Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008727.1 Hibiscus syriacus cultivar Beakdansim tig00111794_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1388410
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 8
Found at i:1180037 original size:37 final size:37
Alignment explanation
Indices: 1179947--1180042 Score: 113
Period size: 37 Copynumber: 2.6 Consensus size: 37
1179937 CATTTTCATC
*
1179947 CTACTAAGATTCAAACTCCTAAAAATAGGATAAAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
* * *
1179984 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGA-T
1 CTACTAGGATTCAAACTCCTAAAAATAGGATA-AAATT
** *
1180021 CTACTATTATTTAAACTCCTAA
1 CTACTAGGATTCAAACTCCTAA
1180043 TGATATGATC
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
37 47 0.96
38 2 0.04
ACGTcount: A:0.43, C:0.17, G:0.10, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
Found at i:1180752 original size:24 final size:22
Alignment explanation
Indices: 1180722--1180777 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
1180712 ATATTTAGTA
1180722 TTTTATTATATTATACATACATT
1 TTTTATTAT-TTATACATACATT
* *
1180745 TTTATATT-TTTATATATATATT
1 TTT-TATTATTTATACATACATT
1180767 TTTTATTATTT
1 TTTTATTATTT
1180778 TATTTATACT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
21 4 0.14
22 17 0.59
23 4 0.14
24 4 0.14
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (22 bp):
TTTTATTATTTATACATACATT
Found at i:1180757 original size:22 final size:21
Alignment explanation
Indices: 1180722--1180800 Score: 59
Period size: 23 Copynumber: 3.4 Consensus size: 21
1180712 ATATTTAGTA
1180722 TTTTATTATATTATACATACATT
1 TTTTATT-T-TTATACATACATT
* *
1180745 TTTATATTTTTATATATATATT
1 TTT-TATTTTTATACATACATT
**
1180767 TTTTATTATTTTATTTATACTATT
1 TTTTA-T-TTTTATACATAC-ATT
1180791 TATTTATTTT
1 T-TTTATTTT
1180801 CATTATATTT
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
21 2 0.04
22 15 0.32
23 17 0.36
24 9 0.19
25 4 0.09
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTTATTTTTATACATACATT
Found at i:1180773 original size:21 final size:21
Alignment explanation
Indices: 1180743--1180812 Score: 63
Period size: 23 Copynumber: 3.1 Consensus size: 21
1180733 TATACATACA
1180743 TTTTTATATTTTTATATATATAT
1 TTTTTATA-TTTTAT-TATATAT
1180766 TTTTTATTATTTTATTTATACTAT
1 TTTTTA-TATTTTA-TTATA-TAT
*
1180790 TTATTTAT-TTTCATTATAT-T
1 TT-TTTATATTTTATTATATAT
1180810 TTT
1 TTT
1180813 AGTTTCTTTG
Statistics
Matches: 42, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
19 1 0.02
20 3 0.07
21 1 0.02
22 5 0.12
23 19 0.45
24 9 0.21
25 4 0.10
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (21 bp):
TTTTTATATTTTATTATATAT
Found at i:1180778 original size:24 final size:23
Alignment explanation
Indices: 1180700--1180808 Score: 80
Period size: 24 Copynumber: 4.6 Consensus size: 23
1180690 TCATTTATTA
* *
1180700 TTATTATTATTA-ATATTTAGTATT
1 TTATTA-TATTATATATATA-TTTT
* *
1180724 TTATTATATTATACATACATTTT
1 TTATTATATTATATATATATTTT
1180747 TATATT-T-TTATATATATATTTT
1 T-TATTATATTATATATATATTTT
* *
1180769 TTATTATTTTATTTATACTATTTAT
1 TTATTATATTATATATA-TATTT-T
*
1180794 TTATTTTCATTATAT
1 TTATTAT-ATTATAT
1180809 TTTTAGTTTC
Statistics
Matches: 68, Mismatches: 10, Indels: 12
0.76 0.11 0.13
Matches are distributed among these distances:
21 4 0.06
22 15 0.22
23 18 0.26
24 19 0.28
25 7 0.10
26 5 0.07
ACGTcount: A:0.31, C:0.04, G:0.01, T:0.64
Consensus pattern (23 bp):
TTATTATATTATATATATATTTT
Found at i:1180808 original size:45 final size:44
Alignment explanation
Indices: 1180722--1180812 Score: 105
Period size: 45 Copynumber: 2.0 Consensus size: 44
1180712 ATATTTAGTA
*
1180722 TTTTATTATATTATACATACATTTTTATATTTTTATATATATATT
1 TTTTATTATATTATACATACATTTTTATATTTTCATATATAT-TT
* **
1180767 TTTTATTATTTTATTTATACTATTTATT-TATTTTCAT-TATATTT
1 TTTTATTATATTATACATAC-ATTT-TTATATTTTCATATATATTT
1180811 TT
1 TT
1180813 AGTTTCTTTG
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
44 4 0.10
45 22 0.55
46 12 0.30
47 2 0.05
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (44 bp):
TTTTATTATATTATACATACATTTTTATATTTTCATATATATTT
Found at i:1180809 original size:28 final size:27
Alignment explanation
Indices: 1180753--1180810 Score: 64
Period size: 28 Copynumber: 2.1 Consensus size: 27
1180743 TTTTTATATT
* *
1180753 TTTATATATATATTTTTTATTATTTTA
1 TTTATATATATATTTTTTATCATTATA
*
1180780 TTTATACTATTTATTTATTT-TCATTATA
1 TTTATA-TATATATTT-TTTATCATTATA
1180808 TTT
1 TTT
1180811 TTAGTTTCTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
27 6 0.23
28 17 0.65
29 3 0.12
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (27 bp):
TTTATATATATATTTTTTATCATTATA
Found at i:1182001 original size:57 final size:57
Alignment explanation
Indices: 1181879--1182386 Score: 770
Period size: 57 Copynumber: 8.9 Consensus size: 57
1181869 CCCATTACCA
* * * *
1181879 ATACAGAAATTCATATACTTATTATGAATTTCTT-AGTTTCTGCACACAAAGTGCCC
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAACTTTTTGCACACAAAGTGCCC
* * *
1181935 ATACGGAAATTCATAAACTCATTATGAATTTCTTAACCTTTTGCACATAAAGTGCCC
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAACTTTTTGCACACAAAGTGCCC
*
1181992 ATACGGAAATTCATAAACTTATTATGAATTTCTTAACTTTTTGCACACAAAGTGTCC
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAACTTTTTGCACACAAAGTGCCC
* *
1182049 ATACGAAAATTCATAAACTCATTATGAATTTCTTAACTTTTTGCACACAAAGTGCCC
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAACTTTTTGCACACAAAGTGCCC
* * * *
1182106 ATATGGAAACTCATAAACTCATTATGAATTTCTTAACCTTTTGCACACAAAGTGCCC
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAACTTTTTGCACACAAAGTGCCC
* * ** **
1182163 ATACGAAAACTT-ATAAATTTATTATGAATTGATTAACTTTTTGCATGCAAAGTGCCC
1 ATACGGAAA-TTCATAAACTTATTATGAATTTCTTAACTTTTTGCACACAAAGTGCCC
* *
1182220 ATAAGGAAATACATAAACTTATTATGAATTTCTTAACTTTTTGCACACAAAGTGCCC
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAACTTTTTGCACACAAAGTGCCC
* *
1182277 ATACGGAAATTTATAAACTTATTATGAATTTCTTAACTTTTTGCACACAAAGTGCTC
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAACTTTTTGCACACAAAGTGCCC
1182334 ATACGGAAATTCATAAACTTATT-TGAATTTCTTAACTTTTTGCACACAAAGTG
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAACTTTTTGCACACAAAGTG
1182387 TCATTCGCTA
Statistics
Matches: 408, Mismatches: 41, Indels: 6
0.90 0.09 0.01
Matches are distributed among these distances:
56 62 0.15
57 345 0.85
58 1 0.00
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.35
Consensus pattern (57 bp):
ATACGGAAATTCATAAACTTATTATGAATTTCTTAACTTTTTGCACACAAAGTGCCC
Found at i:1182777 original size:19 final size:19
Alignment explanation
Indices: 1182709--1182778 Score: 61
Period size: 19 Copynumber: 3.5 Consensus size: 19
1182699 TGGAACAATA
**
1182709 GTATCGATACTCTACCATG
1 GTATCGATACTCTATTATG
*
1182728 GTATCGATAATACTATACTATG
1 GTATCGATACT-CTAT--TATG
*
1182750 GTA-CTGATACTCTATTACG
1 GTATC-GATACTCTATTATG
1182769 GTATCGATAC
1 GTATCGATAC
1182779 CATTTTTGTA
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
19 21 0.51
20 4 0.10
21 5 0.12
22 11 0.27
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.34
Consensus pattern (19 bp):
GTATCGATACTCTATTATG
Found at i:1188845 original size:57 final size:57
Alignment explanation
Indices: 1188726--1189173 Score: 711
Period size: 57 Copynumber: 7.9 Consensus size: 57
1188716 GCCAATACGC
* * * * *
1188726 AAATTCATATACTTATTATGAATTTCTT-AGTTTTTGCACACAAAGTGTCCATTCGG
1 AAATTCATAAACTTATTATGAATTTCTTAACTTTTTGCACACAAAGTGCCCATACAG
* * *
1188782 AAATTCATAAACTCATTATGAATTTCTTAACCTTTTGCACTCAAAGTGCCCATACAG
1 AAATTCATAAACTTATTATGAATTTCTTAACTTTTTGCACACAAAGTGCCCATACAG
* * *
1188839 AAATTCATAAACTTATTATGAATTTCTTAACTTTTTGCACATAAAGTGCCAATACGG
1 AAATTCATAAACTTATTATGAATTTCTTAACTTTTTGCACACAAAGTGCCCATACAG
* *
1188896 AAATTCATAAACTCATTATGAATTTCTTAACCTTTTGCACACAAAGTGCCCATACAG
1 AAATTCATAAACTTATTATGAATTTCTTAACTTTTTGCACACAAAGTGCCCATACAG
*
1188953 AAATTCATAAACTCATTATGAATTTCTTAACTTTTTGCACACAAAGTGCCCATAC-G
1 AAATTCATAAACTTATTATGAATTTCTTAACTTTTTGCACACAAAGTGCCCATACAG
*
1189009 AAAATTCATAAACTTATTATGAATTTCTTAACTTTTTGCACACAAAGTGTCCATACAG
1 -AAATTCATAAACTTATTATGAATTTCTTAACTTTTTGCACACAAAGTGCCCATACAG
* *
1189067 AAATTCATAAACTTATAATGAATTTCTTAACTTTTTGCACACAAAGTGCCCATACGG
1 AAATTCATAAACTTATTATGAATTTCTTAACTTTTTGCACACAAAGTGCCCATACAG
*
1189124 AAATTCATAAACTTATTATGAATTTATTAACTTTTTGCACACAAAGTGCC
1 AAATTCATAAACTTATTATGAATTTCTTAACTTTTTGCACACAAAGTGCC
1189174 ATTCGATAAT
Statistics
Matches: 362, Mismatches: 27, Indels: 5
0.92 0.07 0.01
Matches are distributed among these distances:
56 27 0.07
57 334 0.92
58 1 0.00
ACGTcount: A:0.36, C:0.19, G:0.10, T:0.35
Consensus pattern (57 bp):
AAATTCATAAACTTATTATGAATTTCTTAACTTTTTGCACACAAAGTGCCCATACAG
Found at i:1190609 original size:32 final size:32
Alignment explanation
Indices: 1190498--1190685 Score: 153
Period size: 32 Copynumber: 5.9 Consensus size: 32
1190488 GTCACTCATG
* * * * * *
1190498 TGCATTATCTGAATACAACACTAACTTTGGTG
1 TGCATTATCTGAATGCAACATTGACTCTGTTA
* * * *
1190530 TGCATTATATGAATACAACATTGACTTTGCTA
1 TGCATTATCTGAATGCAACATTGACTCTGTTA
* * *
1190562 TGCATTATCTAAATGCAATATTAACTCTGTTA
1 TGCATTATCTGAATGCAACATTGACTCTGTTA
* * **
1190594 AGCATTATCTGAATGCAATATTGACTCTGTCG
1 TGCATTATCTGAATGCAACATTGACTCTGTTA
* * * *
1190626 TGCATTATCTAAATGTAGCACTGACTCTAG-TA
1 TGCATTATCTGAATGCAACATTGACTCT-GTTA
* *
1190658 TGCATTATCTGAATGCAATACTGACTCT
1 TGCATTATCTGAATGCAACATTGACTCT
1190686 TCTGAACATT
Statistics
Matches: 126, Mismatches: 29, Indels: 2
0.80 0.18 0.01
Matches are distributed among these distances:
32 125 0.99
33 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.14, T:0.36
Consensus pattern (32 bp):
TGCATTATCTGAATGCAACATTGACTCTGTTA
Found at i:1190696 original size:32 final size:31
Alignment explanation
Indices: 1190562--1190703 Score: 135
Period size: 32 Copynumber: 4.5 Consensus size: 31
1190552 GACTTTGCTA
* *
1190562 TGCATTATCTAAATGCAATATTAACTCTGT-
1 TGCATTATCTAAATGCAATACTGACTCTGTC
* *
1190592 TAAGCATTATCTGAATGCAATATTGACTCTGTC
1 T--GCATTATCTAAATGCAATACTGACTCTGTC
* ** *
1190625 GTGCATTATCTAAATGTAGCACTGACTCTAGTA
1 -TGCATTATCTAAATGCAATACTGACTCT-GTC
*
1190658 TGCATTATCTGAATGCAATACTGACTCT-TC
1 TGCATTATCTAAATGCAATACTGACTCTGTC
1190688 TGAACATTATCTAAAT
1 TG--CATTATCTAAAT
1190704 ACATCACTGA
Statistics
Matches: 91, Mismatches: 14, Indels: 12
0.78 0.12 0.10
Matches are distributed among these distances:
30 4 0.04
32 84 0.92
33 2 0.02
34 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.13, T:0.37
Consensus pattern (31 bp):
TGCATTATCTAAATGCAATACTGACTCTGTC
Found at i:1190724 original size:64 final size:64
Alignment explanation
Indices: 1190595--1190725 Score: 160
Period size: 64 Copynumber: 2.0 Consensus size: 64
1190585 ACTCTGTTAA
* ** * *
1190595 GCATTATCTGAATGCAATATTGACTCTGTCGTGCATTATCTAAATGTAGCACTGACTCTAGTAT
1 GCATTATCTGAATGCAATACTGACTCTGTCGTGCATTATCTAAATACAGCACTGACTATACTAT
*
1190659 GCATTATCTGAATGCAATACTGACTCT-TC-TGAACATTATCTAAATACATCACTGA-TAATACT
1 GCATTATCTGAATGCAATACTGACTCTGTCGTG--CATTATCTAAATACAGCACTGACT-ATACT
1190721 AT
63 AT
1190723 GCA
1 GCA
1190726 ACATACAAGC
Statistics
Matches: 58, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
62 2 0.03
63 3 0.05
64 53 0.91
ACGTcount: A:0.32, C:0.20, G:0.14, T:0.34
Consensus pattern (64 bp):
GCATTATCTGAATGCAATACTGACTCTGTCGTGCATTATCTAAATACAGCACTGACTATACTAT
Found at i:1203402 original size:107 final size:107
Alignment explanation
Indices: 1203216--1203424 Score: 346
Period size: 107 Copynumber: 2.0 Consensus size: 107
1203206 GTTCGAGCAC
* * *
1203216 CAACTATTATAACATGATGATTGAACGTTAATTATCAAATAATTGAAAATATTTAAAACAAACAT
1 CAACTATTATAACATAATAATTGAACGTTAATTATCAAATAATTAAAAATATTTAAAACAAACAT
*
1203281 TACTTTAAAATCACTTTAATTTAATAAAAAGAATAAGGGTAT
66 CACTTTAAAATCACTTTAATTTAATAAAAAGAATAAGGGTAT
* * * *
1203323 CAACTATTGTAACATAATAATTGAACGTTAATTATCAAATGATTAAAAATATTTAAACCATACAT
1 CAACTATTATAACATAATAATTGAACGTTAATTATCAAATAATTAAAAATATTTAAAACAAACAT
1203388 CACTTTAAAATCACTTTAATTTAATAAAAAGAATAAG
66 CACTTTAAAATCACTTTAATTTAATAAAAAGAATAAG
1203425 ACCGTTAACG
Statistics
Matches: 94, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
107 94 1.00
ACGTcount: A:0.49, C:0.11, G:0.07, T:0.33
Consensus pattern (107 bp):
CAACTATTATAACATAATAATTGAACGTTAATTATCAAATAATTAAAAATATTTAAAACAAACAT
CACTTTAAAATCACTTTAATTTAATAAAAAGAATAAGGGTAT
Found at i:1205151 original size:19 final size:19
Alignment explanation
Indices: 1205112--1205156 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
1205102 ATTATATATA
* *
1205112 TAAACTAAAAAAATAGGCT
1 TAAACTAAAAAAAAAAGCT
*
1205131 TAAACTAAAAAAAAAATCT
1 TAAACTAAAAAAAAAAGCT
1205150 TAAACTA
1 TAAACTA
1205157 TACTTTTCTG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.62, C:0.11, G:0.04, T:0.22
Consensus pattern (19 bp):
TAAACTAAAAAAAAAAGCT
Found at i:1209812 original size:19 final size:21
Alignment explanation
Indices: 1209788--1209830 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1209778 AAATTCAAAA
1209788 AAATTAAA-TA-TAAAAATAT
1 AAATTAAAGTACTAAAAATAT
*
1209807 AAATTAAAGTACTAAAAATTT
1 AAATTAAAGTACTAAAAATAT
1209828 AAA
1 AAA
1209831 ATATATCATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 8 0.38
20 2 0.10
21 11 0.52
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (21 bp):
AAATTAAAGTACTAAAAATAT
Found at i:1214111 original size:6 final size:6
Alignment explanation
Indices: 1214100--1214152 Score: 88
Period size: 6 Copynumber: 8.8 Consensus size: 6
1214090 GGGGAAAATG
* *
1214100 GGTGGC GGTGGC GGTGGC GGTGGC GGTGGC GGTGGC GGTGGT GGTGGT
1 GGTGGC GGTGGC GGTGGC GGTGGC GGTGGC GGTGGC GGTGGC GGTGGC
1214148 GGTGG
1 GGTGG
1214153 GGATTTTACA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 46 1.00
ACGTcount: A:0.00, C:0.11, G:0.68, T:0.21
Consensus pattern (6 bp):
GGTGGC
Found at i:1215560 original size:30 final size:30
Alignment explanation
Indices: 1215519--1215620 Score: 132
Period size: 30 Copynumber: 3.4 Consensus size: 30
1215509 GTTTTTACTG
*
1215519 TTAGTCCCTTAAGTTTCTATTTTTGTTGTT
1 TTAGTCCCTTAAGTTTCTATTTTTGTTATT
* **
1215549 TTAGTCTCTTAAGTTTCTGCTTTTGTTATT
1 TTAGTCCCTTAAGTTTCTATTTTTGTTATT
* * *
1215579 TTAATCCCTTAAGCTTCTATTTTTGCTATT
1 TTAGTCCCTTAAGTTTCTATTTTTGTTATT
*
1215609 TTAGTCTCTTAA
1 TTAGTCCCTTAA
1215621 ATTCATGTTT
Statistics
Matches: 60, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 60 1.00
ACGTcount: A:0.17, C:0.16, G:0.11, T:0.57
Consensus pattern (30 bp):
TTAGTCCCTTAAGTTTCTATTTTTGTTATT
Found at i:1215651 original size:60 final size:60
Alignment explanation
Indices: 1215486--1215662 Score: 166
Period size: 60 Copynumber: 3.0 Consensus size: 60
1215476 TTTGTAATTA
* * * *
1215486 CTATTTTAGTACT-TTTAGATTTTGTTTTTAC--TGTTAGTCCCTTAAGTTTCTATTTTTG
1 CTATTTTAGT-CTCTTAAGATTCTGCTTTTACTATTTTAGTCCCTTAAGTTTCTATTTTTG
* * * ** * *
1215544 TTGTTTTAGTCTCTTAAGTTTCTGCTTTTGTTATTTTAATCCCTTAAGCTTCTATTTTTG
1 CTATTTTAGTCTCTTAAGATTCTGCTTTTACTATTTTAGTCCCTTAAGTTTCTATTTTTG
* * *
1215604 CTATTTTAGTCTCTTAA-ATTCATG-TTTATACTATTTTGGTCCTTTAAGTTTCTGTTTTT
1 CTATTTTAGTCTCTTAAGATTC-TGCTTT-TACTATTTTAGTCCCTTAAGTTTCTATTTTT
1215663 CACATTCTGG
Statistics
Matches: 93, Mismatches: 21, Indels: 8
0.76 0.17 0.07
Matches are distributed among these distances:
57 2 0.02
58 20 0.22
59 6 0.06
60 65 0.70
ACGTcount: A:0.17, C:0.14, G:0.11, T:0.58
Consensus pattern (60 bp):
CTATTTTAGTCTCTTAAGATTCTGCTTTTACTATTTTAGTCCCTTAAGTTTCTATTTTTG
Found at i:1220348 original size:207 final size:207
Alignment explanation
Indices: 1219993--1220405 Score: 637
Period size: 207 Copynumber: 2.0 Consensus size: 207
1219983 TATATGTATA
* * *
1219993 TATACAATAAAGGTGAGCTATTCCGCTAAAGCAATTAATTATAGAGGAAACTCGAAAGCCTTAGC
1 TATACAACAAAGCTGAGCTATTCCGCTAAAGCAATTAATTATAGAGGAAACTCGAAAGCCCTAGC
* * * *
1220058 TTTATGAATATATTATATTCAAACCATGACATTGATCGGGTATTTAGCAATTCGGTGTTTGCTCC
66 TTTATGAATAGATTACATTCAAACCATGACATTGATCGGGTACTTAGAAATTCGGTGTTTGCTCC
* * * *
1220123 TCTGTGGTTGTCAAGTCGAAGACTTTGTGACAACATGAATCCTTTAGGTAGCCAAATAAAGGCAA
131 ACTGTGGTTGTCAAGTCGAAGACCTTGTGACAACATGAATCCTTCAGCTAGCCAAATAAAGGCAA
*
1220188 TTATAATATATG
196 TTATAAAATATG
**
1220200 TATACAACAAAGCTGAGCTATTCCGCTAAAGCAATTGGTTATAGAGGAAACTCGAAAGCCCTAGC
1 TATACAACAAAGCTGAGCTATTCCGCTAAAGCAATTAATTATAGAGGAAACTCGAAAGCCCTAGC
* * *
1220265 TTTATGAATAGATTACATTCAAACTATGACATTGATCGGGTACTTGGAAATTCGGTGTTTGGTCC
66 TTTATGAATAGATTACATTCAAACCATGACATTGATCGGGTACTTAGAAATTCGGTGTTTGCTCC
** * *
1220330 ACTGTGGTTGTCAAGTCGAAGACCTTGTGATGACATGAATCCTTCATCTAGCCACATAAAGGCAA
131 ACTGTGGTTGTCAAGTCGAAGACCTTGTGACAACATGAATCCTTCAGCTAGCCAAATAAAGGCAA
1220395 TTATAAAATAT
196 TTATAAAATAT
1220406 ATATGTACAA
Statistics
Matches: 185, Mismatches: 21, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
207 185 1.00
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (207 bp):
TATACAACAAAGCTGAGCTATTCCGCTAAAGCAATTAATTATAGAGGAAACTCGAAAGCCCTAGC
TTTATGAATAGATTACATTCAAACCATGACATTGATCGGGTACTTAGAAATTCGGTGTTTGCTCC
ACTGTGGTTGTCAAGTCGAAGACCTTGTGACAACATGAATCCTTCAGCTAGCCAAATAAAGGCAA
TTATAAAATATG
Found at i:1221662 original size:29 final size:29
Alignment explanation
Indices: 1221630--1221722 Score: 78
Period size: 31 Copynumber: 3.0 Consensus size: 29
1221620 GACAATTTAT
1221630 TTTGAAAAAAAAATCTTTGAGTCTGTTTC
1 TTTGAAAAAAAAATCTTTGAGTCTGTTTC
** * * **
1221659 TTTGGGAAAAAAATTGTCTCTTTAGACAATTTC
1 TTT--GAAAAAAA-AATCT-TTGAGTCTGTTTC
*
1221692 TTTTAAGAAAAAAATCTTTGAGTCTGTTTC
1 TTTGAA-AAAAAAATCTTTGAGTCTGTTTC
1221722 T
1 T
1221723 ATGGAAACAA
Statistics
Matches: 46, Mismatches: 13, Indels: 9
0.68 0.19 0.13
Matches are distributed among these distances:
29 3 0.07
30 10 0.22
31 13 0.28
32 8 0.17
33 12 0.26
ACGTcount: A:0.33, C:0.11, G:0.14, T:0.42
Consensus pattern (29 bp):
TTTGAAAAAAAAATCTTTGAGTCTGTTTC
Found at i:1221704 original size:63 final size:64
Alignment explanation
Indices: 1221612--1221830 Score: 213
Period size: 63 Copynumber: 3.4 Consensus size: 64
1221602 ACATTTTTTA
* * *
1221612 TCTCTTGAGACAATTTATTTTGAA-AAAAAAATCTTTGAGTCTGTTTCTTTGGGAAA-AAA-ATT
1 TCTCTTTAGACAATTTCTTTT-AAGAAAAAAATCTTTGAGTCTGTTTCTAT-GGAAACAAAGATT
1221674 G
64 G
* *
1221675 TCTCTTTAGACAATTTCTTTTAAGAAAAAAATCTTTGAGTCTGTTTCTATGGAAACAAAGTTTTT
1 TCTCTTTAGACAATTTCTTTTAAGAAAAAAATCTTTGAGTCTGTTTCTATGGAAACAAAG-ATTG
* * *
1221740 TCTCTATTGAGACAATTTCTTTTGAGAAAAAAAATCTTAGAGTC----TCTA--GAAACAAAGTT
1 TCTCT-TT-AGACAATTTCTTTTAAG-AAAAAAATCTTTGAGTCTGTTTCTATGGAAACAAAG-A
1221799 TTG
62 TTG
*
1221802 TCTCTTTTGAGACAATTTCTTTTGAGAAA
1 TCTC-TTT-AGACAATTTCTTTTAAGAAA
1221831 TTTTTTTTTT
Statistics
Matches: 140, Mismatches: 8, Indels: 18
0.84 0.05 0.11
Matches are distributed among these distances:
61 3 0.02
62 44 0.31
63 48 0.34
64 4 0.03
65 7 0.05
66 2 0.01
67 16 0.11
68 16 0.11
ACGTcount: A:0.34, C:0.12, G:0.14, T:0.40
Consensus pattern (64 bp):
TCTCTTTAGACAATTTCTTTTAAGAAAAAAATCTTTGAGTCTGTTTCTATGGAAACAAAGATTG
Found at i:1221812 original size:62 final size:64
Alignment explanation
Indices: 1221616--1221830 Score: 214
Period size: 62 Copynumber: 3.4 Consensus size: 64
1221606 TTTTTATCTC
* * * *
1221616 TTGAGACAATTTATTTTGA-AAAAAAAATCTTTGAGTCTGTTTCTTTGGGAAA-AAA--ATTGTC
1 TTGAGACAATTTCTTTTGAGAAAAAAAATCTTAGAGTC---TTC--TAGGAAACAAAGTTTTGTC
1221677 TC-T
61 TCTT
* * *
1221680 TT-AGACAATTTCTTTTAAG-AAAAAAATCTTTGAGTCTGTTTCTATGGAAACAAAGTTTTTTCT
1 TTGAGACAATTTCTTTTGAGAAAAAAAATCTTAGAGTC---TTCTA-GGAAACAAAGTTTTGTCT
*
1221743 CTA
62 CTT
1221746 TTGAGACAATTTCTTTTGAGAAAAAAAATCTTAGAGTC-TCTA-GAAACAAAGTTTTGTCTCTT
1 TTGAGACAATTTCTTTTGAGAAAAAAAATCTTAGAGTCTTCTAGGAAACAAAGTTTTGTCTCTT
1221808 TTGAGACAATTTCTTTTGAGAAA
1 TTGAGACAATTTCTTTTGAGAAA
1221831 TTTTTTTTTT
Statistics
Matches: 133, Mismatches: 10, Indels: 18
0.83 0.06 0.11
Matches are distributed among these distances:
61 1 0.01
62 46 0.35
63 40 0.30
64 6 0.05
65 6 0.05
66 2 0.02
67 16 0.12
68 16 0.12
ACGTcount: A:0.34, C:0.11, G:0.14, T:0.40
Consensus pattern (64 bp):
TTGAGACAATTTCTTTTGAGAAAAAAAATCTTAGAGTCTTCTAGGAAACAAAGTTTTGTCTCTT
Found at i:1221839 original size:15 final size:15
Alignment explanation
Indices: 1221804--1221837 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
1221794 AAGTTTTGTC
1221804 TCTTTTGAGACAATT
1 TCTTTTGAGACAATT
1221819 TCTTTTGAGA-AATT
1 TCTTTTGAGACAATT
1221833 T-TTTT
1 TCTTTT
1221838 TTTGAGTATG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 4 0.21
14 5 0.26
15 10 0.53
ACGTcount: A:0.24, C:0.09, G:0.12, T:0.56
Consensus pattern (15 bp):
TCTTTTGAGACAATT
Found at i:1222267 original size:130 final size:128
Alignment explanation
Indices: 1221959--1222317 Score: 392
Period size: 130 Copynumber: 2.8 Consensus size: 128
1221949 TCTTGAAATC
*
1221959 ATCATCCCTAAAGATGG--TTTGCAATCCTCATCACATA-AGAA-CTGTCATCCCCCGACCAGAC
1 ATCATCCCTAAAGATGGCATAT-C-ATCCTCATCACATAGA-AACCTGTCAT-CCCCGACCAGAC
* *
1222020 CTCCTCATCACATAGGAGCTGTGTCACCCCT-GATAAACAATCGTCCTCATCACGTAGGAACCAT
62 CTCCTCATCACGTAGGAGCTGTGTCACCCCTAGAT-AACAATCATCCTCATCACGTAGGAACCAT
1222084 GTT
126 GTT
* * * *
1222087 ATCATCCCTAAAGATGGCATATCGTCCTCATCGCGTAGGAA-CTGTTTCATCCCCGACCAGACCT
1 ATCATCCCTAAAGATGGCATATCATCCTCATCACATAGAAACCTG--TCATCCCCGACCAGACCT
* **
1222151 CCTCATCGCGTAGGAGCTGTGTCACCCCTAGATAACTAATCATCCTCATCACGTAGGAACTGTGT
64 CCTCATCACGTAGGAGCTGTGTCACCCCTAGATAAC-AATCATCCTCATCACGTAGGAACCATGT
1222216 T
128 T
* * * *
1222217 ATCATTCCTAAATATGGTC-TATCATCCTCATCACATAGAAACCATGTCATCCACCGATCATACC
1 ATCATCCCTAAAGATGG-CATATCATCCTCATCACATAGAAACC-TGTCATCC-CCGACCAGACC
* * **
1222281 CCCTCATCATGTAAAAG-TCGTGTCACCCCTAGATAAC
63 TCCTCATCACGTAGGAGCT-GTGTCACCCCTAGATAAC
1222318 CAGCCGCCCT
Statistics
Matches: 196, Mismatches: 23, Indels: 21
0.82 0.10 0.09
Matches are distributed among these distances:
128 33 0.17
129 45 0.23
130 75 0.38
131 41 0.21
132 2 0.01
ACGTcount: A:0.28, C:0.31, G:0.15, T:0.26
Consensus pattern (128 bp):
ATCATCCCTAAAGATGGCATATCATCCTCATCACATAGAAACCTGTCATCCCCGACCAGACCTCC
TCATCACGTAGGAGCTGTGTCACCCCTAGATAACAATCATCCTCATCACGTAGGAACCATGTT
Found at i:1222663 original size:20 final size:20
Alignment explanation
Indices: 1222638--1222675 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1222628 CTACCAAAAA
1222638 TATTATTA-TATTATATTTAT
1 TATTATTATTATTA-ATTTAT
1222658 TATTATTATTATTAATTT
1 TATTATTATTATTAATTT
1222676 TGTTTGCATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (20 bp):
TATTATTATTATTAATTTAT
Found at i:1224119 original size:30 final size:30
Alignment explanation
Indices: 1224083--1224222 Score: 117
Period size: 30 Copynumber: 4.8 Consensus size: 30
1224073 ATTTTTATTA
1224083 TTTAGTCCCTTAAGTTTTTGTTTTTGCTAT
1 TTTAGTCCCTTAAGTTTTTGTTTTTGCTAT
* * * **
1224113 TTTAGTCCTTTAAATTTCTACTTTTGCTAT
1 TTTAGTCCCTTAAGTTTTTGTTTTTGCTAT
*
1224143 TTTAATCCCTTAAG---TT-TTTTTGCTAT
1 TTTAGTCCCTTAAGTTTTTGTTTTTGCTAT
** * ** * *
1224169 TTTAGTATCTTAAATTCATGTTTGTACTAT
1 TTTAGTCCCTTAAGTTTTTGTTTTTGCTAT
* *
1224199 TTTGGTCCTTTAAGTTTTTGTTTT
1 TTTAGTCCCTTAAGTTTTTGTTTT
1224223 CCCATTCTGG
Statistics
Matches: 81, Mismatches: 25, Indels: 8
0.71 0.22 0.07
Matches are distributed among these distances:
26 19 0.23
27 1 0.01
29 1 0.01
30 60 0.74
ACGTcount: A:0.18, C:0.13, G:0.11, T:0.59
Consensus pattern (30 bp):
TTTAGTCCCTTAAGTTTTTGTTTTTGCTAT
Found at i:1225504 original size:22 final size:22
Alignment explanation
Indices: 1225476--1225517 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
1225466 AACTCCTTTC
1225476 TTCTTCTTCTT-TTCCACACTAT
1 TTCTTCTTCTTCTT-CACACTAT
1225498 TTCTTCTTCTTCTTCACACT
1 TTCTTCTTCTTCTTCACACT
1225518 TGAAATCAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.12, C:0.33, G:0.00, T:0.55
Consensus pattern (22 bp):
TTCTTCTTCTTCTTCACACTAT
Found at i:1226446 original size:21 final size:21
Alignment explanation
Indices: 1226422--1226461 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1226412 AATTCTCTTC
*
1226422 ATGAAATGATTAAATCTTTTT
1 ATGAAATGATTAAACCTTTTT
*
1226443 ATGAAATGGTTAAACCTTT
1 ATGAAATGATTAAACCTTT
1226462 CATCAAAAGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.07, G:0.12, T:0.42
Consensus pattern (21 bp):
ATGAAATGATTAAACCTTTTT
Found at i:1226488 original size:22 final size:22
Alignment explanation
Indices: 1226463--1226504 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
1226453 TAAACCTTTC
1226463 ATCAAAAGGATAAGTCTTTTTA
1 ATCAAAAGGATAAGTCTTTTTA
*
1226485 ATCAAAAGGTTAAGTCTTTT
1 ATCAAAAGGATAAGTCTTTT
1226505 CATCGTAAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.38
Consensus pattern (22 bp):
ATCAAAAGGATAAGTCTTTTTA
Found at i:1229523 original size:21 final size:21
Alignment explanation
Indices: 1229499--1229548 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
1229489 AAGCCATTTC
1229499 ATCAAAAGGAGAAGTCTTTTA
1 ATCAAAAGGAGAAGTCTTTTA
** *
1229520 ATCAAAAGGTTAAGTCTTTTC
1 ATCAAAAGGAGAAGTCTTTTA
*
1229541 ATCGAAAG
1 ATCAAAAG
1229549 ATCTTAATCA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.40, C:0.12, G:0.18, T:0.30
Consensus pattern (21 bp):
ATCAAAAGGAGAAGTCTTTTA
Found at i:1230512 original size:180 final size:180
Alignment explanation
Indices: 1230162--1230516 Score: 662
Period size: 181 Copynumber: 2.0 Consensus size: 180
1230152 TGAAGGAGCA
1230162 TAACTTATAAAGCCATGATCAATTTGACTTCTTGTTGGACTGTGTCACTTGAGTTTTTAAAGAGG
1 TAACTTATAAAGCCATGATCAATTTGACTTCTTGTTGGACTGTGTCACTTGAGTTTTTAAAGAGG
1230227 TTTTAGTTACCAGTTTCATTGTGTGTTCCGATGAAGGGATTCAATCCTCTTGGTGAGTTTAGTGA
66 TTTTAGTTACCAGTTTCATTGTGTGTTCCGATGAAGGGATTCAATCCTCTTGGTGAGTTTAGTGA
1230292 ACTGTTAATTATTCTCCTCTGTTTCTTTGCTTCCTACATGTGAAAGGCAT
131 ACTGTTAATTATTCTCCTCTGTTTCTTTGCTTCCTACATGTGAAAGGCAT
1230342 TAACTTA-ATAAGCCATGATCAAATTTGACTTCTTGTTGGACTGTGTCACTTGAGTTTTTAAAGA
1 TAACTTATA-AAGCCATGATC-AATTTGACTTCTTGTTGGACTGTGTCACTTGAGTTTTTAAAGA
1230406 GGTTTTAGTTACCAGTTTCA-T-TGTGTTCCGATGAAGGGATTCAATCCTCTTGGTGAGTTTAGT
64 GGTTTTAGTTACCAGTTTCATTGTGTGTTCCGATGAAGGGATTCAATCCTCTTGGTGAGTTTAGT
1230469 GAACTGTTAATTATTTCTCCTCTGTTTCTTTGCTTCCTACATGTGAAA
129 GAACTGTTAATTA-TTCTCCTCTGTTTCTTTGCTTCCTACATGTGAAA
1230517 AAGAAATACT
Statistics
Matches: 172, Mismatches: 0, Indels: 6
0.97 0.00 0.03
Matches are distributed among these distances:
179 56 0.33
180 53 0.31
181 63 0.37
ACGTcount: A:0.23, C:0.16, G:0.19, T:0.41
Consensus pattern (180 bp):
TAACTTATAAAGCCATGATCAATTTGACTTCTTGTTGGACTGTGTCACTTGAGTTTTTAAAGAGG
TTTTAGTTACCAGTTTCATTGTGTGTTCCGATGAAGGGATTCAATCCTCTTGGTGAGTTTAGTGA
ACTGTTAATTATTCTCCTCTGTTTCTTTGCTTCCTACATGTGAAAGGCAT
Found at i:1231157 original size:14 final size:14
Alignment explanation
Indices: 1231138--1231165 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1231128 CAAAGAACGC
1231138 TAAAAGACTTTCAA
1 TAAAAGACTTTCAA
1231152 TAAAAGACTTTCAA
1 TAAAAGACTTTCAA
1231166 CTTTTTTTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.14, G:0.07, T:0.29
Consensus pattern (14 bp):
TAAAAGACTTTCAA
Found at i:1236340 original size:35 final size:35
Alignment explanation
Indices: 1236300--1236372 Score: 128
Period size: 35 Copynumber: 2.1 Consensus size: 35
1236290 AGAAATCTAA
* *
1236300 GAGAAGCTGCTAAGGGTGTTAATTGTTATCGATCC
1 GAGAAGCTGCTAAGGGCGTTAATTGTTATCAATCC
1236335 GAGAAGCTGCTAAGGGCGTTAATTGTTATCAATCC
1 GAGAAGCTGCTAAGGGCGTTAATTGTTATCAATCC
1236370 GAG
1 GAG
1236373 CTCAAGAGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.29
Consensus pattern (35 bp):
GAGAAGCTGCTAAGGGCGTTAATTGTTATCAATCC
Found at i:1241771 original size:24 final size:24
Alignment explanation
Indices: 1241736--1241786 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 24
1241726 AGTAGTTAGT
*
1241736 TTAAGCAACTGA-TTGATTAGCTGA
1 TTAAGCAACTGATTTGA-TAACTGA
1241760 TTAAG-AATCTGATTTGATAACTGA
1 TTAAGCAA-CTGATTTGATAACTGA
1241784 TTA
1 TTA
1241787 TATAGAATTG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
23 2 0.08
24 18 0.75
25 4 0.17
ACGTcount: A:0.35, C:0.10, G:0.18, T:0.37
Consensus pattern (24 bp):
TTAAGCAACTGATTTGATAACTGA
Found at i:1242662 original size:16 final size:16
Alignment explanation
Indices: 1242637--1242667 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1242627 ATTGAACATA
*
1242637 CAAAATTATAAAATTT
1 CAAAAGTATAAAATTT
1242653 CAAAAGTATAAAATT
1 CAAAAGTATAAAATT
1242668 ATATCATCTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.58, C:0.06, G:0.03, T:0.32
Consensus pattern (16 bp):
CAAAAGTATAAAATTT
Found at i:1243819 original size:30 final size:30
Alignment explanation
Indices: 1243785--1243842 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
1243775 ATAAAAAAAA
* *
1243785 TAAAAAAG-TATAATAATAAAGTAAAAATGT
1 TAAAAAAGAAATAA-AATAAAATAAAAATGT
*
1243815 TAAAAGAGAAATAAAATAAAATAAAAAT
1 TAAAAAAGAAATAAAATAAAATAAAAAT
1243843 AAATGTTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 20 0.83
31 4 0.17
ACGTcount: A:0.69, C:0.00, G:0.09, T:0.22
Consensus pattern (30 bp):
TAAAAAAGAAATAAAATAAAATAAAAATGT
Found at i:1243844 original size:41 final size:41
Alignment explanation
Indices: 1243776--1243886 Score: 108
Period size: 41 Copynumber: 2.8 Consensus size: 41
1243766 AAAGGTTAGA
* *
1243776 TAAAAA-AAATAAAA-AAGT-ATAATAATAAA-GTAAAAATGT
1 TAAAAAGAAATAAAATAAATAATAAAAATAAATGT-AAAAT-T
*
1243815 TAAAAGAGAAATAAAAT-AA-AATAAAAATAAATGTTAAATT
1 TAAAA-AGAAATAAAATAAATAATAAAAATAAATGTAAAATT
* *
1243855 TCAAATGAAATAAAATAAATAATAAAAATAAA
1 TAAAAAGAAATAAAATAAATAATAAAAATAAA
1243887 ATTAAGAAAA
Statistics
Matches: 60, Mismatches: 5, Indels: 12
0.78 0.06 0.16
Matches are distributed among these distances:
39 15 0.25
40 8 0.13
41 35 0.58
42 2 0.03
ACGTcount: A:0.69, C:0.01, G:0.06, T:0.23
Consensus pattern (41 bp):
TAAAAAGAAATAAAATAAATAATAAAAATAAATGTAAAATT
Found at i:1243852 original size:34 final size:35
Alignment explanation
Indices: 1243794--1243880 Score: 97
Period size: 34 Copynumber: 2.5 Consensus size: 35
1243784 ATAAAAAAGT
*
1243794 ATAATAATAAAGTAA-AAATGTTAAAAGAGAAATAAA
1 ATAA-AATAAA-TAATAAATGTTAAAAGACAAATAAA
*** *
1243830 ATAAAATAAA-AATAAATGTTAAATTTCAAATGAA
1 ATAAAATAAATAATAAATGTTAAAAGACAAATAAA
1243864 ATAAAATAAATAATAAA
1 ATAAAATAAATAATAAA
1243881 AATAAAATTA
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
33 2 0.05
34 26 0.59
35 12 0.27
36 4 0.09
ACGTcount: A:0.67, C:0.01, G:0.07, T:0.25
Consensus pattern (35 bp):
ATAAAATAAATAATAAATGTTAAAAGACAAATAAA
Found at i:1245265 original size:36 final size:36
Alignment explanation
Indices: 1245221--1245482 Score: 337
Period size: 36 Copynumber: 7.4 Consensus size: 36
1245211 ATACATATGG
*
1245221 TATATTTTCAAAAGCGTTTT-AAAATTATATATTATA
1 TATATTTTCAAAA-TGTTTTCAAAATTATATATTATA
1245257 TATATTTTCAAAATGTTTTCAAAACTATATATATTATA
1 TATATTTTCAAAATGTTTTCAAAA-T-TATATATTATA
* *
1245295 TATA-TTTCAAAAGGTTTT-TAAA--ATATATTATA
1 TATATTTTCAAAATGTTTTCAAAATTATATATTATA
*
1245327 TATATTTT-AAAATGTTTTCAGAAACTATATATTATA
1 TATATTTTCAAAATGTTTTCA-AAATTATATATTATA
1245363 TATATTTTCAAAATGTTTTCAAAA--ACTATATTATA
1 TATATTTTCAAAATGTTTTCAAAATTA-TATATTATA
*
1245398 TATATTTTCAAAATGTTTTCAAAAACTATATATTATA
1 TATATTTTCAAAATGTTTTC-AAAATTATATATTATA
*
1245435 TATA--TTCAAAATATTTTCAAAATTATATATTATA
1 TATATTTTCAAAATGTTTTCAAAATTATATATTATA
1245469 TATATTTTCGAAAA
1 TATATTTTC-AAAA
1245483 ATTATATATA
Statistics
Matches: 203, Mismatches: 7, Indels: 31
0.84 0.03 0.13
Matches are distributed among these distances:
32 23 0.11
33 3 0.01
34 23 0.11
35 47 0.23
36 48 0.24
37 43 0.21
38 16 0.08
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.47
Consensus pattern (36 bp):
TATATTTTCAAAATGTTTTCAAAATTATATATTATA
Found at i:1245361 original size:106 final size:105
Alignment explanation
Indices: 1245221--1245482 Score: 354
Period size: 106 Copynumber: 2.5 Consensus size: 105
1245211 ATACATATGG
*
1245221 TATATTTTCAAAAGCGTTTT-AAAATTATATATTATATATATTTTCAAAATGTTTTC-AAAACTA
1 TATATTTT-AAAA-TGTTTTCAAAATTATATATTATATATATTTTCAAAATGTTTTCAAAAACTA
*
1245284 TATATATTATATATATTTCAAAAGGTTTT-TAAAA-TATAT-TATA
64 TAT-TA-TATATAT-TTTCAAAAGGTTTTCAAAAACTATATAT-TA
*
1245327 TATATTTTAAAATGTTTTCAGAAACTATATATTATATATATTTTCAAAATGTTTTCAAAAACTAT
1 TATATTTTAAAATGTTTTCA-AAATTATATATTATATATATTTTCAAAATGTTTTCAAAAACTAT
*
1245392 ATTATATATATTTTCAAAATGTTTTCAAAAACTATATATTA
65 ATTATATATATTTTCAAAAGGTTTTCAAAAACTATATATTA
* *
1245433 TATATATTCAAAATATTTTCAAAATTATATATTATATATATTTTCGAAAA
1 TATAT-TTTAAAATGTTTTCAAAATTATATATTATATATATTTTC-AAAA
1245483 ATTATATATA
Statistics
Matches: 141, Mismatches: 7, Indels: 15
0.87 0.04 0.09
Matches are distributed among these distances:
104 18 0.13
105 16 0.11
106 79 0.56
107 28 0.20
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.47
Consensus pattern (105 bp):
TATATTTTAAAATGTTTTCAAAATTATATATTATATATATTTTCAAAATGTTTTCAAAAACTATA
TTATATATATTTTCAAAAGGTTTTCAAAAACTATATATTA
Found at i:1245462 original size:27 final size:28
Alignment explanation
Indices: 1245429--1245493 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 28
1245419 AAAACTATAT
1245429 ATTATATATATTCA-AAATATTTTC-AAA
1 ATTATATATATT-ATAAATATTTTCAAAA
*
1245456 A-T-TATATATTATATATATTTTCGAAAA
1 ATTATATATATTATAAATATTTTC-AAAA
1245483 ATTATATATAT
1 ATTATATATAT
1245494 ATTATATATA
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
24 1 0.03
25 17 0.53
26 1 0.03
27 5 0.16
28 1 0.03
29 7 0.22
ACGTcount: A:0.46, C:0.05, G:0.02, T:0.48
Consensus pattern (28 bp):
ATTATATATATTATAAATATTTTCAAAA
Found at i:1245473 original size:25 final size:28
Alignment explanation
Indices: 1245431--1245502 Score: 87
Period size: 27 Copynumber: 2.6 Consensus size: 28
1245421 AACTATATAT
*
1245431 TATATATATTCAAAATATTTTC-AAAATTA
1 TATATATATT--ATATATTTTCAAAAATTA
1245460 TATAT-TA-TATATATTTTCGAAAAATTA
1 TATATATATTATATATTTTC-AAAAATTA
1245487 TATATATATTATATAT
1 TATATATATTATATAT
1245503 ATTAAATAGA
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
25 9 0.24
27 13 0.34
28 4 0.11
29 12 0.32
ACGTcount: A:0.46, C:0.04, G:0.01, T:0.49
Consensus pattern (28 bp):
TATATATATTATATATTTTCAAAAATTA
Found at i:1250916 original size:58 final size:58
Alignment explanation
Indices: 1250743--1253199 Score: 3187
Period size: 57 Copynumber: 43.6 Consensus size: 58
1250733 TCCAGTTAAT
* * *
1250743 AAATAAATTCAACAATCTATTTT-CTTACAAAGTTATAATCATTAAAGATTCTCAATG
1 AAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAGG
* * * *
1250800 AAATAAAGTCAACAATCTAATTTCCTTAC-AAGTTAGAATTATTTAAGATTCTCAAGA
1 AAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAGG
1250857 AAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAA-G
1 AAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAGG
* *
1250914 -AA-AAATTCAACAATCTATTTTCCTTA-TAA---AGAATCATTTAGGATTCTCAAGG
1 AAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAGG
* * *
1250966 AAATAAATTTAACAATCTATTTTACTTACAAAGTTATAATCATTTAAGATTCTCAAGG
1 AAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAGG
* *
1251024 AAAT-AATTCAACAATCTATTTTCCTTGCAAAGTTAGAATCATTTAAGATTCTCAAGT
1 AAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAGG
* * *
1251081 TAAT-AA-TCAACAATCTATTTTACTTACAAAGTTAGAATCATTTAAGATTCTCAAGT
1 AAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAGG
* *
1251137 TAATAAATTCAACAATCTATTTTCCTTATAAAGTTAGAAT--TGTTAAGATTCTCAAGG
1 AAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCAT-TTAAGATTCTCAAGG
* * * *
1251194 -ATTAAATTAAACAATCTATTTT-CTTACAAAGTTAGAATCATTTAGGATTCTCAATG
1 AAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAGG
* *
1251250 AAAT-AATTCAACAATCTATTTTTCTTACAAAGTTAGAATCGTTTAAGATTCTCAAGG
1 AAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAGG
* * * *
1251307 AATTAAA--AAAC-ATCTATTTTCCTTACAAAGTTAGAATCATTTAGGATTCTCAATG
1 AAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAGG
* *
1251362 AAAT-AATTCATCAATCTATTTTCCTTACAAAGTTAGAATCGTTTAAGA-T-TCAAGG
1 AAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAGG
* * * * *
1251417 AATTAAATTAAACAA--TATTTTTCTTACAAAGTTAGAATCATTTAGGATTCTC-ATG
1 AAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAGG
* * *
1251472 AAATAAATTCAACAATCTA-TTTCCTTACAAAGTTATAATCATTAAAGATTCTCAATG
1 AAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAGG
* * * *
1251529 AAAT-AAGTCAACAATCTATTTT-TTTACAAAATTAGAATCATTTAAGATTCACAA-G
1 AAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAGG
1251584 AAA-AAATTCAACAATCTA-TTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAGG
1 AAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAGG
*
1251640 AAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTT-AGAATTCTCAATG
1 AAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAG-ATTCTCAAGG
* * ** *
1251698 AAATAAATTCAAC-ATATATTTTCCGTACAAAGTTAGAATTGTTTAAGATTCTGAAGG
1 AAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAGG
* * *
1251755 AAATAAATTAAACAA--TATTTTCCTTACAAAGTTAGAATCATTTAGGGTTCTCAAGG
1 AAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAGG
* *
1251811 AAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCA-TTAGGATTCTCAATG
1 AAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAGG
** *
1251868 AAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATTGTTTAAGATTCTGAAGG
1 AAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAGG
* * * *
1251926 AAATAAATTAAACAATATATTTTCCTTACAAAGTTA-AATCATTTAGGGTTCTCAAGG
1 AAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAGG
* * * **
1251983 AAATAAATTCAACAATCTATTTTCCTTACAAATTTATAATCATTAAAGATTCTCAATA
1 AAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAGG
* *
1252041 AAATAAAGTC-ACAATCTATTTTCCTCACAAAGTTAGAATCATTTAAGATTCTCAA-G
1 AAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAGG
*
1252097 AAAT-AATTCAACAATCTATTTTCTTTACAAAGTT--AATCATTTAAGATTCTCAAGG
1 AAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAGG
* *
1252152 AAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAATATTCTCAAGT
1 AAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAGG
* * *
1252210 TAATAAATTCAACAATCTA-TTTCC-TACAAAGTTAG-ATCATTTAATATTCTCAAGT
1 AAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAGG
* *
1252265 TAATAAATTCAACAATCTATTTTCCTTAC-AA---A-AATCGTTTAAGATTCTCAAGG
1 AAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAGG
* * * * **
1252318 AATTAAATTAAACAATCTATTTT-CTTACAAAAGTTAGAATCATTTAGGGTTCTCAATT
1 AAATAAATTCAACAATCTATTTTCCTTAC-AAAGTTAGAATCATTTAAGATTCTCAAGG
* *
1252376 AAATAAATTCAACAATTTATTTTCCTTAC-AA---AGAATCGTTTAAGATTCTCAAGG
1 AAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAGG
* * * * * *
1252430 -AATTAATTAAACAATCTATTTTCCTTATAAAGTTAAAATCATTTAGGATTCTCAATG
1 AAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAGG
* * *
1252487 CAATAAATTCAACAATCTATTTTTCTTACAAAGTTAGAATCGTTTAAGATTCTCAAGG
1 AAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAGG
* * * * * **
1252545 AAATAAA-TCAATAATGTA-TTTCCTGACAAAGTTAGAACCATTTAGGATTCTCAATC
1 AAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAGG
* * * *
1252601 AAATAAATTCAACAATC--TTTTCCTTAC-AAGTTAGAATCGTTTAAGGTTTTCAAGA
1 AAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAGG
* *
1252656 AAATAAATTCAACAATCTATTTTCCTTAGAAAGTTAG-A--ATTTAGGATTCTC-AGG
1 AAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAGG
* * * *
1252710 AAATAAATTAAACAATCTATTTTCATTACAAAGTTATAATCATTAAAGATTCTCAAGG
1 AAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAGG
* * *
1252768 AAAT-AATCCAGCAATTTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAGG
1 AAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAGG
* * *
1252825 AAATAAATTCAACAATCTATTCTCCTTACAAAGTTAGAATAATTTAAGATTCTCAAGT
1 AAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAGG
* *
1252883 TAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCGTTTAAGATTCTCAAGG
1 AAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAGG
* * *
1252941 AATTAAATTAAACAATCTATTTTCCTTACAAAGTTAGAATCATTAAAGATTCTCAAGG
1 AAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAGG
* *
1252999 AAAT-AATTCAACAATCTATTTTCCTTAC-AAGTTAGAATCATTTAAGATTTTCAAGA
1 AAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAGG
* * *
1253055 AAACAAATTCATC-ATTTA-TTTCCTTACAAAGTTAGAATCA-TTAAGTATTCTCAAGG
1 AAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAG-ATTCTCAAGG
*
1253111 AAATAAATTC-ACAATCTATTTTACTTAC-AAGTTAGAATCATTTAAG-TTCTCAAGG
1 AAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAGG
*
1253166 AAATAAATTCAACCA--TATTTTCCTTACAAAGTTA
1 AAATAAATTCAACAATCTATTTTCCTTACAAAGTTA
1253200 CTCAACACAT
Statistics
Matches: 2093, Mismatches: 230, Indels: 156
0.84 0.09 0.06
Matches are distributed among these distances:
51 20 0.01
52 6 0.00
53 64 0.03
54 145 0.07
55 290 0.14
56 443 0.21
57 589 0.28
58 531 0.25
59 5 0.00
ACGTcount: A:0.41, C:0.14, G:0.09, T:0.36
Consensus pattern (58 bp):
AAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAGG
Found at i:1251339 original size:112 final size:115
Alignment explanation
Indices: 1250743--1253199 Score: 3071
Period size: 112 Copynumber: 21.8 Consensus size: 115
1250733 TCCAGTTAAT
* *
1250743 AAATAAATTCAACAATCTATTTT-CTTACAAAGTTATAATCATTAAAGATTCTCAATGAAATAAA
1 AAATAAA-TCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAATGAAATAAA
* * * *
1250807 GTCAACAATCTAATTTCCTTAC-AAGTTAGAATTATTTAAGATTCTCAAGA
65 TTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAGG
1250857 AAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAA-G-AA-AAA
1 AAATAAA-TCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAATGAAATAAA
* *
1250919 TTCAACAATCTATTTTCCTTA-TAA---AGAATCATTTAGGATTCTCAAGG
65 TTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAGG
* * * *
1250966 AAATAAATTTAACAATCTATTTTACTTACAAAGTTATAATCATTTAAGATTCTCAAGGAAAT-AA
1 AAATAAA-TCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAATGAAATAAA
* *
1251030 TTCAACAATCTATTTTCCTTGCAAAGTTAGAATCATTTAAGATTCTCAAGT
65 TTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAGG
* * *
1251081 TAAT-AATCAACAATCTATTTTACTTACAAAGTTAGAATCATTTAAGATTCTCAA-GTTAATAAA
1 AAATAAATCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAATG-AAATAAA
*
1251144 TTCAACAATCTATTTTCCTTATAAAGTTAGAAT--TGTTAAGATTCTCAAGG
65 TTCAACAATCTATTTTCCTTACAAAGTTAGAATCAT-TTAAGATTCTCAAGG
* * *
1251194 -ATTAAATTAAACAATCTATTTT-CTTACAAAGTTAGAATCATTTAGGATTCTCAATGAAAT-AA
1 AAATAAA-TCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAATGAAATAAA
* *
1251256 TTCAACAATCTATTTTTCTTACAAAGTTAGAATCGTTTAAGATTCTCAAGG
65 TTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAGG
* * *
1251307 AATTAAA-AAAC-ATCTATTTTCCTTACAAAGTTAGAATCATTTAGGATTCTCAATGAAAT-AAT
1 AAATAAATCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAATGAAATAAAT
* *
1251369 TCATCAATCTATTTTCCTTACAAAGTTAGAATCGTTTAAGA-T-TCAAGG
66 TCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAGG
* * * *
1251417 AATTAAATTAAACAA--TATTTTTCTTACAAAGTTAGAATCATTTAGGATTCTC-ATGAAATAAA
1 AAATAAA-TCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAATGAAATAAA
* * *
1251479 TTCAACAATCTA-TTTCCTTACAAAGTTATAATCATTAAAGATTCTCAATG
65 TTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAGG
* * * *
1251529 AAATAAGTCAACAATCTATTTT-TTTACAAAATTAGAATCATTTAAGATTCACAA-GAAA-AAAT
1 AAATAAATCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAATGAAATAAAT
1251591 TCAACAATCTA-TTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAGG
66 TCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAGG
1251640 AAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTT-AGAATTCTCAATGAAATAA
1 AAATAAA-TCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAG-ATTCTCAATGAAATAA
* * ** *
1251704 ATTCAAC-ATATATTTTCCGTACAAAGTTAGAATTGTTTAAGATTCTGAAGG
64 ATTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAGG
* * * *
1251755 AAATAAATTAAACAA--TATTTTCCTTACAAAGTTAGAATCATTTAGGGTTCTCAAGGAAATAAA
1 AAATAAA-TCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAATGAAATAAA
* *
1251818 TTCAACAATCTATTTTCCTTACAAAGTTAGAATCA-TTAGGATTCTCAATG
65 TTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAGG
** * *
1251868 AAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATTGTTTAAGATTCTGAAGGAAATAAA
1 AAATAAA-TCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAATGAAATAAA
* * * *
1251933 TTAAACAATATATTTTCCTTACAAAGTTA-AATCATTTAGGGTTCTCAAGG
65 TTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAGG
* * * *
1251983 AAATAAATTCAACAATCTATTTTCCTTACAAATTTATAATCATTAAAGATTCTCAATAAAATAAA
1 AAATAAA-TCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAATGAAATAAA
* *
1252048 GTC-ACAATCTATTTTCCTCACAAAGTTAGAATCATTTAAGATTCTCAA-G
65 TTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAGG
* * *
1252097 AAATAATTCAACAATCTATTTTCTTTACAAAGTT--AATCATTTAAGATTCTCAAGGAAATAAAT
1 AAATAAATCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAATGAAATAAAT
* *
1252160 TCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAATATTCTCAAGT
66 TCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAGG
* * *
1252210 TAATAAATTCAACAATCTA-TTTCC-TACAAAGTTAG-ATCATTTAATATTCTCAA-GTTAATAA
1 AAATAAA-TCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAATG-AAATAA
*
1252271 ATTCAACAATCTATTTTCCTTAC-AA---A-AATCGTTTAAGATTCTCAAGG
64 ATTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAGG
* * * * *
1252318 AATTAAATTAAACAATCTATTTT-CTTACAAAAGTTAGAATCATTTAGGGTTCTCAATTAAATAA
1 AAATAAA-TCAACAATCTATTTTCCTTAC-AAAGTTAGAATCATTTAAGATTCTCAATGAAATAA
* *
1252382 ATTCAACAATTTATTTTCCTTAC-AA---AGAATCGTTTAAGATTCTCAAGG
64 ATTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAGG
* * * * * * *
1252430 AATTAATTAAACAATCTATTTTCCTTATAAAGTTAAAATCATTTAGGATTCTCAATGCAATAAAT
1 AAATAAATCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAATGAAATAAAT
* *
1252495 TCAACAATCTATTTTTCTTACAAAGTTAGAATCGTTTAAGATTCTCAAGG
66 TCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAGG
* * * * * *
1252545 AAATAAATCAATAATGTA-TTTCCTGACAAAGTTAGAACCATTTAGGATTCTCAATCAAATAAAT
1 AAATAAATCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAATGAAATAAAT
* * * *
1252609 TCAACAATC--TTTTCCTTAC-AAGTTAGAATCGTTTAAGGTTTTCAAGA
66 TCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAGG
* * *
1252656 AAATAAATTCAACAATCTATTTTCCTTAGAAAGTTAG-A--ATTTAGGATTCTC-AGGAAATAAA
1 AAATAAA-TCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAATGAAATAAA
* * * *
1252717 TTAAACAATCTATTTTCATTACAAAGTTATAATCATTAAAGATTCTCAAGG
65 TTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAGG
* * *
1252768 AAAT-AATCCAGCAATTTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAGGAAATAAA
1 AAATAAAT-CAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAATGAAATAAA
* * *
1252832 TTCAACAATCTATTCTCCTTACAAAGTTAGAATAATTTAAGATTCTCAAGT
65 TTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAGG
* * * *
1252883 TAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCGTTTAAGATTCTCAAGGAATTAAA
1 AAATAAA-TCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAATGAAATAAA
* *
1252948 TTAAACAATCTATTTTCCTTACAAAGTTAGAATCATTAAAGATTCTCAAGG
65 TTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAGG
* * *
1252999 AAATAATTCAACAATCTATTTTCCTTAC-AAGTTAGAATCATTTAAGATTTTCAA-GAAAACAAA
1 AAATAAATCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAATG-AAATAAA
* *
1253062 TTCATC-ATTTA-TTTCCTTACAAAGTTAGAATCA-TTAAGTATTCTCAAGG
65 TTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAG-ATTCTCAAGG
* *
1253111 AAATAAATTC-ACAATCTATTTTACTTAC-AAGTTAGAATCATTTAAG-TTCTCAAGGAAATAAA
1 AAATAAA-TCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAATGAAATAAA
*
1253173 TTCAACCA--TATTTTCCTTACAAAGTTA
65 TTCAACAATCTATTTTCCTTACAAAGTTA
1253200 CTCAACACAT
Statistics
Matches: 2079, Mismatches: 189, Indels: 153
0.86 0.08 0.06
Matches are distributed among these distances:
108 35 0.02
109 97 0.05
110 71 0.03
111 390 0.19
112 417 0.20
113 326 0.16
114 254 0.12
115 383 0.18
116 105 0.05
117 1 0.00
ACGTcount: A:0.41, C:0.14, G:0.09, T:0.36
Consensus pattern (115 bp):
AAATAAATCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAATGAAATAAAT
TCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAGG
Found at i:1253419 original size:44 final size:44
Alignment explanation
Indices: 1253348--1253461 Score: 137
Period size: 44 Copynumber: 2.6 Consensus size: 44
1253338 GAATTAATCC
*
1253348 TTTAATTTAC-CAACCAATAATCAAAAGGAACTAATCCTTTGAT
1 TTTAATTTTCGCAACCAATAATCAAAAGGAACTAATCCTTTGAT
* *
1253391 TTTAATTTTCGCAATCC-ATAATCGAAAGGAATTAATCCTTTGAT
1 TTTAATTTTCGCAA-CCAATAATCAAAAGGAACTAATCCTTTGAT
* *
1253435 TTTACTTTTGGCAA-C-ATAAATCAAAAG
1 TTTAATTTTCGCAACCAAT-AATCAAAAG
1253462 CCTTGGATTA
Statistics
Matches: 62, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
42 3 0.05
43 17 0.27
44 40 0.65
45 2 0.03
ACGTcount: A:0.39, C:0.17, G:0.10, T:0.35
Consensus pattern (44 bp):
TTTAATTTTCGCAACCAATAATCAAAAGGAACTAATCCTTTGAT
Found at i:1255747 original size:2 final size:2
Alignment explanation
Indices: 1255740--1255777 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1255730 AATGATGTTT
1255740 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1255778 AATTATGTGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1255812 original size:19 final size:19
Alignment explanation
Indices: 1255788--1255826 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
1255778 AATTATGTGA
1255788 ATCTTCTCTAAGTGAAGTT
1 ATCTTCTCTAAGTGAAGTT
*
1255807 ATCTTCTTTAAGTGAAGTT
1 ATCTTCTCTAAGTGAAGTT
1255826 A
1 A
1255827 ACTCAGTGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.28, C:0.13, G:0.15, T:0.44
Consensus pattern (19 bp):
ATCTTCTCTAAGTGAAGTT
Found at i:1266257 original size:12 final size:12
Alignment explanation
Indices: 1266242--1266287 Score: 56
Period size: 12 Copynumber: 3.6 Consensus size: 12
1266232 CGGTTTTTTT
*
1266242 ACCGGATAAAAA
1 ACCGGTTAAAAA
1266254 ACCGGTTTGAAAAAA
1 ACCGG-TT--AAAAA
1266269 ACCGGTTAAAAA
1 ACCGGTTAAAAA
1266281 ACCGGTT
1 ACCGGTT
1266288 TTTATCCGGA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
12 17 0.57
13 1 0.03
14 2 0.07
15 10 0.33
ACGTcount: A:0.46, C:0.17, G:0.20, T:0.17
Consensus pattern (12 bp):
ACCGGTTAAAAA
Found at i:1266269 original size:15 final size:13
Alignment explanation
Indices: 1266248--1266288 Score: 57
Period size: 12 Copynumber: 3.1 Consensus size: 13
1266238 TTTTACCGGA
1266248 TAAAAAACCGGTT
1 TAAAAAACCGGTT
1266261 TGAAAAAAACCGG-T
1 T--AAAAAACCGGTT
1266275 TAAAAAACCGGTT
1 TAAAAAACCGGTT
1266288 T
1 T
1266289 TTATCCGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 10 0.40
13 3 0.12
14 2 0.08
15 10 0.40
ACGTcount: A:0.46, C:0.15, G:0.17, T:0.22
Consensus pattern (13 bp):
TAAAAAACCGGTT
Found at i:1268614 original size:21 final size:21
Alignment explanation
Indices: 1268590--1268631 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1268580 AGTTTATTTT
*
1268590 TAAACTTTATTTTAATTATCG
1 TAAACTTTATTTCAATTATCG
*
1268611 TAAACTTTGTTTCAATTATCG
1 TAAACTTTATTTCAATTATCG
1268632 AACTTGAAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.31, C:0.12, G:0.07, T:0.50
Consensus pattern (21 bp):
TAAACTTTATTTCAATTATCG
Found at i:1268679 original size:33 final size:33
Alignment explanation
Indices: 1268620--1268728 Score: 170
Period size: 33 Copynumber: 3.4 Consensus size: 33
1268610 GTAAACTTTG
1268620 TTTCAA-TTATCGAACTT-GAAGTTTTTAAGTA
1 TTTCAATTTATCGAACTTGGAAGTTTTTAAGTA
*
1268651 TTTGAATTTATCGAACTTGGAAGTTTTTAAGTA
1 TTTCAATTTATCGAACTTGGAAGTTTTTAAGTA
* *
1268684 TTTTAATTTATCGAACTTGGAAGTATTTAAGTA
1 TTTCAATTTATCGAACTTGGAAGTTTTTAAGTA
1268717 TTTCAA-TTATCG
1 TTTCAATTTATCG
1268729 TAAACTTTGT
Statistics
Matches: 72, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
31 5 0.07
32 17 0.24
33 50 0.69
ACGTcount: A:0.31, C:0.08, G:0.15, T:0.46
Consensus pattern (33 bp):
TTTCAATTTATCGAACTTGGAAGTTTTTAAGTA
Found at i:1268822 original size:15 final size:15
Alignment explanation
Indices: 1268770--1268822 Score: 52
Period size: 15 Copynumber: 3.4 Consensus size: 15
1268760 TTTAATAATA
1268770 TTAAAATCGGTTTTT
1 TTAAAATCGGTTTTT
* *
1268785 TTATAACCGGATTTTT
1 TTAAAATCGG-TTTTT
**
1268801 AAAAAAATCGGTTTTT
1 -TTAAAATCGGTTTTT
1268817 TTAAAA
1 TTAAAA
1268823 CCGAAGCCGG
Statistics
Matches: 28, Mismatches: 8, Indels: 4
0.70 0.20 0.10
Matches are distributed among these distances:
15 12 0.43
16 10 0.36
17 6 0.21
ACGTcount: A:0.36, C:0.08, G:0.11, T:0.45
Consensus pattern (15 bp):
TTAAAATCGGTTTTT
Found at i:1270596 original size:14 final size:14
Alignment explanation
Indices: 1270577--1270603 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1270567 TTATTCCGTC
1270577 AAAATTTGAATTTT
1 AAAATTTGAATTTT
1270591 AAAATTTGAATTT
1 AAAATTTGAATTT
1270604 ATTTATCATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.48
Consensus pattern (14 bp):
AAAATTTGAATTTT
Found at i:1275129 original size:16 final size:16
Alignment explanation
Indices: 1275104--1275146 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
1275094 TAGTTAGTAA
*
1275104 TTAGCGGTTAGAAAGG
1 TTAGCGGTTAGAAAAG
*
1275120 TTAGCTGTTAGAAAAG
1 TTAGCGGTTAGAAAAG
1275136 TTAGCGGTTAG
1 TTAGCGGTTAG
1275147 CGGTTAGCAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.30, C:0.07, G:0.33, T:0.30
Consensus pattern (16 bp):
TTAGCGGTTAGAAAAG
Found at i:1275349 original size:119 final size:125
Alignment explanation
Indices: 1275141--1275469 Score: 361
Period size: 119 Copynumber: 2.6 Consensus size: 125
1275131 AAAAGTTAGC
* * * *
1275141 GGTTAGCGGTTAGCATAGTCCGAACCATAATAAAGTGGATCATACCACAG-ATC-TAGTCACCAC
1 GGTTAGTGGTTAGCATGGTCCGAACCATAATAATGTGGATCATACC-CAGTATCGGA-TCACCAC
*
1275204 AAGGTCAAATAGAATAATTCAAAC-A-A-AT-T-AACAAAATAAAATAAATAAAACAAAAAA
64 AAGGTCGAATAGAATAATTCAAACAATATATATAAACAAAATAAAATAAATAAAACAAAAAA
* *
1275261 -GTTAGTGGTTAGCATGGTCCGTACCATAATAATGTGGATCATACCCAGTATCGGATAACCACAA
1 GGTTAGTGGTTAGCATGGTCCGAACCATAATAATGTGGATCATACCCAGTATCGGATCACCACAA
* * * * *
1275325 GGTTGAATATAATTATTCAAACAAATATATAAAAATAAAATAAAATAAAATAAATAAAATAAAAA
66 GGTCGAATAGAATAATTCAAAC-AATATAT----AT-AAACAAAATAAAATAAATAAAACAAAAA
1275390 A
125 A
* * * *
1275391 GGTTAGTGGTTAGCA-GAGTCTGAACCATAATAATGCGGATCATACCCCGTATCGGGTCACCACA
1 GGTTAGTGGTTAGCATG-GTCCGAACCATAATAATGTGGATCATACCCAGTATCGGATCACCACA
*
1275455 AGGTCGAATCGAATA
65 AGGTCGAATAGAATA
1275470 TTAGAAACAA
Statistics
Matches: 172, Mismatches: 22, Indels: 19
0.81 0.10 0.09
Matches are distributed among these distances:
118 3 0.02
119 70 0.41
120 1 0.01
121 1 0.01
122 1 0.01
123 2 0.01
128 1 0.01
130 27 0.16
131 66 0.38
ACGTcount: A:0.45, C:0.16, G:0.16, T:0.23
Consensus pattern (125 bp):
GGTTAGTGGTTAGCATGGTCCGAACCATAATAATGTGGATCATACCCAGTATCGGATCACCACAA
GGTCGAATAGAATAATTCAAACAATATATATAAACAAAATAAAATAAATAAAACAAAAAA
Found at i:1275366 original size:5 final size:5
Alignment explanation
Indices: 1275356--1275388 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
1275346 CAAATATATA
1275356 AAAAT AAAAT AAAAT AAAAT -AAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
1275389 AAGGTTAGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 23 0.85
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:1275381 original size:9 final size:9
Alignment explanation
Indices: 1275357--1275387 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
1275347 AAATATATAA
1275357 AAATAAAAT
1 AAATAAAAT
1275366 AAAATAAAAT
1 -AAATAAAAT
1275376 AAATAAAAT
1 AAATAAAAT
1275385 AAA
1 AAA
1275388 AAAGGTTAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (9 bp):
AAATAAAAT
Found at i:1275381 original size:14 final size:15
Alignment explanation
Indices: 1275356--1275388 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
1275346 CAAATATATA
1275356 AAAATAAAATAAAAT
1 AAAATAAAATAAAAT
1275371 AAAAT-AAATAAAAT
1 AAAATAAAATAAAAT
1275385 AAAA
1 AAAA
1275389 AAGGTTAGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (15 bp):
AAAATAAAATAAAAT
Found at i:1275478 original size:131 final size:129
Alignment explanation
Indices: 1275236--1275487 Score: 346
Period size: 131 Copynumber: 1.9 Consensus size: 129
1275226 ACAAATTAAC
* *
1275236 AAAATAAAATAAATAAAACAAAAAAGTTAGTGGTTAGCATGGTCCGTACCATAATAATGTGGATC
1 AAAATAAAATAAATAAAACAAAAAAGTTAGTGGTTAGCATGGTCCGAACCATAATAATGCGGATC
* * *
1275301 ATACCCAGTATCGGATAACCACAAGGTTGAATATAATTATTCAAACAAATATATAAAAATAAAAT
66 ATACCCAGTATCGGATAACCACAAGGTCGAATAGAATTATTCAAAC-AATAAATAAAAATAAAAT
* *
1275366 AAAATAAAATAAATAAAATAAAAAAGGTTAGTGGTTAGCA-GAGTCTGAACCATAATAATGCGGA
1 AAAATAAAATAAATAAAACAAAAAA-GTTAGTGGTTAGCATG-GTCCGAACCATAATAATGCGGA
* * * * *
1275430 TCATACCCCGTATCGGGTCACCACAAGGTCGAATCGAA-TATTAGAAACAATAAATAAA
64 TCATACCCAGTATCGGATAACCACAAGGTCGAATAGAATTATT-CAAACAATAAATAAA
1275488 TAAATAACAA
Statistics
Matches: 107, Mismatches: 12, Indels: 6
0.86 0.10 0.05
Matches are distributed among these distances:
130 38 0.36
131 69 0.64
ACGTcount: A:0.48, C:0.13, G:0.15, T:0.23
Consensus pattern (129 bp):
AAAATAAAATAAATAAAACAAAAAAGTTAGTGGTTAGCATGGTCCGAACCATAATAATGCGGATC
ATACCCAGTATCGGATAACCACAAGGTCGAATAGAATTATTCAAACAATAAATAAAAATAAAAT
Found at i:1275532 original size:29 final size:29
Alignment explanation
Indices: 1275507--1275562 Score: 112
Period size: 29 Copynumber: 1.9 Consensus size: 29
1275497 ATGGTTAGAG
1275507 TGCAATAAAATAAAAGTTAGTAGTTAATA
1 TGCAATAAAATAAAAGTTAGTAGTTAATA
1275536 TGCAATAAAATAAAAGTTAGTAGTTAA
1 TGCAATAAAATAAAAGTTAGTAGTTAA
1275563 CTTAAAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.52, C:0.04, G:0.14, T:0.30
Consensus pattern (29 bp):
TGCAATAAAATAAAAGTTAGTAGTTAATA
Found at i:1275571 original size:29 final size:29
Alignment explanation
Indices: 1275510--1275573 Score: 94
Period size: 29 Copynumber: 2.2 Consensus size: 29
1275500 GTTAGAGTGC
**
1275510 AATAAAATAAAAGTTAGTAGTTAATATGC
1 AATAAAATAAAAGTTAGTAGTTAATATAA
1275539 AATAAAATAAAAGTTAGTAGTTAACT-TAA
1 AATAAAATAAAAGTTAGTAGTTAA-TATAA
1275568 AATAAA
1 AATAAA
1275574 TAACATAGCA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 31 0.97
30 1 0.03
ACGTcount: A:0.56, C:0.03, G:0.11, T:0.30
Consensus pattern (29 bp):
AATAAAATAAAAGTTAGTAGTTAATATAA
Found at i:1276838 original size:139 final size:139
Alignment explanation
Indices: 1276666--1277312 Score: 669
Period size: 139 Copynumber: 4.7 Consensus size: 139
1276656 ATATTTGAAT
* * * * ** *
1276666 ATAATTTGAAGACAATACGGTTCCTTCATGATGAGGAAGTCTGATTGCCTGAA-GATGATGTTGC
1 ATAATTTGGAGACAACACGGTTCCTACGTGATGAGGAAGTCTGATTATCTGAAGGATGACGTTGC
* * * ** *
1276730 TCATTCGCGTTGAGGAGATCTGGTCGGTGGATGACATTGTTCCTACGTGATGAGGACGTCTAGTC
66 TCCTACGCATTGAGGAGATCTGGTCGGTGGACAACATTGTTCCTACGTGATGAGGACGTCTAGCC
1276795 ATCTTTATGG
131 ATCTTTA-GG
* * *
1276805 ATAATTTGGAGACAACAAGGTTCCTACGTGATGAGGAAGTCT-AGTTAT-TTAAGGATGACGCTG
1 ATAATTTGGAGACAACACGGTTCCTACGTGATGAGGAAGTCTGA-TTATCTGAAGGATGACGTTG
* *
1276868 CTCCTACGCATTGAGGAGATCTGGTCGGGGGACAACATTGTTCCTACGTGATGAGGACTTCTAGC
65 CTCCTACGCATTGAGGAGATCTGGTCGGTGGACAACATTGTTCCTACGTGATGAGGACGTCTAGC
**
1276933 TGTCTTTAGAG
130 CATCTTTAG-G
* * * * **
1276944 ATACTTTGAAGACAACA-GGTTCCTACGTGATGAGAAAGTCTGGTTATCTG-AGGATGGTGTTGC
1 ATAATTTGGAGACAACACGGTTCCTACGTGATGAGGAAGTCTGATTATCTGAAGGATGACGTTGC
** * * * * *
1277007 TCCTACATATTGCGGAGATCTAGTTGGTGGACAACATTGTTCATACGTGATGAGGATGTCTAGCC
66 TCCTACGCATTGAGGAGATCTGGTCGGTGGACAACATTGTTCCTACGTGATGAGGACGTCTAGCC
*
1277072 GTCTTTAGGG
131 ATCTTTA-GG
* * * * *
1277082 ATAATTTGGAGATAACACGGTTCCTACGTGATGAGGACGTCTGGTTATCT-AAGGATGGCGTTGT
1 ATAATTTGGAGACAACACGGTTCCTACGTGATGAGGAAGTCTGATTATCTGAAGGATGACGTTGC
* * * ** * ** * *
1277146 TCCTACGCGTTTAGGAGATTTTATTGGTGGATGACATTGTTTCTACGTGATGAAGACGTCTAGCC
66 TCCTACGCATTGAGGAGATCTGGTCGGTGGACAACATTGTTCCTACGTGATGAGGACGTCTAGCC
1277211 ATCTTTAAGG
131 ATCTTT-AGG
* * * ** *
1277221 ATAATTTGGAGACAACACGGTTCCTACGTGATGAGAAAGTCTGATTGTCT-AAGGGTGACACTAC
1 ATAATTTGGAGACAACACGGTTCCTACGTGATGAGGAAGTCTGATTATCTGAAGGATGACGTTGC
* * * *
1277285 TCCTTCGCGTTTAGGATATCTGGTCGGT
66 TCCTACGCATTGAGGAGATCTGGTCGGT
1277313 TTCCAATGAT
Statistics
Matches: 422, Mismatches: 77, Indels: 18
0.82 0.15 0.03
Matches are distributed among these distances:
138 119 0.28
139 302 0.72
140 1 0.00
ACGTcount: A:0.25, C:0.16, G:0.28, T:0.31
Consensus pattern (139 bp):
ATAATTTGGAGACAACACGGTTCCTACGTGATGAGGAAGTCTGATTATCTGAAGGATGACGTTGC
TCCTACGCATTGAGGAGATCTGGTCGGTGGACAACATTGTTCCTACGTGATGAGGACGTCTAGCC
ATCTTTAGG
Found at i:1277185 original size:277 final size:278
Alignment explanation
Indices: 1276666--1277266 Score: 747
Period size: 277 Copynumber: 2.2 Consensus size: 278
1276656 ATATTTGAAT
* * * * *
1276666 ATAATTTGAAGACAATACGGTTCCTTCATGATGAGGAAGTCTGATTGCCTGAAGATGATGTTGCT
1 ATAATTTGAAGACAACACGGTTCCTACGTGATGAGAAAGTCTGATTACCTGAAGATGATGTTGCT
* * * * ** * *
1276731 CATTCGCGTTGAGGAGATCTGGTCGGTGGATGACATTGTTCCTACGTGATGAGGACGTCTAGTCA
66 CATACACATTGAGGAGATCTAGTCGGTGGACAACATTGTTCATACGTGATGAGGACGTCTAGCCA
* *
1276796 TCTTTATGGATAATTTGGAGACAACAAGGTTCCTACGTGATGAGGAAGTCTAGTTATTTAAGGAT
131 TCTTTAGGGATAATTTGGAGACAACAAGGTTCCTACGTGATGAGGAAGTCTAGTTATCTAAGGAT
* *
1276861 GACGCTGCTCCTACGCATTGAGGAGATCTGGTCGGGGGACAACATTGTTCCTACGTGATGAGGAC
196 GACGCTGCTCCTACGCATTGAGGAGATCTGATCGGGGGACAACATTGTTCCTACGTGATGAAGAC
* **
1276926 TTCTAGCTGTCTTT-AGAG
261 GTCTAGCCATCTTTAAG-G
* * * * *
1276944 ATACTTTGAAGACAACA-GGTTCCTACGTGATGAGAAAGTCTGGTTATCTGAGGATGGTGTTGCT
1 ATAATTTGAAGACAACACGGTTCCTACGTGATGAGAAAGTCTGATTACCTGAAGATGATGTTGCT
* * * * * *
1277008 CCTACATATTGCGGAGATCTAGTTGGTGGACAACATTGTTCATACGTGATGAGGATGTCTAGCCG
66 CATACACATTGAGGAGATCTAGTCGGTGGACAACATTGTTCATACGTGATGAGGACGTCTAGCCA
* * * *
1277073 TCTTTAGGGATAATTTGGAGATAACACGGTTCCTACGTGATGAGGACGTCTGGTTATCTAAGGAT
131 TCTTTAGGGATAATTTGGAGACAACAAGGTTCCTACGTGATGAGGAAGTCTAGTTATCTAAGGAT
* * * * * * * * * ** *
1277138 GGCGTTGTTCCTACGCGTTTAGGAGATTTTATTGGTGGATGACATTGTTTCTACGTGATGAAGAC
196 GACGCTGCTCCTACGCATTGAGGAGATCTGATCGGGGGACAACATTGTTCCTACGTGATGAAGAC
1277203 GTCTAGCCATCTTTAAGG
261 GTCTAGCCATCTTTAAGG
*
1277221 ATAATTTGGAGACAACACGGTTCCTACGTGATGAGAAAGTCTGATT
1 ATAATTTGAAGACAACACGGTTCCTACGTGATGAGAAAGTCTGATT
1277267 GTCTAAGGGT
Statistics
Matches: 271, Mismatches: 50, Indels: 4
0.83 0.15 0.01
Matches are distributed among these distances:
277 227 0.84
278 44 0.16
ACGTcount: A:0.25, C:0.16, G:0.28, T:0.31
Consensus pattern (278 bp):
ATAATTTGAAGACAACACGGTTCCTACGTGATGAGAAAGTCTGATTACCTGAAGATGATGTTGCT
CATACACATTGAGGAGATCTAGTCGGTGGACAACATTGTTCATACGTGATGAGGACGTCTAGCCA
TCTTTAGGGATAATTTGGAGACAACAAGGTTCCTACGTGATGAGGAAGTCTAGTTATCTAAGGAT
GACGCTGCTCCTACGCATTGAGGAGATCTGATCGGGGGACAACATTGTTCCTACGTGATGAAGAC
GTCTAGCCATCTTTAAGG
Found at i:1277995 original size:154 final size:152
Alignment explanation
Indices: 1277657--1278015 Score: 415
Period size: 154 Copynumber: 2.3 Consensus size: 152
1277647 TTGTGTCTTA
* * * * * *
1277657 AGGAAGACTGTCTCAAGTGAGACAAAATTTGTTTGGTGAAAAAAATCTCAAATGTTTATGTTTCA
1 AGGAAAACTGTCTCAAGTGAGACGAAATTTGTTTCGAGAAAACAATCTCAAATATTTATGTTTCA
**
1277722 AGAGAAAATGTCTCAAGCAATACGAAATTTTATTTGGGAAAACAATCTCAAATGAGATCAATTTT
66 AGAGAAAATGTCTCAAGCAATAC-AAATTTTATTTGAAAAAACAATCTCAAATGAGATCAATTTT
*
1277787 GTTTCAAAAATTTCAAAATTTGT
130 GTTTAAAAAATTTCAAAATTTGT
* * * ** *
1277810 A-GAAAGCTGTCTCAAGAGAAACGAAGCTTGTTTCGAGAGAAACAATATC-AATAATTTATGTTT
1 AGGAAAACTGTCTCAAGTGAGACGAAATTTGTTTCGAGA-AAACAATCTCAAAT-ATTTATGTTT
*
1277873 CAAGAG-AAATAGTCTCAAGCGAGATA-AAATTTGT-TTTGAAAGAAACAATCTCAAGTGAGATC
64 CAAGAGAAAAT-GTCTCAAGC-A-ATACAAATTT-TATTTGAAA-AAACAATCTCAAATGAGATC
1277935 AATTTTGTTTAAAAAATTTCAAAATTTG-
124 AATTTTGTTTAAAAAATTTCAAAATTTGT
* * **
1277963 AGGAAAACAGTCTCAAGTGAGATGAAATTTGTTTTAAGAAAAACAATCTCAAA
1 AGGAAAACTGTCTCAAGTGAGACGAAATTTGTTTCGAG-AAAACAATCTCAAA
1278016 GGCTTATAGA
Statistics
Matches: 170, Mismatches: 26, Indels: 18
0.79 0.12 0.08
Matches are distributed among these distances:
152 35 0.21
153 45 0.26
154 84 0.49
155 6 0.04
ACGTcount: A:0.42, C:0.11, G:0.17, T:0.30
Consensus pattern (152 bp):
AGGAAAACTGTCTCAAGTGAGACGAAATTTGTTTCGAGAAAACAATCTCAAATATTTATGTTTCA
AGAGAAAATGTCTCAAGCAATACAAATTTTATTTGAAAAAACAATCTCAAATGAGATCAATTTTG
TTTAAAAAATTTCAAAATTTGT
Found at i:1279727 original size:26 final size:27
Alignment explanation
Indices: 1279698--1279764 Score: 100
Period size: 27 Copynumber: 2.5 Consensus size: 27
1279688 TTTTATTTTC
1279698 AAAATTTTGAAAAA-TATCAATTAAAA
1 AAAATTTTGAAAAATTATCAATTAAAA
* *
1279724 AAAATTTTGAAAAATTTTTAATTAAAA
1 AAAATTTTGAAAAATTATCAATTAAAA
*
1279751 AAAAGTTTGAAAAA
1 AAAATTTTGAAAAA
1279765 ATATTACCCC
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
26 14 0.38
27 23 0.62
ACGTcount: A:0.60, C:0.01, G:0.06, T:0.33
Consensus pattern (27 bp):
AAAATTTTGAAAAATTATCAATTAAAA
Found at i:1280683 original size:24 final size:26
Alignment explanation
Indices: 1280634--1280714 Score: 80
Period size: 24 Copynumber: 3.2 Consensus size: 26
1280624 ATGCTTCTTT
*
1280634 TCTTATTTTTC-TCTCTTTCTTCTTTTG
1 TCTT-TTTTTCAT-TCTTTCTTTTTTTG
*
1280661 TCTTTTTTTTA-TCTTT-TTTTTTTG
1 TCTTTTTTTCATTCTTTCTTTTTTTG
* *
1280685 -CTTTTTTTCATTCTTTGTTTTTTTC
1 TCTTTTTTTCATTCTTTCTTTTTTTG
1280710 TCTTT
1 TCTTT
1280715 GCTTTGATTT
Statistics
Matches: 46, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
23 9 0.20
24 12 0.26
25 12 0.26
26 9 0.20
27 4 0.09
ACGTcount: A:0.04, C:0.16, G:0.04, T:0.77
Consensus pattern (26 bp):
TCTTTTTTTCATTCTTTCTTTTTTTG
Found at i:1280691 original size:14 final size:15
Alignment explanation
Indices: 1280674--1280719 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 15
1280664 TTTTTTTATC
1280674 TTTTT-TTTTTGCTT
1 TTTTTCTTTTTGCTT
1280688 TTTTTCATTCTTTG-TT
1 TTTTTC-TT-TTTGCTT
*
1280704 TTTTTCTCTTTGCTT
1 TTTTTCTTTTTGCTT
1280719 T
1 T
1280720 GATTTGATCT
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
14 9 0.33
15 4 0.15
16 10 0.37
17 4 0.15
ACGTcount: A:0.02, C:0.13, G:0.07, T:0.78
Consensus pattern (15 bp):
TTTTTCTTTTTGCTT
Found at i:1280705 original size:25 final size:24
Alignment explanation
Indices: 1280631--1280708 Score: 72
Period size: 25 Copynumber: 3.2 Consensus size: 24
1280621 CATATGCTTC
*
1280631 TTTT-CTTATTTTTC-TCTCTTTCTTC
1 TTTTGCTT-TTTTTCAT-TCTTT-TTT
*
1280656 TTTTGTCTTTTTTTTA-TCTTTTTT
1 TTTTG-CTTTTTTTCATTCTTTTTT
1280680 TTTTGCTTTTTTTCATTCTTTGTTT
1 TTTTGCTTTTTTTCATTCTTT-TTT
1280705 TTTT
1 TTTT
1280709 CTCTTTGCTT
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
23 9 0.20
24 12 0.27
25 16 0.36
26 5 0.11
27 3 0.07
ACGTcount: A:0.04, C:0.14, G:0.04, T:0.78
Consensus pattern (24 bp):
TTTTGCTTTTTTTCATTCTTTTTT
Found at i:1284636 original size:16 final size:16
Alignment explanation
Indices: 1284595--1284643 Score: 62
Period size: 16 Copynumber: 3.1 Consensus size: 16
1284585 TAGTTTGTAA
*
1284595 TTAGCGGTTAGAAAGG
1 TTAGCGGTTAGAAAAG
**
1284611 TTAGTTGTTAGAAAAG
1 TTAGCGGTTAGAAAAG
*
1284627 TTAGCGGTTAGCAAAG
1 TTAGCGGTTAGAAAAG
1284643 T
1 T
1284644 CTGAACCATA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.33, C:0.06, G:0.31, T:0.31
Consensus pattern (16 bp):
TTAGCGGTTAGAAAAG
Found at i:1284846 original size:121 final size:122
Alignment explanation
Indices: 1284632--1284963 Score: 333
Period size: 121 Copynumber: 2.6 Consensus size: 122
1284622 AAAAGTTAGC
* * *
1284632 GGTTAGCAAAGTCTGAACCATAATAATATGGATCATACCCCGAATCTGGTCACCACAAGGTCGAA
1 GGTTAGCAAAGTCCGAACCATAATAATATGGATCATACCCCGAATCGGGTCAACACAAGGTCGAA
1284697 TCGAATAATTCAAACAAATTAACAAAATAAAAT-AAATAAAACAAAAAAAAAATAGT
66 TCGAATAATTCAAACAAATTAACAAAATAAAATAAAATAAAACAAAAAAAAAATAGT
** * * * * *
1284753 GGTTAGCATGGTCCGAACCTTAATAATGTGGATTATACCCTGGATCGGGTCAACACAAGGTCGAA
1 GGTTAGCAAAGTCCGAACCATAATAATATGGATCATACCCCGAATCGGGTCAACACAAGGTCGAA
* * *
1284818 TCGAATAATTCAAATAATATATAAAAATAAAATAAAATAAATAAAATAAAATAAATAAAATAAAA
66 TCGAATAATTCAAACAA-AT-T---AACAAAAT---A-AAATAAAAT---A-AAACAAAA-AAAA
1284883 AAGGTTAGT
117 AA---TAGT
* * * * *
1284892 GGTTAGCAGAGTCTGAACCATAATAATGTGGATCATACCCCGAATCGAGTCACCACAAGGTCGAA
1 GGTTAGCAAAGTCCGAACCATAATAATATGGATCATACCCCGAATCGGGTCAACACAAGGTCGAA
*
1284957 TTGAATA
66 TCGAATA
1284964 TTAGAAACAA
Statistics
Matches: 170, Mismatches: 23, Indels: 18
0.81 0.11 0.09
Matches are distributed among these distances:
121 71 0.42
122 2 0.01
123 1 0.01
126 7 0.04
129 1 0.01
130 4 0.02
131 4 0.02
134 1 0.01
135 7 0.04
136 6 0.04
139 66 0.39
ACGTcount: A:0.46, C:0.15, G:0.16, T:0.23
Consensus pattern (122 bp):
GGTTAGCAAAGTCCGAACCATAATAATATGGATCATACCCCGAATCGGGTCAACACAAGGTCGAA
TCGAATAATTCAAACAAATTAACAAAATAAAATAAAATAAAACAAAAAAAAAATAGT
Found at i:1284851 original size:5 final size:5
Alignment explanation
Indices: 1284841--1284882 Score: 70
Period size: 5 Copynumber: 8.8 Consensus size: 5
1284831 ATAATATATA
1284841 AAAAT AAAAT AAAAT -AAAT AAAAT AAAAT -AAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
1284883 AAGGTTAGTG
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
4 8 0.23
5 27 0.77
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:1284861 original size:9 final size:9
Alignment explanation
Indices: 1284842--1284881 Score: 55
Period size: 9 Copynumber: 4.3 Consensus size: 9
1284832 TAATATATAA
1284842 AAATAAAAT
1 AAATAAAAT
1284851 AAA-ATAAAT
1 AAATA-AAAT
1284860 AAAATAAAAT
1 -AAATAAAAT
1284870 AAATAAAAT
1 AAATAAAAT
1284879 AAA
1 AAA
1284882 AAAGGTTAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
8 1 0.04
9 19 0.68
10 7 0.25
11 1 0.04
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (9 bp):
AAATAAAAT
Found at i:1284861 original size:14 final size:14
Alignment explanation
Indices: 1284829--1284882 Score: 83
Period size: 14 Copynumber: 3.9 Consensus size: 14
1284819 CGAATAATTC
* *
1284829 AAATAATATATAA-
1 AAATAAAATAAAAT
1284842 AAATAAAATAAAAT
1 AAATAAAATAAAAT
1284856 AAATAAAATAAAAT
1 AAATAAAATAAAAT
1284870 AAATAAAATAAAA
1 AAATAAAATAAAA
1284883 AAGGTTAGTG
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
13 11 0.29
14 27 0.71
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (14 bp):
AAATAAAATAAAAT
Found at i:1284981 original size:139 final size:138
Alignment explanation
Indices: 1284720--1284990 Score: 341
Period size: 139 Copynumber: 2.0 Consensus size: 138
1284710 ACAAATTAAC
*
1284720 AAAATAAAATAAATAAAACAAAAAAAAAATAGTGGTTAGCATGGTCCGAACCTTAATAATGTGGA
1 AAAATAAAATAAATAAAACAAAAAAAAAATAGTGGTTAGCATGGTCCGAACCATAATAATGTGGA
* * * * * * *
1284785 TTATACCCTGGATCGGGTCAACACAAGGTCGAATCGAATAATTCAAATAATATATAAAAATAAAA
66 TCATACCCCGAATCGAGTCAACACAAGGTCGAATCGAATAATTCAAACAAAAAAT-AAAAT-AAA
1284850 TAAAATAAAT
129 TAAAATAAAT
* *** *
1284860 AAAATAAAATAAATAAAA-TAAAAAAGGTTAGTGGTTAGCA-GAGTCTGAACCATAATAATGTGG
1 AAAATAAAATAAATAAAACAAAAAAAAAATAGTGGTTAGCATG-GTCCGAACCATAATAATGTGG
* * *
1284923 ATCATACCCCGAATCGAGTCACCACAAGGTCGAATTGAAT-ATTAGAAACAAAAAATAAAATAAA
65 ATCATACCCCGAATCGAGTCAACACAAGGTCGAATCGAATAATT-CAAACAAAAAATAAAATAAA
1284987 TAAA
129 TAAA
1284991 CAACAATGGT
Statistics
Matches: 113, Mismatches: 16, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
137 7 0.06
138 9 0.08
139 79 0.70
140 18 0.16
ACGTcount: A:0.51, C:0.12, G:0.14, T:0.23
Consensus pattern (138 bp):
AAAATAAAATAAATAAAACAAAAAAAAAATAGTGGTTAGCATGGTCCGAACCATAATAATGTGGA
TCATACCCCGAATCGAGTCAACACAAGGTCGAATCGAATAATTCAAACAAAAAATAAAATAAATA
AAATAAAT
Found at i:1285071 original size:28 final size:29
Alignment explanation
Indices: 1285006--1285060 Score: 103
Period size: 28 Copynumber: 1.9 Consensus size: 29
1284996 ATGGTTAGAG
1285006 TGCAATAAAATAAAAGTTAGTAGTTAATA
1 TGCAATAAAATAAAAGTTAGTAGTTAATA
1285035 TGCAATAAAAT-AAAGTTAGTAGTTAA
1 TGCAATAAAATAAAAGTTAGTAGTTAA
1285061 CTTGGAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
28 15 0.58
29 11 0.42
ACGTcount: A:0.51, C:0.04, G:0.15, T:0.31
Consensus pattern (29 bp):
TGCAATAAAATAAAAGTTAGTAGTTAATA
Found at i:1287426 original size:30 final size:27
Alignment explanation
Indices: 1287371--1287426 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
1287361 TTTCCTTGTT
* *
1287371 CTTACATCATTTCCTTCTTTTCATTTC
1 CTTAAATCATTTCCTTCTTTCCATTTC
1287398 CTTAAATCATTTCTTCTATCTTTCCATTT
1 CTTAAATCATTTC--CT-TCTTTCCATTT
1287427 TTTCTTTTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 12 0.50
29 2 0.08
30 10 0.42
ACGTcount: A:0.18, C:0.27, G:0.00, T:0.55
Consensus pattern (27 bp):
CTTAAATCATTTCCTTCTTTCCATTTC
Found at i:1291645 original size:23 final size:23
Alignment explanation
Indices: 1291619--1291676 Score: 89
Period size: 23 Copynumber: 2.5 Consensus size: 23
1291609 ATACGACGAC
1291619 CGACCACCGACCTCTCCGACAAA
1 CGACCACCGACCTCTCCGACAAA
*
1291642 CGACCACTGACCTCTCCGACAAA
1 CGACCACCGACCTCTCCGACAAA
* *
1291665 CGGCGACCGACC
1 CGACCACCGACC
1291677 ACTAACCGAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.28, C:0.47, G:0.17, T:0.09
Consensus pattern (23 bp):
CGACCACCGACCTCTCCGACAAA
Found at i:1294619 original size:22 final size:20
Alignment explanation
Indices: 1294591--1294644 Score: 81
Period size: 22 Copynumber: 2.6 Consensus size: 20
1294581 CAGTTTTGTT
1294591 TTATTTTAATTTAGTCACTA
1 TTATTTTAATTTAGTCACTA
*
1294611 TTAGTTTTTGATTTAGTCACTA
1 TTA--TTTTAATTTAGTCACTA
1294633 TTATTTTAATTT
1 TTATTTTAATTT
1294645 TTGCATTTGA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 11 0.37
22 19 0.63
ACGTcount: A:0.26, C:0.07, G:0.07, T:0.59
Consensus pattern (20 bp):
TTATTTTAATTTAGTCACTA
Found at i:1295050 original size:13 final size:14
Alignment explanation
Indices: 1295032--1295060 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1295022 TAACTCTTTG
1295032 TTTTT-ATTTATTT
1 TTTTTAATTTATTT
1295045 TTTTTAATTTATTT
1 TTTTTAATTTATTT
1295059 TT
1 TT
1295061 ATTTTTAGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.33
14 10 0.67
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (14 bp):
TTTTTAATTTATTT
Found at i:1295057 original size:18 final size:17
Alignment explanation
Indices: 1295034--1295067 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1295024 ACTCTTTGTT
*
1295034 TTTATTTATTTTTTTTAA
1 TTTATTT-TTATTTTTAA
1295052 TTTATTTTTATTTTTA
1 TTTATTTTTATTTTTA
1295068 GGGATAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTATTTTTATTTTTAA
Found at i:1297638 original size:20 final size:20
Alignment explanation
Indices: 1297615--1297656 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
1297605 GGACGAACCT
1297615 GAGCAATTGAGGCATACCGG
1 GAGCAATTGAGGCATACCGG
*
1297635 GAGCAATTGAGGCATGCCGG
1 GAGCAATTGAGGCATACCGG
1297655 GA
1 GA
1297657 ACAAGAAGCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.29, C:0.19, G:0.38, T:0.14
Consensus pattern (20 bp):
GAGCAATTGAGGCATACCGG
Found at i:1298031 original size:17 final size:16
Alignment explanation
Indices: 1298006--1298037 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
1297996 AAGATCCAAT
1298006 AAAAAAAAGAAAAAGA
1 AAAAAAAAGAAAAAGA
1298022 AAAAACAAAGAAAAAG
1 AAAAA-AAAGAAAAAG
1298038 GGACGAGAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.84, C:0.03, G:0.12, T:0.00
Consensus pattern (16 bp):
AAAAAAAAGAAAAAGA
Found at i:1299105 original size:32 final size:32
Alignment explanation
Indices: 1299056--1299126 Score: 99
Period size: 32 Copynumber: 2.2 Consensus size: 32
1299046 AGGGAATCTT
*
1299056 TTCAA-ATCAAATGTTGGGGCATCTTTCGAGA
1 TTCAACATCAAATATTGGGGCATCTTTCGAGA
* * *
1299087 TTCAACATCGAATATTGGGGCATCTTTGGGGA
1 TTCAACATCAAATATTGGGGCATCTTTCGAGA
1299119 TTCAACAT
1 TTCAACAT
1299127 TCTGATGCGA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
31 5 0.14
32 30 0.86
ACGTcount: A:0.28, C:0.17, G:0.23, T:0.32
Consensus pattern (32 bp):
TTCAACATCAAATATTGGGGCATCTTTCGAGA
Found at i:1299790 original size:43 final size:43
Alignment explanation
Indices: 1299737--1299859 Score: 149
Period size: 43 Copynumber: 2.9 Consensus size: 43
1299727 CGAAGGGGCC
* *
1299737 ATCCATGATTTCAACTCCACGATGGAGGATATCGTACCAACGG
1 ATCCACGATTTCAACTCCACGATGGAGGATATCGTACCAACAG
* * * *
1299780 ATCCACGATTTCAACTCCACGACGGAGGATATCGTGCCCACAT
1 ATCCACGATTTCAACTCCACGATGGAGGATATCGTACCAACAG
* * *
1299823 ATCCACGGTTTCAACTTCACGATGAAGGGA-ATCGTAC
1 ATCCACGATTTCAACTCCACGATGGA-GGATATCGTAC
1299860 ACACAAGTAG
Statistics
Matches: 68, Mismatches: 11, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
43 65 0.96
44 3 0.04
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.23
Consensus pattern (43 bp):
ATCCACGATTTCAACTCCACGATGGAGGATATCGTACCAACAG
Found at i:1300254 original size:84 final size:84
Alignment explanation
Indices: 1300097--1300676 Score: 653
Period size: 84 Copynumber: 6.9 Consensus size: 84
1300087 CTAGAAGGGC
* * * *
1300097 CAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACGTCATTTGCAGCATAACTCAA
1 CAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACGTCATTTGCAGCATAACTCAA
*
1300162 GGCTAGAAGGGTTATCTGT
66 GGCTAGAAGGGCTATCTGT
* * * * * * *
1300181 CAACAAAAGACCTTCTAGTTCGATTATACTCAGCTCAAAGGCACATCATTTGTAGTATAGCTTAA
1 CAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACGTCATTTGCAGCATAACTCAA
* * * *
1300246 GTCGAGAAGTGCTATCTGC
66 GGCTAGAAGGGCTATCTGT
* * * *
1300265 CAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCTAAGGCACGTCATTTGCAGCATAACTCAA
1 CAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACGTCATTTGCAGCATAACTCAA
1300330 GGCTAGAAGGGCTATCT-T
66 GGCTAGAAGGGCTATCTGT
* * * * *
1300348 CCAACCAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACGTCATTTGCAGCATAACTCA
1 -CAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACGTCATTTGCAGCATAACTCA
*
1300413 AGGCTAGAAGGGTTATCTGT
65 AGGCTAGAAGGGCTATCTGT
* * * * ** * * * *
1300433 TAACAAAAGACCTTCGAGTTTGATTATATTCAGCTCAAAGGCATATTATTTGCAGTATAGCTTAA
1 CAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACGTCATTTGCAGCATAACTCAA
* *
1300498 -GTTGAGAAGAGCTATCTGT
66 GGCT-AGAAGGGCTATCTGT
* * * * *
1300517 CATC-AAATACCTTCGAGATTCGATTTCATTCAGCTCCAAGGCACGTCATTTGCAGCATAACTCA
1 CAACAAAAGACCTTCGAG-TTCGATTACACTCAGCTCAAAGGCACGTCATTTGCAGCATAACTCA
*
1300581 AGGCTAGAAGGGTTATCTGT
65 AGGCTAGAAGGGCTATCTGT
* * * * * *
1300601 CAAAAAAAGACCTTTTGAGTTCGATTACACTCAGCTTAAAGACACATCTTTTGCAGCATAACTCA
1 CAACAAAAGACC-TTCGAGTTCGATTACACTCAGCTCAAAGGCACGTCATTTGCAGCATAACTCA
1300666 AGGCTAGAAGG
65 AGGCTAGAAGG
1300677 ATTATCTACC
Statistics
Matches: 412, Mismatches: 77, Indels: 13
0.82 0.15 0.03
Matches are distributed among these distances:
83 14 0.03
84 334 0.81
85 59 0.14
86 5 0.01
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.26
Consensus pattern (84 bp):
CAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACGTCATTTGCAGCATAACTCAA
GGCTAGAAGGGCTATCTGT
Found at i:1300300 original size:168 final size:168
Alignment explanation
Indices: 1299922--1300676 Score: 848
Period size: 168 Copynumber: 4.5 Consensus size: 168
1299912 TCCAACTCAA
*
1299922 AGAAGGGTTATCTGTCAACAAAAGACCTTCGAGTTCGATTATACTCAGCTCAAAGGCACATCATT
1 AGAAGGGTTATCTGTCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATT
* * * * * ** * * *
1299987 TGCAGTATAGCTTAAGTCGAGAACTGCTATATGCCAACCAAAGACCTTCGAGTTCGACTACGCTC
66 TGCAGCATAACTCAAGGCTAGAAGGGCTATCTGTCAACCAAAGACCTTCGAGTTCGACTACACTC
*
1300052 AGCT-CAAGACACGTCATTTGCAGCATAACTCAAGGCT
131 AGCTCCAAGGCACGTCATTTGCAGCATAACTCAAGGCT
* * * * *
1300089 AGAAGGG----C---CAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACGTCATT
1 AGAAGGGTTATCTGTCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATT
* * * * *
1300147 TGCAGCATAACTCAAGGCTAGAAGGGTTATCTGTCAACAAAAGACCTTCTAGTTCGATTATACTC
66 TGCAGCATAACTCAAGGCTAGAAGGGCTATCTGTCAACCAAAGACCTTCGAGTTCGACTACACTC
* * * * * * * *
1300212 AGCTCAAAGGCACATCATTTGTAGTATAGCTTAAGTCG
131 AGCTCCAAGGCACGTCATTTGCAGCATAACTCAAGGCT
* * * * * * * *
1300250 AGAAGTGCTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCTAAGGCACGTCATT
1 AGAAGGGTTATCTGTCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATT
* *
1300315 TGCAGCATAACTCAAGGCTAGAAGGGCTATCT-TCCAACCAAAGACCTTCGAGTTTGACTACGCT
66 TGCAGCATAACTCAAGGCTAGAAGGGCTATCTGT-CAACCAAAGACCTTCGAGTTCGACTACACT
1300379 CAGCTCCAAGGCACGTCATTTGCAGCATAACTCAAGGCT
130 CAGCTCCAAGGCACGTCATTTGCAGCATAACTCAAGGCT
* * * * * *
1300418 AGAAGGGTTATCTGTTAACAAAAGACCTTCGAGTTTGATTATATTCAGCTCAAAGGCATATTATT
1 AGAAGGGTTATCTGTCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATT
* * * * * * * * * *
1300483 TGCAGTATAGCTTAA-GTTGAGAAGAGCTATCTGTC-ATCAAATACCTTCGAGATTCGATTTCAT
66 TGCAGCATAACTCAAGGCT-AGAAGGGCTATCTGTCAACCAAAGACCTTCGAG-TTCGACTACAC
1300546 TCAGCTCCAAGGCACGTCATTTGCAGCATAACTCAAGGCT
129 TCAGCTCCAAGGCACGTCATTTGCAGCATAACTCAAGGCT
* * * * *
1300586 AGAAGGGTTATCTGTCAAAAAAAGACCTTTTGAGTTCGATTACACTCAGCTTAAAGACACATCTT
1 AGAAGGGTTATCTGTCAACAAAAGACC-TTCGAGTTCGATTACACTCAGCTCAAAGGCACATCAT
1300651 TTGCAGCATAACTCAAGGCTAGAAGG
65 TTGCAGCATAACTCAAGGCTAGAAGG
1300677 ATTATCTACC
Statistics
Matches: 485, Mismatches: 89, Indels: 26
0.81 0.15 0.04
Matches are distributed among these distances:
160 98 0.20
161 30 0.06
163 1 0.00
165 1 0.00
167 24 0.05
168 282 0.58
169 47 0.10
170 2 0.00
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.26
Consensus pattern (168 bp):
AGAAGGGTTATCTGTCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATT
TGCAGCATAACTCAAGGCTAGAAGGGCTATCTGTCAACCAAAGACCTTCGAGTTCGACTACACTC
AGCTCCAAGGCACGTCATTTGCAGCATAACTCAAGGCT
Found at i:1300444 original size:252 final size:250
Alignment explanation
Indices: 1299922--1300711 Score: 1128
Period size: 252 Copynumber: 3.2 Consensus size: 250
1299912 TCCAACTCAA
1299922 AGAAGGGTTATCTGTCAACAAAAGACCTTCGAGTTCGATTATACTCAGCTCAAAGGCACATCATT
1 AGAAGGGTTATCTGTCAACAAAAGACCTTCGAGTTCGATTATACTCAGCTCAAAGGCACATCATT
* *
1299987 TGCAGTATAGCTTAAGTCGAGAACTGCTATATGCCAACCAAAGACCTTCGAGTTCGACTACGCTC
66 TGCAGTATAGCTTAAGTCGAGAAGTGCTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTC
*
1300052 AGCTCAAGACACGTCATTTGCAGCATAACTCAAGGCTAGAAGGG------CCAACCAAAGACCTT
131 AGCTCAAGGCACGTCATTTGCAGCATAACTCAAGGCTAGAAGGGTATCTTCCAACCAAAGACCTT
1300111 CGAGTTCGACTACGCTCAGCTCCAAGGCACGTCATTTGCAGCATAACTCAAGGCT
196 CGAGTTCGACTACGCTCAGCTCCAAGGCACGTCATTTGCAGCATAACTCAAGGCT
*
1300166 AGAAGGGTTATCTGTCAACAAAAGACCTTCTAGTTCGATTATACTCAGCTCAAAGGCACATCATT
1 AGAAGGGTTATCTGTCAACAAAAGACCTTCGAGTTCGATTATACTCAGCTCAAAGGCACATCATT
*
1300231 TGTAGTATAGCTTAAGTCGAGAAGTGCTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTC
66 TGCAGTATAGCTTAAGTCGAGAAGTGCTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTC
1300296 AGCTCTAAGGCACGTCATTTGCAGCATAACTCAAGGCTAGAAGGGCTATCTTCCAACCAAAGACC
131 AGCTC-AAGGCACGTCATTTGCAGCATAACTCAAGGCTAGAAGGG-TATCTTCCAACCAAAGACC
*
1300361 TTCGAGTTTGACTACGCTCAGCTCCAAGGCACGTCATTTGCAGCATAACTCAAGGCT
194 TTCGAGTTCGACTACGCTCAGCTCCAAGGCACGTCATTTGCAGCATAACTCAAGGCT
* * * * *
1300418 AGAAGGGTTATCTGTTAACAAAAGACCTTCGAGTTTGATTATATTCAGCTCAAAGGCATATTATT
1 AGAAGGGTTATCTGTCAACAAAAGACCTTCGAGTTCGATTATACTCAGCTCAAAGGCACATCATT
* * * * * * * **
1300483 TGCAGTATAGCTTAAGTTGAGAAGAGCTATCTGTC-ATCAAATACCTTCGAGATTCGATTTCATT
66 TGCAGTATAGCTTAAGTCGAGAAGTGCTATCTGCCAACCAAAGACCTTCGAG-TTCGACTACGCT
**
1300547 CAGCTCCAAGGCACGTCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGT-CAAAAAAAGA
130 CAGCT-CAAGGCACGTCATTTGCAGCATAACTCAAGGCTAGAAGGG-TATCT-TCCAACCAAAGA
* * * ** * * *
1300611 CCTTTTGAGTTCGATTACACTCAGCTTAAAGACACATCTTTTGCAGCATAACTCAAGGCT
192 CC-TTCGAGTTCGACTACGCTCAGCTCCAAGGCACGTCATTTGCAGCATAACTCAAGGCT
* ** * * *
1300671 AGAAGGATTATCTACCAACATCAAGACTTTTGAGTTCGATT
1 AGAAGGGTTATCTGTCAACA-AAAGACCTTCGAGTTCGATT
1300712 TCATTCATCT
Statistics
Matches: 491, Mismatches: 42, Indels: 16
0.89 0.08 0.03
Matches are distributed among these distances:
244 131 0.27
245 38 0.08
251 14 0.03
252 226 0.46
253 66 0.13
254 16 0.03
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.26
Consensus pattern (250 bp):
AGAAGGGTTATCTGTCAACAAAAGACCTTCGAGTTCGATTATACTCAGCTCAAAGGCACATCATT
TGCAGTATAGCTTAAGTCGAGAAGTGCTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTC
AGCTCAAGGCACGTCATTTGCAGCATAACTCAAGGCTAGAAGGGTATCTTCCAACCAAAGACCTT
CGAGTTCGACTACGCTCAGCTCCAAGGCACGTCATTTGCAGCATAACTCAAGGCT
Found at i:1302068 original size:22 final size:20
Alignment explanation
Indices: 1302040--1302093 Score: 81
Period size: 22 Copynumber: 2.6 Consensus size: 20
1302030 CAGTTTTGTT
1302040 TTATTTTAATTTAGTCACTA
1 TTATTTTAATTTAGTCACTA
*
1302060 TTAGTTTTTGATTTAGTCACTA
1 TTA--TTTTAATTTAGTCACTA
1302082 TTATTTTAATTT
1 TTATTTTAATTT
1302094 TTGCATTTGA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 11 0.37
22 19 0.63
ACGTcount: A:0.26, C:0.07, G:0.07, T:0.59
Consensus pattern (20 bp):
TTATTTTAATTTAGTCACTA
Found at i:1302510 original size:17 final size:17
Alignment explanation
Indices: 1302484--1302523 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
1302474 TAACTCTTTG
1302484 TTTTTATTTATTTAT-T
1 TTTTTATTTATTTATAT
*
1302500 TTTTTACTTTATTTTTAT
1 TTTTTA-TTTATTTATAT
1302518 TTTTTA
1 TTTTTA
1302524 GGGATAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 6 0.29
17 8 0.38
18 7 0.33
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80
Consensus pattern (17 bp):
TTTTTATTTATTTATAT
Found at i:1303846 original size:8 final size:9
Alignment explanation
Indices: 1303822--1303856 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
1303812 TAAAAAAGGT
1303822 TTAAAAAATA
1 TTAAAAAA-A
*
1303832 ATAAAAAAA
1 TTAAAAAAA
1303841 TTAAAAAAA
1 TTAAAAAAA
1303850 TTAAAAA
1 TTAAAAA
1303857 GGATAATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 16 0.70
10 7 0.30
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (9 bp):
TTAAAAAAA
Found at i:1303933 original size:4 final size:4
Alignment explanation
Indices: 1303917--1303949 Score: 57
Period size: 4 Copynumber: 8.2 Consensus size: 4
1303907 ATGATAACAT
*
1303917 AATA AATA GATA AATA AATA AATA AATA AATA A
1 AATA AATA AATA AATA AATA AATA AATA AATA A
1303950 TATTTAAGCC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.24
Consensus pattern (4 bp):
AATA
Found at i:1305365 original size:171 final size:171
Alignment explanation
Indices: 1305072--1305432 Score: 497
Period size: 171 Copynumber: 2.1 Consensus size: 171
1305062 GCCCTTGAGA
* * * *
1305072 TGAATGAAATCGAACTCGAAAAGTCTTCATTGACAGATAGTTTTTCTCGACTTAAGGTATGCTGC
1 TGAATGGAATCGAACTCGAAAAGTCTTCATTGACAGATAGCTTTTCTCGACTTAAGATATACTGC
* * * *
1305137 CGGAAAACGGTTTCTTGTCACTAAGGCACGGCTAACCCAAGTCTTCTTCTCGACTTGAAAACCTC
66 CGGAAAACAGTTTCTTGTCACTAAGGCACAGCTAACCCAAGTCTTCTTATCGACTTGAAAAACTC
1305202 GACTGCAACCAGACAGTAGCGTGATTGATGTGTCATCAAGC
131 GACTGCAACCAGACAGTAGCGTGATTGATGTGTCATCAAGC
* * *
1305243 TGAATGGAATCGAACTCGAAAAGTCTTCGTTGACAGATAGCTTTTCTTGACTTAAGATATACTGT
1 TGAATGGAATCGAACTCGAAAAGTCTTCATTGACAGATAGCTTTTCTCGACTTAAGATATACTGC
* * * * * * *
1305308 TGGAAAACATTTTCTTGTCATTAAGGCGCAGCTAACTCAGGTCTTCTTATTGACTTGAAAAACTC
66 CGGAAAACAGTTTCTTGTCACTAAGGCACAGCTAACCCAAGTCTTCTTATCGACTTGAAAAACTC
* * * ** *
1305373 GACTGTAATCGGACAGTATTGTGATTGATGTGTCATCGAGC
131 GACTGCAACCAGACAGTAGCGTGATTGATGTGTCATCAAGC
*
1305414 TGAATGGAATCGCACTCGA
1 TGAATGGAATCGAACTCGA
1305433 CAATTTTTTT
Statistics
Matches: 165, Mismatches: 25, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
171 165 1.00
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.30
Consensus pattern (171 bp):
TGAATGGAATCGAACTCGAAAAGTCTTCATTGACAGATAGCTTTTCTCGACTTAAGATATACTGC
CGGAAAACAGTTTCTTGTCACTAAGGCACAGCTAACCCAAGTCTTCTTATCGACTTGAAAAACTC
GACTGCAACCAGACAGTAGCGTGATTGATGTGTCATCAAGC
Found at i:1305550 original size:84 final size:84
Alignment explanation
Indices: 1305441--1306565 Score: 1483
Period size: 84 Copynumber: 13.4 Consensus size: 84
1305431 GACAATTTTT
* * * * * * *
1305441 TTGACAGATAACCCTTATTGCCTTGAGCTACT-CTGTAAAATGACGTGCCTTTGAGCTGAGTGAA
1 TTGACAGATAACCCTTCTAGCCTTGAGCTA-TGCTG-CAAATGATGTGCCTTGGAGCTGAGCGTA
* * * *
1305505 ATTGAACTCGAACGT-TTTCG
64 GTCGAACTCGAAGGTCTTTGG
* * * * *
1305525 TTGACAAATAGCCCTTCTTGCCTTGAGTTATGCTGCAAATGATGCGCCTTGGAGCTGAGCGTAGT
1 TTGACAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGT
*
1305590 TGAACTCGAAGGTCTTTGG
66 CGAACTCGAAGGTCTTTGG
* * * * * * * *
1305609 TTGGCAGATAACCTTTCTAACCTTGAGTTATACTGCAAATGATTTGCCTTGGAGCTAAGAGTAGT
1 TTGACAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGT
1305674 CGAACTCGAAGGTCTTTTGG
66 CGAACTCGAAGGTC-TTTGG
* * ** *
1305694 TGGA-AGATAACCCTTTTAGCCTTGAGCTATATTGCAAAATGATGTGCCTTAGAGCTGAGCGTAG
1 TTGACAGATAACCCTTCTAGCCTTGAGCTATGCTGC-AAATGATGTGCCTTGGAGCTGAGCGTAG
*
1305758 TCAAACTCGAAGGTCTTTGG
65 TCGAACTCGAAGGTCTTTGG
* * *
1305778 TTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGACGTGCCTTGGAGCTGAGCGTAGT
1 TTGACAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGT
1305843 CGAACTCGAAGGTCTTTGG
66 CGAACTCGAAGGTCTTTGG
* * *
1305862 TTGGCATATAGCCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGT
1 TTGACAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGT
1305927 CGAACTCGAAGGTCTTTGG
66 CGAACTCGAAGGTCTTTGG
* * * * *
1305946 TTGGCAGATAACACTTCTAGCCTTGAGTTATGCTACAAATGATGTGCCTTGGAGCTGAGCTTAGT
1 TTGACAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGT
1306011 CGAACTCGAAGGTCTTTTGG
66 CGAACTCGAAGGTC-TTTGG
* * * * * *
1306031 -TGGCAAAGAACCCTTCTAGCCTTGAGCTATGCTGCAATTGATGTGCCTTGCAGCTGAGCATAGT
1 TTGACAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGT
1306095 CGAACTCGAAGGTCTTTGG
66 CGAACTCGAAGGTCTTTGG
* * *
1306114 TTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGACTTGGAGCTGAGCGTAGT
1 TTGACAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGT
1306179 CGAACTCGAAGGTCTTTTGG
66 CGAACTCGAAGGTC-TTTGG
*
1306199 -TGACAGATATCCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGT
1 TTGACAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGT
*
1306263 CGAACTCAAAGGTCTTTGG
66 CGAACTCGAAGGTCTTTGG
* * *
1306282 GTGGCAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAACTGAGCGTAGT
1 TTGACAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGT
1306347 CGAACTCGAAGGTCTTTGG
66 CGAACTCGAAGGTCTTTGG
* * * *
1306366 TTGGCAGATAA-CCTTCTAGCCTTGAGTTATGCTGCAGATGATGTGCCTTGGAGTTGAGCGTAGT
1 TTGACAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGT
1306430 CGAACTCGAAGGTCTTTTGG
66 CGAACTCGAAGGTC-TTTGG
* * * * * * *
1306450 -TGATAGATATCCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGATGAGTGTAAT
1 TTGACAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGT
* *
1306514 CAAACTCGAAGGT-GTTGG
66 CGAACTCGAAGGTCTTTGG
* * *
1306532 CTGACAGATAACCCTTCTCGCCTTGAGTTATGCT
1 TTGACAGATAACCCTTCTAGCCTTGAGCTATGCT
1306566 ACCGATAGTT
Statistics
Matches: 931, Mismatches: 98, Indels: 25
0.88 0.09 0.02
Matches are distributed among these distances:
82 4 0.00
83 146 0.16
84 699 0.75
85 82 0.09
ACGTcount: A:0.23, C:0.20, G:0.26, T:0.30
Consensus pattern (84 bp):
TTGACAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGT
CGAACTCGAAGGTCTTTGG
Found at i:1307871 original size:94 final size:95
Alignment explanation
Indices: 1307694--1307950 Score: 331
Period size: 94 Copynumber: 2.7 Consensus size: 95
1307684 TAGCTTAATT
* * * * *
1307694 CATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACAGCTTAATATCATTGTATAG-ATATT
1 CATAAAGTCGGGGCGTTTAACCAATTGCTCTAGAGGGACAAC-TCA-AGC-TT-TATTGTATATT
* *
1307758 ATAATCACTTTTATCAGGCTAGTTGAATATTATC
62 ATAATCACCTTTATCAGGCTAGCTGAATATTATC
*
1307792 CATAAAGTCGGGG-GTTTAACCAATTGCTCTAGAGGGAAAACTCAAGCTTTATTGTATATTATAA
1 CATAAAGTCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATATTATAA
*
1307856 TCACCTTTATCAGGCTAGCTGAATCTTATC
66 TCACCTTTATCAGGCTAGCTGAATATTATC
* * * * *
1307886 GATAAAGTTGGGGCGTTTAACCAATTGCTTTAGAGGGACAACTCAAGCTTTAATATATA-TATAA
1 CATAAAGTCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATATTATAA
1307950 T
66 T
1307951 ATTATAATCT
Statistics
Matches: 142, Mismatches: 15, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
93 4 0.03
94 55 0.39
95 43 0.30
96 2 0.01
97 26 0.18
98 12 0.08
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Consensus pattern (95 bp):
CATAAAGTCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATATTATAA
TCACCTTTATCAGGCTAGCTGAATATTATC
Found at i:1310563 original size:9 final size:9
Alignment explanation
Indices: 1310551--1310693 Score: 50
Period size: 9 Copynumber: 15.9 Consensus size: 9
1310541 AAAAAAGGTT
1310551 TAAAAATAA
1 TAAAAATAA
1310560 T-AAAATAA
1 TAAAAATAA
*
1310568 GTAAAAAATAT
1 -T-AAAAATAA
*
1310579 TAAAAATGA
1 TAAAAATAA
1310588 TAATAAAATAA
1 T-A-AAAATAA
*
1310599 TAATGAA-AA
1 TAA-AAATAA
*
1310608 T-AAAGTAA
1 TAAAAATAA
* *
1310616 TAAAAAGAG
1 TAAAAATAA
*
1310625 GAAAAA-AA
1 TAAAAATAA
1310633 -AAAAA-AA
1 TAAAAATAA
1310640 TAAAAAATAA
1 T-AAAAATAA
* **
1310650 TGATGATAA
1 TAAAAATAA
*
1310659 TAATAATAA
1 TAAAAATAA
1310668 T-AAAATAGA
1 TAAAAATA-A
*
1310677 TAAATA-AA
1 TAAAAATAA
1310685 TAAATAATA
1 TAAA-AATA
1310694 TATTTAAGCC
Statistics
Matches: 99, Mismatches: 20, Indels: 29
0.67 0.14 0.20
Matches are distributed among these distances:
7 8 0.08
8 22 0.22
9 44 0.44
10 12 0.12
11 13 0.13
ACGTcount: A:0.71, C:0.00, G:0.07, T:0.22
Consensus pattern (9 bp):
TAAAAATAA
Found at i:1310574 original size:19 final size:19
Alignment explanation
Indices: 1310552--1310650 Score: 61
Period size: 17 Copynumber: 5.5 Consensus size: 19
1310542 AAAAAGGTTT
1310552 AAAAATAATAAAATAAG-TA
1 AAAAATAATAAAA-AAGATA
* *
1310571 AAAAATATTAAAAATGATA
1 AAAAATAATAAAAAAGATA
*
1310590 ATAAAATAATAATGAAA-AT-
1 A-AAAATAATAA-AAAAGATA
* **
1310609 -AAAGTAAT-AAAAAGAGG
1 AAAAATAATAAAAAAGATA
1310626 AAAAA-AA-AAAAAA-ATA
1 AAAAATAATAAAAAAGATA
1310642 AAAAATAAT
1 AAAAATAAT
1310651 GATGATAATA
Statistics
Matches: 60, Mismatches: 11, Indels: 19
0.67 0.12 0.21
Matches are distributed among these distances:
15 3 0.05
16 8 0.13
17 16 0.27
18 5 0.08
19 15 0.25
20 11 0.18
21 2 0.03
ACGTcount: A:0.74, C:0.00, G:0.07, T:0.19
Consensus pattern (19 bp):
AAAAATAATAAAAAAGATA
Found at i:1310595 original size:11 final size:11
Alignment explanation
Indices: 1310555--1310620 Score: 57
Period size: 11 Copynumber: 5.9 Consensus size: 11
1310545 AAGGTTTAAA
1310555 AATAATAAAAT
1 AATAATAAAAT
1310566 AAGTAA-AAAAT
1 AA-TAATAAAAT
*
1310577 -ATTA-AAAAT
1 AATAATAAAAT
*
1310586 GATAATAAAAT
1 AATAATAAAAT
1310597 AATAATGAAAAT
1 AATAAT-AAAAT
1310609 AAAGTAATAAAA
1 -AA-TAATAAAA
1310621 AGAGGAAAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
9 7 0.15
10 4 0.09
11 17 0.37
12 8 0.17
13 6 0.13
14 4 0.09
ACGTcount: A:0.70, C:0.00, G:0.06, T:0.24
Consensus pattern (11 bp):
AATAATAAAAT
Found at i:1310607 original size:23 final size:23
Alignment explanation
Indices: 1310564--1310620 Score: 57
Period size: 23 Copynumber: 2.5 Consensus size: 23
1310554 AAATAATAAA
*
1310564 ATAAGTAAAAAATATTAAAAATG
1 ATAAGTAAAAAATAATAAAAATG
*
1310587 ATAA-TAAAATAATAATGAAAAT-
1 ATAAGTAAAA-AATAATAAAAATG
1310609 A-AAGTAATAAAA
1 ATAAGTAA-AAAA
1310621 AGAGGAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
21 2 0.07
22 11 0.38
23 16 0.55
ACGTcount: A:0.68, C:0.00, G:0.07, T:0.25
Consensus pattern (23 bp):
ATAAGTAAAAAATAATAAAAATG
Found at i:1313629 original size:6 final size:6
Alignment explanation
Indices: 1313618--1313658 Score: 82
Period size: 6 Copynumber: 6.8 Consensus size: 6
1313608 TCTAGCAGGA
1313618 TCACTC TCACTC TCACTC TCACTC TCACTC TCACTC TCACT
1 TCACTC TCACTC TCACTC TCACTC TCACTC TCACTC TCACT
1313659 GGTCCTAATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.17, C:0.49, G:0.00, T:0.34
Consensus pattern (6 bp):
TCACTC
Found at i:1313818 original size:17 final size:19
Alignment explanation
Indices: 1313788--1313828 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
1313778 AATCATTGTA
*
1313788 TTTTA-GATTGATAT-TTT
1 TTTTATGATTGATATATAT
1313805 TTTTATGATT-ATATATAT
1 TTTTATGATTGATATATAT
1313823 TTTTAT
1 TTTTAT
1313829 TAATTTATGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 9 0.43
18 12 0.57
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.66
Consensus pattern (19 bp):
TTTTATGATTGATATATAT
Found at i:1327431 original size:23 final size:21
Alignment explanation
Indices: 1327377--1327433 Score: 60
Period size: 23 Copynumber: 2.6 Consensus size: 21
1327367 CCCATTGATA
1327377 TGTATCGATACACTATAAATG
1 TGTATCGATACACTATAAATG
* * * *
1327398 TGTACCAATACATTCTTTGAATG
1 TGTATCGATACA--CTATAAATG
1327421 TGTATCGATACAC
1 TGTATCGATACAC
1327434 CCCTAAATAT
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
21 11 0.39
23 17 0.61
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.35
Consensus pattern (21 bp):
TGTATCGATACACTATAAATG
Found at i:1328095 original size:4 final size:4
Alignment explanation
Indices: 1328086--1328112 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
1328076 CAATGCATGT
1328086 ATAA ATAA ATAA ATAA ATAA ATAA ATA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATA
1328113 CATAGTTGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAA
Found at i:1335796 original size:6 final size:6
Alignment explanation
Indices: 1335785--1335829 Score: 90
Period size: 6 Copynumber: 7.5 Consensus size: 6
1335775 GAATGTAAAG
1335785 CTCCCT CTCCCT CTCCCT CTCCCT CTCCCT CTCCCT CTCCCT CTC
1 CTCCCT CTCCCT CTCCCT CTCCCT CTCCCT CTCCCT CTCCCT CTC
1335830 TTATTAAACT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.00, C:0.67, G:0.00, T:0.33
Consensus pattern (6 bp):
CTCCCT
Found at i:1338572 original size:87 final size:88
Alignment explanation
Indices: 1338407--1338590 Score: 228
Period size: 87 Copynumber: 2.1 Consensus size: 88
1338397 AACCTTCTTT
* * * * *
1338407 TGTGATGGAATCAAACAAGATGTCGGTGTTGATCTACCTCATTCTATGATAGATTCGAGCAAAAT
1 TGTGATGGAATCAAACAAGATATCGGTGCTGATCTACCTCATTCTATGATAGAATCGAGAAAAAA
* *
1338472 GAAAATGACGACCC-CCTCCTTC
66 GAAAATGACGACCCAACTCCTTA
* *
1338494 TGTGATGGAATCGAACAAGATATCGGTGCTGATCTACCTCATTCTGTGATAGAATCGAGAAAAAA
1 TGTGATGGAATCAAACAAGATATCGGTGCTGATCTACCTCATTCTATGATAGAATCGAGAAAAAA
***
1338559 GTTGATG-CTGACCCAACTCCTTA
66 GAAAATGAC-GACCCAACTCCTTA
*
1338582 TGCGATGGA
1 TGTGATGGA
1338591 TTTGAGCAAA
Statistics
Matches: 82, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
86 1 0.01
87 67 0.82
88 14 0.17
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (88 bp):
TGTGATGGAATCAAACAAGATATCGGTGCTGATCTACCTCATTCTATGATAGAATCGAGAAAAAA
GAAAATGACGACCCAACTCCTTA
Found at i:1338659 original size:132 final size:131
Alignment explanation
Indices: 1338458--1338815 Score: 477
Period size: 132 Copynumber: 2.7 Consensus size: 131
1338448 TTCTATGATA
* * * * * *
1338458 GATTCGAGCAAAATGAAAATGA-CGA-CCCCCTCCTTCTGTGATGGAATCGAACAAGATATCGGT
1 GATTTGAGCAAAATAAAAAT-ATCGATCCACCTCCTTCTGTGATGGAATCGAACGAGAT-TTGAT
*
1338521 GCTGATCTACCTCATTCTGTGATAGAATCGAGAAAAAAGTTGATGCTGACCCAACTCCTTATGCG
64 GCTGATCTACCTCATTCTGTGATAGAATCGAGAAAAAACTTGATGCTGACCCAACTCCTTATGCG
1338586 ATG
129 ATG
1338589 GATTTGAGCAAAATAAAAATATCGATCCACCTCCTTCTGTGATGGAATCGAACGAGATGTTGATG
1 GATTTGAGCAAAATAAAAATATCGATCCACCTCCTTCTGTGATGGAATCGAACGAGAT-TTGATG
* * * ** *
1338654 GTGATCTACCTCCTTCTGTGATAGAATCAAGCTAAAACTTGATGCTGATCCAACTCCTTATGCGA
65 CTGATCTACCTCATTCTGTGATAGAATCGAGAAAAAACTTGATGCTGACCCAACTCCTTATGCGA
1338719 TG
130 TG
* ** * * *
1338721 GATTTGAGCAAAATAAAAATGTCGATCCACCTTATTCTGTGATGAAATCGAACGAGATATCAGTG
1 GATTTGAGCAAAATAAAAATATCGATCCACCTCCTTCTGTGATGGAATCGAACGAGATTTGA-TG
* *
1338786 CTGATATACCACATTCTGTGATAGAATCGA
65 CTGATCTACCTCATTCTGTGATAGAATCGA
1338816 CCAAATAGTT
Statistics
Matches: 199, Mismatches: 25, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
130 1 0.01
131 23 0.12
132 175 0.88
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Consensus pattern (131 bp):
GATTTGAGCAAAATAAAAATATCGATCCACCTCCTTCTGTGATGGAATCGAACGAGATTTGATGC
TGATCTACCTCATTCTGTGATAGAATCGAGAAAAAACTTGATGCTGACCCAACTCCTTATGCGAT
G
Found at i:1338696 original size:44 final size:44
Alignment explanation
Indices: 1338612--1338712 Score: 114
Period size: 44 Copynumber: 2.3 Consensus size: 44
1338602 TAAAAATATC
* * ** *
1338612 GATCCACCTCCTTCTGTGATGGAATCGAACGAGATGTTGATGGT
1 GATCCACCTCCTTCTGTGATAGAATCGAACGAAAACTTGATGCT
* *
1338656 GATCTACCTCCTTCTGTGATAGAATC-AAGCTAAAACTTGATGCT
1 GATCCACCTCCTTCTGTGATAGAATCGAA-CGAAAACTTGATGCT
*
1338700 GATCCAACTCCTT
1 GATCCACCTCCTT
1338713 ATGCGATGGA
Statistics
Matches: 47, Mismatches: 9, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
43 2 0.04
44 45 0.96
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.31
Consensus pattern (44 bp):
GATCCACCTCCTTCTGTGATAGAATCGAACGAAAACTTGATGCT
Found at i:1339414 original size:36 final size:36
Alignment explanation
Indices: 1339367--1339594 Score: 218
Period size: 36 Copynumber: 6.5 Consensus size: 36
1339357 CTCAAAGATT
*
1339367 TTTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* **
1339403 TTTGTTTCAAGAGAAACATAT-TC-A-A-AG---ATT
1 TTTGTTTCAAGAGAAAC-TGTCTCAAGAGAGACAAAA
* *
1339433 TTGTGTTTCAAGAGAAACTATCTCAAGCGAGACAAAA
1 TT-TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
*
1339470 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAG
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* ** * * *
1339506 CTCATTTCAAGGGGAACTGTCTCAAGAGAGACAAAC
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * * * *
1339542 TTCGTTTAAAGAGAAACTGTCTCAAGATATACAAAC
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
*
1339578 TTTGTTTCAAAAGAAAC
1 TTTGTTTCAAGAGAAAC
1339595 AGACTCAGGC
Statistics
Matches: 157, Mismatches: 26, Indels: 18
0.78 0.13 0.09
Matches are distributed among these distances:
30 6 0.04
31 17 0.11
32 1 0.01
33 2 0.01
34 2 0.01
35 1 0.01
36 123 0.78
37 5 0.03
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.27
Consensus pattern (36 bp):
TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
Found at i:1339470 original size:67 final size:67
Alignment explanation
Indices: 1339225--1339494 Score: 296
Period size: 66 Copynumber: 4.1 Consensus size: 67
1339215 GAAACCATAA
* * * * * * ** *
1339225 TCAAAGTTTTTATGTTTCAAGAGATACTGTCACTAGGGAGATAAAATTCATTTCAAGGGAAACGA
1 TCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGAGAAACGA
1339290 TC
66 TC
* ** * * ** ** *
1339292 TCAAATA-TCAGTGTTTCAAGGGAAACTGTCTTAAGAAAGACAAAATTCATTTCAAGGGAAACGA
1 TCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGAGAAACGA
1339356 TC
66 TC
1339358 TCAAAGATTTT-TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGAGAAAC-A
1 TCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGAGAAACGA
*
1339421 TAT
66 T-C
* *
1339424 TCAAAGATTTTGTGTTTCAAGAGAAACTATCTCAAGCGAGACAAAATTTGTTTCAAGAGAAACTG
1 TCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGAGAAAC-G
1339489 -TC
65 ATC
1339491 TCAA
1 TCAA
1339495 GAGAGACAAA
Statistics
Matches: 171, Mismatches: 27, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
65 2 0.01
66 109 0.64
67 59 0.35
68 1 0.01
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (67 bp):
TCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGAGAAACGA
TC
Found at i:1339493 original size:133 final size:133
Alignment explanation
Indices: 1339225--1339494 Score: 312
Period size: 133 Copynumber: 2.0 Consensus size: 133
1339215 GAAACCATAA
* * * * *
1339225 TCAAAGTTTTTATGTTTCAAGAGATACTGTCACTAGGGAGATAAAATTCATTTCAAGGGAAACGA
1 TCAAAGATTTTATGTTTCAAGAGAAACTGTCACAAGGGAGACAAAATTCATTTCAAGAGAAACGA
* * * * *
1339290 TCTCAAATATCAGTGTTTCAAGGGAAACTGTCTTAAGAAAGACAAAATTCATTTCAAGGGAAACG
66 TCTCAAAGATCAGTGTTTCAAGAGAAACTATCTCAAGAAAGACAAAATTCATTTCAAGAGAAACG
1339355 ATC
131 ATC
* **
1339358 TCAAAGATTTT-TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGAGAAAC-A
1 TCAAAGATTTTATGTTTCAAGAGAAACTGTCACAAGGGAGACAAAATTCATTTCAAGAGAAACGA
* ** ** **
1339421 TATTCAAAGATTTTGTGTTTCAAGAGAAACTATCTCAAGCGAGACAAAATTTGTTTCAAGAGAAA
66 T-CTCAAAGA-TCAGTGTTTCAAGAGAAACTATCTCAAGAAAGACAAAATTCATTTCAAGAGAAA
1339486 CTG-TC
129 C-GATC
1339491 TCAA
1 TCAA
1339495 GAGAGACAAA
Statistics
Matches: 114, Mismatches: 20, Indels: 6
0.81 0.14 0.04
Matches are distributed among these distances:
131 2 0.02
132 50 0.44
133 61 0.54
134 1 0.01
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (133 bp):
TCAAAGATTTTATGTTTCAAGAGAAACTGTCACAAGGGAGACAAAATTCATTTCAAGAGAAACGA
TCTCAAAGATCAGTGTTTCAAGAGAAACTATCTCAAGAAAGACAAAATTCATTTCAAGAGAAACG
ATC
Found at i:1339692 original size:21 final size:21
Alignment explanation
Indices: 1339666--1339799 Score: 119
Period size: 21 Copynumber: 6.4 Consensus size: 21
1339656 AAATTGTCTC
*
1339666 AAAGACTTATCATCTTGCTCA
1 AAAGACTTATCATCTTGCTCG
*
1339687 AAAGACTTATCATCTTGCTTG
1 AAAGACTTATCATCTTGCTCG
** * *
1339708 AAAGACTTAT-AGATGGCCCG
1 AAAGACTTATCATCTTGCTCG
* *
1339728 AAGGACTTATCATCTTTCTCG
1 AAAGACTTATCATCTTGCTCG
** * *
1339749 AAAGACTTAT-AGATGGCCCG
1 AAAGACTTATCATCTTGCTCG
* *
1339769 AAGGACTTATGCATCATGCTCG
1 AAAGACTTAT-CATCTTGCTCG
1339791 AAAGACTTA
1 AAAGACTTA
1339800 CTTATGACAC
Statistics
Matches: 84, Mismatches: 26, Indels: 5
0.73 0.23 0.04
Matches are distributed among these distances:
20 28 0.33
21 43 0.51
22 13 0.15
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.29
Consensus pattern (21 bp):
AAAGACTTATCATCTTGCTCG
Found at i:1339740 original size:41 final size:41
Alignment explanation
Indices: 1339690--1339799 Score: 184
Period size: 41 Copynumber: 2.7 Consensus size: 41
1339680 TTGCTCAAAA
*
1339690 GACTTATCATCTTGCTTGAAAGACTTATAGATGGCCCGAAG
1 GACTTATCATCTTGCTCGAAAGACTTATAGATGGCCCGAAG
*
1339731 GACTTATCATCTTTCTCGAAAGACTTATAGATGGCCCGAAG
1 GACTTATCATCTTGCTCGAAAGACTTATAGATGGCCCGAAG
*
1339772 GACTTATGCATCATGCTCGAAAGACTTA
1 GACTTAT-CATCTTGCTCGAAAGACTTA
1339800 CTTATGACAC
Statistics
Matches: 64, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
41 46 0.72
42 18 0.28
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.29
Consensus pattern (41 bp):
GACTTATCATCTTGCTCGAAAGACTTATAGATGGCCCGAAG
Found at i:1339775 original size:20 final size:20
Alignment explanation
Indices: 1339711--1339778 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
1339701 TTGCTTGAAA
1339711 GACTTATAGATGGCCCGAAG
1 GACTTATAGATGGCCCGAAG
** ** * *
1339731 GACTTATCATCTTTCTCGAAA
1 GACTTAT-AGATGGCCCGAAG
1339752 GACTTATAGATGGCCCGAAG
1 GACTTATAGATGGCCCGAAG
1339772 GACTTAT
1 GACTTAT
1339779 GCATCATGCT
Statistics
Matches: 35, Mismatches: 12, Indels: 2
0.71 0.24 0.04
Matches are distributed among these distances:
20 21 0.60
21 14 0.40
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28
Consensus pattern (20 bp):
GACTTATAGATGGCCCGAAG
Found at i:1339815 original size:42 final size:41
Alignment explanation
Indices: 1339685--1339825 Score: 167
Period size: 41 Copynumber: 3.4 Consensus size: 41
1339675 TCATCTTGCT
* *
1339685 CAAAAGACTTATCATCTTGCTTGAAAGACTTATAGATGGCC
1 CAAAGGACTTATCATCTTGCTCGAAAGACTTATAGATGGCC
* *
1339726 CGAAGGACTTATCATCTTTCTCGAAAGACTTATAGATGGCC
1 CAAAGGACTTATCATCTTGCTCGAAAGACTTATAGATGGCC
* * * * *
1339767 CGAAGGACTTATGCATCATGCTCGAAAGACTTACT-TATGACA
1 CAAAGGACTTAT-CATCTTGCTCGAAAGACTTA-TAGATGGCC
1339809 CAAAGGACTTACTCATC
1 CAAAGGACTTA-TCATC
1339826 AAGAAACCCT
Statistics
Matches: 87, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
41 49 0.56
42 36 0.41
43 2 0.02
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.28
Consensus pattern (41 bp):
CAAAGGACTTATCATCTTGCTCGAAAGACTTATAGATGGCC
Found at i:1340074 original size:42 final size:40
Alignment explanation
Indices: 1339976--1340089 Score: 95
Period size: 42 Copynumber: 2.7 Consensus size: 40
1339966 GCCTGAAGGT
* * * *
1339976 CTTATGGATGGCCCGAAGGATTTATCATCTTGCTCGAATGA
1 CTTATAGAT-GCCCGAAGGATTTATCATCATGCTCAAAAGA
*
1340017 CTTATAGATGACCCGAAGGATTTA-CGTATCATGCTTAAAAGA
1 CTTATAGATG-CCCGAAGGATTTATC--ATCATGCTCAAAAGA
* * *
1340059 CTTATTGATAGCCCGAATGACTTACTCATCA
1 CTTATAGAT-GCCCGAAGGATTTA-TCATCA
1340090 AGAAACCCTT
Statistics
Matches: 59, Mismatches: 8, Indels: 11
0.76 0.10 0.14
Matches are distributed among these distances:
40 2 0.03
41 21 0.36
42 34 0.58
43 1 0.02
44 1 0.02
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31
Consensus pattern (40 bp):
CTTATAGATGCCCGAAGGATTTATCATCATGCTCAAAAGA
Found at i:1340174 original size:42 final size:42
Alignment explanation
Indices: 1340128--1340287 Score: 189
Period size: 42 Copynumber: 3.8 Consensus size: 42
1340118 CTTATTTGCT
*
1340128 ATCAAGGAACCCCTACATATCACGATGGTCCCTCTAGTTGTC
1 ATCAAGGAACCCCTACATATCACGATGGTCCCTCAAGTTGTC
* * * *
1340170 ATCAAGGAACGTCC-ACATTTCACGTTGGTCCCTCAAGCTTGCC
1 ATCAAGGAAC-CCCTACATATCACGATGGTCCCTCAAG-TTGTC
* *
1340213 ATCAAGGAACCCCTACATATCA-TATTGGTCCCTCGAGTTGTC
1 ATCAAGGAACCCCTACATATCACGA-TGGTCCCTCAAGTTGTC
* * *
1340255 ATCATGGAACCCCTACAAATCACGTTGGTCCCT
1 ATCAAGGAACCCCTACATATCACGATGGTCCCT
1340288 TAAGCTTAGT
Statistics
Matches: 98, Mismatches: 15, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
42 64 0.65
43 34 0.35
ACGTcount: A:0.26, C:0.31, G:0.17, T:0.26
Consensus pattern (42 bp):
ATCAAGGAACCCCTACATATCACGATGGTCCCTCAAGTTGTC
Found at i:1340278 original size:85 final size:85
Alignment explanation
Indices: 1340123--1340294 Score: 240
Period size: 85 Copynumber: 2.0 Consensus size: 85
1340113 AGTTACTTAT
* * * *
1340123 TTGCTATCAAGGAACCCCTACATATCACGATGGTCCCTCTAGTTGTCATCAAGGAACGTCCACAT
1 TTGCCATCAAGGAACCCCTACATATCACGATGGTCCCTCGAGTTGTCATCAAGGAACGCCCACAA
*
1340188 TTCACGTTGGTCCCTCAAGC
66 ATCACGTTGGTCCCTCAAGC
* *
1340208 TTGCCATCAAGGAACCCCTACATATCA-TATTGGTCCCTCGAGTTGTCATCATGGAAC-CCCTAC
1 TTGCCATCAAGGAACCCCTACATATCACGA-TGGTCCCTCGAGTTGTCATCAAGGAACGCCC-AC
*
1340271 AAATCACGTTGGTCCCTTAAGC
64 AAATCACGTTGGTCCCTCAAGC
1340293 TT
1 TT
1340295 AGTTTCTTAT
Statistics
Matches: 77, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
84 3 0.04
85 74 0.96
ACGTcount: A:0.25, C:0.30, G:0.17, T:0.28
Consensus pattern (85 bp):
TTGCCATCAAGGAACCCCTACATATCACGATGGTCCCTCGAGTTGTCATCAAGGAACGCCCACAA
ATCACGTTGGTCCCTCAAGC
Found at i:1351850 original size:20 final size:20
Alignment explanation
Indices: 1351825--1351866 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
1351815 GTGGTACGAC
1351825 ATGTTAACATATTACTCTAA
1 ATGTTAACATATTACTCTAA
1351845 ATGTTAACATATTACTCTAA
1 ATGTTAACATATTACTCTAA
1351865 AT
1 AT
1351867 CTGTCACCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.40, C:0.14, G:0.05, T:0.40
Consensus pattern (20 bp):
ATGTTAACATATTACTCTAA
Found at i:1352157 original size:7 final size:7
Alignment explanation
Indices: 1352147--1352173 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
1352137 GAACAAAGAA
1352147 AAAAATT
1 AAAAATT
1352154 AAAAATT
1 AAAAATT
1352161 AAAAATT
1 AAAAATT
1352168 AAAAAT
1 AAAAAT
1352174 GGGGCCAGCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (7 bp):
AAAAATT
Found at i:1356034 original size:16 final size:16
Alignment explanation
Indices: 1356013--1356043 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1356003 ATCATTGAGT
*
1356013 AAATATTCAATTCATA
1 AAATATTCAAATCATA
1356029 AAATATTCAAATCAT
1 AAATATTCAAATCAT
1356044 TTTTTAAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.35
Consensus pattern (16 bp):
AAATATTCAAATCATA
Done.