Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008213.1 Hibiscus syriacus cultivar Beakdansim tig00110839_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: 2348840
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 9
Found at i:963744 original size:114 final size:114
Alignment explanation
Indices: 963491--963841 Score: 501
Period size: 114 Copynumber: 3.1 Consensus size: 114
963481 TAGAAGATGT
* * *
963491 ATCAACATTTCAGTGGAGAGTTCATAATGAGAAGAACCCATCCGATGAGGGAGAAGAAGTTCAAA
1 ATCAACATTTCAGTGGAGAGTTCATAATGAGAAGAACTCATCTGATGAGGGAGAAGAAGTTCATA
* * *
963556 ATGAGAA-AACCTGTTAAACCTTAGTTTGATTCCATCACAGAAGGAGGTGG
66 ATGAGAAGAACTTGTTCAACCTT-G-GTGATTCCATCACAGAAGGAGGTGG
*
963606 ATCAACATTTCAGTGGAGAG-TCATAATGAGAAGAACTCATCTGATGAGGGAGAAGAAATTCATA
1 ATCAACATTTCAGTGGAGAGTTCATAATGAGAAGAACTCATCTGATGAGGGAGAAGAAGTTCATA
* *
963670 ATGAGAAGAACTTGTTCAACCTTGGTGATTTCATCACAGAAGTAGGTGG
66 ATGAGAAGAACTTGTTCAACCTTGGTGATTCCATCACAGAAGGAGGTGG
* * * *
963719 ATCAATATTTCAGGGGAGAGTTCATAATGAGAAGAACTCAT-TCGATGAGAGAGAATAAGTTCAT
1 ATCAACATTTCAGTGGAGAGTTCATAATGAGAAGAACTCATCT-GATGAGGGAGAAGAAGTTCAT
* *
963783 AATGAGAAGAACTTGTTCAACCTTGGCTCGATTCCATCACATAAGGAGTTGG
65 AATGAGAAGAACTTGTTCAACCTTGG-T-GATTCCATCACAGAAGGAGGTGG
963835 ATCAACA
1 ATCAACA
963842 CCAACCTTGG
Statistics
Matches: 212, Mismatches: 19, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
113 41 0.19
114 112 0.53
115 34 0.16
116 25 0.12
ACGTcount: A:0.37, C:0.15, G:0.24, T:0.25
Consensus pattern (114 bp):
ATCAACATTTCAGTGGAGAGTTCATAATGAGAAGAACTCATCTGATGAGGGAGAAGAAGTTCATA
ATGAGAAGAACTTGTTCAACCTTGGTGATTCCATCACAGAAGGAGGTGG
Found at i:963789 original size:19 final size:20
Alignment explanation
Indices: 963737--963795 Score: 52
Period size: 19 Copynumber: 3.0 Consensus size: 20
963727 TTCAGGGGAG
*
963737 AGTTCATAATGAGAAGAACTC
1 AGTTCATAATGAG-AGAACTA
*
963758 A-TTCGATGA-GAGAGAA-TA
1 AGTTC-ATAATGAGAGAACTA
963776 AGTTCATAATGAGAAGAACT
1 AGTTCATAATGAG-AGAACT
963796 TGTTCAACCT
Statistics
Matches: 30, Mismatches: 3, Indels: 10
0.70 0.07 0.23
Matches are distributed among these distances:
18 5 0.17
19 10 0.33
20 10 0.33
21 5 0.17
ACGTcount: A:0.44, C:0.10, G:0.22, T:0.24
Consensus pattern (20 bp):
AGTTCATAATGAGAGAACTA
Found at i:963800 original size:20 final size:20
Alignment explanation
Indices: 963737--963801 Score: 57
Period size: 20 Copynumber: 3.3 Consensus size: 20
963727 TTCAGGGGAG
963737 AGTTCATAATGAGAAGAACT
1 AGTTCATAATGAGAAGAACT
*
963757 CA-TTC--GATGAGAGAGAA-T
1 -AGTTCATAATGAGA-AGAACT
963775 AAGTTCATAATGAGAAGAACT
1 -AGTTCATAATGAGAAGAACT
*
963796 TGTTCA
1 AGTTCA
963802 ACCTTGGCTC
Statistics
Matches: 35, Mismatches: 4, Indels: 11
0.70 0.08 0.22
Matches are distributed among these distances:
18 8 0.23
19 7 0.20
20 12 0.34
21 8 0.23
ACGTcount: A:0.42, C:0.11, G:0.22, T:0.26
Consensus pattern (20 bp):
AGTTCATAATGAGAAGAACT
Found at i:970170 original size:25 final size:26
Alignment explanation
Indices: 970143--970193 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
970133 TTAATGAATA
970143 TTTAATTTACAAAAATTAAATAAGAT
1 TTTAATTTACAAAAATTAAATAAGAT
* ** *
970169 TTTATTTTGGAATAATTAAATAAGA
1 TTTAATTTACAAAAATTAAATAAGA
970194 GCTTAATTAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.49, C:0.02, G:0.08, T:0.41
Consensus pattern (26 bp):
TTTAATTTACAAAAATTAAATAAGAT
Found at i:986043 original size:17 final size:17
Alignment explanation
Indices: 986023--986055 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
986013 AACAAAATCA
*
986023 AATTAAACTTCTTCAAT
1 AATTAAACCTCTTCAAT
986040 AATTAAACCTCTTCAA
1 AATTAAACCTCTTCAA
986056 CCTTTATCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.42, C:0.21, G:0.00, T:0.36
Consensus pattern (17 bp):
AATTAAACCTCTTCAAT
Found at i:986300 original size:17 final size:17
Alignment explanation
Indices: 986278--986310 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
986268 TTTTGGGTTT
986278 TTTATTA-ATTTTATTAA
1 TTTATTATA-TTTATTAA
986295 TTTATTATATTTATTA
1 TTTATTATATTTATTA
986311 TCACCAAGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 14 0.93
18 1 0.07
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTATTATATTTATTAA
Found at i:987686 original size:47 final size:47
Alignment explanation
Indices: 987614--987936 Score: 529
Period size: 47 Copynumber: 6.9 Consensus size: 47
987604 TTTTATTTCT
* *
987614 TTTCATGCCTTAATGCATCCATTCATGCATTTTTGGTTATGGCATCC
1 TTTCATGCCTTAATGCATCCTTTCATGCATTTTTAGTTATGGCATCC
* *
987661 TTTCATGCCTTAATGCACCCGTTCATGCATTTTTAGTTATGGCATCC
1 TTTCATGCCTTAATGCATCCTTTCATGCATTTTTAGTTATGGCATCC
987708 TTTCATGCCTTAATGCATCCTTTCATGCATTTTTAGTTATGGCATCC
1 TTTCATGCCTTAATGCATCCTTTCATGCATTTTTAGTTATGGCATCC
* * *
987755 TTTCATGCCTTAATGTATCATTTCATGCATTTTTAGTTATGGCAGCC
1 TTTCATGCCTTAATGCATCCTTTCATGCATTTTTAGTTATGGCATCC
* *
987802 TTTCATGCCTTAATGCATCATTTCATGCATTTTTAGTTATGGTATCC
1 TTTCATGCCTTAATGCATCCTTTCATGCATTTTTAGTTATGGCATCC
** *
987849 TTTCATGCCTTAATGCATCCTTTCACACATTTTTAGTTATGGCATCA
1 TTTCATGCCTTAATGCATCCTTTCATGCATTTTTAGTTATGGCATCC
*
987896 TTTCAGGCCTTAATGCATCCTTTCATGCATTTTTAGTTATG
1 TTTCATGCCTTAATGCATCCTTTCATGCATTTTTAGTTATG
987937 AATTCGGTTT
Statistics
Matches: 257, Mismatches: 19, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 257 1.00
ACGTcount: A:0.20, C:0.22, G:0.14, T:0.44
Consensus pattern (47 bp):
TTTCATGCCTTAATGCATCCTTTCATGCATTTTTAGTTATGGCATCC
Found at i:988513 original size:94 final size:94
Alignment explanation
Indices: 988343--988519 Score: 241
Period size: 94 Copynumber: 1.9 Consensus size: 94
988333 ACTCCCCTGG
* * * *
988343 TATCGATACTTCTATACTATGATACTGATACCCCTTTCAATATCGATACCATTTCTATATTCTGT
1 TATCGATACTACTACACTATGATACCGATACCCCTTTCAATATCGATACCATTTCTATAGTCTGT
* * *
988408 GTTGCATGGTATCGATACCATTATTTCAA
66 GATCCAAGGTATCGATACCATTATTTCAA
* *
988437 TATCGATACTACTACACTATGGTACCGATACTCCCTTTCAGTATCGATACCATTT-TGATAGTCT
1 TATCGATACTACTACACTATGATACCGATAC-CCCTTTCAATATCGATACCATTTCT-ATAGTCT
988501 G-GATCCAAGGTATCGATAC
64 GTGATCCAAGGTATCGATAC
988520 TTCCCTTTGT
Statistics
Matches: 72, Mismatches: 9, Indels: 4
0.85 0.11 0.05
Matches are distributed among these distances:
94 43 0.60
95 29 0.40
ACGTcount: A:0.28, C:0.23, G:0.13, T:0.37
Consensus pattern (94 bp):
TATCGATACTACTACACTATGATACCGATACCCCTTTCAATATCGATACCATTTCTATAGTCTGT
GATCCAAGGTATCGATACCATTATTTCAA
Found at i:995511 original size:20 final size:20
Alignment explanation
Indices: 995486--995554 Score: 66
Period size: 20 Copynumber: 3.1 Consensus size: 20
995476 TGGTTATGGT
995486 ATCCTTTCATGCCTTAATGC
1 ATCCTTTCATGCCTTAATGC
*
995506 ATCCTTTCATGCATTTTTAGTTATGAC
1 ATCCTTTCATGC---CTTA---ATG-C
995533 ATCCTTTCATGCCTTAATGC
1 ATCCTTTCATGCCTTAATGC
995553 AT
1 AT
995555 AATTTAATGC
Statistics
Matches: 40, Mismatches: 2, Indels: 14
0.71 0.04 0.25
Matches are distributed among these distances:
20 15 0.38
21 3 0.08
23 3 0.08
24 3 0.08
26 3 0.08
27 13 0.32
ACGTcount: A:0.22, C:0.25, G:0.10, T:0.43
Consensus pattern (20 bp):
ATCCTTTCATGCCTTAATGC
Found at i:995541 original size:47 final size:47
Alignment explanation
Indices: 995442--995672 Score: 293
Period size: 47 Copynumber: 4.9 Consensus size: 47
995432 TATGGCCTCT
* * * * **
995442 TTTCATGGCTTAATGCACCCGTTCATGCATTTTTTGGTTATGGTATCC
1 TTTCATGCCTTAATGCATCCTTTCATGCA-TTTTTAGTTATGACATCC
995490 TTTCATGCCTTAATGCATCCTTTCATGCATTTTTAGTTATGACATCC
1 TTTCATGCCTTAATGCATCCTTTCATGCATTTTTAGTTATGACATCC
** *
995537 TTTCATGCCTTAATGCATAATTTAATGCATTTTTAGTTAT-ATCATCC
1 TTTCATGCCTTAATGCATCCTTTCATGCATTTTTAGTTATGA-CATCC
* * * *
995584 TTCCATACCTTAATGCATCCTTTCATGCATTTTTAGCTATGGCATCC
1 TTTCATGCCTTAATGCATCCTTTCATGCATTTTTAGTTATGACATCC
* * *
995631 TTTCATGCCTTAATGCATCATTTCATGTAATTTTAGTTATGA
1 TTTCATGCCTTAATGCATCCTTTCATGCATTTTTAGTTATGA
995673 ATTCGGTTTA
Statistics
Matches: 158, Mismatches: 23, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
46 1 0.01
47 131 0.83
48 26 0.16
ACGTcount: A:0.23, C:0.21, G:0.12, T:0.45
Consensus pattern (47 bp):
TTTCATGCCTTAATGCATCCTTTCATGCATTTTTAGTTATGACATCC
Found at i:996252 original size:94 final size:94
Alignment explanation
Indices: 996078--996255 Score: 207
Period size: 94 Copynumber: 1.9 Consensus size: 94
996068 TACTACCTTG
* * *
996078 GTATCGACACTTCTATACTATGGTACCGATACCCCTTTCAATATCGATACCATTTCTATATAATG
1 GTATCGACACTACTATACTATGGTACCGATACCCCTTTCAATATCGATACCATTTCGACATAATG
* * * *
996143 TGTTGCATGGTATCGATACCATTCTCTCA
66 TGATCCAAGGCATCGATACCATTCTCTCA
* * * * **
996172 GTATCGATACTACTATACTATGGTACTGATACTCCCTTTTAGTATCGATACCATTAT-GACATTT
1 GTATCGACACTACTATACTATGGTACCGATAC-CCCTTTCAATATCGATACCATT-TCGACATAA
996236 TG-GATCCAAGGCATCGATAC
64 TGTGATCCAAGGCATCGATAC
996256 TTCCTTTTAT
Statistics
Matches: 69, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
94 43 0.62
95 25 0.36
96 1 0.01
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (94 bp):
GTATCGACACTACTATACTATGGTACCGATACCCCTTTCAATATCGATACCATTTCGACATAATG
TGATCCAAGGCATCGATACCATTCTCTCA
Found at i:1006966 original size:25 final size:25
Alignment explanation
Indices: 1006918--1006967 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
1006908 AGGTTAATTC
*
1006918 TTTTATGAGATTTACTGTAGTATGA
1 TTTTATGAGATTTACTGTACTATGA
1006943 TTTTATGAGATTTACTAGT-CTATGA
1 TTTTATGAGATTTACT-GTACTATGA
1006968 CTTGTTTAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 21 0.91
26 2 0.09
ACGTcount: A:0.28, C:0.06, G:0.18, T:0.48
Consensus pattern (25 bp):
TTTTATGAGATTTACTGTACTATGA
Found at i:1009476 original size:20 final size:21
Alignment explanation
Indices: 1009444--1009486 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
1009434 CAAATTAAGT
1009444 TAAATGAATTTTA-AGATTTTA
1 TAAATGAATTTTACA-ATTTTA
1009465 TAAATG-ATTTTACAATTTTA
1 TAAATGAATTTTACAATTTTA
1009485 TA
1 TA
1009487 TTCGATTCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 14 0.67
21 7 0.33
ACGTcount: A:0.42, C:0.02, G:0.07, T:0.49
Consensus pattern (21 bp):
TAAATGAATTTTACAATTTTA
Found at i:1009747 original size:19 final size:17
Alignment explanation
Indices: 1009704--1009750 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 17
1009694 TTAATTGAAA
1009704 CATCGAATGCATTCTATG
1 CATCG-ATGCATTCTATG
*
1009722 CACCGATGCATTCTCCATG
1 CATCGATGCATTCT--ATG
1009741 CATCGATGCA
1 CATCGATGCA
1009751 CTCAGGCTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 9 0.36
18 4 0.16
19 12 0.48
ACGTcount: A:0.26, C:0.30, G:0.17, T:0.28
Consensus pattern (17 bp):
CATCGATGCATTCTATG
Found at i:1017977 original size:20 final size:21
Alignment explanation
Indices: 1017940--1017979 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
1017930 AAATTAAGTT
1017940 AAATGAATTTTAAGATTTTAC
1 AAATGAATTTTAAGATTTTAC
1017961 AAATG-ATTTTACA-ATTTTA
1 AAATGAATTTTA-AGATTTTA
1017980 TATTCGATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.45
Consensus pattern (21 bp):
AAATGAATTTTAAGATTTTAC
Found at i:1022989 original size:129 final size:128
Alignment explanation
Indices: 1022736--1022969 Score: 312
Period size: 129 Copynumber: 1.8 Consensus size: 128
1022726 TCGTTGACCA
* * *
1022736 TTGACTTTGACCAAAAAGTTAAATTTTTCAAAAAGTCATATATTATTATTTTGACGTCCTGAGTC
1 TTGACTTTGACCAAAAAATAAAATTTTTCAAAAAGACATATATTATTATTTTGACGTCCTGAGTC
* * *
1022801 TGAATTCGAAGTTCATTTTTCGAAATTCAAACCCGAAAGCCACGAGATCGTCAGTCAAACCCG
66 TCAATTCGAAGTTCATTTTGCCAAATTCAAACCCGAAAGCCACGAGATCGTCAGTCAAACCCG
* * *
1022864 TTGACTTTGACCAAAAAATCAAAATTTTT-GAAAAGACATATTTTATGT-TTTTCGATGTCCTGA
1 TTGACTTTGACCAAAAAAT-AAAATTTTTCAAAAAGACATATATTAT-TATTTT-GACGTCCTGA
* *
1022927 GT-TCAATTCCGCAGTTCATTTTGCCAAATTCAAAGCCGAAAGC
63 GTCTCAATT-CGAAGTTCATTTTGCCAAATTCAAACCCGAAAGC
1022970 GTCCTAATTG
Statistics
Matches: 91, Mismatches: 11, Indels: 7
0.83 0.10 0.06
Matches are distributed among these distances:
128 41 0.45
129 50 0.55
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.33
Consensus pattern (128 bp):
TTGACTTTGACCAAAAAATAAAATTTTTCAAAAAGACATATATTATTATTTTGACGTCCTGAGTC
TCAATTCGAAGTTCATTTTGCCAAATTCAAACCCGAAAGCCACGAGATCGTCAGTCAAACCCG
Found at i:1023747 original size:25 final size:25
Alignment explanation
Indices: 1023699--1023748 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
1023689 AGGTTAACTC
*
1023699 TTTTATGAGATTTACTGTAGTATGA
1 TTTTATGAGATTTACTGTACTATGA
1023724 TTTTATGAGATTTACT-TGACTATGA
1 TTTTATGAGATTTACTGT-ACTATGA
1023749 CTTGTTTAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 1 0.04
25 22 0.96
ACGTcount: A:0.28, C:0.06, G:0.18, T:0.48
Consensus pattern (25 bp):
TTTTATGAGATTTACTGTACTATGA
Found at i:1028274 original size:33 final size:33
Alignment explanation
Indices: 1028221--1028287 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1028211 CCTAGTACAG
* *
1028221 ATGGTGGATACGACCATATGTGTCATATGGATT
1 ATGGTGGACACGACCATATGTGTCATACGGATT
* *
1028254 ATGGTGGACATGACCTTATGTGTCATACGGATT
1 ATGGTGGACACGACCATATGTGTCATACGGATT
1028287 A
1 A
1028288 GCACTATGGT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.27, C:0.13, G:0.27, T:0.33
Consensus pattern (33 bp):
ATGGTGGACACGACCATATGTGTCATACGGATT
Found at i:1028408 original size:44 final size:44
Alignment explanation
Indices: 1028359--1028462 Score: 129
Period size: 44 Copynumber: 2.3 Consensus size: 44
1028349 TGGTATATGG
* * *
1028359 TTATGGA-ATAATGGCAAGTGTATTGGTAAAATAAGCATACTAGC
1 TTATGGATA-AATGGCAAGTATATTGGTAAAACAAGCATACGAGC
* *
1028403 TTATGGATAAATGGTAAGTATATTGGTAAAACAAGCTTACGAGC
1 TTATGGATAAATGGCAAGTATATTGGTAAAACAAGCATACGAGC
1028447 TTATGGTATTAAATGG
1 TTATGG-A-TAAATGG
1028463 TAAAATATTG
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
44 43 0.83
45 2 0.04
46 7 0.13
ACGTcount: A:0.38, C:0.08, G:0.23, T:0.32
Consensus pattern (44 bp):
TTATGGATAAATGGCAAGTATATTGGTAAAACAAGCATACGAGC
Found at i:1035758 original size:14 final size:14
Alignment explanation
Indices: 1035739--1035767 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1035729 AAATAAAACA
1035739 TGGTTTCTGATCTC
1 TGGTTTCTGATCTC
1035753 TGGTTTCTGATCTC
1 TGGTTTCTGATCTC
1035767 T
1 T
1035768 AGGTAGGATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.07, C:0.21, G:0.21, T:0.52
Consensus pattern (14 bp):
TGGTTTCTGATCTC
Found at i:1036755 original size:29 final size:29
Alignment explanation
Indices: 1036723--1036829 Score: 101
Period size: 29 Copynumber: 3.7 Consensus size: 29
1036713 CTTTTTCATA
* *
1036723 TTACTGAATGAGATCATATCCTCGTCCTG
1 TTACTGAATGAGATCATATCCTCATTCTG
*
1036752 TTACT-ACATGGGATCATATCCTCATTCTG
1 TTACTGA-ATGAGATCATATCCTCATTCTG
* * * *
1036781 TTATTGTATGGGATCATATCC-CTTTCTG
1 TTACTGAATGAGATCATATCCTCATTCTG
* * *
1036809 GTACTGCATGAGATCAAATCC
1 TTACTGAATGAGATCATATCC
1036830 CCATGTTGTT
Statistics
Matches: 65, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
28 23 0.35
29 42 0.65
ACGTcount: A:0.24, C:0.22, G:0.17, T:0.36
Consensus pattern (29 bp):
TTACTGAATGAGATCATATCCTCATTCTG
Found at i:1036840 original size:57 final size:58
Alignment explanation
Indices: 1036734--1036865 Score: 142
Period size: 57 Copynumber: 2.3 Consensus size: 58
1036724 TACTGAATGA
* * * *
1036734 GATCATATCCTCGTCCTGTTACTACATGGGATCATATCCTCATTCTGTTATTGTATGG
1 GATCATATCCTCGTCCTGGTACTACATGAGATCAAATCCCCATTCTGTTATTGTATGG
* * * **
1036792 GATCATATCC-CTTTCTGGTACTGCATGAGATCAAATCCCCATGT-TGTTATTGTATAC
1 GATCATATCCTCGTCCTGGTACTACATGAGATCAAATCCCCAT-TCTGTTATTGTATGG
* *
1036849 GATCGTATCCTTGTCCT
1 GATCATATCCTCGTCCT
1036866 ATTACTGCTT
Statistics
Matches: 59, Mismatches: 13, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
57 45 0.76
58 14 0.24
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.39
Consensus pattern (58 bp):
GATCATATCCTCGTCCTGGTACTACATGAGATCAAATCCCCATTCTGTTATTGTATGG
Found at i:1038499 original size:20 final size:20
Alignment explanation
Indices: 1038470--1038507 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1038460 GTTTTTCACA
*
1038470 TATATGTATATTTATATTTT
1 TATATATATATTTATATTTT
1038490 TATATATATATTTATATT
1 TATATATATATTTATATT
1038508 ACTTACATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (20 bp):
TATATATATATTTATATTTT
Found at i:1038519 original size:20 final size:20
Alignment explanation
Indices: 1038476--1038521 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
1038466 CACATATATG
* *
1038476 TATATTTATATTTTTATATA
1 TATATTTATATTCTTACATA
1038496 TATATTTATATTACTTACAT-
1 TATATTTATATT-CTTACATA
1038516 TATATT
1 TATATT
1038522 CGTGTGTGTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 18 0.78
21 5 0.22
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (20 bp):
TATATTTATATTCTTACATA
Found at i:1049173 original size:77 final size:77
Alignment explanation
Indices: 1049046--1049200 Score: 310
Period size: 77 Copynumber: 2.0 Consensus size: 77
1049036 AGGAGATACC
1049046 AAAGAAATAGTGATAACTGTAGAAGTACAAAGAGAGGAATAAAAGCCAAGTGATCAGGATTTGTT
1 AAAGAAATAGTGATAACTGTAGAAGTACAAAGAGAGGAATAAAAGCCAAGTGATCAGGATTTGTT
1049111 ATATGAGAATTT
66 ATATGAGAATTT
1049123 AAAGAAATAGTGATAACTGTAGAAGTACAAAGAGAGGAATAAAAGCCAAGTGATCAGGATTTGTT
1 AAAGAAATAGTGATAACTGTAGAAGTACAAAGAGAGGAATAAAAGCCAAGTGATCAGGATTTGTT
1049188 ATATGAGAATTT
66 ATATGAGAATTT
1049200 A
1 A
1049201 CTTCCGATAT
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
77 78 1.00
ACGTcount: A:0.46, C:0.06, G:0.23, T:0.25
Consensus pattern (77 bp):
AAAGAAATAGTGATAACTGTAGAAGTACAAAGAGAGGAATAAAAGCCAAGTGATCAGGATTTGTT
ATATGAGAATTT
Found at i:1051290 original size:3 final size:3
Alignment explanation
Indices: 1051282--1051313 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
1051272 GTTGACGTTT
1051282 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1051314 TTCTCATTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:1053410 original size:148 final size:149
Alignment explanation
Indices: 1053237--1053534 Score: 580
Period size: 148 Copynumber: 2.0 Consensus size: 149
1053227 TTTTCTAGAT
1053237 TTAATCCATATATATATTATTATATTTTTAAATTAAAAATATATATGAACTACGTTAGATAAATT
1 TTAATCCA-ATATATATTATTATATTTTTAAATTAAAAATATATATGAACTACGTTAGATAAATT
1053302 TTTAGTTATATTTTTATTGACCAAACCTATTTATTTTTTCTAGATTCATCGACGATAGAAGTAGC
65 TTTAGTTATATTTTTATTGACCAAACCTATTTATTTTTTCTAGATTCATCGACGATAGAAGTAGC
1053367 ACCGCCTGTGTAGATTTCTA
130 ACCGCCTGTGTAGATTTCTA
1053387 TTAATCC-ATATATATTATTATATTTTTAAATTAAAAATATATATGAACTACGTTAGATAAATTT
1 TTAATCCAATATATATTATTATATTTTTAAATTAAAAATATATATGAACTACGTTAGATAAATTT
1053451 TTAGTTATATTTTTATTGACCAAACCTATTTATTTTTTCTAGATTCATCGACGATAGAAGTAGCA
66 TTAGTTATATTTTTATTGACCAAACCTATTTATTTTTTCTAGATTCATCGACGATAGAAGTAGCA
1053516 CCGCCTGTGTAGATTTCTA
131 CCGCCTGTGTAGATTTCTA
1053535 AGGTAATTCA
Statistics
Matches: 148, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
148 141 0.95
150 7 0.05
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.43
Consensus pattern (149 bp):
TTAATCCAATATATATTATTATATTTTTAAATTAAAAATATATATGAACTACGTTAGATAAATTT
TTAGTTATATTTTTATTGACCAAACCTATTTATTTTTTCTAGATTCATCGACGATAGAAGTAGCA
CCGCCTGTGTAGATTTCTA
Found at i:1068890 original size:43 final size:44
Alignment explanation
Indices: 1068843--1068925 Score: 132
Period size: 43 Copynumber: 1.9 Consensus size: 44
1068833 TCCTACTCTA
*
1068843 ATGTTAGAGCTATTACCAG-TTTTTCAACTTATTTCCTAAGACT
1 ATGTTAGAGCTATTACCAGCTTTTCCAACTTATTTCCTAAGACT
* *
1068886 ATGTTGGAGCTATTACCAGCTTTTCCAACTTATTTTCTAA
1 ATGTTAGAGCTATTACCAGCTTTTCCAACTTATTTCCTAA
1068926 TTTTAATTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
43 18 0.50
44 18 0.50
ACGTcount: A:0.27, C:0.19, G:0.12, T:0.42
Consensus pattern (44 bp):
ATGTTAGAGCTATTACCAGCTTTTCCAACTTATTTCCTAAGACT
Found at i:1097532 original size:24 final size:24
Alignment explanation
Indices: 1097505--1097554 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
1097495 CTAAGCAGAT
1097505 GATGACAAGAGGAGGAGGGCATCC
1 GATGACAAGAGGAGGAGGGCATCC
1097529 GATGACAAGAGGAGGAGGGCATCC
1 GATGACAAGAGGAGGAGGGCATCC
1097553 GA
1 GA
1097555 GAGTTCTCCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.34, C:0.16, G:0.42, T:0.08
Consensus pattern (24 bp):
GATGACAAGAGGAGGAGGGCATCC
Found at i:1098395 original size:17 final size:16
Alignment explanation
Indices: 1098373--1098420 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 16
1098363 TTATGTTGTT
1098373 TTTTATATTTCACTTTA
1 TTTTATATTT-ACTTTA
1098390 TTTTAT-TTTA-TTTA
1 TTTTATATTTACTTTA
1098404 TTTTATTATTTTACTTT
1 TTTTA-TA-TTTACTTT
1098421 TTTGGAGATT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
14 9 0.33
15 2 0.07
16 3 0.11
17 10 0.37
18 3 0.11
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.73
Consensus pattern (16 bp):
TTTTATATTTACTTTA
Found at i:1098398 original size:22 final size:21
Alignment explanation
Indices: 1098341--1098400 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 21
1098331 ATTTTGTCTC
*
1098341 ATTT-TGTTTATTTTTTATTT
1 ATTTATGTTTATTTTATATTT
*
1098361 ATTTATGTTGTTTTTTATATTT
1 ATTTATGTT-TATTTTATATTT
1098383 CACTTTAT-TTTATTTTAT
1 -A-TTTATGTTTATTTTAT
1098401 TTATTTTATT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
20 4 0.12
21 4 0.12
22 17 0.52
23 3 0.09
24 5 0.15
ACGTcount: A:0.18, C:0.03, G:0.05, T:0.73
Consensus pattern (21 bp):
ATTTATGTTTATTTTATATTT
Found at i:1098414 original size:8 final size:9
Alignment explanation
Indices: 1098341--1098416 Score: 54
Period size: 9 Copynumber: 8.7 Consensus size: 9
1098331 ATTTTGTCTC
*
1098341 ATTTTGTTT
1 ATTTTATTT
1098350 A-TTT-TTT
1 ATTTTATTT
1098357 A-TTTATTT
1 ATTTTATTT
* *
1098365 ATGTTGTTT
1 ATTTTATTT
1098374 -TTTATATTT
1 ATTT-TATTT
*
1098383 CACTTTATTTT
1 -ATTTTA-TTT
1098394 ATTTTATTT
1 ATTTTATTT
1098403 ATTTTA-TT
1 ATTTTATTT
1098411 ATTTTA
1 ATTTTA
1098417 CTTTTTTGGA
Statistics
Matches: 55, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
7 7 0.13
8 17 0.31
9 19 0.35
10 7 0.13
11 5 0.09
ACGTcount: A:0.20, C:0.03, G:0.04, T:0.74
Consensus pattern (9 bp):
ATTTTATTT
Found at i:1109210 original size:354 final size:354
Alignment explanation
Indices: 1108561--1109269 Score: 1418
Period size: 354 Copynumber: 2.0 Consensus size: 354
1108551 TTCATACTTC
1108561 ATTATGTATTCACTTTTCAGAATGTTTGTCATGTATTCACTTTTCAGAATGTATTCCTTTTAACA
1 ATTATGTATTCACTTTTCAGAATGTTTGTCATGTATTCACTTTTCAGAATGTATTCCTTTTAACA
1108626 ATATTGGGTTGAATTTAAACCTAATGATTTATTCACCACTGAAAAAAGATAATTGAATATTATTG
66 ATATTGGGTTGAATTTAAACCTAATGATTTATTCACCACTGAAAAAAGATAATTGAATATTATTG
1108691 TACAAAGATTGTTTTAAAAAGTACAGATACTCGGAAGCCAGTCAAGGGTCATGCATAATACTAGA
131 TACAAAGATTGTTTTAAAAAGTACAGATACTCGGAAGCCAGTCAAGGGTCATGCATAATACTAGA
1108756 AGTGGTTAAAAAATATTTCCAAAATCAAGGATAAAAAAACTTTGTACACCGGGTTTAAACGTGTT
196 AGTGGTTAAAAAATATTTCCAAAATCAAGGATAAAAAAACTTTGTACACCGGGTTTAAACGTGTT
1108821 GAAGAATTCAAGATTATGAATTAGAAAGTCAGATTCCATAATCAAGAGTCATCAAGACTAACAAC
261 GAAGAATTCAAGATTATGAATTAGAAAGTCAGATTCCATAATCAAGAGTCATCAAGACTAACAAC
1108886 TAGAGATTTGGATTTCTCTTCAGATCCTA
326 TAGAGATTTGGATTTCTCTTCAGATCCTA
1108915 ATTATGTATTCACTTTTCAGAATGTTTGTCATGTATTCACTTTTCAGAATGTATTCCTTTTAACA
1 ATTATGTATTCACTTTTCAGAATGTTTGTCATGTATTCACTTTTCAGAATGTATTCCTTTTAACA
1108980 ATATTGGGTTGAATTTAAACCTAATGATTTATTCACCACTGAAAAAAGATAATTGAATATTATTG
66 ATATTGGGTTGAATTTAAACCTAATGATTTATTCACCACTGAAAAAAGATAATTGAATATTATTG
1109045 TACAAAGATTGTTTTAAAAAGTACAGATACTCGGAAGCCAGTCAAGGGTCATGCATAATACTAGA
131 TACAAAGATTGTTTTAAAAAGTACAGATACTCGGAAGCCAGTCAAGGGTCATGCATAATACTAGA
1109110 AGTGGTTAAAAAATATTTCCAAAATCAAGGATAAAAAAACTTTGTACACCGGGTTTAAACGTGTT
196 AGTGGTTAAAAAATATTTCCAAAATCAAGGATAAAAAAACTTTGTACACCGGGTTTAAACGTGTT
1109175 GAAGAATTCAAGATTATGAATTAGAAAGTCAGATTCCATAATCAAGAGTCATCAAGACTAACAAC
261 GAAGAATTCAAGATTATGAATTAGAAAGTCAGATTCCATAATCAAGAGTCATCAAGACTAACAAC
1109240 TAGAGATTTGGATTTCTCTTCAGATCCTA
326 TAGAGATTTGGATTTCTCTTCAGATCCTA
1109269 A
1 A
1109270 AATAACATAT
Statistics
Matches: 355, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
354 355 1.00
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.33
Consensus pattern (354 bp):
ATTATGTATTCACTTTTCAGAATGTTTGTCATGTATTCACTTTTCAGAATGTATTCCTTTTAACA
ATATTGGGTTGAATTTAAACCTAATGATTTATTCACCACTGAAAAAAGATAATTGAATATTATTG
TACAAAGATTGTTTTAAAAAGTACAGATACTCGGAAGCCAGTCAAGGGTCATGCATAATACTAGA
AGTGGTTAAAAAATATTTCCAAAATCAAGGATAAAAAAACTTTGTACACCGGGTTTAAACGTGTT
GAAGAATTCAAGATTATGAATTAGAAAGTCAGATTCCATAATCAAGAGTCATCAAGACTAACAAC
TAGAGATTTGGATTTCTCTTCAGATCCTA
Found at i:1111070 original size:2 final size:2
Alignment explanation
Indices: 1111063--1111097 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1111053 CCTCTATTAT
1111063 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1111098 TTATTTTTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1111228 original size:2 final size:2
Alignment explanation
Indices: 1111221--1111257 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1111211 CTAACATTCT
1111221 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1111258 TCATCATTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1111420 original size:22 final size:21
Alignment explanation
Indices: 1111393--1111447 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 21
1111383 TTTTTCTCCC
1111393 TTATTTTTT-TGTCTCATTTTCT
1 TTATTTTTTATGT-T-ATTTTCT
* *
1111415 TTATTTATTTATGTTGTTTTGT
1 TTATTT-TTTATGTTATTTTCT
1111437 TTATTTTTTAT
1 TTATTTTTTAT
1111448 TTCCCTTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
21 5 0.17
22 17 0.59
23 4 0.14
24 3 0.10
ACGTcount: A:0.13, C:0.05, G:0.07, T:0.75
Consensus pattern (21 bp):
TTATTTTTTATGTTATTTTCT
Found at i:1111457 original size:31 final size:32
Alignment explanation
Indices: 1111422--1111481 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 32
1111412 TCTTTATTTA
* *
1111422 TTTATGTTGTTTTGTTTATTTT-TTATTTCCC
1 TTTATGTTATTTTATTTATTTTATTATTTCCC
*
1111453 TTTATTTTATTTTATTTATTTTATTATTT
1 TTTATGTTATTTTATTTATTTTATTATTT
1111482 TTCTTTTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 19 0.76
32 6 0.24
ACGTcount: A:0.15, C:0.05, G:0.05, T:0.75
Consensus pattern (32 bp):
TTTATGTTATTTTATTTATTTTATTATTTCCC
Found at i:1111463 original size:5 final size:5
Alignment explanation
Indices: 1111453--1111531 Score: 51
Period size: 5 Copynumber: 16.2 Consensus size: 5
1111443 TTTATTTCCC
* * * **
1111453 TTTAT TTTAT TTTA- TTTAT TTTAT TAT-T TTTCT TTT-T TTCTGAT TAGTCC
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TT-T-AT T-TTAT
1111503 TTTAT TTT-T TTTAT TTT-T TTTAT TTTAT T
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT T
1111532 GTTTATCTAT
Statistics
Matches: 58, Mismatches: 8, Indels: 16
0.71 0.10 0.20
Matches are distributed among these distances:
4 18 0.31
5 36 0.62
6 1 0.02
7 3 0.05
ACGTcount: A:0.15, C:0.05, G:0.03, T:0.77
Consensus pattern (5 bp):
TTTAT
Found at i:1111483 original size:9 final size:9
Alignment explanation
Indices: 1111453--1111528 Score: 62
Period size: 9 Copynumber: 7.9 Consensus size: 9
1111443 TTTATTTCCC
1111453 TTTATTTTAT
1 TTTATTTT-T
*
1111463 TTTATTTAT
1 TTTATTTTT
*
1111472 TTTATTATT
1 TTTATTTTT
*
1111481 TTTCTTTTT
1 TTTATTTTT
**
1111490 TTCTGATTAGTCC
1 TT-T-ATT--TTT
1111503 TTTATTTTT
1 TTTATTTTT
1111512 TTTATTTTT
1 TTTATTTTT
1111521 TTTATTTT
1 TTTATTTT
1111529 ATTGTTTATC
Statistics
Matches: 52, Mismatches: 10, Indels: 9
0.73 0.14 0.13
Matches are distributed among these distances:
9 35 0.67
10 8 0.15
11 5 0.10
12 1 0.02
13 3 0.06
ACGTcount: A:0.14, C:0.05, G:0.03, T:0.78
Consensus pattern (9 bp):
TTTATTTTT
Found at i:1115223 original size:12 final size:12
Alignment explanation
Indices: 1115171--1115212 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
1115161 TATTTTTTTC
*
1115171 AAAAAAA-CAAA
1 AAAAAAAGCCAA
*
1115182 AAAAAAAGGCAA
1 AAAAAAAGCCAA
*
1115194 AAAAAAGGCCAA
1 AAAAAAAGCCAA
1115206 AAAAAAA
1 AAAAAAA
1115213 AAAATCCAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
11 7 0.28
12 18 0.72
ACGTcount: A:0.81, C:0.10, G:0.10, T:0.00
Consensus pattern (12 bp):
AAAAAAAGCCAA
Found at i:1129369 original size:23 final size:23
Alignment explanation
Indices: 1129343--1129438 Score: 75
Period size: 23 Copynumber: 4.2 Consensus size: 23
1129333 CACCGAAGTG
*
1129343 CCACATAGAAATGTCCCGAAGGA
1 CCACATAGAAATGTCCCGAAAGA
* * *
1129366 CCACATAGTATTGTCTCGAAAGA
1 CCACATAGAAATGTCCCGAAAGA
** * * *
1129389 CTGCGTATAAATGTCCCAAAAGA
1 CCACATAGAAATGTCCCGAAAGA
** * *
1129412 CCATGTAGAATTGTCCCGAATGA
1 CCACATAGAAATGTCCCGAAAGA
1129435 CCAC
1 CCAC
1129439 GTAAAATCCT
Statistics
Matches: 53, Mismatches: 20, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
23 53 1.00
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.21
Consensus pattern (23 bp):
CCACATAGAAATGTCCCGAAAGA
Found at i:1129554 original size:16 final size:15
Alignment explanation
Indices: 1129532--1129584 Score: 56
Period size: 16 Copynumber: 3.5 Consensus size: 15
1129522 ACATATCTTG
1129532 TATCACATAGACATA
1 TATCACATAGACATA
*
1129547 TAATCACATATATCAT-
1 T-ATCACATAGA-CATA
*
1129563 TATCACATA-ACTTA
1 TATCACATAGACATA
1129577 TATCACAT
1 TATCACAT
1129585 GTCCATATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
13 2 0.06
14 9 0.27
15 9 0.27
16 10 0.30
17 3 0.09
ACGTcount: A:0.43, C:0.21, G:0.02, T:0.34
Consensus pattern (15 bp):
TATCACATAGACATA
Found at i:1129615 original size:45 final size:45
Alignment explanation
Indices: 1129543--1129652 Score: 123
Period size: 45 Copynumber: 2.4 Consensus size: 45
1129533 ATCACATAGA
** * *
1129543 CATATAATCACATATATCATTATCACATAACTTATATCACATGTC-
1 CATATAATCACATAGGTCAGTACCACATAACTTATATCACAT-TCT
** * *
1129588 CATATAATCATTTAGGTCAGTACCACATAGCTTATATCATATTCT
1 CATATAATCACATAGGTCAGTACCACATAACTTATATCACATTCT
*
1129633 CATGTAATCACATAGGTCAG
1 CATATAATCACATAGGTCAG
1129653 ATAGAACACT
Statistics
Matches: 53, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
44 2 0.04
45 51 0.96
ACGTcount: A:0.36, C:0.21, G:0.08, T:0.35
Consensus pattern (45 bp):
CATATAATCACATAGGTCAGTACCACATAACTTATATCACATTCT
Found at i:1132433 original size:36 final size:36
Alignment explanation
Indices: 1132393--1132480 Score: 113
Period size: 36 Copynumber: 2.4 Consensus size: 36
1132383 AGAAATATTT
* * * *
1132393 TCAAGCGAGTTAAAATTTCTTTTAAGGAAAACAATC
1 TCAAGTGAGATAAAATCTCTTTTAAGAAAAACAATC
* *
1132429 TCAAGTGAGATAAAATCTGTTTTAAGAAAAATAATC
1 TCAAGTGAGATAAAATCTCTTTTAAGAAAAACAATC
*
1132465 TTAAGTGAGATAAAAT
1 TCAAGTGAGATAAAAT
1132481 ATAATTTAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
36 45 1.00
ACGTcount: A:0.45, C:0.09, G:0.15, T:0.31
Consensus pattern (36 bp):
TCAAGTGAGATAAAATCTCTTTTAAGAAAAACAATC
Found at i:1132489 original size:36 final size:36
Alignment explanation
Indices: 1132413--1132496 Score: 105
Period size: 36 Copynumber: 2.3 Consensus size: 36
1132403 TAAAATTTCT
* * **
1132413 TTTAAGGAAAACAATCTCAAGTGAGATAAAATCTGT
1 TTTAAGAAAAACAATCTCAAGTGAGATAAAATATAA
* *
1132449 TTTAAGAAAAATAATCTTAAGTGAGATAAAATATAA
1 TTTAAGAAAAACAATCTCAAGTGAGATAAAATATAA
*
1132485 TTTAATAAAAAC
1 TTTAAGAAAAAC
1132497 TTATTGATAG
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.51, C:0.07, G:0.12, T:0.30
Consensus pattern (36 bp):
TTTAAGAAAAACAATCTCAAGTGAGATAAAATATAA
Found at i:1137852 original size:15 final size:14
Alignment explanation
Indices: 1137832--1137900 Score: 66
Period size: 15 Copynumber: 4.6 Consensus size: 14
1137822 ATTCAATCAG
*
1137832 AACAAAAAGAGCAAA
1 AACAAAAA-AGAAAA
1137847 AACAAAAAAGAAAA
1 AACAAAAAAGAAAA
*
1137861 GAAGAAAAAAAGAAGAA
1 -AA-CAAAAAAGAA-AA
*
1137878 AACAAAAAAAAAAA
1 AACAAAAAAGAAAA
1137892 GAACAAAAA
1 -AACAAAAA
1137901 TCAAAAAGAA
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
14 7 0.15
15 26 0.57
16 11 0.24
17 2 0.04
ACGTcount: A:0.81, C:0.07, G:0.12, T:0.00
Consensus pattern (14 bp):
AACAAAAAAGAAAA
Found at i:1137873 original size:11 final size:11
Alignment explanation
Indices: 1137857--1137900 Score: 56
Period size: 11 Copynumber: 4.2 Consensus size: 11
1137847 AACAAAAAAG
1137857 AAAAGAAGAAA
1 AAAAGAAGAAA
1137868 AAAAGAAGAAA
1 AAAAGAAGAAA
*
1137879 ACAA-AA-AAA
1 AAAAGAAGAAA
*
1137888 AAAAGAACAAA
1 AAAAGAAGAAA
1137899 AA
1 AA
1137901 TCAAAAAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
9 6 0.21
10 4 0.14
11 19 0.66
ACGTcount: A:0.84, C:0.05, G:0.11, T:0.00
Consensus pattern (11 bp):
AAAAGAAGAAA
Found at i:1137906 original size:16 final size:15
Alignment explanation
Indices: 1137847--1137910 Score: 67
Period size: 16 Copynumber: 4.1 Consensus size: 15
1137837 AAAGAGCAAA
*
1137847 AACAAAAAAGAAAAG
1 AACAAAAAAAAAAAG
*
1137862 AAGAAAAAAAGAAGAA-
1 AACAAAAAAA-AA-AAG
1137878 AACAAAAAAAAAAAG
1 AACAAAAAAAAAAAG
*
1137893 AACAAAAATCAAAAAG
1 AACAAAAA-AAAAAAG
1137909 AA
1 AA
1137911 AAAGGGACAA
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
14 2 0.05
15 18 0.44
16 19 0.46
17 2 0.05
ACGTcount: A:0.81, C:0.06, G:0.11, T:0.02
Consensus pattern (15 bp):
AACAAAAAAAAAAAG
Found at i:1140269 original size:423 final size:424
Alignment explanation
Indices: 1139468--1140530 Score: 1738
Period size: 423 Copynumber: 2.5 Consensus size: 424
1139458 ATATCGTGCC
* * * *
1139468 ACTCGAGACAACACAAGTTCAACTTCACGATGAAGGGACGGCTGGTTGTCAACAAACAACTTCCC
1 ACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
* *
1139533 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
66 AATTTCGGAGCCAATTTCAACTTCACAGCGAAAGATATTGGACTCCAGACAACGCAAGTTCAACT
* *
1139598 TCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTC
131 TCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGACAATTTCAACTTC
*
1139663 ACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACTGCGGGTTG
196 ACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCGGGTTG
* *
1139728 TCAATAAACAATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAG
261 TCAACAAACAATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTAGACTCCAG
* *
1139793 ACAACGCAAGTTCAACTTCACGACGAAGGGATCGCTGGTTGTCAACAAACAACTTCCCAATTTCA
326 ACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCA
* **
1139858 GAGCCCATATCAACTTCACAGCGAATTATATTGG
391 GAGCCAATATCAACTTCACAGCGAAGGATATTGG
1139892 ACTCGAGACAACGC-AGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
1 ACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
*
1139956 AATTTTGGAGCCAATTTCAACTTCACAGCGAAAGATATTGGACTCCAGACAACGCAAGTTCAACT
66 AATTTCGGAGCCAATTTCAACTTCACAGCGAAAGATATTGGACTCCAGACAACGCAAGTTCAACT
* * *
1140021 TCACGATGAAGGGACCGCTAGTTGTCAACAAACAATTTCCCAATTTCGGAGACAATTTCAACTTC
131 TCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGACAATTTCAACTTC
*
1140086 ACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTG
196 ACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCGGGTTG
1140151 TCAACAAAC-ATCTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTAGACTCCA
261 TCAACAAACAAT-TTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTAGACTCCA
*
1140215 GACAACACAAGTTCAACTTCACGATGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTC
325 GACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTC
*
1140280 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
390 AGAGCCAATATCAACTTCACAGCGAAGGATATTGG
* * *
1140315 ACTCGAGACAACGCAAGTTCAACTTCATGACGAACGGACCGCTGGTTGTCAACAAATAATTTCCC
1 ACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
* * * *
1140380 AATTTCGGAGCTAATTTCAACTTCACA-AGAAAGGATATTGGACTCGAGACAACACAAGTTCAAC
66 AATTTCGGAGCCAATTTCAACTTCACAGCGAAA-GATATTGGACTCCAGACAACGCAAGTTCAAC
* * * * * *
1140444 TTCACAACGAAGGGACGGCTGGTTGTCAACAAATAATTTCCCGATTCCAGAGATAATTTCAACTT
130 TTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGACAATTTCAACTT
*
1140509 CAC-GACGGAGGATATTGGACTC
195 CACAG-CGAAGGATATTGGACTC
1140531 GGAACAATGC
Statistics
Matches: 594, Mismatches: 41, Indels: 8
0.92 0.06 0.01
Matches are distributed among these distances:
422 2 0.00
423 403 0.68
424 189 0.32
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.23
Consensus pattern (424 bp):
ACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
AATTTCGGAGCCAATTTCAACTTCACAGCGAAAGATATTGGACTCCAGACAACGCAAGTTCAACT
TCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGACAATTTCAACTTC
ACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCGGGTTG
TCAACAAACAATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTAGACTCCAG
ACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCA
GAGCCAATATCAACTTCACAGCGAAGGATATTGG
Found at i:1140531 original size:106 final size:106
Alignment explanation
Indices: 1139437--1140530 Score: 1640
Period size: 106 Copynumber: 10.3 Consensus size: 106
1139427 GCCATCCGCT
* * * * *
1139437 ATTTCAACTCCAC-GACGAAGGATATCGTGCCACTCGAGACAACACAAGTTCAACTTCACGATGA
1 ATTTCAACTTCACAG-CGAAGGATAT--TG-GACTCCAGACAACGCAAGTTCAACTTCACGACGA
* *
1139501 AGGGACGGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
62 AGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
1139546 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
1139611 ACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCA
66 ACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
1139652 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * * *
1139717 ACTGCGGGTTGTCAATAAACAATTTCTCAATTTCAGAGCCA
66 ACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
*
1139758 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * *
1139823 ATCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCC
66 ACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
* ** *
1139864 ATATCAACTTCACAGCGAATTATATTGGACTCGAGACAACGC-AGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
**
1139928 ACCGCTGGTTGTCAACAAACAATTTCCCAATTTTGGAGCCA
66 ACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
* *
1139969 ATTTCAACTTCACAGCGAAAGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGATGAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * *
1140034 ACCGCTAGTTGTCAACAAACAATTTCCCAATTTCGGAGACA
66 ACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
1140075 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
1140140 ACCGCTGGTTGTCAACAAAC-ATCTTCTCAATTTCAGAGCCA
66 ACCGCTGGTTGTCAACAAACAAT-TTCCCAATTTCAGAGCCA
* * * *
1140181 ATTTCAACTTCACAACGAAGGATATTAGACTCCAGACAACACAAGTTCAACTTCACGATGAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
1140246 ACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
66 ACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
* * *
1140287 ATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACGCAAGTTCAACTTCATGACGAACGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * *
1140352 ACCGCTGGTTGTCAACAAATAATTTCCCAATTTCGGAGCTA
66 ACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
* * * *
1140393 ATTTCAACTTCACAAG-AAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGG
1 ATTTCAACTTCAC-AGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
* * * * **
1140457 GACGGCTGGTTGTCAACAAATAATTTCCCGATTCCAGAGATA
65 GACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
*
1140499 ATTTCAACTTCAC-GACGGAGGATATTGGACTC
1 ATTTCAACTTCACAG-CGAAGGATATTGGACTC
1140531 GGAACAATGC
Statistics
Matches: 906, Mismatches: 72, Indels: 17
0.91 0.07 0.02
Matches are distributed among these distances:
104 1 0.00
105 98 0.11
106 779 0.86
107 5 0.01
109 22 0.02
110 1 0.00
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (106 bp):
ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
ACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
Found at i:1143169 original size:45 final size:45
Alignment explanation
Indices: 1143105--1143238 Score: 225
Period size: 45 Copynumber: 3.0 Consensus size: 45
1143095 GTAACTATGC
1143105 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
1143150 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
* *
1143195 AAATAAGCTTACGAGCTTAAGGTTAATAAATGGTAA-AATATTGG
1 AAATAAGCTTACGAGCTTATGG--AATAAATGGTAAGTATATTGG
1143239 ATATGCAAAT
Statistics
Matches: 85, Mismatches: 2, Indels: 3
0.94 0.02 0.03
Matches are distributed among these distances:
45 66 0.78
46 7 0.08
47 12 0.14
ACGTcount: A:0.41, C:0.07, G:0.22, T:0.31
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
Found at i:1145527 original size:4 final size:4
Alignment explanation
Indices: 1145518--1145587 Score: 90
Period size: 4 Copynumber: 18.0 Consensus size: 4
1145508 GGTGTTGTAA
1145518 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT -TAT -TAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
* * * *
1145564 TTAT ATTT ATTT ATTT ATAT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT
1145588 GTGATTATGC
Statistics
Matches: 62, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
3 6 0.10
4 56 0.90
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (4 bp):
ATAT
Found at i:1145529 original size:6 final size:6
Alignment explanation
Indices: 1145518--1145587 Score: 90
Period size: 6 Copynumber: 12.0 Consensus size: 6
1145508 GGTGTTGTAA
1145518 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATAT-T AT-TAT
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT
* * * *
1145564 TTATAT TTATTT ATTTAT ATATAT
1 ATATAT ATATAT ATATAT ATATAT
1145588 GTGATTATGC
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
4 1 0.02
5 5 0.09
6 50 0.89
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (6 bp):
ATATAT
Found at i:1145533 original size:10 final size:10
Alignment explanation
Indices: 1145518--1145587 Score: 90
Period size: 10 Copynumber: 7.2 Consensus size: 10
1145508 GGTGTTGTAA
1145518 ATATATATAT
1 ATATATATAT
1145528 ATATATATAT
1 ATATATATAT
1145538 ATATATATAT
1 ATATATATAT
1145548 ATATATATAT
1 ATATATATAT
*
1145558 -TAT-TATTT
1 ATATATATAT
* *
1145566 ATATTTATTT
1 ATATATATAT
*
1145576 ATTTATATAT
1 ATATATATAT
1145586 AT
1 AT
1145588 GTGATTATGC
Statistics
Matches: 54, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
8 4 0.07
9 6 0.11
10 44 0.81
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (10 bp):
ATATATATAT
Found at i:1149821 original size:132 final size:131
Alignment explanation
Indices: 1149583--1149826 Score: 391
Period size: 132 Copynumber: 1.9 Consensus size: 131
1149573 TTTAAAATTT
* *
1149583 GTGAAATTTTGAAACTCGAATTCTTCATTTTCAAAAATTTCATCTTCTTAAAACTTCATTTTCCA
1 GTGAAATTTTGAAAATCGAATTCTTCATTTTCAAAAATTTCATCTTCTTAAAACATCATTTTCCA
*
1149648 TTTTCAAATTCATTTGAAAACATCCTACCCGAAGGTTTTATGGATGGCCCGAAGGACTTACAAAT
66 TTTTCAAATTCATTTGAAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTACAAAT
1149713 C
131 C
* ** *
1149714 GTGAAATTTTGAAAATCGCATTCTTTGTTTTC-AAAATTTCCATCTTCTTAAAACATCATTTTTT
1 GTGAAATTTTGAAAATCGAATTCTTCATTTTCAAAAATTT-CATCTTCTTAAAACATCA-TTTTC
*
1149778 CATTTTTAAATTCATTTGAAAACATCCTACCCGAAGGTCTTATGGATGG
64 CATTTTCAAATTCATTTGAAAACATCCTACCCGAAGGTCTTATGGATGG
1149827 TTTGCTTCAC
Statistics
Matches: 103, Mismatches: 8, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
130 7 0.07
131 45 0.44
132 51 0.50
ACGTcount: A:0.31, C:0.18, G:0.11, T:0.39
Consensus pattern (131 bp):
GTGAAATTTTGAAAATCGAATTCTTCATTTTCAAAAATTTCATCTTCTTAAAACATCATTTTCCA
TTTTCAAATTCATTTGAAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTACAAAT
C
Found at i:1149990 original size:244 final size:245
Alignment explanation
Indices: 1149607--1150095 Score: 971
Period size: 244 Copynumber: 2.0 Consensus size: 245
1149597 CTCGAATTCT
1149607 TCATTTTCAAAAATTTCATCTTCTTAAAACTTCATTTTCCATTTTCAAATTCATTTGAAAACATC
1 TCATTTTCAAAAATTTCATCTTCTTAAAACTTCATTTTCCATTTTCAAATTCATTTGAAAACATC
1149672 CTACCCGAAGGTTTTATGGATGGCCCGAAGGACTTACAAATCGTGAAATTTTGAAAATCGCATTC
66 CTACCCGAAGGTTTTATGGATGGCCCGAAGGACTTACAAATCGTGAAATTTTGAAAATCGCATTC
1149737 TTTGTTTTCAAAATTTCCATCTTCTTAAAACATCATTTTTTCATTTTTAAATTCATTTGAAAACA
131 TTTGTTTTCAAAATTTCCATCTTCTTAAAACATCATTTTTTCATTTTTAAATTCATTTGAAAACA
1149802 TCCTACCCGAAGGTCTTATGGATGGTTTGCTTCACTGCTATTTTAGGGTG
196 TCCTACCCGAAGGTCTTATGGATGGTTTGCTTCACTGCTATTTTAGGGTG
1149852 TCATTTTCAAAAA-TTCATCTTCTTAAAACTTCATTTTCCATTTTCAAATTCATTTGAAAACATC
1 TCATTTTCAAAAATTTCATCTTCTTAAAACTTCATTTTCCATTTTCAAATTCATTTGAAAACATC
1149916 CTACCCGAAGGTTTTATGGATGGCCCGAAGGACTTACAAATCGTGAAATTTTGAAAATCGCATTC
66 CTACCCGAAGGTTTTATGGATGGCCCGAAGGACTTACAAATCGTGAAATTTTGAAAATCGCATTC
1149981 TTTGTTTTCAAAATTTCCATCTTCTTAAAACATCATTTTTTCATTTTTAAATTCATTTGAAAACA
131 TTTGTTTTCAAAATTTCCATCTTCTTAAAACATCATTTTTTCATTTTTAAATTCATTTGAAAACA
1150046 TCCTACCCGAAGGTCTTATGGATGGTTTGCTTCACTGCTATTTTAGGGTG
196 TCCTACCCGAAGGTCTTATGGATGGTTTGCTTCACTGCTATTTTAGGGTG
1150096 AGTCTTGAAA
Statistics
Matches: 244, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
244 231 0.95
245 13 0.05
ACGTcount: A:0.29, C:0.19, G:0.12, T:0.40
Consensus pattern (245 bp):
TCATTTTCAAAAATTTCATCTTCTTAAAACTTCATTTTCCATTTTCAAATTCATTTGAAAACATC
CTACCCGAAGGTTTTATGGATGGCCCGAAGGACTTACAAATCGTGAAATTTTGAAAATCGCATTC
TTTGTTTTCAAAATTTCCATCTTCTTAAAACATCATTTTTTCATTTTTAAATTCATTTGAAAACA
TCCTACCCGAAGGTCTTATGGATGGTTTGCTTCACTGCTATTTTAGGGTG
Found at i:1150231 original size:53 final size:52
Alignment explanation
Indices: 1150175--1150794 Score: 718
Period size: 53 Copynumber: 11.7 Consensus size: 52
1150165 ATCTTTAACA
* * *
1150175 ATCGTGTCTGCCCCCTATATCTTCAGAGAGTATAAGACCCACAATCTTCATG
1 ATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCCACAATCTTCACG
* *
1150227 AATCGCGCCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACG
1 -ATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGAC-C-CACAATCTTC-ACG
* * *
1150283 ATCGTGTCTGCCCCCTATATATTCAGAGAGTATAAGACCCACAATCTTCAACG
1 ATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCCACAATCTTC-ACG
* * *
1150336 ATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACCCACAATCTTCATCA
1 ATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCCACAATCTTCA-CG
* * *
1150389 ATCGCGTCTG-CCCCTATTTCTTCAGAGAGTATAAGACTCGAATAATCTT--CT
1 ATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGAC-C-CACAATCTTCACG
* * * *
1150440 TTTGC-T-T---CACTACTTT-TTCATAGAGTATAAGACCCACAATCTTCAACG
1 ATCGCGTCTGCCCCCTA-TTTCTTCAGAGAGTATAAGACCCACAATCTTC-ACG
**
1150488 ATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTTGAACAATCTTCAACG
1 ATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGAC--CCACAATCTTC-ACG
* * * *
1150543 ATTGCGTCTGCCCCCTATTTCTTTAGAGAGTATAAGACTCACAATCTTCATCA
1 ATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCCACAATCTTCA-CG
* *
1150596 ATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACT
1 ATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGAC-C-CACAATCTTC-ACG
* *
1150651 ATCGTGTCTGCCCCCTATATCTTCAGAGAGTATAAGACCCACAATCTTCAACG
1 ATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCCACAATCTTC-ACG
* * * *
1150704 ACCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACCCACAATCTTCATCA
1 ATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCCACAATCTTCA-CG
1150757 ATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGAC
1 ATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGAC
1150795 TCGAATAATC
Statistics
Matches: 491, Mismatches: 53, Indels: 46
0.83 0.09 0.08
Matches are distributed among these distances:
45 7 0.01
46 1 0.00
47 20 0.04
48 7 0.01
49 2 0.00
50 2 0.00
51 4 0.01
52 32 0.07
53 265 0.54
54 10 0.02
55 138 0.28
56 3 0.01
ACGTcount: A:0.27, C:0.28, G:0.15, T:0.30
Consensus pattern (52 bp):
ATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCCACAATCTTCACG
Found at i:1150298 original size:108 final size:107
Alignment explanation
Indices: 1150164--1150807 Score: 728
Period size: 108 Copynumber: 6.1 Consensus size: 107
1150154 GAACTCGAAT
* * * *
1150164 AATCTTTAACAATCGTGTCTGCCCCCTATATCTTCAGAGAGTATAAGAC-CCACAATCTTCATGA
1 AATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCAACAATCTTCATG-
*
1150228 ATCGCGCCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
65 ATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTC-AAC
* * * * * *
1150272 AATCTTCAACGATCGTGTCTGCCCCCTATATATTCAGAGAGTATAAGAC-CCACAATCTTCAACG
1 AATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCAACAATCTTC-ATG
* * *
1150336 ATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGAC-CCAC
65 ATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCAAC
* *
1150378 AATCTTCATCAATCGCGTCTG-CCCCTATTTCTTCAGAGAGTATAAGACTCGAATAATCTTC-T-
1 AATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTC-AACAATCTTCATG
* * * * *
1150440 TTTGC-T-T---CACTACTTT-TTCATAGAGTATAAGAC-CCAC
65 ATCGCGTCTGCCCCCTA-TTTCTTCAGAGAGTATAAGACTCAAC
* * *
1150477 AATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTTGAACAATCTTCAAC
1 AATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGAC-TCAACAATCTTC-AT
* *
1150542 GATTGCGTCTGCCCCCTATTTCTTTAGAGAGTATAAGACTC-AC
64 GATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCAAC
*
1150585 AATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAAC
1 AATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTC-AACAATCTTC-A-
* * *
1150650 T-ATCGTGTCTGCCCCCTATATCTTCAGAGAGTATAAGAC-CCAC
63 TGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCAAC
* * * * * *
1150693 AATCTTCAACGACCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGAC-CCACAATCTTCATCA
1 AATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCAACAATCTTCAT-G
*
1150757 ATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAT
65 ATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTC-AAC
1150801 AATCTTC
1 AATCTTC
1150808 TTTTGCTTCA
Statistics
Matches: 465, Mismatches: 48, Indels: 46
0.83 0.09 0.08
Matches are distributed among these distances:
99 43 0.09
100 39 0.08
101 1 0.00
102 1 0.00
103 5 0.01
104 4 0.01
105 27 0.06
106 66 0.14
107 16 0.03
108 260 0.56
109 3 0.01
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.30
Consensus pattern (107 bp):
AATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCAACAATCTTCATGA
TCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCAAC
Found at i:1151798 original size:124 final size:125
Alignment explanation
Indices: 1151552--1151852 Score: 448
Period size: 124 Copynumber: 2.4 Consensus size: 125
1151542 CTCAATAATT
* * *
1151552 CTTGGTCT-AATCTTTTCA--TCAACATGACGTGGGTTTGGTCGCGCCCCAACATTATCTTACAC
1 CTTGGTCTGAATCTTTTCATCTCAACATGATGTGGGTTTAGTCGTGCCCCAACATTATCTTACAC
* * * *
1151614 TGGTACGAGCCTTCAAAATGCCCCATCACCTCAAATTGTAAGGCTCATTCTTCATGCCTC
66 TGGTACGAGCCATCAAAATGCCCCAACACCTCAAATTGTAAGGCTCATTCTTAATACCTC
* * * *
1151674 CTTGGTCTGAATCTTTTCATCTCAACATAATGTGGGTTCAGTCATGCCCCAACATTATCTTATAC
1 CTTGGTCTGAATCTTTTCATCTCAACATGATGTGGGTTTAGTCGTGCCCCAACATTATCTTACAC
*
1151739 TGGTACG-GGCATCAAAATGCCCCAACACCTCAAATTGTAAGGCTCATTCTTAATACCTC
66 TGGTACGAGCCATCAAAATGCCCCAACACCTCAAATTGTAAGGCTCATTCTTAATACCTC
* *
1151798 CTTGGTCTGAATCTTGTCTTCTCAACATGATGTGGGTTTAGTCGTGCCCCAACAT
1 CTTGGTCTGAATCTTTTCATCTCAACATGATGTGGGTTTAGTCGTGCCCCAACAT
1151853 ATCACAACTT
Statistics
Matches: 159, Mismatches: 17, Indels: 4
0.88 0.09 0.02
Matches are distributed among these distances:
122 8 0.05
123 10 0.06
124 97 0.61
125 44 0.28
ACGTcount: A:0.24, C:0.27, G:0.17, T:0.32
Consensus pattern (125 bp):
CTTGGTCTGAATCTTTTCATCTCAACATGATGTGGGTTTAGTCGTGCCCCAACATTATCTTACAC
TGGTACGAGCCATCAAAATGCCCCAACACCTCAAATTGTAAGGCTCATTCTTAATACCTC
Found at i:1153070 original size:16 final size:15
Alignment explanation
Indices: 1153046--1153075 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
1153036 TTTCATTCTT
1153046 TTTTCATTTTTCTCA
1 TTTTCATTTTTCTCA
1153061 TTTTCAATTTTTCTC
1 TTTTC-ATTTTTCTC
1153076 TTTCTTTTCC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.13, C:0.20, G:0.00, T:0.67
Consensus pattern (15 bp):
TTTTCATTTTTCTCA
Found at i:1153095 original size:23 final size:23
Alignment explanation
Indices: 1153069--1153158 Score: 78
Period size: 23 Copynumber: 3.9 Consensus size: 23
1153059 CATTTTCAAT
1153069 TTTTCTCTTTCTTTTCCTTTTTA
1 TTTTCTCTTTCTTTTCCTTTTTA
* * *
1153092 TTTTCTTTTTCATTTCATTTTT-
1 TTTTCTCTTTCTTTTCCTTTTTA
*
1153114 TTTATCT-TTTCTTTTTCTCTTTCTA
1 TTT-TCTCTTTC-TTTTC-CTTTTTA
*
1153139 TATTTCTC-TTCTTTTTCTTT
1 T-TTTCTCTTTCTTTTCCTTT
1153159 ATGATGTCAA
Statistics
Matches: 54, Mismatches: 7, Indels: 12
0.74 0.10 0.16
Matches are distributed among these distances:
22 7 0.13
23 30 0.56
24 8 0.15
25 7 0.13
26 2 0.04
ACGTcount: A:0.07, C:0.19, G:0.00, T:0.74
Consensus pattern (23 bp):
TTTTCTCTTTCTTTTCCTTTTTA
Found at i:1153101 original size:6 final size:6
Alignment explanation
Indices: 1153045--1153158 Score: 58
Period size: 6 Copynumber: 18.5 Consensus size: 6
1153035 CTTTCATTCT
* * *
1153045 TTTTTC ATTTTTC TCATTTTC AATTTTTC TCTTTC TTTTCC TTTTT- ATTTTC
1 TTTTTC -TTTTTC T--TTTTC --TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC
* * *
1153097 TTTTTC -ATTTC ATTTTT- TTTATC -TTTTC TTTTTC TCTTTC TATATTTC
1 TTTTTC TTTTTC -TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC T-T-TTTC
*
1153145 -TCTTC TTTTTC TTT
1 TTTTTC TTTTTC TTT
1153159 ATGATGTCAA
Statistics
Matches: 81, Mismatches: 14, Indels: 25
0.68 0.12 0.21
Matches are distributed among these distances:
5 19 0.23
6 38 0.47
7 9 0.11
8 14 0.17
10 1 0.01
ACGTcount: A:0.09, C:0.18, G:0.00, T:0.73
Consensus pattern (6 bp):
TTTTTC
Found at i:1156916 original size:13 final size:13
Alignment explanation
Indices: 1156898--1156922 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1156888 AAATACATGC
1156898 AATGCAAATGCAA
1 AATGCAAATGCAA
1156911 AATGCAAATGCA
1 AATGCAAATGCA
1156923 CGAGGTGCTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.16, G:0.16, T:0.16
Consensus pattern (13 bp):
AATGCAAATGCAA
Found at i:1157189 original size:21 final size:21
Alignment explanation
Indices: 1157165--1157262 Score: 119
Period size: 21 Copynumber: 4.7 Consensus size: 21
1157155 ATGTGATGTA
*
1157165 GTCTTCAT-GTCTTTATGAAGG
1 GTCTTC-TCGTCTTTATGAACG
* *
1157186 GTCTTCAT-GTCTCTATGAATG
1 GTCTTC-TCGTCTTTATGAACG
*
1157207 GTCTTCTCATCTTTATGAACG
1 GTCTTCTCGTCTTTATGAACG
1157228 GTCTTCTCGTCTTTATGAACG
1 GTCTTCTCGTCTTTATGAACG
*
1157249 GTCTTCTCATCTTT
1 GTCTTCTCGTCTTT
1157263 GGTACGACTA
Statistics
Matches: 69, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
20 1 0.01
21 68 0.99
ACGTcount: A:0.16, C:0.21, G:0.17, T:0.45
Consensus pattern (21 bp):
GTCTTCTCGTCTTTATGAACG
Found at i:1157212 original size:42 final size:42
Alignment explanation
Indices: 1157174--1157262 Score: 135
Period size: 42 Copynumber: 2.1 Consensus size: 42
1157164 AGTCTTCATG
* *
1157174 TCTTTATGAAGGGTCTTCAT-GTCTCTATGAATGGTCTTCTCA
1 TCTTTATGAACGGTCTTC-TCGTCTCTATGAACGGTCTTCTCA
*
1157216 TCTTTATGAACGGTCTTCTCGTCTTTATGAACGGTCTTCTCA
1 TCTTTATGAACGGTCTTCTCGTCTCTATGAACGGTCTTCTCA
1157258 TCTTT
1 TCTTT
1157263 GGTACGACTA
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
41 1 0.02
42 42 0.98
ACGTcount: A:0.17, C:0.21, G:0.17, T:0.45
Consensus pattern (42 bp):
TCTTTATGAACGGTCTTCTCGTCTCTATGAACGGTCTTCTCA
Found at i:1161631 original size:63 final size:64
Alignment explanation
Indices: 1161552--1161695 Score: 227
Period size: 63 Copynumber: 2.3 Consensus size: 64
1161542 ATGCACTATA
* *
1161552 GTAGTGCATCAATACACAATATTAATTTGAAGTTTTGGTGCATCGATGCACTATTCACG-TACT
1 GTAGTGCATCAATACACAATATTAATTCGAAGTTTTGGTGCATCGATGCACTATTCACGTTAAT
* *
1161615 GTAGTGCATCGATACACAATATTAATTCGAAGTTTTGGTGCATCGATGCACTGTTCACGTTAAT
1 GTAGTGCATCAATACACAATATTAATTCGAAGTTTTGGTGCATCGATGCACTATTCACGTTAAT
* *
1161679 GTAGCGCATCAGTACAC
1 GTAGTGCATCAATACAC
1161696 TGTTCACGGG
Statistics
Matches: 73, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
63 56 0.77
64 17 0.23
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (64 bp):
GTAGTGCATCAATACACAATATTAATTCGAAGTTTTGGTGCATCGATGCACTATTCACGTTAAT
Found at i:1161661 original size:34 final size:34
Alignment explanation
Indices: 1161555--1161661 Score: 107
Period size: 34 Copynumber: 3.3 Consensus size: 34
1161545 CACTATAGTA
* *
1161555 GTGCATCAATACACAATATTAATTTGAAGTTTTG
1 GTGCATCGATACACAATATTAATTCGAAGTTTTG
* * * * * *
1161589 GTGCATCGATGCAC--TATTCA--CGTA-CTGTA
1 GTGCATCGATACACAATATTAATTCGAAGTTTTG
1161618 GTGCATCGATACACAATATTAATTCGAAGTTTTG
1 GTGCATCGATACACAATATTAATTCGAAGTTTTG
1161652 GTGCATCGAT
1 GTGCATCGAT
1161662 GCACTGTTCA
Statistics
Matches: 54, Mismatches: 14, Indels: 10
0.69 0.18 0.13
Matches are distributed among these distances:
29 15 0.28
30 2 0.04
31 5 0.09
32 5 0.09
33 3 0.06
34 24 0.44
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.35
Consensus pattern (34 bp):
GTGCATCGATACACAATATTAATTCGAAGTTTTG
Found at i:1161738 original size:22 final size:22
Alignment explanation
Indices: 1161693--1161763 Score: 97
Period size: 22 Copynumber: 3.2 Consensus size: 22
1161683 CGCATCAGTA
* * *
1161693 CACTGTTCACGGGTATTATACAT
1 CACTGTTCAC-GGTACTGTTCAT
1161716 CACTGTTCACGGTACTGTTCAT
1 CACTGTTCACGGTACTGTTCAT
*
1161738 CACTATTCACGGTACTGTTCAT
1 CACTGTTCACGGTACTGTTCAT
1161760 CACT
1 CACT
1161764 ATTAATAAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
22 34 0.77
23 10 0.23
ACGTcount: A:0.23, C:0.27, G:0.15, T:0.35
Consensus pattern (22 bp):
CACTGTTCACGGTACTGTTCAT
Found at i:1161764 original size:22 final size:22
Alignment explanation
Indices: 1161713--1161766 Score: 99
Period size: 22 Copynumber: 2.5 Consensus size: 22
1161703 GGGTATTATA
*
1161713 CATCACTGTTCACGGTACTGTT
1 CATCACTATTCACGGTACTGTT
1161735 CATCACTATTCACGGTACTGTT
1 CATCACTATTCACGGTACTGTT
1161757 CATCACTATT
1 CATCACTATT
1161767 AATAAAAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.22, C:0.28, G:0.13, T:0.37
Consensus pattern (22 bp):
CATCACTATTCACGGTACTGTT
Found at i:1171025 original size:20 final size:20
Alignment explanation
Indices: 1171000--1171038 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
1170990 CTTGGCTTGC
1171000 TTTCTTTT-TGAATTTTTCTT
1 TTTCTTTTCTG-ATTTTTCTT
1171020 TTTCTTTTCTGATTTTTCT
1 TTTCTTTTCTGATTTTTCT
1171039 CTTCTTTTGC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 16 0.89
21 2 0.11
ACGTcount: A:0.08, C:0.13, G:0.05, T:0.74
Consensus pattern (20 bp):
TTTCTTTTCTGATTTTTCTT
Found at i:1171043 original size:19 final size:20
Alignment explanation
Indices: 1171001--1171046 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
1170991 TTGGCTTGCT
*
1171001 TTCTTTTTGAATTTTTCTTT
1 TTCTTTTTGAATTTTTCTTC
1171021 TTCTTTTCTG-ATTTTTC-TC
1 TTCTTTT-TGAATTTTTCTTC
1171040 TTCTTTT
1 TTCTTTT
1171047 GCCTTTTTCT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 8 0.33
20 14 0.58
21 2 0.08
ACGTcount: A:0.07, C:0.15, G:0.04, T:0.74
Consensus pattern (20 bp):
TTCTTTTTGAATTTTTCTTC
Found at i:1177278 original size:15 final size:15
Alignment explanation
Indices: 1177258--1177289 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1177248 GAAAATTACC
*
1177258 ATTTTCCATTAAAAT
1 ATTTTCCATCAAAAT
1177273 ATTTTCCATCAAAAT
1 ATTTTCCATCAAAAT
1177288 AT
1 AT
1177290 CTGAAACAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.41, C:0.16, G:0.00, T:0.44
Consensus pattern (15 bp):
ATTTTCCATCAAAAT
Found at i:1177880 original size:39 final size:39
Alignment explanation
Indices: 1177826--1177919 Score: 127
Period size: 39 Copynumber: 2.4 Consensus size: 39
1177816 CATCAACCTC
* * *
1177826 ACCTTAGGCGTTATCGCCTTTACTGCACTCGATA-TCCTA
1 ACCTTAGGCATTATCGCCTTTACTGCACTCAACATTCC-A
* *
1177865 ACCTTAGGCATTATCGCCTTTATTGCACTCAACATTCCC
1 ACCTTAGGCATTATCGCCTTTACTGCACTCAACATTCCA
1177904 ACCTTAGGCATTATCG
1 ACCTTAGGCATTATCG
1177920 TCTTAATTAC
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
39 46 0.94
40 3 0.06
ACGTcount: A:0.22, C:0.31, G:0.14, T:0.33
Consensus pattern (39 bp):
ACCTTAGGCATTATCGCCTTTACTGCACTCAACATTCCA
Found at i:1179639 original size:18 final size:18
Alignment explanation
Indices: 1179604--1179638 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1179594 AATAATCAAA
1179604 CCTATATTGTTTCTTTTT
1 CCTATATTGTTTCTTTTT
1179622 CCTATATTG-TTCTTTTT
1 CCTATATTGTTTCTTTTT
1179639 TAGTTCATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.11, C:0.17, G:0.06, T:0.66
Consensus pattern (18 bp):
CCTATATTGTTTCTTTTT
Found at i:1179902 original size:48 final size:48
Alignment explanation
Indices: 1179802--1179919 Score: 155
Period size: 48 Copynumber: 2.4 Consensus size: 48
1179792 CACATAGTGC
* *
1179802 CAGGAGTACATGAATGTACTAAATACATGAGTACCTAATAGTACTAACA
1 CAGGAGTACACGAATGTACT-AATACATGAGTACCAAATAGTACTAACA
* * * * *
1179851 CAGGAGTGCACGAATGCACTAATATATGAGTACCAAATGGTACTAATA
1 CAGGAGTACACGAATGTACTAATACATGAGTACCAAATAGTACTAACA
*
1179899 CAGGAGTACACGGATGTACTA
1 CAGGAGTACACGAATGTACTA
1179920 GAATTAGTAT
Statistics
Matches: 59, Mismatches: 10, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
48 42 0.71
49 17 0.29
ACGTcount: A:0.40, C:0.17, G:0.20, T:0.23
Consensus pattern (48 bp):
CAGGAGTACACGAATGTACTAATACATGAGTACCAAATAGTACTAACA
Found at i:1179917 original size:24 final size:24
Alignment explanation
Indices: 1179802--1179919 Score: 105
Period size: 24 Copynumber: 4.9 Consensus size: 24
1179792 CACATAGTGC
*
1179802 CAGGAGTACATGAATGTACTAAATA
1 CAGGAGTACACGAATGTACT-AATA
* * *
1179827 CATGAGTAC-CTAATAGTACTAACA
1 CAGGAGTACACGAAT-GTACTAATA
* *
1179851 CAGGAGTGCACGAATGCACTAATA
1 CAGGAGTACACGAATGTACTAATA
* * *
1179875 TATGAGTAC-CAAATGGTACTAATA
1 CAGGAGTACACGAAT-GTACTAATA
*
1179899 CAGGAGTACACGGATGTACTA
1 CAGGAGTACACGAATGTACTA
1179920 GAATTAGTAT
Statistics
Matches: 71, Mismatches: 18, Indels: 9
0.72 0.18 0.09
Matches are distributed among these distances:
23 4 0.06
24 47 0.66
25 20 0.28
ACGTcount: A:0.40, C:0.17, G:0.20, T:0.23
Consensus pattern (24 bp):
CAGGAGTACACGAATGTACTAATA
Found at i:1189413 original size:2 final size:2
Alignment explanation
Indices: 1189408--1189447 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
1189398 ATTTATTTTC
*
1189408 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT CT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1189448 GTTATTATGA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1208494 original size:5 final size:5
Alignment explanation
Indices: 1208475--1208543 Score: 84
Period size: 5 Copynumber: 13.8 Consensus size: 5
1208465 GTCAGTCCGT
* * * * * *
1208475 CTCGT CTCGT CTCGG CTCGG CACGG CACGG CTTGG CTTGG CTCGG CTCGG
1 CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG
1208525 CTCGG CTCGG CTCGG CTCG
1 CTCGG CTCGG CTCGG CTCG
1208544 TGGTCGTGGT
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 59 1.00
ACGTcount: A:0.03, C:0.38, G:0.36, T:0.23
Consensus pattern (5 bp):
CTCGG
Found at i:1208552 original size:6 final size:6
Alignment explanation
Indices: 1208541--1208601 Score: 95
Period size: 6 Copynumber: 10.2 Consensus size: 6
1208531 TCGGCTCGGC
* * *
1208541 TCGTGG TCGTGG TCGTGG TCGAGG TCGAGG TCGAGG TCGTGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
1208589 TCGTGG TCGTGG T
1 TCGTGG TCGTGG T
1208602 AATACGTGTC
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 53 1.00
ACGTcount: A:0.05, C:0.16, G:0.49, T:0.30
Consensus pattern (6 bp):
TCGTGG
Found at i:1208901 original size:22 final size:22
Alignment explanation
Indices: 1208876--1208930 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
1208866 TCAGGAGTTA
* *
1208876 CAGGAGTTATTTGATTTAATTC
1 CAGGAGTTATATGATATAATTC
* * *
1208898 CAGGGGTTACATGATATAATTT
1 CAGGAGTTATATGATATAATTC
*
1208920 CGGGAGTTATA
1 CAGGAGTTATA
1208931 ACAGCTATAT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (22 bp):
CAGGAGTTATATGATATAATTC
Found at i:1217068 original size:17 final size:17
Alignment explanation
Indices: 1217046--1217080 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1217036 AAACAATAAA
*
1217046 TATACTTTATCTTGTGG
1 TATACTTTATCTGGTGG
*
1217063 TATACTTTCTCTGGTGG
1 TATACTTTATCTGGTGG
1217080 T
1 T
1217081 GTAAGATCTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.14, C:0.14, G:0.20, T:0.51
Consensus pattern (17 bp):
TATACTTTATCTGGTGG
Found at i:1219439 original size:20 final size:20
Alignment explanation
Indices: 1219410--1219447 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1219400 AAGAAATTTA
*
1219410 TTGAATATTTAGGGTAATAT
1 TTGAAGATTTAGGGTAATAT
1219430 TTGAAGATTTAGGGTAAT
1 TTGAAGATTTAGGGTAAT
1219448 GTTATGGTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.00, G:0.24, T:0.42
Consensus pattern (20 bp):
TTGAAGATTTAGGGTAATAT
Found at i:1225180 original size:54 final size:54
Alignment explanation
Indices: 1224787--1225159 Score: 530
Period size: 54 Copynumber: 6.9 Consensus size: 54
1224777 AATTCTAGGA
* ** *
1224787 AAATGGACACTTAGTGAAGAAACGGTTATTCATCCACATAGGATGAATTTCGTG
1 AAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTG
* *
1224841 AAATGCACACTTAGTGCCAAAACGATTATTCATCCACATAGGATGAATTCCGTG
1 AAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTG
** *
1224895 AAATGCACACTTAGTGCCGAAACATTTATTCATCCATATAGGATGAATTCCGTG
1 AAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTG
* * *
1224949 AAATGCACACTTAGTGCCGAAACAGTTATTCATCTATATAGGATGAATTCCGTG
1 AAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTG
*** * *
1225003 AAACATACACTTAGTGCCAAAACGATTATTCATCCACATAGGATGAATTCCGTG
1 AAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTG
* * * *
1225057 AAATACACACTTAGTGCCGAAACGGTTATTCATTCGCATAGGATTAATTCCGTG
1 AAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTG
* * *
1225111 AAATGCACACTTAGTGTCGAAACGGTTAGTCATCCATATAGGATGAATT
1 AAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATT
1225160 TTGTACTTTG
Statistics
Matches: 285, Mismatches: 34, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 285 1.00
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.28
Consensus pattern (54 bp):
AAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTG
Found at i:1238101 original size:215 final size:216
Alignment explanation
Indices: 1237724--1238226 Score: 596
Period size: 215 Copynumber: 2.3 Consensus size: 216
1237714 AATTATGGGA
* * * * * *
1237724 AAATGCACACTTAGTGCCGAAACGGTTATTTATCCACCTAGGATGAATTCCGTGGAATGCACAAT
1 AAATGAACACTTAATGCCAAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACAAT
* * * * *
1237789 TAGTGTCGAAACGATTATTCATACACATAGGATGAATTCCGTAAAATGTACACTTAGTGCTGGAA
66 TAGTGCCGAAACGATTATTCATACACATAGGATGAATTCCATAAAATGTACACTTAGTACCGAAA
* * * * *
1237854 CGGTTATTCATCCATATATGATGAATTCCATGAAATGAACCCTTAGTGCCGAAACGGTTATTCAT
131 CGGTTATTCATCCACATAGGATGAATTCCATGAAATGAACACTTAATGCCGAAACGGTTATTCAC
*
1237919 CCACATAGGATGAATTCCATG
196 CCACATAGGATAAATTCCATG
* * * * * *
1237940 AACT-AACACTTAATGCTAAAATGTTTATTCATCCACATAGGATGAATTCTGTGAAATGCACACT
1 AAATGAACACTTAATGCCAAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACAAT
* * * * *
1238004 TAGTGCCGAAACGGTTATTCATCCACATATGATGAATTCTATGAAATGTACACTTAGTACCGAAA
66 TAGTGCCGAAACGATTATTCATACACATAGGATGAATTCCATAAAATGTACACTTAGTACCGAAA
* * * * *
1238069 TGGTTATTCATCCACATAGGATGAATTCCATGAAATGCACACTTAATGTCTAAATGGTTATTCAC
131 CGGTTATTCATCCACATAGGATGAATTCCATGAAATGAACACTTAATGCCGAAACGGTTATTCAC
* * *
1238134 CCGCATAGGATAAATTTCGTG
196 CCACATAGGATAAATTCCATG
* * * * * **
1238155 AAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAAGATGAATTTCGT-ACTTTGCACAA
1 AAATGAACACTTAATGCCAAAACGGTTATTCATCCACATAGGATGAATTCCGTGA-AATGCACAA
1238219 TTAGTGCC
65 TTAGTGCC
1238227 TATTTGTTAA
Statistics
Matches: 236, Mismatches: 49, Indels: 4
0.82 0.17 0.01
Matches are distributed among these distances:
215 180 0.76
216 56 0.24
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.30
Consensus pattern (216 bp):
AAATGAACACTTAATGCCAAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACAAT
TAGTGCCGAAACGATTATTCATACACATAGGATGAATTCCATAAAATGTACACTTAGTACCGAAA
CGGTTATTCATCCACATAGGATGAATTCCATGAAATGAACACTTAATGCCGAAACGGTTATTCAC
CCACATAGGATAAATTCCATG
Found at i:1238207 original size:54 final size:54
Alignment explanation
Indices: 1237724--1238203 Score: 584
Period size: 54 Copynumber: 8.9 Consensus size: 54
1237714 AATTATGGGA
* *
1237724 AAATGCACACTTAGTGCCGAAACGGTTATTTATCCACCTAGGATGAATTCCGTG
1 AAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTG
* * * * * *
1237778 GAATGCACAATTAGTGTCGAAACGATTATTCATACACATAGGATGAATTCCGTA
1 AAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTG
* * * * * *
1237832 AAATGTACACTTAGTGCTGGAACGGTTATTCATCCATATATGATGAATTCCATG
1 AAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTG
* * *
1237886 AAATGAACCCTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCATG
1 AAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTG
* * * ** * * *
1237940 AACT-AACACTTAATGCTAAAATGTTTATTCATCCACATAGGATGAATTCTGTG
1 AAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTG
* **
1237993 AAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATATGATGAATTCTATG
1 AAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTG
* * * *
1238047 AAATGTACACTTAGTACCGAAATGGTTATTCATCCACATAGGATGAATTCCATG
1 AAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTG
* * * * * * * *
1238101 AAATGCACACTTAATGTCTAAATGGTTATTCACCCGCATAGGATAAATTTCGTG
1 AAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTG
*
1238155 AAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAAGATGAATT
1 AAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATT
1238204 TCGTACTTTG
Statistics
Matches: 358, Mismatches: 67, Indels: 2
0.84 0.16 0.00
Matches are distributed among these distances:
53 44 0.12
54 314 0.88
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Consensus pattern (54 bp):
AAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTG
Found at i:1243023 original size:13 final size:13
Alignment explanation
Indices: 1243005--1243041 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
1242995 AAGTTTATGA
*
1243005 AAATGATTTTTAC
1 AAATGATTTTAAC
1243018 AAATGATTTTAAC
1 AAATGATTTTAAC
*
1243031 GAATGATTTTA
1 AAATGATTTTA
1243042 GGGTATGAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.41, C:0.05, G:0.11, T:0.43
Consensus pattern (13 bp):
AAATGATTTTAAC
Found at i:1245092 original size:18 final size:18
Alignment explanation
Indices: 1245069--1245108 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
1245059 TTTATGGAGT
1245069 TTGTATGAGATTTTTGGA
1 TTGTATGAGATTTTTGGA
*
1245087 TTGTATGAGATTTTTGGG
1 TTGTATGAGATTTTTGGA
1245105 TTGT
1 TTGT
1245109 GGATATTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.17, C:0.00, G:0.30, T:0.53
Consensus pattern (18 bp):
TTGTATGAGATTTTTGGA
Found at i:1245363 original size:20 final size:20
Alignment explanation
Indices: 1245334--1245374 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
1245324 AAGAGATTTA
*
1245334 TTGAATATTTAGGGTAATGT
1 TTGAAGATTTAGGGTAATGT
1245354 TTGAAGATTTAGGGTAATGT
1 TTGAAGATTTAGGGTAATGT
1245374 T
1 T
1245375 ATAGTATATG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.29, C:0.00, G:0.27, T:0.44
Consensus pattern (20 bp):
TTGAAGATTTAGGGTAATGT
Found at i:1246635 original size:20 final size:20
Alignment explanation
Indices: 1246572--1246646 Score: 60
Period size: 20 Copynumber: 3.7 Consensus size: 20
1246562 AGATGAACAA
* *
1246572 GTATCCATACTAGAGGCTTG
1 GTATTCATACTAGAAGCTTG
* * **
1246592 ATATTCATACCAGATAATTTG
1 GTATTCATACTAGA-AGCTTG
*
1246613 GTATTGATACTAGAAGCTTG
1 GTATTCATACTAGAAGCTTG
* *
1246633 GTATCCATAGTAGA
1 GTATTCATACTAGA
1246647 TGTACTGATA
Statistics
Matches: 40, Mismatches: 14, Indels: 2
0.71 0.25 0.04
Matches are distributed among these distances:
20 26 0.65
21 14 0.35
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.33
Consensus pattern (20 bp):
GTATTCATACTAGAAGCTTG
Found at i:1259165 original size:35 final size:35
Alignment explanation
Indices: 1259119--1259189 Score: 124
Period size: 35 Copynumber: 2.0 Consensus size: 35
1259109 TGCATTGAGA
1259119 GTATTAGGTACAATTGGCATGCCATGAAGTGAAGT
1 GTATTAGGTACAATTGGCATGCCATGAAGTGAAGT
* *
1259154 GTATTAGGTACAATTGGTATGCCATGAAGTGGAGT
1 GTATTAGGTACAATTGGCATGCCATGAAGTGAAGT
1259189 G
1 G
1259190 ATTCTATGGT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.30, C:0.10, G:0.31, T:0.30
Consensus pattern (35 bp):
GTATTAGGTACAATTGGCATGCCATGAAGTGAAGT
Found at i:1259237 original size:23 final size:23
Alignment explanation
Indices: 1259211--1259259 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
1259201 CATATTTGTA
*
1259211 CATTTTACATGGCACTACATGTG
1 CATTATACATGGCACTACATGTG
** *
1259234 CATTATATGTGGCACTATATGTG
1 CATTATACATGGCACTACATGTG
1259257 CAT
1 CAT
1259260 AATGGGTTTC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.37
Consensus pattern (23 bp):
CATTATACATGGCACTACATGTG
Found at i:1262998 original size:143 final size:143
Alignment explanation
Indices: 1262735--1263018 Score: 496
Period size: 143 Copynumber: 2.0 Consensus size: 143
1262725 GTTGCACCTA
* *
1262735 AGTGCCGAAATGGTAATTCATAAACTCATTATGAATTCCATTGATGCACAAATAGTGCCGAAAGT
1 AGTGCCGAAATGGTAATTCACAAACTCATTATGAATTCCATGGATGCACAAATAGTGCCGAAAGT
*
1262800 AAATATAGTACTGATACGAAAATGCAATATATGCATTAAACAAAATCGATCGATAACCATCATAC
66 AAATATAGTACTGATACGAAAATGCAACATATGCATTAAACAAAATCGATCGATAACCATCATAC
1262865 ACAAAGTATGTCG
131 ACAAAGTATGTCG
* * *
1262878 AGTGTCGAAATGGTAATTCACAAACTCATTATTAATTCCATGGATGCACATATAGTGCCGAAAGT
1 AGTGCCGAAATGGTAATTCACAAACTCATTATGAATTCCATGGATGCACAAATAGTGCCGAAAGT
* *
1262943 ACATATAGTACTGATACGAAAATGCAACATATGCATTAAACAAAATCGATCGATAACCATCATAT
66 AAATATAGTACTGATACGAAAATGCAACATATGCATTAAACAAAATCGATCGATAACCATCATAC
1263008 ACAAAGTATGT
131 ACAAAGTATGT
1263019 TGAAATGCAC
Statistics
Matches: 133, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
143 133 1.00
ACGTcount: A:0.42, C:0.17, G:0.15, T:0.26
Consensus pattern (143 bp):
AGTGCCGAAATGGTAATTCACAAACTCATTATGAATTCCATGGATGCACAAATAGTGCCGAAAGT
AAATATAGTACTGATACGAAAATGCAACATATGCATTAAACAAAATCGATCGATAACCATCATAC
ACAAAGTATGTCG
Found at i:1269615 original size:143 final size:143
Alignment explanation
Indices: 1269349--1269768 Score: 651
Period size: 143 Copynumber: 2.9 Consensus size: 143
1269339 CTAAGTGCCA
**
1269349 AAATGGTAATTCACAAACTCATTATGAATTAAATGGATGCACACATAGTGTCGAAAGTACATATA
1 AAATGGTAATTCACAAACTCATTATGAATTCCATGGATGCACACATAGTGTCGAAAGTACATATA
* * * * * *
1269414 GTACTTATACGAAATTACAACATATACAATAAACAGAATCGATCGATAACCATCATACACAAAGT
66 GTACTGATACGAAAATGCAACATATGCATTAAACAAAATCGATCGATAACCATCATACACAAAGT
1269479 ATGTAGAGAATCG
131 ATGTAGAGAATCG
* * *
1269492 AAATAGTAATTCATAAACTCATTATGAATTCCATGGATGCACAAATAGTGTCGAAAGTACATATA
1 AAATGGTAATTCACAAACTCATTATGAATTCCATGGATGCACACATAGTGTCGAAAGTACATATA
* *
1269557 GTACTGATACGAAAATGCAACATATGCATTAAACAAAATCGATCGATAACCATTATACACAAAAT
66 GTACTGATACGAAAATGCAACATATGCATTAAACAAAATCGATCGATAACCATCATACACAAAGT
* **
1269622 ATGTCGAGTGTCG
131 ATGTAGAGAATCG
*
1269635 AAATGGTAATTCACAAACTCATTATTAATTCCATGGATGCACACATAGTGTCGAAAGTACATATA
1 AAATGGTAATTCACAAACTCATTATGAATTCCATGGATGCACACATAGTGTCGAAAGTACATATA
* * * *
1269700 GTATTGATACAAAAATGCAACATATGCATTAGACAAAATCGATCGATAACCATCATATACAAAGT
66 GTACTGATACGAAAATGCAACATATGCATTAAACAAAATCGATCGATAACCATCATACACAAAGT
1269765 ATGT
131 ATGT
1269769 CGAAATGCAC
Statistics
Matches: 251, Mismatches: 26, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
143 251 1.00
ACGTcount: A:0.43, C:0.16, G:0.14, T:0.26
Consensus pattern (143 bp):
AAATGGTAATTCACAAACTCATTATGAATTCCATGGATGCACACATAGTGTCGAAAGTACATATA
GTACTGATACGAAAATGCAACATATGCATTAAACAAAATCGATCGATAACCATCATACACAAAGT
ATGTAGAGAATCG
Found at i:1270651 original size:15 final size:15
Alignment explanation
Indices: 1270633--1270664 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
1270623 TCATTAAACT
1270633 CATCATCACTTAACC
1 CATCATCACTTAACC
1270648 CATCATCACTTAACC
1 CATCATCACTTAACC
1270663 CA
1 CA
1270665 ACTAATTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.34, C:0.41, G:0.00, T:0.25
Consensus pattern (15 bp):
CATCATCACTTAACC
Found at i:1276887 original size:12 final size:12
Alignment explanation
Indices: 1276870--1276896 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1276860 GTTACTGTTT
1276870 ACTGCTACAGTA
1 ACTGCTACAGTA
1276882 ACTGCTACAGTA
1 ACTGCTACAGTA
1276894 ACT
1 ACT
1276897 TTTGTAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.33, C:0.26, G:0.15, T:0.26
Consensus pattern (12 bp):
ACTGCTACAGTA
Found at i:1277767 original size:30 final size:30
Alignment explanation
Indices: 1277722--1277780 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
1277712 ATCGCGTAGA
* *
1277722 CATATTATTTCCATACCTTTATCACATAGG
1 CATATCATTTACATACCTTTATCACATAGG
1277752 CATATCATTTACATACCTTTATCACATAG
1 CATATCATTTACATACCTTTATCACATAG
1277781 CTCATATAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.32, C:0.24, G:0.05, T:0.39
Consensus pattern (30 bp):
CATATCATTTACATACCTTTATCACATAGG
Found at i:1277881 original size:34 final size:29
Alignment explanation
Indices: 1277802--1277873 Score: 144
Period size: 29 Copynumber: 2.5 Consensus size: 29
1277792 TTTTCTGCAT
1277802 ATTCATGTCATGTAATACATATAATATGA
1 ATTCATGTCATGTAATACATATAATATGA
1277831 ATTCATGTCATGTAATACATATAATATGA
1 ATTCATGTCATGTAATACATATAATATGA
1277860 ATTCATGTCATGTA
1 ATTCATGTCATGTA
1277874 TCATAATATG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.39
Consensus pattern (29 bp):
ATTCATGTCATGTAATACATATAATATGA
Found at i:1281948 original size:18 final size:18
Alignment explanation
Indices: 1281925--1281959 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1281915 TTCCATCCGG
*
1281925 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
1281943 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
1281960 GTCCTTTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:1283131 original size:19 final size:19
Alignment explanation
Indices: 1283109--1283191 Score: 113
Period size: 19 Copynumber: 4.6 Consensus size: 19
1283099 CTAGGCGGCT
*
1283109 CGGCTTGGCTCAGCTCAAA
1 CGGCTCGGCTCAGCTCAAA
1283128 CGGCTCGGCTCAGCTCAAA
1 CGGCTCGGCTCAGCTCAAA
1283147 CGGCTC-G----GCTCAAA
1 CGGCTCGGCTCAGCTCAAA
*
1283161 CGGCTCGGCTCAGCTCAAG
1 CGGCTCGGCTCAGCTCAAA
1283180 CGGCTCGGCTCA
1 CGGCTCGGCTCA
1283192 AACGGCTCCT
Statistics
Matches: 57, Mismatches: 2, Indels: 10
0.83 0.03 0.14
Matches are distributed among these distances:
14 13 0.23
15 1 0.02
18 1 0.02
19 42 0.74
ACGTcount: A:0.18, C:0.36, G:0.29, T:0.17
Consensus pattern (19 bp):
CGGCTCGGCTCAGCTCAAA
Found at i:1283138 original size:14 final size:14
Alignment explanation
Indices: 1283133--1283199 Score: 80
Period size: 14 Copynumber: 4.4 Consensus size: 14
1283123 TCAAACGGCT
*
1283133 CGGCTCAGCTCAAA
1 CGGCTCGGCTCAAA
1283147 CGGCTCGGCTCAAA
1 CGGCTCGGCTCAAA
1283161 CGGCTCGGCTCAGCTCAA
1 CGGCTCGGCTCA----AA
1283179 GCGGCTCGGCTCAAA
1 -CGGCTCGGCTCAAA
1283194 CGGCTC
1 CGGCTC
1283200 CTCAGGCTTC
Statistics
Matches: 47, Mismatches: 1, Indels: 10
0.81 0.02 0.17
Matches are distributed among these distances:
14 31 0.66
15 2 0.04
18 2 0.04
19 12 0.26
ACGTcount: A:0.19, C:0.37, G:0.28, T:0.15
Consensus pattern (14 bp):
CGGCTCGGCTCAAA
Found at i:1283158 original size:33 final size:33
Alignment explanation
Indices: 1283115--1283199 Score: 152
Period size: 33 Copynumber: 2.6 Consensus size: 33
1283105 GGCTCGGCTT
*
1283115 GGCTCAGCTCAAACGGCTCGGCTCAGCTCAAAC
1 GGCTCGGCTCAAACGGCTCGGCTCAGCTCAAAC
*
1283148 GGCTCGGCTCAAACGGCTCGGCTCAGCTCAAGC
1 GGCTCGGCTCAAACGGCTCGGCTCAGCTCAAAC
1283181 GGCTCGGCTCAAACGGCTC
1 GGCTCGGCTCAAACGGCTC
1283200 CTCAGGCTTC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 50 1.00
ACGTcount: A:0.20, C:0.36, G:0.28, T:0.15
Consensus pattern (33 bp):
GGCTCGGCTCAAACGGCTCGGCTCAGCTCAAAC
Found at i:1286963 original size:18 final size:18
Alignment explanation
Indices: 1286940--1286974 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1286930 TTCCATCCGG
*
1286940 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
1286958 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
1286975 GTCCTTTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:1288149 original size:19 final size:19
Alignment explanation
Indices: 1288127--1288209 Score: 113
Period size: 19 Copynumber: 4.6 Consensus size: 19
1288117 CTAGGCGGCT
*
1288127 CGGCTTGGCTCAGCTCAAA
1 CGGCTCGGCTCAGCTCAAA
1288146 CGGCTCGGCTCAGCTCAAA
1 CGGCTCGGCTCAGCTCAAA
1288165 CGGCTC-G----GCTCAAA
1 CGGCTCGGCTCAGCTCAAA
*
1288179 CGGCTCGGCTCAGCTCAAG
1 CGGCTCGGCTCAGCTCAAA
1288198 CGGCTCGGCTCA
1 CGGCTCGGCTCA
1288210 AACGGCTCCT
Statistics
Matches: 57, Mismatches: 2, Indels: 10
0.83 0.03 0.14
Matches are distributed among these distances:
14 13 0.23
15 1 0.02
18 1 0.02
19 42 0.74
ACGTcount: A:0.18, C:0.36, G:0.29, T:0.17
Consensus pattern (19 bp):
CGGCTCGGCTCAGCTCAAA
Found at i:1288156 original size:14 final size:14
Alignment explanation
Indices: 1288151--1288217 Score: 80
Period size: 14 Copynumber: 4.4 Consensus size: 14
1288141 TCAAACGGCT
*
1288151 CGGCTCAGCTCAAA
1 CGGCTCGGCTCAAA
1288165 CGGCTCGGCTCAAA
1 CGGCTCGGCTCAAA
1288179 CGGCTCGGCTCAGCTCAA
1 CGGCTCGGCTCA----AA
1288197 GCGGCTCGGCTCAAA
1 -CGGCTCGGCTCAAA
1288212 CGGCTC
1 CGGCTC
1288218 CTCAGGCTTC
Statistics
Matches: 47, Mismatches: 1, Indels: 10
0.81 0.02 0.17
Matches are distributed among these distances:
14 31 0.66
15 2 0.04
18 2 0.04
19 12 0.26
ACGTcount: A:0.19, C:0.37, G:0.28, T:0.15
Consensus pattern (14 bp):
CGGCTCGGCTCAAA
Found at i:1288176 original size:33 final size:33
Alignment explanation
Indices: 1288133--1288217 Score: 152
Period size: 33 Copynumber: 2.6 Consensus size: 33
1288123 GGCTCGGCTT
*
1288133 GGCTCAGCTCAAACGGCTCGGCTCAGCTCAAAC
1 GGCTCGGCTCAAACGGCTCGGCTCAGCTCAAAC
*
1288166 GGCTCGGCTCAAACGGCTCGGCTCAGCTCAAGC
1 GGCTCGGCTCAAACGGCTCGGCTCAGCTCAAAC
1288199 GGCTCGGCTCAAACGGCTC
1 GGCTCGGCTCAAACGGCTC
1288218 CTCAGGCTTC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 50 1.00
ACGTcount: A:0.20, C:0.36, G:0.28, T:0.15
Consensus pattern (33 bp):
GGCTCGGCTCAAACGGCTCGGCTCAGCTCAAAC
Found at i:1290253 original size:164 final size:170
Alignment explanation
Indices: 1290054--1290534 Score: 507
Period size: 183 Copynumber: 2.8 Consensus size: 170
1290044 TAGCGCCTAT
* ** *
1290054 AAAGTGTCGATACTTTA--AAAAAATATCGATCCATAACAATATAACAGGTAAAAATTTGATAAA
1 AAAGTGTCGAAACTTTATGAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGATAAA
* * *
1290117 ACATGTCTCAAAATTGACAAAACCAGTAAAACGATACTGGATATGTTGAAAGTATCGATACTTTA
66 ACACGTCTCAAAA-TGACAAAACCGGTAAAACGATACTGGATATGTTGAAAGTGTCGATACTTTA
*
1290182 ATATAAGTATCGACACTTTC-T-G-A-AA-TTA-A-ACAAA
130 ATATAAGTATCAACACTTTCATAGAAGAAGTTATAGACAAA
1290216 AAAGTGTCGAAACTTTATGAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGATAAA
1 AAAGTGTCGAAACTTTATGAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGATAAA
* * * * * * * *
1290281 ACAGGTCTAAAAAATGACAAAACCGGAAAAAAGATACCGGATATATTGAAAGTGTTGATAATTTA
66 ACACGTCT-CAAAATGACAAAACCGGTAAAACGATACTGGATATGTTGAAAGTGTCGATACTTTA
* * *
1290346 ATATAAGTTTCAACACTTTCGGAATTTAAAAGAGAAGAAGTTATAGCGCCTAA
130 ATATAAGTATCAACACTTTC---A--T-----AGAAGAAGTTATA--GACAAA
* * *
1290399 AAAGTGTC-AACACTTTATGAAAATGTATCGATCTATAACAATATAACAGCTAAAAATATAATAA
1 AAAGTGTCGAA-ACTTTATGAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGATAA
* * *
1290463 AAC-CGATCTCAACAATGAAAAAACCGGTAAAACAATACTGAATATGTTGAAAGTGTCGATACTT
65 AACACG-TCTCAA-AATGACAAAACCGGTAAAACGATACTGGATATGTTGAAAGTGTCGATACTT
1290527 TAATATAA
128 TAATATAA
1290535 CTTTAATATA
Statistics
Matches: 262, Mismatches: 32, Indels: 29
0.81 0.10 0.09
Matches are distributed among these distances:
162 16 0.06
164 111 0.42
165 4 0.02
170 1 0.00
176 1 0.00
177 1 0.00
178 2 0.01
179 3 0.01
180 1 0.00
182 5 0.02
183 117 0.45
ACGTcount: A:0.47, C:0.13, G:0.14, T:0.27
Consensus pattern (170 bp):
AAAGTGTCGAAACTTTATGAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGATAAA
ACACGTCTCAAAATGACAAAACCGGTAAAACGATACTGGATATGTTGAAAGTGTCGATACTTTAA
TATAAGTATCAACACTTTCATAGAAGAAGTTATAGACAAA
Found at i:1290531 original size:183 final size:182
Alignment explanation
Indices: 1290214--1290907 Score: 847
Period size: 183 Copynumber: 3.7 Consensus size: 182
1290204 AAATTAAACA
* *
1290214 AAAAAGTGTCGAA-ACTTTATGAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGAT
1 AAAAAGTGTC-AATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGAT
* * * *
1290278 AAAACAGGTCTAAAAAATGACAAAACCGG-AAAAAAGATACCGGATATATTGAAAGTGTTGATAA
65 AAAACAGGTCT-CAAAATGACAAAACCGGTAAAACA-ATACCGGATATGTTGAAAGTGTCGATAA
*
1290342 TTTAATATAAGTTTCAACACTTTCGGAATTTAAAAGAGAAGAAGTTATAGCGCCT
128 TTTAATATAAGTTTCAACACTTTAGGAATTTAAAAGAGAAGAAGTTATAGCGCCT
* * * *
1290397 AAAAAGTGTCAACACTTTATGAAAATGTATCGATCTATAACAATATAACA-GCTAAAAATATAAT
1 AAAAAGTGTCAATACTTTATAAAAATGTATCGATCCATAACAATATAACATG-TAAAAATATGAT
* * * * * *
1290461 AAAACCGATCTCAACAATGAAAAAACCGGTAAAACAATACTGAATATGTTGAAAGTGTCGATACT
65 AAAACAGGTCTCAA-AATGACAAAACCGGTAAAACAATACCGGATATGTTGAAAGTGTCGATAAT
* * * *
1290526 TTAATATAACTTTAATATAACTATCGACACTTTTGGAATTTAAAAGAGAATAAATTATAGCGCCT
129 TTAATATAA--GT--T-T--C-A---ACACTTTAGGAATTTAAAAGAGAAGAAGTTATAGCGCCT
* * * *
1290591 ATAAAGTGTCGATACTTTAAAAAAATGTATCGATACATAACAATATAACATGTAAAAATATGATA
1 AAAAAGTGTCAATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGATA
* **
1290656 AAACAGGTCTCAAAATTGACAAAACCAGTAAAACGCTACCGGATATGTTGAAAGTGTCGATAATT
66 AAACAGGTCTCAAAA-TGACAAAACCGGTAAAACAATACCGGATATGTTGAAAGTGTCGATAATT
* * *
1290721 TAATATAAGTATCGACACTTTATGAATTTAAAAGAGAAGAAGTTATAGCGCCT
130 TAATATAAGTTTCAACACTTTAGGAATTTAAAAGAGAAGAAGTTATAGCGCCT
* *
1290774 ATAAAGTGTCGATACTTT-TAAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGAT
1 AAAAAGTGTCAATACTTTAT-AAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGAT
* * * ** *
1290838 AAAACCGGTCTCAAAATGACAAAATCGGTAAAGCGCTACCGGATATGTTGAAAGTGTCGATACTT
65 AAAACAGGTCTCAAAATGACAAAACCGGTAAAACAATACCGGATATGTTGAAAGTGTCGATAATT
1290903 TAATA
130 TAATA
1290908 AGTACGCGTA
Statistics
Matches: 446, Mismatches: 47, Indels: 37
0.84 0.09 0.07
Matches are distributed among these distances:
182 55 0.12
183 223 0.50
184 5 0.01
185 1 0.00
187 2 0.00
188 1 0.00
189 1 0.00
190 1 0.00
191 1 0.00
192 1 0.00
193 2 0.00
194 152 0.34
195 1 0.00
ACGTcount: A:0.45, C:0.13, G:0.15, T:0.27
Consensus pattern (182 bp):
AAAAAGTGTCAATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGATA
AAACAGGTCTCAAAATGACAAAACCGGTAAAACAATACCGGATATGTTGAAAGTGTCGATAATTT
AATATAAGTTTCAACACTTTAGGAATTTAAAAGAGAAGAAGTTATAGCGCCT
Found at i:1290539 original size:11 final size:11
Alignment explanation
Indices: 1290523--1290547 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1290513 AAGTGTCGAT
1290523 ACTTTAATATA
1 ACTTTAATATA
1290534 ACTTTAATATA
1 ACTTTAATATA
1290545 ACT
1 ACT
1290548 ATCGACACTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.12, G:0.00, T:0.44
Consensus pattern (11 bp):
ACTTTAATATA
Found at i:1290807 original size:377 final size:376
Alignment explanation
Indices: 1290216--1290907 Score: 1064
Period size: 377 Copynumber: 1.8 Consensus size: 376
1290206 ATTAAACAAA
** *
1290216 AAAGTGTCGAAACTTTATGAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGATAAA
1 AAAGTGTCGAAACTTTAAAAAAATGTATCGATACATAACAATATAACAGGTAAAAATATGATAAA
* *
1290281 ACAGGTCTAAAAAATGACAAAACCGGAAAAAAGATACCGGATATATTGAAAGTGTTGATAATTTA
66 ACAGGTCTAAAAAATGACAAAACCAGAAAAAAGATACCGGATATATTGAAAGTGTCGATAATTTA
* *
1290346 ATATAAGTTTCAACACTTTCGGAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCAACA
131 ATATAAGTATCAACACTTTAGGAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCAACA
* *
1290411 CTTTATGAAAATGTATCGATCTATAACAATATAACA-GCTAAAAATATAATAAAACCGATCTCAA
196 CTTTATAAAAATGTATCGATCCATAACAATATAACATG-TAAAAATATAATAAAACCGATCTCAA
*
1290475 CAATGAAAAAACCGGTAAAACAATACTGAATATGTTGAAAGTGTCGATACTTTAATATAACTTTA
260 -AATGAAAAAACCGGTAAAACAATACCGAATATGTTGAAAGTGTCGATACTTTAATATAACTTTA
1290540 ATATAACTATCGACACTTTTGGAATTTAAAAGAGAATAAATTATAGCGCCTAT
324 ATATAACTATCGACACTTTTGGAATTTAAAAGAGAATAAATTATAGCGCCTAT
* *
1290593 AAAGTGTCGATACTTTAAAAAAATGTATCGATACATAACAATATAACATGTAAAAATATGATAAA
1 AAAGTGTCGAAACTTTAAAAAAATGTATCGATACATAACAATATAACAGGTAAAAATATGATAAA
* * * * * *
1290658 ACAGGTCTCAAAATTGACAAAACCAGTAAAACGCTACCGGATATGTTGAAAGTGTCGATAATTTA
66 ACAGGTCTAAAAAATGACAAAACCAGAAAAAAGATACCGGATATATTGAAAGTGTCGATAATTTA
* * * * *
1290723 ATATAAGTATCGACACTTTATGAATTTAAAAGAGAAGAAGTTATAGCGCCTATAAAGTGTCGATA
131 ATATAAGTATCAACACTTTAGGAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCAACA
* *
1290788 CTTT-TAAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGATAAAACCGGTCTCAA
196 CTTTAT-AAAAATGTATCGATCCATAACAATATAACATGTAAAAATATAATAAAACCGATCTCAA
* * * ** *
1290852 AATGACAAAATCGGTAAAGCGCTACCGGATATGTTGAAAGTGTCGATACTTTAATA
260 AATGAAAAAACCGGTAAAACAATACCGAATATGTTGAAAGTGTCGATACTTTAATA
1290908 AGTACGCGTA
Statistics
Matches: 282, Mismatches: 31, Indels: 5
0.89 0.10 0.02
Matches are distributed among these distances:
376 50 0.18
377 231 0.82
378 1 0.00
ACGTcount: A:0.45, C:0.13, G:0.15, T:0.27
Consensus pattern (376 bp):
AAAGTGTCGAAACTTTAAAAAAATGTATCGATACATAACAATATAACAGGTAAAAATATGATAAA
ACAGGTCTAAAAAATGACAAAACCAGAAAAAAGATACCGGATATATTGAAAGTGTCGATAATTTA
ATATAAGTATCAACACTTTAGGAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCAACA
CTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATAATAAAACCGATCTCAAA
ATGAAAAAACCGGTAAAACAATACCGAATATGTTGAAAGTGTCGATACTTTAATATAACTTTAAT
ATAACTATCGACACTTTTGGAATTTAAAAGAGAATAAATTATAGCGCCTAT
Found at i:1291321 original size:19 final size:19
Alignment explanation
Indices: 1291297--1291342 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
1291287 TATTTAATAT
1291297 TTATAGGTAAAAAATGATA
1 TTATAGGTAAAAAATGATA
*
1291316 TTATAGGTAGAAAATGATA
1 TTATAGGTAAAAAATGATA
*
1291335 TTTTAGGT
1 TTATAGGT
1291343 TGTATAAATG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.43, C:0.00, G:0.20, T:0.37
Consensus pattern (19 bp):
TTATAGGTAAAAAATGATA
Found at i:1292653 original size:22 final size:24
Alignment explanation
Indices: 1292602--1292657 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
1292592 GAATGTTTTT
*
1292602 GTTTTTTATATAAAATGATAGTATA
1 GTTTATTATATAAAATGATAG-ATA
*
1292627 G-TTATTATATAAAATGATA-A-C
1 GTTTATTATATAAAATGATAGATA
1292648 GTTTATTATA
1 GTTTATTATA
1292658 AATGTAGGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
21 1 0.04
22 9 0.32
24 17 0.61
25 1 0.04
ACGTcount: A:0.41, C:0.02, G:0.11, T:0.46
Consensus pattern (24 bp):
GTTTATTATATAAAATGATAGATA
Found at i:1292906 original size:9 final size:9
Alignment explanation
Indices: 1292895--1292937 Score: 59
Period size: 9 Copynumber: 4.8 Consensus size: 9
1292885 TAAAGGAGTT
*
1292895 AGAGGAGGT
1 AGAGGAGGC
1292904 AGAGGAGGC
1 AGAGGAGGC
*
1292913 AGAGGAAGC
1 AGAGGAGGC
1292922 AGAGGAGGC
1 AGAGGAGGC
*
1292931 AGTGGAG
1 AGAGGAG
1292938 AATGAAGAAG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 30 1.00
ACGTcount: A:0.35, C:0.07, G:0.53, T:0.05
Consensus pattern (9 bp):
AGAGGAGGC
Found at i:1293394 original size:22 final size:18
Alignment explanation
Indices: 1293345--1293383 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
1293335 GAAAAAATTT
*
1293345 GAAGAAGAGAAGATGGAG
1 GAAGAAGAAAAGATGGAG
1293363 GAAGAAGAAAAGATGGAG
1 GAAGAAGAAAAGATGGAG
1293381 GAA
1 GAA
1293384 ATGAGGAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.54, C:0.00, G:0.41, T:0.05
Consensus pattern (18 bp):
GAAGAAGAAAAGATGGAG
Found at i:1294897 original size:19 final size:18
Alignment explanation
Indices: 1294854--1294902 Score: 80
Period size: 18 Copynumber: 2.7 Consensus size: 18
1294844 AAATGCAGGG
1294854 TTAATTTTGTATAAGATT
1 TTAATTTTGTATAAGATT
*
1294872 TTAATTTTGTATACGATT
1 TTAATTTTGTATAAGATT
1294890 TATAATTTTGTAT
1 T-TAATTTTGTAT
1294903 GTGAATGTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
18 18 0.62
19 11 0.38
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.57
Consensus pattern (18 bp):
TTAATTTTGTATAAGATT
Found at i:1296164 original size:199 final size:198
Alignment explanation
Indices: 1295230--1296285 Score: 1689
Period size: 199 Copynumber: 5.3 Consensus size: 198
1295220 GTAAACTTAT
* * *
1295230 GTGTCGATACATTAATAACAAGTTTCGATCCCAAAAACATCGAAAATCAT-A--ATAATGTAATA
1 GTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACTCATAATGATAATGTAATA
*
1295292 GGTAAATTAGCAATATAACCGGTCTAAATATACAGGTTTTTGAGAAAACAGGTGTACAAAAAGTA
66 GGTAAATTAGCAATATAACC-GTCTAAATATACCGGTTTTTGAGAAAACAGGTGTACAAAAAGTA
*
1295357 TCGACACAAATCAAACAACTGTCGATACTTTTGGTCCAGAATGTATTTCAAAACCAAGTGCACTA
130 TCGACACAAATCAAACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCAAAACCAAGTGCACTA
1295422 AAAA
195 AAAA
* *
1295426 GTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACCCATAATAATAATGTAATA
1 GTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACTCATAATGATAATGTAATA
* *
1295491 GG-----TAGCAATATAACCGTTCTAAATATACCGGTTTTTGAGAAAACATGTGTACAAAAAGAA
66 GGTAAATTAGCAATATAACCG-TCTAAATATACCGGTTTTTGAGAAAACAGGTGTACAAAAAGTA
1295551 TCGACACAAATCAAACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCAAAACCAAGTGCACTA
130 TCGACACAAATCAAACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCAAAACCAAGTGCACTA
1295616 AAAA
195 AAAA
* * **
1295620 GTGTCGATACATTTCTAACAAGTGTCGATCCCAAAAATATATAAAACTCATAATGATAATGTAAT
1 GTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACAT-CGAAACTCATAATGATAATGTAAT
* * *
1295685 AGGTAAATTAACAATATAACCGATCTAAATATATCGATTTTTGAGAAAACAGGTGTACAAAAAGT
65 AGGTAAATTAGCAATATAACCG-TCTAAATATACCGGTTTTTGAGAAAACAGGTGTACAAAAAGT
* *
1295750 ATCGACACAAATCAAACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCCAAACCATGTGCACT
129 ATCGACACAAATCAAACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCAAAACCAAGTGCACT
1295815 AAAAA
194 AAAAA
* *
1295820 GTGTCGATACATTTATAACAAGTGTTGATCCC-AAAACATCGAAACCCATAATGATAATGTAATA
1 GTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACTCATAATGATAATGTAATA
* * *
1295884 GGTAAATTAGCAATATAATCGGTCTAAATATACCGATTTTTGAGAAAATAGGTGTACAAAAAGTA
66 GGTAAATTAGCAATATAA-CCGTCTAAATATACCGGTTTTTGAGAAAACAGGTGTACAAAAAGTA
* * * *
1295949 TCGACACAAATCAAACAAATGTCGATACTTTTGATCCATAATGTATTTCAAAACCATGTGCACTA
130 TCGACACAAATCAAACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCAAAACCAAGTGCACTA
1296014 AAAA
195 AAAA
*
1296018 GTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACTCATAATGTTAATGTAATA
1 GTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACTCATAATGATAATGTAATA
*
1296083 GGTAAATTAGCAATATAACCAGTCTAAATATATCGGTTTTTGAGAAAACAGGTGTACAAAAAGTA
66 GGTAAATTAGCAATATAACC-GTCTAAATATACCGGTTTTTGAGAAAACAGGTGTACAAAAAGTA
* * *
1296148 TTGTCACAAATCAAACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCAAAACCAAGTGCATTA
130 TCGACACAAATCAAACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCAAAACCAAGTGCACTA
1296213 AAAA
195 AAAA
* *
1296217 GTGTTGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACTCATAATTATAATGTAATA
1 GTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACTCATAATGATAATGTAATA
1296282 GGTA
66 GGTA
1296286 GCAATGTAAC
Statistics
Matches: 794, Mismatches: 53, Indels: 23
0.91 0.06 0.03
Matches are distributed among these distances:
193 1 0.00
194 159 0.20
195 23 0.03
196 46 0.06
197 1 0.00
198 177 0.22
199 238 0.30
200 149 0.19
ACGTcount: A:0.42, C:0.16, G:0.15, T:0.28
Consensus pattern (198 bp):
GTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACTCATAATGATAATGTAATA
GGTAAATTAGCAATATAACCGTCTAAATATACCGGTTTTTGAGAAAACAGGTGTACAAAAAGTAT
CGACACAAATCAAACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCAAAACCAAGTGCACTAA
AAA
Found at i:1296682 original size:15 final size:15
Alignment explanation
Indices: 1296662--1296719 Score: 71
Period size: 15 Copynumber: 3.7 Consensus size: 15
1296652 TTTCTCAAAT
1296662 CTCTTCTCAACCCAC
1 CTCTTCTCAACCCAC
* *
1296677 CTCTTCCCAACCCAG
1 CTCTTCTCAACCCAC
1296692 CTCTTCTCAACCACAAC
1 CTCTTCTCAACC-C-AC
1296709 CTCCTTCTCAA
1 CT-CTTCTCAA
1296720 ACAATCATCC
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
15 24 0.67
16 1 0.03
17 3 0.08
18 8 0.22
ACGTcount: A:0.22, C:0.50, G:0.02, T:0.26
Consensus pattern (15 bp):
CTCTTCTCAACCCAC
Found at i:1297046 original size:2 final size:2
Alignment explanation
Indices: 1297039--1297088 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
1297029 ATAGGGAAAG
1297039 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1297081 AT AT AT AT
1 AT AT AT AT
1297089 CTCCGGAAAT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1297902 original size:3 final size:3
Alignment explanation
Indices: 1297877--1297917 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
1297867 CAAGCGGTCA
* * *
1297877 ATG AAG ATG ACG ATG AAG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
1297918 CCAAACAAGT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.39, C:0.02, G:0.32, T:0.27
Consensus pattern (3 bp):
ATG
Found at i:1297917 original size:12 final size:12
Alignment explanation
Indices: 1297877--1297916 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
1297867 CAAGCGGTCA
*
1297877 ATGAAGATGACG
1 ATGAAGATGATG
1297889 ATGAAGATGATG
1 ATGAAGATGATG
*
1297901 ATGATGATGATG
1 ATGAAGATGATG
1297913 ATGA
1 ATGA
1297917 TCCAAACAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.40, C:0.03, G:0.33, T:0.25
Consensus pattern (12 bp):
ATGAAGATGATG
Found at i:1299919 original size:22 final size:19
Alignment explanation
Indices: 1299877--1299920 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
1299867 CGAAAAACAT
*
1299877 AATTATAATGTAATAGGTA
1 AATTATAATGTAATAGCTA
1299896 AATTATTAATGTAATCAGTCTA
1 AATTA-TAATGTAAT-AG-CTA
1299918 AAT
1 AAT
1299921 ATACCGGTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 5 0.24
20 9 0.43
21 2 0.10
22 5 0.24
ACGTcount: A:0.45, C:0.05, G:0.11, T:0.39
Consensus pattern (19 bp):
AATTATAATGTAATAGCTA
Done.