Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008033.1 Hibiscus syriacus cultivar Beakdansim tig00110515_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: 3048429
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 14
Found at i:1149675 original size:14 final size:14
Alignment explanation
Indices: 1149647--1149682 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
1149637 TTACTGATAG
1149647 TTGTATATACAATTA
1 TTGT-TATACAATTA
*
1149662 TTGTTATACTATTA
1 TTGTTATACAATTA
1149676 TTGTTAT
1 TTGTTAT
1149683 CATTAGCCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 16 0.80
15 4 0.20
ACGTcount: A:0.31, C:0.06, G:0.08, T:0.56
Consensus pattern (14 bp):
TTGTTATACAATTA
Found at i:1153527 original size:29 final size:32
Alignment explanation
Indices: 1153478--1153549 Score: 82
Period size: 29 Copynumber: 2.4 Consensus size: 32
1153468 ATTTTGAATG
*
1153478 GTGACCAAAATGAAAA-TTTTGAAAA-TTT-A
1 GTGACCAAAATGAAAACTTTGGAAAAGTTTAA
*
1153507 GTGACCAAAGT-ATAAACTTTGGAAAAGTTTAA
1 GTGACCAAAATGA-AAACTTTGGAAAAGTTTAA
1153539 G-GACCAAAATG
1 GTGACCAAAATG
1153550 GTAATTTTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
28 1 0.03
29 13 0.37
30 8 0.23
31 11 0.31
32 2 0.06
ACGTcount: A:0.46, C:0.10, G:0.18, T:0.26
Consensus pattern (32 bp):
GTGACCAAAATGAAAACTTTGGAAAAGTTTAA
Found at i:1158072 original size:15 final size:15
Alignment explanation
Indices: 1158054--1158106 Score: 88
Period size: 15 Copynumber: 3.5 Consensus size: 15
1158044 GAGTTGATAA
**
1158054 GATGGGAGAGGAAGG
1 GATGGGAGAGGCGGG
1158069 GATGGGAGAGGCGGG
1 GATGGGAGAGGCGGG
1158084 GATGGGAGAGGCGGG
1 GATGGGAGAGGCGGG
1158099 GATGGGAG
1 GATGGGAG
1158107 GAATACAATG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 36 1.00
ACGTcount: A:0.25, C:0.04, G:0.64, T:0.08
Consensus pattern (15 bp):
GATGGGAGAGGCGGG
Found at i:1158327 original size:31 final size:31
Alignment explanation
Indices: 1158287--1158351 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
1158277 GATGATAGAA
*
1158287 TGACCGTTTTGTTACAAATCGATAATGTTAG
1 TGACCGTTTTGTTACAAATCGATAACGTTAG
* *
1158318 TGACTGTTTTGTTATAAATCGATAACGTTAG
1 TGACCGTTTTGTTACAAATCGATAACGTTAG
1158349 TGA
1 TGA
1158352 TTAATATGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.29, C:0.11, G:0.20, T:0.40
Consensus pattern (31 bp):
TGACCGTTTTGTTACAAATCGATAACGTTAG
Found at i:1158362 original size:31 final size:31
Alignment explanation
Indices: 1158296--1158363 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
1158286 ATGACCGTTT
* ** *
1158296 TGTTACAAATCGATAATGTTAGTGACTGTTT
1 TGTTACAAATCGATAACGTTAGTGACTAATA
* *
1158327 TGTTATAAATCGATAACGTTAGTGATTAATA
1 TGTTACAAATCGATAACGTTAGTGACTAATA
1158358 TGTTAC
1 TGTTAC
1158364 TTTTAAATTT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.32, C:0.09, G:0.18, T:0.41
Consensus pattern (31 bp):
TGTTACAAATCGATAACGTTAGTGACTAATA
Found at i:1158652 original size:19 final size:18
Alignment explanation
Indices: 1158630--1158677 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 18
1158620 TATATTATGC
1158630 ATATATTTT-TATGTGTTAA
1 ATATATTTTGTAT-T-TTAA
1158649 ATATATTTATGTATTTTAA
1 ATATATTT-TGTATTTTAA
1158668 ATATTATTTT
1 ATA-TATTTT
1158678 AGAAAAAACA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
19 16 0.62
20 7 0.27
21 3 0.12
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.60
Consensus pattern (18 bp):
ATATATTTTGTATTTTAA
Found at i:1159809 original size:19 final size:19
Alignment explanation
Indices: 1159785--1159822 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1159775 TTCATGTAAT
1159785 TCATAAATCAATACATAAC
1 TCATAAATCAATACATAAC
* *
1159804 TCATAAATTAATATATAAC
1 TCATAAATCAATACATAAC
1159823 GAATAAAACA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.32
Consensus pattern (19 bp):
TCATAAATCAATACATAAC
Found at i:1159828 original size:19 final size:19
Alignment explanation
Indices: 1159787--1159829 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
1159777 CATGTAATTC
**
1159787 ATAAATCAATACATAACTC
1 ATAAATCAATACATAACGA
* *
1159806 ATAAATTAATATATAACGA
1 ATAAATCAATACATAACGA
1159825 ATAAA
1 ATAAA
1159830 ACAGAAAACA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.58, C:0.12, G:0.02, T:0.28
Consensus pattern (19 bp):
ATAAATCAATACATAACGA
Found at i:1161671 original size:46 final size:46
Alignment explanation
Indices: 1161626--1161999 Score: 595
Period size: 46 Copynumber: 8.1 Consensus size: 46
1161616 TTAATTTCAT
* * * *
1161626 TTATGGCATCCTTTCATGCCTTAATGCATCCTGTCATGCATTTCAT
1 TTATGACATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAG
*
1161672 TTATGACATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTGAG
1 TTATGACATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAG
*
1161718 TTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAG
1 TTATGACATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAG
** *
1161764 TTATGGGATCCTTTCATGCCTTAATGCATCCTTTCATGCCTTTTAG
1 TTATGACATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAG
* * *
1161810 TTATGACATCCTTTCATGCCTTAATGCATCATTTCATGCATTTCAT
1 TTATGACATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAG
* *
1161856 TTATGGCATCCTTTCATGCCTTAAAGCATCCTTTCATGCATTTTAG
1 TTATGACATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAG
* *
1161902 TTATGACATGCTTTCATGCCTTAATGCATCCTTTCATGAATTTTAG
1 TTATGACATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAG
*
1161948 TTATGACATCCTTTCATGCCTTAATGCATCATTTCATGCATTTTAG
1 TTATGACATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAG
1161994 TTATGA
1 TTATGA
1162000 ATTCATTTTA
Statistics
Matches: 302, Mismatches: 26, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 302 1.00
ACGTcount: A:0.22, C:0.23, G:0.13, T:0.43
Consensus pattern (46 bp):
TTATGACATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAG
Found at i:1163179 original size:3 final size:3
Alignment explanation
Indices: 1163171--1163208 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
1163161 CTACCCACGT
* *
1163171 GAA GAA GAA GAA GAA GAA GAA GAA CAA GAA GAA TAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1163209 GTAGAAATAG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.66, C:0.03, G:0.29, T:0.03
Consensus pattern (3 bp):
GAA
Found at i:1168805 original size:46 final size:46
Alignment explanation
Indices: 1168755--1169203 Score: 675
Period size: 46 Copynumber: 9.8 Consensus size: 46
1168745 TTATGGTATT
* *
1168755 CTTTCATGCCTTAATGCATCTTTTCATGCATTTTATTTATGACATC
1 CTTTCATGCCTTAATGCATCATTTCATGCATTTTAGTTATGACATC
* * *
1168801 CTTTCATGCCTTAATGCATCATATCATGCATTTCATTTATGACATC
1 CTTTCATGCCTTAATGCATCATTTCATGCATTTTAGTTATGACATC
*
1168847 CTTTCATGCCTTAATGCATCATTTCATGCATTTTAGTTATGGCATC
1 CTTTCATGCCTTAATGCATCATTTCATGCATTTTAGTTATGACATC
*
1168893 CTTTCATGCCTTAATGCATCATTTCATGCATTTTAGTTATGGCATC
1 CTTTCATGCCTTAATGCATCATTTCATGCATTTTAGTTATGACATC
1168939 CTTTCATGCCTTAATGCATCATTTCATGCATTTTAGTTATGGA-ATC
1 CTTTCATGCCTTAATGCATCATTTCATGCATTTTAGTTAT-GACATC
* * *
1168985 CTTTCATGCCTTAATGCATCCTTTCATGCCTTTTAGTTATGATATC
1 CTTTCATGCCTTAATGCATCATTTCATGCATTTTAGTTATGACATC
* * * *
1169031 CTTTCATGCCTTGATTCATCCTTTCATGCATTTTAGTTATGGCATC
1 CTTTCATGCCTTAATGCATCATTTCATGCATTTTAGTTATGACATC
* * * *
1169077 CTTTCATTCCTTAATGCATCCTTTCATGCATTTTAGTAATCACATC
1 CTTTCATGCCTTAATGCATCATTTCATGCATTTTAGTTATGACATC
* *
1169123 CTTTCATGCCTTAATGCATCCTTTCATGCATTTTAGTTATGGCATC
1 CTTTCATGCCTTAATGCATCATTTCATGCATTTTAGTTATGACATC
* * *
1169169 TTTTCATGCCTTAATGCATCTTTTCATGTATTTTA
1 CTTTCATGCCTTAATGCATCATTTCATGCATTTTA
1169204 TTGATGAATT
Statistics
Matches: 373, Mismatches: 28, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
45 2 0.01
46 370 0.99
47 1 0.00
ACGTcount: A:0.22, C:0.22, G:0.11, T:0.45
Consensus pattern (46 bp):
CTTTCATGCCTTAATGCATCATTTCATGCATTTTAGTTATGACATC
Found at i:1169784 original size:95 final size:94
Alignment explanation
Indices: 1169626--1169803 Score: 234
Period size: 95 Copynumber: 1.9 Consensus size: 94
1169616 ACTACCCTGG
* * *
1169626 TATCGATACTTCTATACTATGGTACCGATACCCTCTTTCAGTATCGATACCATTTCTATATTATG
1 TATCGATACTACTATACTATGGTACCGATACCCTCTTTCAGTATCGATACCATTTCGACATTATG
* *
1169691 TGTTGCATGGTATCAATACATTTCTCTCAT
66 -GATCCATGGTATCAATACATTTCTCTCAT
* * *
1169721 TATCGATACTACTATACTATGGTATCGATACTCC-CTTTCAGTGTCGATAGCATGTT-GACATTA
1 TATCGATACTACTATACTATGGTACCGATAC-CCTCTTTCAGTATCGATACCAT-TTCGACATTA
*
1169784 TGGATCCATGGTATCTATAC
64 TGGATCCATGGTATCAATAC
1169804 TTCCCCTTTT
Statistics
Matches: 72, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
94 15 0.21
95 53 0.74
96 4 0.06
ACGTcount: A:0.26, C:0.21, G:0.14, T:0.39
Consensus pattern (94 bp):
TATCGATACTACTATACTATGGTACCGATACCCTCTTTCAGTATCGATACCATTTCGACATTATG
GATCCATGGTATCAATACATTTCTCTCAT
Found at i:1172661 original size:49 final size:48
Alignment explanation
Indices: 1172606--1172742 Score: 139
Period size: 49 Copynumber: 2.8 Consensus size: 48
1172596 CTGGTGTTCG
* *
1172606 CAAAGAGACGATGAAGAAAATCAACCAACTTTTTCATATTCGTCATTCA
1 CAAAGAGACGATGAAGCAAATCAACCAACTTTTT-ATATTCGTCATTAA
* * * ** * * * *
1172655 CGAAGAGAGGAGGAAGCAAATCAACCTTCTTTTGAAATTTGTCCTTAA
1 CAAAGAGACGATGAAGCAAATCAACCAACTTTTTATATTCGTCATTAA
* *
1172703 CAAAGAGACGATGGAGCAAATCAACTAACATTTTTATATT
1 CAAAGAGACGATGAAGCAAATCAACCAAC-TTTTTATATT
1172743 TGACCTTTAC
Statistics
Matches: 67, Mismatches: 20, Indels: 2
0.75 0.22 0.02
Matches are distributed among these distances:
48 32 0.48
49 35 0.52
ACGTcount: A:0.39, C:0.18, G:0.16, T:0.27
Consensus pattern (48 bp):
CAAAGAGACGATGAAGCAAATCAACCAACTTTTTATATTCGTCATTAA
Found at i:1172724 original size:48 final size:49
Alignment explanation
Indices: 1172606--1172737 Score: 124
Period size: 48 Copynumber: 2.7 Consensus size: 49
1172596 CTGGTGTTCG
* * * *
1172606 CAAAGAGACGATGAAGAAAATCAACCAACTTTTTCATATTCGTCATTCA
1 CAAAGAGACGATGGAGCAAATCAACCAACTTTTTCAAATTCGTCATTAA
* * ** * * *
1172655 CGAAGAGAGGA-GGAAGCAAATCAACCTTC-TTTTGAAATTTGTCCTTAA
1 CAAAGAGACGATGG-AGCAAATCAACCAACTTTTTCAAATTCGTCATTAA
*
1172703 CAAAGAGACGATGGAGCAAATCAACTAACATTTTT
1 CAAAGAGACGATGGAGCAAATCAACCAAC-TTTTT
1172738 ATATTTGACC
Statistics
Matches: 63, Mismatches: 16, Indels: 7
0.73 0.19 0.08
Matches are distributed among these distances:
48 36 0.57
49 23 0.37
50 4 0.06
ACGTcount: A:0.39, C:0.18, G:0.17, T:0.26
Consensus pattern (49 bp):
CAAAGAGACGATGGAGCAAATCAACCAACTTTTTCAAATTCGTCATTAA
Found at i:1174235 original size:21 final size:19
Alignment explanation
Indices: 1174186--1174227 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
1174176 TAAATATCCG
1174186 TAAAAGA-AAAGAAAAAAA
1 TAAAAGAGAAAGAAAAAAA
*
1174204 TAAAAGAGAAAGTAAAAAA
1 TAAAAGAGAAAGAAAAAAA
*
1174223 CAAAA
1 TAAAA
1174228 CAGAGAAATG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 7 0.33
19 14 0.67
ACGTcount: A:0.79, C:0.02, G:0.12, T:0.07
Consensus pattern (19 bp):
TAAAAGAGAAAGAAAAAAA
Found at i:1174529 original size:28 final size:28
Alignment explanation
Indices: 1174482--1174535 Score: 67
Period size: 28 Copynumber: 1.9 Consensus size: 28
1174472 GGAAGAGAGT
*
1174482 ATTAATAAATAATAATAAAAATTAAATG
1 ATTAATAAATAATAATAAAAAATAAATG
1174510 ATTATATAAA-AAGTAA-AAAAAATAAA
1 ATTA-ATAAATAA-TAATAAAAAATAAA
1174536 AAGGATAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
28 15 0.65
29 8 0.35
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.28
Consensus pattern (28 bp):
ATTAATAAATAATAATAAAAAATAAATG
Found at i:1174805 original size:32 final size:32
Alignment explanation
Indices: 1174759--1174894 Score: 143
Period size: 32 Copynumber: 4.2 Consensus size: 32
1174749 TTCCTTTCCA
**
1174759 GATATTTAAAATTATATTATAATTAAATTTTG
1 GATATTTATTATTATATTATAATTAAATTTTG
* * *
1174791 GATATTTATTATTATATTCTGATTAAAATTTG
1 GATATTTATTATTATATTATAATTAAATTTTG
*
1174823 GATATTTATTATTATATTCA-AATTAAATTTTA
1 GATATTTATTATTATATT-ATAATTAAATTTTG
* *
1174855 GATATTTCA-TATTATATT-TATTGTAAATTTTC
1 GATATTT-ATTATTATATTATAAT-TAAATTTTG
*
1174887 AATATTTA
1 GATATTTA
1174895 AAAATAGCGA
Statistics
Matches: 88, Mismatches: 12, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
31 3 0.03
32 84 0.95
33 1 0.01
ACGTcount: A:0.38, C:0.03, G:0.06, T:0.53
Consensus pattern (32 bp):
GATATTTATTATTATATTATAATTAAATTTTG
Found at i:1174892 original size:64 final size:64
Alignment explanation
Indices: 1174760--1174897 Score: 158
Period size: 64 Copynumber: 2.2 Consensus size: 64
1174750 TCCTTTCCAG
* **
1174760 ATATTTAAAATTATATTATAATTAAATTTTGGATATTTATTATTATATTCTGATTAAAATTTGG
1 ATATTTAAAATTATATTATAATTAAATTTTAGATATTTATTATTATATTCTGATTAAAATTTCA
** *
1174824 ATATTTATTATTATATTCA-AATTAAATTTTAGATATTTCA-TATTATATT-T-ATTGTAAATTT
1 ATATTTAAAATTATATT-ATAATTAAATTTTAGATATTT-ATTATTATATTCTGA-T-TAAAATT
1174885 TCA
62 TCA
1174888 ATATTTAAAA
1 ATATTTAAAA
1174898 ATAGCGAAAC
Statistics
Matches: 62, Mismatches: 8, Indels: 8
0.79 0.10 0.10
Matches are distributed among these distances:
62 1 0.02
63 2 0.03
64 57 0.92
65 2 0.03
ACGTcount: A:0.40, C:0.03, G:0.05, T:0.52
Consensus pattern (64 bp):
ATATTTAAAATTATATTATAATTAAATTTTAGATATTTATTATTATATTCTGATTAAAATTTCA
Found at i:1175937 original size:22 final size:21
Alignment explanation
Indices: 1175912--1175952 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
1175902 TATAAAAAAT
1175912 TATTTTTATTGAATATTTTTGG
1 TATTTTTATTGAAT-TTTTTGG
*
1175934 TATTTTTATTTAATTTTTT
1 TATTTTTATTGAATTTTTT
1175953 AAATAATTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.22, C:0.00, G:0.07, T:0.71
Consensus pattern (21 bp):
TATTTTTATTGAATTTTTTGG
Found at i:1176921 original size:20 final size:20
Alignment explanation
Indices: 1176896--1177343 Score: 205
Period size: 20 Copynumber: 19.7 Consensus size: 20
1176886 TTTAATTATG
1176896 GCATCCTTTCATGCCTTAAT
1 GCATCCTTTCATGCCTTAAT
* *
1176916 GCATCCCTTCATGCATTTTATTTTAT
1 GCATCCTTTCATGC--CTTA----AT
1176942 GGCATCCTTTCATGCCTTAAT
1 -GCATCCTTTCATGCCTTAAT
* * *
1176963 GCATCATTTCATGCATTTTAGTTTGT
1 GCATCCTTTCATGC--CTTA----AT
*
1176989 GGCACCCTTTCATGCCTTAAT
1 -GCATCCTTTCATGCCTTAAT
* *
1177010 TCATCCTTTCATGCATTTTAGTTTAT
1 GCATCCTTTCATGC--CTTA----AT
* *
1177036 GGCACCCTTTCATGTCTTAAT
1 -GCATCCTTTCATGCCTTAAT
*
1177057 GCATCCTTTCATGCAATTTAATTAT
1 GCATCCTTTCATGC--CTT-A--AT
1177082 GACATCCTTTCATGCCTTAAT
1 G-CATCCTTTCATGCCTTAAT
* *
1177103 GCATTCTTTCATGCATTTTAGTTTAT
1 GCATCCTTTCATGC--CTTA----AT
1177129 GGCATCCTTTCATGCCTTAAT
1 -GCATCCTTTCATGCCTTAAT
*
1177150 GCATCCTTTCATGCGTTTTAGTTTAT
1 GCATCCTTTCATGC--CTTA----AT
*
1177176 GATATCCTTTCATGCCTTAAT
1 G-CATCCTTTCATGCCTTAAT
*
1177197 GCATCCTTTCATGCCTTAAC
1 GCATCCTTTCATGCCTTAAT
*
1177217 GCATCCTTTCATGCATTTTAATTAT
1 GCATCCTTTCATGC--CTT-A--AT
* *
1177242 GGCATTCTTTCATGCCTTAAG
1 -GCATCCTTTCATGCCTTAAT
*
1177263 GCATCCTTTCATGCCTTAAG
1 GCATCCTTTCATGCCTTAAT
*
1177283 GCATCCTTTCATGCATTTTAGTTTAT
1 GCATCCTTTCATGC--CTTA----AT
1177309 GGCATCCTTTCATGCCTTAAT
1 -GCATCCTTTCATGCCTTAAT
1177330 -CTATCCTTTCATGC
1 GC-ATCCTTTCATGC
1177344 ATTTTAGTTT
Statistics
Matches: 333, Mismatches: 40, Indels: 110
0.69 0.08 0.23
Matches are distributed among these distances:
19 1 0.00
20 152 0.46
21 16 0.05
22 22 0.07
23 4 0.01
24 4 0.01
25 22 0.07
26 37 0.11
27 75 0.23
ACGTcount: A:0.20, C:0.25, G:0.12, T:0.44
Consensus pattern (20 bp):
GCATCCTTTCATGCCTTAAT
Found at i:1176950 original size:47 final size:47
Alignment explanation
Indices: 1176872--1177357 Score: 592
Period size: 47 Copynumber: 10.6 Consensus size: 47
1176862 AGGTCATATT
*
1176872 ATCCTTTCATGCATTTTA-ATTATGGCATCCTTTCATGCCTTAATGC
1 ATCCTTTCATGCATTTTAGTTTATGGCATCCTTTCATGCCTTAATGC
* *
1176918 ATCCCTTCATGCATTTTATTTTATGGCATCCTTTCATGCCTTAATGC
1 ATCCTTTCATGCATTTTAGTTTATGGCATCCTTTCATGCCTTAATGC
* * * *
1176965 ATCATTTCATGCATTTTAGTTTGTGGCACCCTTTCATGCCTTAATTC
1 ATCCTTTCATGCATTTTAGTTTATGGCATCCTTTCATGCCTTAATGC
* *
1177012 ATCCTTTCATGCATTTTAGTTTATGGCACCCTTTCATGTCTTAATGC
1 ATCCTTTCATGCATTTTAGTTTATGGCATCCTTTCATGCCTTAATGC
* * *
1177059 ATCCTTTCATGCAATTTA-ATTATGACATCCTTTCATGCCTTAATGC
1 ATCCTTTCATGCATTTTAGTTTATGGCATCCTTTCATGCCTTAATGC
*
1177105 ATTCTTTCATGCATTTTAGTTTATGGCATCCTTTCATGCCTTAATGC
1 ATCCTTTCATGCATTTTAGTTTATGGCATCCTTTCATGCCTTAATGC
* **
1177152 ATCCTTTCATGCGTTTTAGTTTATGATATCCTTTCATGCCTTAATGC
1 ATCCTTTCATGCATTTTAGTTTATGGCATCCTTTCATGCCTTAATGC
* * *
1177199 ATCCTTTCATGC--CTTA----A-CGCATCCTTTCATGCATTTTAATTATGGC
1 ATCCTTTCATGCATTTTAGTTTATGGCATCCTTTCATGC--CTT-A--AT-GC
* * *
1177245 ATTCTTTCATGC--CTTA----A-GGCATCCTTTCATGCCTTAAGGC
1 ATCCTTTCATGCATTTTAGTTTATGGCATCCTTTCATGCCTTAATGC
1177285 ATCCTTTCATGCATTTTAGTTTATGGCATCCTTTCATGCCTTAAT-C
1 ATCCTTTCATGCATTTTAGTTTATGGCATCCTTTCATGCCTTAATGC
1177331 TATCCTTTCATGCATTTTAGTTTATGG
1 -ATCCTTTCATGCATTTTAGTTTATGG
1177358 ATTCAATTTA
Statistics
Matches: 387, Mismatches: 37, Indels: 31
0.85 0.08 0.07
Matches are distributed among these distances:
40 25 0.06
41 2 0.01
42 5 0.01
43 2 0.01
44 2 0.01
45 5 0.01
46 91 0.24
47 255 0.66
ACGTcount: A:0.20, C:0.23, G:0.12, T:0.44
Consensus pattern (47 bp):
ATCCTTTCATGCATTTTAGTTTATGGCATCCTTTCATGCCTTAATGC
Found at i:1177124 original size:140 final size:138
Alignment explanation
Indices: 1176872--1177349 Score: 588
Period size: 140 Copynumber: 3.5 Consensus size: 138
1176862 AGGTCATATT
* *
1176872 ATCCTTTCATGCATTTTA-ATTATGGCATCCTTTCATGCCTTAATGCATCCCTTCATGCATTTTA
1 ATCCTTTCATGCATTTTAGTTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTA
* *
1176936 TTTTATGGCATCCTTTCATGCCTTAATGCA-TCATTTCATGCATTTTAGTTTGTGGCACCCTTTC
66 -ATTAT-GCATCCTTTCATGCCTTAATGCATTC-TTTCATGCATTTTAGTTT-TGGCATCCTTTC
*
1177000 ATGCCTTAATTC
127 ATGCCTTAATGC
* * *
1177012 ATCCTTTCATGCATTTTAGTTTATGGCACCCTTTCATGTCTTAATGCATCCTTTCATGCAATTTA
1 ATCCTTTCATGCATTTTAGTTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTA
1177077 ATTATGACATCCTTTCATGCCTTAATGCATTCTTTCATGCATTTTAGTTTATGGCATCCTTTCAT
66 ATTATG-CATCCTTTCATGCCTTAATGCATTCTTTCATGCATTTTAGTTT-TGGCATCCTTTCAT
1177142 GCCTTAATGC
129 GCCTTAATGC
* ** *
1177152 ATCCTTTCATGCGTTTTAGTTTATGATATCCTTTCATGCCTTAATGCATCCTTTCATGC--CTT-
1 ATCCTTTCATGCATTTTAGTTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTA
* * * *
1177214 A--ACGCATCCTTTCATGCATTTTAATTATGGCATTCTTTCATGC--CTTA----AGGCATCCTT
66 ATTATGCATCCTTTCATGC--CTT-A--AT-GCATTCTTTCATGCATTTTAGTTTTGGCATCCTT
*
1177271 TCATGCCTTAAGGC
125 TCATGCCTTAATGC
1177285 ATCCTTTCATGCATTTTAGTTTATGGCATCCTTTCATGCCTTAAT-CTATCCTTTCATGCATTTT
1 ATCCTTTCATGCATTTTAGTTTATGGCATCCTTTCATGCCTTAATGC-ATCCTTTCATGCATTTT
1177349 A
65 A
1177350 GTTTATGGAT
Statistics
Matches: 301, Mismatches: 24, Indels: 30
0.85 0.07 0.08
Matches are distributed among these distances:
132 1 0.00
133 76 0.25
134 13 0.04
135 4 0.01
136 2 0.01
137 2 0.01
138 5 0.02
139 3 0.01
140 152 0.50
141 43 0.14
ACGTcount: A:0.21, C:0.24, G:0.12, T:0.44
Consensus pattern (138 bp):
ATCCTTTCATGCATTTTAGTTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTA
ATTATGCATCCTTTCATGCCTTAATGCATTCTTTCATGCATTTTAGTTTTGGCATCCTTTCATGC
CTTAATGC
Found at i:1184060 original size:47 final size:47
Alignment explanation
Indices: 1183975--1184416 Score: 692
Period size: 47 Copynumber: 9.5 Consensus size: 47
1183965 AGGTCATATT
* *
1183975 ATCCTTTCTTGCATTTTA-ATTATGGCATCCTTTCATGCCTTAATGC
1 ATCCTTTCATGCATTTTAGTTTATGGCATCCTTTCATGCCTTAATGC
* *
1184021 ATCCTTTCATGCATTTTAGTTTATGACATCCTTTTATGCCTTAATGC
1 ATCCTTTCATGCATTTTAGTTTATGGCATCCTTTCATGCCTTAATGC
* * *
1184068 ATTCTTTCATGCATTTTAGTTTATGACATCCTTTCATGTCTTAATGC
1 ATCCTTTCATGCATTTTAGTTTATGGCATCCTTTCATGCCTTAATGC
* *
1184115 ATCCTTTCATGCATTTTAGTTTATGGCATCCTTTTAAGCCTTAATGC
1 ATCCTTTCATGCATTTTAGTTTATGGCATCCTTTCATGCCTTAATGC
* *
1184162 ATCCTTTCATGCATTTTA-ATTATGGCATCCTTTTATGCCTTAATGC
1 ATCCTTTCATGCATTTTAGTTTATGGCATCCTTTCATGCCTTAATGC
*
1184208 ATCCTTTCATGCATTTTAGTTTATGACATCCTTTCATGCCTTAATGC
1 ATCCTTTCATGCATTTTAGTTTATGGCATCCTTTCATGCCTTAATGC
*
1184255 ATCCTTTCATGCATTTTAGTTTATGGCATCCTTTCATGCCTTAATGT
1 ATCCTTTCATGCATTTTAGTTTATGGCATCCTTTCATGCCTTAATGC
* * *
1184302 ATCATTTCATGCATTTTA-ATTATGGCATCCTTTCATGCCTTAATGT
1 ATCCTTTCATGCATTTTAGTTTATGGCATCCTTTCATGCCTTAATGC
*
1184348 ATCCTTTCATGCATTTTAGTTTATGGCATCATTTCATGCCTTAATGC
1 ATCCTTTCATGCATTTTAGTTTATGGCATCCTTTCATGCCTTAATGC
**
1184395 ATAATTTCATGCATTTTAGTTT
1 ATCCTTTCATGCATTTTAGTTT
1184417 GTGGATTCGA
Statistics
Matches: 366, Mismatches: 27, Indels: 5
0.92 0.07 0.01
Matches are distributed among these distances:
46 105 0.29
47 261 0.71
ACGTcount: A:0.21, C:0.21, G:0.11, T:0.46
Consensus pattern (47 bp):
ATCCTTTCATGCATTTTAGTTTATGGCATCCTTTCATGCCTTAATGC
Found at i:1184227 original size:140 final size:140
Alignment explanation
Indices: 1183975--1184416 Score: 724
Period size: 140 Copynumber: 3.2 Consensus size: 140
1183965 AGGTCATATT
* *
1183975 ATCCTTTCTTGCATTTTA-ATTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTA
1 ATCCTTTCATGCATTTTAGTTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTA
* * *
1184039 GTTTATGACATCCTTTTATGCCTTAATGCATTCTTTCATGCATTTTAGTTTATGACATCCTTTCA
66 -ATTATGGCATCCTTTTATGCCTTAATGCATCCTTTCATGCATTTTAGTTTATGACATCCTTTCA
*
1184104 TGTCTTAATGC
130 TGCCTTAATGC
* *
1184115 ATCCTTTCATGCATTTTAGTTTATGGCATCCTTTTAAGCCTTAATGCATCCTTTCATGCATTTTA
1 ATCCTTTCATGCATTTTAGTTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTA
1184180 ATTATGGCATCCTTTTATGCCTTAATGCATCCTTTCATGCATTTTAGTTTATGACATCCTTTCAT
66 ATTATGGCATCCTTTTATGCCTTAATGCATCCTTTCATGCATTTTAGTTTATGACATCCTTTCAT
1184245 GCCTTAATGC
131 GCCTTAATGC
* *
1184255 ATCCTTTCATGCATTTTAGTTTATGGCATCCTTTCATGCCTTAATGTATCATTTCATGCATTTTA
1 ATCCTTTCATGCATTTTAGTTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTA
* * * *
1184320 ATTATGGCATCCTTTCATGCCTTAATGTATCCTTTCATGCATTTTAGTTTATGGCATCATTTCAT
66 ATTATGGCATCCTTTTATGCCTTAATGCATCCTTTCATGCATTTTAGTTTATGACATCCTTTCAT
1184385 GCCTTAATGC
131 GCCTTAATGC
**
1184395 ATAATTTCATGCATTTTAGTTT
1 ATCCTTTCATGCATTTTAGTTT
1184417 GTGGATTCGA
Statistics
Matches: 283, Mismatches: 18, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
140 240 0.85
141 43 0.15
ACGTcount: A:0.21, C:0.21, G:0.11, T:0.46
Consensus pattern (140 bp):
ATCCTTTCATGCATTTTAGTTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTA
ATTATGGCATCCTTTTATGCCTTAATGCATCCTTTCATGCATTTTAGTTTATGACATCCTTTCAT
GCCTTAATGC
Found at i:1184290 original size:187 final size:186
Alignment explanation
Indices: 1183975--1184416 Score: 722
Period size: 187 Copynumber: 2.4 Consensus size: 186
1183965 AGGTCATATT
*
1183975 ATCCTTTCTTGCATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAG
1 ATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAG
* *
1184040 TTTATGACATCCTTTTATGCCTTAATGCATTCTTTCATGCATTTTAGTTTATGACATCCTTTCAT
66 TTTATGACATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAGTTTATGACATCCTTTCAT
* * * *
1184105 GTCTTAATGCATCCTTTCATGCATTTTAGTTTATGGCATCCTTTTAAGCCTTAATGC
131 GCCTTAATGCATCATTTCATGCATTTTA-ATTATGGCATCCTTTCAAGCCTTAATGC
*
1184162 ATCCTTTCATGCATTTTAATTATGGCATCCTTTTATGCCTTAATGCATCCTTTCATGCATTTTAG
1 ATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAG
*
1184227 TTTATGACATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAGTTTATGGCATCCTTTCAT
66 TTTATGACATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAGTTTATGACATCCTTTCAT
* * *
1184292 GCCTTAATGTATCATTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATGT
131 GCCTTAATGCATCATTTCATGCATTTTAATTATGGCATCCTTTCAAGCCTTAATGC
* * **
1184348 ATCCTTTCATGCATTTTAGTTTATGGCATCATTTCATGCCTTAATGCATAATTTCATGCATTTTA
1 ATCCTTTCATGCATTTTA-ATTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTA
1184413 GTTT
65 GTTT
1184417 GTGGATTCGA
Statistics
Matches: 237, Mismatches: 17, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
186 42 0.18
187 195 0.82
ACGTcount: A:0.21, C:0.21, G:0.11, T:0.46
Consensus pattern (186 bp):
ATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAG
TTTATGACATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAGTTTATGACATCCTTTCAT
GCCTTAATGCATCATTTCATGCATTTTAATTATGGCATCCTTTCAAGCCTTAATGC
Found at i:1184856 original size:22 final size:19
Alignment explanation
Indices: 1184812--1184883 Score: 72
Period size: 22 Copynumber: 3.6 Consensus size: 19
1184802 TGGCTCCTCA
* *
1184812 GTATCAATACCCTTACCATG
1 GTATCGATACCC-TACTATG
1184832 GTATCGATACTACCATACTATG
1 GTATCGATAC--CC-TACTATG
* *
1184854 GTACCGATACCCTATTATG
1 GTATCGATACCCTACTATG
1184873 GTATCGATACC
1 GTATCGATACC
1184884 ATTTTTGCAT
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
19 16 0.36
20 11 0.25
22 17 0.39
ACGTcount: A:0.29, C:0.26, G:0.14, T:0.31
Consensus pattern (19 bp):
GTATCGATACCCTACTATG
Found at i:1185122 original size:19 final size:18
Alignment explanation
Indices: 1185096--1185174 Score: 51
Period size: 19 Copynumber: 4.4 Consensus size: 18
1185086 TAAATTTAGT
1185096 TATACTAATACCATATAA
1 TATACTAATACCATATAA
* * *
1185114 TACTACTAA-ACTCTTCT-T
1 TA-TACTAATAC-CATATAA
1185132 TA-ACT-AT-CCATACTAA
1 TATACTAATACCATA-TAA
*
1185148 TATACTAACACCATATAA
1 TATACTAATACCATATAA
1185166 TACTACTAA
1 TA-TACTAA
1185175 ACTCTTCTTT
Statistics
Matches: 45, Mismatches: 7, Indels: 17
0.65 0.10 0.25
Matches are distributed among these distances:
14 2 0.04
15 3 0.07
16 5 0.11
17 3 0.07
18 12 0.27
19 20 0.44
ACGTcount: A:0.43, C:0.23, G:0.00, T:0.34
Consensus pattern (18 bp):
TATACTAATACCATATAA
Found at i:1185174 original size:52 final size:52
Alignment explanation
Indices: 1185096--1185202 Score: 205
Period size: 52 Copynumber: 2.1 Consensus size: 52
1185086 TAAATTTAGT
*
1185096 TATACTAATACCATATAATACTACTAAACTCTTCTTTAACTATCCATACTAA
1 TATACTAACACCATATAATACTACTAAACTCTTCTTTAACTATCCATACTAA
1185148 TATACTAACACCATATAATACTACTAAACTCTTCTTTAACTATCCATACTAA
1 TATACTAACACCATATAATACTACTAAACTCTTCTTTAACTATCCATACTAA
1185200 TAT
1 TAT
1185203 TTCTTCATCT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 54 1.00
ACGTcount: A:0.40, C:0.23, G:0.00, T:0.36
Consensus pattern (52 bp):
TATACTAACACCATATAATACTACTAAACTCTTCTTTAACTATCCATACTAA
Found at i:1185198 original size:28 final size:28
Alignment explanation
Indices: 1185113--1185198 Score: 74
Period size: 28 Copynumber: 3.2 Consensus size: 28
1185103 ATACCATATA
1185113 ATACTACTAAACTCTTCTTTAACTATCC
1 ATACTACTAAACTCTTCTTTAACTATCC
* * ** * *
1185141 ATACTAATATACT-AAC---ACCATAT-A
1 ATACTACTAAACTCTTCTTTAAC-TATCC
1185165 ATACTACTAAACTCTTCTTTAACTATCC
1 ATACTACTAAACTCTTCTTTAACTATCC
1185193 ATACTA
1 ATACTA
1185199 ATATTTCTTC
Statistics
Matches: 40, Mismatches: 12, Indels: 12
0.62 0.19 0.19
Matches are distributed among these distances:
24 13 0.32
25 4 0.10
27 4 0.10
28 19 0.47
ACGTcount: A:0.38, C:0.26, G:0.00, T:0.36
Consensus pattern (28 bp):
ATACTACTAAACTCTTCTTTAACTATCC
Found at i:1186322 original size:24 final size:24
Alignment explanation
Indices: 1186273--1186322 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
1186263 TAAGTAATAA
**
1186273 AATAGTATAATATTAACATGTTTG
1 AATAGTATAATATTAACATGCATG
* *
1186297 AATATTATAATATTAACTTGCATG
1 AATAGTATAATATTAACATGCATG
1186321 AA
1 AA
1186323 CCAACTTACC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.44, C:0.06, G:0.10, T:0.40
Consensus pattern (24 bp):
AATAGTATAATATTAACATGCATG
Found at i:1186843 original size:21 final size:21
Alignment explanation
Indices: 1186814--1186859 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
1186804 AAAAAACATG
*
1186814 TATCTAAATTATCGGATTGAA
1 TATCCAAATTATCGGATTGAA
*
1186835 TATCCAAATTTTCGGATTGAA
1 TATCCAAATTATCGGATTGAA
1186856 TATC
1 TATC
1186860 ATAATATATG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.39
Consensus pattern (21 bp):
TATCCAAATTATCGGATTGAA
Found at i:1188057 original size:2 final size:2
Alignment explanation
Indices: 1188045--1188137 Score: 177
Period size: 2 Copynumber: 46.5 Consensus size: 2
1188035 ATAAAATTTG
*
1188045 TC TC CC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1188087 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1188129 TC TC TC TC T
1 TC TC TC TC T
1188138 ATATATATAT
Statistics
Matches: 89, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
2 89 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
TC
Found at i:1188185 original size:2 final size:2
Alignment explanation
Indices: 1188137--1188166 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1188127 TCTCTCTCTC
1188137 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1188167 GGTTAAGTCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1189449 original size:18 final size:17
Alignment explanation
Indices: 1189426--1189469 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
1189416 TTATTGGGTG
1189426 AAAATATTATTATTGTAA
1 AAAATATTATTATT-TAA
*
1189444 AAAATATAATTATTTAA
1 AAAATATTATTATTTAA
1189461 AATAATATT
1 AA-AATATT
1189470 TAGTTTTGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 5 0.22
18 18 0.78
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (17 bp):
AAAATATTATTATTTAA
Found at i:1192646 original size:3 final size:3
Alignment explanation
Indices: 1192638--1192696 Score: 118
Period size: 3 Copynumber: 19.7 Consensus size: 3
1192628 AGTGCATTTC
1192638 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1192686 ATT ATT ATT AT
1 ATT ATT ATT AT
1192697 ATATATACTC
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:1197290 original size:36 final size:36
Alignment explanation
Indices: 1197243--1197338 Score: 158
Period size: 36 Copynumber: 2.7 Consensus size: 36
1197233 GTCAATCCAA
1197243 CCTTCACAAAAGAGTAGTGAAGCAATGCAAATCAAG
1 CCTTCACAAAAGAGTAGTGAAGCAATGCAAATCAAG
*
1197279 CCTTCATAAAAGAGTAGTGAA-CTAATGCAAATCAAG
1 CCTTCACAAAAGAGTAGTGAAGC-AATGCAAATCAAG
*
1197315 CTTTCACAAAAGAGTAGTGAAGCA
1 CCTTCACAAAAGAGTAGTGAAGCA
1197339 GAAACATATC
Statistics
Matches: 55, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
35 1 0.02
36 53 0.96
37 1 0.02
ACGTcount: A:0.44, C:0.18, G:0.19, T:0.20
Consensus pattern (36 bp):
CCTTCACAAAAGAGTAGTGAAGCAATGCAAATCAAG
Found at i:1197535 original size:8 final size:8
Alignment explanation
Indices: 1197515--1197552 Score: 53
Period size: 8 Copynumber: 4.9 Consensus size: 8
1197505 TTCCGATTCG
1197515 TTATAAGTA
1 TTATAA-TA
1197524 TTATAATA
1 TTATAATA
1197532 TTAT--TA
1 TTATAATA
1197538 TTATAATA
1 TTATAATA
1197546 TTATAAT
1 TTATAAT
1197553 TAATTATTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
6 6 0.22
8 15 0.56
9 6 0.22
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (8 bp):
TTATAATA
Found at i:1197541 original size:14 final size:14
Alignment explanation
Indices: 1197522--1197554 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
1197512 TCGTTATAAG
1197522 TATTATAATATTAT
1 TATTATAATATTAT
1197536 TATTATAATATTAT
1 TATTATAATATTAT
*
1197550 AATTA
1 TATTA
1197555 ATTATTATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
TATTATAATATTAT
Found at i:1197638 original size:25 final size:27
Alignment explanation
Indices: 1197603--1197653 Score: 79
Period size: 25 Copynumber: 2.0 Consensus size: 27
1197593 CGAAGGCCCA
1197603 ATTACAACTCGAAGGCCCAT-TTACAC
1 ATTACAACTCGAAGGCCCATGTTACAC
*
1197629 ATTA-AACTCGAATGCCCATGTTACA
1 ATTACAACTCGAAGGCCCATGTTACA
1197654 ATGAGATCCG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 14 0.61
26 9 0.39
ACGTcount: A:0.35, C:0.27, G:0.12, T:0.25
Consensus pattern (27 bp):
ATTACAACTCGAAGGCCCATGTTACAC
Found at i:1199617 original size:45 final size:45
Alignment explanation
Indices: 1199549--1199865 Score: 481
Period size: 45 Copynumber: 7.0 Consensus size: 45
1199539 TTTATTAGAG
* ** *
1199549 ATGAAATGCATAACAATTTATTAAAGGCATGAAAGGATACCATAA
1 ATGAAATGCATAACGATGCATTAAAGGCATGAAAGGATGCCATAA
*
1199594 ATGAAATACATAACGATGCATTAAAGGCATGAAAGGATGCCATAA
1 ATGAAATGCATAACGATGCATTAAAGGCATGAAAGGATGCCATAA
* *
1199639 ATAAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGCCATAA
1 ATGAAATGCATAACGATGCATTAAAGGCATGAAAGGATGCCATAA
* *
1199684 ATGAAATGCATAATGATGCATTAAAGGCATGAAAGGATACCATAA
1 ATGAAATGCATAACGATGCATTAAAGGCATGAAAGGATGCCATAA
* *
1199729 ATGAAATGCATAACGATGCATTAAAGGCGTGAAAGGATGTCATAA
1 ATGAAATGCATAACGATGCATTAAAGGCATGAAAGGATGCCATAA
* * *
1199774 ATGAAATGTATAATGATGCATTAAAGGTATGAAAGGATGCCATAA
1 ATGAAATGCATAACGATGCATTAAAGGCATGAAAGGATGCCATAA
* * *
1199819 ATGAAATGCATAACGGTGCATTAAATGCATGAAATGATGCCATAA
1 ATGAAATGCATAACGATGCATTAAAGGCATGAAAGGATGCCATAA
1199864 AT
1 AT
1199866 AAAAATAATG
Statistics
Matches: 245, Mismatches: 27, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 245 1.00
ACGTcount: A:0.45, C:0.11, G:0.21, T:0.23
Consensus pattern (45 bp):
ATGAAATGCATAACGATGCATTAAAGGCATGAAAGGATGCCATAA
Found at i:1199931 original size:21 final size:23
Alignment explanation
Indices: 1199907--1199950 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
1199897 GGGAAAATGT
1199907 ACATA-AAGAA-ATGTATGATGG
1 ACATACAAGAATATGTATGATGG
*
1199928 ACATACTAAGAATATTTATGATG
1 ACATAC-AAGAATATGTATGATG
1199951 ATAGTATGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 5 0.26
23 5 0.26
24 9 0.47
ACGTcount: A:0.45, C:0.07, G:0.18, T:0.30
Consensus pattern (23 bp):
ACATACAAGAATATGTATGATGG
Found at i:1206641 original size:45 final size:45
Alignment explanation
Indices: 1206573--1207118 Score: 810
Period size: 45 Copynumber: 12.2 Consensus size: 45
1206563 TTTCATTACT
* * *
1206573 TAAATGAAATCCATAACGGTGCATTATAGGCATGAAAGGATGCCA
1 TAAATGAAATGCATAACGATGCATTAAAGGCATGAAAGGATGCCA
*
1206618 TAAATGACATGCATAACGATGCATTAAAGGCATGAAAGGATGCCA
1 TAAATGAAATGCATAACGATGCATTAAAGGCATGAAAGGATGCCA
* *
1206663 TAAATGAAATGCATAACGGTGCATTAAAGGCATGAAATGATGCCA
1 TAAATGAAATGCATAACGATGCATTAAAGGCATGAAAGGATGCCA
* * * *
1206708 TAAATGAAATGTATAACGGTGCATTAAAGGAATGAAATGATGCCA
1 TAAATGAAATGCATAACGATGCATTAAAGGCATGAAAGGATGCCA
* * *
1206753 TAAATGAAATGCATAACGATGCATTAAAGGCATAAAATGATGCTA
1 TAAATGAAATGCATAACGATGCATTAAAGGCATGAAAGGATGCCA
* *
1206798 TAAATGAAATGCACAACGGTGCATTAAAGGCATGAAAGGATGCCA
1 TAAATGAAATGCATAACGATGCATTAAAGGCATGAAAGGATGCCA
* * *
1206843 TAAATGAAATGCACAACGGTGCATTAAAGGCATGAAAGGATGACA
1 TAAATGAAATGCATAACGATGCATTAAAGGCATGAAAGGATGCCA
* *
1206888 TAAATGAAATGCATAACGATGCATTAAATGCATGAAAGGATGTCA
1 TAAATGAAATGCATAACGATGCATTAAAGGCATGAAAGGATGCCA
* * *
1206933 TAAATGAAATGCATAATGATGCATTAAAGGAATGGAAGGATGCCA
1 TAAATGAAATGCATAACGATGCATTAAAGGCATGAAAGGATGCCA
* * *
1206978 TAAATGAAATACATAACGATGCATTAAAGGCATGAAAAGATTCCA
1 TAAATGAAATGCATAACGATGCATTAAAGGCATGAAAGGATGCCA
1207023 T--A-GAAATGCATAACGATGCATTAAAGGCATGAAAGGATGCCA
1 TAAATGAAATGCATAACGATGCATTAAAGGCATGAAAGGATGCCA
* * *
1207065 TAAATGAAATGCATAATGGTGCATTAAAGGCATGAAAGGTTGCCA
1 TAAATGAAATGCATAACGATGCATTAAAGGCATGAAAGGATGCCA
1207110 TAAATGAAA
1 TAAATGAAA
1207119 ATAATGAATA
Statistics
Matches: 457, Mismatches: 41, Indels: 6
0.91 0.08 0.01
Matches are distributed among these distances:
42 38 0.08
43 1 0.00
44 1 0.00
45 417 0.91
ACGTcount: A:0.44, C:0.12, G:0.22, T:0.22
Consensus pattern (45 bp):
TAAATGAAATGCATAACGATGCATTAAAGGCATGAAAGGATGCCA
Found at i:1207912 original size:30 final size:30
Alignment explanation
Indices: 1207816--1207911 Score: 131
Period size: 30 Copynumber: 3.2 Consensus size: 30
1207806 TAGCAGTATA
*
1207816 GTGTGTAAGGACACTTAGTGA-AGCACTATG
1 GTGTGTAAGGACACTTAGT-ACAGCACTGTG
*
1207846 GTGTGTAAGGACACTTAGTACAGCACTGTA
1 GTGTGTAAGGACACTTAGTACAGCACTGTG
* * *
1207876 GTGTGTTAGGACGCTTAGTACAACACTGTG
1 GTGTGTAAGGACACTTAGTACAGCACTGTG
1207906 GTGTGT
1 GTGTGT
1207912 TTATAAATTG
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
29 1 0.02
30 58 0.98
ACGTcount: A:0.26, C:0.15, G:0.30, T:0.29
Consensus pattern (30 bp):
GTGTGTAAGGACACTTAGTACAGCACTGTG
Found at i:1218428 original size:14 final size:14
Alignment explanation
Indices: 1218409--1218435 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1218399 TGTTAGCTCA
1218409 TTTATATTGACGAG
1 TTTATATTGACGAG
1218423 TTTATATTGACGA
1 TTTATATTGACGA
1218436 ATAAATTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.07, G:0.19, T:0.44
Consensus pattern (14 bp):
TTTATATTGACGAG
Found at i:1219426 original size:15 final size:15
Alignment explanation
Indices: 1219402--1219460 Score: 64
Period size: 15 Copynumber: 3.7 Consensus size: 15
1219392 ATAAAATAGC
*
1219402 ATTATTTATTTGTTA
1 ATTAATTATTTGTTA
* *
1219417 ATTAACTATTTTTATA
1 ATTAATTATTTGT-TA
1219433 GTATTAATTATTTGTTA
1 --ATTAATTATTTGTTA
1219450 ATTAATTATTT
1 ATTAATTATTT
1219461 TTATATATCG
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
15 21 0.58
16 2 0.06
17 2 0.06
18 11 0.31
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.61
Consensus pattern (15 bp):
ATTAATTATTTGTTA
Found at i:1219449 original size:33 final size:33
Alignment explanation
Indices: 1219397--1219465 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 33
1219387 TAACTATAAA
*
1219397 ATAGCATTATTTATTTGTTAATTAACTATTTTT
1 ATAGCATTAATTATTTGTTAATTAACTATTTTT
* *
1219430 ATAGTATTAATTATTTGTTAATTAATTATTTTT
1 ATAGCATTAATTATTTGTTAATTAACTATTTTT
1219463 ATA
1 ATA
1219466 TATCGAGTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.33, C:0.03, G:0.06, T:0.58
Consensus pattern (33 bp):
ATAGCATTAATTATTTGTTAATTAACTATTTTT
Found at i:1219527 original size:23 final size:23
Alignment explanation
Indices: 1219499--1219553 Score: 110
Period size: 23 Copynumber: 2.4 Consensus size: 23
1219489 TAAAATAATT
1219499 ATTTTAATAAACCTTGGGTGATA
1 ATTTTAATAAACCTTGGGTGATA
1219522 ATTTTAATAAACCTTGGGTGATA
1 ATTTTAATAAACCTTGGGTGATA
1219545 ATTTTAATA
1 ATTTTAATA
1219554 TTATACCTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.36, C:0.07, G:0.15, T:0.42
Consensus pattern (23 bp):
ATTTTAATAAACCTTGGGTGATA
Found at i:1219926 original size:23 final size:25
Alignment explanation
Indices: 1219883--1219932 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 25
1219873 ATATAACATT
*
1219883 AAAATTATATTTGAAATTTAC-CAA
1 AAAATCATATTTGAAATTTACTCAA
1219907 AAAATCATATTAT-AAA-TTACTCAA
1 AAAATCATATT-TGAAATTTACTCAA
1219931 AA
1 AA
1219933 TTTTATAATC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
23 4 0.17
24 18 0.78
25 1 0.04
ACGTcount: A:0.54, C:0.10, G:0.02, T:0.34
Consensus pattern (25 bp):
AAAATCATATTTGAAATTTACTCAA
Found at i:1222469 original size:5 final size:5
Alignment explanation
Indices: 1222459--1222496 Score: 60
Period size: 5 Copynumber: 7.8 Consensus size: 5
1222449 AACGGTCAAC
*
1222459 GGTCG GGTC- GGTCA GGTCG GGTCG GGTCG GGTCG GGTC
1 GGTCG GGTCG GGTCG GGTCG GGTCG GGTCG GGTCG GGTC
1222497 AGACCGGTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
4 4 0.13
5 27 0.87
ACGTcount: A:0.03, C:0.21, G:0.55, T:0.21
Consensus pattern (5 bp):
GGTCG
Found at i:1222544 original size:20 final size:19
Alignment explanation
Indices: 1222493--1222565 Score: 92
Period size: 19 Copynumber: 3.7 Consensus size: 19
1222483 GGTCGGGTCG
*
1222493 GGTCAGACCGGTTTAGACC
1 GGTCAAACCGGTTTAGACC
1222512 GGTCAAACCGGTTTAGACC
1 GGTCAAACCGGTTTAGACC
* * *
1222531 GGTCGAAACTGGTTCAAAACC
1 GGTC-AAACCGGTT-TAGACC
1222552 GGTCAAACCGGTTT
1 GGTCAAACCGGTTT
1222566 TCAGCCACTC
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
19 22 0.48
20 16 0.35
21 8 0.17
ACGTcount: A:0.26, C:0.25, G:0.27, T:0.22
Consensus pattern (19 bp):
GGTCAAACCGGTTTAGACC
Found at i:1228402 original size:113 final size:114
Alignment explanation
Indices: 1228204--1228439 Score: 447
Period size: 113 Copynumber: 2.1 Consensus size: 114
1228194 GCTCGAACCG
1228204 AGAAATCTAACCAACAGTATCTGAAAGGGGAAAAAATTTTCGAAAAGTGAGCTAGGCTCAGTGTC
1 AGAAATCTAACCAACAGTATCTGAAAGGGGAAAAAATTTTCGAAAAGTGAGCTAGGCTCAGTGTC
1228269 CCAATATTACCTTAAAATCACAATAGGTACATTAAACAAATCATAGT-C
66 CCAATATTACCTTAAAATCACAATAGGTACATTAAACAAATCATAGTCC
*
1228317 AGAAATCTAACCAACAGTATCTGAAAGGGGAAAAACTTTTCGAAAAGTGAGCTAGGCTCAGTGTC
1 AGAAATCTAACCAACAGTATCTGAAAGGGGAAAAAATTTTCGAAAAGTGAGCTAGGCTCAGTGTC
1228382 CCAATATTACCTTAAAATCACAATAGGTACATTAAACAAATCATAGTCC
66 CCAATATTACCTTAAAATCACAATAGGTACATTAAACAAATCATAGTCC
1228431 AGTAAATCT
1 AG-AAATCT
1228440 CATAAATTCA
Statistics
Matches: 120, Mismatches: 1, Indels: 2
0.98 0.01 0.02
Matches are distributed among these distances:
113 111 0.93
114 3 0.03
115 6 0.05
ACGTcount: A:0.42, C:0.18, G:0.16, T:0.24
Consensus pattern (114 bp):
AGAAATCTAACCAACAGTATCTGAAAGGGGAAAAAATTTTCGAAAAGTGAGCTAGGCTCAGTGTC
CCAATATTACCTTAAAATCACAATAGGTACATTAAACAAATCATAGTCC
Found at i:1229495 original size:5 final size:5
Alignment explanation
Indices: 1229485--1229521 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
1229475 AACGATCAAC
*
1229485 GGTCG GGTCG GGTC- GGT-A GGTCG GGTCG GGTCG GGTC
1 GGTCG GGTCG GGTCG GGTCG GGTCG GGTCG GGTCG GGTC
1229522 AGACCGGTTC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
4 6 0.21
5 23 0.79
ACGTcount: A:0.03, C:0.19, G:0.57, T:0.22
Consensus pattern (5 bp):
GGTCG
Found at i:1236774 original size:19 final size:19
Alignment explanation
Indices: 1236733--1236774 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
1236723 CGGGTCAGAC
* *
1236733 CGGTCAAACCGGTTCGAAT
1 CGGTCAAACCGGTTCAAAA
1236752 CGGTCAAAACCGG-TCAAAA
1 CGGTC-AAACCGGTTCAAAA
1236771 CGGT
1 CGGT
1236775 TTTCAGCCAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.31, C:0.26, G:0.26, T:0.17
Consensus pattern (19 bp):
CGGTCAAACCGGTTCAAAA
Found at i:1238248 original size:36 final size:35
Alignment explanation
Indices: 1238075--1238247 Score: 193
Period size: 36 Copynumber: 5.1 Consensus size: 35
1238065 CTATTGGAAA
1238075 AAAAATGCTCAAATTAGGTATTT-C-C-AC-TTGG
1 AAAAATGCTCAAATTAGGTATTTCCACTACATTGG
1238106 AAAAATGCTCAAATTAGGTATTT-C-C-AC-TTGG
1 AAAAATGCTCAAATTAGGTATTTCCACTACATTGG
* *
1238137 AAAAATGCTGAAGTTAGGGT-TTTCCACTAGCATTGG
1 AAAAATGCTCAAATTA-GGTATTTCCACTA-CATTGG
* * *
1238173 ATAAATGCTCAAGTTAGGTTTTTCCACTAGCATTGG
1 AAAAATGCTCAAATTAGGTATTTCCACTA-CATTGG
*
1238209 AAATATGCTCAAATTAGGTATTTCCACTACTATTGG
1 AAAAATGCTCAAATTAGGTATTTCCACTAC-ATTGG
1238245 AAA
1 AAA
1238248 TGACTATTTT
Statistics
Matches: 126, Mismatches: 8, Indels: 11
0.87 0.06 0.08
Matches are distributed among these distances:
31 48 0.38
32 4 0.03
33 1 0.01
34 1 0.01
35 5 0.04
36 67 0.53
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.33
Consensus pattern (35 bp):
AAAAATGCTCAAATTAGGTATTTCCACTACATTGG
Found at i:1243432 original size:36 final size:35
Alignment explanation
Indices: 1243350--1243493 Score: 227
Period size: 36 Copynumber: 4.1 Consensus size: 35
1243340 ACTATTGGAA
1243350 AAAATGCTCAA-TTAGGTATTTCCACTAGCATTGG
1 AAAATGCTCAAGTTAGGTATTTCCACTAGCATTGG
*
1243384 AAAATGCTCAAGTTAGGTTTTTCCACTAGCATTGG
1 AAAATGCTCAAGTTAGGTATTTCCACTAGCATTGG
*
1243419 ATAAATGCTCAAGTTAGGTTTTTCCACTAGCATTGG
1 A-AAATGCTCAAGTTAGGTATTTCCACTAGCATTGG
* *
1243455 AAATATGCTCAAATTAGGTATTTCCACTAGTATTGG
1 AAA-ATGCTCAAGTTAGGTATTTCCACTAGCATTGG
1243491 AAA
1 AAA
1243494 TGACTATTTT
Statistics
Matches: 103, Mismatches: 4, Indels: 4
0.93 0.04 0.04
Matches are distributed among these distances:
34 11 0.11
35 25 0.24
36 67 0.65
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (35 bp):
AAAATGCTCAAGTTAGGTATTTCCACTAGCATTGG
Found at i:1248278 original size:24 final size:22
Alignment explanation
Indices: 1248255--1248307 Score: 61
Period size: 24 Copynumber: 2.3 Consensus size: 22
1248245 AAATTGAAAT
1248255 TAATAACAAATAAATATAATAAA
1 TAATAACAAATAAATA-AATAAA
* *
1248278 TAAGTAATAAATAATTAAATATAA
1 TAA-TAACAAATAAATAAATA-AA
1248302 TAATAA
1 TAATAA
1248308 ATAAACATAG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
23 10 0.38
24 16 0.62
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (22 bp):
TAATAACAAATAAATAAATAAA
Found at i:1248279 original size:4 final size:4
Alignment explanation
Indices: 1248262--1248312 Score: 52
Period size: 4 Copynumber: 12.8 Consensus size: 4
1248252 AATTAATAAC
* *
1248262 AAAT AAAT ATAAT AAAT AAGT -AAT AAAT AATT AAAT ATAAT -AAT AAAT
1 AAAT AAAT A-AAT AAAT AAAT AAAT AAAT AAAT AAAT A-AAT AAAT AAAT
1248310 AAA
1 AAA
1248313 CATAGTAATT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
3 5 0.13
4 27 0.69
5 7 0.18
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (4 bp):
AAAT
Found at i:1248286 original size:20 final size:20
Alignment explanation
Indices: 1248263--1248312 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
1248253 ATTAATAACA
*
1248263 AATAAATATAATAAATA-AGT
1 AATAAATA-AATAAATATAAT
*
1248283 AATAAATAATTAAATATAAT
1 AATAAATAAATAAATATAAT
1248303 AATAAATAAA
1 AATAAATAAA
1248313 CATAGTAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
19 7 0.27
20 19 0.73
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (20 bp):
AATAAATAAATAAATATAAT
Found at i:1248346 original size:25 final size:25
Alignment explanation
Indices: 1248318--1248365 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
1248308 ATAAACATAG
* *
1248318 TAATTAAAATATATTTTTTAAATAA
1 TAATTAAAAGATATTTTGTAAATAA
*
1248343 TAATTATAAGATATTTTGTAAAT
1 TAATTAAAAGATATTTTGTAAAT
1248366 TTTGAAATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (25 bp):
TAATTAAAAGATATTTTGTAAATAA
Found at i:1253663 original size:35 final size:35
Alignment explanation
Indices: 1253623--1253691 Score: 95
Period size: 35 Copynumber: 2.0 Consensus size: 35
1253613 AATCTGTGTC
* *
1253623 TGATAACTGTAAAA-CATCTGATATCTGTAAATATT
1 TGATAACT-TAAAATCATCTAATAACTGTAAATATT
*
1253658 TGATAACTTAAAATCGTCTAATAACTGTAAATAT
1 TGATAACTTAAAATCATCTAATAACTGTAAATAT
1253692 CTGCTAATGG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
34 5 0.17
35 25 0.83
ACGTcount: A:0.42, C:0.12, G:0.10, T:0.36
Consensus pattern (35 bp):
TGATAACTTAAAATCATCTAATAACTGTAAATATT
Found at i:1253671 original size:17 final size:18
Alignment explanation
Indices: 1253621--1253723 Score: 88
Period size: 18 Copynumber: 5.8 Consensus size: 18
1253611 TTAATCTGTG
*
1253621 TCTGATAACTGTAAAACA
1 TCTGATAACTGTAAAATA
*
1253639 TCTGATATCTGT-AAATA
1 TCTGATAACTGTAAAATA
* *
1253656 TTTGATAACT-TAAAATCG
1 TCTGATAACTGTAAAAT-A
*
1253674 TCTAATAACTGT-AAATA
1 TCTGATAACTGTAAAATA
* *
1253691 TCTGCTAA-TGGTGAAATA
1 TCTGATAACT-GTAAAATA
*
1253709 TCTGATAATTGTAAA
1 TCTGATAACTGTAAA
1253724 CATTTAGAAT
Statistics
Matches: 67, Mismatches: 12, Indels: 12
0.74 0.13 0.13
Matches are distributed among these distances:
16 2 0.03
17 24 0.36
18 39 0.58
19 2 0.03
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.36
Consensus pattern (18 bp):
TCTGATAACTGTAAAATA
Found at i:1260775 original size:13 final size:13
Alignment explanation
Indices: 1260757--1260855 Score: 55
Period size: 14 Copynumber: 7.3 Consensus size: 13
1260747 TCAAAATATA
1260757 TTATAATTATTAT
1 TTATAATTATTAT
*
1260770 TTATAAAATATCTAT
1 TTAT-AATTAT-TAT
1260785 TT-TAATTAATATAT
1 TTATAATT-AT-TAT
*
1260799 TAATATATTATTAT
1 TTATA-ATTATTAT
*
1260813 ATT-TAATAATTAAT
1 -TTATAATTATT-AT
1260827 ATTATTAATTATTA-
1 -TTA-TAATTATTAT
1260841 TTAT-ATTA-TAT
1 TTATAATTATTAT
1260852 TTAT
1 TTAT
1260856 TATATTTATT
Statistics
Matches: 69, Mismatches: 7, Indels: 22
0.70 0.07 0.22
Matches are distributed among these distances:
10 2 0.03
11 8 0.12
12 1 0.01
13 15 0.22
14 22 0.32
15 11 0.16
16 10 0.14
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (13 bp):
TTATAATTATTAT
Found at i:1260803 original size:24 final size:22
Alignment explanation
Indices: 1260776--1260859 Score: 62
Period size: 23 Copynumber: 3.5 Consensus size: 22
1260766 TTATTTATAA
*
1260776 AATATCTATTTTAATTAATATATT
1 AATAT-TATTATAATTAATA-ATT
*
1260800 AATATATTATTATATTTAATAATT
1 -A-ATATTATTATAATTAATAATT
* *
1260824 AATATTATTAATTATTATTATATT
1 AATATTATT-ATAATTAATA-ATT
1260848 -ATATTTATTATA
1 AATA-TTATTATA
1260860 TTTATTTGTT
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
22 8 0.16
23 13 0.27
24 11 0.22
25 13 0.27
26 4 0.08
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (22 bp):
AATATTATTATAATTAATAATT
Found at i:1260808 original size:16 final size:16
Alignment explanation
Indices: 1260789--1260861 Score: 82
Period size: 16 Copynumber: 4.7 Consensus size: 16
1260779 ATCTATTTTA
*
1260789 ATTAATATATTAATAT
1 ATTATTATATTAATAT
1260805 ATTATTATATTTAATA-
1 ATTATTATA-TTAATAT
*
1260821 ATTAATATTATTAAT-T
1 ATTATTA-TATTAATAT
1260837 ATTATTATATT-ATAT
1 ATTATTATATTAATAT
1260852 -TTATTATATT
1 ATTATTATATT
1260862 TATTTGTTAT
Statistics
Matches: 50, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
14 12 0.24
15 5 0.10
16 25 0.50
17 8 0.16
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
ATTATTATATTAATAT
Found at i:1260823 original size:32 final size:32
Alignment explanation
Indices: 1260787--1260847 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
1260777 ATATCTATTT
1260787 TAATTAATA-TATTAATATATTATTATATTTAA
1 TAATTAATATTATTAAT-TATTATTATATTTAA
1260819 TAATTAATATTATTAATTATTATTATATT
1 TAATTAATATTATTAATTATTATTATATT
1260848 ATATTTATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
32 21 0.75
33 7 0.25
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (32 bp):
TAATTAATATTATTAATTATTATTATATTTAA
Found at i:1270523 original size:15 final size:15
Alignment explanation
Indices: 1270505--1270548 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
1270495 ATCATCTATG
* *
1270505 TGCTCATCTGCTTCA
1 TGCTCATCTCCATCA
1270520 TGCTCATCTCCATCA
1 TGCTCATCTCCATCA
1270535 TGCTCATCCTCCAT
1 TGCTCAT-CTCCAT
1270549 TTCCTCTCCA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
15 20 0.77
16 6 0.23
ACGTcount: A:0.16, C:0.39, G:0.09, T:0.36
Consensus pattern (15 bp):
TGCTCATCTCCATCA
Found at i:1273150 original size:27 final size:26
Alignment explanation
Indices: 1273119--1273178 Score: 84
Period size: 27 Copynumber: 2.2 Consensus size: 26
1273109 ATTATTATCT
*
1273119 TTTTACAACATAAGGGTATTTTTGTAA
1 TTTTAC-ACATAAGGGTATTTTTATAA
*
1273146 TTTTATCTCATAAGGGTATTTTTATAA
1 TTTTA-CACATAAGGGTATTTTTATAA
1273173 TTTTAC
1 TTTTAC
1273179 CTAACAGAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
26 1 0.03
27 28 0.93
28 1 0.03
ACGTcount: A:0.30, C:0.08, G:0.12, T:0.50
Consensus pattern (26 bp):
TTTTACACATAAGGGTATTTTTATAA
Found at i:1278426 original size:42 final size:42
Alignment explanation
Indices: 1278359--1278440 Score: 119
Period size: 42 Copynumber: 2.0 Consensus size: 42
1278349 TTCTACGTGG
1278359 TCCTTCGGGACATATATGTGATCCTTGGGAACATATATGTTA
1 TCCTTCGGGACATATATGTGATCCTTGGGAACATATATGTTA
* * * * *
1278401 TCCTTCGGGATATATGTTTGGTCCTTTGGAACATATATGT
1 TCCTTCGGGACATATATGTGATCCTTGGGAACATATATGT
1278441 GGTCATACAA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.23, C:0.16, G:0.22, T:0.39
Consensus pattern (42 bp):
TCCTTCGGGACATATATGTGATCCTTGGGAACATATATGTTA
Found at i:1278443 original size:21 final size:21
Alignment explanation
Indices: 1278355--1278444 Score: 90
Period size: 21 Copynumber: 4.3 Consensus size: 21
1278345 AGGATTCTAC
*
1278355 GTGGTCCTTCGGGACATATAT
1 GTGGTCCTTCGGAACATATAT
* *
1278376 GTGATCCTTGGGAACATATAT
1 GTGGTCCTTCGGAACATATAT
** * * *
1278397 GTTATCCTTCGGGATATATGT
1 GTGGTCCTTCGGAACATATAT
* *
1278418 TTGGTCCTTTGGAACATATAT
1 GTGGTCCTTCGGAACATATAT
1278439 GTGGTC
1 GTGGTC
1278445 ATACAAGACA
Statistics
Matches: 53, Mismatches: 16, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 53 1.00
ACGTcount: A:0.21, C:0.16, G:0.26, T:0.38
Consensus pattern (21 bp):
GTGGTCCTTCGGAACATATAT
Found at i:1281859 original size:13 final size:13
Alignment explanation
Indices: 1281816--1281859 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
1281806 TCTATGACAT
*
1281816 GCATTTATGACAC
1 GCATTTATGACGC
* *
1281829 GCATATATGATGC
1 GCATTTATGACGC
*
1281842 TCATTTATGACGC
1 GCATTTATGACGC
1281855 GCATT
1 GCATT
1281860 GCACGTCATT
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.34
Consensus pattern (13 bp):
GCATTTATGACGC
Found at i:1288745 original size:21 final size:21
Alignment explanation
Indices: 1288721--1288803 Score: 80
Period size: 21 Copynumber: 3.9 Consensus size: 21
1288711 CCTTCGGGAC
1288721 ATATATGTGATCCTTGGGAAG
1 ATATATGTGATCCTTGGGAAG
*
1288742 ATATATGTGATCCTTCGG--G
1 ATATATGTGATCCTTGGGAAG
* * *
1288761 ATATATGTTTGGTCCTTTGGAAC
1 ATATATG--TGATCCTTGGGAAG
*
1288784 ATATATGTGGTCCTATGGGA
1 ATATATGTGATCCT-TGGGA
1288804 CAATTCTACG
Statistics
Matches: 52, Mismatches: 5, Indels: 9
0.79 0.08 0.14
Matches are distributed among these distances:
19 8 0.15
21 33 0.63
22 4 0.08
23 7 0.13
ACGTcount: A:0.24, C:0.12, G:0.27, T:0.37
Consensus pattern (21 bp):
ATATATGTGATCCTTGGGAAG
Found at i:1288763 original size:19 final size:19
Alignment explanation
Indices: 1288710--1288768 Score: 73
Period size: 21 Copynumber: 2.9 Consensus size: 19
1288700 TTCTACGCGG
1288710 TCCTTCGGGACATATATGTGA
1 TCCTTCGGG--ATATATGTGA
*
1288731 TCCTTGGGAAGATATATGTGA
1 TCCTTCGG--GATATATGTGA
1288752 TCCTTCGGGATATATGT
1 TCCTTCGGGATATATGT
1288769 TTGGTCCTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
19 9 0.26
21 24 0.71
23 1 0.03
ACGTcount: A:0.24, C:0.15, G:0.25, T:0.36
Consensus pattern (19 bp):
TCCTTCGGGATATATGTGA
Found at i:1288777 original size:42 final size:42
Alignment explanation
Indices: 1288710--1288805 Score: 113
Period size: 42 Copynumber: 2.3 Consensus size: 42
1288700 TTCTACGCGG
*
1288710 TCCTTCGGGACATATATGTGATCCTTGGGAAGATATATGTGA
1 TCCTTCGGGACATATATGTGATCCTTGGGAACATATATGTGA
* * * * * *
1288752 TCCTTCGGGATATATGTTTGGTCCTTTGGAACATATATGTGG
1 TCCTTCGGGACATATATGTGATCCTTGGGAACATATATGTGA
1288794 TCCTAT-GGGACA
1 TCCT-TCGGGACA
1288806 ATTCTACGTG
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
42 44 0.98
43 1 0.02
ACGTcount: A:0.23, C:0.16, G:0.26, T:0.35
Consensus pattern (42 bp):
TCCTTCGGGACATATATGTGATCCTTGGGAACATATATGTGA
Found at i:1288820 original size:23 final size:22
Alignment explanation
Indices: 1288790--1288846 Score: 64
Period size: 22 Copynumber: 2.5 Consensus size: 22
1288780 GAACATATAT
1288790 GTGGTCCTAT-GGGACAATTCTAC
1 GTGGTCCT-TCGGGAC-ATTCTAC
*
1288813 GTGGTCCTTCGGGACATTCTAT
1 GTGGTCCTTCGGGACATTCTAC
1288835 GTGG-CACTTCGG
1 GTGGTC-CTTCGG
1288847 TGCATATTCT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
21 1 0.03
22 17 0.55
23 13 0.42
ACGTcount: A:0.16, C:0.23, G:0.30, T:0.32
Consensus pattern (22 bp):
GTGGTCCTTCGGGACATTCTAC
Found at i:1290043 original size:21 final size:21
Alignment explanation
Indices: 1290019--1290073 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
1290009 CCTTTAAGGG
1290019 AAGGGATCGATCCTTTTCATC
1 AAGGGATCGATCCTTTTCATC
* * ** *
1290040 AAGGGGTCGATTCTTTTGGTG
1 AAGGGATCGATCCTTTTCATC
1290061 AAGGGATCGATCC
1 AAGGGATCGATCC
1290074 AAAACTCACA
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.22, C:0.18, G:0.29, T:0.31
Consensus pattern (21 bp):
AAGGGATCGATCCTTTTCATC
Found at i:1301559 original size:12 final size:12
Alignment explanation
Indices: 1301524--1301565 Score: 57
Period size: 12 Copynumber: 3.2 Consensus size: 12
1301514 AATACGACAT
1301524 AAGCTATGTGAA
1 AAGCTATGTGAA
1301536 AATGGTCTATGTGAA
1 AA--G-CTATGTGAA
1301551 AAGCTATGTGAA
1 AAGCTATGTGAA
1301563 AAG
1 AAG
1301566 GTATAAATGG
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
12 14 0.52
13 1 0.04
14 1 0.04
15 11 0.41
ACGTcount: A:0.40, C:0.07, G:0.26, T:0.26
Consensus pattern (12 bp):
AAGCTATGTGAA
Found at i:1301774 original size:25 final size:25
Alignment explanation
Indices: 1301727--1301776 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
1301717 CTTTTGGGAC
* * **
1301727 ATTTTTATGTGGCACTTTGGTGCAA
1 ATTTCTATGCGGCACTTCAGTGCAA
1301752 ATTTCTATGCGGCACTTCAGTGCAA
1 ATTTCTATGCGGCACTTCAGTGCAA
1301777 TTTATACGAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.38
Consensus pattern (25 bp):
ATTTCTATGCGGCACTTCAGTGCAA
Found at i:1301919 original size:32 final size:32
Alignment explanation
Indices: 1301883--1301947 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
1301873 ATGAATGAAT
* *
1301883 AGTGCATAATATTACATGTTCTTGTTTGGTGA
1 AGTGCATAACATTACATGTTATTGTTTGGTGA
* * *
1301915 AGTGCGTAACGTTACATGTTATTGTTTTGTGA
1 AGTGCATAACATTACATGTTATTGTTTGGTGA
1301947 A
1 A
1301948 ATATATGATG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.25, C:0.09, G:0.23, T:0.43
Consensus pattern (32 bp):
AGTGCATAACATTACATGTTATTGTTTGGTGA
Found at i:1302501 original size:5 final size:5
Alignment explanation
Indices: 1302491--1302515 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
1302481 AAATGTGTTT
1302491 AAATA AAATA AAATA AAATA AAATA
1 AAATA AAATA AAATA AAATA AAATA
1302516 TGCATGCCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAATA
Found at i:1308116 original size:23 final size:23
Alignment explanation
Indices: 1308090--1308158 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
1308080 CACCACAGCT
* * *
1308090 CGTATAAATGTACCGAAATGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * *
1308113 CGTAGAATTGCACCGCAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
1308136 CGTAGAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
1308159 TATAAGATGT
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.32, C:0.26, G:0.25, T:0.17
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:1313481 original size:23 final size:23
Alignment explanation
Indices: 1313455--1313523 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
1313445 CACCATAGCT
*
1313455 CGTATAAATGCACCGAAGTGCCA
1 CGTAAAAATGCACCGAAGTGCCA
* * * *
1313478 CGTAGAATTGCACCGTAGTGCCG
1 CGTAAAAATGCACCGAAGTGCCA
1313501 CGTAAAAATGCACCGAAGTGCCA
1 CGTAAAAATGCACCGAAGTGCCA
1313524 TATGAGATAT
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.32, C:0.26, G:0.25, T:0.17
Consensus pattern (23 bp):
CGTAAAAATGCACCGAAGTGCCA
Found at i:1335387 original size:23 final size:23
Alignment explanation
Indices: 1335361--1335429 Score: 102
Period size: 23 Copynumber: 3.0 Consensus size: 23
1335351 TAGGGTTCTT
* *
1335361 TCCTTCGAGACAATTCTACGTGG
1 TCCTTCGGGACATTTCTACGTGG
**
1335384 TCCTTCGGGACATTTCTACGCAG
1 TCCTTCGGGACATTTCTACGTGG
1335407 TCCTTCGGGACATTTCTACGTGG
1 TCCTTCGGGACATTTCTACGTGG
1335430 CACTTTGGTG
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.17, C:0.28, G:0.23, T:0.32
Consensus pattern (23 bp):
TCCTTCGGGACATTTCTACGTGG
Found at i:1335611 original size:32 final size:32
Alignment explanation
Indices: 1335575--1335639 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
1335565 ATGAATGAAT
*
1335575 AGTGTATAATATTACATGTTCTTGTTTGGTGA
1 AGTGTATAATATTACATGTTATTGTTTGGTGA
* * *
1335607 AGTGTGTAATGTTACATGTTATTGTTTTGTGA
1 AGTGTATAATATTACATGTTATTGTTTGGTGA
1335639 A
1 A
1335640 ATATATGATA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.25, C:0.05, G:0.23, T:0.48
Consensus pattern (32 bp):
AGTGTATAATATTACATGTTATTGTTTGGTGA
Found at i:1337383 original size:30 final size:30
Alignment explanation
Indices: 1337360--1337444 Score: 161
Period size: 30 Copynumber: 2.8 Consensus size: 30
1337350 ATCTATCAAC
1337360 ACAAGCTTGAAATGCAAGCCATCTAACAGA
1 ACAAGCTTGAAATGCAAGCCATCTAACAGA
*
1337390 ACAAGCTTGAAATGCAAGCTATCTAACAGA
1 ACAAGCTTGAAATGCAAGCCATCTAACAGA
1337420 ACAAGCTTGAAATGCAAGCCATCTA
1 ACAAGCTTGAAATGCAAGCCATCTA
1337445 GCCACATCTA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 53 1.00
ACGTcount: A:0.42, C:0.22, G:0.16, T:0.19
Consensus pattern (30 bp):
ACAAGCTTGAAATGCAAGCCATCTAACAGA
Found at i:1337695 original size:4 final size:4
Alignment explanation
Indices: 1337686--1337710 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
1337676 ATTTAACACA
1337686 TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT T
1337711 TAAAAATATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:1345952 original size:22 final size:20
Alignment explanation
Indices: 1345926--1345965 Score: 62
Period size: 22 Copynumber: 1.9 Consensus size: 20
1345916 AATTTCGTCC
1345926 TTATATTATACAATATATATAT
1 TTATATTATA-AAT-TATATAT
1345948 TTATATTATAAATTATAT
1 TTATATTATAAATTATAT
1345966 TTACATTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 3 0.17
22 10 0.56
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (20 bp):
TTATATTATAAATTATATAT
Found at i:1346229 original size:20 final size:21
Alignment explanation
Indices: 1346194--1346232 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
1346184 GGACTCTATG
1346194 ACTAAAAATAGGATGTAATAA
1 ACTAAAAATAGGATGTAATAA
*
1346215 ACTATAAAT-GGATGTAAT
1 ACTAAAAATAGGATGTAAT
1346233 CAGAAACCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.51, C:0.05, G:0.15, T:0.28
Consensus pattern (21 bp):
ACTAAAAATAGGATGTAATAA
Found at i:1347023 original size:27 final size:28
Alignment explanation
Indices: 1346992--1347050 Score: 72
Period size: 26 Copynumber: 2.2 Consensus size: 28
1346982 ATATATTACG
*
1346992 TTATTTATTATATATATTAT-TAT-TGTA
1 TTATTTATTAT-TATACTATATATATGTA
1347019 TTA-TTATTATTATACTATATATATGTA
1 TTATTTATTATTATACTATATATATGTA
1347046 -TATTT
1 TTATTT
1347051 TAGTTCTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
25 7 0.25
26 12 0.43
27 9 0.32
ACGTcount: A:0.34, C:0.02, G:0.03, T:0.61
Consensus pattern (28 bp):
TTATTTATTATTATACTATATATATGTA
Found at i:1347501 original size:8 final size:9
Alignment explanation
Indices: 1347486--1347527 Score: 52
Period size: 8 Copynumber: 4.7 Consensus size: 9
1347476 TTTGCTATAT
1347486 TATTATTTA
1 TATTATTTA
1347495 T-TTATTTA
1 TATTATTTA
1347503 TATTATATTA
1 TATTAT-TTA
1347513 TATT-TTTA
1 TATTATTTA
1347521 TTATTAT
1 -TATTAT
1347528 ATTCGTATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
8 11 0.38
9 10 0.34
10 8 0.28
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (9 bp):
TATTATTTA
Found at i:1347525 original size:14 final size:15
Alignment explanation
Indices: 1347481--1347530 Score: 59
Period size: 14 Copynumber: 3.4 Consensus size: 15
1347471 TACTTTTTGC
*
1347481 TATATTATTATTTAT
1 TATATTTTTATTTAT
*
1347496 T-TATTTATATTATAT
1 TATATTTTTATT-TAT
1347511 TATATTTTTA-TTAT
1 TATATTTTTATTTAT
1347525 TATATT
1 TATATT
1347531 CGTATAAGTA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
14 17 0.57
15 6 0.20
16 7 0.23
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (15 bp):
TATATTTTTATTTAT
Found at i:1347619 original size:13 final size:13
Alignment explanation
Indices: 1347601--1347625 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1347591 TATATACTTT
1347601 ATTATATTTCATC
1 ATTATATTTCATC
1347614 ATTATATTTCAT
1 ATTATATTTCAT
1347626 TACTATTTTA
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:0.32, C:0.12, G:0.00, T:0.56
Consensus pattern (13 bp):
ATTATATTTCATC
Found at i:1351075 original size:76 final size:76
Alignment explanation
Indices: 1350950--1351101 Score: 288
Period size: 76 Copynumber: 2.0 Consensus size: 76
1350940 TTTGTCTGAA
1350950 CAAGGGTTATTTATAATAATGACACTTTTCTGGATCAATGCCTCCAATTGCATA-ATCATACATT
1 CAAGGGTTATTTATAATAATGACACTTTTCTGGATCAATGCCTCCAATTGCATACATCATACATT
1351014 GCATACATTGC
66 GCATACATTGC
1351025 CAAGGGTTATTTATAATAATGAACACTTTTCTGGATCAATGCCTCCAATTGCATACATCATACAT
1 CAAGGGTTATTTATAATAATG-ACACTTTTCTGGATCAATGCCTCCAATTGCATACATCATACAT
1351090 TGCATACATTGC
65 TGCATACATTGC
1351102 ATTTTTATTT
Statistics
Matches: 75, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
75 21 0.28
76 33 0.44
77 21 0.28
ACGTcount: A:0.32, C:0.20, G:0.13, T:0.34
Consensus pattern (76 bp):
CAAGGGTTATTTATAATAATGACACTTTTCTGGATCAATGCCTCCAATTGCATACATCATACATT
GCATACATTGC
Found at i:1351097 original size:9 final size:9
Alignment explanation
Indices: 1351072--1351103 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
1351062 AATGCCTCCA
1351072 ATTGCATAC
1 ATTGCATAC
1351081 A-T-CATAC
1 ATTGCATAC
1351088 ATTGCATAC
1 ATTGCATAC
1351097 ATTGCAT
1 ATTGCAT
1351104 TTTTATTTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
7 6 0.29
8 2 0.10
9 13 0.62
ACGTcount: A:0.34, C:0.22, G:0.09, T:0.34
Consensus pattern (9 bp):
ATTGCATAC
Found at i:1351674 original size:21 final size:21
Alignment explanation
Indices: 1351628--1351684 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 21
1351618 ACTTTGATGA
*
1351628 AGAAGATAAAGCTAAAAAGAT
1 AGAAGATAAAGATAAAAAGAT
* *
1351649 GGAAGA-AAAGATAAAAATATT
1 AGAAGATAAAGATAAAAAGA-T
*
1351670 AGAAGATCAA-ATAAA
1 AGAAGATAAAGATAAA
1351685 GATGGTCCAG
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
20 11 0.38
21 16 0.55
22 2 0.07
ACGTcount: A:0.63, C:0.04, G:0.18, T:0.16
Consensus pattern (21 bp):
AGAAGATAAAGATAAAAAGAT
Found at i:1355279 original size:45 final size:45
Alignment explanation
Indices: 1355228--1355319 Score: 184
Period size: 45 Copynumber: 2.0 Consensus size: 45
1355218 GTACAATCAG
1355228 ATCAAGATGCATCCCGAAGACATGGAGAAGACCACTTTCGTCACA
1 ATCAAGATGCATCCCGAAGACATGGAGAAGACCACTTTCGTCACA
1355273 ATCAAGATGCATCCCGAAGACATGGAGAAGACCACTTTCGTCACA
1 ATCAAGATGCATCCCGAAGACATGGAGAAGACCACTTTCGTCACA
1355318 AT
1 AT
1355320 GTGGGGAACT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.18
Consensus pattern (45 bp):
ATCAAGATGCATCCCGAAGACATGGAGAAGACCACTTTCGTCACA
Found at i:1358128 original size:12 final size:10
Alignment explanation
Indices: 1358079--1358130 Score: 56
Period size: 9 Copynumber: 5.4 Consensus size: 10
1358069 TCCTAAGTTG
1358079 AAAAAAA-AA
1 AAAAAAAGAA
*
1358088 AAAAGAAG-A
1 AAAAAAAGAA
1358097 AAAAAAAGAA
1 AAAAAAAGAA
1358107 AAAAAAA-AA
1 AAAAAAAGAA
*
1358116 AAAAAGAGGAA
1 AAAAA-AAGAA
1358127 AAAA
1 AAAA
1358131 CGTTTTGGGG
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
9 21 0.58
10 9 0.25
11 6 0.17
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (10 bp):
AAAAAAAGAA
Found at i:1358130 original size:1 final size:1
Alignment explanation
Indices: 1358079--1358120 Score: 57
Period size: 1 Copynumber: 42.0 Consensus size: 1
1358069 TCCTAAGTTG
* * *
1358079 AAAAAAAAAAAAAGAAGAAAAAAAAGAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1358121 GAGGAAAAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
1 35 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (1 bp):
A
Found at i:1358130 original size:17 final size:15
Alignment explanation
Indices: 1358079--1358122 Score: 63
Period size: 14 Copynumber: 3.0 Consensus size: 15
1358069 TCCTAAGTTG
1358079 AAAAAAAAAAAAAGA
1 AAAAAAAAAAAAAGA
* *
1358094 AGAAAAAAAAGAA-A
1 AAAAAAAAAAAAAGA
1358108 AAAAAAAAAAAAAGA
1 AAAAAAAAAAAAAGA
1358123 GGAAAAAACG
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
14 12 0.50
15 12 0.50
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAAAAGA
Found at i:1359230 original size:105 final size:105
Alignment explanation
Indices: 1358929--1359563 Score: 1162
Period size: 105 Copynumber: 6.0 Consensus size: 105
1358919 AGGTTTTACC
1358929 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1358994 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
*
1359034 CAGAGCCAATTTCAAACTTCACAACGAAGGATATTGGGCTCCAGACAACGTAAGTTCAACTTCAC
1 CAGAGCCAATTTC-AACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCAC
*
1359099 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTC
65 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
*
1359140 CGGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1359205 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
* *
1359245 CAGAGCCAATTTCAAACTTCACAACGAAAGATATTGGGCTCCAGACAACGTAAGTTCAACTTCAC
1 CAGAGCCAATTTC-AACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCAC
1359310 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
65 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
*
1359351 CAGAGCAAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
*
1359416 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
* *
1359456 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGGCAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
*
1359521 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCCCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
1359561 CAG
1 CAG
1359564 CTCCACAACG
Statistics
Matches: 511, Mismatches: 17, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
105 307 0.60
106 204 0.40
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (105 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
Found at i:1359295 original size:211 final size:211
Alignment explanation
Indices: 1358928--1359559 Score: 1176
Period size: 211 Copynumber: 3.0 Consensus size: 211
1358918 CAGGTTTTAC
1358928 CCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCAC
1 CCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCAC
1358993 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTCAAACTTCACAA
66 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTCAAACTTCACAA
1359058 CGAAGGATATTGGGCTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA
131 CGAAGGATATTGGGCTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA
1359123 CAAACATTTCTCAATT
196 CAAACATTTCTCAATT
*
1359139 CCGGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCAC
1 CCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCAC
1359204 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTCAAACTTCACAA
66 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTCAAACTTCACAA
*
1359269 CGAAAGATATTGGGCTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA
131 CGAAGGATATTGGGCTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA
1359334 CAAACATTTCTCAATT
196 CAAACATTTCTCAATT
* *
1359350 TCAGAGCAAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCAC
1 CCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCAC
*
1359415 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAGAGCCAATTTC-AACTTCACAA
66 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTCAAACTTCACAA
* * *
1359479 CGAAGGATATTGGACTCCAGGCAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA
131 CGAAGGATATTGGGCTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA
*
1359544 CAAACATTTCCCAATT
196 CAAACATTTCTCAATT
1359560 TCAGCTCCAC
Statistics
Matches: 410, Mismatches: 11, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
210 86 0.21
211 324 0.79
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (211 bp):
CCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCAC
GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTCAAACTTCACAA
CGAAGGATATTGGGCTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA
CAAACATTTCTCAATT
Found at i:1359512 original size:316 final size:316
Alignment explanation
Indices: 1358929--1359563 Score: 1166
Period size: 316 Copynumber: 2.0 Consensus size: 316
1358919 AGGTTTTACC
*
1358929 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAAGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
*
1358994 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTCAAACTTCACAAC
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCAAATTTCAAACTTCACAAC
*
1359059 GAAGGATATTGGGCTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAC
131 GAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAC
*
1359124 AAACATTTCTCAATTCCGGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
196 AAACATTTCTCAATTCCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
* *
1359189 TAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
261 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCCCAATTT
*
1359245 CAGAGCCAATTTCAAACTTCACAACGAAAGATATTGGGCTCCAGACAACGTAAGTTCAACTTCAC
1 CAGAGCCAATTTC-AACTTCACAACGAAAGATATTGGACTCCAGACAACGTAAGTTCAACTTCAC
1359310 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCAAATTTC-AACTTCACAA
65 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCAAATTTCAAACTTCACAA
1359374 CGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA
130 CGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA
*
1359439 CAAACATTTCTCAAATT-CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGGCAA
195 CAAACATTTCTC-AATTCCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAA
1359503 CGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCCCAATTT
259 CGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCCCAATTT
1359561 CAG
1 CAG
1359564 CTCCACAACG
Statistics
Matches: 309, Mismatches: 8, Indels: 4
0.96 0.02 0.01
Matches are distributed among these distances:
316 203 0.66
317 106 0.34
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (316 bp):
CAGAGCCAATTTCAACTTCACAACGAAAGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCAAATTTCAAACTTCACAAC
GAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAC
AAACATTTCTCAATTCCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCCCAATTT
Found at i:1359659 original size:20 final size:20
Alignment explanation
Indices: 1359621--1359662 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
1359611 CCAGAACTCT
*
1359621 GAGTTCGATTTCAGCTTCAC
1 GAGTTCGATTTCAACTTCAC
* *
1359641 GAGTTTGATTTCAATTTCAC
1 GAGTTCGATTTCAACTTCAC
1359661 GA
1 GA
1359663 CGAAGGATTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.24, C:0.19, G:0.19, T:0.38
Consensus pattern (20 bp):
GAGTTCGATTTCAACTTCAC
Found at i:1361106 original size:18 final size:18
Alignment explanation
Indices: 1361059--1361107 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
1361049 TTATTTTTGT
* *
1361059 TATTATTATTATTCTTTA
1 TATTATTACTATTATTTA
** *
1361077 TATTATCCCTATTATTTC
1 TATTATTACTATTATTTA
1361095 TATTATTACTATT
1 TATTATTACTATT
1361108 TTTTTTTGTG
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.12, G:0.00, T:0.61
Consensus pattern (18 bp):
TATTATTACTATTATTTA
Found at i:1361504 original size:26 final size:25
Alignment explanation
Indices: 1361465--1361523 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 25
1361455 TATTTCTCCC
*
1361465 TTTTACTTTTTGCTATTATTATTAT-T
1 TTTTA-TTTATGCTATTA-TATTATAT
1361491 TATTTATTTATGCTATTATATTATAT
1 T-TTTATTTATGCTATTATATTATAT
1361517 TTTTATT
1 TTTTATT
1361524 ATTATATTCG
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
25 12 0.40
26 14 0.47
27 4 0.13
ACGTcount: A:0.24, C:0.05, G:0.03, T:0.68
Consensus pattern (25 bp):
TTTTATTTATGCTATTATATTATAT
Found at i:1364870 original size:15 final size:15
Alignment explanation
Indices: 1364850--1364905 Score: 62
Period size: 15 Copynumber: 3.9 Consensus size: 15
1364840 TGGTTTTCTA
1364850 GAAAATGAATTACTG
1 GAAAATGAATTACTG
* *
1364865 GAAAATAAATTATTG
1 GAAAATGAATTACTG
**
1364880 GAATTTGAATT-CT-
1 GAAAATGAATTACTG
1364893 GAAAATGAATTAC
1 GAAAATGAATTAC
1364906 ATTTTTTGAA
Statistics
Matches: 32, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
13 9 0.28
14 2 0.06
15 21 0.66
ACGTcount: A:0.46, C:0.05, G:0.16, T:0.32
Consensus pattern (15 bp):
GAAAATGAATTACTG
Found at i:1365297 original size:23 final size:23
Alignment explanation
Indices: 1365248--1365298 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
1365238 GTGTTATATT
**
1365248 ATATTTTAAAAATATTAATTAGT
1 ATATTTTAAAAATATTAATTAAA
* * *
1365271 ATATTTTAAATATCTTTATTAAA
1 ATATTTTAAAAATATTAATTAAA
1365294 ATATT
1 ATATT
1365299 ATTAGATTAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (23 bp):
ATATTTTAAAAATATTAATTAAA
Found at i:1365375 original size:27 final size:28
Alignment explanation
Indices: 1365311--1365375 Score: 82
Period size: 27 Copynumber: 2.4 Consensus size: 28
1365301 TAGATTATTA
* *
1365311 TATTA-ATATTAAATATATAAATAATAT
1 TATTATATATTAAATATACAAATAAAAT
1365338 TATTCAT-TATTAAATATACAAA-AAAAT
1 TATT-ATATATTAAATATACAAATAAAAT
1365365 TATTATATATT
1 TATTATATATT
1365376 TATTAAAACA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
26 2 0.06
27 16 0.48
28 15 0.45
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (28 bp):
TATTATATATTAAATATACAAATAAAAT
Found at i:1365425 original size:23 final size:23
Alignment explanation
Indices: 1365386--1365438 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
1365376 TATTAAAACA
*
1365386 AAAATATAATATCTTATATTATT
1 AAAATATAATATATTATATTATT
*
1365409 AAAATATAAT-TGATTATTTTATT
1 AAAATATAATAT-ATTATATTATT
*
1365432 ATAATAT
1 AAAATAT
1365439 TACAAATAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
22 1 0.04
23 25 0.96
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (23 bp):
AAAATATAATATATTATATTATT
Found at i:1365440 original size:31 final size:29
Alignment explanation
Indices: 1365399--1365472 Score: 76
Period size: 31 Copynumber: 2.4 Consensus size: 29
1365389 ATATAATATC
* * *
1365399 TTATATTATTAAAATATAATTGATTATTTTA
1 TTATAATATTAAAATAGAA-T-ATTATATTA
1365430 TTATAATATTACAAATAGAATATTATATTA
1 TTATAATATTA-AAATAGAATATTATATTA
*
1365460 TAATAAATATTAA
1 TTAT-AATATTAA
1365473 TAAATATATT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
30 12 0.32
31 18 0.49
32 7 0.19
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.47
Consensus pattern (29 bp):
TTATAATATTAAAATAGAATATTATATTA
Found at i:1365752 original size:42 final size:42
Alignment explanation
Indices: 1365691--1365785 Score: 118
Period size: 42 Copynumber: 2.3 Consensus size: 42
1365681 TTCCTCCAAC
* ** ***
1365691 CAAACACTGGAAAACATTTTCCGGAAAACGAATTGTGTGAAA
1 CAAACACGGGAAAACATTTTCCAAAAAACGAATTACATGAAA
*
1365733 CAAACACGGGAAAATATTTTCCAAAAAACGAATTACATGAAA
1 CAAACACGGGAAAACATTTTCCAAAAAACGAATTACATGAAA
*
1365775 CAAACATGGGA
1 CAAACACGGGA
1365786 TTTCGGGAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.47, C:0.17, G:0.17, T:0.19
Consensus pattern (42 bp):
CAAACACGGGAAAACATTTTCCAAAAAACGAATTACATGAAA
Found at i:1367056 original size:21 final size:21
Alignment explanation
Indices: 1367032--1367096 Score: 60
Period size: 21 Copynumber: 3.1 Consensus size: 21
1367022 CTCAGTTTCA
1367032 AAATTCGCAACGCGAATATGT
1 AAATTCGCAACGCGAATATGT
** * * **
1367053 AAA-TCGCATTGCGATTTTCC
1 AAATTCGCAACGCGAATATGT
*
1367073 AATTTCGCAACGCGAATATGT
1 AAATTCGCAACGCGAATATGT
1367094 AAA
1 AAA
1367097 ATTTGTAATT
Statistics
Matches: 29, Mismatches: 14, Indels: 2
0.64 0.31 0.04
Matches are distributed among these distances:
20 13 0.45
21 16 0.55
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (21 bp):
AAATTCGCAACGCGAATATGT
Found at i:1367128 original size:20 final size:20
Alignment explanation
Indices: 1367103--1367151 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
1367093 TAAAATTTGT
1367103 AATTCGCAACACAGAAGTCA
1 AATTCGCAACACAGAAGTCA
1367123 AATTCGCAACACAGAAGTCA
1 AATTCGCAACACAGAAGTCA
1367143 AATTCGCAA
1 AATTCGCAA
1367152 AGCGCGTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.45, C:0.24, G:0.14, T:0.16
Consensus pattern (20 bp):
AATTCGCAACACAGAAGTCA
Found at i:1367183 original size:20 final size:19
Alignment explanation
Indices: 1367158--1367214 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
1367148 GCAAAGCGCG
*
1367158 TTTATTTTCGCAACGCGAAT
1 TTTATTTTCGCAACAC-AAT
*
1367178 TTTATTTTCGAAACACAAT
1 TTTATTTTCGCAACACAAT
* *
1367197 ATTAATTTCGCAACACAA
1 TTTATTTTCGCAACACAA
1367215 ATGTAAACAA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 18 0.56
20 14 0.44
ACGTcount: A:0.35, C:0.19, G:0.09, T:0.37
Consensus pattern (19 bp):
TTTATTTTCGCAACACAAT
Found at i:1367669 original size:20 final size:20
Alignment explanation
Indices: 1367632--1367669 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1367622 ATTCATTCAA
* *
1367632 GTTGCGATTTTCATTTTCGC
1 GTTGCGATTTTAAGTTTCGC
1367652 GTTGCGATTTTAAGTTTC
1 GTTGCGATTTTAAGTTTC
1367670 AGAAACTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATTTTAAGTTTCGC
Found at i:1369381 original size:21 final size:21
Alignment explanation
Indices: 1369338--1369387 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
1369328 GTTAGGGGAG
*
1369338 TTACGTGATG-AGGTCAATGCT
1 TTACGTGA-GAAGGTCAATACT
* *
1369359 TTGCGTGAGAAGGTCAGTACT
1 TTACGTGAGAAGGTCAATACT
1369380 TTACGTGA
1 TTACGTGA
1369388 CGACAATGGT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
20 1 0.04
21 23 0.96
ACGTcount: A:0.24, C:0.14, G:0.30, T:0.32
Consensus pattern (21 bp):
TTACGTGAGAAGGTCAATACT
Found at i:1369487 original size:63 final size:63
Alignment explanation
Indices: 1369379--1369500 Score: 147
Period size: 63 Copynumber: 1.9 Consensus size: 63
1369369 AGGTCAGTAC
* * * * *
1369379 TTTACGTGACGACAATGGTGCATGGCGTGATGAGGTATGGTCTTTACTTGGTGAGGTAGAGGT
1 TTTACGCGACGACAATGGTGCATGACGTGATGAGGTATGCTCTTTACGTGATGAGGTAGAGGT
* * * *
1369442 TTTACGCGATGACAATGGTGCTTTACGTGGTGAGGTAT-CTACTTTACGTGATGAGGTAG
1 TTTACGCGACGACAATGGTGCATGACGTGATGAGGTATGCT-CTTTACGTGATGAGGTAG
1369501 CCGCTCTACG
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
62 1 0.02
63 48 0.98
ACGTcount: A:0.21, C:0.12, G:0.34, T:0.33
Consensus pattern (63 bp):
TTTACGCGACGACAATGGTGCATGACGTGATGAGGTATGCTCTTTACGTGATGAGGTAGAGGT
Found at i:1369838 original size:42 final size:42
Alignment explanation
Indices: 1369791--1369893 Score: 143
Period size: 42 Copynumber: 2.5 Consensus size: 42
1369781 GCTCGATTCA
* * *
1369791 CCTATCATCATTCAAGAGGCCTCGCCTATCGTTCAAAAGGCC
1 CCTATCATCATTCAAGAGGCCCCGCCCACCGTTCAAAAGGCC
* *
1369833 CCTATCATCATTCAAGAGGCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCATTCAAGAGGCCCCGCCCACCGTTCAAAAGGCC
* *
1369875 CCTGTCATCGTTCAAGAGG
1 CCTATCATCATTCAAGAGG
1369894 TCATTCTCAC
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 54 1.00
ACGTcount: A:0.24, C:0.35, G:0.18, T:0.22
Consensus pattern (42 bp):
CCTATCATCATTCAAGAGGCCCCGCCCACCGTTCAAAAGGCC
Found at i:1369846 original size:21 final size:21
Alignment explanation
Indices: 1369791--1369893 Score: 102
Period size: 21 Copynumber: 4.9 Consensus size: 21
1369781 GCTCGATTCA
*
1369791 CCTATCATCATTCAAGAGGCC
1 CCTATCATCGTTCAAGAGGCC
* *
1369812 TCGC-CT-ATCGTTCAAAAGGCC
1 -C-CTATCATCGTTCAAGAGGCC
*
1369833 CCTATCATCATTCAAGAGGCC
1 CCTATCATCGTTCAAGAGGCC
** *
1369854 CCTCCCACCGTTCAAGAGGCC
1 CCTATCATCGTTCAAGAGGCC
*
1369875 CCTGTCATCGTTCAAGAGG
1 CCTATCATCGTTCAAGAGG
1369894 TCATTCTCAC
Statistics
Matches: 65, Mismatches: 13, Indels: 7
0.76 0.15 0.08
Matches are distributed among these distances:
19 1 0.02
20 2 0.03
21 59 0.91
22 2 0.03
23 1 0.02
ACGTcount: A:0.24, C:0.35, G:0.18, T:0.22
Consensus pattern (21 bp):
CCTATCATCGTTCAAGAGGCC
Found at i:1369910 original size:42 final size:42
Alignment explanation
Indices: 1369791--1369913 Score: 129
Period size: 42 Copynumber: 2.9 Consensus size: 42
1369781 GCTCGATTCA
* * * * * *
1369791 CCTATCATCATTCAAGAGGCCTCGCCTATCGTTCAAAAGGCC
1 CCTATCATCATTCAAGAGGCCACTCCCACCATTCAAGAGGCC
* *
1369833 CCTATCATCATTCAAGAGGCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCATTCAAGAGGCCACTCCCACCATTCAAGAGGCC
* * * * *
1369875 CCTGTCATCGTTCAAGAGGTCATTCTCACCATTCAAGAG
1 CCTATCATCATTCAAGAGGCCACTCCCACCATTCAAGAG
1369914 CCCGATTCAC
Statistics
Matches: 69, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 69 1.00
ACGTcount: A:0.25, C:0.34, G:0.17, T:0.24
Consensus pattern (42 bp):
CCTATCATCATTCAAGAGGCCACTCCCACCATTCAAGAGGCC
Found at i:1371319 original size:14 final size:14
Alignment explanation
Indices: 1371300--1371336 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
1371290 TGCTGTTTAA
1371300 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
1371314 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
1371328 TTGATTTGT
1 TTGATTTGT
1371337 TTAATTGATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.30, C:0.00, G:0.22, T:0.49
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Done.