Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001129.1 Hibiscus syriacus cultivar Beakdansim tig00002237_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: 21326069
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 89
Found at i:1075293 original size:17 final size:16
Alignment explanation
Indices: 1075257--1075289 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1075247 CGGAAAATAA
1075257 TAAATATTATTTATTT
1 TAAATATTATTTATTT
1075273 TAAATA-TATATTATTT
1 TAAATATTAT-TTATTT
1075289 T
1 T
1075290 TAAAATTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 3 0.19
16 13 0.81
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TAAATATTATTTATTT
Found at i:1075494 original size:18 final size:18
Alignment explanation
Indices: 1075474--1075509 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1075464 CTCAATATTT
1075474 AAAATTATCATATATTTTA
1 AAAATT-TCATATATTTTA
*
1075493 AAAATTTTATATATTTT
1 AAAATTTCATATATTTT
1075510 TATTAAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (18 bp):
AAAATTTCATATATTTTA
Found at i:1075517 original size:21 final size:20
Alignment explanation
Indices: 1075472--1075523 Score: 54
Period size: 19 Copynumber: 2.6 Consensus size: 20
1075462 CTCTCAATAT
*
1075472 TTAAAATTATCATATATTTTA
1 TTAAAATT-TTATATATTTTA
1075493 --AAAATTTTATATATTTTTA
1 TTAAAATTTTATATA-TTTTA
*
1075512 TTAAAAATTTAT
1 TTAAAATTTTAT
1075524 TTTCACCTCC
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
18 6 0.23
19 11 0.42
21 9 0.35
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (20 bp):
TTAAAATTTTATATATTTTA
Found at i:1076378 original size:24 final size:24
Alignment explanation
Indices: 1076333--1076390 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
1076323 TCATAATCAA
*
1076333 TAAAAATATAATAGATATATTT-T
1 TAAAAATATAATAGATACATTTAT
**
1076356 TAAAAATCATAATATTTACATTTAT
1 TAAAAAT-ATAATAGATACATTTAT
*
1076381 CAAAAATATA
1 TAAAAATATA
1076391 TTTTACTATT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
23 7 0.24
24 15 0.52
25 7 0.24
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (24 bp):
TAAAAATATAATAGATACATTTAT
Found at i:1077196 original size:66 final size:68
Alignment explanation
Indices: 1077022--1077199 Score: 245
Period size: 68 Copynumber: 2.6 Consensus size: 68
1077012 CATTTGCATC
* * *
1077022 GTTAGAAGTATAATAACATGAGATCATAATCACATATGAGAAGAATGATTTTACTATGTCTTAAG
1 GTTAGAAGTATAATAATATGAGACCATAATCACATATGAGAAGAATGAGTTTACTATGTCTTAAG
1077087 ATT
66 ATT
* * * * *
1077090 GTTAGAAGTATAACAATCTGAGACCATAATCACATTTGAGAAGAATGAGTTTATTTTGTCTT-AG
1 GTTAGAAGTATAATAATATGAGACCATAATCACATATGAGAAGAATGAGTTTACTATGTCTTAAG
1077154 AATT
66 -ATT
*
1077158 GTT-G-AGTATAATAATATGAGACCATAATCACATCTGAGAAGA
1 GTTAGAAGTATAATAATATGAGACCATAATCACATATGAGAAGA
1077200 TAAAATAAAC
Statistics
Matches: 98, Mismatches: 11, Indels: 4
0.87 0.10 0.04
Matches are distributed among these distances:
66 35 0.36
67 3 0.03
68 60 0.61
ACGTcount: A:0.40, C:0.10, G:0.17, T:0.33
Consensus pattern (68 bp):
GTTAGAAGTATAATAATATGAGACCATAATCACATATGAGAAGAATGAGTTTACTATGTCTTAAG
ATT
Found at i:1078316 original size:37 final size:37
Alignment explanation
Indices: 1078275--1078392 Score: 123
Period size: 37 Copynumber: 3.2 Consensus size: 37
1078265 AATTCGTATT
* *
1078275 TTAATATATTTATATTTAATCATATATAAATTTATAA
1 TTAATATATTCATATTTAATCATATATAAATTCATAA
*
1078312 TTAATATATTCCTATTTCAATC-TAATATAAATTCATAA
1 TTAATATATTCATATTT-AATCAT-ATATAAATTCATAA
* * * *
1078350 -TAATATATTCACATTTTAATTAAATATAAATTCTTAA
1 TTAATATATTCATA-TTTAATCATATATAAATTCATAA
*
1078387 CTAATA
1 TTAATA
1078393 GAATACTATC
Statistics
Matches: 68, Mismatches: 8, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
37 43 0.63
38 25 0.37
ACGTcount: A:0.45, C:0.08, G:0.00, T:0.47
Consensus pattern (37 bp):
TTAATATATTCATATTTAATCATATATAAATTCATAA
Found at i:1078534 original size:14 final size:14
Alignment explanation
Indices: 1078515--1078549 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
1078505 TTCTTTCACT
1078515 GAAAATATTTTTCA
1 GAAAATATTTTTCA
1078529 GAAAATATTTTTCA
1 GAAAATATTTTTCA
*
1078543 TAAAATA
1 GAAAATA
1078550 AATTACATCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.06, G:0.06, T:0.40
Consensus pattern (14 bp):
GAAAATATTTTTCA
Found at i:1078938 original size:35 final size:32
Alignment explanation
Indices: 1078815--1078940 Score: 91
Period size: 35 Copynumber: 3.8 Consensus size: 32
1078805 TATTGAAATA
* * *
1078815 AAAATATTA-TAAATTATATTAATTATTTATTA
1 AAAATATTATTATATTATATTAAATATTT-TTT
*
1078847 AAGTAATAGTATTATATTATATT--ATATTTTTT
1 AA--AATATTATTATATTATATTAAATATTTTTT
* *
1078879 AAAA-ACTAATTA-ATTTATTTTAAATATCTTTATT
1 AAAATA-TTATTATA-TTATATTAAATAT-TTT-TT
1078913 AAAATATTATTATATTAATATTAAATAT
1 AAAATATTATTATATT-ATATTAAATAT
1078941 ATAAATAATA
Statistics
Matches: 73, Mismatches: 9, Indels: 21
0.71 0.09 0.20
Matches are distributed among these distances:
29 2 0.03
30 12 0.16
32 10 0.14
33 8 0.11
34 19 0.26
35 22 0.30
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (32 bp):
AAAATATTATTATATTATATTAAATATTTTTT
Found at i:1079104 original size:20 final size:19
Alignment explanation
Indices: 1079081--1079137 Score: 60
Period size: 22 Copynumber: 2.8 Consensus size: 19
1079071 ATAATTGAGT
1079081 ATATTATTATAATATTAAAA
1 ATATTATTA-AATATTAAAA
*
1079101 ATATAATATTAAATTATTAGAA
1 ATAT--TATTAAA-TATTAAAA
*
1079123 ATATTAATAAATATT
1 ATATTATTAAATATT
1079138 TTTTAAAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
19 4 0.12
20 10 0.31
21 2 0.06
22 16 0.50
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (19 bp):
ATATTATTAAATATTAAAA
Found at i:1079110 original size:22 final size:22
Alignment explanation
Indices: 1079080--1079131 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 22
1079070 TATAATTGAG
*
1079080 TATATTATTATAA-TATTAAAAA
1 TATAATATTA-AATTATTAAAAA
*
1079102 TATAATATTAAATTATTAGAAA
1 TATAATATTAAATTATTAAAAA
1079124 TATTAATA
1 TA-TAATA
1079132 AATATTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 2 0.08
22 19 0.73
23 5 0.19
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (22 bp):
TATAATATTAAATTATTAAAAA
Found at i:1080594 original size:15 final size:15
Alignment explanation
Indices: 1080574--1080605 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
1080564 TTAAAATTAA
1080574 ATATAATTAAAAAAT
1 ATATAATTAAAAAAT
1080589 ATATAATTAAAAAAT
1 ATATAATTAAAAAAT
1080604 AT
1 AT
1080606 CAATTTTTTT
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:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
ATATAATTAAAAAAT
Found at i:1085712 original size:18 final size:18
Alignment explanation
Indices: 1085689--1085726 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
1085679 AAAACTAGCC
1085689 ACCTCGAGGTGACGAGTT
1 ACCTCGAGGTGACGAGTT
1085707 ACCTCGAGGTGACGAGTT
1 ACCTCGAGGTGACGAGTT
1085725 AC
1 AC
1085727 TGAGGATTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.24, C:0.24, G:0.32, T:0.21
Consensus pattern (18 bp):
ACCTCGAGGTGACGAGTT
Found at i:1086706 original size:18 final size:19
Alignment explanation
Indices: 1086685--1086725 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
1086675 ATTTATTTAT
*
1086685 TTTTATTTGTTTAT-AATA
1 TTTTATTTATTTATAAATA
*
1086703 TTTT-TTTATTTTTAAATA
1 TTTTATTTATTTATAAATA
1086721 TTTTA
1 TTTTA
1086726 GATGGTATCA
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (19 bp):
TTTTATTTATTTATAAATA
Found at i:1096513 original size:2 final size:2
Alignment explanation
Indices: 1096502--1096540 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
1096492 CAAATACTAC
1096502 AT AT -T 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
1096541 TAGTTAGGGA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1098909 original size:30 final size:30
Alignment explanation
Indices: 1098869--1098927 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
1098859 GATCAAACAG
1098869 ATCCAGATCCAAAAGAAAAAAGAAAATTAT
1 ATCCAGATCCAAAAGAAAAAAGAAAATTAT
*
1098899 ATCCATATCCAAAAGAAAAAAGAAAATTA
1 ATCCAGATCCAAAAGAAAAAAGAAAATTA
1098928 AATCTTTCAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.61, C:0.14, G:0.08, T:0.17
Consensus pattern (30 bp):
ATCCAGATCCAAAAGAAAAAAGAAAATTAT
Found at i:1101957 original size:13 final size:13
Alignment explanation
Indices: 1101939--1101963 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1101929 TGCGAAAATG
1101939 ATTTTACACAAGT
1 ATTTTACACAAGT
1101952 ATTTTACACAAG
1 ATTTTACACAAG
1101964 GGTAGTGATA
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:0.40, C:0.16, G:0.08, T:0.36
Consensus pattern (13 bp):
ATTTTACACAAGT
Found at i:1107580 original size:20 final size:20
Alignment explanation
Indices: 1107557--1107627 Score: 108
Period size: 20 Copynumber: 3.5 Consensus size: 20
1107547 TTGAGTGCGT
1107557 AGTATCGATACTCTAGGTGT-
1 AGTATCGATACTCTAGG-GTA
1107577 AGTATCGATACTCTAGGGTA
1 AGTATCGATACTCTAGGGTA
*
1107597 AGTTTCGATACTCTAGGGTA
1 AGTATCGATACTCTAGGGTA
*
1107617 AGTTTCGATAC
1 AGTATCGATAC
1107628 CAAAATGGAT
Statistics
Matches: 49, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
19 2 0.04
20 47 0.96
ACGTcount: A:0.27, C:0.15, G:0.24, T:0.34
Consensus pattern (20 bp):
AGTATCGATACTCTAGGGTA
Found at i:1107671 original size:19 final size:19
Alignment explanation
Indices: 1107647--1107725 Score: 88
Period size: 19 Copynumber: 4.1 Consensus size: 19
1107637 TTCTGTTGCT
*
1107647 GAAAGTATCAATACTCTTG
1 GAAAGTATCGATACTCTTG
1107666 GAAAGTATCGATACT-TTGAG
1 GAAAGTATCGATACTCTT--G
* *
1107686 GTAAAGTTTTGATACTCTTG
1 G-AAAGTATCGATACTCTTG
*
1107706 AAAAGTATCGATACTCTTG
1 GAAAGTATCGATACTCTTG
1107725 G
1 G
1107726 CTTGAAATCC
Statistics
Matches: 49, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
18 2 0.04
19 30 0.61
20 3 0.06
21 12 0.24
22 2 0.04
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.34
Consensus pattern (19 bp):
GAAAGTATCGATACTCTTG
Found at i:1108290 original size:27 final size:24
Alignment explanation
Indices: 1108257--1108305 Score: 71
Period size: 27 Copynumber: 1.9 Consensus size: 24
1108247 AGGAGGGAAG
1108257 AAGAGAAAATGAGAAGATAGGAAAATA
1 AAGAGAAAAT-AG-AGAT-GGAAAATA
1108284 AAGAGAAAATAGAGATGGAAAA
1 AAGAGAAAATAGAGATGGAAAA
1108306 GATAAAAAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 6 0.27
25 4 0.18
26 2 0.09
27 10 0.45
ACGTcount: A:0.63, C:0.00, G:0.27, T:0.10
Consensus pattern (24 bp):
AAGAGAAAATAGAGATGGAAAATA
Found at i:1112178 original size:12 final size:12
Alignment explanation
Indices: 1112161--1112185 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1112151 TTACTATTAT
1112161 TGATTTTGTTTC
1 TGATTTTGTTTC
1112173 TGATTTTGTTTC
1 TGATTTTGTTTC
1112185 T
1 T
1112186 ATTACTGAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.08, G:0.16, T:0.68
Consensus pattern (12 bp):
TGATTTTGTTTC
Found at i:1115560 original size:17 final size:17
Alignment explanation
Indices: 1115535--1115576 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
1115525 GTTATAATCC
*
1115535 AATTTCTCCTTAAAATA
1 AATTCCTCCTTAAAATA
*
1115552 AATTCCTCCTTAAAATC
1 AATTCCTCCTTAAAATA
1115569 AATTCCTC
1 AATTCCTC
1115577 AAACCTTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.36, C:0.26, G:0.00, T:0.38
Consensus pattern (17 bp):
AATTCCTCCTTAAAATA
Found at i:1117905 original size:13 final size:13
Alignment explanation
Indices: 1117889--1117919 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1117879 GTCAACGGGT
*
1117889 CGGGTCGGGTCAA
1 CGGGTCGGGTAAA
1117902 CGGGTCGGGTAAA
1 CGGGTCGGGTAAA
1117915 CGGGT
1 CGGGT
1117920 AAACGGGTCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.16, C:0.19, G:0.48, T:0.16
Consensus pattern (13 bp):
CGGGTCGGGTAAA
Found at i:1117952 original size:10 final size:10
Alignment explanation
Indices: 1117932--1117995 Score: 80
Period size: 9 Copynumber: 6.6 Consensus size: 10
1117922 ACGGGTCGTG
1117932 ACCGGTC-AA
1 ACCGGTCAAA
1117941 ACCGGTCAAA
1 ACCGGTCAAA
1117951 ACCGGTTCAAA
1 ACCGG-TCAAA
*
1117962 ACCGGT-TAA
1 ACCGGTCAAA
*
1117971 ACCGGT-TAA
1 ACCGGTCAAA
1117980 ACCGGTCAAA
1 ACCGGTCAAA
1117990 ACCGGT
1 ACCGGT
1117996 TTCAAGCGTT
Statistics
Matches: 50, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
9 24 0.48
10 16 0.32
11 10 0.20
ACGTcount: A:0.34, C:0.28, G:0.22, T:0.16
Consensus pattern (10 bp):
ACCGGTCAAA
Found at i:1125118 original size:18 final size:18
Alignment explanation
Indices: 1125095--1125135 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
1125085 CACCGGTCAA
1125095 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
1125113 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
1125131 CGGGT
1 CGGGT
1125136 AAACGGGTCG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.10, C:0.22, G:0.51, T:0.17
Consensus pattern (18 bp):
CGGGTCGGGTCAACGGGT
Found at i:1125135 original size:13 final size:13
Alignment explanation
Indices: 1125089--1125118 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
1125079 GAATAGCACC
1125089 GGTCAACGGGTCG
1 GGTCAACGGGTCG
1125102 GGTCAACGGGTCG
1 GGTCAACGGGTCG
1125115 GGTC
1 GGTC
1125119 GGGTCAACGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.13, C:0.23, G:0.47, T:0.17
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:1125140 original size:13 final size:13
Alignment explanation
Indices: 1125113--1125145 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
1125103 GTCAACGGGT
*
1125113 CGGGTCGGGTCAA
1 CGGGTCGGGTAAA
1125126 CGGGTCGGGTAAA
1 CGGGTCGGGTAAA
1125139 CGGGTCG
1 CGGGTCG
1125146 TGACCGGTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.15, C:0.21, G:0.48, T:0.15
Consensus pattern (13 bp):
CGGGTCGGGTAAA
Found at i:1125155 original size:31 final size:31
Alignment explanation
Indices: 1125086--1125156 Score: 106
Period size: 31 Copynumber: 2.3 Consensus size: 31
1125076 CCAGAATAGC
*
1125086 ACCGGTCAACGGGTCGGGTCAACGGGTCGGG
1 ACCGGTCAACGGGTCGGGTAAACGGGTCGGG
* * *
1125117 TCGGGTCAACGGGTCGGGTAAACGGGTCGTG
1 ACCGGTCAACGGGTCGGGTAAACGGGTCGGG
1125148 ACCGGTCAA
1 ACCGGTCAA
1125157 ACCGGTCAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.18, C:0.24, G:0.42, T:0.15
Consensus pattern (31 bp):
ACCGGTCAACGGGTCGGGTAAACGGGTCGGG
Found at i:1132999 original size:29 final size:27
Alignment explanation
Indices: 1132950--1133008 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 27
1132940 CTAGTTGCAC
*
1132950 AAAAAATTCGAATATCCGATTTTGTGAA
1 AAAAAATTCGAATATCCGA-TTTGGGAA
*
1132978 AAAAAATATCCGAA-ATCGGATTTGGGAA
1 AAAAAAT-T-CGAATATCCGATTTGGGAA
1133006 AAA
1 AAA
1133009 TCGGTTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 17 0.63
29 6 0.22
30 4 0.15
ACGTcount: A:0.47, C:0.10, G:0.17, T:0.25
Consensus pattern (27 bp):
AAAAAATTCGAATATCCGATTTGGGAA
Found at i:1134052 original size:31 final size:30
Alignment explanation
Indices: 1134017--1134091 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 30
1134007 TGTAAGATTG
*
1134017 TATATGAATAGATTTATAAAATGTAATATGT
1 TATAT-AATAGATTTATAAAATATAATATGT
* *
1134048 TATATAGATGGGTTTATAAAATATAATATGT
1 TATATA-ATAGATTTATAAAATATAATATGT
*
1134079 TAAATAAATAGAT
1 TATAT-AATAGAT
1134092 ATTGACAATT
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
30 1 0.03
31 34 0.94
32 1 0.03
ACGTcount: A:0.47, C:0.00, G:0.13, T:0.40
Consensus pattern (30 bp):
TATATAATAGATTTATAAAATATAATATGT
Found at i:1147354 original size:52 final size:52
Alignment explanation
Indices: 1147294--1147466 Score: 319
Period size: 52 Copynumber: 3.3 Consensus size: 52
1147284 AAATGAATCC
1147294 TTCAGCTAGCCGAACAAAGGCAATTATAAGATATATGTACAATAAAGCTGAA
1 TTCAGCTAGCCGAACAAAGGCAATTATAAGATATATGTACAATAAAGCTGAA
* *
1147346 TTTAGCTAGCCGAACAAAGGCAATTATAAGATTTATGTACAATAAAGCTGAA
1 TTCAGCTAGCCGAACAAAGGCAATTATAAGATATATGTACAATAAAGCTGAA
1147398 TTCAGCTAGCCGAACAAAGGCAATTATAAGATATATGTACAATAAAGCTGAA
1 TTCAGCTAGCCGAACAAAGGCAATTATAAGATATATGTACAATAAAGCTGAA
*
1147450 TTCAGCTAGCCAAACAA
1 TTCAGCTAGCCGAACAA
1147467 TGAGAAATTA
Statistics
Matches: 116, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 116 1.00
ACGTcount: A:0.43, C:0.16, G:0.17, T:0.24
Consensus pattern (52 bp):
TTCAGCTAGCCGAACAAAGGCAATTATAAGATATATGTACAATAAAGCTGAA
Found at i:1148280 original size:14 final size:14
Alignment explanation
Indices: 1148250--1148294 Score: 67
Period size: 14 Copynumber: 3.3 Consensus size: 14
1148240 ATTGAGAAAA
1148250 ACATACAT-CAT-C
1 ACATACATACATAC
1148262 ACATACATACATAC
1 ACATACATACATAC
1148276 ACATACATACATGAC
1 ACATACATACAT-AC
1148291 ACAT
1 ACAT
1148295 GAAATTTGCA
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
12 8 0.27
13 3 0.10
14 13 0.43
15 6 0.20
ACGTcount: A:0.47, C:0.29, G:0.02, T:0.22
Consensus pattern (14 bp):
ACATACATACATAC
Found at i:1148940 original size:67 final size:66
Alignment explanation
Indices: 1148835--1148994 Score: 196
Period size: 67 Copynumber: 2.4 Consensus size: 66
1148825 ACAATTTACA
* * * * *
1148835 ATCTTTGAGTCTTGTTCTCTTAAAACTAAATTTTGTCTCTCTTGAGACAGTTTCTCTTAAAACAA
1 ATCTTTGAGTCGT-TTCCCTTGAAACTAAATTTTGTCTCTCCTGAGACAATTTCTCTTAAAAC--
1148900 AATC
63 AATC
* * * *
1148904 ATCTTTGAGTCGTTTCCCTTGAAA-TGAATTTTGTCTCTCCTGATATAATTTCTCTTGAAACAAT
1 ATCTTTGAGTCGTTTCCCTTGAAACTAAATTTTGTCTCTCCTGAGACAATTTCTCTTAAAACAAT
1148968 C
66 C
1148969 ATCTTTGAGTCTGTTTCCCTTGAAAC
1 ATCTTTGAGTC-GTTTCCCTTGAAAC
1148995 CATTATCCCT
Statistics
Matches: 80, Mismatches: 9, Indels: 6
0.84 0.09 0.06
Matches are distributed among these distances:
65 15 0.19
66 13 0.16
67 31 0.39
68 9 0.11
69 12 0.15
ACGTcount: A:0.26, C:0.20, G:0.12, T:0.42
Consensus pattern (66 bp):
ATCTTTGAGTCGTTTCCCTTGAAACTAAATTTTGTCTCTCCTGAGACAATTTCTCTTAAAACAAT
C
Found at i:1149075 original size:40 final size:41
Alignment explanation
Indices: 1149020--1149121 Score: 116
Period size: 43 Copynumber: 2.5 Consensus size: 41
1149010 TGGTTTGTCA
** * *
1149020 TCCTCATCTTGTAGGAACCGTGTCATCCC-ATGACCAGATC
1 TCCTCATCACGTAGGAACCGTGTCACCCCAATAACCAGATC
* * *
1149060 TCCTCATCACGTAGGAGCCGTGTCACCCCTAGATAACCAGGTG
1 TCCTCATCACGTAGGAACCGTGTCACCCC-A-ATAACCAGATC
1149103 TCCTCATCACGTAGGAACC
1 TCCTCATCACGTAGGAACC
1149122 ATGTTATCAT
Statistics
Matches: 51, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
40 25 0.49
43 26 0.51
ACGTcount: A:0.24, C:0.33, G:0.20, T:0.24
Consensus pattern (41 bp):
TCCTCATCACGTAGGAACCGTGTCACCCCAATAACCAGATC
Found at i:1149330 original size:134 final size:132
Alignment explanation
Indices: 1149002--1149617 Score: 613
Period size: 131 Copynumber: 4.6 Consensus size: 132
1148992 AACCATTATC
* * ** * * *
1149002 CCTAAAGATGGTTTGTCATCCTCATCTTGTAGGAACCGTGTCATCC-CATGACCAGATCTCCTCA
1 CCTAAAGATGGCTT-ACATCCTCATCACGTAGGAACCGTGTCATCCAC-CGACCATACCTCCTCA
** *
1149066 TCACGTAGGAGCCGTGTCACCCCTAGATAACCAGGTGTCCTCATCACGTAGGAACCATGTTATCA
64 TCACGTAGGAGCCGTGTCACCCCTAGATAACCAGCCGTCCTCATCACATAGGAA-CATGTTATCA
1149131 TC-TT
128 TCATT
1149135 --TAAAGATGG-TCTACCATCCTCATCACGTAGGAACCGTGTCATCCACCGACCATACCTCCTCA
1 CCTAAAGATGGCT-TA-CATCCTCATCACGTAGGAACCGTGTCATCCACCGACCATACCTCCTCA
* * * **
1149197 TCATGTGGGAGCCGTGTCACCCCTAGATAACTAGCCGTCCTCATCGTATAGGAAC-TGAGTTATC
64 TCACGTAGGAGCCGTGTCACCCCTAGATAACCAGCCGTCCTCATCACATAGGAACAT--GTTATC
*
1149261 ACCATT
127 ATCATT
* * *
1149267 CCTAAAGATGGCGTGCAATCCTCATCACGTAGGAACCATGTCATCCACCGACCATACCTCCTCAT
1 CCTAAAGATGGCTTAC-ATCCTCATCACGTAGGAACCGTGTCATCCACCGACCATACCTCCTCAT
* * * * *
1149332 CACGTAGGAGCAGTGTCACCCCTAAATAACCAGCCGTCCTCATCATATAGGAATCGTGTTAGCAT
65 CACGTAGGAGCCGTGTCACCCCTAGATAACCAGCCGTCCTCATCACATAGGAA-CATGTTATCAT
1149397 C---
129 CATT
* * * *
1149398 CCTAAAGATGGCTTACCATCCTCATCACATAGGAACCGTGTCATCCACCAACCAGACCTCTTCAT
1 CCTAAAGATGGCTTA-CATCCTCATCACGTAGGAACCGTGTCATCCACCGACCATACCTCCTCAT
* * * * *
1149463 CACGTAGGAGCCATGTCACCCTTAGATAACTAGCCGTCCTCATCGCGTAGGAACAATGTTATCAT
65 CACGTAGGAGCCGTGTCACCCCTAGATAACCAGCCGTCCTCATCACATAGGAAC-ATGTTATCAT
*
1149528 TATT
129 CATT
* * ** ** ** *
1149532 CCCTAAAGATGGCCAATT-CGTCCTCGTCACGTAGGAACAATGTCATCCTTCGACCATATATCTT
1 -CCTAAAGATGG-C--TTACATCCTCATCACGTAGGAACCGTGTCATCCACCGACCATACCTCCT
* * *
1149596 CATCACTTAGGAGTCGAGTCAC
62 CATCACGTAGGAGCCGTGTCAC
1149618 TCTTAGACGA
Statistics
Matches: 403, Mismatches: 59, Indels: 39
0.80 0.12 0.08
Matches are distributed among these distances:
129 1 0.00
130 3 0.01
131 214 0.53
132 4 0.01
133 1 0.00
134 111 0.28
135 12 0.03
136 55 0.14
138 2 0.00
ACGTcount: A:0.27, C:0.31, G:0.18, T:0.25
Consensus pattern (132 bp):
CCTAAAGATGGCTTACATCCTCATCACGTAGGAACCGTGTCATCCACCGACCATACCTCCTCATC
ACGTAGGAGCCGTGTCACCCCTAGATAACCAGCCGTCCTCATCACATAGGAACATGTTATCATCA
TT
Found at i:1149482 original size:265 final size:264
Alignment explanation
Indices: 1149000--1149608 Score: 747
Period size: 265 Copynumber: 2.3 Consensus size: 264
1148990 GAAACCATTA
** ** * * *
1149000 TCCCTAAAGATGGTTTGTCATCCTCATCTTGTAGGAACCGTGTCATCCCATGACCAGATCTCCTC
1 TCCCTAAAGATGGCATG-CATCCTCATCACGTAGGAACCATGTCATCCC-CGACCATATCTCCTC
* * ** * *
1149065 ATCACGTAGGAGCCGTGTCACCCCTAGATAACCAGGTGTCCTCATCACGTAGGAACCATGTTATC
64 ATCACGTAGGAGCAGTGTCACCCCTAAATAACCAGCCGTCCTCATCACATAGGAACCATGTTAGC
** * * *
1149130 ATCTTTAAAGATGGTCTACCATCCTCATCACGTAGGAACCGTGTCATCCACCGACCATACCTCCT
129 ATCCCTAAAGATGGTCTACCATCCTCATCACATAGGAACCGTGTCATCCACCAACCAGACCTCCT
* * * * *
1149195 CATCATGTGGGAGCCGTGTCACCCCTAGATAACTAGCCGTCCTCATCGTATAGGAACTGA-GTTA
194 CATCACGTAGGAGCCATGTCACCCCTAGATAACTAGCCGTCCTCATCGCATAGGAAC-AATGTTA
1149259 TCACCAT
258 TCACCAT
* *
1149266 T-CCTAAAGATGGCGTGCAATCCTCATCACGTAGGAACCATGTCATCCACCGACCATACCTCCTC
1 TCCCTAAAGATGGCATGC-ATCCTCATCACGTAGGAACCATGTCATCC-CCGACCATATCTCCTC
* * *
1149330 ATCACGTAGGAGCAGTGTCACCCCTAAATAACCAGCCGTCCTCATCATATAGGAATCGTGTTAGC
64 ATCACGTAGGAGCAGTGTCACCCCTAAATAACCAGCCGTCCTCATCACATAGGAACCATGTTAGC
*
1149395 ATCCCTAAAGATGG-CTTACCATCCTCATCACATAGGAACCGTGTCATCCACCAACCAGACCTCT
129 ATCCCTAAAGATGGTC-TACCATCCTCATCACATAGGAACCGTGTCATCCACCAACCAGACCTCC
* *
1149459 TCATCACGTAGGAGCCATGTCACCCTTAGATAACTAGCCGTCCTCATCGCGTAGGAACAATGTTA
193 TCATCACGTAGGAGCCATGTCACCCCTAGATAACTAGCCGTCCTCATCGCATAGGAACAATGTTA
**
1149524 TCATTAT
258 TCACCAT
* * * * * * *
1149531 TCCCTAAAGATGGCCAATTCGTCCTCGTCACGTAGGAACAATGTCATCCTTCGACCATATATCTT
1 TCCCTAAAGATGG-C-ATGCATCCTCATCACGTAGGAACCATGTCATCC-CCGACCATATCTCCT
*
1149596 CATCACTTAGGAG
63 CATCACGTAGGAG
1149609 TCGAGTCACT
Statistics
Matches: 293, Mismatches: 43, Indels: 13
0.84 0.12 0.04
Matches are distributed among these distances:
264 3 0.01
265 225 0.77
266 13 0.04
267 50 0.17
268 2 0.01
ACGTcount: A:0.27, C:0.31, G:0.17, T:0.25
Consensus pattern (264 bp):
TCCCTAAAGATGGCATGCATCCTCATCACGTAGGAACCATGTCATCCCCGACCATATCTCCTCAT
CACGTAGGAGCAGTGTCACCCCTAAATAACCAGCCGTCCTCATCACATAGGAACCATGTTAGCAT
CCCTAAAGATGGTCTACCATCCTCATCACATAGGAACCGTGTCATCCACCAACCAGACCTCCTCA
TCACGTAGGAGCCATGTCACCCCTAGATAACTAGCCGTCCTCATCGCATAGGAACAATGTTATCA
CCAT
Found at i:1149831 original size:12 final size:12
Alignment explanation
Indices: 1149814--1149873 Score: 56
Period size: 12 Copynumber: 5.2 Consensus size: 12
1149804 TCTAAAAATG
1149814 TTATTAATTATA
1 TTATTAATTATA
1149826 TTATT-ATTATTA
1 TTATTAATTA-TA
1149838 TTATTAA-TAT-
1 TTATTAATTATA
*
1149848 TAATTAATTA-A
1 TTATTAATTATA
*
1149859 TTAATTAATAATA
1 TT-ATTAATTATA
1149872 TT
1 TT
1149874 TTTTTGCAGG
Statistics
Matches: 39, Mismatches: 3, Indels: 11
0.74 0.06 0.21
Matches are distributed among these distances:
10 6 0.15
11 8 0.21
12 21 0.54
13 4 0.10
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (12 bp):
TTATTAATTATA
Found at i:1153179 original size:29 final size:29
Alignment explanation
Indices: 1153137--1153195 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
1153127 ATTTTCACCT
1153137 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
1153166 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
1153195 A
1 A
1153196 TTAATTTAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGACATCAA
Found at i:1157765 original size:29 final size:29
Alignment explanation
Indices: 1157723--1157781 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
1157713 ATTTTTACCT
1157723 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
1157752 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
1157781 A
1 A
1157782 TTAATTTAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGACATCAA
Found at i:1164773 original size:10 final size:10
Alignment explanation
Indices: 1164758--1164782 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1164748 ATATAACTTG
1164758 TTCATGTTCA
1 TTCATGTTCA
1164768 TTCATGTTCA
1 TTCATGTTCA
1164778 TTCAT
1 TTCAT
1164783 TTAAACGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.20, C:0.20, G:0.08, T:0.52
Consensus pattern (10 bp):
TTCATGTTCA
Found at i:1164832 original size:13 final size:13
Alignment explanation
Indices: 1164802--1164860 Score: 52
Period size: 13 Copynumber: 4.7 Consensus size: 13
1164792 AAACGAACAC
*
1164802 AAACGAACAAACAT
1 AAACGAACATA-AT
*
1164816 AAATGAACATAAT
1 AAACGAACATAAT
*
1164829 AAATG-A-AT-AT
1 AAACGAACATAAT
*
1164839 AAACGAACACAAT
1 AAACGAACATAAT
1164852 AAACGAACA
1 AAACGAACA
1164861 ACACAAACAC
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
10 6 0.16
11 3 0.08
12 2 0.05
13 18 0.47
14 9 0.24
ACGTcount: A:0.63, C:0.15, G:0.08, T:0.14
Consensus pattern (13 bp):
AAACGAACATAAT
Found at i:1169289 original size:22 final size:21
Alignment explanation
Indices: 1169261--1169324 Score: 73
Period size: 20 Copynumber: 3.1 Consensus size: 21
1169251 TAGATGATTC
1169261 TTTTTTCTCTTCTTTCCTC-CTT
1 TTTTTTCTC-T-TTTCCTCTCTT
1169283 TTTTTTCTCTTTTCCTCTCTT
1 TTTTTTCTCTTTTCCTCTCTT
*
1169304 TTTTGTCT-TTTTCC-CT-TT
1 TTTTTTCTCTTTTCCTCTCTT
1169322 TTT
1 TTT
1169325 CTTGTCCTAA
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
18 5 0.12
19 2 0.05
20 13 0.32
21 11 0.28
22 9 0.22
ACGTcount: A:0.00, C:0.27, G:0.02, T:0.72
Consensus pattern (21 bp):
TTTTTTCTCTTTTCCTCTCTT
Found at i:1169329 original size:20 final size:18
Alignment explanation
Indices: 1169279--1169330 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 18
1169269 CTTCTTTCCT
*
1169279 CCTTTTTTTTCTCTTTTC
1 CCTTTTTTTTGTCTTTTC
*
1169297 CTCTCTTTTTTGTCTTTTTC
1 C-CTTTTTTTTGTC-TTTTC
1169317 CCTTTTTTCTTGTC
1 CCTTTTTT-TTGTC
1169331 CTAAAGTGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
18 1 0.04
19 16 0.57
20 11 0.39
ACGTcount: A:0.00, C:0.27, G:0.04, T:0.69
Consensus pattern (18 bp):
CCTTTTTTTTGTCTTTTC
Found at i:1173712 original size:105 final size:105
Alignment explanation
Indices: 1173593--1174070 Score: 722
Period size: 105 Copynumber: 4.6 Consensus size: 105
1173583 TTTGTCGGAT
* * *
1173593 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTCGATTCACCTCCTTCTGGGGTGAATTTGAAA
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGTTCACCTCCTTCTGGGGTGGATTTGAAA
*
1173658 GGAACATGCTCTTCTCATTACGAACCTTCTCCTTTAAGAC
66 GGAACAGGCTCTTCTCATTACGAACCTTCTCCTTTAAGAC
*
1173698 GAGTTCTTCTCATTATGAAACTCTTCTGGAAATGTTGGTTCACCTCCTTC-GCGGTGGATTTGAA
1 GAGTTCTTCTCATTATG-AACTCTTCTGGAAATGTTGGTTCACCTCCTTCTGGGGTGGATTTGAA
** *
1173762 AGGAACATACTCTTTTCATTACGAACCTTCTCCTTTAAGAC
65 AGGAACAGGCTCTTCTCATTACGAACCTTCTCCTTTAAGAC
1173803 GAGTTCTTCTCATTATGAACTCTTCTGGAAA--TTGGTTCACCT-CTTCTGCGGGGGTGGATTTG
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGTTCACCTCCTTCT---GGGGTGGATTTG
*
1173865 AAAGGAACAGGCTCTTCTCATTACGAACCTTCTCCTTTAGGAC
63 AAAGGAACAGGCTCTTCTCATTACGAACCTTCTCCTTTAAGAC
* *
1173908 GAGTTCTT-TCATTATGAACTCTTCTAGAAATGTTGGTTCACCTCCTTCT-GCGTGGA-TTGAAA
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGTTCACCTCCTTCTGGGGTGGATTTGAAA
* *
1173970 GG-ATAGGCT-TTCTCATTACGAACCTTCTCCTTTAGGAC
66 GGAACAGGCTCTTCTCATTACGAACCTTCTCCTTTAAGAC
* *
1174008 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGGTCACCTCCTTCTGTGGTGGATTTGA
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGTTCACCTCCTTCTGGGGTGGATTTGA
1174071 TTGTTATTGA
Statistics
Matches: 344, Mismatches: 18, Indels: 24
0.89 0.05 0.06
Matches are distributed among these distances:
100 37 0.11
101 49 0.14
102 24 0.07
103 10 0.03
104 35 0.10
105 143 0.42
106 41 0.12
107 5 0.01
ACGTcount: A:0.22, C:0.22, G:0.19, T:0.36
Consensus pattern (105 bp):
GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGTTCACCTCCTTCTGGGGTGGATTTGAAA
GGAACAGGCTCTTCTCATTACGAACCTTCTCCTTTAAGAC
Found at i:1175016 original size:17 final size:17
Alignment explanation
Indices: 1174980--1175031 Score: 61
Period size: 17 Copynumber: 2.9 Consensus size: 17
1174970 TCGAACCCTT
*
1174980 ATTTTTCTTTTTTCTTTTC
1 ATTTTT-TTCTTT-TTTTC
1174999 A-TTTTTTCATTTTTTTC
1 ATTTTTTTC-TTTTTTTC
1175016 ATTTTTTTCTTTTTTT
1 ATTTTTTTCTTTTTTT
1175032 TTTCAAGCAT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
17 15 0.50
18 14 0.47
19 1 0.03
ACGTcount: A:0.08, C:0.12, G:0.00, T:0.81
Consensus pattern (17 bp):
ATTTTTTTCTTTTTTTC
Found at i:1175028 original size:8 final size:9
Alignment explanation
Indices: 1174994--1175031 Score: 62
Period size: 9 Copynumber: 4.4 Consensus size: 9
1174984 TTCTTTTTTC
1174994 TTTTCA-TT
1 TTTTCATTT
1175002 TTTTCATTT
1 TTTTCATTT
1175011 TTTTCATTT
1 TTTTCATTT
1175020 TTTTC-TTT
1 TTTTCATTT
1175028 TTTT
1 TTTT
1175032 TTTCAAGCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
8 13 0.45
9 16 0.55
ACGTcount: A:0.08, C:0.11, G:0.00, T:0.82
Consensus pattern (9 bp):
TTTTCATTT
Found at i:1175032 original size:9 final size:9
Alignment explanation
Indices: 1174981--1175032 Score: 52
Period size: 9 Copynumber: 5.6 Consensus size: 9
1174971 CGAACCCTTA
1174981 TTTTTCTTT
1 TTTTTCTTT
1174990 TTTCTT-TTCAT
1 TTT-TTCTT--T
*
1175001 TTTTTCATT
1 TTTTTCTTT
*
1175010 TTTTTCATT
1 TTTTTCTTT
1175019 TTTTTCTTT
1 TTTTTCTTT
1175028 TTTTT
1 TTTTT
1175033 TTCAAGCATA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
9 28 0.76
10 4 0.11
11 5 0.14
ACGTcount: A:0.06, C:0.12, G:0.00, T:0.83
Consensus pattern (9 bp):
TTTTTCTTT
Found at i:1192191 original size:23 final size:26
Alignment explanation
Indices: 1192156--1192211 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 26
1192146 AAAATATACA
* *
1192156 TAAAAAGATACATTAA-GT-TAAAAT
1 TAAAAAGAAACATGAATGTATAAAAT
1192180 TAAAAA-AAACATGAATGTATAAAAT
1 TAAAAAGAAACATGAATGTATAAAAT
*
1192205 TTAAAAG
1 TAAAAAG
1192212 TAAATAAAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
23 7 0.27
24 8 0.31
25 11 0.42
ACGTcount: A:0.61, C:0.04, G:0.09, T:0.27
Consensus pattern (26 bp):
TAAAAAGAAACATGAATGTATAAAAT
Found at i:1193685 original size:48 final size:48
Alignment explanation
Indices: 1193585--1194287 Score: 567
Period size: 48 Copynumber: 14.6 Consensus size: 48
1193575 TGGGTTTCCT
* * * * * * **
1193585 CATCTCTTCGTGAAGGTTAAATCTCAAGAACTTTGACGATTTGCCCCGT
1 CATCTCTTCGTGGAGATCAAATCTGAA-AACTTTGATGATTTGTCCCAC
* * *
1193634 CATCTCTTCAG-GGAGATAAAATCTGAAAACTTTGATGATTTGTTCCAT
1 CATCTCTTC-GTGGAGATCAAATCTGAAAACTTTGATGATTTGTCCCAC
* * * * *
1193682 CATCTCTTCATGGA-ATCATATATGAAAAACCTTGATGATTCG-CTCCAC
1 CATCTCTTCGTGGAGATCAAATCTG-AAAACTTTGATGATTTGTC-CCAC
* * * * *
1193730 CATCACTTCGTGGAAATCCAATCTGGAAACTTTGGTGATTTGTCCCAC
1 CATCTCTTCGTGGAGATCAAATCTGAAAACTTTGATGATTTGTCCCAC
* * * *
1193778 CAACTCTTCTTGGAGATCAAATCTGAAAACTTTGACGATCTT-CCCCAC
1 CATCTCTTCGTGGAGATCAAATCTGAAAACTTTGATGAT-TTGTCCCAC
*** * * * * *
1193826 CATCTCTTCGCAAATATCAAATATGAAAATTTTGATGATTTGTTCCAT
1 CATCTCTTCGTGGAGATCAAATCTGAAAACTTTGATGATTTGTCCCAC
* * * * * * *
1193874 TATCTCTTCATGGAAATCAAATTTGAAAAACCTTGATGATTCGTTCCAC
1 CATCTCTTCGTGGAGATCAAATCTG-AAAACTTTGATGATTTGTCCCAC
* * * *
1193923 CATCACTTCGTGGAGATCTAATCTGAAAACTTTGGTGATTTGTCCCAT
1 CATCTCTTCGTGGAGATCAAATCTGAAAACTTTGATGATTTGTCCCAC
**
1193971 CATCTCTTCGTGGAGATCAAATCTGAAAACTTTGACAATTT-TCCCCAC
1 CATCTCTTCGTGGAGATCAAATCTGAAAACTTTGATGATTTGT-CCCAC
* * * ***
1194019 CACCTCTTCGCGGATATCAAATCTGAAAACTTTGGCAATTTGTCCCAC
1 CATCTCTTCGTGGAGATCAAATCTGAAAACTTTGATGATTTGTCCCAC
* * * *
1194067 CATCTCTTCGTGGAAATCAAATTTGAAAACTTTGACGATTTGCCCCAC
1 CATCTCTTCGTGGAGATCAAATCTGAAAACTTTGATGATTTGTCCCAC
* * * * *
1194115 CATCTCTTCGTAGAGATCAAATATGAAAACTTTGATGATTCGTTCCAT
1 CATCTCTTCGTGGAGATCAAATCTGAAAACTTTGATGATTTGTCCCAC
* * * * * **
1194163 CATCTCTTCATGG-GAATCAAATATAAAAAACCTTGATGGTCCG-CTCCAC
1 CATCTCTTCGTGGAG-ATCAAATCT-GAAAACTTTGATGATTTGTC-CCAC
* * * * ** *
1194212 CATC-ATTCTTGGAGATCCAATCTGGAAACTTTGGCGATTTATCCCAC
1 CATCTCTTCGTGGAGATCAAATCTGAAAACTTTGATGATTTGTCCCAC
* *
1194259 CATCTCTTAGTAGAGATCAAATCTGAAAA
1 CATCTCTTCGTGGAGATCAAATCTGAAAA
1194288 GTTGACGACT
Statistics
Matches: 517, Mismatches: 120, Indels: 35
0.77 0.18 0.05
Matches are distributed among these distances:
47 28 0.05
48 396 0.77
49 92 0.18
50 1 0.00
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.32
Consensus pattern (48 bp):
CATCTCTTCGTGGAGATCAAATCTGAAAACTTTGATGATTTGTCCCAC
Found at i:1193962 original size:193 final size:193
Alignment explanation
Indices: 1193652--1194154 Score: 704
Period size: 193 Copynumber: 2.6 Consensus size: 193
1193642 CAGGGAGATA
* *
1193652 AAATCTGAAAACTTTGATGATTTGTTCCATCATCTCTTCATGG-AATCATATATGAAAAACCTTG
1 AAATCTGAAAACTTTGATGATTTGTTCCATCATCTCTTCATGGAAATCAAATTTGAAAAACCTTG
* * *
1193716 ATGATTCGCTCCACCATCACTTCGTGGAAATCCAATCTGGAAACTTTGGTGATTTGTCCCACCAA
66 ATGATTCGCTCCACCATCACTTCGTGGAGATCAAATCTGAAAACTTTGGTGATTTGTCCCACCAA
* * *
1193781 CTCTTCTTGGAGATCAAATCTGAAAACTTTGACGATCTTCCCCACCATCTCTTCGCAAATATC
131 CTCTTCGTGGAGATCAAATCTGAAAACTTTGACAATCTTCCCCACCACCTCTTCGCAAATATC
* * *
1193844 AAATATGAAAATTTTGATGATTTGTTCCATTATCTCTTCATGGAAATCAAATTTGAAAAACCTTG
1 AAATCTGAAAACTTTGATGATTTGTTCCATCATCTCTTCATGGAAATCAAATTTGAAAAACCTTG
* * * *
1193909 ATGATTCGTTCCACCATCACTTCGTGGAGATCTAATCTGAAAACTTTGGTGATTTGTCCCATCAT
66 ATGATTCGCTCCACCATCACTTCGTGGAGATCAAATCTGAAAACTTTGGTGATTTGTCCCACCAA
* **
1193974 CTCTTCGTGGAGATCAAATCTGAAAACTTTGACAATTTTCCCCACCACCTCTTCGCGGATATC
131 CTCTTCGTGGAGATCAAATCTGAAAACTTTGACAATCTTCCCCACCACCTCTTCGCAAATATC
*** * * * *
1194037 AAATCTGAAAACTTTGGCAATTTGTCCCACCATCTCTTCGTGGAAATCAAATTTG-AAAACTTTG
1 AAATCTGAAAACTTTGATGATTTGTTCCATCATCTCTTCATGGAAATCAAATTTGAAAAACCTTG
* * * * * * *
1194101 ACGATTTGCCCCACCATCTCTTCGTAGAGATCAAATATGAAAACTTTGATGATT
66 ATGATTCGCTCCACCATCACTTCGTGGAGATCAAATCTGAAAACTTTGGTGATT
1194155 CGTTCCATCA
Statistics
Matches: 274, Mismatches: 36, Indels: 2
0.88 0.12 0.01
Matches are distributed among these distances:
192 93 0.34
193 181 0.66
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (193 bp):
AAATCTGAAAACTTTGATGATTTGTTCCATCATCTCTTCATGGAAATCAAATTTGAAAAACCTTG
ATGATTCGCTCCACCATCACTTCGTGGAGATCAAATCTGAAAACTTTGGTGATTTGTCCCACCAA
CTCTTCGTGGAGATCAAATCTGAAAACTTTGACAATCTTCCCCACCACCTCTTCGCAAATATC
Found at i:1201229 original size:21 final size:21
Alignment explanation
Indices: 1201199--1201249 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
1201189 CAACCCTAAC
* *
1201199 ATATATAAAATAAATTAACAA
1 ATATAGAAAACAAATTAACAA
**
1201220 ATATAGAAAACAAATTAATTA
1 ATATAGAAAACAAATTAACAA
1201241 ATATAGAAA
1 ATATAGAAA
1201250 TTGTCAACAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.65, C:0.04, G:0.04, T:0.27
Consensus pattern (21 bp):
ATATAGAAAACAAATTAACAA
Found at i:1202033 original size:27 final size:27
Alignment explanation
Indices: 1202002--1202096 Score: 167
Period size: 27 Copynumber: 3.6 Consensus size: 27
1201992 TCTATTTACA
*
1202002 AAATCATATCTCTATAGGAATTGTAAC
1 AAATCATATCTCTATAGGAATGGTAAC
1202029 AAATCATATCTCTATAGGAATGGTAAC
1 AAATCATATCTCTATAGGAATGGTAAC
1202056 AAATCATATCTCTATAGGAATGGTAAC
1 AAATCATATCTCTATAGGAATGGTAAC
1202083 AAATC--ATCTCTATA
1 AAATCATATCTCTATA
1202097 ATTCCTACAC
Statistics
Matches: 67, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
25 9 0.13
27 58 0.87
ACGTcount: A:0.41, C:0.16, G:0.12, T:0.32
Consensus pattern (27 bp):
AAATCATATCTCTATAGGAATGGTAAC
Found at i:1204191 original size:22 final size:22
Alignment explanation
Indices: 1204163--1204210 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
1204153 TTAGGCTCTT
*
1204163 GTTTATTGTCCTTAACATAATA
1 GTTTATTGTCCTTAAAATAATA
1204185 GTTTATTGTCCTTAAAATAATA
1 GTTTATTGTCCTTAAAATAATA
1204207 GTTT
1 GTTT
1204211 CTTGACAATG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.31, C:0.10, G:0.10, T:0.48
Consensus pattern (22 bp):
GTTTATTGTCCTTAAAATAATA
Found at i:1206411 original size:21 final size:21
Alignment explanation
Indices: 1206387--1206426 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1206377 TTGGATTTTT
*
1206387 TATTAACTTGATCACAATAAA
1 TATTAAATTGATCACAATAAA
1206408 TATTAAATTGATCACAATA
1 TATTAAATTGATCACAATA
1206427 TTAGTGTCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.12, G:0.05, T:0.35
Consensus pattern (21 bp):
TATTAAATTGATCACAATAAA
Found at i:1206896 original size:18 final size:17
Alignment explanation
Indices: 1206874--1206911 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
1206864 AGATATAACT
* *
1206874 TAAAATTAATTTTTTTA
1 TAAAAATAATTTATTTA
1206891 TAAAAATAATTTATTTA
1 TAAAAATAATTTATTTA
1206908 TAAA
1 TAAA
1206912 TCAAATATAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TAAAAATAATTTATTTA
Found at i:1208877 original size:3 final size:3
Alignment explanation
Indices: 1208869--1208918 Score: 63
Period size: 3 Copynumber: 18.0 Consensus size: 3
1208859 TTTGTTTTAT
*
1208869 TTA TTA TTA TTA TTA TT- TTG TT- TTA TTA TTA -TA TTA -TA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1208913 TTA TTA
1 TTA TTA
1208919 AATAATTAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
2 8 0.19
3 35 0.81
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1208896 original size:19 final size:19
Alignment explanation
Indices: 1208866--1208918 Score: 69
Period size: 16 Copynumber: 3.0 Consensus size: 19
1208856 TCATTTGTTT
1208866 TATT-TATTATTATTATTA
1 TATTATATTATTATTATTA
*
1208884 T-TT-TGTT-TTATTATTA
1 TATTATATTATTATTATTA
1208900 TATTATATTATTATTATTA
1 TATTATATTATTATTATTA
1208919 AATAATTAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
16 10 0.33
17 7 0.23
18 4 0.13
19 9 0.30
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (19 bp):
TATTATATTATTATTATTA
Found at i:1213818 original size:22 final size:22
Alignment explanation
Indices: 1213793--1213836 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1213783 ACTATACGGT
1213793 ATGAACAATA-CAGTGAACAGTA
1 ATGAACAATACCA-TGAACAGTA
*
1213815 ATGAACAGTACCATGAACAGTA
1 ATGAACAATACCATGAACAGTA
1213837 CCGAATGCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 18 0.90
23 2 0.10
ACGTcount: A:0.48, C:0.16, G:0.18, T:0.18
Consensus pattern (22 bp):
ATGAACAATACCATGAACAGTA
Found at i:1213838 original size:12 final size:11
Alignment explanation
Indices: 1213793--1213837 Score: 56
Period size: 12 Copynumber: 4.0 Consensus size: 11
1213783 ACTATACGGT
*
1213793 ATGAACAATAC
1 ATGAACAGTAC
1213804 AGTGAACAGTA-
1 A-TGAACAGTAC
1213815 ATGAACAGTACC
1 ATGAACAGTA-C
1213827 ATGAACAGTAC
1 ATGAACAGTAC
1213838 CGAATGCTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
10 9 0.30
11 3 0.10
12 18 0.60
ACGTcount: A:0.47, C:0.18, G:0.18, T:0.18
Consensus pattern (11 bp):
ATGAACAGTAC
Found at i:1216234 original size:2 final size:2
Alignment explanation
Indices: 1216227--1216271 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1216217 AAGCATTTAT
1216227 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1216269 TA T
1 TA T
1216272 GTATGTGAGA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1216487 original size:29 final size:28
Alignment explanation
Indices: 1216446--1216504 Score: 84
Period size: 30 Copynumber: 2.1 Consensus size: 28
1216436 TATACCTTTA
*
1216446 GTTCTATTTATGTCTAATG-TTTATTTC
1 GTTCTATTTATGTCTAACGTTTTATTTC
1216473 GTTCTAATTTAATGTCTAACGTTTTATTTC
1 GTTCT-ATTT-ATGTCTAACGTTTTATTTC
1216503 GT
1 GT
1216505 AAATATTATC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
27 5 0.18
28 4 0.14
29 9 0.32
30 10 0.36
ACGTcount: A:0.20, C:0.12, G:0.12, T:0.56
Consensus pattern (28 bp):
GTTCTATTTATGTCTAACGTTTTATTTC
Found at i:1221773 original size:19 final size:20
Alignment explanation
Indices: 1221734--1221771 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
1221724 TACCAGCACT
1221734 ACAAACTTCAATTTTTTTTA
1 ACAAACTTCAATTTTTTTTA
1221754 ACAAACTTCAATTTTTTT
1 ACAAACTTCAATTTTTTT
1221772 AAAGACAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.34, C:0.16, G:0.00, T:0.50
Consensus pattern (20 bp):
ACAAACTTCAATTTTTTTTA
Found at i:1225240 original size:20 final size:20
Alignment explanation
Indices: 1225215--1225258 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
1225205 ATGTAGTGTT
1225215 TGATTAACTTTTCCTGCATA
1 TGATTAACTTTTCCTGCATA
*
1225235 TGATTAATTTTTCCTGCATA
1 TGATTAACTTTTCCTGCATA
1225255 TGAT
1 TGAT
1225259 ATATCTAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.25, C:0.16, G:0.11, T:0.48
Consensus pattern (20 bp):
TGATTAACTTTTCCTGCATA
Found at i:1226389 original size:38 final size:37
Alignment explanation
Indices: 1226328--1226420 Score: 143
Period size: 38 Copynumber: 2.5 Consensus size: 37
1226318 TTTTCACCCT
*
1226328 AAACCCGAACCCTACCCGACCCGAATATCACACTTAAAA
1 AAACCCG-ACCCGACCCGACCCGAATATCACACTT-AAA
*
1226367 AAACCCGACCCGACTCGACCCGAATATCACACTTAAA
1 AAACCCGACCCGACCCGACCCGAATATCACACTTAAA
1226404 AAACCCGA-CCGACCCGA
1 AAACCCGACCCGACCCGA
1226421 ACAAAATAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
36 8 0.16
37 11 0.22
38 25 0.49
39 7 0.14
ACGTcount: A:0.39, C:0.40, G:0.11, T:0.11
Consensus pattern (37 bp):
AAACCCGACCCGACCCGACCCGAATATCACACTTAAA
Found at i:1229151 original size:13 final size:14
Alignment explanation
Indices: 1229133--1229163 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
1229123 TGCAGAGTCC
1229133 CAACTCCCAAC-AA
1 CAACTCCCAACAAA
1229146 CAACTCCCAACAAA
1 CAACTCCCAACAAA
1229160 CAAC
1 CAAC
1229164 ATTGGGAGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.65
14 6 0.35
ACGTcount: A:0.48, C:0.45, G:0.00, T:0.06
Consensus pattern (14 bp):
CAACTCCCAACAAA
Found at i:1234788 original size:41 final size:41
Alignment explanation
Indices: 1234702--1234896 Score: 132
Period size: 41 Copynumber: 4.7 Consensus size: 41
1234692 CGTTTTGTAC
* ** * *
1234702 AAACGCCGCTAAA-ACTCGTACGTTAGTGGCATTTTTTA-TA
1 AAACGCCGCTAAATACTTGTAATTTAGTGGCA-TTTTAAGCA
* *
1234742 TAAACGCCGCTAAATA-TTATATTTTAGTGGCATTTTAAGCA
1 -AAACGCCGCTAAATACTTGTAATTTAGTGGCATTTTAAGCA
** * * *
1234783 CAAACGTAGCTAAATACTGGTACTTTAGTGGCATTAATATA--A
1 -AAACGCCGCTAAATACTTGTAATTTAGTGGCATT-TTA-AGCA
* * * *
1234825 AAATGCCGCCAAAGACTTGTAATTTAGTGGCGTTTTAAGCA
1 AAACGCCGCTAAATACTTGTAATTTAGTGGCATTTTAAGCA
*
1234866 TAAACGCCGCTAAATA-TTGGTACTTTAGTGG
1 -AAACGCCGCTAAATACTT-GTAATTTAGTGG
1234897 AACTTTTATA
Statistics
Matches: 119, Mismatches: 26, Indels: 17
0.73 0.16 0.10
Matches are distributed among these distances:
39 1 0.01
40 7 0.06
41 68 0.57
42 40 0.34
43 2 0.02
44 1 0.01
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.32
Consensus pattern (41 bp):
AAACGCCGCTAAATACTTGTAATTTAGTGGCATTTTAAGCA
Found at i:1234907 original size:83 final size:81
Alignment explanation
Indices: 1234684--1234908 Score: 231
Period size: 83 Copynumber: 2.8 Consensus size: 81
1234674 ATACTCATAC
* * * * *
1234684 TTTAGTGGCGTTTT--GTACAAACGCCGCTAAA-ACTCGTACGTTAGTGGCATTTTTTATATAAA
1 TTTAGTGGCGTTTTAAGCACAAACGCCGCTAAATACTGGTACTTTAGTGG-A-ATTTTATAAAAA
* * *
1234746 CGCCGCTAAATATTATAT
64 CGCCGCCAAAGATTATAA
* ** * * *
1234764 TTTAGTGGCATTTTAAGCACAAACGTAGCTAAATACTGGTACTTTAGTGGCATTAATATAAAAAT
1 TTTAGTGGCGTTTTAAGCACAAACGCCGCTAAATACTGGTACTTTAGTGGAATT-TTATAAAAAC
*
1234829 GCCGCCAAAGACTTGTAA
65 GCCGCCAAAGA-TTATAA
* *
1234847 TTTAGTGGCGTTTTAAGCATAAACGCCGCTAAATATTGGTACTTTAGTGGAACTTTTATAAA
1 TTTAGTGGCGTTTTAAGCACAAACGCCGCTAAATACTGGTACTTTAGTGGAA-TTTTATAAA
1234909 CGCCGTTAAA
Statistics
Matches: 117, Mismatches: 22, Indels: 9
0.79 0.15 0.06
Matches are distributed among these distances:
80 13 0.11
81 2 0.02
82 30 0.26
83 70 0.60
84 2 0.02
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (81 bp):
TTTAGTGGCGTTTTAAGCACAAACGCCGCTAAATACTGGTACTTTAGTGGAATTTTATAAAAACG
CCGCCAAAGATTATAA
Found at i:1234910 original size:122 final size:121
Alignment explanation
Indices: 1234741--1235045 Score: 272
Period size: 122 Copynumber: 2.5 Consensus size: 121
1234731 CATTTTTTAT
* * * * *
1234741 ATAAACGCCGCTAAATATTATATTTTAGTGGCATTTTAAGCACAAACGTAGCTAAATACTGGTAC
1 ATAAACGCCGCTAAATATTGTACTTTAGTGGAATTTT-A--ACAAACGCAGCTAAATAAT-GTAC
** *
1234806 TTTAGTGGCATTAAT-ATAAAAATGCCGCCAAAGACTTGTAATTTAGTGGCGTTTTAAGC
62 TTTAGTGGCATTAATGATAAAAATGCCGCCAAAGACTAATAATTTAGTGGCGTTTTAACC
* * *
1234865 ATAAACGCCGCTAAATATTGGTACTTTAGTGGAACTTTT-ATAAACGCCGTTAAATAATGTACTT
1 ATAAACGCCGCTAAATATT-GTACTTTAGTGGAA-TTTTAACAAACGCAGCTAAATAATGTACTT
* ** * * * ** *
1234929 TAGTGGCGTTTCTGCTTAAAATGCTGCCAAATTCTAATACTTTAGTGGCGTTTTAACC
64 TAGTGGCATTAATGATAAAAATGCCGCCAAAGACTAATAATTTAGTGGCGTTTTAACC
* * * ** * *
1234987 ACAAACGCTGCTAAATACTTGTTCTTTAGTGGTGTATTTATATAAACGCCGCTAAATAA
1 ATAAACGCCGCTAAATA-TTGTACTTTAGTGGAAT-TTTA-ACAAACGCAGCTAAATAA
1235046 ATAAAACCAA
Statistics
Matches: 148, Mismatches: 26, Indels: 14
0.79 0.14 0.07
Matches are distributed among these distances:
121 17 0.11
122 78 0.53
123 2 0.01
124 36 0.24
125 11 0.07
126 4 0.03
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.34
Consensus pattern (121 bp):
ATAAACGCCGCTAAATATTGTACTTTAGTGGAATTTTAACAAACGCAGCTAAATAATGTACTTTA
GTGGCATTAATGATAAAAATGCCGCCAAAGACTAATAATTTAGTGGCGTTTTAACC
Found at i:1239307 original size:42 final size:42
Alignment explanation
Indices: 1239179--1239496 Score: 325
Period size: 42 Copynumber: 7.4 Consensus size: 42
1239169 AAGGTAATTA
* *
1239179 GCGGCGTTTGTCCCAAAAACGCCGCTATAAATATGACCTTTT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAAATCTGACCTTTT
* * * * * *
1239221 GCGGCGTTTGTT-AAAAAACATACCACTATAGATCTCACATTTT
1 GCGGCGTTTGTTCCAAAAAC--GCCGCTATAAATCTGACCTTTT
* * *
1239264 GCGGCGTTTGTTCAAAAAATGCCGCTATAAATCTGACTTTTT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAAATCTGACCTTTT
* *
1239306 GCGACGTTTGTTCCAAAAACGCCGCTATAGATCTGACCTTTT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAAATCTGACCTTTT
* * * * *
1239348 ACGGTGTTTGTTCCATAAACGCCGCTATAGATCTCGACATTTT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAAATCT-GACCTTTT
* * **
1239391 ACTGCGTTTGTTCCAAAATACGCCATTATAGATATC-GACCTTTT
1 GCGGCGTTTGTTCCAAAA-ACGCCGCTATA-A-ATCTGACCTTTT
* *
1239435 GCGGCGTTTGTTCCAAAAACGCTGCTATAAATATAGACCTTTT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAAATCT-GACCTTTT
1239478 GCGGCGTTTTGTTCTCAAA
1 GCGGCG-TTTGTTC-CAAA
1239497 CGTCGCAAGC
Statistics
Matches: 228, Mismatches: 37, Indels: 19
0.80 0.13 0.07
Matches are distributed among these distances:
41 8 0.04
42 96 0.42
43 72 0.32
44 45 0.20
45 4 0.02
46 3 0.01
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.33
Consensus pattern (42 bp):
GCGGCGTTTGTTCCAAAAACGCCGCTATAAATCTGACCTTTT
Found at i:1240166 original size:45 final size:44
Alignment explanation
Indices: 1240116--1240288 Score: 168
Period size: 45 Copynumber: 3.8 Consensus size: 44
1240106 ATAAACTGGA
**
1240116 AAAATAAGCTTACAAGCTTATGGAATAATGACAAGTATATTGGT
1 AAAATAAGCTTACAAGCTTATGGAATAATGGTAAGTATATTGGT
* * * *
1240160 AAAAATAAGCTTATGAA-ATTAATGGAACAAATGGTAAGTATAATGGT
1 -AAAATAAGCTTA-CAAGCTT-ATGGAA-TAATGGTAAGTATATTGGT
* * * *
1240207 AAGATAAGCTTACGAGCTTATGGGATAAATGGTAAGTATTTTGGT
1 AAAATAAGCTTACAAGCTTATGGAAT-AATGGTAAGTATATTGGT
*
1240252 AAAATAAGCTTACGAGCTTATGGTTAATAAATGGTAA
1 AAAATAAGCTTACAAGCTTATGG--AAT-AATGGTAA
1240289 AATATTGAAT
Statistics
Matches: 105, Mismatches: 16, Indels: 12
0.79 0.12 0.09
Matches are distributed among these distances:
45 58 0.55
46 21 0.20
47 26 0.25
ACGTcount: A:0.42, C:0.07, G:0.21, T:0.30
Consensus pattern (44 bp):
AAAATAAGCTTACAAGCTTATGGAATAATGGTAAGTATATTGGT
Found at i:1240661 original size:13 final size:12
Alignment explanation
Indices: 1240643--1240694 Score: 50
Period size: 13 Copynumber: 4.1 Consensus size: 12
1240633 CCGATTCCCC
1240643 TACTGTTCACATA
1 TACTGTTCAC-TA
*
1240656 TACTGTTCACTG
1 TACTGTTCACTA
**
1240668 TCACTGTTCACGGG
1 T-ACTGTTCAC-TA
1240682 TACTGTTCACTA
1 TACTGTTCACTA
1240694 T
1 T
1240695 TCATAAAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
12 3 0.09
13 28 0.85
14 2 0.06
ACGTcount: A:0.21, C:0.25, G:0.15, T:0.38
Consensus pattern (12 bp):
TACTGTTCACTA
Found at i:1241145 original size:45 final size:44
Alignment explanation
Indices: 1241074--1241250 Score: 266
Period size: 45 Copynumber: 4.0 Consensus size: 44
1241064 AAATTTCTTT
1241074 CCAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTA
1 CCAATATACTTACCATTTA-CCCATAAGCTCGTAAGCTTATTTTA
* *
1241119 CTAATATACTTATCATTTACCACATAAGCTCGTAAGCTTATTTTA
1 CCAATATACTTACCATTTACC-CATAAGCTCGTAAGCTTATTTTA
* *
1241164 CCAATATACTTACCATTTACCCCTTATGCTCGTAAGCTTATTTTA
1 CCAATATACTTACCATTTA-CCCATAAGCTCGTAAGCTTATTTTA
*
1241209 CCAATATACTTGCCA-TTACTCCATAAGCTCGTAAGCTTATTT
1 CCAATATACTTACCATTTAC-CCATAAGCTCGTAAGCTTATTT
1241251 GCATGGTTAC
Statistics
Matches: 120, Mismatches: 9, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
43 1 0.01
44 25 0.21
45 92 0.77
46 2 0.02
ACGTcount: A:0.30, C:0.24, G:0.07, T:0.38
Consensus pattern (44 bp):
CCAATATACTTACCATTTACCCATAAGCTCGTAAGCTTATTTTA
Found at i:1241527 original size:40 final size:40
Alignment explanation
Indices: 1241362--1241511 Score: 246
Period size: 40 Copynumber: 3.8 Consensus size: 40
1241352 ACCGTAGTGC
* * *
1241362 TACACATAAGGTCGTGCTCACCATATACACCAAAGTATAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1241402 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
* *
1241442 TACATATAAGGTCGTGCCCATCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
*
1241482 TACACATAAGGTCGTGCCTACCATATACAC
1 TACACATAAGGTCGTGCCCACCATATACAC
1241512 TTAGTGTCCT
Statistics
Matches: 102, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 102 1.00
ACGTcount: A:0.34, C:0.26, G:0.15, T:0.25
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
Found at i:1241859 original size:24 final size:24
Alignment explanation
Indices: 1241827--1241875 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
1241817 AGTCTTCCTG
1241827 ATGATGTATAAAACATCTATGTAC
1 ATGATGTATAAAACATCTATGTAC
1241851 ATGATGTATAAAACATCTATGTAC
1 ATGATGTATAAAACATCTATGTAC
1241875 A
1 A
1241876 ATGTCATGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.33
Consensus pattern (24 bp):
ATGATGTATAAAACATCTATGTAC
Found at i:1242587 original size:30 final size:31
Alignment explanation
Indices: 1242528--1242596 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 31
1242518 AACCATTCCC
* * *
1242528 AACTTTTCCAAAATTACTGAATTGGTCCCCT
1 AACTTTTCAAAAATTACTGAATTGATCCCCA
1242559 AACTTTTCAAAAATTA-TAGAA-TGATCCCCA
1 AACTTTTCAAAAATTACT-GAATTGATCCCCA
*
1242589 AATTTTTC
1 AACTTTTC
1242597 TAAGGCCTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
30 15 0.45
31 18 0.55
ACGTcount: A:0.35, C:0.22, G:0.07, T:0.36
Consensus pattern (31 bp):
AACTTTTCAAAAATTACTGAATTGATCCCCA
Found at i:1243085 original size:14 final size:14
Alignment explanation
Indices: 1243066--1243104 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
1243056 TAACGGGGAG
1243066 TAATCCCTGCAAAA
1 TAATCCCTGCAAAA
*
1243080 TAATCCCTGCGAAA
1 TAATCCCTGCAAAA
* *
1243094 GAATCTCTGCA
1 TAATCCCTGCA
1243105 TATAGACAGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.28, G:0.13, T:0.23
Consensus pattern (14 bp):
TAATCCCTGCAAAA
Found at i:1246206 original size:2 final size:2
Alignment explanation
Indices: 1246199--1246246 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
1246189 CATTTCTCTT
1246199 TA TA TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1246240 TA TA TA T
1 TA TA TA T
1246247 TAGATTATTT
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1255634 original size:15 final size:15
Alignment explanation
Indices: 1255616--1255647 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1255606 ATTCTTCTCA
1255616 TTCTCATTCTCATTC
1 TTCTCATTCTCATTC
*
1255631 TTCTCATTCTCCTTC
1 TTCTCATTCTCATTC
1255646 TT
1 TT
1255648 ATTCTTCTCC
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:0.09, C:0.34, G:0.00, T:0.56
Consensus pattern (15 bp):
TTCTCATTCTCATTC
Found at i:1255666 original size:21 final size:21
Alignment explanation
Indices: 1255605--1255656 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
1255595 TCATTATTAG
*
1255605 TATTCTTCTCATTCTCATTCT
1 TATTCTTCTCATTCTCCTTCT
*
1255626 CATTCTTCTCATTCTCCTTCT
1 TATTCTTCTCATTCTCCTTCT
1255647 TATTCTTCTC
1 TATTCTTCTC
1255657 CTCATCCTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.12, C:0.33, G:0.00, T:0.56
Consensus pattern (21 bp):
TATTCTTCTCATTCTCCTTCT
Found at i:1257140 original size:7 final size:7
Alignment explanation
Indices: 1257128--1257162 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
1257118 TTTATGTTGT
1257128 AAATATA
1 AAATATA
1257135 AAATATA
1 AAATATA
1257142 AAATATA
1 AAATATA
*
1257149 AAATTTA
1 AAATATA
*
1257156 AATTATA
1 AAATATA
1257163 TTTACACTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (7 bp):
AAATATA
Found at i:1261816 original size:23 final size:23
Alignment explanation
Indices: 1261775--1261862 Score: 83
Period size: 23 Copynumber: 3.9 Consensus size: 23
1261765 GGTTCTATAC
* * * *
1261775 GGTCCTTCGGGATAATTCTACGT
1 GGTCATTCGGGACATTTCTATGT
*
1261798 GGTCATTCGGGACATTTCTATAT
1 GGTCATTCGGGACATTTCTATGT
* *
1261821 GGTTCCTTCAGGACA--TCTATGT
1 GG-TCATTCGGGACATTTCTATGT
1261843 GGTCATTCGGGACA-TTCTAT
1 GGTCATTCGGGACATTTCTAT
1261863 ATGGCACTTT
Statistics
Matches: 53, Mismatches: 10, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
21 10 0.19
22 13 0.25
23 20 0.38
24 10 0.19
ACGTcount: A:0.19, C:0.20, G:0.24, T:0.36
Consensus pattern (23 bp):
GGTCATTCGGGACATTTCTATGT
Found at i:1261845 original size:22 final size:22
Alignment explanation
Indices: 1261797--1261866 Score: 79
Period size: 22 Copynumber: 3.1 Consensus size: 22
1261787 TAATTCTACG
*
1261797 TGGTCATTCGGGACATTTCTATA
1 TGGTCATTCAGGACA-TTCTATA
* *
1261820 TGGTTCCTTCAGGACA-TCTATG
1 TGG-TCATTCAGGACATTCTATA
*
1261842 TGGTCATTCGGGACATTCTATA
1 TGGTCATTCAGGACATTCTATA
1261864 TGG
1 TGG
1261867 CACTTTGGTG
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
21 10 0.26
22 16 0.41
23 3 0.08
24 10 0.26
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.37
Consensus pattern (22 bp):
TGGTCATTCAGGACATTCTATA
Found at i:1267621 original size:14 final size:15
Alignment explanation
Indices: 1267597--1267626 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
1267587 GTATGAATGG
1267597 TATGATTATATGATA
1 TATGATTATATGATA
1267612 TATG-TTATATGATA
1 TATGATTATATGATA
1267626 T
1 T
1267627 GAGATGGATG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.37, C:0.00, G:0.13, T:0.50
Consensus pattern (15 bp):
TATGATTATATGATA
Found at i:1267841 original size:32 final size:31
Alignment explanation
Indices: 1267772--1267875 Score: 163
Period size: 31 Copynumber: 3.3 Consensus size: 31
1267762 GAGTCATGGG
* *
1267772 TTACCTATGTCTTTCAATACATATGGACAGA
1 TTACCTATGTCTTTCGAGACATATGGACAGA
1267803 TTACCTATGTCTTTCGAGACATATGGACAAGA
1 TTACCTATGTCTTTCGAGACATATGGAC-AGA
* *
1267835 TTACCTATGTCTTTCGGGACATATGGACAGT
1 TTACCTATGTCTTTCGAGACATATGGACAGA
1267866 TTACCTATGT
1 TTACCTATGT
1267876 TCTTAGGAAC
Statistics
Matches: 68, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
31 38 0.56
32 30 0.44
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.36
Consensus pattern (31 bp):
TTACCTATGTCTTTCGAGACATATGGACAGA
Found at i:1267888 original size:31 final size:30
Alignment explanation
Indices: 1267772--1267890 Score: 121
Period size: 31 Copynumber: 3.8 Consensus size: 30
1267762 GAGTCATGGG
***
1267772 TTACCTATGTCTTTCAATACATATGGACAGA
1 TTACCTATGTCTTAGGA-ACATATGGACAGA
**
1267803 TTACCTATGTCTTTCGAGACATATGGACAAGA
1 TTACCTATGTCTTAGGA-ACATATGGAC-AGA
* * *
1267835 TTACCTATGTCTTTCGGGACATATGGACAGT
1 TTACCTATGTC-TTAGGAACATATGGACAGA
1267866 TTACCTATGTTCTTAGGAACATATG
1 TTACCTATG-TCTTAGGAACATATG
1267891 TACATGTCAT
Statistics
Matches: 77, Mismatches: 8, Indels: 6
0.85 0.09 0.07
Matches are distributed among these distances:
31 48 0.62
32 26 0.34
33 3 0.04
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (30 bp):
TTACCTATGTCTTAGGAACATATGGACAGA
Found at i:1267888 original size:63 final size:63
Alignment explanation
Indices: 1267772--1267890 Score: 168
Period size: 63 Copynumber: 1.9 Consensus size: 63
1267762 GAGTCATGGG
* *
1267772 TTACCTATGTCTTTCAATACATATGGACAGATTACCTATGTCTTTCGAGACATATGGACAAGA
1 TTACCTATGTCTTTCAAGACATATGGACAGATTACCTATGTCTTACGAGACATATGGACAAGA
** * *
1267835 TTACCTATGTCTTTCGGGACATATGGACAGTTTACCTATGTTCTTAGGA-ACATATG
1 TTACCTATGTCTTTCAAGACATATGGACAGATTACCTATG-TCTTACGAGACATATG
1267891 TACATGTCAT
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
63 43 0.88
64 6 0.12
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (63 bp):
TTACCTATGTCTTTCAAGACATATGGACAGATTACCTATGTCTTACGAGACATATGGACAAGA
Found at i:1271930 original size:2 final size:2
Alignment explanation
Indices: 1271919--1271976 Score: 93
Period size: 2 Copynumber: 30.0 Consensus size: 2
1271909 AATCTATGTG
*
1271919 AT AT AT -T AT AT AT AT AT AT AT AT AT AT AC AT A- 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
1271959 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
1271977 CACCATAGAG
Statistics
Matches: 52, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
1 2 0.04
2 50 0.96
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1272180 original size:18 final size:19
Alignment explanation
Indices: 1272139--1272185 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
1272129 TATATGAGTT
**
1272139 ATATGTTATTGTATGTGTG
1 ATATGTTATTGTATGAATG
1272158 ATATGTT-TTGTATGAATG
1 ATATGTTATTGTATGAATG
*
1272176 GTATGATTAT
1 ATATG-TTAT
1272186 ATGATATATG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
18 13 0.57
19 9 0.39
20 1 0.04
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (19 bp):
ATATGTTATTGTATGAATG
Found at i:1272201 original size:14 final size:15
Alignment explanation
Indices: 1272177--1272206 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
1272167 GTATGAATGG
1272177 TATGATTATATGATA
1 TATGATTATATGATA
1272192 TATG-TTATATGATA
1 TATGATTATATGATA
1272206 T
1 T
1272207 GAGATGGATG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.37, C:0.00, G:0.13, T:0.50
Consensus pattern (15 bp):
TATGATTATATGATA
Found at i:1272391 original size:31 final size:32
Alignment explanation
Indices: 1272353--1272473 Score: 149
Period size: 31 Copynumber: 3.8 Consensus size: 32
1272343 GAGTCGAGGG
1272353 TTACCTATGTCTTTCGAGACATATGGACA-TA
1 TTACCTATGTCTTTCGAGACATATGGACAGTA
* *
1272384 TTACCTATGTCTTTTGAGACATATGGACAGGA
1 TTACCTATGTCTTTCGAGACATATGGACAGTA
* * *
1272416 TTGCCTATGTCCTTCGGGACATATGGACAGT-
1 TTACCTATGTCTTTCGAGACATATGGACAGTA
**
1272447 TTACCTATGTTCTTAGGA-ACATATGGA
1 TTACCTATG-TCTTTCGAGACATATGGA
1272474 TAGGTCATTC
Statistics
Matches: 76, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
31 45 0.59
32 31 0.41
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.35
Consensus pattern (32 bp):
TTACCTATGTCTTTCGAGACATATGGACAGTA
Found at i:1274552 original size:20 final size:20
Alignment explanation
Indices: 1274523--1274561 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1274513 ATAGCCCATA
*
1274523 TAGGATCATATAGATGCATT
1 TAGGAGCATATAGATGCATT
*
1274543 TAGGAGCATATAGTTGCAT
1 TAGGAGCATATAGATGCAT
1274562 GTTGTGAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.10, G:0.23, T:0.33
Consensus pattern (20 bp):
TAGGAGCATATAGATGCATT
Found at i:1277334 original size:5 final size:5
Alignment explanation
Indices: 1277286--1277344 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
1277276 AATTAACCTA
* * *
1277286 AAAAT AAAAC AAAAT AAACT AAAGT AATAAT AATAAT GAAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AA-AAT AA-AAT -AAAAT AAAAT
1277334 AAAAAT AAAAT
1 -AAAAT AAAAT
1277345 GATAATATAT
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
5 28 0.61
6 16 0.35
7 2 0.04
ACGTcount: A:0.73, C:0.03, G:0.03, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:1277349 original size:28 final size:28
Alignment explanation
Indices: 1277296--1277350 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
1277286 AAAATAAAAC
* *
1277296 AAAATAAACTAAAGTAATAATAATAATG
1 AAAATAAAATAAAATAATAATAATAATG
*
1277324 AAAATAAAATAAAAATAA-AATGATAAT
1 AAAATAAAAT-AAAATAATAATAATAAT
1277351 ATATATTATC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 17 0.74
29 6 0.26
ACGTcount: A:0.69, C:0.02, G:0.05, T:0.24
Consensus pattern (28 bp):
AAAATAAAATAAAATAATAATAATAATG
Found at i:1278052 original size:11 final size:11
Alignment explanation
Indices: 1278038--1278062 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1278028 TAAGATTAGA
1278038 AAAAGATAAAT
1 AAAAGATAAAT
1278049 AAAAGATAAAT
1 AAAAGATAAAT
1278060 AAA
1 AAA
1278063 TTTAAAATAA
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:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (11 bp):
AAAAGATAAAT
Found at i:1282385 original size:25 final size:25
Alignment explanation
Indices: 1282349--1282405 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 25
1282339 ATTTTCAAAC
*
1282349 TTTTTTGGCTTTTTGGCTT-TT-TTTT
1 TTTTTTGCCTTTTT--CTTCTTCTTTT
1282374 TTTTTTGCCTTTTTCTTCTTCTTTT
1 TTTTTTGCCTTTTTCTTCTTCTTTT
1282399 TTTTTTG
1 TTTTTTG
1282406 AAAAAAAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
23 3 0.10
24 2 0.07
25 24 0.83
ACGTcount: A:0.00, C:0.12, G:0.11, T:0.77
Consensus pattern (25 bp):
TTTTTTGCCTTTTTCTTCTTCTTTT
Found at i:1283832 original size:24 final size:24
Alignment explanation
Indices: 1283804--1283874 Score: 69
Period size: 24 Copynumber: 3.1 Consensus size: 24
1283794 AATATGATGC
1283804 TGATCCAACTCCTTATGTGATGGA
1 TGATCCAACTCCTTATGTGATGGA
*** * *
1283828 TGATCCAA---GAAATGTG-TTGT
1 TGATCCAACTCCTTATGTGATGGA
1283848 TGATCCAACTCCTTATGTGATGGA
1 TGATCCAACTCCTTATGTGATGGA
1283872 TGA
1 TGA
1283875 GCCGAGGTTG
Statistics
Matches: 33, Mismatches: 10, Indels: 8
0.65 0.20 0.16
Matches are distributed among these distances:
20 10 0.30
21 5 0.15
23 5 0.15
24 13 0.39
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.34
Consensus pattern (24 bp):
TGATCCAACTCCTTATGTGATGGA
Found at i:1283868 original size:44 final size:44
Alignment explanation
Indices: 1283753--1283877 Score: 169
Period size: 44 Copynumber: 2.8 Consensus size: 44
1283743 ATGAGACAAA
* * * **
1283753 ATGATGTTGATCTAACTGCTTATGTGACGGACAAGCCAAGAAAT
1 ATGATGTTGATCCAACTCCTTATGTGATGGATGAGCCAAGAAAT
* *
1283797 ATGATGCTGATCCAACTCCTTATGTGATGGATGATCCAAGAAAT
1 ATGATGTTGATCCAACTCCTTATGTGATGGATGAGCCAAGAAAT
* *
1283841 GTGTTGTTGATCCAACTCCTTATGTGATGGATGAGCC
1 ATGATGTTGATCCAACTCCTTATGTGATGGATGAGCC
1283878 GAGGTTGAAT
Statistics
Matches: 70, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
44 70 1.00
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.30
Consensus pattern (44 bp):
ATGATGTTGATCCAACTCCTTATGTGATGGATGAGCCAAGAAAT
Found at i:1285090 original size:20 final size:21
Alignment explanation
Indices: 1285067--1285121 Score: 71
Period size: 19 Copynumber: 2.8 Consensus size: 21
1285057 TTTTTTCAAT
1285067 TTTTTTCTTCTTTTC-CTTTC
1 TTTTTTCTTCTTTTCTCTTTC
*
1285087 -TTTTTCTTCTTTTCTTTTTC
1 TTTTTTCTTCTTTTCTCTTTC
*
1285107 TTATTT-TTCTTTTCT
1 TTTTTTCTTCTTTTCT
1285122 TCTAAGTGTA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 14 0.45
20 13 0.42
21 4 0.13
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (21 bp):
TTTTTTCTTCTTTTCTCTTTC
Found at i:1285102 original size:14 final size:14
Alignment explanation
Indices: 1285069--1285124 Score: 62
Period size: 14 Copynumber: 4.1 Consensus size: 14
1285059 TTTTCAATTT
*
1285069 TTTTCTTCTT-TTC
1 TTTTCTTTTTCTTC
*
1285082 CTTTCTTTTTCTTC
1 TTTTCTTTTTCTTC
*
1285096 TTTTCTTTTTCTTA
1 TTTTCTTTTTCTTC
1285110 TTTT-TCTTTTCTTC
1 TTTTCT-TTTTCTTC
1285124 T
1 T
1285125 AAGTGTAGTA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
13 9 0.25
14 27 0.75
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTTCTTTTTCTTC
Found at i:1285122 original size:20 final size:20
Alignment explanation
Indices: 1285068--1285122 Score: 78
Period size: 20 Copynumber: 2.8 Consensus size: 20
1285058 TTTTTCAATT
*
1285068 TTTTTCTTCTTTTC-CTTTC
1 TTTTTCTTCTTTTCTTTTTC
1285087 TTTTTCTTCTTTTCTTTTTC
1 TTTTTCTTCTTTTCTTTTTC
1285107 TTATTT-TTCTTTTCTT
1 TT-TTTCTTCTTTTCTT
1285123 CTAAGTGTAG
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
19 14 0.42
20 16 0.48
21 3 0.09
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (20 bp):
TTTTTCTTCTTTTCTTTTTC
Found at i:1294821 original size:15 final size:15
Alignment explanation
Indices: 1294801--1294834 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1294791 TAATGAATGA
1294801 TTAAGTATGTTTTTG
1 TTAAGTATGTTTTTG
* *
1294816 TTAAGTGTTTTTTTG
1 TTAAGTATGTTTTTG
1294831 TTAA
1 TTAA
1294835 CTGTTTAACC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.21, C:0.00, G:0.18, T:0.62
Consensus pattern (15 bp):
TTAAGTATGTTTTTG
Found at i:1294839 original size:15 final size:15
Alignment explanation
Indices: 1294810--1294840 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1294800 ATTAAGTATG
*
1294810 TTTTTGTTAAGTGTT
1 TTTTTGTTAACTGTT
1294825 TTTTTGTTAACTGTT
1 TTTTTGTTAACTGTT
1294840 T
1 T
1294841 AACCTTTTGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.03, G:0.16, T:0.68
Consensus pattern (15 bp):
TTTTTGTTAACTGTT
Found at i:1298751 original size:101 final size:102
Alignment explanation
Indices: 1298612--1298815 Score: 313
Period size: 101 Copynumber: 2.0 Consensus size: 102
1298602 TCACAGGATG
*
1298612 ACTCTACCTGACTAGCTCGGGGGTGGAAGTTATACTCCCTTTCACTTAGAGTGT-GAGATGGTAG
1 ACTCTACCTGACTAGCTCGGGGGTGGAAGGTATACTCCCTTTCACTTAGAGTGTAG-GATGGTAG
* * *
1298676 TATGATGAGCTGAATCCTCTTAAAGTATGC-TAAAAAA
65 TACGATGAGATGAATCCCCTTAAAGTATGCTTAAAAAA
* *
1298713 ACTCTACTTGACTAGCTCGGGGGTGGAAGGTATGCTCCCTTTCACTTAGAGTGTAGGATGGTAGT
1 ACTCTACCTGACTAGCTCGGGGGTGGAAGGTATACTCCCTTTCACTTAGAGTGTAGGATGGTAGT
* *
1298778 GCGATGAGATGACTCCCCTTAAAGTATGCTTAAAAAA
66 ACGATGAGATGAATCCCCTTAAAGTATGCTTAAAAAA
1298815 A
1 A
1298816 GAGTTGAAGT
Statistics
Matches: 93, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
101 84 0.90
102 9 0.10
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.29
Consensus pattern (102 bp):
ACTCTACCTGACTAGCTCGGGGGTGGAAGGTATACTCCCTTTCACTTAGAGTGTAGGATGGTAGT
ACGATGAGATGAATCCCCTTAAAGTATGCTTAAAAAA
Found at i:1300971 original size:32 final size:33
Alignment explanation
Indices: 1300930--1300999 Score: 90
Period size: 33 Copynumber: 2.2 Consensus size: 33
1300920 AAAGTTAAAA
* *
1300930 ATAATTACAAGAAAACAAAA-ATTC-AATAAATC
1 ATAAATACAA-AAAACAAAACATCCAAATAAATC
*
1300962 ATAAATACAATAAACAAAACATCCAAATAAATC
1 ATAAATACAAAAAACAAAACATCCAAATAAATC
1300995 ATAAA
1 ATAAA
1301000 CCTTAACCAG
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
31 8 0.24
32 12 0.36
33 13 0.39
ACGTcount: A:0.64, C:0.14, G:0.01, T:0.20
Consensus pattern (33 bp):
ATAAATACAAAAAACAAAACATCCAAATAAATC
Found at i:1300972 original size:16 final size:16
Alignment explanation
Indices: 1300948--1300999 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
1300938 AAGAAAACAA
*
1300948 AAATTCAATAAATCAT
1 AAATACAATAAATCAT
*
1300964 AAATACAATAAA-CAA
1 AAATACAATAAATCAT
*
1300979 AACATCCAAATAAATCAT
1 AA-ATAC-AATAAATCAT
1300997 AAA
1 AAA
1301000 CCTTAACCAG
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
15 4 0.14
16 14 0.48
17 7 0.24
18 4 0.14
ACGTcount: A:0.63, C:0.15, G:0.00, T:0.21
Consensus pattern (16 bp):
AAATACAATAAATCAT
Found at i:1304018 original size:23 final size:23
Alignment explanation
Indices: 1303992--1304044 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
1303982 TCTAAATATA
1303992 TAAAATTATGAGAGAAGTTAAAG
1 TAAAATTATGAGAGAAGTTAAAG
*
1304015 TAAAATTATGGGAGAAGTTAAAG
1 TAAAATTATGAGAGAAGTTAAAG
1304038 TAAAATT
1 TAAAATT
1304045 CAAACTCGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.51, C:0.00, G:0.21, T:0.28
Consensus pattern (23 bp):
TAAAATTATGAGAGAAGTTAAAG
Found at i:1305690 original size:60 final size:61
Alignment explanation
Indices: 1305572--1305691 Score: 145
Period size: 60 Copynumber: 2.0 Consensus size: 61
1305562 TTTGTATTTT
* * * *
1305572 TTTTTCATTGATCTTGTTAAAATTTTCTGGCTTAAGCTTCTTTTAAGTTATTAGTTTGCAC
1 TTTTTCATTGATCTTGTTAAAAGTTTCTGGCTTAAGCTTCATTTAAGTTATGAATTTGCAC
* * * *
1305633 TTTTTCATTGAT-TTGTTTAAAGTTTCTGGTTTGA-CTTGATTTAAGTTCATGAATTTGCA
1 TTTTTCATTGATCTTGTTAAAAGTTTCTGGCTTAAGCTTCATTTAAGTT-ATGAATTTGCA
1305692 GGATTGAGAT
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
59 11 0.22
60 27 0.54
61 12 0.24
ACGTcount: A:0.22, C:0.11, G:0.15, T:0.53
Consensus pattern (61 bp):
TTTTTCATTGATCTTGTTAAAAGTTTCTGGCTTAAGCTTCATTTAAGTTATGAATTTGCAC
Found at i:1310943 original size:12 final size:12
Alignment explanation
Indices: 1310926--1310955 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1310916 CTTTACTTTA
1310926 TTTGTTCAATAC
1 TTTGTTCAATAC
*
1310938 TTTGTTCTATAC
1 TTTGTTCAATAC
1310950 TTTGTT
1 TTTGTT
1310956 GCATGTGCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.17, C:0.13, G:0.10, T:0.60
Consensus pattern (12 bp):
TTTGTTCAATAC
Found at i:1313894 original size:22 final size:22
Alignment explanation
Indices: 1313866--1313921 Score: 112
Period size: 22 Copynumber: 2.5 Consensus size: 22
1313856 ATTTTATCTT
1313866 TAGAGTAGAGATAGAGATGTTG
1 TAGAGTAGAGATAGAGATGTTG
1313888 TAGAGTAGAGATAGAGATGTTG
1 TAGAGTAGAGATAGAGATGTTG
1313910 TAGAGTAGAGAT
1 TAGAGTAGAGAT
1313922 GAGGGCTAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.38, C:0.00, G:0.36, T:0.27
Consensus pattern (22 bp):
TAGAGTAGAGATAGAGATGTTG
Found at i:1316747 original size:13 final size:13
Alignment explanation
Indices: 1316729--1316753 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1316719 AGAAGATATT
1316729 TTATTAATTTTAA
1 TTATTAATTTTAA
1316742 TTATTAATTTTA
1 TTATTAATTTTA
1316754 TTTTATTTTG
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:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TTATTAATTTTAA
Found at i:1317396 original size:26 final size:26
Alignment explanation
Indices: 1317366--1317420 Score: 67
Period size: 25 Copynumber: 2.0 Consensus size: 26
1317356 ATTTAATGTT
1317366 TATATATATAAATTATATAAAAA-ATAAA
1 TATA-ATATAAA--ATATAAAAATATAAA
*
1317394 TATAATTTAAAATATAAAAATATAAA
1 TATAATATAAAATATAAAAATATAAA
1317420 T
1 T
1317421 TTTACTTTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
25 9 0.36
26 6 0.24
27 6 0.24
28 4 0.16
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (26 bp):
TATAATATAAAATATAAAAATATAAA
Found at i:1317409 original size:36 final size:35
Alignment explanation
Indices: 1317320--1317414 Score: 84
Period size: 36 Copynumber: 2.6 Consensus size: 35
1317310 GATTTTTTAT
* * *
1317320 ATATAATTATAAAA-ATTATTAATTGTATTAAAAATA
1 ATATAATT-TAAAATA-TATAAATTATATAAAAAATA
* * *
1317356 ATTTAATGTTTATATATATAAATTATATAAAAAATAA
1 ATATAAT-TTAAAATATATAAATTATATAAAAAAT-A
*
1317393 ATATAATTTAAAATATAAAAAT
1 ATATAATTTAAAATATATAAAT
1317415 ATAAATTTTA
Statistics
Matches: 46, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
36 37 0.80
37 9 0.20
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (35 bp):
ATATAATTTAAAATATATAAATTATATAAAAAATA
Found at i:1320830 original size:20 final size:20
Alignment explanation
Indices: 1320807--1320854 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
1320797 GTTCTGACAG
1320807 TATTGATACTATATGAACAA
1 TATTGATACTATATGAACAA
1320827 TATTGATACTATATGAACAA
1 TATTGATACTATATGAACAA
1320847 TATTGATA
1 TATTGATA
1320855 TTATTCATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.44, C:0.08, G:0.10, T:0.38
Consensus pattern (20 bp):
TATTGATACTATATGAACAA
Found at i:1321174 original size:16 final size:18
Alignment explanation
Indices: 1321145--1321194 Score: 61
Period size: 17 Copynumber: 2.8 Consensus size: 18
1321135 ATATGAATGA
1321145 ATTATTTGTAATTAAA-TT
1 ATTATTT-TAATTAAAGTT
1321163 -TTATTTTAATTAAAAGTT
1 ATTATTTTAATT-AAAGTT
1321181 ATT-TTTTAATTAAA
1 ATTATTTTAATTAAA
1321195 ATGTTTTCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
16 5 0.17
17 12 0.41
18 10 0.34
19 2 0.07
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (18 bp):
ATTATTTTAATTAAAGTT
Found at i:1321186 original size:17 final size:17
Alignment explanation
Indices: 1321146--1321195 Score: 57
Period size: 16 Copynumber: 2.9 Consensus size: 17
1321136 TATGAATGAA
* **
1321146 TTATTTGTAATTAAATT
1 TTATTTTTAATTAAAAG
1321163 TTA-TTTTAATTAAAAG
1 TTATTTTTAATTAAAAG
1321179 TTATTTTTTAATTAAAA
1 TTA-TTTTTAATTAAAA
1321196 TGTTTTCATT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
16 13 0.46
17 3 0.11
18 12 0.43
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (17 bp):
TTATTTTTAATTAAAAG
Found at i:1326075 original size:20 final size:20
Alignment explanation
Indices: 1326050--1326157 Score: 173
Period size: 20 Copynumber: 5.4 Consensus size: 20
1326040 TCACGGAATG
1326050 TAAGATTATCAGTGGAAATA
1 TAAGATTATCAGTGGAAATA
1326070 TAAGATTATCAGTGGAAATA
1 TAAGATTATCAGTGGAAATA
*
1326090 TAAGATTATCAGTGGGAATA
1 TAAGATTATCAGTGGAAATA
*
1326110 TAAGATTATCAGTGGGAATA
1 TAAGATTATCAGTGGAAATA
*
1326130 TAAGATTACCAGT-GAGAATA
1 TAAGATTATCAGTGGA-AATA
1326150 TAAGATTA
1 TAAGATTA
1326158 CCAGGGAATA
Statistics
Matches: 84, Mismatches: 3, Indels: 2
0.94 0.03 0.02
Matches are distributed among these distances:
19 1 0.01
20 83 0.99
ACGTcount: A:0.44, C:0.06, G:0.21, T:0.30
Consensus pattern (20 bp):
TAAGATTATCAGTGGAAATA
Found at i:1326158 original size:20 final size:19
Alignment explanation
Indices: 1326044--1326167 Score: 169
Period size: 20 Copynumber: 6.3 Consensus size: 19
1326034 TTTGGTTCAC
*
1326044 GGAATGTAAGATTATCAGT
1 GGAATATAAGATTATCAGT
1326063 GGAAATATAAGATTATCAGT
1 GG-AATATAAGATTATCAGT
1326083 GGAAATATAAGATTATCAGT
1 GG-AATATAAGATTATCAGT
1326103 GGGAATATAAGATTATCAGT
1 -GGAATATAAGATTATCAGT
*
1326123 GGGAATATAAGATTACCAGT
1 -GGAATATAAGATTATCAGT
*
1326143 GAGAATATAAGATTACCAG-
1 G-GAATATAAGATTATCAGT
1326162 GGAATA
1 GGAATA
1326168 AGATTACTGA
Statistics
Matches: 100, Mismatches: 2, Indels: 7
0.92 0.02 0.06
Matches are distributed among these distances:
18 5 0.05
19 4 0.04
20 89 0.89
21 2 0.02
ACGTcount: A:0.43, C:0.06, G:0.23, T:0.27
Consensus pattern (19 bp):
GGAATATAAGATTATCAGT
Found at i:1328297 original size:29 final size:30
Alignment explanation
Indices: 1328217--1328297 Score: 78
Period size: 30 Copynumber: 2.7 Consensus size: 30
1328207 TTTTATTTTC
* * *
1328217 TATTTAGTCCCTTAAGTTT-TTATTGTTGT
1 TATTTAGTCCCTTTAGTTTCTAAATGTTGT
* *
1328246 TATTTTAGT-CCTTTAAATGTCTAAAT-TTGT
1 TA-TTTAGTCCCTTT-AGTTTCTAAATGTTGT
1328276 TATTTAGTCCCTTTAGTTTCTA
1 TATTTAGTCCCTTTAGTTTCTA
1328298 TTTTTTCTAT
Statistics
Matches: 41, Mismatches: 7, Indels: 8
0.73 0.12 0.14
Matches are distributed among these distances:
29 18 0.44
30 20 0.49
31 3 0.07
ACGTcount: A:0.21, C:0.12, G:0.11, T:0.56
Consensus pattern (30 bp):
TATTTAGTCCCTTTAGTTTCTAAATGTTGT
Found at i:1330171 original size:32 final size:32
Alignment explanation
Indices: 1330127--1330188 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
1330117 TCTTACCTAT
* *
1330127 ACTAACTAATTTCTTTTCTTTTGTTTGTGTAC
1 ACTAACTAATTTCTTCTCTTTTATTTGTGTAC
*
1330159 ACTAACTTATTTCTTCTCTTTTATTTGTGT
1 ACTAACTAATTTCTTCTCTTTTATTTGTGT
1330189 CATTTTGTCA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.18, C:0.16, G:0.08, T:0.58
Consensus pattern (32 bp):
ACTAACTAATTTCTTCTCTTTTATTTGTGTAC
Found at i:1336490 original size:21 final size:21
Alignment explanation
Indices: 1336464--1336522 Score: 109
Period size: 21 Copynumber: 2.8 Consensus size: 21
1336454 GTCCGAGTTA
1336464 CCCGCGACGGCCGCAATAGCG
1 CCCGCGACGGCCGCAATAGCG
1336485 CCCGCGACGGCCGCAATAGCG
1 CCCGCGACGGCCGCAATAGCG
*
1336506 CCCGCGACGGCCACAAT
1 CCCGCGACGGCCGCAAT
1336523 CACGGTAAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.20, C:0.44, G:0.31, T:0.05
Consensus pattern (21 bp):
CCCGCGACGGCCGCAATAGCG
Found at i:1337525 original size:18 final size:18
Alignment explanation
Indices: 1337467--1337525 Score: 59
Period size: 18 Copynumber: 3.2 Consensus size: 18
1337457 AAAACTATTG
1337467 GTTTTTAAAATATCATAT
1 GTTTTTAAAATATCATAT
**
1337485 GTTTATTTTAATA-C-TATT
1 GTTT-TTAAAATATCATA-T
1337503 GGTTTTTAAAATATCATAT
1 -GTTTTTAAAATATCATAT
1337522 GTTT
1 GTTT
1337526 AATTTTAATA
Statistics
Matches: 32, Mismatches: 4, Indels: 10
0.70 0.09 0.22
Matches are distributed among these distances:
17 2 0.06
18 16 0.50
19 12 0.38
20 2 0.06
ACGTcount: A:0.32, C:0.05, G:0.08, T:0.54
Consensus pattern (18 bp):
GTTTTTAAAATATCATAT
Done.