Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D06
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: 68668488
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1920000 characters in sequence are not A, C, G, or T
File 4 of 230
Found at i:1092950 original size:4 final size:4
Alignment explanation
Indices: 1092941--1092996 Score: 51
Period size: 4 Copynumber: 14.2 Consensus size: 4
1092931 CAGAGAAGGG
* * * * * *
1092941 AGAA AGAA AGAA AGCA A-AA CGAA ACAG AGAA GGAA AGAA GGAA AGAA
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA
1092988 AGAA AGAA A
1 AGAA AGAA A
1092997 AAGAGAAATT
Statistics
Matches: 39, Mismatches: 12, Indels: 2
0.74 0.23 0.04
Matches are distributed among these distances:
3 1 0.03
4 38 0.97
ACGTcount: A:0.68, C:0.05, G:0.27, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:1092959 original size:34 final size:35
Alignment explanation
Indices: 1092896--1092989 Score: 109
Period size: 34 Copynumber: 2.6 Consensus size: 35
1092886 TATATGACAA
* *
1092896 AGAAAGAAAGAAAAGAAACAGAGAGCAAAACAAAACAG
1 AGAAGGAAAG-AAAG-AA-AGAAAGCAAAACAAAACAG
* *
1092934 AGAAGG-GAGAAAGAAAGAAAGCAAAACGAAACAG
1 AGAAGGAAAGAAAGAAAGAAAGCAAAACAAAACAG
*
1092968 AGAAGGAAAGAAGGAAAGAAAG
1 AGAAGGAAAGAAAGAAAGAAAG
1092990 AAAGAAAAAG
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
34 23 0.47
35 15 0.31
36 4 0.08
37 2 0.04
38 5 0.10
ACGTcount: A:0.65, C:0.07, G:0.28, T:0.00
Consensus pattern (35 bp):
AGAAGGAAAGAAAGAAAGAAAGCAAAACAAAACAG
Found at i:1094036 original size:25 final size:24
Alignment explanation
Indices: 1094008--1094091 Score: 93
Period size: 25 Copynumber: 3.5 Consensus size: 24
1093998 ACTTTAGCGC
*
1094008 GCTCTCTGATTATTAGCACGTTGGT
1 GCTCTCTGA-TATTAGCACGTTAGT
*
1094033 GCTCTCTGATATTTAGCACGTCAGT
1 GCTCTCTGATA-TTAGCACGTTAGT
* *
1094058 GCTCTCTG-T-TTAGCACATTTGT
1 GCTCTCTGATATTAGCACGTTAGT
1094080 GCTCTCTG-TATT
1 GCTCTCTGATATT
1094092 TGTTCCGTAT
Statistics
Matches: 52, Mismatches: 5, Indels: 6
0.83 0.08 0.10
Matches are distributed among these distances:
22 19 0.37
23 2 0.04
24 3 0.06
25 28 0.54
ACGTcount: A:0.15, C:0.23, G:0.20, T:0.42
Consensus pattern (24 bp):
GCTCTCTGATATTAGCACGTTAGT
Found at i:1094072 original size:22 final size:22
Alignment explanation
Indices: 1094020--1094088 Score: 75
Period size: 22 Copynumber: 3.0 Consensus size: 22
1094010 TCTCTGATTA
*
1094020 TTAGCACGTTGGTGCTCTCTGATAT
1 TTAGCACGTTAGTGCTCTCTG---T
*
1094045 TTAGCACGTCAGTGCTCTCTGT
1 TTAGCACGTTAGTGCTCTCTGT
* *
1094067 TTAGCACATTTGTGCTCTCTGT
1 TTAGCACGTTAGTGCTCTCTGT
1094089 ATTTGTTCCG
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
22 20 0.51
25 19 0.49
ACGTcount: A:0.14, C:0.23, G:0.22, T:0.41
Consensus pattern (22 bp):
TTAGCACGTTAGTGCTCTCTGT
Found at i:1094747 original size:21 final size:22
Alignment explanation
Indices: 1094708--1094748 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1094698 TGTAGACATA
1094708 AATTAAATGTATATAATTTGTC
1 AATTAAATGTATATAATTTGTC
1094730 AATTAATAT-TAT-TAATTTG
1 AATTAA-ATGTATATAATTTG
1094749 AATTATGGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.39
22 9 0.50
23 2 0.11
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.49
Consensus pattern (22 bp):
AATTAAATGTATATAATTTGTC
Found at i:1094924 original size:17 final size:17
Alignment explanation
Indices: 1094902--1094935 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1094892 ATGTGGCATG
*
1094902 TACCTAGGTAATGTATA
1 TACCTAAGTAATGTATA
*
1094919 TACCTAAGTGATGTATA
1 TACCTAAGTAATGTATA
1094936 GGGGTTAGTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (17 bp):
TACCTAAGTAATGTATA
Found at i:1103609 original size:13 final size:14
Alignment explanation
Indices: 1103586--1103615 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
1103576 GAGAAAAACA
1103586 AAAATGCAAAAAAG
1 AAAATGCAAAAAAG
1103600 AAAATG-AAAAAAG
1 AAAATGCAAAAAAG
1103613 AAA
1 AAA
1103616 CCAAATTGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.62
14 6 0.38
ACGTcount: A:0.77, C:0.03, G:0.13, T:0.07
Consensus pattern (14 bp):
AAAATGCAAAAAAG
Found at i:1120979 original size:7 final size:7
Alignment explanation
Indices: 1120959--1120998 Score: 64
Period size: 7 Copynumber: 5.9 Consensus size: 7
1120949 TAGATTGGTG
1120959 AATTAAA
1 AATTAAA
*
1120966 AA-AAAA
1 AATTAAA
1120972 AATTAAA
1 AATTAAA
1120979 AATTAAA
1 AATTAAA
1120986 AATTAAA
1 AATTAAA
1120993 AATTAA
1 AATTAA
1120999 TTATAAAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
6 5 0.17
7 25 0.83
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (7 bp):
AATTAAA
Found at i:1121006 original size:19 final size:18
Alignment explanation
Indices: 1120979--1121014 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
1120969 AAAAATTAAA
1120979 AATTAAAAATTAAAAATT
1 AATTAAAAATTAAAAATT
*
1120997 AATTATAAAATTATAAAT
1 AATTA-AAAATTAAAAAT
1121015 ATAAATAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
AATTAAAAATTAAAAATT
Found at i:1131368 original size:19 final size:19
Alignment explanation
Indices: 1131344--1131384 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
1131334 GAAATCCCCA
1131344 TTTGAAATTACTAATA-AAT
1 TTTGAAATT-CTAATATAAT
*
1131363 TTTGAAATTCTATTATAAT
1 TTTGAAATTCTAATATAAT
1131382 TTT
1 TTT
1131385 ACCCAAACAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.39, C:0.05, G:0.05, T:0.51
Consensus pattern (19 bp):
TTTGAAATTCTAATATAAT
Found at i:1136233 original size:29 final size:29
Alignment explanation
Indices: 1136175--1136235 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
1136165 ATAAATTAAT
*
1136175 AAATGATTAAATTATTTTTAGTCCTCTTA
1 AAATGATTAAATTATTTTTAATCCTCTTA
*
1136204 AAATGA-TAAATTTTTAATTTAATCCT-TTA
1 AAATGATTAAATTATT--TTTAATCCTCTTA
1136233 AAA
1 AAA
1136236 ATTATAAAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 8 0.29
29 12 0.43
30 8 0.29
ACGTcount: A:0.41, C:0.08, G:0.05, T:0.46
Consensus pattern (29 bp):
AAATGATTAAATTATTTTTAATCCTCTTA
Found at i:1143310 original size:22 final size:22
Alignment explanation
Indices: 1143285--1143327 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1143275 TATTCAAATA
1143285 ATAACAATAAAAT-AGTAGTAAC
1 ATAACAATAAAATGA-TAGTAAC
*
1143307 ATAACAATGAAATGATAGTAA
1 ATAACAATAAAATGATAGTAA
1143328 AACAGTGAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 18 0.95
23 1 0.05
ACGTcount: A:0.58, C:0.07, G:0.12, T:0.23
Consensus pattern (22 bp):
ATAACAATAAAATGATAGTAAC
Found at i:1147292 original size:18 final size:18
Alignment explanation
Indices: 1147265--1147357 Score: 132
Period size: 18 Copynumber: 5.2 Consensus size: 18
1147255 TACGACCGTT
1147265 TACGGTACTATTCACGTA
1 TACGGTACTATTCACGTA
** *
1147283 TACGACACTATTCACATA
1 TACGGTACTATTCACGTA
*
1147301 TACGGTACTATTCACATA
1 TACGGTACTATTCACGTA
1147319 TACGGTACTATTCACGTA
1 TACGGTACTATTCACGTA
* *
1147337 TATGGTACTGTTCACGTA
1 TACGGTACTATTCACGTA
1147355 TAC
1 TAC
1147358 AGTAGTTGGG
Statistics
Matches: 66, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 66 1.00
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (18 bp):
TACGGTACTATTCACGTA
Found at i:1153007 original size:25 final size:25
Alignment explanation
Indices: 1152967--1153016 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
1152957 GTGCTCTGGT
**
1152967 AAAAAAATATAAGTACTTAATTGAA
1 AAAAAAATATAAGTACCAAATTGAA
* *
1152992 AAAAAAATTTAGGTACCAAATTGAA
1 AAAAAAATATAAGTACCAAATTGAA
1153017 TATTAAAAAA
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:0.58, C:0.06, G:0.10, T:0.26
Consensus pattern (25 bp):
AAAAAAATATAAGTACCAAATTGAA
Found at i:1153582 original size:17 final size:20
Alignment explanation
Indices: 1153541--1153583 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
1153531 TTGCTACTAC
1153541 TTTGTTGTTATTGTATAACT
1 TTTGTTGTTATTGTATAACT
*
1153561 CTTGTT-TTATTGT-TAA-T
1 TTTGTTGTTATTGTATAACT
1153578 TTTGTT
1 TTTGTT
1153584 ACTACTTTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 6 0.29
18 3 0.14
19 7 0.33
20 5 0.24
ACGTcount: A:0.16, C:0.05, G:0.14, T:0.65
Consensus pattern (20 bp):
TTTGTTGTTATTGTATAACT
Found at i:1157576 original size:22 final size:24
Alignment explanation
Indices: 1157541--1157598 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 24
1157531 AATTGTGTAT
* *
1157541 TTTTATTATATTAA-AG-ATATAA
1 TTTTATAATTTTAATAGTATATAA
* *
1157563 TTTTATAATTTTAATAGTTTATAT
1 TTTTATAATTTTAATAGTATATAA
1157587 TTTTATAATTTT
1 TTTTATAATTTT
1157599 TAAATTATTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
22 12 0.40
23 2 0.07
24 16 0.53
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.60
Consensus pattern (24 bp):
TTTTATAATTTTAATAGTATATAA
Found at i:1158961 original size:20 final size:19
Alignment explanation
Indices: 1158945--1158984 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
1158935 ACCAAAAATT
1158945 TATTTTAAAAATTAAAAAAA
1 TATTTT-AAAATTAAAAAAA
1158965 TATTTTAAAATTAAAAAAA
1 TATTTTAAAATTAAAAAAA
1158984 T
1 T
1158985 TTAAAAAACG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
TATTTTAAAATTAAAAAAA
Found at i:1162135 original size:29 final size:28
Alignment explanation
Indices: 1162053--1162136 Score: 114
Period size: 29 Copynumber: 2.9 Consensus size: 28
1162043 CACGACCTAC
*
1162053 CACATGGCCGTGTGGTCGTCGTGTGGAT
1 CACATGGCCGTGTGGTCGCCGTGTGGAT
* *
1162081 CACATGGCCGTGTGGTTGCCCATGTGGAT
1 CACATGGCCGTGTGGTCG-CCGTGTGGAT
*
1162110 CACACGGCCGTGTGGTCGCCTGTGTGG
1 CACATGGCCGTGTGGTCGCC-GTGTGG
1162137 CTCCTATGGC
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
28 19 0.40
29 29 0.60
ACGTcount: A:0.11, C:0.25, G:0.38, T:0.26
Consensus pattern (28 bp):
CACATGGCCGTGTGGTCGCCGTGTGGAT
Found at i:1167774 original size:12 final size:12
Alignment explanation
Indices: 1167757--1167782 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1167747 AGCTAGATAA
1167757 TGATGCGGTTTT
1 TGATGCGGTTTT
1167769 TGATGCGGTTTT
1 TGATGCGGTTTT
1167781 TG
1 TG
1167783 TGTCACGTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.08, G:0.35, T:0.50
Consensus pattern (12 bp):
TGATGCGGTTTT
Found at i:1169557 original size:11 final size:11
Alignment explanation
Indices: 1169530--1169572 Score: 61
Period size: 11 Copynumber: 4.0 Consensus size: 11
1169520 TGACCTTTCC
1169530 AAGGTATGGG-
1 AAGGTATGGGA
*
1169540 TAGGTATGGGA
1 AAGGTATGGGA
*
1169551 AAGGTATGGGC
1 AAGGTATGGGA
1169562 AAGGTATGGGA
1 AAGGTATGGGA
1169573 TATATTCTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
10 9 0.32
11 19 0.68
ACGTcount: A:0.30, C:0.02, G:0.47, T:0.21
Consensus pattern (11 bp):
AAGGTATGGGA
Found at i:1169569 original size:22 final size:21
Alignment explanation
Indices: 1169530--1169572 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
1169520 TGACCTTTCC
*
1169530 AAGGTATGGGTAGGTATGGGA
1 AAGGTATGGGAAGGTATGGGA
1169551 AAGGTATGGGCAAGGTATGGGA
1 AAGGTATGGG-AAGGTATGGGA
1169573 TATATTCTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.30, C:0.02, G:0.47, T:0.21
Consensus pattern (21 bp):
AAGGTATGGGAAGGTATGGGA
Found at i:1173641 original size:18 final size:18
Alignment explanation
Indices: 1173618--1173710 Score: 114
Period size: 18 Copynumber: 5.2 Consensus size: 18
1173608 CCCAACTACT
*
1173618 GTATACGTGAACAGTACC
1 GTATACGTGAATAGTACC
**
1173636 GTATACGTGAATAGTGTC
1 GTATACGTGAATAGTACC
* *
1173654 GTATACGTAAATAGTACT
1 GTATACGTGAATAGTACC
* *
1173672 GTATACATGAATAGTGCC
1 GTATACGTGAATAGTACC
*
1173690 GTATACGTGAATAGTATC
1 GTATACGTGAATAGTACC
1173708 GTA
1 GTA
1173711 AACGATCGTA
Statistics
Matches: 61, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 61 1.00
ACGTcount: A:0.33, C:0.14, G:0.23, T:0.30
Consensus pattern (18 bp):
GTATACGTGAATAGTACC
Found at i:1173670 original size:36 final size:36
Alignment explanation
Indices: 1173618--1173710 Score: 132
Period size: 36 Copynumber: 2.6 Consensus size: 36
1173608 CCCAACTACT
* * *
1173618 GTATACGTGAACAGTACCGTATACGTGAATAGTGTC
1 GTATACGTGAATAGTACCGTATACATGAATAGTGCC
* *
1173654 GTATACGTAAATAGTACTGTATACATGAATAGTGCC
1 GTATACGTGAATAGTACCGTATACATGAATAGTGCC
*
1173690 GTATACGTGAATAGTATCGTA
1 GTATACGTGAATAGTACCGTA
1173711 AACGATCGTA
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 49 1.00
ACGTcount: A:0.33, C:0.14, G:0.23, T:0.30
Consensus pattern (36 bp):
GTATACGTGAATAGTACCGTATACATGAATAGTGCC
Found at i:1174270 original size:11 final size:11
Alignment explanation
Indices: 1174243--1174285 Score: 61
Period size: 11 Copynumber: 4.0 Consensus size: 11
1174233 TGACCTTTCC
1174243 AAGGTATGGG-
1 AAGGTATGGGA
*
1174253 TAGGTATGGGA
1 AAGGTATGGGA
*
1174264 AAGGTATGGGC
1 AAGGTATGGGA
1174275 AAGGTATGGGA
1 AAGGTATGGGA
1174286 TATATTCTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
10 9 0.32
11 19 0.68
ACGTcount: A:0.30, C:0.02, G:0.47, T:0.21
Consensus pattern (11 bp):
AAGGTATGGGA
Found at i:1174282 original size:22 final size:21
Alignment explanation
Indices: 1174243--1174285 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
1174233 TGACCTTTCC
*
1174243 AAGGTATGGGTAGGTATGGGA
1 AAGGTATGGGAAGGTATGGGA
1174264 AAGGTATGGGCAAGGTATGGGA
1 AAGGTATGGG-AAGGTATGGGA
1174286 TATATTCTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.30, C:0.02, G:0.47, T:0.21
Consensus pattern (21 bp):
AAGGTATGGGAAGGTATGGGA
Found at i:1176313 original size:36 final size:36
Alignment explanation
Indices: 1176273--1176345 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
1176263 GCCTACAAAT
1176273 AAGCTTGATTGTCCCTTGGTAAATAACGACAGAGAG
1 AAGCTTGATTGTCCCTTGGTAAATAACGACAGAGAG
1176309 AAGCTTGATTGTCCCTTGGTAAATAACGACAGAGAG
1 AAGCTTGATTGTCCCTTGGTAAATAACGACAGAGAG
1176345 A
1 A
1176346 GCTGGGACGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.34, C:0.16, G:0.25, T:0.25
Consensus pattern (36 bp):
AAGCTTGATTGTCCCTTGGTAAATAACGACAGAGAG
Found at i:1177228 original size:36 final size:36
Alignment explanation
Indices: 1177181--1177253 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
1177171 ATTAATAGTA
1177181 ATACAAAGGAGACTATTTCCCAACCCCTAATTTGTG
1 ATACAAAGGAGACTATTTCCCAACCCCTAATTTGTG
1177217 ATACAAAGGAGACTATTTCCCAACCCCTAATTTGTG
1 ATACAAAGGAGACTATTTCCCAACCCCTAATTTGTG
1177253 A
1 A
1177254 GACATTTATA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.34, C:0.25, G:0.14, T:0.27
Consensus pattern (36 bp):
ATACAAAGGAGACTATTTCCCAACCCCTAATTTGTG
Found at i:1177837 original size:20 final size:19
Alignment explanation
Indices: 1177779--1177837 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 19
1177769 AGATATGTTG
1177779 AAAATCATAGAAAATTA-TT
1 AAAATCATA-AAAATTATTT
**
1177798 AGAAATCATATTAATTATTT
1 A-AAATCATAAAAATTATTT
1177818 AAAACTCATAAAAATTATTT
1 AAAA-TCATAAAAATTATTT
1177838 TTTTGGCATT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
19 9 0.27
20 24 0.73
ACGTcount: A:0.53, C:0.07, G:0.03, T:0.37
Consensus pattern (19 bp):
AAAATCATAAAAATTATTT
Found at i:1192858 original size:41 final size:41
Alignment explanation
Indices: 1192776--1192881 Score: 131
Period size: 41 Copynumber: 2.6 Consensus size: 41
1192766 CATCGGCACG
***
1192776 AAGCCTGCTAGGCATAAAGCCTGATCTGATACACCAACATA
1 AAGCCTGCTAGGCATAAAGCCTGATAAAATACACCAACATA
** **
1192817 AAGCCTGCTAGGCATAAAGCCTGATAAAATTTACCGGCATA
1 AAGCCTGCTAGGCATAAAGCCTGATAAAATACACCAACATA
* *
1192858 AAGCCTGCTAGGCACAGAGCCTGA
1 AAGCCTGCTAGGCATAAAGCCTGA
1192882 ATATCACTGA
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 56 1.00
ACGTcount: A:0.35, C:0.25, G:0.21, T:0.19
Consensus pattern (41 bp):
AAGCCTGCTAGGCATAAAGCCTGATAAAATACACCAACATA
Found at i:1203019 original size:18 final size:18
Alignment explanation
Indices: 1202996--1203031 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1202986 TGAATTTTAG
*
1202996 ACCTTCATACATATCAAT
1 ACCTTCACACATATCAAT
*
1203014 ACCTTCACATATATCAAT
1 ACCTTCACACATATCAAT
1203032 TACTTCATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.39, C:0.28, G:0.00, T:0.33
Consensus pattern (18 bp):
ACCTTCACACATATCAAT
Found at i:1205956 original size:15 final size:14
Alignment explanation
Indices: 1205908--1205957 Score: 52
Period size: 15 Copynumber: 3.6 Consensus size: 14
1205898 GTACTAAGAA
1205908 AATATATA-TATA-
1 AATATATAGTATAG
1205920 AATA-ATAGTATTAG
1 AATATATAGTA-TAG
1205934 AATCATATAGTATAG
1 AAT-ATATAGTATAG
1205949 AGATATATA
1 A-ATATATA
1205958 ACTGATAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
11 3 0.09
12 6 0.19
13 2 0.06
14 3 0.09
15 10 0.31
16 8 0.25
ACGTcount: A:0.52, C:0.02, G:0.10, T:0.36
Consensus pattern (14 bp):
AATATATAGTATAG
Found at i:1206016 original size:22 final size:24
Alignment explanation
Indices: 1205962--1206016 Score: 64
Period size: 22 Copynumber: 2.5 Consensus size: 24
1205952 TATATAACTG
1205962 ATAATAT-TA-AAATATATACATA
1 ATAATATATATAAATATATACATA
* *
1205984 ATATTATATATAAAT-TATTCAT-
1 ATAATATATATAAATATATACATA
1206006 ATAATATATAT
1 ATAATATATAT
1206017 TAAAAAAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
22 16 0.57
23 8 0.29
24 4 0.14
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.44
Consensus pattern (24 bp):
ATAATATATATAAATATATACATA
Found at i:1206317 original size:3 final size:3
Alignment explanation
Indices: 1206309--1206346 Score: 58
Period size: 3 Copynumber: 12.3 Consensus size: 3
1206299 ACTAATGTAC
*
1206309 AAT AAT AAT AAT AAT AAT AAT AAAT AAT ATT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT A
1206347 TGAAAATAAC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:1207226 original size:35 final size:35
Alignment explanation
Indices: 1207180--1207248 Score: 138
Period size: 35 Copynumber: 2.0 Consensus size: 35
1207170 GGGTGTGTGA
1207180 TGGTGCTGGTGGCAGACAGCATGGGAGAGTGGGAG
1 TGGTGCTGGTGGCAGACAGCATGGGAGAGTGGGAG
1207215 TGGTGCTGGTGGCAGACAGCATGGGAGAGTGGGA
1 TGGTGCTGGTGGCAGACAGCATGGGAGAGTGGGA
1207249 AGAGGCAAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.20, C:0.12, G:0.51, T:0.17
Consensus pattern (35 bp):
TGGTGCTGGTGGCAGACAGCATGGGAGAGTGGGAG
Found at i:1208316 original size:75 final size:74
Alignment explanation
Indices: 1207850--1208493 Score: 798
Period size: 74 Copynumber: 8.7 Consensus size: 74
1207840 CTCAACTCAT
* * *
1207850 TCAGCGTGTCCTGAGGCTCAATTCACCTCTCGCAATATGAGTTGA--TTTTTGAAACATACAAAA
1 TCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAA-AT---AGA
*
1207913 AATTGACAA-TACC
62 AATT-AAAATTACC
* ** ** * * * * *
1207926 TAAGTATGTCTTGAGGCTCAACTCGCCTCTCGCAATACGAGTTGATTTTTTTGACAACACAAATT
1 TCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAATAGAAATT
*
1207991 GAAATTACC
66 AAAATTACC
**
1208000 TCAGCATGTGAACCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGAAAATAGAAA
1 TCAGC--GTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAATAGAAA
1208063 TTGAAAA-TACC
64 TT-AAAATTACC
** ** ** *
1208074 TCAATGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTTTGAAAACAGAAATT
1 TCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAATAGAAATT
*
1208139 GAAATTACC
66 AAAATTACC
** * * * * *
1208148 TCAGCGTGTCCTAAGGCTCAATTTATCTCTCGCAATATGAGTTGATTTTTTTTAAAAAAGAAATT
1 TCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAATAGAAATT
1208213 AAAATTACC
66 AAAATTACC
* * *
1208222 TCAGCGTGTCCCGAGGCTCAATTCATCTCTCGCAATATGAGTTGATTTTTTTTAAAAATAGAAAT
1 TCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTTGAAAATAGAAAT
1208287 TAAAATTACC
65 TAAAATTACC
* * *
1208297 TCAGCATGTCCCGAGGCTCAATTCATCTCTCGCAATATGAGTTGATTTTTTTTGAAAATAGAAAT
1 TCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTTGAAAATAGAAAT
1208362 TAAAATTACC
65 TAAAATTACC
*
1208372 TCAGCGTGTCCCGAGGCTCACCTCACCTCTCGCAATATGAGTTGATTTTTTT-AAAATAGAAATT
1 TCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAATAGAAATT
1208436 AAAATTACC
66 AAAATTACC
1208445 TCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
1 TCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
1208494 GAAAAACAAA
Statistics
Matches: 501, Mismatches: 57, Indels: 23
0.86 0.10 0.04
Matches are distributed among these distances:
72 34 0.07
73 74 0.15
74 169 0.34
75 144 0.29
76 71 0.14
77 1 0.00
78 8 0.02
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Consensus pattern (74 bp):
TCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAATAGAAATT
AAAATTACC
Found at i:1208798 original size:194 final size:193
Alignment explanation
Indices: 1208362--1208878 Score: 876
Period size: 193 Copynumber: 2.7 Consensus size: 193
1208352 AAATAGAAAT
* * * * *
1208362 TAAAATTACCTCAGCGTGTCCCGAGGCTCACCTCACCTCTCGCAATATGAGTTGATTTTTTTAAA
1 TAAAAATACCTCGGCGTGCCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTAAA
* * * ** **
1208427 ATAGAAATTAAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATT
66 A-A-AATTTAAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATT
1208492 TTGAAAAACAAAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGTCAATTTAAAACATAAAC
129 TTGAAAAACAAAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGTCAATTTAAAACATAAAC
*
1208557 TAAAAA-ACCTCGGCGTGCCCCGAGGCTCAACTCACTTCTCACAATATGAGTTGATTTTTTTTAA
1 TAAAAATACCTCGGCGTGCCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGA-TTTTTTTAA
1208621 AAAAATTTAAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTT
65 AAAAATTTAAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTT
1208686 TGAAAAACAAAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGTCAATTTAAAACATAAAC
130 TGAAAAACAAAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGTCAATTTAAAACATAAAC
1208750 TAAAAATACCTCGGCGTGCCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTT-AA
1 TAAAAATACCTCGGCGTGCCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTAAA
1208814 AAAATTTAAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTT
66 AAAATTTAAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTT
1208879 CCTTGGAAAG
Statistics
Matches: 306, Mismatches: 14, Indels: 7
0.94 0.04 0.02
Matches are distributed among these distances:
192 67 0.22
193 132 0.43
194 91 0.30
195 16 0.05
ACGTcount: A:0.34, C:0.22, G:0.14, T:0.30
Consensus pattern (193 bp):
TAAAAATACCTCGGCGTGCCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTAAA
AAAATTTAAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTT
GAAAAACAAAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGTCAATTTAAAACATAAAC
Found at i:1220003 original size:14 final size:15
Alignment explanation
Indices: 1219973--1220005 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1219963 AAACTAAACC
*
1219973 AAAATTAAAACCATA
1 AAAATTAAAAACATA
1219988 AAAATTAAAAAC-TA
1 AAAATTAAAAACATA
1220002 AAAA
1 AAAA
1220006 CAACCAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.73, C:0.09, G:0.00, T:0.18
Consensus pattern (15 bp):
AAAATTAAAAACATA
Found at i:1220891 original size:18 final size:18
Alignment explanation
Indices: 1220722--1221240 Score: 120
Period size: 18 Copynumber: 28.1 Consensus size: 18
1220712 TTTTATTTTT
* *
1220722 AAACAAGAAAAATTTT-A
1 AAACACGAAAATTTTTGA
* *
1220739 AAACACGAGAATTTTAG-
1 AAACACGAAAATTTTTGA
* *
1220756 AGACACGAAAATTCTT-A
1 AAACACGAAAATTTTTGA
*
1220773 AAACATGAAAATTTTTGA
1 AAACACGAAAATTTTTGA
* *
1220791 GAACACGACAA-TTTTGA
1 AAACACGAAAATTTTTGA
**
1220808 AATACACGAATTTTTTTGA
1 AA-ACACGAAAATTTTTGA
***
1220827 AAAC-CTGATTTTTTTTG-
1 AAACAC-GAAAATTTTTGA
* * **
1220844 AAGCGCGAAAATTCGTG-
1 AAACACGAAAATTTTTGA
* * *
1220861 AAACATGAGAATTGTTGA
1 AAACACGAAAATTTTTGA
1220879 AAACACGAAAATTTTTG-
1 AAACACGAAAATTTTTGA
*
1220896 AAACATGAAAATTTTTTGA
1 AAACACGAAAA-TTTTTGA
* **
1220915 AAACAC-AAATTTTTTTTT
1 AAACACGAAA-ATTTTTGA
* * * **
1220933 GATCATGGGAATTTTTGA
1 AAACACGAAAATTTTTGA
**
1220951 AAACGTGAAAATTTTTG-
1 AAACACGAAAATTTTTGA
* *
1220968 AAACACGAAAGTTTTCTTTTTAAAAA
1 AAACACGAAA-----ATTTTT---GA
1220994 AGAACACGAAAAAATTTTTTTTGA
1 A-AACACG--AAAA---TTTTTGA
* *
1221018 ACACGA-GAAAATTTTTTAA
1 AAAC-ACGAAAA-TTTTTGA
* *
1221037 AAACATGAAAAATTTTG-
1 AAACACGAAAATTTTTGA
*
1221054 AAACACCG-AAA-TCTTGA
1 AAACA-CGAAAATTTTTGA
*
1221071 AAACACGAAGATTTTTGA
1 AAACACGAAAATTTTTGA
** ** *
1221089 AAACAATTATTATTTTTTTTAA
1 AAAC-ACGA--A-AATTTTTGA
* *
1221111 AAAAACGAAAATTTATGA
1 AAACACGAAAATTTTTGA
* *** *
1221129 AACACAAGATTTTTTTTTAAAA
1 AA-ACACGA-AAATTTTT--GA
* *
1221151 AAACAC-AAAAATTTTCA
1 AAACACGAAAATTTTTGA
1221168 AAACACTG-AAATTTTTGA
1 AAACAC-GAAAATTTTTGA
**
1221186 AAACACGAGGATTTTT-A
1 AAACACGAAAATTTTTGA
*
1221203 AAACACGCAAAA-TTTTGG
1 AAACACG-AAAATTTTTGA
1221221 AAACACGAAAATTTTTGA
1 AAACACGAAAATTTTTGA
1221239 AA
1 AA
1221241 TACGAATTTT
Statistics
Matches: 355, Mismatches: 100, Indels: 93
0.65 0.18 0.17
Matches are distributed among these distances:
16 6 0.02
17 122 0.34
18 134 0.38
19 40 0.11
20 5 0.01
21 10 0.03
22 17 0.05
23 3 0.01
24 3 0.01
26 1 0.00
27 11 0.03
29 3 0.01
ACGTcount: A:0.45, C:0.11, G:0.12, T:0.32
Consensus pattern (18 bp):
AAACACGAAAATTTTTGA
Found at i:1220909 original size:17 final size:17
Alignment explanation
Indices: 1220716--1220982 Score: 114
Period size: 17 Copynumber: 15.3 Consensus size: 17
1220706 TTTTATTTTT
*
1220716 ATTTTT-AAACAAGAAA
1 ATTTTTGAAACACGAAA
* * *
1220732 AATTTTAAAACACGAGA
1 ATTTTTGAAACACGAAA
* *
1220749 ATTTTAGAGACACGAAA
1 ATTTTTGAAACACGAAA
* * *
1220766 ATTCTTAAAACATGAAA
1 ATTTTTGAAACACGAAA
*
1220783 ATTTTTGAGAACACGACA
1 ATTTTTGA-AACACGAAA
*
1220801 A-TTTTGAAATACACGAAT
1 ATTTTTG-AA-ACACGAAA
* **
1220819 TTTTTTGAAA-ACCTGATT
1 ATTTTTGAAACA-C-GAAA
* * *
1220837 TTTTTTGAAGCGCGAAA
1 ATTTTTGAAACACGAAA
** * *
1220854 ATTCGTGAAACATGAGA
1 ATTTTTGAAACACGAAA
*
1220871 ATTGTTGAAAACACGAAA
1 ATTTTTG-AAACACGAAA
*
1220889 ATTTTTGAAACATGAAA
1 ATTTTTGAAACACGAAA
1220906 ATTTTTTGAAAACAC-AAA
1 A-TTTTTG-AAACACGAAA
* * * **
1220924 TTTTTTTTTG-ATCATGGGA
1 ---ATTTTTGAAACACGAAA
1220943 ATTTTTGAAA-ACGTGAAA
1 ATTTTTGAAACAC--GAAA
1220961 ATTTTTGAAACACGAAA
1 ATTTTTGAAACACGAAA
*
1220978 GTTTT
1 ATTTT
1220983 CTTTTTAAAA
Statistics
Matches: 182, Mismatches: 50, Indels: 37
0.68 0.19 0.14
Matches are distributed among these distances:
16 13 0.07
17 82 0.45
18 68 0.37
19 13 0.07
20 6 0.03
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.34
Consensus pattern (17 bp):
ATTTTTGAAACACGAAA
Found at i:1220928 original size:88 final size:88
Alignment explanation
Indices: 1220761--1220930 Score: 202
Period size: 88 Copynumber: 1.9 Consensus size: 88
1220751 TTTAGAGACA
* * * * *
1220761 CGAAAATTCTTAAAACATGAAAATTTTTGAGAACACGACAATTTTGAAATACACGAATTTTTTTG
1 CGAAAATTCGTAAAACATGAAAATTGTTGAAAACACGAAAATTTTGAAATACACGAAATTTTTTG
* *
1220826 AAAACCTGATTTTTTTTGAAGCG
66 AAAACCTAAATTTTTTTGAAGCG
* * *
1220849 CGAAAATTCGTGAAACATGAGAATTGTTGAAAACACGAAAATTTTTG-AA-ACATGAAAATTTTT
1 CGAAAATTCGTAAAACATGAAAATTGTTGAAAACACGAAAA-TTTTGAAATACACG-AAATTTTT
1220912 TGAAAACAC-AAATTTTTTT
64 TGAAAAC-CTAAATTTTTTT
1220931 TTGATCATGG
Statistics
Matches: 69, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
87 4 0.06
88 59 0.86
89 6 0.09
ACGTcount: A:0.41, C:0.11, G:0.14, T:0.34
Consensus pattern (88 bp):
CGAAAATTCGTAAAACATGAAAATTGTTGAAAACACGAAAATTTTGAAATACACGAAATTTTTTG
AAAACCTAAATTTTTTTGAAGCG
Found at i:1220929 original size:35 final size:35
Alignment explanation
Indices: 1220716--1220929 Score: 127
Period size: 35 Copynumber: 6.2 Consensus size: 35
1220706 TTTTATTTTT
* *
1220716 ATTTTT-AAACAAGAAAAATT-TT-AAAACACGAGA
1 ATTTTTGAAACATG-AAAATTGTTGAAAACACGAAA
* * * * *
1220749 ATTTTAGAGACACGAAAATTCTT-AAAACATGAAA
1 ATTTTTGAAACATGAAAATTGTTGAAAACACGAAA
* * *
1220783 ATTTTTGAGAACACGACAATT-TTGAAATACACGAAT
1 ATTTTTGA-AACATGAAAATTGTTGAAA-ACACGAAA
* * *** * * *
1220819 TTTTTTGAAAACCTGATTTTTTTTG-AAGCGCGAAA
1 ATTTTTG-AAACATGAAAATTGTTGAAAACACGAAA
** *
1220854 ATTCGTGAAACATGAGAATTGTTGAAAACACGAAA
1 ATTTTTGAAACATGAAAATTGTTGAAAACACGAAA
*
1220889 ATTTTTGAAACATGAAAATTTTTTGAAAACAC-AAA
1 ATTTTTGAAACATGAAAA-TTGTTGAAAACACGAAA
*
1220924 TTTTTT
1 ATTTTT
1220930 TTTGATCATG
Statistics
Matches: 138, Mismatches: 34, Indels: 16
0.73 0.18 0.09
Matches are distributed among these distances:
33 11 0.08
34 37 0.27
35 53 0.38
36 33 0.24
37 4 0.03
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.33
Consensus pattern (35 bp):
ATTTTTGAAACATGAAAATTGTTGAAAACACGAAA
Found at i:1221020 original size:21 final size:21
Alignment explanation
Indices: 1220995--1221034 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1220985 TTTTAAAAAA
1220995 GAACACGAAAAAATTTTTTTT
1 GAACACGAAAAAATTTTTTTT
*
1221016 GAACACGAGAAAATTTTTT
1 GAACACGAAAAAATTTTTT
1221035 AAAAACATGA
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:0.42, C:0.10, G:0.12, T:0.35
Consensus pattern (21 bp):
GAACACGAAAAAATTTTTTTT
Found at i:1221041 original size:21 final size:20
Alignment explanation
Indices: 1220996--1221052 Score: 60
Period size: 21 Copynumber: 2.8 Consensus size: 20
1220986 TTTAAAAAAG
***
1220996 AACACGAAAAAATTTTTTTTG
1 AACACG-AAAAATTTTTTAAA
1221017 AACACGAGAAAATTTTTTAAA
1 AACACGA-AAAATTTTTTAAA
*
1221038 AACATGAAAAATTTT
1 AACACGAAAAATTTT
1221053 GAAACACCGA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
20 9 0.29
21 22 0.71
ACGTcount: A:0.49, C:0.09, G:0.09, T:0.33
Consensus pattern (20 bp):
AACACGAAAAATTTTTTAAA
Found at i:1221130 original size:40 final size:37
Alignment explanation
Indices: 1221083--1221172 Score: 99
Period size: 39 Copynumber: 2.3 Consensus size: 37
1221073 ACACGAAGAT
* *
1221083 TTTTGAAAACAATTATTATTTTTTTTAAAAAAACGAAAA
1 TTTTGAAAACAA-GATT-TTTTTTTAAAAAAAACGAAAA
*
1221122 TTTATGAAACACAAGATTTTTTTTTAAAAAAACACAAAAA
1 TTT-TGAAA-ACAAGATTTTTTTTTAAAAAAA-ACGAAAA
*
1221162 TTTTCAAAACA
1 TTTTGAAAACA
1221173 CTGAAATTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
38 3 0.07
39 20 0.45
40 17 0.39
41 4 0.09
ACGTcount: A:0.50, C:0.09, G:0.04, T:0.37
Consensus pattern (37 bp):
TTTTGAAAACAAGATTTTTTTTTAAAAAAAACGAAAA
Found at i:1221235 original size:35 final size:35
Alignment explanation
Indices: 1221150--1221236 Score: 104
Period size: 35 Copynumber: 2.5 Consensus size: 35
1221140 TTTTTTTAAA
* * *
1221150 AAAACACAAAAATTTTCAAAACACTGAAATTTTTG
1 AAAACACGAAAATTTTTAAAACACTGAAAATTTTG
**
1221185 AAAACACGAGGATTTTTAAAACAC-GCAAAATTTTG
1 AAAACACGAAAATTTTTAAAACACTG-AAAATTTTG
*
1221220 GAAACACGAAAATTTTT
1 AAAACACGAAAATTTTT
1221237 GAAATACGAA
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
34 1 0.02
35 42 0.98
ACGTcount: A:0.48, C:0.14, G:0.10, T:0.28
Consensus pattern (35 bp):
AAAACACGAAAATTTTTAAAACACTGAAAATTTTG
Found at i:1221245 original size:17 final size:17
Alignment explanation
Indices: 1221151--1221246 Score: 86
Period size: 17 Copynumber: 5.5 Consensus size: 17
1221141 TTTTTTAAAA
* **
1221151 AAACACAAAAATTTTCA
1 AAACACGAAAATTTTTG
1221168 AAACACTG-AAATTTTTG
1 AAACAC-GAAAATTTTTG
** *
1221185 AAAACACGAGGATTTTTA
1 -AAACACGAAAATTTTTG
*
1221203 AAACACGCAAAATTTTGG
1 AAACACG-AAAATTTTTG
1221221 AAACACGAAAATTTTTG
1 AAACACGAAAATTTTTG
*
1221238 AAATACGAA
1 AAACACGAA
1221247 TTTTTTTTTT
Statistics
Matches: 63, Mismatches: 12, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
17 38 0.60
18 25 0.40
ACGTcount: A:0.49, C:0.14, G:0.11, T:0.26
Consensus pattern (17 bp):
AAACACGAAAATTTTTG
Found at i:1221289 original size:20 final size:19
Alignment explanation
Indices: 1221197--1221289 Score: 59
Period size: 20 Copynumber: 4.9 Consensus size: 19
1221187 AACACGAGGA
*
1221197 TTTTTAAAACACGCAAAA--
1 TTTTTGAAACACG-AAAATT
*
1221215 TTTTGGAAACACGAAAA--
1 TTTTTGAAACACGAAAATT
* **
1221232 TTTTTGAAATACGAATTTTT
1 TTTTTGAAACACGAA-AATT
* * *
1221252 TTTTTAAAACGCGGAAATT
1 TTTTTGAAACACGAAAATT
1221271 TCTTTTGAAACACGAAAAT
1 T-TTTTGAAACACGAAAAT
1221290 CCGAGCGATA
Statistics
Matches: 56, Mismatches: 15, Indels: 6
0.73 0.19 0.08
Matches are distributed among these distances:
17 17 0.30
18 11 0.20
19 3 0.05
20 25 0.45
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.35
Consensus pattern (19 bp):
TTTTTGAAACACGAAAATT
Found at i:1221848 original size:8 final size:8
Alignment explanation
Indices: 1221823--1221890 Score: 86
Period size: 8 Copynumber: 8.5 Consensus size: 8
1221813 AATTGAACCC
1221823 TCTTTTTCT
1 TCTTTTT-T
*
1221832 TCCTTTTT
1 TCTTTTTT
1221840 TCTTTTTT
1 TCTTTTTT
1221848 TC-TTTTT
1 TCTTTTTT
1221855 TCTTTTTT
1 TCTTTTTT
1221863 TC-TTTTT
1 TCTTTTTT
*
1221870 TCCTTTTT
1 TCTTTTTT
1221878 TCTTCTTTT
1 TCTT-TTTT
1221887 TCTT
1 TCTT
1221891 GCTTTTTTTT
Statistics
Matches: 53, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
7 14 0.26
8 25 0.47
9 14 0.26
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (8 bp):
TCTTTTTT
Found at i:1221854 original size:15 final size:15
Alignment explanation
Indices: 1221823--1221886 Score: 92
Period size: 15 Copynumber: 4.1 Consensus size: 15
1221813 AATTGAACCC
1221823 TCTTTTTCTTCCTTTTT
1 TCTTTTT-TT-CTTTTT
1221840 TCTTTTTTTCTTTTT
1 TCTTTTTTTCTTTTT
1221855 TCTTTTTTTCTTTTT
1 TCTTTTTTTCTTTTT
*
1221870 TCCTTTTTTCTTCTTT
1 TCTTTTTTTCTT-TTT
1221886 T
1 T
1221887 TCTTGCTTTT
Statistics
Matches: 45, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
15 32 0.71
16 6 0.13
17 7 0.16
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (15 bp):
TCTTTTTTTCTTTTT
Found at i:1221865 original size:23 final size:23
Alignment explanation
Indices: 1221826--1221903 Score: 95
Period size: 23 Copynumber: 3.3 Consensus size: 23
1221816 TGAACCCTCT
*
1221826 TTTTCTTCCTTTTTTCTTTTTTTC
1 TTTT-TTCTTTTTTTCTTTTTTTC
*
1221850 TTTTTTCTTTTTTTCTTTTTTCC
1 TTTTTTCTTTTTTTCTTTTTTTC
**
1221873 TTTTTTCTTCTTTTTCTTGCTTT-
1 TTTTTTCTT-TTTTTCTTTTTTTC
1221896 TTTTTTCT
1 TTTTTTCT
1221904 GCTGGGCTGC
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
23 34 0.71
24 14 0.29
ACGTcount: A:0.00, C:0.18, G:0.01, T:0.81
Consensus pattern (23 bp):
TTTTTTCTTTTTTTCTTTTTTTC
Found at i:1222026 original size:12 final size:11
Alignment explanation
Indices: 1222005--1222049 Score: 72
Period size: 11 Copynumber: 4.0 Consensus size: 11
1221995 GGCCTGCCCT
1222005 CTTTTTTTTTG
1 CTTTTTTTTTG
1222016 CTTTGTTTTTTG
1 CTTT-TTTTTTG
*
1222028 CTTTTTTTTTT
1 CTTTTTTTTTG
1222039 CTTTTTTTTTG
1 CTTTTTTTTTG
1222050 TTGGGCTACT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
11 20 0.65
12 11 0.35
ACGTcount: A:0.00, C:0.09, G:0.09, T:0.82
Consensus pattern (11 bp):
CTTTTTTTTTG
Found at i:1222035 original size:23 final size:22
Alignment explanation
Indices: 1222005--1222049 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 22
1221995 GGCCTGCCCT
1222005 CTTTTTTTTTGCTTTGTTTTTTG
1 CTTTTTTTTTGCTTT-TTTTTTG
*
1222028 CTTTTTTTTTTCTTTTTTTTTG
1 CTTTTTTTTTGCTTTTTTTTTG
1222050 TTGGGCTACT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 7 0.33
23 14 0.67
ACGTcount: A:0.00, C:0.09, G:0.09, T:0.82
Consensus pattern (22 bp):
CTTTTTTTTTGCTTTTTTTTTG
Found at i:1222102 original size:18 final size:18
Alignment explanation
Indices: 1222074--1222116 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
1222064 GCTTGGCTAA
*
1222074 TGGGCTTGCTGGGTCGGGT
1 TGGG-TTGCTGGATCGGGT
1222093 TGGGTTGCTGGATCGGGT
1 TGGGTTGCTGGATCGGGT
*
1222111 CGGGTT
1 TGGGTT
1222117 ATACCCGGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 18 0.82
19 4 0.18
ACGTcount: A:0.02, C:0.14, G:0.51, T:0.33
Consensus pattern (18 bp):
TGGGTTGCTGGATCGGGT
Found at i:1222174 original size:3 final size:3
Alignment explanation
Indices: 1222168--1222226 Score: 73
Period size: 3 Copynumber: 18.0 Consensus size: 3
1222158 TTTCTTTTTT
1222168 TTC TTC TTTC TTC TTC TCTC TTTC TTTC TTC TTC TTC TTC TTCC TTC
1 TTC TTC -TTC TTC TTC T-TC -TTC -TTC TTC TTC TTC TTC TT-C TTC
1222215 TTC TTC TTC TTC
1 TTC TTC TTC TTC
1222227 AAAACCGAGC
Statistics
Matches: 52, Mismatches: 0, Indels: 8
0.87 0.00 0.13
Matches are distributed among these distances:
3 37 0.71
4 14 0.27
5 1 0.02
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TTC
Found at i:1222179 original size:16 final size:16
Alignment explanation
Indices: 1222158--1222225 Score: 91
Period size: 16 Copynumber: 4.1 Consensus size: 16
1222148 TTAAATTTTT
* *
1222158 TTTCTTTTTTTTCTTC
1 TTTCTTCTTCTTCTTC
1222174 TTTCTTCTTCTCTCTTTC
1 TTTCTTCTTCT-TC-TTC
1222192 TTTCTTCTTCTTCTTC
1 TTTCTTCTTCTTCTTC
*
1222208 TTCCTTCTTCTTCTTC
1 TTTCTTCTTCTTCTTC
1222224 TT
1 TT
1222226 CAAAACCGAG
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
16 29 0.62
17 4 0.09
18 14 0.30
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTCTTCTTCTTCTTC
Found at i:1222206 original size:34 final size:33
Alignment explanation
Indices: 1222158--1222222 Score: 94
Period size: 34 Copynumber: 1.9 Consensus size: 33
1222148 TTAAATTTTT
* * *
1222158 TTTCTTTTTTTTCTTCTTTCTTCTTCTCTCTTTC
1 TTTCTTCTTCTTCTTCTTCCTTCTTCT-TCTTTC
1222192 TTTCTTCTTCTTCTTCTTCCTTCTTCTTCTT
1 TTTCTTCTTCTTCTTCTTCCTTCTTCTTCTT
1222223 CTTCAAAACC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 4 0.14
34 24 0.86
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (33 bp):
TTTCTTCTTCTTCTTCTTCCTTCTTCTTCTTTC
Found at i:1222350 original size:18 final size:18
Alignment explanation
Indices: 1222327--1222369 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
1222317 TCTCTCCCCT
* *
1222327 TTTTTTTATTTTTGAAGC
1 TTTTTTTATCTTTGAAAC
*
1222345 TTTTTTTCTCTTTGAAAC
1 TTTTTTTATCTTTGAAAC
1222363 TTTTTTT
1 TTTTTTT
1222370 TTGGAGATTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.14, C:0.09, G:0.07, T:0.70
Consensus pattern (18 bp):
TTTTTTTATCTTTGAAAC
Found at i:1222617 original size:29 final size:30
Alignment explanation
Indices: 1222584--1222700 Score: 96
Period size: 30 Copynumber: 3.9 Consensus size: 30
1222574 TGTAATTTTT
*
1222584 AGAAAATTT-AGGATTAAAATGAAATTTAA
1 AGAAAATTTAAGGGTTAAAATGAAATTTAA
* * *
1222613 TGAAAGTTTAAGGGTCT-AAGTGAAATTTAA
1 AGAAAATTTAAGGGT-TAAAATGAAATTTAA
* * *
1222643 AGAAAGTTTAAGGGTCAAAACGAAATTT-A
1 AGAAAATTTAAGGGTTAAAATGAAATTTAA
* * * *
1222672 GGAAAAGTTTAGGGGTCAAAATGCAATTT
1 AGAAAA-TTTAAGGGTTAAAATGAAATTT
1222701 TTATTTTTTT
Statistics
Matches: 71, Mismatches: 13, Indels: 7
0.78 0.14 0.08
Matches are distributed among these distances:
29 12 0.17
30 58 0.82
31 1 0.01
ACGTcount: A:0.45, C:0.04, G:0.21, T:0.29
Consensus pattern (30 bp):
AGAAAATTTAAGGGTTAAAATGAAATTTAA
Found at i:1222668 original size:30 final size:30
Alignment explanation
Indices: 1222599--1222700 Score: 125
Period size: 30 Copynumber: 3.4 Consensus size: 30
1222589 ATTTAGGATT
*
1222599 AAAATGAAATTTAATGAAAGTTTAAGGGTC
1 AAAATGAAATTTAAAGAAAGTTTAAGGGTC
* *
1222629 TAAGTGAAATTTAAAGAAAGTTTAAGGGTC
1 AAAATGAAATTTAAAGAAAGTTTAAGGGTC
* * *
1222659 AAAACGAAATTT-AGGAAAAGTTTAGGGGTC
1 AAAATGAAATTTAAAG-AAAGTTTAAGGGTC
*
1222689 AAAATGCAATTT
1 AAAATGAAATTT
1222701 TTATTTTTTT
Statistics
Matches: 61, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
29 2 0.03
30 59 0.97
ACGTcount: A:0.45, C:0.05, G:0.22, T:0.28
Consensus pattern (30 bp):
AAAATGAAATTTAAAGAAAGTTTAAGGGTC
Found at i:1222722 original size:15 final size:16
Alignment explanation
Indices: 1222696--1222732 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
1222686 GTCAAAATGC
*
1222696 AATTTTTATTTTTTTA
1 AATTTTTATTTTTTGA
1222712 AATTTTT-TTTTTTGA
1 AATTTTTATTTTTTGA
1222727 AATTTT
1 AATTTT
1222733 GAAAATTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 13 0.65
16 7 0.35
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (16 bp):
AATTTTTATTTTTTGA
Found at i:1227457 original size:31 final size:31
Alignment explanation
Indices: 1227422--1227515 Score: 179
Period size: 31 Copynumber: 3.0 Consensus size: 31
1227412 GAGATGGAAA
1227422 AAAGTTGAAGAATGGAAGAAAAAGAAGGCTT
1 AAAGTTGAAGAATGGAAGAAAAAGAAGGCTT
1227453 AAAGTTGAAGAATGGAAGAAAAAGAAGGCTT
1 AAAGTTGAAGAATGGAAGAAAAAGAAGGCTT
*
1227484 AAAGTTGAAGAACGGAAGAAAAAGAAGGCTT
1 AAAGTTGAAGAATGGAAGAAAAAGAAGGCTT
1227515 A
1 A
1227516 CCTGGATGAA
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 62 1.00
ACGTcount: A:0.52, C:0.04, G:0.29, T:0.15
Consensus pattern (31 bp):
AAAGTTGAAGAATGGAAGAAAAAGAAGGCTT
Found at i:1230435 original size:25 final size:25
Alignment explanation
Indices: 1230384--1230435 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
1230374 AGCTAAATAT
* *
1230384 AACTTTGAATGAATTGCATAATAAA
1 AACTGTGAATGAATTGCATAAAAAA
*
1230409 AACTGTGAATGAA-TGTATAAAACAA
1 AACTGTGAATGAATTGCATAAAA-AA
1230434 AA
1 AA
1230436 TAGATTGCAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 7 0.30
25 16 0.70
ACGTcount: A:0.52, C:0.08, G:0.13, T:0.27
Consensus pattern (25 bp):
AACTGTGAATGAATTGCATAAAAAA
Found at i:1233127 original size:21 final size:21
Alignment explanation
Indices: 1233101--1233141 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1233091 ATCTGCTCAA
* *
1233101 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
1233122 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
1233142 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:1236913 original size:31 final size:31
Alignment explanation
Indices: 1236860--1236920 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
1236850 TTTTGGTTTA
*
1236860 TTTTTTTTTTTGTATGTATTTTTTTTTTTTC
1 TTTTTTTTTTTATATGTATTTTTTTTTTTTC
*
1236891 TTTTTTTTTTTA-ATAGTTTTTTTTTTTTTT
1 TTTTTTTTTTTATAT-GTATTTTTTTTTTTT
1236921 ATTATTATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 2 0.07
31 25 0.93
ACGTcount: A:0.08, C:0.02, G:0.05, T:0.85
Consensus pattern (31 bp):
TTTTTTTTTTTATATGTATTTTTTTTTTTTC
Found at i:1236935 original size:19 final size:18
Alignment explanation
Indices: 1236856--1236943 Score: 69
Period size: 18 Copynumber: 4.9 Consensus size: 18
1236846 AGCTTTTTGG
1236856 TTTATTTTTTTT-TTTGTA
1 TTTATTTTTTTTATTT-TA
* *
1236874 TGTATTTTTTTT-TTTTC
1 TTTATTTTTTTTATTTTA
1236891 TTT-TTTTTTTTAATAGTTT-
1 TTTATTTTTTTT-AT--TTTA
1236910 TTT-TTTTTTTTATTATTA
1 TTTATTTTTTTTATT-TTA
*
1236928 TTTATTTTATTTATTT
1 TTTATTTTTTTTATTT
1236944 GATTCATGTG
Statistics
Matches: 59, Mismatches: 4, Indels: 14
0.77 0.05 0.18
Matches are distributed among these distances:
16 9 0.15
17 5 0.08
18 21 0.36
19 21 0.36
20 3 0.05
ACGTcount: A:0.14, C:0.01, G:0.03, T:0.82
Consensus pattern (18 bp):
TTTATTTTTTTTATTTTA
Found at i:1252437 original size:22 final size:24
Alignment explanation
Indices: 1252383--1252437 Score: 64
Period size: 22 Copynumber: 2.5 Consensus size: 24
1252373 TATATAACTG
1252383 ATAATAT-TA-AAATATATACATA
1 ATAATATATATAAATATATACATA
* *
1252405 ATATTATATATAAAT-TATTCAT-
1 ATAATATATATAAATATATACATA
1252427 ATAATATATAT
1 ATAATATATAT
1252438 TAAAAAAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
22 16 0.57
23 8 0.29
24 4 0.14
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.44
Consensus pattern (24 bp):
ATAATATATATAAATATATACATA
Found at i:1252740 original size:3 final size:3
Alignment explanation
Indices: 1252732--1252769 Score: 58
Period size: 3 Copynumber: 12.3 Consensus size: 3
1252722 ACTAATGTAC
*
1252732 AAT AAT AAT AAT AAT AAT AAAT AAT AAT ATT AAT AAT A
1 AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT A
1252770 TGAAAATAAC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:1252754 original size:16 final size:16
Alignment explanation
Indices: 1252735--1252767 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1252725 AATGTACAAT
1252735 AATAATAATAATAATA
1 AATAATAATAATAATA
*
1252751 AATAATAATATTAATA
1 AATAATAATAATAATA
1252767 A
1 A
1252768 TATGAAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
AATAATAATAATAATA
Found at i:1252754 original size:19 final size:19
Alignment explanation
Indices: 1252732--1252769 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
1252722 ACTAATGTAC
1252732 AATAATAATAATAATAATA
1 AATAATAATAATAATAATA
*
1252751 AATAATAATATTAATAATA
1 AATAATAATAATAATAATA
1252770 TGAAAATAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (19 bp):
AATAATAATAATAATAATA
Found at i:1253650 original size:35 final size:35
Alignment explanation
Indices: 1253604--1253672 Score: 129
Period size: 35 Copynumber: 2.0 Consensus size: 35
1253594 GGGTGTGTGA
*
1253604 TGGTGCTGGTGGCAGACAGCATGGGAGAGTGGGAG
1 TGGTGCTGGTGGCAGACAACATGGGAGAGTGGGAG
1253639 TGGTGCTGGTGGCAGACAACATGGGAGAGTGGGA
1 TGGTGCTGGTGGCAGACAACATGGGAGAGTGGGA
1253673 AGAGGCAAGT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.22, C:0.12, G:0.49, T:0.17
Consensus pattern (35 bp):
TGGTGCTGGTGGCAGACAACATGGGAGAGTGGGAG
Found at i:1262557 original size:16 final size:17
Alignment explanation
Indices: 1262536--1262567 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1262526 TTATAAACAA
1262536 AAGAAAG-AACAGAAAT
1 AAGAAAGAAACAGAAAT
1262552 AAGAAAGAAACAGAAA
1 AAGAAAGAAACAGAAA
1262568 GCTTAAAACG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.72, C:0.06, G:0.19, T:0.03
Consensus pattern (17 bp):
AAGAAAGAAACAGAAAT
Found at i:1266930 original size:50 final size:50
Alignment explanation
Indices: 1266855--1266958 Score: 199
Period size: 50 Copynumber: 2.1 Consensus size: 50
1266845 CCATAAAAAG
1266855 ATCAACAATGAATTAATAGCATTTCCAACTTCTGTATGTTATTAATGGAA
1 ATCAACAATGAATTAATAGCATTTCCAACTTCTGTATGTTATTAATGGAA
*
1266905 ATCAACAATGAATTAATAGCATTTCCAACTTCTGTATGTTATTAATGGCA
1 ATCAACAATGAATTAATAGCATTTCCAACTTCTGTATGTTATTAATGGAA
1266955 ATCA
1 ATCA
1266959 GTTTGGTTAA
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 53 1.00
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.36
Consensus pattern (50 bp):
ATCAACAATGAATTAATAGCATTTCCAACTTCTGTATGTTATTAATGGAA
Found at i:1268678 original size:164 final size:161
Alignment explanation
Indices: 1268408--1268734 Score: 503
Period size: 164 Copynumber: 2.0 Consensus size: 161
1268398 GTAAACCACA
* * *
1268408 CAGTTGGTCACTCAACTTTTATATGTATTCATTTTGGGCACCAAATTTAAAAGTTTACAATTTAG
1 CAGTTGGCCACTCAACTTTTATAAGTATTCATTTTGGACACCAAATTTAAAAGTTTACAATTTAG
* * *
1268473 GTACTGTCGTTATATACTTTTATCATTTTAGTCACTATCGTTACATACTTTATTTTATCATTTTA
66 GTACTGTCATTATATACTTTTATCATTTTAGCCACTATCGTTACATAC-TT-TTATATCATTTTA
* * *
1268538 GTCACCCATCGTTAATTTGT-CATTAAATGTACT
129 GTCACCCACCATTAATTT-TCCATTAAATATACT
*
1268571 CAGTTGGCCACTCAACTTTTATAAGTATTCATTTTGGACACCAAAATTTAAAAGTTTGCAATTTA
1 CAGTTGGCCACTCAACTTTTATAAGTATTCATTTTGGACACC-AAATTTAAAAGTTTACAATTTA
*
1268636 GGTACTGTTATTATATACTTTTATCATTTTAGCCACTATCGTTACATACTTTTATATCATTTTAG
65 GGTACTGTCATTATATACTTTTATCATTTTAGCCACTATCGTTACATACTTTTATATCATTTTAG
*
1268701 TCGCCCACCATTAATTTTCCATTAAATATACT
130 TCACCCACCATTAATTTTCCATTAAATATACT
1268733 CA
1 CA
1268735 TTTTTAATCA
Statistics
Matches: 150, Mismatches: 12, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
161 1 0.01
162 41 0.27
163 41 0.27
164 67 0.45
ACGTcount: A:0.29, C:0.18, G:0.10, T:0.43
Consensus pattern (161 bp):
CAGTTGGCCACTCAACTTTTATAAGTATTCATTTTGGACACCAAATTTAAAAGTTTACAATTTAG
GTACTGTCATTATATACTTTTATCATTTTAGCCACTATCGTTACATACTTTTATATCATTTTAGT
CACCCACCATTAATTTTCCATTAAATATACT
Found at i:1268872 original size:23 final size:23
Alignment explanation
Indices: 1268837--1268891 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 23
1268827 AAAAAGAAAA
* *
1268837 ATAAAAAGATAAATTAGTTTTTC-
1 ATAAAAA-CTAAAGTAGTTTTTCT
*
1268860 AGTAAAAACTAAAGTATTTTTTCT
1 A-TAAAAACTAAAGTAGTTTTTCT
1268884 ATAAAAAC
1 ATAAAAAC
1268892 CTAGGTAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
23 20 0.74
24 7 0.26
ACGTcount: A:0.49, C:0.07, G:0.07, T:0.36
Consensus pattern (23 bp):
ATAAAAACTAAAGTAGTTTTTCT
Found at i:1269121 original size:24 final size:24
Alignment explanation
Indices: 1269090--1269137 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
1269080 AAAAGGATAA
1269090 AATGAGTGACCAAAATAAAAACTT
1 AATGAGTGACCAAAATAAAAACTT
1269114 AATGAGTGACCAAAATAAAAACTT
1 AATGAGTGACCAAAATAAAAACTT
1269138 TCTAAATTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.12, G:0.12, T:0.21
Consensus pattern (24 bp):
AATGAGTGACCAAAATAAAAACTT
Found at i:1270433 original size:17 final size:17
Alignment explanation
Indices: 1270402--1270453 Score: 54
Period size: 17 Copynumber: 3.0 Consensus size: 17
1270392 ACCTTTTTAT
1270402 TTTTATTTT-TGTTTTCG
1 TTTTATTTTAT-TTTTCG
*
1270419 TTTTATTTTATTTTTATG
1 TTTTATTTTATTTTT-CG
1270437 TTTT-TTTTATTATTTCG
1 TTTTATTTTATT-TTTCG
1270454 AAATATGGCT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
17 21 0.70
18 9 0.30
ACGTcount: A:0.12, C:0.04, G:0.08, T:0.77
Consensus pattern (17 bp):
TTTTATTTTATTTTTCG
Found at i:1272491 original size:19 final size:19
Alignment explanation
Indices: 1272467--1272505 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
1272457 TCACATATAG
*
1272467 TTATATGTCTCATCAATAA
1 TTATATGTCACATCAATAA
1272486 TTATATGTCACATCAATAA
1 TTATATGTCACATCAATAA
1272505 T
1 T
1272506 ACAAATAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.38, C:0.15, G:0.05, T:0.41
Consensus pattern (19 bp):
TTATATGTCACATCAATAA
Found at i:1279297 original size:68 final size:69
Alignment explanation
Indices: 1279218--1279355 Score: 242
Period size: 69 Copynumber: 2.0 Consensus size: 69
1279208 TTAATTTCTA
1279218 TAATCGGTCCCC-CTTTTTTTTCATTTTTAGCAATTTCATTTTTTCTTTTATGCTATTTTATCTT
1 TAATCGGTCCCCGCTTTTTTTTCATTTTTAGCAATTTCATTTTTTCTTTTATGCTATTTTATCTT
1279282 TTTT
66 TTTT
* * *
1279286 TAATCGGTCCCCGTTTTTTTTTCATTTTTAGCAATTTTATTTTTTCTTTTATGCTATTTTTTCTT
1 TAATCGGTCCCCGCTTTTTTTTCATTTTTAGCAATTTCATTTTTTCTTTTATGCTATTTTATCTT
1279351 TTTT
66 TTTT
1279355 T
1 T
1279356 TTCTTTTTTT
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
68 12 0.18
69 54 0.82
ACGTcount: A:0.14, C:0.16, G:0.07, T:0.64
Consensus pattern (69 bp):
TAATCGGTCCCCGCTTTTTTTTCATTTTTAGCAATTTCATTTTTTCTTTTATGCTATTTTATCTT
TTTT
Found at i:1279344 original size:22 final size:23
Alignment explanation
Indices: 1279233--1279345 Score: 58
Period size: 22 Copynumber: 5.0 Consensus size: 23
1279223 GGTCCCCCTT
*
1279233 TTTTTTCATTTT-TAGCAATTTCA
1 TTTTTTC-TTTTATAGCAATTTTA
*
1279256 TTTTTTCTTTTAT-GCTATTTTA
1 TTTTTTCTTTTATAGCAATTTTA
* * * ***
1279278 TCTTTT-TTTAATCGGTCCCCGTTT-
1 TTTTTTCTTTTAT-AG--CAATTTTA
1279302 TTTTTTCATTTT-TAGCAATTTTA
1 TTTTTTC-TTTTATAGCAATTTTA
*
1279325 TTTTTTCTTTTAT-GCTATTTT
1 TTTTTTCTTTTATAGCAATTTT
1279346 TTCTTTTTTT
Statistics
Matches: 67, Mismatches: 14, Indels: 19
0.67 0.14 0.19
Matches are distributed among these distances:
21 5 0.07
22 31 0.46
23 17 0.25
24 6 0.09
25 5 0.07
26 3 0.04
ACGTcount: A:0.15, C:0.13, G:0.06, T:0.65
Consensus pattern (23 bp):
TTTTTTCTTTTATAGCAATTTTA
Found at i:1279356 original size:11 final size:10
Alignment explanation
Indices: 1279342--1279368 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
1279332 TTTTATGCTA
1279342 TTTTTTCTTT
1 TTTTTTCTTT
1279352 TTTTTTCTTT
1 TTTTTTCTTT
1279362 TTTTTTC
1 TTTTTTC
1279369 ATTCTCTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (10 bp):
TTTTTTCTTT
Found at i:1279357 original size:22 final size:21
Alignment explanation
Indices: 1279310--1279357 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 21
1279300 TTTTTTTTCA
1279310 TTTTTAGCAATTTTATTTTTT
1 TTTTTAGCAATTTTATTTTTT
* *
1279331 CTTTTATGCTATTTT-TTCTTTT
1 TTTTTA-GCAATTTTATT-TTTT
1279353 TTTTT
1 TTTTT
1279358 CTTTTTTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
21 7 0.32
22 15 0.68
ACGTcount: A:0.12, C:0.08, G:0.04, T:0.75
Consensus pattern (21 bp):
TTTTTAGCAATTTTATTTTTT
Found at i:1281021 original size:169 final size:169
Alignment explanation
Indices: 1280704--1281021 Score: 374
Period size: 169 Copynumber: 1.9 Consensus size: 169
1280694 ATAATTATAG
* * * *
1280704 GTAAACATAAGTAGGAATGTGATGGGTTATATAAACTTCTAATGGAGTTGCTTTAGGACTCATTA
1 GTAAACAAAAGCAGGAATGCGATGGGTTATATAAACTTCTAATGGAGTTGCTTTAGAACTCATTA
*** * ** * * *
1280769 ATTTGACTGCTTCAGACATATCGACTGGATTGTTTGATGGAGTTTCAAACTCGAATCAATGCAGC
66 ATCCAACTCCTTCAGACATATCGACTGGATTGCCTGATGGAGTTTCAAACTCAAACCAATGCAAC
**
1280834 AAATTACCCAGGGTAAGCTCTAATGGAGTTAGTGGAATT
131 AAATTACCCAACGTAAGCTCTAATGGAGTTAGTGGAATT
*
1280873 GTAAACAAAAGCAGGAATGCGA-GGAGTTATATGAACTTCTAATGGAGTTGCTTTAGAACTC-TT
1 GTAAACAAAAGCAGGAATGCGATGG-GTTATATAAACTTCTAATGGAGTTGCTTTAGAACTCATT
* * * *
1280936 TATCCCAAGTCCTTCACG-CATATCGACT-GCTATGCCTGATGGGGTTTCAAACTCAAACCAATG
65 AAT-CCAACTCCTTCA-GACATATCGACTGGAT-TGCCTGATGGAGTTTCAAACTCAAACCAATG
* *
1280999 CAACACATTAGCCAACGTAAGCT
127 CAACAAATTACCCAACGTAAGCT
1281022 GTAAAACTTG
Statistics
Matches: 123, Mismatches: 22, Indels: 8
0.80 0.14 0.05
Matches are distributed among these distances:
168 8 0.07
169 114 0.93
170 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (169 bp):
GTAAACAAAAGCAGGAATGCGATGGGTTATATAAACTTCTAATGGAGTTGCTTTAGAACTCATTA
ATCCAACTCCTTCAGACATATCGACTGGATTGCCTGATGGAGTTTCAAACTCAAACCAATGCAAC
AAATTACCCAACGTAAGCTCTAATGGAGTTAGTGGAATT
Found at i:1283944 original size:18 final size:17
Alignment explanation
Indices: 1283921--1283969 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 17
1283911 TATTATTTTC
1283921 AAAATTTATTATTAAAAT
1 AAAATTTATTATT-AAAT
*
1283939 AAAATTAATTTATTAAAT
1 AAAATTTA-TTATTAAAT
1283957 AATAATTTATTAT
1 AA-AATTTATTAT
1283970 ATGATTAGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 17 0.63
19 10 0.37
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
AAAATTTATTATTAAAT
Found at i:1286150 original size:50 final size:50
Alignment explanation
Indices: 1286091--1286194 Score: 199
Period size: 50 Copynumber: 2.1 Consensus size: 50
1286081 CCATAAAAAG
*
1286091 ATCAACAATGAATTAATAGCATTTCCAACTTCTGTATGTTATTAATGGCA
1 ATCAACAATGAATTAATAGCATTTCCAACTTCTGTATGATATTAATGGCA
1286141 ATCAACAATGAATTAATAGCATTTCCAACTTCTGTATGATATTAATGGCA
1 ATCAACAATGAATTAATAGCATTTCCAACTTCTGTATGATATTAATGGCA
1286191 ATCA
1 ATCA
1286195 GTTTGGTTAA
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 53 1.00
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.35
Consensus pattern (50 bp):
ATCAACAATGAATTAATAGCATTTCCAACTTCTGTATGATATTAATGGCA
Found at i:1287769 original size:31 final size:32
Alignment explanation
Indices: 1287727--1287789 Score: 92
Period size: 34 Copynumber: 1.9 Consensus size: 32
1287717 TTAAGTACTG
*
1287727 TCGTTATATAC-TTTTATCATTTTAGTCACTA
1 TCGTTACATACTTTTTATCATTTTAGTCACTA
1287758 TCGTTACATACTTTTTTTATCATTTTAGTCAC
1 TCGTTACATAC--TTTTTATCATTTTAGTCAC
1287790 CCACTGTTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 10 0.36
34 18 0.64
ACGTcount: A:0.24, C:0.17, G:0.06, T:0.52
Consensus pattern (32 bp):
TCGTTACATACTTTTTATCATTTTAGTCACTA
Found at i:1288567 original size:21 final size:22
Alignment explanation
Indices: 1288525--1288574 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
1288515 CACATGCGTG
*
1288525 GGATTTTTCTTGAAATTATCTT
1 GGATTTTTCTGGAAATTATCTT
* *
1288547 GGATTTTTC-GGATATTTTCTT
1 GGATTTTTCTGGAAATTATCTT
1288568 GG-TTTTT
1 GGATTTTT
1288575 ATTGAGTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 5 0.20
21 11 0.44
22 9 0.36
ACGTcount: A:0.16, C:0.08, G:0.18, T:0.58
Consensus pattern (22 bp):
GGATTTTTCTGGAAATTATCTT
Found at i:1289164 original size:19 final size:19
Alignment explanation
Indices: 1289140--1289178 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
1289130 TCACAGATAG
*
1289140 TTATATTTCTCATCAATAA
1 TTATATGTCTCATCAATAA
1289159 TTATATGTCTCATCAATAA
1 TTATATGTCTCATCAATAA
1289178 T
1 T
1289179 ACAAATAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.36, C:0.15, G:0.03, T:0.46
Consensus pattern (19 bp):
TTATATGTCTCATCAATAA
Found at i:1290459 original size:46 final size:45
Alignment explanation
Indices: 1290389--1290527 Score: 179
Period size: 46 Copynumber: 3.0 Consensus size: 45
1290379 ACAATGCTAT
* *
1290389 AACTCAGTATGGCTTTCTTCACTGAAATACCATACCTACTTTTCAC
1 AACTCAGTATGG-TTTCTTAACTGAAATACCATACCTACATTTCAC
* *
1290435 GACTCAGTACGGTTATCTTAACTGAAATACCATACCTACATTTCAC
1 AACTCAGTATGGTT-TCTTAACTGAAATACCATACCTACATTTCAC
* * * *
1290481 AACTCAATATGGTTTACTTTACTGAAATACCACACCTACATTCCAC
1 AACTCAGTATGGTTT-CTTAACTGAAATACCATACCTACATTTCAC
1290527 A
1 A
1290528 CTTTTCCATG
Statistics
Matches: 81, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
45 3 0.04
46 78 0.96
ACGTcount: A:0.32, C:0.27, G:0.09, T:0.32
Consensus pattern (45 bp):
AACTCAGTATGGTTTCTTAACTGAAATACCATACCTACATTTCAC
Found at i:1301087 original size:17 final size:17
Alignment explanation
Indices: 1301065--1301098 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1301055 TACATCAATG
1301065 ATCAATCCATTTCCATT
1 ATCAATCCATTTCCATT
* *
1301082 ATCAATTCTTTTCCATT
1 ATCAATCCATTTCCATT
1301099 TTTCTTGTTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.26, C:0.26, G:0.00, T:0.47
Consensus pattern (17 bp):
ATCAATCCATTTCCATT
Found at i:1304916 original size:169 final size:169
Alignment explanation
Indices: 1304623--1304940 Score: 390
Period size: 169 Copynumber: 1.9 Consensus size: 169
1304613 ATGATTATAG
* * * * *
1304623 GTAAACATAAGTAGGAATGTGAGGAGTTATATAAACTTCTAATGGAGTTGCTTTAGGACTCATTA
1 GTAAACAAAAGCAGGAAGGCGAGGAGTTATATAAACTTCTAATGGAGTTGCTTTAGAACTCATTA
*** * ** * * *
1304688 ATTTGACTGCTTCAGACATATCGACTGGATTGTTTGATGGAGTTTGAAACTCGAACCAATGCAGC
66 ATCCAACTCCTTCAGACATATCGACTGGATTGCCTGATGGAGTTTCAAACTCAAACCAATGCAAC
*
1304753 AAATTACCCAAGGTAAGCTCTAATGGAGTTAGTGGAATT
131 AAATTACCCAACGTAAGCTCTAATGGAGTTAGTGGAATT
* *
1304792 GTAAACAAAAGCAGGAAGGCGAGGAGTTATATGAACTTCTAATGGAGTTGCTTTAGAACTCGTT-
1 GTAAACAAAAGCAGGAAGGCGAGGAGTTATATAAACTTCTAATGGAGTTGCTTTAGAACTCATTA
* * *
1304856 ATCCCAAGTCCTTCACG-CATATCGACT-GCTATGCCTGATGGGGTTTCAAACTCAAACCAATGC
66 AT-CCAACTCCTTCA-GACATATCGACTGGAT-TGCCTGATGGAGTTTCAAACTCAAACCAATGC
* *
1304919 AACACATTAGCCAACGTAAGCT
128 AACAAATTACCCAACGTAAGCT
1304941 GTAAAACTTG
Statistics
Matches: 124, Mismatches: 22, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
168 4 0.03
169 119 0.96
170 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28
Consensus pattern (169 bp):
GTAAACAAAAGCAGGAAGGCGAGGAGTTATATAAACTTCTAATGGAGTTGCTTTAGAACTCATTA
ATCCAACTCCTTCAGACATATCGACTGGATTGCCTGATGGAGTTTCAAACTCAAACCAATGCAAC
AAATTACCCAACGTAAGCTCTAATGGAGTTAGTGGAATT
Found at i:1306722 original size:16 final size:18
Alignment explanation
Indices: 1306703--1306767 Score: 71
Period size: 18 Copynumber: 3.7 Consensus size: 18
1306693 TATTTTCTTG
1306703 AAAA-TGATTTTT-AAAA
1 AAAATTGATTTTTGAAAA
1306719 AAAATTGATTTTTGAAAA
1 AAAATTGATTTTTGAAAA
** * *
1306737 ATGATTTATTTTTTAAAA
1 AAAATTGATTTTTGAAAA
*
1306755 AAAATTAATTTTT
1 AAAATTGATTTTT
1306768 TATGGTGTTT
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
16 4 0.10
17 8 0.20
18 28 0.70
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.46
Consensus pattern (18 bp):
AAAATTGATTTTTGAAAA
Found at i:1306768 original size:18 final size:18
Alignment explanation
Indices: 1306710--1306769 Score: 75
Period size: 18 Copynumber: 3.3 Consensus size: 18
1306700 TTGAAAATGA
*
1306710 TTTTTAAAAAAAATTGAT
1 TTTTTAAAAAAAATTAAT
* ** *
1306728 TTTTGAAAAATGATTTAT
1 TTTTTAAAAAAAATTAAT
1306746 TTTTTAAAAAAAATTAAT
1 TTTTTAAAAAAAATTAAT
1306764 TTTTTA
1 TTTTTA
1306770 TGGTGTTTAA
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (18 bp):
TTTTTAAAAAAAATTAAT
Found at i:1307029 original size:22 final size:22
Alignment explanation
Indices: 1307004--1307077 Score: 64
Period size: 22 Copynumber: 3.4 Consensus size: 22
1306994 ATTATTAAGC
1307004 TAGAATACAAACAATAACAAAT
1 TAGAATACAAACAATAACAAAT
** *
1307026 TAGAA-A-AATTACCCT-TCTAAAT
1 TAGAATACAA--ACAATAAC-AAAT
*
1307048 TAGAATACAAATAATAACAAAT
1 TAGAATACAAACAATAACAAAT
1307070 TAGAATAC
1 TAGAATAC
1307078 CAAGTACCAT
Statistics
Matches: 39, Mismatches: 7, Indels: 12
0.67 0.12 0.21
Matches are distributed among these distances:
20 2 0.05
21 2 0.05
22 31 0.79
23 2 0.05
24 2 0.05
ACGTcount: A:0.57, C:0.14, G:0.05, T:0.24
Consensus pattern (22 bp):
TAGAATACAAACAATAACAAAT
Found at i:1314818 original size:18 final size:18
Alignment explanation
Indices: 1314795--1314830 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1314785 TGAATTTTAG
*
1314795 ACCTTCATACATATCAAT
1 ACCTTCACACATATCAAT
*
1314813 ACCTTCACATATATCAAT
1 ACCTTCACACATATCAAT
1314831 TACTTCATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.39, C:0.28, G:0.00, T:0.33
Consensus pattern (18 bp):
ACCTTCACACATATCAAT
Found at i:1324342 original size:15 final size:16
Alignment explanation
Indices: 1324316--1324349 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
1324306 AAAATGTATA
1324316 TAAATAAATAATAAAT
1 TAAATAAATAATAAAT
*
1324332 TAAAT-AATAATATAT
1 TAAATAAATAATAAAT
1324347 TAA
1 TAA
1324350 CATTTTCCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
TAAATAAATAATAAAT
Found at i:1325734 original size:37 final size:37
Alignment explanation
Indices: 1325673--1325865 Score: 255
Period size: 37 Copynumber: 5.0 Consensus size: 37
1325663 TACGTATGAT
*
1325673 CACTTATCAC-TTGTC-CCTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
* *
1325708 CACCTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
1325745 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
1325782 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGC
1 CACTTATCACTTTGTCTCTTGATCAGATAA--GT-G-T--AGC
*
1325825 TATCACTTATCACTTTGTCTCTTGATCAGATAAGTATAGC
1 ---CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
1325865 C
1 C
1325866 GAAGCTATCA
Statistics
Matches: 141, Mismatches: 6, Indels: 20
0.84 0.04 0.12
Matches are distributed among these distances:
35 9 0.06
36 4 0.03
37 85 0.60
39 2 0.01
40 4 0.03
41 1 0.01
42 1 0.01
43 3 0.02
44 2 0.01
46 30 0.21
ACGTcount: A:0.26, C:0.22, G:0.16, T:0.36
Consensus pattern (37 bp):
CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
Found at i:1325835 original size:46 final size:46
Alignment explanation
Indices: 1325782--1326050 Score: 340
Period size: 46 Copynumber: 5.6 Consensus size: 46
1325772 TAAGTGTAGC
* **
1325782 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* *
1325828 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
1325874 CACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
1 CACTTATCAC---T---TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
*
1325926 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* ** *
1325972 TACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCAC--T----TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
1326024 CACTTATCACTTTGTCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
1326051 AGTACTCAAA
Statistics
Matches: 199, Mismatches: 12, Indels: 24
0.85 0.05 0.10
Matches are distributed among these distances:
46 112 0.56
48 1 0.01
49 2 0.01
50 1 0.01
52 83 0.42
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.35
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
Found at i:1325901 original size:52 final size:52
Alignment explanation
Indices: 1325825--1326044 Score: 299
Period size: 52 Copynumber: 4.3 Consensus size: 52
1325815 TAGCTAAAGC
* *
1325825 TATCACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACT
1 TATCACTTTTCAC-TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
1325878 TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
1325930 TATCAC---T---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
* * ** *
1325976 TATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
1326028 TATCACTTTGTCACTTG
1 TATCACTTT-TCACTTG
1326045 ATCAGAAGTA
Statistics
Matches: 148, Mismatches: 12, Indels: 14
0.85 0.07 0.08
Matches are distributed among these distances:
46 43 0.29
49 1 0.01
52 86 0.58
53 18 0.12
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (52 bp):
TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
Found at i:1325947 original size:98 final size:98
Alignment explanation
Indices: 1325782--1326050 Score: 457
Period size: 98 Copynumber: 2.7 Consensus size: 98
1325772 TAAGTGTAGC
* * *
1325782 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCTCT
1 CACTTTTCAC-TTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACT
1325847 TGATCAGATAAGTATAGCCGAAGCTATCACTTAT
65 TGATCAGATAAGTATAGCCGAAGCTATCACTTAT
**
1325881 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTGTCACTT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
*
1325946 GATCAGATAAGTATAGCCGAAGCTATTACTTAT
66 GATCAGATAAGTATAGCCGAAGCTATCACTTAT
* *
1325979 CACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
1326044 GATCAGA
66 GATCAGA
1326051 AGTACTCAAA
Statistics
Matches: 160, Mismatches: 10, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
98 151 0.94
99 9 0.06
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.35
Consensus pattern (98 bp):
CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
GATCAGATAAGTATAGCCGAAGCTATCACTTAT
Found at i:1329228 original size:49 final size:50
Alignment explanation
Indices: 1329173--1329481 Score: 327
Period size: 49 Copynumber: 5.9 Consensus size: 50
1329163 TTCGTTTTCT
* *
1329173 CGATGCCATAGTCCAACTATGGTCTTACACGTAATCACA-AATCACATAC
1 CGATGCCATAGCCCAACTATGGTCTTACACGTAATCACACAATCACTTAC
* * * *
1329222 CGATGCCAGAGCCCAACTACGGTCTTACACGAAATCACA-TATCACTTAC
1 CGATGCCATAGCCCAACTATGGTCTTACACGTAATCACACAATCACTTAC
*
1329271 CGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACATATCACACATATCACTTAC
1 CGATGCCATAGCCCAACTATGGTCTTACAC-G--T---A-ATCACACA-ATCACTTAC
* * *
1329329 CGATGCCATAGCCCAACTACGGTCTTACACGAAATCACA-TATCACTTAC
1 CGATGCCATAGCCCAACTATGGTCTTACACGTAATCACACAATCACTTAC
*
1329378 CGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACATATCACACATATCACTTAC
1 CGATGCCATAGCCCAACTATGGTCTTACAC-G--T---A-ATCACACA-ATCACTTAC
* * *
1329436 CGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACATAATCAC
1 CGATGCCATAGCCCAACTATGGTCTTACACGTAATCACACAATCAC
1329482 ATGTTCACAT
Statistics
Matches: 221, Mismatches: 21, Indels: 35
0.80 0.08 0.13
Matches are distributed among these distances:
49 107 0.48
50 7 0.03
51 13 0.06
52 2 0.01
55 2 0.01
56 12 0.05
57 2 0.01
58 76 0.34
ACGTcount: A:0.32, C:0.31, G:0.14, T:0.23
Consensus pattern (50 bp):
CGATGCCATAGCCCAACTATGGTCTTACACGTAATCACACAATCACTTAC
Found at i:1329343 original size:58 final size:58
Alignment explanation
Indices: 1329257--1329482 Score: 362
Period size: 58 Copynumber: 4.0 Consensus size: 58
1329247 TACACGAAAT
1329257 CACATATCACTTACCGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACATATCA
1 CACATATCACTTACCGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACATATCA
* *
1329315 CACATATCACTTACCGATGCCATAGCCCAACTACGGTCTTACAC-G----A-A-AT--
1 CACATATCACTTACCGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACATATCA
1329364 CACATATCACTTACCGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACATATCA
1 CACATATCACTTACCGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACATATCA
1329422 CACATATCACTTACCGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACATAATCA
1 CACATATCACTTACCGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACAT-ATCA
1329481 CA
1 CA
1329483 TGTTCACATG
Statistics
Matches: 154, Mismatches: 4, Indels: 19
0.87 0.02 0.11
Matches are distributed among these distances:
49 42 0.27
50 1 0.01
51 2 0.01
52 1 0.01
53 1 0.01
54 1 0.01
55 1 0.01
56 2 0.01
57 1 0.01
58 96 0.62
59 6 0.04
ACGTcount: A:0.32, C:0.31, G:0.13, T:0.23
Consensus pattern (58 bp):
CACATATCACTTACCGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACATATCA
Found at i:1329399 original size:107 final size:107
Alignment explanation
Indices: 1329208--1329481 Score: 485
Period size: 107 Copynumber: 2.6 Consensus size: 107
1329198 TACACGTAAT
* * *
1329208 CACAAATCACATACCGATGCCAGAGCCCAACTACGGTCTTACACGAAATCACATATCACTTACCG
1 CACATATCACTTACCGATGCCATAGCCCAACTACGGTCTTACACGAAATCACATATCACTTACCG
1329273 ATGCCATAGCCCAGCTATGGTCTTACACGGAATCACATATCA
66 ATGCCATAGCCCAGCTATGGTCTTACACGGAATCACATATCA
1329315 CACATATCACTTACCGATGCCATAGCCCAACTACGGTCTTACACGAAATCACATATCACTTACCG
1 CACATATCACTTACCGATGCCATAGCCCAACTACGGTCTTACACGAAATCACATATCACTTACCG
1329380 ATGCCATAGCCCAGCTATGGTCTTACACGGAATCACATATCA
66 ATGCCATAGCCCAGCTATGGTCTTACACGGAATCACATATCA
* * *
1329422 CACATATCACTTACCGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACATAATCAC
1 CACATATCACTTACCGATGCCATAGCCCAACTACGGTCTTACACGAAATCACAT-ATCAC
1329482 ATGTTCACAT
Statistics
Matches: 160, Mismatches: 6, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
107 155 0.97
108 5 0.03
ACGTcount: A:0.32, C:0.32, G:0.14, T:0.22
Consensus pattern (107 bp):
CACATATCACTTACCGATGCCATAGCCCAACTACGGTCTTACACGAAATCACATATCACTTACCG
ATGCCATAGCCCAGCTATGGTCTTACACGGAATCACATATCA
Found at i:1329463 original size:28 final size:28
Alignment explanation
Indices: 1329373--1329463 Score: 80
Period size: 28 Copynumber: 3.2 Consensus size: 28
1329363 TCACATATCA
1329373 CTTACCGATGCCATAGCCCAGCTATGGT
1 CTTACCGATGCCATAGCCCAGCTATGGT
* * **
1329401 CTTACACGGAAT-CACATATCACA-CATAT-CA
1 CTTAC-C-G-ATGC-CATAGCCCAGC-TATGGT
1329431 CTTACCGATGCCATAGCCCAGCTATGGT
1 CTTACCGATGCCATAGCCCAGCTATGGT
1329459 CTTAC
1 CTTAC
1329464 ACGGAATCAC
Statistics
Matches: 47, Mismatches: 8, Indels: 16
0.66 0.11 0.23
Matches are distributed among these distances:
27 12 0.26
28 13 0.28
29 2 0.04
30 8 0.17
31 12 0.26
ACGTcount: A:0.27, C:0.32, G:0.15, T:0.25
Consensus pattern (28 bp):
CTTACCGATGCCATAGCCCAGCTATGGT
Found at i:1330797 original size:37 final size:37
Alignment explanation
Indices: 1330740--1330890 Score: 171
Period size: 37 Copynumber: 3.9 Consensus size: 37
1330730 TATGATCACT
*
1330740 TATCAC-TTGTC-CCTGATCAGATAAGTGTAGCCACC
1 TATCACTTTGTCTCTTGATCAGATAAGTGTAGCCACC
* *
1330775 TATCACTTTGTTTCTTGATCAGATAAGTGTAGCCACT
1 TATCACTTTGTCTCTTGATCAGATAAGTGTAGCCACC
1330812 TATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCAC
1 TATCACTTTGTCTCTTGATCAGATAAGTGTAGC-----C-A-C-C
*
1330857 TTATCACTTTGTCTCTTGATCAGATAAGTATAGC
1 -TATCACTTTGTCTCTTGATCAGATAAGTGTAGC
1330891 TGAAGCTATC
Statistics
Matches: 99, Mismatches: 6, Indels: 11
0.85 0.05 0.09
Matches are distributed among these distances:
35 6 0.06
36 4 0.04
37 54 0.55
42 1 0.01
43 1 0.01
44 1 0.01
46 32 0.32
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.36
Consensus pattern (37 bp):
TATCACTTTGTCTCTTGATCAGATAAGTGTAGCCACC
Found at i:1330875 original size:46 final size:46
Alignment explanation
Indices: 1330808--1331076 Score: 340
Period size: 46 Copynumber: 5.6 Consensus size: 46
1330798 TAAGTGTAGC
* *
1330808 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTAT
* *
1330854 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCTGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTAT
*
1330900 CACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
1 CACTTATCAC---T---TTGTCACTTGATCAGATAAGTGTAGCTGAAGCTAT
* *
1330952 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTAT
* * *
1330998 TACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCAC--T----TTGTCACTTGATCAGATAAGTGTAGCTGAAGCTAT
1331050 CACTTATCACTTTGTCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
1331077 AGTACTCAAA
Statistics
Matches: 199, Mismatches: 12, Indels: 24
0.85 0.05 0.10
Matches are distributed among these distances:
46 113 0.57
48 1 0.01
49 2 0.01
50 1 0.01
52 82 0.41
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.35
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTAT
Found at i:1330927 original size:52 final size:52
Alignment explanation
Indices: 1330851--1331070 Score: 290
Period size: 52 Copynumber: 4.3 Consensus size: 52
1330841 TAGCTAAAGC
* * *
1330851 TATCACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCTGAAGCTATCACT
1 TATCACTTTTCAC-TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
1330904 TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
1330956 TATCAC---T---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
* * ** *
1331002 TATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
1331054 TATCACTTTGTCACTTG
1 TATCACTTT-TCACTTG
1331071 ATCAGAAGTA
Statistics
Matches: 147, Mismatches: 13, Indels: 14
0.84 0.07 0.08
Matches are distributed among these distances:
46 43 0.29
49 1 0.01
52 85 0.58
53 18 0.12
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.36
Consensus pattern (52 bp):
TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
Found at i:1330973 original size:98 final size:98
Alignment explanation
Indices: 1330808--1331076 Score: 448
Period size: 98 Copynumber: 2.7 Consensus size: 98
1330798 TAAGTGTAGC
* * *
1330808 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCTCT
1 CACTTTTCAC-TTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACT
*
1330873 TGATCAGATAAGTATAGCTGAAGCTATCACTTAT
65 TGATCAGATAAGTATAGCCGAAGCTATCACTTAT
**
1330907 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTGTCACTT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
*
1330972 GATCAGATAAGTATAGCCGAAGCTATTACTTAT
66 GATCAGATAAGTATAGCCGAAGCTATCACTTAT
* *
1331005 CACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
1331070 GATCAGA
66 GATCAGA
1331077 AGTACTCAAA
Statistics
Matches: 159, Mismatches: 11, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
98 150 0.94
99 9 0.06
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.35
Consensus pattern (98 bp):
CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
GATCAGATAAGTATAGCCGAAGCTATCACTTAT
Found at i:1334255 original size:49 final size:50
Alignment explanation
Indices: 1334200--1334508 Score: 327
Period size: 49 Copynumber: 5.9 Consensus size: 50
1334190 TTCGTTTTCT
* *
1334200 CGATGCCATAGTCCAACTATGGTCTTACACGTAATCACA-AATCACATAC
1 CGATGCCATAGCCCAACTATGGTCTTACACGTAATCACACAATCACTTAC
* * * *
1334249 CGATGCCAGAGCCCAACTACGGTCTTACACGAAATCACA-TATCACTTAC
1 CGATGCCATAGCCCAACTATGGTCTTACACGTAATCACACAATCACTTAC
*
1334298 CGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACATATCACACATATCACTTAC
1 CGATGCCATAGCCCAACTATGGTCTTACAC-G--T---A-ATCACACA-ATCACTTAC
* * *
1334356 CGATGCCATAGCCCAACTACGGTCTTACACGAAATCACA-TATCACTTAC
1 CGATGCCATAGCCCAACTATGGTCTTACACGTAATCACACAATCACTTAC
*
1334405 CGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACATATCACACATATCACTTAC
1 CGATGCCATAGCCCAACTATGGTCTTACAC-G--T---A-ATCACACA-ATCACTTAC
* * *
1334463 CGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACATAATCAC
1 CGATGCCATAGCCCAACTATGGTCTTACACGTAATCACACAATCAC
1334509 ATGTTCACAT
Statistics
Matches: 221, Mismatches: 21, Indels: 35
0.80 0.08 0.13
Matches are distributed among these distances:
49 107 0.48
50 7 0.03
51 13 0.06
52 2 0.01
55 2 0.01
56 12 0.05
57 2 0.01
58 76 0.34
ACGTcount: A:0.32, C:0.31, G:0.14, T:0.23
Consensus pattern (50 bp):
CGATGCCATAGCCCAACTATGGTCTTACACGTAATCACACAATCACTTAC
Found at i:1334370 original size:58 final size:58
Alignment explanation
Indices: 1334284--1334509 Score: 362
Period size: 58 Copynumber: 4.0 Consensus size: 58
1334274 TACACGAAAT
1334284 CACATATCACTTACCGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACATATCA
1 CACATATCACTTACCGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACATATCA
* *
1334342 CACATATCACTTACCGATGCCATAGCCCAACTACGGTCTTACAC-G----A-A-AT--
1 CACATATCACTTACCGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACATATCA
1334391 CACATATCACTTACCGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACATATCA
1 CACATATCACTTACCGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACATATCA
1334449 CACATATCACTTACCGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACATAATCA
1 CACATATCACTTACCGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACAT-ATCA
1334508 CA
1 CA
1334510 TGTTCACATG
Statistics
Matches: 154, Mismatches: 4, Indels: 19
0.87 0.02 0.11
Matches are distributed among these distances:
49 42 0.27
50 1 0.01
51 2 0.01
52 1 0.01
53 1 0.01
54 1 0.01
55 1 0.01
56 2 0.01
57 1 0.01
58 96 0.62
59 6 0.04
ACGTcount: A:0.32, C:0.31, G:0.13, T:0.23
Consensus pattern (58 bp):
CACATATCACTTACCGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACATATCA
Found at i:1334426 original size:107 final size:107
Alignment explanation
Indices: 1334235--1334508 Score: 485
Period size: 107 Copynumber: 2.6 Consensus size: 107
1334225 TACACGTAAT
* * *
1334235 CACAAATCACATACCGATGCCAGAGCCCAACTACGGTCTTACACGAAATCACATATCACTTACCG
1 CACATATCACTTACCGATGCCATAGCCCAACTACGGTCTTACACGAAATCACATATCACTTACCG
1334300 ATGCCATAGCCCAGCTATGGTCTTACACGGAATCACATATCA
66 ATGCCATAGCCCAGCTATGGTCTTACACGGAATCACATATCA
1334342 CACATATCACTTACCGATGCCATAGCCCAACTACGGTCTTACACGAAATCACATATCACTTACCG
1 CACATATCACTTACCGATGCCATAGCCCAACTACGGTCTTACACGAAATCACATATCACTTACCG
1334407 ATGCCATAGCCCAGCTATGGTCTTACACGGAATCACATATCA
66 ATGCCATAGCCCAGCTATGGTCTTACACGGAATCACATATCA
* * *
1334449 CACATATCACTTACCGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACATAATCAC
1 CACATATCACTTACCGATGCCATAGCCCAACTACGGTCTTACACGAAATCACAT-ATCAC
1334509 ATGTTCACAT
Statistics
Matches: 160, Mismatches: 6, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
107 155 0.97
108 5 0.03
ACGTcount: A:0.32, C:0.32, G:0.14, T:0.22
Consensus pattern (107 bp):
CACATATCACTTACCGATGCCATAGCCCAACTACGGTCTTACACGAAATCACATATCACTTACCG
ATGCCATAGCCCAGCTATGGTCTTACACGGAATCACATATCA
Found at i:1334490 original size:28 final size:28
Alignment explanation
Indices: 1334400--1334490 Score: 80
Period size: 28 Copynumber: 3.2 Consensus size: 28
1334390 TCACATATCA
1334400 CTTACCGATGCCATAGCCCAGCTATGGT
1 CTTACCGATGCCATAGCCCAGCTATGGT
* * **
1334428 CTTACACGGAAT-CACATATCACA-CATAT-CA
1 CTTAC-C-G-ATGC-CATAGCCCAGC-TATGGT
1334458 CTTACCGATGCCATAGCCCAGCTATGGT
1 CTTACCGATGCCATAGCCCAGCTATGGT
1334486 CTTAC
1 CTTAC
1334491 ACGGAATCAC
Statistics
Matches: 47, Mismatches: 8, Indels: 16
0.66 0.11 0.23
Matches are distributed among these distances:
27 12 0.26
28 13 0.28
29 2 0.04
30 8 0.17
31 12 0.26
ACGTcount: A:0.27, C:0.32, G:0.15, T:0.25
Consensus pattern (28 bp):
CTTACCGATGCCATAGCCCAGCTATGGT
Found at i:1335824 original size:37 final size:37
Alignment explanation
Indices: 1335767--1335917 Score: 171
Period size: 37 Copynumber: 3.9 Consensus size: 37
1335757 TATGATCACT
*
1335767 TATCAC-TTGTC-CCTGATCAGATAAGTGTAGCCACC
1 TATCACTTTGTCTCTTGATCAGATAAGTGTAGCCACC
* *
1335802 TATCACTTTGTTTCTTGATCAGATAAGTGTAGCCACT
1 TATCACTTTGTCTCTTGATCAGATAAGTGTAGCCACC
1335839 TATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCAC
1 TATCACTTTGTCTCTTGATCAGATAAGTGTAGC-----C-A-C-C
*
1335884 TTATCACTTTGTCTCTTGATCAGATAAGTATAGC
1 -TATCACTTTGTCTCTTGATCAGATAAGTGTAGC
1335918 TGAAGCTATC
Statistics
Matches: 99, Mismatches: 6, Indels: 11
0.85 0.05 0.09
Matches are distributed among these distances:
35 6 0.06
36 4 0.04
37 54 0.55
42 1 0.01
43 1 0.01
44 1 0.01
46 32 0.32
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.36
Consensus pattern (37 bp):
TATCACTTTGTCTCTTGATCAGATAAGTGTAGCCACC
Found at i:1335902 original size:46 final size:46
Alignment explanation
Indices: 1335835--1336103 Score: 340
Period size: 46 Copynumber: 5.6 Consensus size: 46
1335825 TAAGTGTAGC
* *
1335835 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTAT
* *
1335881 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCTGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTAT
*
1335927 CACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
1 CACTTATCAC---T---TTGTCACTTGATCAGATAAGTGTAGCTGAAGCTAT
* *
1335979 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTAT
* * *
1336025 TACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCAC--T----TTGTCACTTGATCAGATAAGTGTAGCTGAAGCTAT
1336077 CACTTATCACTTTGTCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
1336104 AGTACTCAAA
Statistics
Matches: 199, Mismatches: 12, Indels: 24
0.85 0.05 0.10
Matches are distributed among these distances:
46 113 0.57
48 1 0.01
49 2 0.01
50 1 0.01
52 82 0.41
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.35
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTAT
Found at i:1335954 original size:52 final size:52
Alignment explanation
Indices: 1335878--1336097 Score: 290
Period size: 52 Copynumber: 4.3 Consensus size: 52
1335868 TAGCTAAAGC
* * *
1335878 TATCACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCTGAAGCTATCACT
1 TATCACTTTTCAC-TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
1335931 TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
1335983 TATCAC---T---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
* * ** *
1336029 TATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
1336081 TATCACTTTGTCACTTG
1 TATCACTTT-TCACTTG
1336098 ATCAGAAGTA
Statistics
Matches: 147, Mismatches: 13, Indels: 14
0.84 0.07 0.08
Matches are distributed among these distances:
46 43 0.29
49 1 0.01
52 85 0.58
53 18 0.12
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.36
Consensus pattern (52 bp):
TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
Found at i:1336000 original size:98 final size:98
Alignment explanation
Indices: 1335835--1336103 Score: 448
Period size: 98 Copynumber: 2.7 Consensus size: 98
1335825 TAAGTGTAGC
* * *
1335835 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCTCT
1 CACTTTTCAC-TTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACT
*
1335900 TGATCAGATAAGTATAGCTGAAGCTATCACTTAT
65 TGATCAGATAAGTATAGCCGAAGCTATCACTTAT
**
1335934 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTGTCACTT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
*
1335999 GATCAGATAAGTATAGCCGAAGCTATTACTTAT
66 GATCAGATAAGTATAGCCGAAGCTATCACTTAT
* *
1336032 CACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
1336097 GATCAGA
66 GATCAGA
1336104 AGTACTCAAA
Statistics
Matches: 159, Mismatches: 11, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
98 150 0.94
99 9 0.06
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.35
Consensus pattern (98 bp):
CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
GATCAGATAAGTATAGCCGAAGCTATCACTTAT
Found at i:1347733 original size:2 final size:2
Alignment explanation
Indices: 1347726--1347771 Score: 65
Period size: 2 Copynumber: 23.0 Consensus size: 2
1347716 ATGTATATCA
* * *
1347726 AG AG AG AG AG AG AG GG AG AG AG GG GG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1347768 AG AG
1 AG AG
1347772 CTATTTTCTA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.43, C:0.00, G:0.57, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1353752 original size:5 final size:5
Alignment explanation
Indices: 1353742--1353814 Score: 64
Period size: 5 Copynumber: 14.8 Consensus size: 5
1353732 TGTTAAAAAA
* * *
1353742 ATATT ATATT ATAGTA ATGATT ATGTT -TTTT ATATT ATATT ATTATT
1 ATATT ATATT ATA-TT AT-ATT ATATT ATATT ATATT ATATT A-TATT
1353789 A-A-T ATATT ATATT ATATT ATA-T ATAT
1 ATATT ATATT ATATT ATATT ATATT ATAT
1353815 ACATAAAACA
Statistics
Matches: 56, Mismatches: 5, Indels: 14
0.75 0.07 0.19
Matches are distributed among these distances:
3 2 0.04
4 9 0.16
5 33 0.59
6 11 0.20
7 1 0.02
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (5 bp):
ATATT
Found at i:1353794 original size:19 final size:19
Alignment explanation
Indices: 1353772--1353814 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
1353762 TTATGTTTTT
1353772 TATATTATATTATTATTA-A
1 TATATTATATTA-TATTATA
1353791 TATATTATATTATATTATA
1 TATATTATATTATATTATA
1353810 TATAT
1 TATAT
1353815 ACATAAAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 5 0.22
19 18 0.78
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
TATATTATATTATATTATA
Found at i:1353847 original size:18 final size:19
Alignment explanation
Indices: 1353819--1353858 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
1353809 ATATATACAT
*
1353819 AAAACAAAAGAAAGAATAG
1 AAAACAAAAGAAAGAAAAG
1353838 AAAA-AAAAGAAAGAAAAG
1 AAAACAAAAGAAAGAAAAG
1353856 AAA
1 AAA
1353859 CAGAATAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.80, C:0.03, G:0.15, T:0.03
Consensus pattern (19 bp):
AAAACAAAAGAAAGAAAAG
Found at i:1354822 original size:44 final size:45
Alignment explanation
Indices: 1354727--1354860 Score: 162
Period size: 44 Copynumber: 3.0 Consensus size: 45
1354717 ACAGGACAGA
* *
1354727 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG
* *
1354773 ACAGGATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
* ** * *
1354817 ACAGGAATAATTCATGTAAGTCCATGTTAAAGACATGGCATTGG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
1354861 CAGGATATTG
Statistics
Matches: 75, Mismatches: 11, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
44 37 0.49
45 1 0.01
46 37 0.49
ACGTcount: A:0.35, C:0.13, G:0.24, T:0.28
Consensus pattern (45 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
Done.