Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032249.1 Gossypioides kirkii chromosome KI_07
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: 37252039
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 2100 characters in sequence are not A, C, G, or T
File 101 of 120
Found at i:29109171 original size:13 final size:12
Alignment explanation
Indices: 29109133--29109172 Score: 55
Period size: 12 Copynumber: 3.2 Consensus size: 12
29109123 AATTTTAAAA
29109133 TTTAAAACATAT
1 TTTAAAACATAT
29109145 TTTAAAAGCA-AT
1 TTTAAAA-CATAT
29109157 TTTCAAAACATAT
1 TTT-AAAACATAT
29109170 TTT
1 TTT
29109173 TGTAAATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
12 14 0.56
13 11 0.44
ACGTcount: A:0.45, C:0.10, G:0.03, T:0.42
Consensus pattern (12 bp):
TTTAAAACATAT
Found at i:29111795 original size:31 final size:31
Alignment explanation
Indices: 29111735--29111795 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
29111725 TTTGTTATTA
*
29111735 AATTATTCGAAAATTTTTATTGAAATCATTG
1 AATTATTCGAAAATTTTCATTGAAATCATTG
* *
29111766 AATTATTC-AAAAGTTTTCATTTAAGTCATT
1 AATTATTCGAAAA-TTTTCATTGAAATCATT
29111796 AGGATGCTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 4 0.15
31 22 0.85
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (31 bp):
AATTATTCGAAAATTTTCATTGAAATCATTG
Found at i:29151351 original size:20 final size:21
Alignment explanation
Indices: 29151326--29151375 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
29151316 TTATATTTTA
29151326 TATTATTAATAATAA-AATAT
1 TATTATTAATAATAATAATAT
* *
29151346 TATTATTTATTATAATAATAT
1 TATTATTAATAATAATAATAT
29151367 TA--ATTAATA
1 TATTATTAATA
29151376 TATCTTTTGA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
19 5 0.20
20 13 0.52
21 7 0.28
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
TATTATTAATAATAATAATAT
Found at i:29151360 original size:23 final size:24
Alignment explanation
Indices: 29151318--29151363 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
29151308 TTCTTTACTT
29151318 ATATTTTATATTATTAATAATAAA
1 ATATTTTATATTATTAATAATAAA
29151342 ATATTATTAT-TTATT-ATAATAA
1 ATATT-TTATATTATTAATAATAA
29151364 TATTAATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 7 0.33
24 10 0.48
25 4 0.19
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (24 bp):
ATATTTTATATTATTAATAATAAA
Found at i:29151377 original size:18 final size:18
Alignment explanation
Indices: 29151329--29151377 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 18
29151319 TATTTTATAT
* *
29151329 TATTAA-TAATAAAATAT
1 TATTAATTAATATAATAA
* *
29151346 TATTATTTATTATAATAA
1 TATTAATTAATATAATAA
29151364 TATTAATTAATATA
1 TATTAATTAATATA
29151378 TCTTTTGATA
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
17 5 0.20
18 20 0.80
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TATTAATTAATATAATAA
Found at i:29158882 original size:118 final size:118
Alignment explanation
Indices: 29158674--29158933 Score: 511
Period size: 118 Copynumber: 2.2 Consensus size: 118
29158664 ATTAAGTGAA
29158674 TGAAGCATATATAGCAAATATTTACAAAATAAAAATAAACAAGGACACTCATTCACTTAATGAAA
1 TGAAGCATATATAGCAAATATTTACAAAATAAAAATAAACAAGGACACTCATTCACTTAATGAAA
29158739 TCAATACAGAAAGCAAGATAAGGAGATGAAAAATAAAGCTCTATTAACACGAT
66 TCAATACAGAAAGCAAGATAAGGAGATGAAAAATAAAGCTCTATTAACACGAT
29158792 TGAAGCATATATAGCAAATATTTACAAAATAAAAATAAACAAGGACACTCATTCACTTAATGAAA
1 TGAAGCATATATAGCAAATATTTACAAAATAAAAATAAACAAGGACACTCATTCACTTAATGAAA
29158857 TCAATACAGAAAGCAAGATAAGGAGATGAAAAATAAAGCTCTATTAACACGAT
66 TCAATACAGAAAGCAAGATAAGGAGATGAAAAATAAAGCTCTATTAACACGAT
*
29158910 TGAAGCATATATAGCACATATTTA
1 TGAAGCATATATAGCAAATATTTA
29158934 GTGTTTAGAA
Statistics
Matches: 141, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
118 141 1.00
ACGTcount: A:0.51, C:0.13, G:0.13, T:0.23
Consensus pattern (118 bp):
TGAAGCATATATAGCAAATATTTACAAAATAAAAATAAACAAGGACACTCATTCACTTAATGAAA
TCAATACAGAAAGCAAGATAAGGAGATGAAAAATAAAGCTCTATTAACACGAT
Found at i:29166977 original size:14 final size:13
Alignment explanation
Indices: 29166944--29166995 Score: 63
Period size: 13 Copynumber: 4.1 Consensus size: 13
29166934 TTAATTAACT
29166944 AAAT-TATTTAAA
1 AAATATATTTAAA
*
29166956 ATATATATTTAAA
1 AAATATATTTAAA
*
29166969 ACAATATA-TTATA
1 A-AATATATTTAAA
29166982 AAATATATTTAAA
1 AAATATATTTAAA
29166995 A
1 A
29166996 TAATTAAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
12 9 0.27
13 19 0.58
14 5 0.15
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (13 bp):
AAATATATTTAAA
Found at i:29167004 original size:9 final size:11
Alignment explanation
Indices: 29166944--29167008 Score: 53
Period size: 12 Copynumber: 5.5 Consensus size: 11
29166934 TTAATTAACT
29166944 AAAT-TATTTAA
1 AAATATATTT-A
29166955 AATATATATTTAAA
1 AA-ATATATTT--A
29166969 ACAATATATTATA
1 A-AATATATT-TA
29166982 AAATATATTTA
1 AAATATATTTA
*
29166993 AAATA-ATTAA
1 AAATATATTTA
29167003 AAATAT
1 AAATAT
29167009 TAAATATTAA
Statistics
Matches: 47, Mismatches: 1, Indels: 12
0.78 0.02 0.20
Matches are distributed among these distances:
10 9 0.19
11 9 0.19
12 10 0.21
13 7 0.15
14 10 0.21
15 2 0.04
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (11 bp):
AAATATATTTA
Found at i:29167005 original size:10 final size:11
Alignment explanation
Indices: 29166951--29167008 Score: 55
Period size: 10 Copynumber: 4.9 Consensus size: 11
29166941 ACTAAATTAT
29166951 TTAAAATATATA
1 TTAAAA-ATATA
29166963 TTTAAAACAATATA
1 -TT-AAA-AATATA
29166977 TTATAAAATATA
1 TTA-AAAATATA
*
29166989 TTTAAAATA-A
1 TTAAAAATATA
29166999 TTAAAAATAT
1 TTAAAAATAT
29167009 TAAATATTAA
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
10 9 0.23
11 6 0.15
12 9 0.23
13 6 0.15
14 8 0.21
15 1 0.03
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.40
Consensus pattern (11 bp):
TTAAAAATATA
Found at i:29171933 original size:6 final size:6
Alignment explanation
Indices: 29171922--29171956 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
29171912 TAGGTTTACA
* *
29171922 AGAAGT AGAAGT AGAAGT AGAAGC AGAAGC AGAAG
1 AGAAGT AGAAGT AGAAGT AGAAGT AGAAGT AGAAG
29171957 ATCAAGCTCG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.51, C:0.06, G:0.34, T:0.09
Consensus pattern (6 bp):
AGAAGT
Found at i:29174640 original size:12 final size:13
Alignment explanation
Indices: 29174623--29174656 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
29174613 AAAAAAATTG
29174623 TAAAAATTAAA-A
1 TAAAAATTAAATA
*
29174635 TTAAAATTAAATA
1 TAAAAATTAAATA
29174648 TAAAAATTA
1 TAAAAATTA
29174657 CTAAGGTAGC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 10 0.53
13 9 0.47
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
TAAAAATTAAATA
Found at i:29175221 original size:29 final size:30
Alignment explanation
Indices: 29175175--29175241 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 30
29175165 TGTACATTTG
29175175 AAATTTAGTTTTCATA-TTTTT-ATTTTCAA
1 AAATTTAGTTTTCATATTTTTTAATTTT-AA
* *
29175204 TAATTTAGTTATT-TTATTTTTTAATTTTAA
1 AAATTTAGTT-TTCATATTTTTTAATTTTAA
29175234 AAATTTAG
1 AAATTTAG
29175242 GTCAAATTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
29 11 0.34
30 16 0.50
31 5 0.16
ACGTcount: A:0.33, C:0.03, G:0.04, T:0.60
Consensus pattern (30 bp):
AAATTTAGTTTTCATATTTTTTAATTTTAA
Found at i:29175824 original size:31 final size:31
Alignment explanation
Indices: 29175766--29175824 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
29175756 ATTGAAAATT
* * *
29175766 TAAAAAGAAATTATATAAAATCTAAAATATA
1 TAAAAAGAAATTATAAAAAAACAAAAATATA
29175797 TAAAAA-AAAGTTATAAAAAAACAAAAAT
1 TAAAAAGAAA-TTATAAAAAAACAAAAAT
29175825 TTTAAGATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 3 0.12
31 21 0.88
ACGTcount: A:0.69, C:0.03, G:0.03, T:0.24
Consensus pattern (31 bp):
TAAAAAGAAATTATAAAAAAACAAAAATATA
Found at i:29176219 original size:13 final size:12
Alignment explanation
Indices: 29176201--29176240 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
29176191 TAATATTTAT
29176201 TTATATATAATAA
1 TTATATATAAT-A
*
29176214 TTATATATAATG
1 TTATATATAATA
29176226 TTATATATAAT-
1 TTATATATAATA
29176237 TTAT
1 TTAT
29176241 CATTAAATCT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
11 4 0.15
12 11 0.42
13 11 0.42
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (12 bp):
TTATATATAATA
Found at i:29177887 original size:3 final size:3
Alignment explanation
Indices: 29177881--29177924 Score: 81
Period size: 3 Copynumber: 15.0 Consensus size: 3
29177871 TGTAAAAAAA
29177881 AAT AAT -AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
29177925 TGAGAAGTAC
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 38 0.95
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:29178267 original size:29 final size:29
Alignment explanation
Indices: 29178225--29178283 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
29178215 TTAGCAAGAG
29178225 GGAGAATTCCAGAATGTAATGATAATGTT
1 GGAGAATTCCAGAATGTAATGATAATGTT
29178254 GGAGAATTCCAGAATGTAATGATAATGTT
1 GGAGAATTCCAGAATGTAATGATAATGTT
29178283 G
1 G
29178284 ATGATATTTG
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:0.37, C:0.07, G:0.25, T:0.31
Consensus pattern (29 bp):
GGAGAATTCCAGAATGTAATGATAATGTT
Found at i:29178362 original size:23 final size:25
Alignment explanation
Indices: 29178319--29178371 Score: 74
Period size: 23 Copynumber: 2.2 Consensus size: 25
29178309 AATTAATTAG
29178319 TTAAATTATTTAATTAATATTTTAC
1 TTAAATTATTTAATTAATATTTTAC
* *
29178344 TTAAA-TATTT-ATTATTATTTTAT
1 TTAAATTATTTAATTAATATTTTAC
29178367 TTAAA
1 TTAAA
29178372 AAATGGTAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
23 16 0.62
24 5 0.19
25 5 0.19
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (25 bp):
TTAAATTATTTAATTAATATTTTAC
Found at i:29180649 original size:19 final size:21
Alignment explanation
Indices: 29180606--29180654 Score: 66
Period size: 22 Copynumber: 2.4 Consensus size: 21
29180596 GAAAAATGAT
*
29180606 TTATTTTTTGTTGATCCGTAAA
1 TTATTTTTCGTTGATCCG-AAA
29180628 TTATTTTTCGTTGAT-C-AAA
1 TTATTTTTCGTTGATCCGAAA
29180647 TTATTTTT
1 TTATTTTT
29180655 TATGAAACAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 11 0.42
21 1 0.04
22 14 0.54
ACGTcount: A:0.22, C:0.08, G:0.10, T:0.59
Consensus pattern (21 bp):
TTATTTTTCGTTGATCCGAAA
Found at i:29183262 original size:31 final size:31
Alignment explanation
Indices: 29183224--29183282 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
29183214 TTAAACTTGG
* *
29183224 TAATTATT-TTATTATTGAAATTTGAATTAAA
1 TAATTATTATT-TCATTAAAATTTGAATTAAA
29183255 TAATTATTATTTCATTAAAATTTGAATT
1 TAATTATTATTTCATTAAAATTTGAATT
29183283 TTTTTAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
31 23 0.92
32 2 0.08
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.53
Consensus pattern (31 bp):
TAATTATTATTTCATTAAAATTTGAATTAAA
Found at i:29184465 original size:24 final size:23
Alignment explanation
Indices: 29184429--29184476 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 23
29184419 TAGAATTATT
* *
29184429 TTAAAACTTATTAAATAAATATA
1 TTAAAAATTATTAAATAAAAATA
29184452 TTAAAAATTGATTAAATAAAAATA
1 TTAAAAATT-ATTAAATAAAAATA
29184476 T
1 T
29184477 ATATTTTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 8 0.36
24 14 0.64
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (23 bp):
TTAAAAATTATTAAATAAAAATA
Found at i:29185999 original size:16 final size:16
Alignment explanation
Indices: 29185980--29186021 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
29185970 ATATTATATT
*
29185980 ATTTTAATATTTAATA
1 ATTTTTATATTTAATA
*
29185996 ATTTTTTTATTTAATA
1 ATTTTTATATTTAATA
29186012 ATTTTTATAT
1 ATTTTTATAT
29186022 AATCATCTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
ATTTTTATATTTAATA
Found at i:29187112 original size:18 final size:18
Alignment explanation
Indices: 29187089--29187124 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
29187079 ACCAAGACTT
* *
29187089 TATTTTGATTTTTTTATA
1 TATTTTAATTTTATTATA
29187107 TATTTTAATTTTATTATA
1 TATTTTAATTTTATTATA
29187125 CGCGATTCAT
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:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (18 bp):
TATTTTAATTTTATTATA
Found at i:29187574 original size:7 final size:7
Alignment explanation
Indices: 29187562--29187586 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
29187552 CCACCACCTA
29187562 TTCCCTC
1 TTCCCTC
29187569 TTCCCTC
1 TTCCCTC
29187576 TTCCCTC
1 TTCCCTC
29187583 TTCC
1 TTCC
29187587 TCTCCATTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.00, C:0.56, G:0.00, T:0.44
Consensus pattern (7 bp):
TTCCCTC
Found at i:29191965 original size:14 final size:14
Alignment explanation
Indices: 29191938--29191966 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
29191928 TGTGTGTAAG
29191938 AATAACTTTGAAAA
1 AATAACTTTGAAAA
29191952 AATAA-TTTGAAAA
1 AATAACTTTGAAAA
29191965 AA
1 AA
29191967 GAAAACAAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.62, C:0.03, G:0.07, T:0.28
Consensus pattern (14 bp):
AATAACTTTGAAAA
Found at i:29199534 original size:6 final size:6
Alignment explanation
Indices: 29199521--29199553 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
29199511 ACAATTCATA
*
29199521 TCACTT TCAATT TCACTT TCACTT TCACTT TCA
1 TCACTT TCACTT TCACTT TCACTT TCACTT TCA
29199554 ATTTTGATCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.21, C:0.30, G:0.00, T:0.48
Consensus pattern (6 bp):
TCACTT
Found at i:29199536 original size:12 final size:12
Alignment explanation
Indices: 29199521--29199557 Score: 65
Period size: 12 Copynumber: 3.1 Consensus size: 12
29199511 ACAATTCATA
29199521 TCACTTTCAATT
1 TCACTTTCAATT
*
29199533 TCACTTTCACTT
1 TCACTTTCAATT
29199545 TCACTTTCAATT
1 TCACTTTCAATT
29199557 T
1 T
29199558 TGATCACAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.22, C:0.27, G:0.00, T:0.51
Consensus pattern (12 bp):
TCACTTTCAATT
Found at i:29208181 original size:18 final size:18
Alignment explanation
Indices: 29208145--29208182 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
29208135 AGGCATGCTA
*
29208145 AAACCATTGTGGAACTTG
1 AAACCATTATGGAACTTG
29208163 AAACCATTTATGGAA-TTG
1 AAACCA-TTATGGAACTTG
29208181 AA
1 AA
29208183 CTCCGAACCC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.29
Consensus pattern (18 bp):
AAACCATTATGGAACTTG
Found at i:29214014 original size:7 final size:7
Alignment explanation
Indices: 29214002--29214035 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
29213992 ATTAGGCGTG
29214002 TGGAAAC
1 TGGAAAC
29214009 TGGAAAC
1 TGGAAAC
*
29214016 TGGAATC
1 TGGAAAC
*
29214023 TGGAATC
1 TGGAAAC
29214030 TGGAAA
1 TGGAAA
29214036 TGTTTTTGCG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.38, C:0.12, G:0.29, T:0.21
Consensus pattern (7 bp):
TGGAAAC
Found at i:29214800 original size:22 final size:23
Alignment explanation
Indices: 29214775--29214841 Score: 100
Period size: 24 Copynumber: 2.9 Consensus size: 23
29214765 AGTTTGACTT
*
29214775 AAACAA-ATACAGAGTTTAATTG
1 AAACAATAAACAGAGTTTAATTG
29214797 AAACAATTAAACAGAGTTTAATTG
1 AAACAA-TAAACAGAGTTTAATTG
29214821 AAACAATTAAACAGAGTTTAA
1 AAACAA-TAAACAGAGTTTAA
29214842 ATGGAAGATT
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
22 6 0.14
24 36 0.86
ACGTcount: A:0.52, C:0.09, G:0.12, T:0.27
Consensus pattern (23 bp):
AAACAATAAACAGAGTTTAATTG
Found at i:29214813 original size:24 final size:24
Alignment explanation
Indices: 29214783--29214841 Score: 118
Period size: 24 Copynumber: 2.5 Consensus size: 24
29214773 TTAAACAAAT
29214783 ACAGAGTTTAATTGAAACAATTAA
1 ACAGAGTTTAATTGAAACAATTAA
29214807 ACAGAGTTTAATTGAAACAATTAA
1 ACAGAGTTTAATTGAAACAATTAA
29214831 ACAGAGTTTAA
1 ACAGAGTTTAA
29214842 ATGGAAGATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.49, C:0.08, G:0.14, T:0.29
Consensus pattern (24 bp):
ACAGAGTTTAATTGAAACAATTAA
Found at i:29216790 original size:24 final size:24
Alignment explanation
Indices: 29216774--29216842 Score: 129
Period size: 24 Copynumber: 2.9 Consensus size: 24
29216764 AGTTTGACTC
29216774 AAACAAATAAACAGAGTTTAATTG
1 AAACAAATAAACAGAGTTTAATTG
29216798 AAACAAATAAACAGAGTTTAATTG
1 AAACAAATAAACAGAGTTTAATTG
*
29216822 AAACAATTAAACAGAGTTTAA
1 AAACAAATAAACAGAGTTTAA
29216843 CTAAAAGATT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
24 44 1.00
ACGTcount: A:0.55, C:0.09, G:0.12, T:0.25
Consensus pattern (24 bp):
AAACAAATAAACAGAGTTTAATTG
Found at i:29220254 original size:3 final size:3
Alignment explanation
Indices: 29220246--29220283 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
29220236 GTTAACCAAT
29220246 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
29220284 ATTTAGATGG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:29222105 original size:3 final size:3
Alignment explanation
Indices: 29222097--29222131 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
29222087 ATCAGTTATC
29222097 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
29222132 TTTTGCATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:29223055 original size:36 final size:36
Alignment explanation
Indices: 29223008--29223078 Score: 97
Period size: 36 Copynumber: 2.0 Consensus size: 36
29222998 GGAATGATTC
* *
29223008 ATGCATGGATGGACTGAAACTCATTTAATTAATTTG
1 ATGCATAGATGGACTGAAACTCATTGAATTAATTTG
** *
29223044 ATGCATAGATGGGTTGAAATTCATTGAATTAATTT
1 ATGCATAGATGGACTGAAACTCATTGAATTAATTT
29223079 CATCAAGGGA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.34, C:0.08, G:0.20, T:0.38
Consensus pattern (36 bp):
ATGCATAGATGGACTGAAACTCATTGAATTAATTTG
Found at i:29229379 original size:14 final size:14
Alignment explanation
Indices: 29229360--29229388 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
29229350 CCCCCTCTCG
29229360 CTCTCTCTTCTCTT
1 CTCTCTCTTCTCTT
29229374 CTCTCTCTTCTCTT
1 CTCTCTCTTCTCTT
29229388 C
1 C
29229389 CCTTCCCTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55
Consensus pattern (14 bp):
CTCTCTCTTCTCTT
Found at i:29229405 original size:12 final size:12
Alignment explanation
Indices: 29229388--29229412 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
29229378 CTCTTCTCTT
29229388 CCCTTCCCTTCC
1 CCCTTCCCTTCC
29229400 CCCTTCCCTTCC
1 CCCTTCCCTTCC
29229412 C
1 C
29229413 TACAGATTTG
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:0.00, C:0.68, G:0.00, T:0.32
Consensus pattern (12 bp):
CCCTTCCCTTCC
Found at i:29231153 original size:16 final size:16
Alignment explanation
Indices: 29231132--29231164 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
29231122 ATCTATCCAT
29231132 CGGCTTCGATTTGGTG
1 CGGCTTCGATTTGGTG
29231148 CGGCTTCGATTTGGTG
1 CGGCTTCGATTTGGTG
29231164 C
1 C
29231165 AACTTTAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.21, G:0.36, T:0.36
Consensus pattern (16 bp):
CGGCTTCGATTTGGTG
Found at i:29239022 original size:3 final size:3
Alignment explanation
Indices: 29239005--29239037 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
29238995 GTGATATGTG
*
29239005 TAT TAT TAG TA- TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
29239038 CCCGTACCAG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:29239540 original size:1 final size:1
Alignment explanation
Indices: 29239534--29239568 Score: 61
Period size: 1 Copynumber: 35.0 Consensus size: 1
29239524 TAAAGAGGAA
*
29239534 GGGGGGGGGGGGGGGAGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
29239569 ATGGATTGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:0.03, C:0.00, G:0.97, T:0.00
Consensus pattern (1 bp):
G
Found at i:29244900 original size:23 final size:22
Alignment explanation
Indices: 29244874--29244920 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
29244864 TTTAAAATAC
29244874 TAAATA-AAAAATAGTTAAGATTT
1 TAAATATAAAAA-AG-TAAGATTT
*
29244897 TAAATATAAAAAAGTAATATTT
1 TAAATATAAAAAAGTAAGATTT
29244919 TA
1 TA
29244921 TTATAGAAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 9 0.41
23 8 0.36
24 5 0.23
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.36
Consensus pattern (22 bp):
TAAATATAAAAAAGTAAGATTT
Found at i:29249596 original size:62 final size:59
Alignment explanation
Indices: 29249527--29249644 Score: 155
Period size: 62 Copynumber: 1.9 Consensus size: 59
29249517 AAATGATTAT
* * * * *
29249527 TTTAATATTAAATTTAATTTGATGTTTATCTACAAGATAAATATTCTATTATTTTAATAAGA
1 TTTAATATTAAATTTAATCTAATATTTATCT---AGATAAATATTATATTAATTTAATAAGA
*
29249589 TTTAATATTAAATTTAATCTAATATTTATCTTGATAAATATTATATTAATTTAATA
1 TTTAATATTAAATTTAATCTAATATTTATCTAGATAAATATTATATTAATTTAATA
29249645 TTTAAAGAGA
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
59 22 0.44
62 28 0.56
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.50
Consensus pattern (59 bp):
TTTAATATTAAATTTAATCTAATATTTATCTAGATAAATATTATATTAATTTAATAAGA
Found at i:29257875 original size:20 final size:20
Alignment explanation
Indices: 29257837--29257875 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
29257827 TTTTTTACCC
* *
29257837 TAAAAAAATTCAAATTCAAT
1 TAAAAAAATTAAAAATCAAT
*
29257857 TAAAAATATTAAAAATCAA
1 TAAAAAAATTAAAAATCAA
29257876 GAGAAAGAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (20 bp):
TAAAAAAATTAAAAATCAAT
Found at i:29271697 original size:1 final size:1
Alignment explanation
Indices: 29271691--29271721 Score: 53
Period size: 1 Copynumber: 31.0 Consensus size: 1
29271681 TTGATGTCCT
*
29271691 CCCCCCCCCCCCCCCCCCCCCCACCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
29271722 ACCCATTGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.03, C:0.97, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:29271726 original size:13 final size:12
Alignment explanation
Indices: 29271691--29271726 Score: 56
Period size: 11 Copynumber: 3.0 Consensus size: 12
29271681 TTGATGTCCT
29271691 CCCCCCCCCCC-
1 CCCCCCCCCCCA
29271702 CCCCCCCCCCCA
1 CCCCCCCCCCCA
29271714 CCCCCCCCACCCA
1 CCCCCCCC-CCCA
29271727 TTGATTTGCC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 11 0.48
12 8 0.35
13 4 0.17
ACGTcount: A:0.08, C:0.92, G:0.00, T:0.00
Consensus pattern (12 bp):
CCCCCCCCCCCA
Found at i:29277683 original size:59 final size:60
Alignment explanation
Indices: 29277571--29277685 Score: 135
Period size: 59 Copynumber: 1.9 Consensus size: 60
29277561 AAAACCCTCA
* * * **
29277571 TCAAATGAAAATAATTTTTTGTGATGTTTTTCATATCTTTTCGTGATGCTTTTAAACATCG
1 TCAAATGAAAATAATTTTTTGTGATG-TTTTCACATATTTGCGTGACACTTTTAAACATCG
* *
29277632 TCAAATTAAAAT-ATTTTTTGGTGATG-TTTCACATATTTGCGTGACATTTTTAAA
1 TCAAATGAAAATAATTTTTT-GTGATGTTTTCACATATTTGCGTGACACTTTTAAA
29277686 TCTCACCAAG
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
59 22 0.48
60 7 0.15
61 17 0.37
ACGTcount: A:0.30, C:0.10, G:0.13, T:0.47
Consensus pattern (60 bp):
TCAAATGAAAATAATTTTTTGTGATGTTTTCACATATTTGCGTGACACTTTTAAACATCG
Found at i:29278853 original size:41 final size:41
Alignment explanation
Indices: 29278787--29278893 Score: 135
Period size: 41 Copynumber: 2.6 Consensus size: 41
29278777 GTTTCTCAAT
* * * * *
29278787 AAACACCGCAAAAGGT-AAAGCATTAGTGGTGCTTATGGAA
1 AAACGCCGCTAAAGGTCAGAGCATTAGCGGCGCTTATGGAA
*
29278827 AAACGCCGCTAAAGGTCAGAGCATTAGCGGCGCTTGTGGAA
1 AAACGCCGCTAAAGGTCAGAGCATTAGCGGCGCTTATGGAA
* *
29278868 AAGCGCCGTTAAAGGTCAGAGCATTA
1 AAACGCCGCTAAAGGTCAGAGCATTA
29278894 CAAGCGTCGC
Statistics
Matches: 58, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
40 14 0.24
41 44 0.76
ACGTcount: A:0.35, C:0.19, G:0.28, T:0.19
Consensus pattern (41 bp):
AAACGCCGCTAAAGGTCAGAGCATTAGCGGCGCTTATGGAA
Found at i:29278907 original size:27 final size:27
Alignment explanation
Indices: 29278868--29278920 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
29278858 GCTTGTGGAA
*
29278868 AAGCGCCGTTAAAGGTCAGAGCATTAC
1 AAGCGCCGCTAAAGGTCAGAGCATTAC
* *
29278895 AAGCGTCGCTAAAGGTTAGAGCATTA
1 AAGCGCCGCTAAAGGTCAGAGCATTA
29278921 GCGGTGCTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (27 bp):
AAGCGCCGCTAAAGGTCAGAGCATTAC
Found at i:29278949 original size:68 final size:68
Alignment explanation
Indices: 29278833--29278961 Score: 204
Period size: 68 Copynumber: 1.9 Consensus size: 68
29278823 GGAAAAACGC
* *
29278833 CGCTAAAGGTCAGAGCATTAGCGGCGCTTGTGGAAAAGCGCCGTTAAAGGTCAGAGCATTACAAG
1 CGCTAAAGGTCAGAGCATTAGCGGCGCTTGTGGAAAAGAGCCGCTAAAGGTCAGAGCATTACAAG
29278898 CGT
66 CGT
* * * *
29278901 CGCTAAAGGTTAGAGCATTAGCGGTGCTTGTGGGAAAGATCCGCTAAAGGTCAGAGCATTA
1 CGCTAAAGGTCAGAGCATTAGCGGCGCTTGTGGAAAAGAGCCGCTAAAGGTCAGAGCATTA
29278962 GCGGCGCTTA
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
68 55 1.00
ACGTcount: A:0.29, C:0.19, G:0.31, T:0.21
Consensus pattern (68 bp):
CGCTAAAGGTCAGAGCATTAGCGGCGCTTGTGGAAAAGAGCCGCTAAAGGTCAGAGCATTACAAG
CGT
Found at i:29280773 original size:42 final size:43
Alignment explanation
Indices: 29280714--29280806 Score: 125
Period size: 43 Copynumber: 2.2 Consensus size: 43
29280704 TTTGTTAATG
* * * *
29280714 TTAGCGACGTTTGTGAG-AAAGTGCCGCTAAAGACCATATTCT
1 TTAGCGGCATTTGTGAGAAAAGCGCCGCTAAAAACCATATTCT
*
29280756 TTAGCGGCATTTGTGAGAAAAGCGCCGCTAAAAACCATGTTCT
1 TTAGCGGCATTTGTGAGAAAAGCGCCGCTAAAAACCATATTCT
*
29280799 ATAGCGGC
1 TTAGCGGC
29280807 GTTTTTCCTC
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
42 15 0.34
43 29 0.66
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.26
Consensus pattern (43 bp):
TTAGCGGCATTTGTGAGAAAAGCGCCGCTAAAAACCATATTCT
Found at i:29281384 original size:36 final size:36
Alignment explanation
Indices: 29281337--29281407 Score: 133
Period size: 36 Copynumber: 2.0 Consensus size: 36
29281327 CAAGAGGTCT
29281337 AATTTTTTGAGGTAATTGATGAGATTTGAGAGCTTC
1 AATTTTTTGAGGTAATTGATGAGATTTGAGAGCTTC
*
29281373 AATTTTTTGAGGTAGTTGATGAGATTTGAGAGCTT
1 AATTTTTTGAGGTAATTGATGAGATTTGAGAGCTT
29281408 TCTTTCTTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.27, C:0.04, G:0.27, T:0.42
Consensus pattern (36 bp):
AATTTTTTGAGGTAATTGATGAGATTTGAGAGCTTC
Found at i:29296004 original size:28 final size:28
Alignment explanation
Indices: 29295970--29296025 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
29295960 GGGAGGATTA
29295970 GGGAAAGAAAAGATGGTGGGATTTAGAT
1 GGGAAAGAAAAGATGGTGGGATTTAGAT
29295998 GGGAAAGAAAAGATGGTGGGATTTAGAT
1 GGGAAAGAAAAGATGGTGGGATTTAGAT
29296026 CCTTATAGGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.39, C:0.00, G:0.39, T:0.21
Consensus pattern (28 bp):
GGGAAAGAAAAGATGGTGGGATTTAGAT
Found at i:29329156 original size:17 final size:16
Alignment explanation
Indices: 29329138--29329168 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
29329128 TGATTATTTT
29329138 TTTTAT-TATTCCCTC
1 TTTTATATATTCCCTC
29329153 TTTTATATATTCCCTC
1 TTTTATATATTCCCTC
29329169 ATCCCTTTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.16, C:0.26, G:0.00, T:0.58
Consensus pattern (16 bp):
TTTTATATATTCCCTC
Found at i:29333503 original size:18 final size:18
Alignment explanation
Indices: 29333480--29333541 Score: 63
Period size: 18 Copynumber: 3.4 Consensus size: 18
29333470 AATAATTCTA
29333480 TTTTAAAATTAAAACAAT
1 TTTTAAAATTAAAACAAT
*
29333498 TTTTAAAATTAATAACTAT
1 TTTTAAAATTAA-AACAAT
* **
29333517 AATTT-AAATTCTAACAAT
1 -TTTTAAAATTAAAACAAT
29333535 TTTTAAA
1 TTTTAAA
29333542 TGTGTAATTA
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
17 3 0.09
18 19 0.54
19 10 0.29
20 3 0.09
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (18 bp):
TTTTAAAATTAAAACAAT
Found at i:29342129 original size:29 final size:28
Alignment explanation
Indices: 29342097--29342406 Score: 148
Period size: 29 Copynumber: 10.5 Consensus size: 28
29342087 CATTCGGGAA
29342097 AAAATGGTAATTTTTGAAAGTTTCGGGTC
1 AAAAT-GTAATTTTTGAAAGTTTCGGGTC
* * *
29342126 AAAAAATG-AAGTTTTTGGACA--TCCGAGGGTA
1 --AAAATGTAA-TTTTT-GAAAGTTTC--GGGTC
* *
29342157 AAAACGTAATTTTTGAAAGTTTTGGGCTC
1 AAAATGTAATTTTTGAAAGTTTCGGG-TC
* *
29342186 AAAAATGGAATTTTTGAAAG-TTCGGGGGTA
1 -AAAATGTAATTTTTGAAAGTTTC--GGGTC
* * *
29342216 AAAATGTAATTTTTGGAAGTTTCAAGATC
1 AAAATGTAATTTTTGAAAGTTTC-GGGTC
* * *
29342245 AAGAATGGAATTTTTGGAAGTTTAGGGGT-
1 AA-AATGTAATTTTTGAAAGTTT-CGGGTC
* * *
29342274 AAAATGTAATTTTT-AGAAGTTTTAAGGTTA
1 AAAATGTAATTTTTGA-AAG-TTT-CGGGTC
* * * * **
29342304 AAAATGGAATTTTTAAAAATTTAGGGGAA
1 AAAATGTAATTTTTGAAAGTTT-CGGGTC
*
29342333 AAAATGTAATTTTTGTAAGTTTCGAGGTC
1 AAAATGTAATTTTTGAAAGTTTCG-GGTC
* *
29342362 AAAATGTAATTTTGGTAAAGTTTGGGGGTC
1 AAAATGTAATTTTTG-AAAGTTT-CGGGTC
29342392 AAAA-GATAATTTTTG
1 AAAATG-TAATTTTTG
29342407 GACAGTTTAG
Statistics
Matches: 215, Mismatches: 42, Indels: 45
0.71 0.14 0.15
Matches are distributed among these distances:
28 21 0.10
29 89 0.41
30 88 0.41
31 17 0.08
ACGTcount: A:0.36, C:0.05, G:0.24, T:0.36
Consensus pattern (28 bp):
AAAATGTAATTTTTGAAAGTTTCGGGTC
Found at i:29342198 original size:30 final size:29
Alignment explanation
Indices: 29342096--29342417 Score: 187
Period size: 30 Copynumber: 10.9 Consensus size: 29
29342086 ACATTCGGGA
*
29342096 AAAAATGGTAATTTTTGAAAGTTTCGGGTC
1 AAAAAT-GTAATTTTTGAAAGTTTAGGGTC
* **
29342126 AAAAAATG-AAGTTTTTGGACA-TCCGAGGGT-
1 -AAAAATGTAA-TTTTT-GAAAGT-TTAGGGTC
* *
29342156 AAAAACGTAATTTTTGAAAGTTTTGGGCTC
1 AAAAATGTAATTTTTGAAAGTTTAGGG-TC
* **
29342186 AAAAATGGAATTTTTGAAAGTTCGGGGGT-
1 AAAAATGTAATTTTTGAAAGTT-TAGGGTC
* * *
29342215 AAAAATGTAATTTTTGGAAGTTTCAAGATC
1 AAAAATGTAATTTTTGAAAGTTT-AGGGTC
* * *
29342245 AAGAATGGAATTTTTGGAAGTTTAGGGGT-
1 AAAAATGTAATTTTTGAAAGTTTA-GGGTC
* *
29342274 -AAAATGTAATTTTT-AGAAGTTTTAAGGTT
1 AAAAATGTAATTTTTGA-AAG-TTTAGGGTC
* * * **
29342303 AAAAATGGAATTTTTAAAAATTTAGGGGA
1 AAAAATGTAATTTTTGAAAGTTTAGGGTC
* *
29342332 AAAAATGTAATTTTTGTAAGTTTCGAGGTC
1 AAAAATGTAATTTTTGAAAGTTTAG-GGTC
* *
29342362 -AAAATGTAATTTTGGTAAAGTTTGGGGGTC
1 AAAAATGTAATTTTTG-AAAGTTT-AGGGTC
*
29342392 -AAAA-GATAATTTTTGGACAGTTTAGG
1 AAAAATG-TAATTTTT-GAAAGTTTAGG
29342418 AACTTTTAGG
Statistics
Matches: 225, Mismatches: 45, Indels: 44
0.72 0.14 0.14
Matches are distributed among these distances:
28 24 0.11
29 85 0.38
30 97 0.43
31 19 0.08
ACGTcount: A:0.36, C:0.05, G:0.24, T:0.35
Consensus pattern (29 bp):
AAAAATGTAATTTTTGAAAGTTTAGGGTC
Found at i:29342266 original size:59 final size:59
Alignment explanation
Indices: 29342069--29342414 Score: 264
Period size: 59 Copynumber: 5.9 Consensus size: 59
29342059 AATCGAGATT
* * * *
29342069 AAAAATGGAATTATTGGACA-TTC--GGGAAAAAATGGTAATTTTTGAAAGTTTC-GGGTC
1 AAAAATGGAATTTTTGGA-AGTTCGGGGGTAAAAAT-GTAATTTTTGGAAGTTTCAAGGTC
* * * * **
29342126 AAAAAAT-GAAGTTTTTGGACA-TCCGAGGGTAAAAACGTAATTTTTGAAAGTTT-TGGGCTC
1 -AAAAATGGAA-TTTTTGGA-AGTTCGGGGGTAAAAATGTAATTTTTGGAAGTTTCAAGG-TC
* *
29342186 AAAAATGGAATTTTTGAAAGTTCGGGGGTAAAAATGTAATTTTTGGAAGTTTCAAGATC
1 AAAAATGGAATTTTTGGAAGTTCGGGGGTAAAAATGTAATTTTTGGAAGTTTCAAGGTC
* ** * * *
29342245 AAGAATGGAATTTTTGGAAGTTTAGGGGT-AAAATGTAATTTTTAGAAGTTTTAAGGTT
1 AAAAATGGAATTTTTGGAAGTTCGGGGGTAAAAATGTAATTTTTGGAAGTTTCAAGGTC
** * ** * * *
29342303 AAAAATGGAATTTTTAAAAATTTAGGGGAAAAAATGTAATTTTTGTAAGTTTCGAGGTC
1 AAAAATGGAATTTTTGGAAGTTCGGGGGTAAAAATGTAATTTTTGGAAGTTTCAAGGTC
* * *
29342362 -AAAATGTAA-TTTTGGTAAAGTTTGGGGGTCAAAA-GATAATTTTTGGACAGTTT
1 AAAAATGGAATTTTTGG--AAGTTCGGGGGTAAAAATG-TAATTTTTGGA-AGTTT
29342415 AGGAACTTTT
Statistics
Matches: 237, Mismatches: 38, Indels: 24
0.79 0.13 0.08
Matches are distributed among these distances:
57 7 0.03
58 76 0.32
59 135 0.57
60 19 0.08
ACGTcount: A:0.36, C:0.05, G:0.24, T:0.35
Consensus pattern (59 bp):
AAAAATGGAATTTTTGGAAGTTCGGGGGTAAAAATGTAATTTTTGGAAGTTTCAAGGTC
Found at i:29342284 original size:117 final size:117
Alignment explanation
Indices: 29342152--29342414 Score: 302
Period size: 117 Copynumber: 2.2 Consensus size: 117
29342142 GGACATCCGA
* * * * *
29342152 GGGTAAAAACGTAATTTTTGA-AAGTTTT-GGGCTCAAAAATGGAATTTTTGAAAGTTCGGGGGT
1 GGGTAAAAA-GTAATTTTTGAGAAGTTTTAAGG-TCAAAAATGGAATTTTTAAAAATTCAGGGGA
29342215 AAAAATGTAATTTTTGGAAGTTTCAAGATCAAGAATGGAATTTTTGG-AAGTTTAG
64 AAAAATGTAATTTTTGGAAGTTTCAAGATCAA-AATGGAA-TTTTGGAAAGTTTAG
* * *
29342270 GGGTAAAATGTAATTTTT-AGAAGTTTTAAGGTTAAAAATGGAATTTTTAAAAATTTAGGGGAAA
1 GGGTAAAAAGTAATTTTTGAGAAGTTTTAAGGTCAAAAATGGAATTTTTAAAAATTCAGGGGAAA
* * * * *
29342334 AAATGTAATTTTTGTAAGTTTCGAGGTCAAAATGTAATTTTGGTAAAGTTTGG
66 AAATGTAATTTTTGGAAGTTTCAAGATCAAAATGGAATTTTGG-AAAGTTTAG
*
29342387 GGGTCAAAAGATAATTTTTG-GACAGTTT
1 GGGTAAAAAG-TAATTTTTGAGA-AGTTT
29342415 AGGAACTTTT
Statistics
Matches: 123, Mismatches: 15, Indels: 13
0.81 0.10 0.09
Matches are distributed among these distances:
115 6 0.05
116 7 0.06
117 85 0.69
118 20 0.16
119 5 0.04
ACGTcount: A:0.36, C:0.04, G:0.24, T:0.37
Consensus pattern (117 bp):
GGGTAAAAAGTAATTTTTGAGAAGTTTTAAGGTCAAAAATGGAATTTTTAAAAATTCAGGGGAAA
AAATGTAATTTTTGGAAGTTTCAAGATCAAAATGGAATTTTGGAAAGTTTAG
Found at i:29344423 original size:17 final size:16
Alignment explanation
Indices: 29344401--29344478 Score: 77
Period size: 17 Copynumber: 4.7 Consensus size: 16
29344391 AATGAACATT
29344401 TTAAATTTACAA-TAATA
1 TTAAATTTA-AATTAA-A
29344418 TTAAATTTAAATTAAA
1 TTAAATTTAAATTAAA
*
29344434 TTAAAATTAAATTTAAA
1 TTAAATTTAAA-TTAAA
* *
29344451 ATAAATTTAATTTCAAA
1 TTAAATTTAAATT-AAA
*
29344468 GTAAATTTAAA
1 TTAAATTTAAA
29344479 ATGGTTTGGG
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
16 15 0.29
17 37 0.71
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (16 bp):
TTAAATTTAAATTAAA
Found at i:29344427 original size:6 final size:6
Alignment explanation
Indices: 29344418--29344478 Score: 51
Period size: 5 Copynumber: 10.8 Consensus size: 6
29344408 TACAATAATA
* *
29344418 TTAAAT TTAAA- TTAAA- TTAAAA TTAAAT TTAAA- ATAAAT TT-AAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
*
29344462 TTCAAA- GTAAAT TTAAA
1 TT-AAAT TTAAAT TTAAA
29344479 ATGGTTTGGG
Statistics
Matches: 45, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
5 22 0.49
6 21 0.47
7 2 0.04
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (6 bp):
TTAAAT
Found at i:29344433 original size:11 final size:11
Alignment explanation
Indices: 29344417--29344460 Score: 70
Period size: 11 Copynumber: 4.0 Consensus size: 11
29344407 TTACAATAAT
29344417 ATTAAATTTAA
1 ATTAAATTTAA
*
29344428 ATTAAATTAAA
1 ATTAAATTTAA
29344439 ATTAAATTTAA
1 ATTAAATTTAA
*
29344450 AATAAATTTAA
1 ATTAAATTTAA
29344461 TTTCAAAGTA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 30 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (11 bp):
ATTAAATTTAA
Found at i:29344445 original size:22 final size:22
Alignment explanation
Indices: 29344400--29344457 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
29344390 TAATGAACAT
*
29344400 TTTAAATTTACAA-TAATATTAAA
1 TTTAAA-TTA-AATTAAAATTAAA
29344423 TTTAAATTAAATTAAAATTAAA
1 TTTAAATTAAATTAAAATTAAA
*
29344445 TTTAAAATAAATT
1 TTTAAATTAAATT
29344458 TAATTTCAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
21 2 0.06
22 24 0.75
23 6 0.19
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (22 bp):
TTTAAATTAAATTAAAATTAAA
Found at i:29344957 original size:92 final size:91
Alignment explanation
Indices: 29344734--29345877 Score: 1747
Period size: 92 Copynumber: 12.5 Consensus size: 91
29344724 ATGTCGAGGT
* * * *
29344734 TTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGTTATCTAACTTTACTACAACTTT
1 TTCATCTTACTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTTC
29344799 AAGAGGATAGG-ATTGATGTTTGAAAC
66 AAGAGGATAGGAATTGA-GTTTGAAAC
*
29344825 TTCATCTTACTCTTACTACCACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTTC
1 TTCATCTTACTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTTC
* *
29344890 AAGAGGATAGGAATTTG-GTATCGAAGC
66 AAGAGGATAGGAA-TTGAGT-TTGAAAC
29344917 TTCATCTTACTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTTC
1 TTCATCTTACTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTTC
* *
29344982 AAGAGGATAGGGATTGATGTTTGAAGC
66 AAGAGGATAGGAATTGA-GTTTGAAAC
* * * * * * *
29345009 TTTATCTTGCTTTTACTACAACTTTAGAGAGATAAAGACTTGTTATCCAACTTTACTGCAACTTT
1 TTCATCTTACTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTTC
* * * *
29345074 GAGAGGACAAGAATTGATGTTTGAAGC
66 AAGAGGATAGGAATTGA-GTTTGAAAC
* * *
29345101 TTCATCTTGCTCTTATTACAACTTCAGAGAGATAAAGACTTACTATCCAACTTTACTACAACTTC
1 TTCATCTTACTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTTC
*
29345166 AAGAGGATAGGAAATGATGTTTGAAAC
66 AAGAGGATAGGAATTGA-GTTTGAAAC
* * *
29345193 TTTATCTTGCTCTTACTACAACTTCAAAGAGATAAAGACTTGCTATCCAACTTTACTACAACTTC
1 TTCATCTTACTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTTC
29345258 AAGAGGATAGGAATTGATGTTTGAAAC
66 AAGAGGATAGGAATTGA-GTTTGAAAC
29345285 TTCATCTTACTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTTC
1 TTCATCTTACTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTTC
*
29345350 AAGAGGATAGGAAATGATGTTTGAAAC
66 AAGAGGATAGGAATTGA-GTTTGAAAC
* * *
29345377 TTCATCTTACTCTTACTATAACTTCAAAGAGATAAAGACTTGCTATCCAACTTTACTATAACTTC
1 TTCATCTTACTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTTC
*
29345442 AAGAGGATAGGAAATGATGTTTGAAAC
66 AAGAGGATAGGAATTGA-GTTTGAAAC
* *
29345469 TTCATCTTGCTCTTACTACAACTTTAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTTC
1 TTCATCTTACTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTTC
29345534 AAGAGGATAGGAAATT-ATGTTTGAAAC
66 AAGAGGATAGG-AATTGA-GTTTGAAAC
*
29345561 TTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTTC
1 TTCATCTTACTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTTC
*
29345626 AAGAGGATAGGAATTGATGTTTGAAGC
66 AAGAGGATAGGAATTGA-GTTTGAAAC
*
29345653 TTCATCTTACTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTTA
1 TTCATCTTACTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTTC
*
29345718 AAGAGGATAGGAATTGATGTTTGAAGC
66 AAGAGGATAGGAATTGA-GTTTGAAAC
* *
29345745 TTCATCTTACTCTTACTCCAAGTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTTC
1 TTCATCTTACTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTTC
*
29345810 AAGAGGATAGGAATTGATGTCT-AAAGC
66 AAGAGGATAGGAATTGA-GTTTGAAA-C
*
29345837 TTTATCTTACTCTTACTACAACTTCAGAGAGATAAAGACTT
1 TTCATCTTACTCTTACTACAACTTCAGAGAGATAAAGACTT
29345878 TTCCCTTTAT
Statistics
Matches: 981, Mismatches: 64, Indels: 15
0.93 0.06 0.01
Matches are distributed among these distances:
91 82 0.08
92 891 0.91
93 8 0.01
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.32
Consensus pattern (91 bp):
TTCATCTTACTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTTC
AAGAGGATAGGAATTGAGTTTGAAAC
Found at i:29347280 original size:6 final size:6
Alignment explanation
Indices: 29347262--29347311 Score: 66
Period size: 6 Copynumber: 8.2 Consensus size: 6
29347252 CGACCTCTCC
*
29347262 TTTTCT ATTTTCT TTTTCT TTTTCT TTTTGC- TTTTCT TTTTCT TTCTCT
1 TTTTCT -TTTTCT TTTTCT TTTTCT TTTT-CT TTTTCT TTTTCT TTTTCT
29347311 T
1 T
29347312 CTTTTTTATT
Statistics
Matches: 40, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
5 1 0.03
6 32 0.80
7 7 0.17
ACGTcount: A:0.02, C:0.18, G:0.02, T:0.78
Consensus pattern (6 bp):
TTTTCT
Found at i:29348149 original size:14 final size:15
Alignment explanation
Indices: 29348130--29348161 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
29348120 ATCTTGACTT
29348130 TTTCTTC-CTTTTTC
1 TTTCTTCTCTTTTTC
29348144 TTTCTTCTCTTTTTC
1 TTTCTTCTCTTTTTC
29348159 TTT
1 TTT
29348162 TTTTGTGTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (15 bp):
TTTCTTCTCTTTTTC
Found at i:29348177 original size:12 final size:12
Alignment explanation
Indices: 29348160--29348189 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
29348150 CTCTTTTTCT
29348160 TTTTTTGTGTTG
1 TTTTTTGTGTTG
*
29348172 TTTTTTGTTTTG
1 TTTTTTGTGTTG
29348184 TTTTTT
1 TTTTTT
29348190 TTATAACACG
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:0.00, C:0.00, G:0.17, T:0.83
Consensus pattern (12 bp):
TTTTTTGTGTTG
Found at i:29351865 original size:10 final size:10
Alignment explanation
Indices: 29351850--29351878 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
29351840 GGTAATATCA
29351850 TATGCAAATG
1 TATGCAAATG
29351860 TATGCAAATG
1 TATGCAAATG
29351870 TATGCAAAT
1 TATGCAAAT
29351879 TTATACTAGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.41, C:0.10, G:0.17, T:0.31
Consensus pattern (10 bp):
TATGCAAATG
Found at i:29353142 original size:29 final size:28
Alignment explanation
Indices: 29353107--29353260 Score: 121
Period size: 29 Copynumber: 5.3 Consensus size: 28
29353097 GGACATCCGC
29353107 GGGTAAAAATGTAATTTTGGAAGTTTCAA
1 GGGTAAAAATGTAATTTTGGAAGTTT-AA
* * * * **
29353136 GGTTAAAAATGGATTTTTAGAAGTTTGG
1 GGGTAAAAATGTAATTTTGGAAGTTTAA
* * *
29353164 GGGT-AAAATGTAATTTTTGAAAATTTGA
1 GGGTAAAAATGTAA-TTTTGGAAGTTTAA
** *
29353192 GGGTAAAAATGTAATTTTCATAAGTTTCA
1 GGGTAAAAATGTAATTTT-GGAAGTTTAA
*
29353221 GGGTCAAAAATGTAATTTTGGTAAAGTTTAG
1 GGGT-AAAAATGTAATTTTGG--AAGTTTAA
*
29353252 GGGTCAAAA
1 GGGTAAAAA
29353261 CATAATTTCT
Statistics
Matches: 97, Mismatches: 22, Indels: 11
0.75 0.17 0.08
Matches are distributed among these distances:
27 7 0.07
28 21 0.22
29 41 0.42
30 18 0.19
31 10 0.10
ACGTcount: A:0.37, C:0.03, G:0.24, T:0.36
Consensus pattern (28 bp):
GGGTAAAAATGTAATTTTGGAAGTTTAA
Found at i:29353143 original size:28 final size:28
Alignment explanation
Indices: 29353107--29353241 Score: 128
Period size: 29 Copynumber: 4.7 Consensus size: 28
29353097 GGACATCCGC
29353107 GGGTAAAAATGTAATTTTGGAAGTTTCAA
1 GGGTAAAAATGTAATTTTGGAAGTTTC-A
* * * * **
29353136 GGTTAAAAATGGATTTTTAGAAGTTTGG
1 GGGTAAAAATGTAATTTTGGAAGTTTCA
* * *
29353164 GGGT-AAAATGTAATTTTTGAAAATTTGA
1 GGGTAAAAATGTAA-TTTTGGAAGTTTCA
**
29353192 GGGTAAAAATGTAATTTTCATAAGTTTCA
1 GGGTAAAAATGTAATTTT-GGAAGTTTCA
29353221 GGGTCAAAAATGTAATTTTGG
1 GGGT-AAAAATGTAATTTTGG
29353242 TAAAGTTTAG
Statistics
Matches: 83, Mismatches: 19, Indels: 8
0.75 0.17 0.07
Matches are distributed among these distances:
27 7 0.08
28 21 0.25
29 41 0.49
30 14 0.17
ACGTcount: A:0.36, C:0.03, G:0.24, T:0.37
Consensus pattern (28 bp):
GGGTAAAAATGTAATTTTGGAAGTTTCA
Found at i:29353209 original size:57 final size:58
Alignment explanation
Indices: 29353107--29353239 Score: 146
Period size: 57 Copynumber: 2.3 Consensus size: 58
29353097 GGACATCCGC
* * * * * **
29353107 GGGTAAAAATGTAA-TTTTGGAAGTTTCAAGGTTAAAAATGGATTTTTAGAAGTTTGG
1 GGGTAAAAATGTAATTTTTGAAAATTTCAAGGGTAAAAATGAATTTTCAGAAGTTTCA
* *
29353164 GGGT-AAAATGTAATTTTTGAAAATTT-GAGGGTAAAAATGTAATTTTCATAAGTTTCA
1 GGGTAAAAATGTAATTTTTGAAAATTTCAAGGGTAAAAATG-AATTTTCAGAAGTTTCA
29353221 GGGTCAAAAATGTAATTTT
1 GGGT-AAAAATGTAATTTT
29353240 GGTAAAGTTT
Statistics
Matches: 63, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
56 20 0.32
57 30 0.48
59 13 0.21
ACGTcount: A:0.37, C:0.03, G:0.23, T:0.38
Consensus pattern (58 bp):
GGGTAAAAATGTAATTTTTGAAAATTTCAAGGGTAAAAATGAATTTTCAGAAGTTTCA
Found at i:29355274 original size:17 final size:16
Alignment explanation
Indices: 29355252--29355337 Score: 84
Period size: 17 Copynumber: 5.1 Consensus size: 16
29355242 AATGGACATT
29355252 TTAAATTTACAA-TAATA
1 TTAAATTTA-AATTAA-A
29355269 TTAAATTTAAATTAAA
1 TTAAATTTAAATTAAA
*
29355285 TTCAAGTTTAAATTAAAA
1 TT-AAATTTAAATT-AAA
*
29355303 TTAAATTTAAAATAAA
1 TTAAATTTAAATTAAA
* *
29355319 TTTAATTTCAAAGTAAA
1 TTAAATTT-AAATTAAA
29355336 TT
1 TT
29355338 TAAAATGATT
Statistics
Matches: 60, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
16 15 0.25
17 40 0.67
18 5 0.08
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.42
Consensus pattern (16 bp):
TTAAATTTAAATTAAA
Found at i:29355284 original size:11 final size:11
Alignment explanation
Indices: 29355268--29355323 Score: 67
Period size: 11 Copynumber: 5.0 Consensus size: 11
29355258 TTACAATAAT
29355268 ATTAAATTTAA
1 ATTAAATTTAA
*
29355279 ATTAAATTCAA
1 ATTAAATTTAA
* *
29355290 GTTTAAATTAAA
1 -ATTAAATTTAA
29355302 ATTAAATTTAA
1 ATTAAATTTAA
*
29355313 AATAAATTTAA
1 ATTAAATTTAA
29355324 TTTCAAAGTA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
11 29 0.76
12 9 0.24
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (11 bp):
ATTAAATTTAA
Found at i:29355322 original size:28 final size:29
Alignment explanation
Indices: 29355268--29355343 Score: 84
Period size: 28 Copynumber: 2.7 Consensus size: 29
29355258 TTACAATAAT
* * *
29355268 ATTAAATTTAAA-TTAAATTCAAGTTTAA
1 ATTAAAATTAAATTTAAAATCAAATTTAA
29355296 ATTAAAATTAAATTTAAAAT-AAATTTAA
1 ATTAAAATTAAATTTAAAATCAAATTTAA
* * *
29355324 TTTCAAAGTAAATTTAAAAT
1 ATTAAAATTAAATTTAAAAT
29355344 GATTTGGGCC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
28 35 0.85
29 6 0.15
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (29 bp):
ATTAAAATTAAATTTAAAATCAAATTTAA
Found at i:29358035 original size:2 final size:2
Alignment explanation
Indices: 29358028--29358064 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
29358018 TCCACAATAT
29358028 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
29358065 GTGAGAACTC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:29362024 original size:24 final size:24
Alignment explanation
Indices: 29361997--29362045 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
29361987 TTTTTTACAA
*
29361997 TAATAAAATATAAT-TTTACAATTT
1 TAATAAAATAT-ATCTTTAAAATTT
*
29362021 TAATAACATATATCTTTAAAATTT
1 TAATAAAATATATCTTTAAAATTT
29362045 T
1 T
29362046 TAAAAGACTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 2 0.09
24 20 0.91
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (24 bp):
TAATAAAATATATCTTTAAAATTT
Found at i:29364378 original size:3 final size:3
Alignment explanation
Indices: 29364370--29364398 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
29364360 AACCTGTTTA
29364370 TCC TCC TCC TCC TCC TCC TCC TCC TCC TC
1 TCC TCC TCC TCC TCC TCC TCC TCC TCC TC
29364399 ATGGCACCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.66, G:0.00, T:0.34
Consensus pattern (3 bp):
TCC
Found at i:29366980 original size:42 final size:41
Alignment explanation
Indices: 29366921--29367001 Score: 135
Period size: 41 Copynumber: 2.0 Consensus size: 41
29366911 GCTTTGAGTC
29366921 GGTGTATTTGTATCAAGCCTTGGGCCTAGCAAGCTCTGAGAT
1 GGTGTATTTGTATCAAG-CTTGGGCCTAGCAAGCTCTGAGAT
* *
29366963 GGTGTATTTGTATCAAGCTTGGGCCTAGCAGGCTTTGAG
1 GGTGTATTTGTATCAAGCTTGGGCCTAGCAAGCTCTGAG
29367002 CCGATGAATA
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
41 20 0.54
42 17 0.46
ACGTcount: A:0.20, C:0.17, G:0.31, T:0.32
Consensus pattern (41 bp):
GGTGTATTTGTATCAAGCTTGGGCCTAGCAAGCTCTGAGAT
Found at i:29368454 original size:18 final size:18
Alignment explanation
Indices: 29368431--29368465 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
29368421 TTTAATAATT
*
29368431 TTTTTATCTCAAAAATAA
1 TTTTTATCCCAAAAATAA
29368449 TTTTTATCCCAAAAATA
1 TTTTTATCCCAAAAATA
29368466 CTTTCTAAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.43, C:0.14, G:0.00, T:0.43
Consensus pattern (18 bp):
TTTTTATCCCAAAAATAA
Found at i:29370448 original size:7 final size:7
Alignment explanation
Indices: 29370433--29370463 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
29370423 ATTGATTGTG
29370433 TTGCCAA
1 TTGCCAA
*
29370440 TTTCCAA
1 TTGCCAA
29370447 TTGCCAA
1 TTGCCAA
29370454 TTGCCAA
1 TTGCCAA
29370461 TTG
1 TTG
29370464 TTTAGGTTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.26, C:0.26, G:0.13, T:0.35
Consensus pattern (7 bp):
TTGCCAA
Found at i:29371989 original size:6 final size:6
Alignment explanation
Indices: 29371978--29372003 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
29371968 TTGAAGCCCT
29371978 CCTTCC CCTTCC CCTTCC CCTTCC CC
1 CCTTCC CCTTCC CCTTCC CCTTCC CC
29372004 ATCTCTTTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.69, G:0.00, T:0.31
Consensus pattern (6 bp):
CCTTCC
Found at i:29380032 original size:28 final size:27
Alignment explanation
Indices: 29379988--29380060 Score: 78
Period size: 28 Copynumber: 2.6 Consensus size: 27
29379978 TTAATTAATT
29379988 TTTTATAATTTTT-AATAATT-TCAATGA
1 TTTT-TAATTTTTAAATAATTAT-AATGA
**
29380015 TTTTTAATTTTTAAAATAATTATAATTT
1 TTTTTAATTTTT-AAATAATTATAATGA
29380043 TTTTTAATTTTTTAAATA
1 TTTTTAA-TTTTTAAATA
29380061 TTAATTAAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
26 8 0.20
27 4 0.10
28 22 0.55
29 6 0.15
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.60
Consensus pattern (27 bp):
TTTTTAATTTTTAAATAATTATAATGA
Found at i:29380296 original size:3 final size:3
Alignment explanation
Indices: 29380288--29380318 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
29380278 AACTATCCAA
29380288 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
29380319 TATTATAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:29398758 original size:15 final size:15
Alignment explanation
Indices: 29398740--29398775 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
29398730 CCTCCGTTGG
29398740 CTTCTCAGCAGGCTT
1 CTTCTCAGCAGGCTT
*
29398755 CTTCTCAGCGGGCTT
1 CTTCTCAGCAGGCTT
*
29398770 TTTCTC
1 CTTCTC
29398776 GGCTTTCGGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.08, C:0.33, G:0.19, T:0.39
Consensus pattern (15 bp):
CTTCTCAGCAGGCTT
Found at i:29401359 original size:8 final size:8
Alignment explanation
Indices: 29401346--29401370 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
29401336 ATTTGTGTGT
29401346 TCAATTTC
1 TCAATTTC
29401354 TCAATTTC
1 TCAATTTC
29401362 TCAATTTC
1 TCAATTTC
29401370 T
1 T
29401371 TCCGCTATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.52
Consensus pattern (8 bp):
TCAATTTC
Found at i:29403229 original size:17 final size:17
Alignment explanation
Indices: 29403203--29403246 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
29403193 GTCCCATCCT
*
29403203 TTTTTATTTCTCATTTC
1 TTTTTCTTTCTCATTTC
**
29403220 TTTTTCTTTCTTTTTTC
1 TTTTTCTTTCTCATTTC
29403237 TTCTTTCTTT
1 TT-TTTCTTT
29403247 TCTTCAAACT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 16 0.70
18 7 0.30
ACGTcount: A:0.05, C:0.18, G:0.00, T:0.77
Consensus pattern (17 bp):
TTTTTCTTTCTCATTTC
Found at i:29403236 original size:24 final size:24
Alignment explanation
Indices: 29403201--29403247 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
29403191 CCGTCCCATC
29403201 CTTTTTTATTTC-TCATTTCTTTTT
1 CTTTTTTATTTCTTC-TTTCTTTTT
29403225 CTTTCTTT-TTTCTTCTTTCTTTT
1 CTTT-TTTATTTCTTCTTTCTTTT
29403248 CTTCAAACTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 16 0.76
25 5 0.24
ACGTcount: A:0.04, C:0.19, G:0.00, T:0.77
Consensus pattern (24 bp):
CTTTTTTATTTCTTCTTTCTTTTT
Found at i:29403750 original size:30 final size:30
Alignment explanation
Indices: 29403716--29403780 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
29403706 TATTTTTTTA
**
29403716 AAACCC-TTCAAACCCAAATTCATTTAAACC
1 AAACCCATTCAAA-CCAAACCCATTTAAACC
* *
29403746 AAACCCATTTAAACCAAACCCATTTGAACC
1 AAACCCATTCAAACCAAACCCATTTAAACC
29403776 AAACC
1 AAACC
29403781 AAATGAACCA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 25 0.83
31 5 0.17
ACGTcount: A:0.45, C:0.34, G:0.02, T:0.20
Consensus pattern (30 bp):
AAACCCATTCAAACCAAACCCATTTAAACC
Found at i:29403754 original size:15 final size:15
Alignment explanation
Indices: 29403736--29403780 Score: 81
Period size: 15 Copynumber: 3.0 Consensus size: 15
29403726 AACCCAAATT
29403736 CATTTAAACCAAACC
1 CATTTAAACCAAACC
29403751 CATTTAAACCAAACC
1 CATTTAAACCAAACC
*
29403766 CATTTGAACCAAACC
1 CATTTAAACCAAACC
29403781 AAATGAACCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.44, C:0.33, G:0.02, T:0.20
Consensus pattern (15 bp):
CATTTAAACCAAACC
Found at i:29403860 original size:21 final size:21
Alignment explanation
Indices: 29403836--29403875 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
29403826 GTTGACTGAC
*
29403836 GTTGACCGACCCTTGACCGGT
1 GTTGACCGACCATTGACCGGT
**
29403857 GTTGATTGACCATTGACCG
1 GTTGACCGACCATTGACCG
29403876 TTGACCGTTG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.17, C:0.28, G:0.28, T:0.28
Consensus pattern (21 bp):
GTTGACCGACCATTGACCGGT
Found at i:29403898 original size:20 final size:20
Alignment explanation
Indices: 29403869--29403910 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
29403859 TGATTGACCA
* *
29403869 TTGACCGTTGACCGTTGACT
1 TTGACAGTTGACCATTGACT
29403889 TTGACAGTTGACCATTGACT
1 TTGACAGTTGACCATTGACT
29403909 TT
1 TT
29403911 TTCGAAAAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.38
Consensus pattern (20 bp):
TTGACAGTTGACCATTGACT
Found at i:29404949 original size:3 final size:3
Alignment explanation
Indices: 29404941--29404969 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
29404931 AATATTCTAT
29404941 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
29404970 TTGAGATGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:29406625 original size:16 final size:18
Alignment explanation
Indices: 29406604--29406637 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
29406594 TTAAACACAA
29406604 AATTAA-AC-AAATTCAT
1 AATTAACACTAAATTCAT
29406620 AATTAACACTAAATTCAT
1 AATTAACACTAAATTCAT
29406638 TCTATTGACA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 2 0.12
18 8 0.50
ACGTcount: A:0.53, C:0.15, G:0.00, T:0.32
Consensus pattern (18 bp):
AATTAACACTAAATTCAT
Found at i:29426407 original size:28 final size:30
Alignment explanation
Indices: 29426371--29426435 Score: 82
Period size: 28 Copynumber: 2.2 Consensus size: 30
29426361 TTTAGTTTAG
*
29426371 TTTATAATTTAATCTT-TTTATTTT-TTAT-T
1 TTTA-AATTTAAT-TTCTCTATTTTCTTATAT
29426400 TTTAAATTTAATTTCTCTATTTTCTTATAT
1 TTTAAATTTAATTTCTCTATTTTCTTATAT
29426430 TTTAAA
1 TTTAAA
29426436 ATTCACGTTC
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
27 2 0.06
28 15 0.47
29 8 0.25
30 7 0.22
ACGTcount: A:0.28, C:0.06, G:0.00, T:0.66
Consensus pattern (30 bp):
TTTAAATTTAATTTCTCTATTTTCTTATAT
Found at i:29427182 original size:30 final size:30
Alignment explanation
Indices: 29427148--29427223 Score: 81
Period size: 30 Copynumber: 2.6 Consensus size: 30
29427138 TTAAAATTAG
29427148 AATTAAATTTTGAAATTTAAAAAGTA-AAAA
1 AATTAAATTTTGAAATTTAAAAA-TACAAAA
*
29427178 AATTAAAATTATAGAAA--TAAAAATACAAAA
1 AATT-AAATT-TTGAAATTTAAAAATACAAAA
29427208 AA-TAAATTTT-AAATTT
1 AATTAAATTTTGAAATTT
29427224 TAAATTTACA
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
26 3 0.08
27 1 0.03
28 6 0.15
29 3 0.08
30 16 0.41
31 5 0.13
32 5 0.13
ACGTcount: A:0.62, C:0.01, G:0.04, T:0.33
Consensus pattern (30 bp):
AATTAAATTTTGAAATTTAAAAATACAAAA
Found at i:29428261 original size:23 final size:22
Alignment explanation
Indices: 29428208--29428249 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
29428198 TATGATTTTT
*
29428208 AATTAATTTTAATATTTTTATA
1 AATTATTTTTAATATTTTTATA
*
29428230 AATTATTTTTAATGTTTTTA
1 AATTATTTTTAATATTTTTA
29428250 ATTATTTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (22 bp):
AATTATTTTTAATATTTTTATA
Found at i:29429856 original size:2 final size:2
Alignment explanation
Indices: 29429849--29429898 Score: 86
Period size: 2 Copynumber: 26.0 Consensus size: 2
29429839 CTGATGATTG
29429849 AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29429890 AT AT -T AT AT
1 AT AT AT AT AT
29429899 TTTGAAAATT
Statistics
Matches: 46, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 2 0.04
2 44 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:29429883 original size:25 final size:25
Alignment explanation
Indices: 29429849--29429898 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
29429839 CTGATGATTG
29429849 ATATATATATATATATATATTATAT
1 ATATATATATATATATATATTATAT
29429874 ATATATATATATATATATATTATAT
1 ATATATATATATATATATATTATAT
29429899 TTTGAAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (25 bp):
ATATATATATATATATATATTATAT
Found at i:29430992 original size:59 final size:57
Alignment explanation
Indices: 29430929--29431176 Score: 157
Period size: 59 Copynumber: 4.2 Consensus size: 57
29430919 TTGGATACCC
*
29430929 GGGGGCAAAATGGTAGATTTTGGTGAAA-TCGGGGTTTAAAATG-AGATTTTT-GAAAGTTT
1 GGGGGCAAAATGGTA-ATTTT--TGAAATTCGGGG-TAAAAATGTA-ATTTTTGGAAAGTTT
* *
29430988 GGGGGTAAAATGGTAATTTTTGAAAGTTTCGGGGTAAAAATGTAATTTTTGGAAATTTT
1 GGGGGCAAAATGGTAATTTTTGAAA--TTCGGGGTAAAAATGTAATTTTTGGAAAGTTT
* * * * ** * *
29431047 GGGGTCAAAAT-ATGATTTTGGAAAAGTTTTAGGGTCAAAATGTAA-TTTTAGAAAGTTTT
1 GGGGGCAAAATGGTAATTTTTG-AAA--TTCGGGGTAAAAATGTAATTTTTGGAAAG-TTT
* * * * **
29431106 GGGGTCAAAAT-GTAATTTTTAGAAAGTTTCGAGGTCAAAATATAATTTTTAAAAAGTTT
1 GGGGGCAAAATGGTAATTTTT-GAAA--TTCGGGGTAAAAATGTAATTTTTGGAAAGTTT
*
29431165 CGGGGTCAAAAT
1 -GGGGGCAAAAT
29431177 ATAATTTCTA
Statistics
Matches: 158, Mismatches: 21, Indels: 19
0.80 0.11 0.10
Matches are distributed among these distances:
56 5 0.03
58 33 0.21
59 99 0.63
60 21 0.13
ACGTcount: A:0.34, C:0.04, G:0.26, T:0.36
Consensus pattern (57 bp):
GGGGGCAAAATGGTAATTTTTGAAATTCGGGGTAAAAATGTAATTTTTGGAAAGTTT
Found at i:29430993 original size:30 final size:29
Alignment explanation
Indices: 29430966--29431183 Score: 235
Period size: 30 Copynumber: 7.4 Consensus size: 29
29430956 ATCGGGGTTT
*
29430966 AAAATG-AGATTTTTGAAAGTTTGGGGGT-
1 AAAATGTA-ATTTTTGAAAGTTTTGGGGTC
* *
29430994 AAAATGGTAATTTTTGAAAGTTTCGGGGTA
1 AAAAT-GTAATTTTTGAAAGTTTTGGGGTC
29431024 AAAATGTAATTTTTGGAAA-TTTTGGGGTC
1 AAAATGTAATTTTT-GAAAGTTTTGGGGTC
* * * *
29431053 AAAATATGATTTTGGAAAAGTTTTAGGGTC
1 AAAATGTAATTTTTG-AAAGTTTTGGGGTC
*
29431083 AAAATGTAATTTTAGAAAGTTTTGGGGTC
1 AAAATGTAATTTTTGAAAGTTTTGGGGTC
* *
29431112 AAAATGTAATTTTTAGAAAGTTTCGAGGTC
1 AAAATGTAATTTTT-GAAAGTTTTGGGGTC
* * *
29431142 AAAATATAATTTTTAAAAAGTTTCGGGGTC
1 AAAATGTAATTTTT-GAAAGTTTTGGGGTC
*
29431172 AAAATATAATTT
1 AAAATGTAATTT
29431184 CTAAATAATT
Statistics
Matches: 166, Mismatches: 17, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
28 6 0.04
29 77 0.46
30 83 0.50
ACGTcount: A:0.36, C:0.04, G:0.22, T:0.38
Consensus pattern (29 bp):
AAAATGTAATTTTTGAAAGTTTTGGGGTC
Found at i:29432621 original size:209 final size:209
Alignment explanation
Indices: 29432261--29432681 Score: 842
Period size: 209 Copynumber: 2.0 Consensus size: 209
29432251 TTATTATTAT
29432261 TAATAAAATATTATTAATATTTATTGAAACATTTAATACCCTTAGTAATATTATATTATTTACAT
1 TAATAAAATATTATTAATATTTATTGAAACATTTAATACCCTTAGTAATATTATATTATTTACAT
29432326 TATTATTGTTGCTCATTAATGCCGATTATTAATGTTTATTAATGCATTCAAAACGGTGCAATGAA
66 TATTATTGTTGCTCATTAATGCCGATTATTAATGTTTATTAATGCATTCAAAACGGTGCAATGAA
29432391 TGCTAAAAGGCTATTAAAGCATGCATTAATACATATCCTCGGAATCTGATAAGTTTAGAAATTTC
131 TGCTAAAAGGCTATTAAAGCATGCATTAATACATATCCTCGGAATCTGATAAGTTTAGAAATTTC
29432456 ATCATAAATGAAAG
196 ATCATAAATGAAAG
29432470 TAATAAAATATTATTAATATTTATTGAAACATTTAATACCCTTAGTAATATTATATTATTTACAT
1 TAATAAAATATTATTAATATTTATTGAAACATTTAATACCCTTAGTAATATTATATTATTTACAT
29432535 TATTATTGTTGCTCATTAATGCCGATTATTAATGTTTATTAATGCATTCAAAACGGTGCAATGAA
66 TATTATTGTTGCTCATTAATGCCGATTATTAATGTTTATTAATGCATTCAAAACGGTGCAATGAA
29432600 TGCTAAAAGGCTATTAAAGCATGCATTAATACATATCCTCGGAATCTGATAAGTTTAGAAATTTC
131 TGCTAAAAGGCTATTAAAGCATGCATTAATACATATCCTCGGAATCTGATAAGTTTAGAAATTTC
29432665 ATCATAAATGAAAG
196 ATCATAAATGAAAG
29432679 TAA
1 TAA
29432682 GTGTGCATTG
Statistics
Matches: 212, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
209 212 1.00
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.38
Consensus pattern (209 bp):
TAATAAAATATTATTAATATTTATTGAAACATTTAATACCCTTAGTAATATTATATTATTTACAT
TATTATTGTTGCTCATTAATGCCGATTATTAATGTTTATTAATGCATTCAAAACGGTGCAATGAA
TGCTAAAAGGCTATTAAAGCATGCATTAATACATATCCTCGGAATCTGATAAGTTTAGAAATTTC
ATCATAAATGAAAG
Found at i:29433256 original size:6 final size:6
Alignment explanation
Indices: 29433239--29433314 Score: 81
Period size: 6 Copynumber: 13.0 Consensus size: 6
29433229 TTAATTTTAT
*
29433239 TTTAAA TTTAAA TTTAAA -TTAAA TCTAAA TAATTAAA TTTAAA TTTAAGA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T--TTAAA TTTAAA TTTAA-A
29433289 --TAAA TTTAAA TTTAAA --TAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
29433315 ATCAATTTAA
Statistics
Matches: 60, Mismatches: 2, Indels: 16
0.77 0.03 0.21
Matches are distributed among these distances:
4 5 0.08
5 8 0.13
6 41 0.68
7 1 0.02
8 5 0.08
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (6 bp):
TTTAAA
Found at i:29433260 original size:11 final size:11
Alignment explanation
Indices: 29433239--29433324 Score: 66
Period size: 11 Copynumber: 7.5 Consensus size: 11
29433229 TTAATTTTAT
29433239 TTTAAATTTAAA
1 TTTAAA-TTAAA
29433251 TTTAAATTAAA
1 TTTAAATTAAA
*
29433262 TCTAAATAATTAAA
1 T-T-TA-AATTAAA
*
29433276 TTTAAATTTAA
1 TTTAAATTAAA
**
29433287 GATAAATTTAAA
1 TTTAAA-TTAAA
29433299 TTTAAA-TAAA
1 TTTAAATTAAA
* *
29433309 TTTAAAATCAA
1 TTTAAATTAAA
29433320 TTTAA
1 TTTAA
29433325 CTCCAAATTA
Statistics
Matches: 60, Mismatches: 9, Indels: 11
0.75 0.11 0.14
Matches are distributed among these distances:
10 10 0.17
11 24 0.40
12 16 0.27
13 2 0.03
14 8 0.13
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.43
Consensus pattern (11 bp):
TTTAAATTAAA
Found at i:29433276 original size:31 final size:32
Alignment explanation
Indices: 29433240--29433314 Score: 100
Period size: 31 Copynumber: 2.3 Consensus size: 32
29433230 TAATTTTATT
29433240 TTAAATTTAAATTTAA-ATTAAATCTAAA-TAA
1 TTAAATTTAAATTTAAGA-TAAATCTAAATTAA
*
29433271 TTAAATTTAAATTTAAGATAAATTTAAATTTAA
1 TTAAATTTAAATTTAAGATAAATCTAAA-TTAA
*
29433304 ATAAATTTAAA
1 TTAAATTTAAA
29433315 ATCAATTTAA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
31 25 0.64
32 1 0.03
33 13 0.33
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (32 bp):
TTAAATTTAAATTTAAGATAAATCTAAATTAA
Found at i:29433316 original size:17 final size:16
Alignment explanation
Indices: 29433241--29433314 Score: 98
Period size: 17 Copynumber: 4.6 Consensus size: 16
29433231 AATTTTATTT
29433241 TAAATTTAAATTTAAA
1 TAAATTTAAATTTAAA
* *
29433257 TTAAATCTAAA--TAAT
1 -TAAATTTAAATTTAAA
29433272 TAAATTTAAATTTAAGA
1 TAAATTTAAATTTAA-A
29433289 TAAATTTAAATTTAAA
1 TAAATTTAAATTTAAA
29433305 TAAATTTAAA
1 TAAATTTAAA
29433315 ATCAATTTAA
Statistics
Matches: 50, Mismatches: 4, Indels: 7
0.82 0.07 0.11
Matches are distributed among these distances:
14 9 0.18
15 3 0.06
16 14 0.28
17 24 0.48
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (16 bp):
TAAATTTAAATTTAAA
Found at i:29433332 original size:27 final size:27
Alignment explanation
Indices: 29433278--29433332 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
29433268 TAATTAAATT
* **
29433278 TAAATTTAAGATAAATTTAAATTTAAA
1 TAAATTTAAAATAAATTTAAATCCAAA
* *
29433305 TAAATTTAAAATCAATTTAACTCCAAA
1 TAAATTTAAAATAAATTTAAATCCAAA
29433332 T
1 T
29433333 TAAAACAAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.53, C:0.07, G:0.02, T:0.38
Consensus pattern (27 bp):
TAAATTTAAAATAAATTTAAATCCAAA
Found at i:29434185 original size:21 final size:23
Alignment explanation
Indices: 29434160--29434203 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
29434150 GTGTTGAAAC
29434160 TTGATAT-T-TAATTTTTATAAT
1 TTGATATATCTAATTTTTATAAT
*
29434181 TTGATATATCTATTTTTTATAAT
1 TTGATATATCTAATTTTTATAAT
29434204 GTTATTAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 7 0.35
22 1 0.05
23 12 0.60
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.61
Consensus pattern (23 bp):
TTGATATATCTAATTTTTATAAT
Found at i:29434343 original size:13 final size:14
Alignment explanation
Indices: 29434325--29434353 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
29434315 TTCTACTATG
29434325 TTTAATA-TTTAAT
1 TTTAATATTTTAAT
29434338 TTTAATATTTTAAT
1 TTTAATATTTTAAT
29434352 TT
1 TT
29434354 CTAACATAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (14 bp):
TTTAATATTTTAAT
Found at i:29435072 original size:2 final size:2
Alignment explanation
Indices: 29435065--29435089 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
29435055 TATATGATTT
29435065 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
29435090 TACATTATAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:29437833 original size:7 final size:7
Alignment explanation
Indices: 29437821--29437866 Score: 92
Period size: 7 Copynumber: 6.6 Consensus size: 7
29437811 ACCCACTGTT
29437821 TGAGTGA
1 TGAGTGA
29437828 TGAGTGA
1 TGAGTGA
29437835 TGAGTGA
1 TGAGTGA
29437842 TGAGTGA
1 TGAGTGA
29437849 TGAGTGA
1 TGAGTGA
29437856 TGAGTGA
1 TGAGTGA
29437863 TGAG
1 TGAG
29437867 CAGTGTCTCA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 39 1.00
ACGTcount: A:0.28, C:0.00, G:0.43, T:0.28
Consensus pattern (7 bp):
TGAGTGA
Found at i:29438316 original size:20 final size:21
Alignment explanation
Indices: 29438286--29438340 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 21
29438276 GCTTTTTTTT
29438286 TAAATTAAAAAACATC-TTTCC
1 TAAA-TAAAAAACATCTTTTCC
*
29438307 TAAAT-AAAAATATCTTTTCC
1 TAAATAAAAAACATCTTTTCC
*
29438327 AATAATAAAAAACA
1 TA-AATAAAAAACA
29438341 CGAAAATATC
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
19 8 0.29
20 7 0.25
21 7 0.25
22 6 0.21
ACGTcount: A:0.55, C:0.15, G:0.00, T:0.31
Consensus pattern (21 bp):
TAAATAAAAAACATCTTTTCC
Found at i:29444745 original size:21 final size:22
Alignment explanation
Indices: 29444716--29444756 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
29444706 TTTATTTTAA
29444716 TTTGATATTTGATA-TTTTTCTT
1 TTTGATATTT-ATACTTTTTCTT
29444738 TTTG-TATTTATACTTTTTC
1 TTTGATATTTATACTTTTTC
29444757 ATAAAATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 3 0.17
21 11 0.61
22 4 0.22
ACGTcount: A:0.17, C:0.07, G:0.07, T:0.68
Consensus pattern (22 bp):
TTTGATATTTATACTTTTTCTT
Found at i:29446512 original size:61 final size:61
Alignment explanation
Indices: 29446390--29446511 Score: 237
Period size: 60 Copynumber: 2.0 Consensus size: 61
29446380 ATAATAAATA
29446390 TCGTGGTTATAATATTTACTCTTTTTTATTTTATTTTATAACACGTAATCAACACGATTTT
1 TCGTGGTTATAATATTTACTCTTTTTTATTTTATTTTATAACACGTAATCAACACGATTTT
29446451 TCGTGGTTATAATATTTACTC-TTTTTATTTTATTTTATAACACGTAATCAACACGATTTT
1 TCGTGGTTATAATATTTACTCTTTTTTATTTTATTTTATAACACGTAATCAACACGATTTT
29446511 T
1 T
29446512 TTTAAGGAAG
Statistics
Matches: 61, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
60 40 0.66
61 21 0.34
ACGTcount: A:0.28, C:0.13, G:0.08, T:0.51
Consensus pattern (61 bp):
TCGTGGTTATAATATTTACTCTTTTTTATTTTATTTTATAACACGTAATCAACACGATTTT
Found at i:29457802 original size:20 final size:20
Alignment explanation
Indices: 29457777--29457843 Score: 66
Period size: 20 Copynumber: 3.3 Consensus size: 20
29457767 ATGAATTTAT
29457777 TAAATTATTTAGAATTAGGA
1 TAAATTATTTAGAATTAGGA
** *
29457797 TAAATTGATAGATGAATTTA--T
1 TAAATT-ATTTA-GAA-TTAGGA
29457818 TAAATTATTTAGAATTAGGA
1 TAAATTATTTAGAATTAGGA
29457838 TAAATT
1 TAAATT
29457844 GATAGAATAT
Statistics
Matches: 36, Mismatches: 6, Indels: 10
0.69 0.12 0.19
Matches are distributed among these distances:
18 3 0.08
19 3 0.08
20 15 0.42
21 9 0.25
22 3 0.08
23 3 0.08
ACGTcount: A:0.45, C:0.00, G:0.13, T:0.42
Consensus pattern (20 bp):
TAAATTATTTAGAATTAGGA
Found at i:29457823 original size:41 final size:41
Alignment explanation
Indices: 29457766--29457849 Score: 168
Period size: 41 Copynumber: 2.0 Consensus size: 41
29457756 TATGCCTTGG
29457766 GATGAATTTATTAAATTATTTAGAATTAGGATAAATTGATA
1 GATGAATTTATTAAATTATTTAGAATTAGGATAAATTGATA
29457807 GATGAATTTATTAAATTATTTAGAATTAGGATAAATTGATA
1 GATGAATTTATTAAATTATTTAGAATTAGGATAAATTGATA
29457848 GA
1 GA
29457850 ATATGTAAGT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.44, C:0.00, G:0.15, T:0.40
Consensus pattern (41 bp):
GATGAATTTATTAAATTATTTAGAATTAGGATAAATTGATA
Found at i:29460528 original size:21 final size:21
Alignment explanation
Indices: 29460504--29460546 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
29460494 TTTAATAATG
*
29460504 TTTATATTTATGATAATTTTA
1 TTTATATTTATAATAATTTTA
*
29460525 TTTATTTTTATAATAATTTTA
1 TTTATATTTATAATAATTTTA
29460546 T
1 T
29460547 ACATAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (21 bp):
TTTATATTTATAATAATTTTA
Found at i:29467873 original size:24 final size:25
Alignment explanation
Indices: 29467834--29467892 Score: 63
Period size: 21 Copynumber: 2.4 Consensus size: 25
29467824 AAGAACTAAG
29467834 AAAAAAAAG-GGAAAAT-A-G-AAA
1 AAAAAAAAGAGGAAAATAATGTAAA
29467855 AAAAAAAAGAGAGAGAAATAATGTAAA
1 AAAAAAAAGAG-GA-AAATAATGTAAA
29467882 ATAAAAAAAGA
1 A-AAAAAAAGA
29467893 CAATAAAAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
21 9 0.29
22 1 0.03
23 2 0.06
24 4 0.13
25 1 0.03
26 1 0.03
27 4 0.13
28 9 0.29
ACGTcount: A:0.75, C:0.00, G:0.17, T:0.08
Consensus pattern (25 bp):
AAAAAAAAGAGGAAAATAATGTAAA
Found at i:29468720 original size:24 final size:24
Alignment explanation
Indices: 29468675--29468721 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
29468665 AATAATAAGT
* **
29468675 TCTCTGTCTTTTGACATGTTTTTC
1 TCTCTATCTTTTGACACATTTTTC
29468699 TCTCTATCTTTTGACACATTTTT
1 TCTCTATCTTTTGACACATTTTT
29468722 TTCTTTCTTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.13, C:0.21, G:0.09, T:0.57
Consensus pattern (24 bp):
TCTCTATCTTTTGACACATTTTTC
Found at i:29470974 original size:30 final size:30
Alignment explanation
Indices: 29470938--29471000 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
29470928 TTGGTGATAT
*
29470938 AGTGGATATAAAGTTAGCTATTAATCTCGA
1 AGTGGATATAAAGTTAGCCATTAATCTCGA
29470968 AGTGGATATAAAGTTAGCCATTAATCTCGA
1 AGTGGATATAAAGTTAGCCATTAATCTCGA
29470998 AGT
1 AGT
29471001 AGACAAGGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.37, C:0.11, G:0.21, T:0.32
Consensus pattern (30 bp):
AGTGGATATAAAGTTAGCCATTAATCTCGA
Found at i:29479824 original size:30 final size:31
Alignment explanation
Indices: 29479773--29479843 Score: 90
Period size: 30 Copynumber: 2.3 Consensus size: 31
29479763 ATGGTCGTTA
*
29479773 AACTATTAAAAAGTTTTTATTTAAGCCATTG
1 AACTATTAAAAAGTGTTTATTTAAGCCATTG
* *
29479804 AACTATTCAAAA-TGTTTATTTAAGTCATTG
1 AACTATTAAAAAGTGTTTATTTAAGCCATTG
**
29479834 GGCTATTAAA
1 AACTATTAAA
29479844 GTTTTTTTTA
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
30 23 0.68
31 11 0.32
ACGTcount: A:0.38, C:0.10, G:0.11, T:0.41
Consensus pattern (31 bp):
AACTATTAAAAAGTGTTTATTTAAGCCATTG
Found at i:29484489 original size:17 final size:19
Alignment explanation
Indices: 29484457--29484494 Score: 62
Period size: 17 Copynumber: 2.1 Consensus size: 19
29484447 TCCTAATTCT
29484457 AAAAATGCAAAGAATATAA
1 AAAAATGCAAAGAATATAA
29484476 AAAAATG-AAA-AATATAA
1 AAAAATGCAAAGAATATAA
29484493 AA
1 AA
29484495 TAATTGAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 9 0.47
18 3 0.16
19 7 0.37
ACGTcount: A:0.74, C:0.03, G:0.08, T:0.16
Consensus pattern (19 bp):
AAAAATGCAAAGAATATAA
Found at i:29486734 original size:33 final size:30
Alignment explanation
Indices: 29486703--29486761 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
29486693 TGGATTAATG
*
29486703 ATTTAATATAAATATATAAT-TAATA-ATTTA
1 ATTTTATA-AAAT-TATAATATAATATATTTA
29486733 ATTTTATAAAATTATAATATAATATATTT
1 ATTTTATAAAATTATAATATAATATATTT
29486762 GGGTCAAGCT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
28 6 0.23
29 9 0.35
30 11 0.42
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (30 bp):
ATTTTATAAAATTATAATATAATATATTTA
Done.