Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 ID=Chr05-JGI_221_v2.0
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: 64140413
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 820884 characters in sequence are not A, C, G, or T
File 204 of 208
Found at i:62089849 original size:21 final size:20
Alignment explanation
Indices: 62089811--62089852 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 20
62089801 AATAATGTTC
62089811 AAAAAATATATTACTAATAT
1 AAAAAATATATTACTAATAT
62089831 AAAAAATACTATATA-TAATAT
1 AAAAAATA-TAT-TACTAATAT
62089852 A
1 A
62089853 TATTATTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 8 0.40
21 10 0.50
22 2 0.10
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (20 bp):
AAAAAATATATTACTAATAT
Found at i:62108931 original size:381 final size:381
Alignment explanation
Indices: 62108228--62109116 Score: 1652
Period size: 381 Copynumber: 2.3 Consensus size: 381
62108218 AGAAAGCTTG
*
62108228 AGGACAGAATGAAGATGGCTGAAGATGACCTGAGAAATGCATCTACTTGTGCATCTGTTGCTTTT
1 AGGACAGAATGAAGATGGCTGAAGATGACCTGAGAAATGCATCTACTTGTGCAACTGTTGCTTTT
*
62108293 GTACTTGTGAATAGATTACCAGAGGCAAACCATAATCATCTCAATGCATTGAAGGGTAAGGACGA
66 GTACTTGTGAATAGATTATCAGAGGCAAACCATAATCATCTCAATGCATTGAAGGGTAAGGACGA
62108358 ACAACTTGCAGAATCAGCAGAGGCGATCTTGAGTAAGGATGCTCTTTTGATCAACCAAGCTACCA
131 ACAACTTGCAGAATCAGCAGAGGCGATCTTGAGTAAGGATGCTCTTTTGATCAACCAAGCTACCA
62108423 TGATTGAAGAAGCAGAAAAACATATTCATTCCCTTGAAACTGAAGTTGAAAAGTCAGAGGAAGCT
196 TGATTGAAGAAGCAGAAAAACATATTCATTCCCTTGAAACTGAAGTTGAAAAGTCAGAGGAAGCT
*
62108488 TGCACTGAACTTAGCCAGAGGCTTCTGGAGGAGGAGCAGCGTGCTGCTGCTATTGAACAAAAGCT
261 TGCACTGAACTTAGCAAGAGGCTTCTGGAGGAGGAGCAGCGTGCTGCTGCTATTGAACAAAAGCT
* * *
62108553 TGAAGATATGGTGGAGAATGACATTTTGAAGACACAGGAGGAGCTGTCTAATCTTA
326 TGAAGATATGGTGGAGAATAACATTTTGAACACACAGGAGGAGCTGTCTAAACTTA
*
62108609 AGGACAGAATGAAGATGGCTGAAGATGACCTGAGAAATGCATCTACTTGTGCAACCGTTGCTTTT
1 AGGACAGAATGAAGATGGCTGAAGATGACCTGAGAAATGCATCTACTTGTGCAACTGTTGCTTTT
62108674 GTACTTGTGAATAGATTATCAGAGGCAAACCATAATCATCTCAATGCATTGAAGGGTAAGGACGA
66 GTACTTGTGAATAGATTATCAGAGGCAAACCATAATCATCTCAATGCATTGAAGGGTAAGGACGA
62108739 ACAACTTGCAGAATCAGCAGAGGCGATCTTGAGTAAGGATGCTCTTTTGATCAACCAAGCTACCA
131 ACAACTTGCAGAATCAGCAGAGGCGATCTTGAGTAAGGATGCTCTTTTGATCAACCAAGCTACCA
* *
62108804 TGATTGAAGAAGCAGAAACACGTATTCATTCCCTTGAAACTGAAGTTGAAAAGTCAGAGGAAGCT
196 TGATTGAAGAAGCAGAAAAACATATTCATTCCCTTGAAACTGAAGTTGAAAAGTCAGAGGAAGCT
* *
62108869 TGCACTGAACTTCGCAAGAGGCTTCTGGAGGAGGAGCAGTGTGCTGCTGCTATTGAACAAAAGCT
261 TGCACTGAACTTAGCAAGAGGCTTCTGGAGGAGGAGCAGCGTGCTGCTGCTATTGAACAAAAGCT
* *
62108934 TGAAGATATGGTGGAGAATAACTTTTTGAACACACAGGAGGAGCTGTCTAAACTTG
326 TGAAGATATGGTGGAGAATAACATTTTGAACACACAGGAGGAGCTGTCTAAACTTA
*
62108990 AGGACAGAATGAAGATGGCTGAAGATGACCTAAGAAATGCATCTACTTGTGCAACTGTTGCTTTT
1 AGGACAGAATGAAGATGGCTGAAGATGACCTGAGAAATGCATCTACTTGTGCAACTGTTGCTTTT
62109055 GTACTTGTGAATAGATTATCAGAGGCAAACCATAATCATCTCAATGCATTGAAGGGTAAGGA
66 GTACTTGTGAATAGATTATCAGAGGCAAACCATAATCATCTCAATGCATTGAAGGGTAAGGA
62109117 TGCTCTTCTA
Statistics
Matches: 493, Mismatches: 15, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
381 493 1.00
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.25
Consensus pattern (381 bp):
AGGACAGAATGAAGATGGCTGAAGATGACCTGAGAAATGCATCTACTTGTGCAACTGTTGCTTTT
GTACTTGTGAATAGATTATCAGAGGCAAACCATAATCATCTCAATGCATTGAAGGGTAAGGACGA
ACAACTTGCAGAATCAGCAGAGGCGATCTTGAGTAAGGATGCTCTTTTGATCAACCAAGCTACCA
TGATTGAAGAAGCAGAAAAACATATTCATTCCCTTGAAACTGAAGTTGAAAAGTCAGAGGAAGCT
TGCACTGAACTTAGCAAGAGGCTTCTGGAGGAGGAGCAGCGTGCTGCTGCTATTGAACAAAAGCT
TGAAGATATGGTGGAGAATAACATTTTGAACACACAGGAGGAGCTGTCTAAACTTA
Found at i:62111701 original size:222 final size:222
Alignment explanation
Indices: 62111415--62111978 Score: 844
Period size: 222 Copynumber: 2.5 Consensus size: 222
62111405 TTGTCCACTT
* *
62111415 AGCTGACTCTGGGAAAAAGCTTACCAATGCTTATGCTGTC-CTTGATGGTTTAAAGAAGGAAATG
1 AGCTGACTCTGGAAAAAAGCTTACCAATGCTTATGCTGTCAC-TGATGGTTTAAAGAAAGAAATG
* * *
62111479 ACTTTTACAAAATTAGATGCATGTTTGAAAGAGCAGCTATTGGTGGAGCGGGAAAGTGAGTTGTC
65 ATTTTTGCAAAATTAGATGCATGTTTGAAAGAGCAGCTATTGGTGGAGCAGGAAAGTGAGTTGTC
* * * * * *
62111544 TTTTCTCCAAGAAAAAGTTGAAGAAGCACAGATTGAGTTAAGAATGTTGAAGAAAGAGAACTGTC
130 TTTTCTACAAGAAAAAGTTGAAGAAGCACAAATTGAGGTAAGAAAGATGAAGAAAGAAAACTGTC
* * *
62111609 TACTTCTCCAGGATTTGGAGGAGCAGAA
195 TACTTCTCCAGAATTTGGACGAGAAGAA
* *
62111637 AGCTGACTCTGGAAAAAAGCTTGCCAATGCTTATTCTGTCACTGATGGTTTAAAGAAAGAAATGA
1 AGCTGACTCTGGAAAAAAGCTTACCAATGCTTATGCTGTCACTGATGGTTTAAAGAAAGAAATGA
* *
62111702 TTTTTGCAAAATTAGATGCATGCTTGAAAGGGCAGCTATTGGTGGAGCAGGACAA-TGAGTTGTC
66 TTTTTGCAAAATTAGATGCATGTTTGAAAGAGCAGCTATTGGTGGAGCAGGA-AAGTGAGTTGTC
*
62111766 TTTTCTACAAGAAAAAGTTGAAGAAGCACAAATTGAGGTAAGAAAGATGCAGAAAGAAAACTGTC
130 TTTTCTACAAGAAAAAGTTGAAGAAGCACAAATTGAGGTAAGAAAGATGAAGAAAGAAAACTGTC
* *
62111831 TGCTTCTCCAGAATTTGGACGAGAAGGA
195 TACTTCTCCAGAATTTGGACGAGAAGAA
* * * * *
62111859 AGCAGACACCGGAAAAAAGCTTACCAATGCTTATGCTGTCATTGATGGTTTAAAGAAAGAAATAA
1 AGCTGACTCTGGAAAAAAGCTTACCAATGCTTATGCTGTCACTGATGGTTTAAAGAAAGAAATGA
* *
62111924 TTTTTGCAAAAGTAGATGCATGTTTGAAAGAGCAACTATTGGTGGAGCAGGAAAG
66 TTTTTGCAAAATTAGATGCATGTTTGAAAGAGCAGCTATTGGTGGAGCAGGAAAG
62111979 GATATCAAAG
Statistics
Matches: 307, Mismatches: 32, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
221 2 0.01
222 302 0.98
223 3 0.01
ACGTcount: A:0.36, C:0.13, G:0.25, T:0.26
Consensus pattern (222 bp):
AGCTGACTCTGGAAAAAAGCTTACCAATGCTTATGCTGTCACTGATGGTTTAAAGAAAGAAATGA
TTTTTGCAAAATTAGATGCATGTTTGAAAGAGCAGCTATTGGTGGAGCAGGAAAGTGAGTTGTCT
TTTCTACAAGAAAAAGTTGAAGAAGCACAAATTGAGGTAAGAAAGATGAAGAAAGAAAACTGTCT
ACTTCTCCAGAATTTGGACGAGAAGAA
Found at i:62116180 original size:15 final size:15
Alignment explanation
Indices: 62116160--62116207 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
62116150 GTCCGATATG
62116160 TACATGCAAGTTTCA
1 TACATGCAAGTTTCA
62116175 TACATGC-A---T-A
1 TACATGCAAGTTTCA
*
62116185 CACATGCAAGTTTCA
1 TACATGCAAGTTTCA
62116200 TACATGCA
1 TACATGCA
62116208 TACACATGCA
Statistics
Matches: 26, Mismatches: 2, Indels: 10
0.68 0.05 0.26
Matches are distributed among these distances:
10 7 0.27
11 2 0.08
14 2 0.08
15 15 0.58
ACGTcount: A:0.35, C:0.23, G:0.12, T:0.29
Consensus pattern (15 bp):
TACATGCAAGTTTCA
Found at i:62116189 original size:25 final size:25
Alignment explanation
Indices: 62116161--62116217 Score: 114
Period size: 25 Copynumber: 2.3 Consensus size: 25
62116151 TCCGATATGT
62116161 ACATGCAAGTTTCATACATGCATAC
1 ACATGCAAGTTTCATACATGCATAC
62116186 ACATGCAAGTTTCATACATGCATAC
1 ACATGCAAGTTTCATACATGCATAC
62116211 ACATGCA
1 ACATGCA
62116218 TATGTACATG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.37, C:0.25, G:0.12, T:0.26
Consensus pattern (25 bp):
ACATGCAAGTTTCATACATGCATAC
Found at i:62118758 original size:18 final size:18
Alignment explanation
Indices: 62118735--62118772 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
62118725 GTACTAGGAG
62118735 TCAGATTGCATTTTGCAC
1 TCAGATTGCATTTTGCAC
62118753 TCAGATTGCATTTTGCAC
1 TCAGATTGCATTTTGCAC
62118771 TC
1 TC
62118773 TATACTCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.21, C:0.24, G:0.16, T:0.39
Consensus pattern (18 bp):
TCAGATTGCATTTTGCAC
Found at i:62123218 original size:42 final size:42
Alignment explanation
Indices: 62123155--62123238 Score: 143
Period size: 42 Copynumber: 2.0 Consensus size: 42
62123145 AAGTTAAACC
*
62123155 GATTTATCAGTTTTT-AGTTTTTTACACTTTTTATGAATTTTT
1 GATTTATCAGTTTTTAATTTTTTTACA-TTTTTATGAATTTTT
62123197 GATTTATCAGTTTTTAATTTTTTTACATTTTTATGAATTTTT
1 GATTTATCAGTTTTTAATTTTTTTACATTTTTATGAATTTTT
62123239 AAGTATTTAT
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
42 30 0.75
43 10 0.25
ACGTcount: A:0.23, C:0.06, G:0.08, T:0.63
Consensus pattern (42 bp):
GATTTATCAGTTTTTAATTTTTTTACATTTTTATGAATTTTT
Found at i:62125234 original size:27 final size:27
Alignment explanation
Indices: 62125202--62125293 Score: 78
Period size: 27 Copynumber: 3.2 Consensus size: 27
62125192 ATTTGATCCT
62125202 AAAAAAAAGCTTAGGTACCAAATTAGG
1 AAAAAAAAGCTTAGGTACCAAATTAGG
* *
62125229 AAAAAAAAGGTCAAGTTCAAGTACCAAATTGAGC
1 AAAAAAAA-G-C---TT-AGGTACCAAATT-AGG
* *
62125263 TAAAAAAA-TTTAGGTACCAAATTAGG
1 AAAAAAAAGCTTAGGTACCAAATTAGG
62125289 AAAAA
1 AAAAA
62125294 GTGTCAAGTT
Statistics
Matches: 51, Mismatches: 7, Indels: 15
0.70 0.10 0.21
Matches are distributed among these distances:
26 6 0.12
27 19 0.37
28 3 0.06
29 1 0.02
32 2 0.04
33 11 0.22
34 9 0.18
ACGTcount: A:0.53, C:0.11, G:0.16, T:0.20
Consensus pattern (27 bp):
AAAAAAAAGCTTAGGTACCAAATTAGG
Found at i:62125283 original size:60 final size:61
Alignment explanation
Indices: 62125203--62125376 Score: 191
Period size: 60 Copynumber: 2.9 Consensus size: 61
62125193 TTTGATCCTA
* *
62125203 AAAAAAAGCTTAGGTACCAAATTAGGAAAAAAAAGGTCAAGTTCAAGTACCAAATTGAGCT
1 AAAAAAAGTTTAGGTACCAAATTAGGAAAAAAAAGGTCAAGTTCAAGTACCAAATTGAGCC
* * *
62125264 AAAAAAA-TTTAGGTACCAAATTAGG---AAAAAGTGTCAAGTTCAGGTACCAATTTGGGCC
1 AAAAAAAGTTTAGGTACCAAATTAGGAAAAAAAAG-GTCAAGTTCAAGTACCAAATTGAGCC
* * *
62125322 AAATAAAAGTTCATGTACCAAAATA-GAAAAAAAA--TACAAAGTTCAAGTACCAAAT
1 AAA-AAAAGTTTAGGTACCAAATTAGGAAAAAAAAGGT-C-AAGTTCAAGTACCAAAT
62125377 GTTATATTAA
Statistics
Matches: 95, Mismatches: 10, Indels: 16
0.79 0.08 0.13
Matches are distributed among these distances:
57 6 0.06
58 25 0.26
59 6 0.06
60 31 0.33
61 22 0.23
62 5 0.05
ACGTcount: A:0.49, C:0.13, G:0.16, T:0.21
Consensus pattern (61 bp):
AAAAAAAGTTTAGGTACCAAATTAGGAAAAAAAAGGTCAAGTTCAAGTACCAAATTGAGCC
Found at i:62130476 original size:66 final size:66
Alignment explanation
Indices: 62130370--62130562 Score: 241
Period size: 66 Copynumber: 3.0 Consensus size: 66
62130360 TGAAGACAAC
* *
62130370 GATGATTCTGCATCCATGAATGCTGAAAGTGCGAAGGGAGAAGTGAAAGAAGAGGAAAAGG-AGA
1 GATGATTCTGAATCCATGAATGCTGAAAGTGCGAAGGGAGAAGAGAAAGAAGAGGAAAAGGAAG-
62130434 AA
65 AA
* * *
62130436 GATGATTCTGTATCCATGAATGCTGAAAGTGCGAAGGGAGAAGAGAACGAAGAGGGAAAGGAAGA
1 GATGATTCTGAATCCATGAATGCTGAAAGTGCGAAGGGAGAAGAGAAAGAAGAGGAAAAGGAAGA
62130501 A
66 A
* ** * * * *
62130502 GATGACTCTGAATCTTTAAATGCTGAAAATTC-AA--AAGAAGAGAAAGAAGAGGAAAAGGAAG
1 GATGATTCTGAATCCATGAATGCTGAAAGTGCGAAGGGAGAAGAGAAAGAAGAGGAAAAGGAAG
62130563 GGGAGCAGGA
Statistics
Matches: 112, Mismatches: 14, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
63 24 0.21
65 2 0.02
66 84 0.75
67 2 0.02
ACGTcount: A:0.44, C:0.09, G:0.31, T:0.16
Consensus pattern (66 bp):
GATGATTCTGAATCCATGAATGCTGAAAGTGCGAAGGGAGAAGAGAAAGAAGAGGAAAAGGAAGA
A
Found at i:62135408 original size:16 final size:16
Alignment explanation
Indices: 62135387--62135417 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
62135377 AAATATTAAA
62135387 TTTATCAAGATATTTT
1 TTTATCAAGATATTTT
62135403 TTTATCAAGATATTT
1 TTTATCAAGATATTT
62135418 GTATGTTATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.32, C:0.06, G:0.06, T:0.55
Consensus pattern (16 bp):
TTTATCAAGATATTTT
Found at i:62137668 original size:13 final size:13
Alignment explanation
Indices: 62137646--62137678 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
62137636 TATAAATATG
62137646 GTAC-AATTATCC
1 GTACAAATTATCC
62137658 GTACAAATTATCC
1 GTACAAATTATCC
62137671 GTACAAAT
1 GTACAAAT
62137679 ATATGCTCGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 4 0.20
13 16 0.80
ACGTcount: A:0.39, C:0.21, G:0.09, T:0.30
Consensus pattern (13 bp):
GTACAAATTATCC
Found at i:62138530 original size:6 final size:6
Alignment explanation
Indices: 62138521--62138554 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
62138511 GTTGTAGTAG
* *
62138521 TGGTAA TGGTAA TGGTAA TGGCAA TGGCAA TGGT
1 TGGTAA TGGTAA TGGTAA TGGTAA TGGTAA TGGT
62138555 GTGACGTTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.29, C:0.06, G:0.35, T:0.29
Consensus pattern (6 bp):
TGGTAA
Found at i:62143410 original size:19 final size:18
Alignment explanation
Indices: 62143388--62143429 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
62143378 AAATTACAAA
*
62143388 AAAAATCAAAATAATTTTT
1 AAAAATCAAAAT-ATTTAT
*
62143407 AAAATTCAAAATATTTAT
1 AAAAATCAAAATATTTAT
62143425 AAAAA
1 AAAAA
62143430 ATTTAAATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (18 bp):
AAAAATCAAAATATTTAT
Found at i:62148328 original size:29 final size:30
Alignment explanation
Indices: 62148280--62148338 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
62148270 GAACTGGATC
* *
62148280 AAATAAAAATTTTATGTATAAAATTGTATA
1 AAATAAAAATTATATGTATAAAAGTGTATA
*
62148310 AAATCAAAATTAT-TGTATAAAAGTGTATA
1 AAATAAAAATTATATGTATAAAAGTGTATA
62148339 TTAGACCAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 15 0.58
30 11 0.42
ACGTcount: A:0.53, C:0.02, G:0.08, T:0.37
Consensus pattern (30 bp):
AAATAAAAATTATATGTATAAAAGTGTATA
Found at i:62154409 original size:30 final size:30
Alignment explanation
Indices: 62154353--62154409 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
62154343 ACGATTTAAT
*
62154353 TTGAATTTTAAAAACTAAAAAGTAGAGGGA
1 TTGAATTTTAAAAACTAAAAAATAGAGGGA
62154383 TTGAATTTT-AAAACTAAAAATATAGAG
1 TTGAATTTTAAAAACTAAAAA-ATAGAG
62154410 ACTAAATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
29 11 0.44
30 14 0.56
ACGTcount: A:0.51, C:0.04, G:0.16, T:0.30
Consensus pattern (30 bp):
TTGAATTTTAAAAACTAAAAAATAGAGGGA
Found at i:62154418 original size:28 final size:29
Alignment explanation
Indices: 62154356--62154423 Score: 84
Period size: 28 Copynumber: 2.3 Consensus size: 29
62154346 ATTTAATTTG
* * *
62154356 AATTTTAAAAACTAAAAAGTAGAGGGATTG
1 AATTTT-AAAACTAAAAAGTAGAGAGACTA
*
62154386 AATTTTAAAACTAAAAA-TATAGAGACTA
1 AATTTTAAAACTAAAAAGTAGAGAGACTA
62154414 AATTTTAAAA
1 AATTTTAAAA
62154424 TTAAGAAAAG
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 17 0.50
29 11 0.32
30 6 0.18
ACGTcount: A:0.54, C:0.04, G:0.12, T:0.29
Consensus pattern (29 bp):
AATTTTAAAACTAAAAAGTAGAGAGACTA
Found at i:62163238 original size:17 final size:19
Alignment explanation
Indices: 62163212--62163250 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 19
62163202 CCCGACCTTT
62163212 AAATAAATTT-AATTAA-A
1 AAATAAATTTAAATTAAGA
*
62163229 AAATATATTTAAATTAAGA
1 AAATAAATTTAAATTAAGA
62163248 AAA
1 AAA
62163251 CAATAAGGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 9 0.47
18 6 0.32
19 4 0.21
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (19 bp):
AAATAAATTTAAATTAAGA
Found at i:62165386 original size:3 final size:3
Alignment explanation
Indices: 62165378--62165416 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
62165368 CTTTCTTTCT
** *
62165378 TTC TTC TTC TTC TTC TTC TTC TAG ATC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
62165417 CTTTACAATG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.05, C:0.31, G:0.03, T:0.62
Consensus pattern (3 bp):
TTC
Found at i:62166900 original size:204 final size:205
Alignment explanation
Indices: 62166549--62167071 Score: 766
Period size: 204 Copynumber: 2.6 Consensus size: 205
62166539 GCTCAGCCGA
* *
62166549 AAAAAAAAAACAAATGGTTTGTGTTGTAGTTGATTGCAAACCATTATCCGGGTTTGGTACCATTC
1 AAAAAAAAAACAAATGGTTTGTGTTGTAGTTGATTGCAAATCGTTATCCGGGTTTGGTACCATTC
* * * *
62166614 ATTCGTATGATAAAAGCG--TGTGTTTTTGGTTGTCGAGGTGTCCGTTTATTCTAGGAAATCAAC
66 ATTCATATGATAAAAGTGTTTGTGTTTTTGGTAGTCGAGGTGTCCGTTTATTCTAGGAAATAAAC
*
62166677 GACGTTGTTGTGATAATTATAGCCTGTTAACCAATACGGTGTTTTCTTTTACCAGCTTGT-CCT-
131 GACGTTATTGTGATAATTATAGCCTGTTAACCAATACGGTGTTTTCTTTTACCAGCTTGTACCTA
* *
62166740 TGGCTTCACCC
196 TGCCTT-AACC
*** *
62166751 CCCAAAAAAACAAATGGTTTGTGTTGTAGTTGATTGCAAATCGTTATCCGGGTTTGGTACCGTTC
1 AAAAAAAAAACAAATGGTTTGTGTTGTAGTTGATTGCAAATCGTTATCCGGGTTTGGTACCATTC
* *
62166816 ATTCATATGATAAAAGTGTTTGTGTTTTTGGTAGTCGAGGTGTCGGTTTATTCTAGGAAATAAAG
66 ATTCATATGATAAAAGTGTTTGTGTTTTTGGTAGTCGAGGTGTCCGTTTATTCTAGGAAATAAAC
* * * *
62166881 GGCGTTATTGTGATAATTATAGCCTGTTAACTAATACGGTGTTTTCTTTTACCGGCTTGTACTTA
131 GACGTTATTGTGATAATTATAGCCTGTTAACCAATACGGTGTTTTCTTTTACCAGCTTGTACCTA
62166946 TGCCTTAACC
196 TGCCTTAACC
* * *
62166956 AAAAAAAAAAGAAATGGTTTGTGTTGTAGTTGATTGCAAATTGTTATCCGGGTTTGGTACCAATC
1 AAAAAAAAAACAAATGGTTTGTGTTGTAGTTGATTGCAAATCGTTATCCGGGTTTGGTACCATTC
* * * *
62167021 ATTCACATGATAAAAGTGTTTGTGTTTTTTGCTAGTCGAGGTATCCATTTA
66 ATTCATATGATAAAAGTGTTTGTG-TTTTTGGTAGTCGAGGTGTCCGTTTA
62167072 GGAAATAAAG
Statistics
Matches: 285, Mismatches: 31, Indels: 6
0.89 0.10 0.02
Matches are distributed among these distances:
202 75 0.26
204 97 0.34
205 86 0.30
206 27 0.09
ACGTcount: A:0.26, C:0.14, G:0.22, T:0.38
Consensus pattern (205 bp):
AAAAAAAAAACAAATGGTTTGTGTTGTAGTTGATTGCAAATCGTTATCCGGGTTTGGTACCATTC
ATTCATATGATAAAAGTGTTTGTGTTTTTGGTAGTCGAGGTGTCCGTTTATTCTAGGAAATAAAC
GACGTTATTGTGATAATTATAGCCTGTTAACCAATACGGTGTTTTCTTTTACCAGCTTGTACCTA
TGCCTTAACC
Found at i:62170430 original size:31 final size:31
Alignment explanation
Indices: 62170372--62170431 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
62170362 CTTATTTTAA
* * *
62170372 GCTTCAATGGTTAATTTGGTACTTGAGTTCG
1 GCTTCAATGGTTAATTCGATACATGAGTTCG
* *
62170403 GCTTCAATGTTTAGTTCGATACATGAGTT
1 GCTTCAATGGTTAATTCGATACATGAGTT
62170432 TTTTTAAATT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.22, C:0.13, G:0.23, T:0.42
Consensus pattern (31 bp):
GCTTCAATGGTTAATTCGATACATGAGTTCG
Found at i:62176283 original size:22 final size:24
Alignment explanation
Indices: 62176236--62176296 Score: 65
Period size: 22 Copynumber: 2.7 Consensus size: 24
62176226 GTAGCGAGGA
*
62176236 AAGAA-AGGAGAGAAGCGAGAGTG
1 AAGAAGAGGAGAGAAGCGAGAGCG
*
62176259 AAGAAGAGGAGAGGAGC-AG-GCG
1 AAGAAGAGGAGAGAAGCGAGAGCG
* *
62176281 AAGAAGATGAAAGAAG
1 AAGAAGAGGAGAGAAG
62176297 AGAAGATGGA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
22 15 0.47
23 7 0.22
24 10 0.31
ACGTcount: A:0.49, C:0.05, G:0.43, T:0.03
Consensus pattern (24 bp):
AAGAAGAGGAGAGAAGCGAGAGCG
Found at i:62182471 original size:19 final size:19
Alignment explanation
Indices: 62182422--62182471 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
62182412 ATATATAAAC
*
62182422 AAAACATGAAAAATAGTTT
1 AAAACATGAAAAATAGTTA
* *
62182441 AAAGCATTAAAAATA-TATA
1 AAAACATGAAAAATAGT-TA
62182460 AAAACATGAAAA
1 AAAACATGAAAA
62182472 TCTCTTTCAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
18 1 0.04
19 24 0.96
ACGTcount: A:0.64, C:0.06, G:0.08, T:0.22
Consensus pattern (19 bp):
AAAACATGAAAAATAGTTA
Found at i:62183793 original size:96 final size:96
Alignment explanation
Indices: 62183614--62183812 Score: 263
Period size: 96 Copynumber: 2.1 Consensus size: 96
62183604 CCTCGAATTA
* * * * * * *
62183614 GAAACTGAACTGATACTCTCAGTAGACCGGAAGCTTGCATTTTTCACATCCTCCGATTCTTTCCT
1 GAAACCGAACCGATACTCTCAGTAGACCGAAAACTTGCACTCTGCACATCCTCCGATTCTTTCCT
*
62183679 AGACAAAACGGCACAATTCAACTCGTGAACC
66 AGACAAAACAGCACAATTCAACTCGTGAACC
* *
62183710 GAAACCGAACCGATACTCTCGGTAGACCGAAAACTTGCACTCTGCACATCCTCCGGTTCTTTCCT
1 GAAACCGAACCGATACTCTCAGTAGACCGAAAACTTGCACTCTGCACATCCTCCGATTCTTTCCT
* * * * *
62183775 ATACAGAACATCATAATTCAACTCGTGAGCC
66 AGACAAAACAGCACAATTCAACTCGTGAACC
62183806 GAAACCG
1 GAAACCG
62183813 GTCTTCTCCT
Statistics
Matches: 88, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
96 88 1.00
ACGTcount: A:0.30, C:0.30, G:0.16, T:0.24
Consensus pattern (96 bp):
GAAACCGAACCGATACTCTCAGTAGACCGAAAACTTGCACTCTGCACATCCTCCGATTCTTTCCT
AGACAAAACAGCACAATTCAACTCGTGAACC
Found at i:62184025 original size:120 final size:123
Alignment explanation
Indices: 62183710--62184104 Score: 575
Period size: 123 Copynumber: 3.2 Consensus size: 123
62183700 CTCGTGAACC
* * *
62183710 GAAACCGAACCGATACTCTCGGTAGACCGAAAACTTGCACTCTGCACATCCTCCGGTTCTTTCCT
1 GAAACCGAACCGATACTCTCAGTAGACCGAAAACTTGCATTCTTCACATCCTCCGGTTCTTTCCT
*
62183775 ATACAGAACATCATAATTCAACTCGTGAGCCGAAACCGGTCTTCTCCTCCTCGAGT-TA
66 ATACAAAACATCATAATTCAACTCGTGAGCCGAAACCGGTC-TCTCCTCCTCGAGTCTA
* * * * * * *
62183833 GACACCAAACCGATACTCTCACTAGACCGAAAGCTTACATTTTTTACATCCTCCGGTTCTTTCCT
1 GAAACCGAACCGATACTCTCAGTAGACCGAAAACTTGCATTCTTCACATCCTCCGGTTCTTTCCT
* * *
62183898 ATACAAAACAGCACAATTCAACTCGTGAGCCGAATCCGGTC-CT-CTCCTC-AGTCTA
66 ATACAAAACATCATAATTCAACTCGTGAGCCGAAACCGGTCTCTCCTCCTCGAGTCTA
*
62183953 GAAACCGAACCGATACTCTCAGTAGACCGAAAACTTGCATTCTTCACATCCTCCGGTTCTTTCCC
1 GAAACCGAACCGATACTCTCAGTAGACCGAAAACTTGCATTCTTCACATCCTCCGGTTCTTTCCT
* *
62184018 ATACAAAACATCATGATTCAACTCGTGAGCCGAAACCGGTCCTCTCCTCCTCGAG-CTC
66 ATACAAAACATCATAATTCAACTCGTGAGCCGAAACCGGT-CTCTCCTCCTCGAGTCTA
*
62184076 GAAACCGAACCGATACTCTCAGTGGACCG
1 GAAACCGAACCGATACTCTCAGTAGACCG
62184105 GAAGCTTACA
Statistics
Matches: 239, Mismatches: 28, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
119 3 0.01
120 101 0.42
121 3 0.01
122 2 0.01
123 128 0.54
124 2 0.01
ACGTcount: A:0.28, C:0.33, G:0.15, T:0.25
Consensus pattern (123 bp):
GAAACCGAACCGATACTCTCAGTAGACCGAAAACTTGCATTCTTCACATCCTCCGGTTCTTTCCT
ATACAAAACATCATAATTCAACTCGTGAGCCGAAACCGGTCTCTCCTCCTCGAGTCTA
Found at i:62185023 original size:22 final size:22
Alignment explanation
Indices: 62184995--62185041 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
62184985 AATTTATCCA
62184995 TTTATACTGTTAAAAATTAGCT
1 TTTATACTGTTAAAAATTAGCT
*
62185017 TTTATACTGTTAAAACTTAGCT
1 TTTATACTGTTAAAAATTAGCT
62185039 TTT
1 TTT
62185042 GTATGCTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.32, C:0.11, G:0.09, T:0.49
Consensus pattern (22 bp):
TTTATACTGTTAAAAATTAGCT
Found at i:62193240 original size:90 final size:88
Alignment explanation
Indices: 62193016--62193328 Score: 312
Period size: 91 Copynumber: 3.5 Consensus size: 88
62193006 TTACACCACA
* * * *
62193016 ATACTCAAGCTCAAGTGCCCCAGAAATGAAATATAATAAATAACAAAATTTATAATTATCTCGAA
1 ATACTCAAGCTCAAGTGCCCCA-AAATGAAATATAATAAATAA-TAATTTTATAGTTATCCCGAA
* * *
62193081 AAAATTTAAAAAAAATTGCATCATC
64 AAAATTCAAAAAAAATTGCAGCACC
*
62193106 ATACTCAAAGCTCAAGTGCTCCAAAAGTGAAATATAATAAATAATAATTTTAATAGTTATCCCGA
1 ATACTC-AAGCTCAAGTGCCCCAAAA-TGAAATATAATAAATAATAATTTT-ATAGTTATCCCGA
** *
62193171 AAGTATTCAAAAAAAATTTG-GGCACC
63 AAAAATTCAAAAAAAA-TTGCAGCACC
* * *
62193197 ATACTCAAGCCCAAGTACCCCGAAAATGAAATATAATAAATAATAATTTTTATAGTTATCCTG--
1 ATACTCAAGCTCAAGTGCCCC-AAAATGAAATATAATAAATAATAA-TTTTATAGTTATCCCGAA
* *
62193260 AAAATT-AAAAAAACA-AGCATCACC
64 AAAATTCAAAAAAA-ATTGCAGCACC
* * * *
62193284 GTACTCAAGCCCAAGTGCCTCAAAAAATGAAATGTAATAAATAAT
1 ATACTCAAGCTCAAGTGCC-C-CAAAATGAAATATAATAAATAAT
62193329 TTTAGCACCA
Statistics
Matches: 189, Mismatches: 24, Indels: 22
0.80 0.10 0.09
Matches are distributed among these distances:
86 1 0.01
87 28 0.15
88 27 0.14
90 57 0.30
91 73 0.39
92 3 0.02
ACGTcount: A:0.48, C:0.17, G:0.10, T:0.26
Consensus pattern (88 bp):
ATACTCAAGCTCAAGTGCCCCAAAATGAAATATAATAAATAATAATTTTATAGTTATCCCGAAAA
AATTCAAAAAAAATTGCAGCACC
Found at i:62193551 original size:140 final size:139
Alignment explanation
Indices: 62193192--62193551 Score: 368
Period size: 140 Copynumber: 2.6 Consensus size: 139
62193182 AAAAATTTGG
* * *
62193192 GCACCATACTCAAGCCCAAGTACCCCGAAAATGAAATATAATAAATAATAATTTTTATAGTTATC
1 GCACCATACTAAAACCCAAGTGCCCCG-AAATGAAATATAATAAATAATAA-TTTTATA-TTATC
** ** * * * *
62193257 -CTGAAAATTAAAAAAACAAGCATCACCGTACTCAAGCCCAAGTGCCTCAAAAAATGAAATGTAA
63 TCAAAAAATTAAAAAAACAAGCAGAACCATACTCAAACCCAAATGCCTCAAAAAATGAAATATAA
62193321 TAAATAATTTTA
128 TAAATAATTTTA
* * ** * * *
62193333 GCACCATACTCAAGCATAAGTGCCCCCGAAATAAAATATAATACATAATAATTTTACAATTATCT
1 GCACCATACTAAAACCCAAGTG-CCCCGAAATGAAATATAATAAATAATAATTTTA-TATTATC-
** * *** * **
62193398 TGGAAAAATAAAAAAAATTTG-AGAACCATACTCAAACTCAAATGCC-CTGAAAATGAAATATAA
63 TCAAAAAATTAAAAAAACAAGCAGAACCATACTCAAACCCAAATGCCTCAAAAAATGAAATATAA
62193461 TAAATAATTGTTA
128 TAAATAATT-TTA
*
62193474 -CACCGTACTAAAACCCAAGTGCCCCGAAATTGAAATATAATAAATAATAATTTTATATTATCTC
1 GCACCATACTAAAACCCAAGTGCCCCGAAA-TGAAATATAATAAATAATAATTTTATATTATCTC
62193538 AAAAAATTAAAAAA
65 AAAAAATTAAAAAA
62193552 TATTTTTGCA
Statistics
Matches: 180, Mismatches: 33, Indels: 15
0.79 0.14 0.07
Matches are distributed among these distances:
138 13 0.07
139 14 0.08
140 72 0.40
141 63 0.35
142 18 0.10
ACGTcount: A:0.48, C:0.17, G:0.09, T:0.26
Consensus pattern (139 bp):
GCACCATACTAAAACCCAAGTGCCCCGAAATGAAATATAATAAATAATAATTTTATATTATCTCA
AAAAATTAAAAAAACAAGCAGAACCATACTCAAACCCAAATGCCTCAAAAAATGAAATATAATAA
ATAATTTTA
Found at i:62193827 original size:92 final size:92
Alignment explanation
Indices: 62193499--62194018 Score: 320
Period size: 92 Copynumber: 5.7 Consensus size: 92
62193489 CAAGTGCCCC
* * *
62193499 GAAATTGAAATATAATAAATAATA-ATTTTATA-TTATCTCAAAAAATT-AAA-AAATATTTTTG
1 GAAAATGAAATATAATAAATAATATTTTTTACAGTTATCTCAAAAAATTAAAATAAATATTTTTG
*** *
62193560 CACCACCATA-ATTAAGCCCAAATACC-T
66 GTGCACCATACA-T-AGCCCAAATGCCAT
* * **
62193587 CGAAAATGAGATATAATAAATAATATTTTTTACAGTTATCCCGGAAAATTAAAATATATATATTT
1 -GAAAATGAAATATAATAAATAATATTTTTTACAGTTATCTCAAAAAATTAAAATA-A-ATA-TT
* *
62193652 TTTGGTGCACCATACTAAAGCCCAAGTGCCCA-
62 TTTGGTGCACCATAC-ATAGCCCAAATG-CCAT
* **
62193684 -AAAATTG-AATATAATAAATCATATTTTTTACAGTTATC-CTGAAAA-TATAAA-AAATATTTT
1 GAAAA-TGAAATATAATAAATAATATTTTTTACAGTTATCTCAAAAAATTA-AAATAAATATTTT
*
62193744 TGGTGCACCATACACTAGCTCAAAATGCCAT
64 TGGTGCACCATACA-TAGC-CCAAATGCCAT
* *** *
62193775 GAACATGAAATATAATAAATAATATTTTTCGTAGTTGTCTCAAAAAATTAAAATAAATATTTTTG
1 GAAAATGAAATATAATAAATAATATTTTTTACAGTTATCTCAAAAAATTAAAATAAATATTTTTG
* * * *
62193840 CAT-CACCATAC-TCAATCCTATATGCCCA-
66 -GTGCACCATACAT--AGCCCAAATG-CCAT
* * * * ** *
62193868 -AAAATGAAATATAAAAAATAATAATTTTTATAGTTATCCCGGAAAATT-AAAT-CATATTTTTG
1 GAAAATGAAATATAATAAATAATATTTTTTACAGTTATCTCAAAAAATTAAAATAAATATTTTTG
*** * * * * ***
62193930 CACCACCGTACTAAAGCTCAATTGTTTT
66 GTGCACCATAC-ATAGCCCAAATGCCAT
* * * * *
62193958 GAAAATGAAATATAATAAATAATAATTTTTACATTTATCCCATAAAATTAAATATATATAT
1 GAAAATGAAATATAATAAATAATATTTTTTACAGTTATCTCAAAAAATTAAA-ATAAATAT
62194019 ATATATATAT
Statistics
Matches: 339, Mismatches: 59, Indels: 61
0.74 0.13 0.13
Matches are distributed among these distances:
89 23 0.07
90 50 0.15
91 69 0.20
92 75 0.22
93 19 0.06
94 40 0.12
95 37 0.11
96 23 0.07
97 2 0.01
98 1 0.00
ACGTcount: A:0.44, C:0.14, G:0.08, T:0.34
Consensus pattern (92 bp):
GAAAATGAAATATAATAAATAATATTTTTTACAGTTATCTCAAAAAATTAAAATAAATATTTTTG
GTGCACCATACATAGCCCAAATGCCAT
Found at i:62193837 original size:185 final size:185
Alignment explanation
Indices: 62193474--62194020 Score: 510
Period size: 184 Copynumber: 3.0 Consensus size: 185
62193464 ATAATTGTTA
* ** *
62193474 CACCGTACTAAAACCCAAGTGCCCCGAAATTGAAATATAATAAATAATAATTTTATA-TTAT-CT
1 CACCATACTAAAACCCAAGTGCCCAAAAATTGAAATATAATAAATAATATTTTTATAGTTATCCT
* * * * *
62193537 CAAAAAATTAAAAAATATTTTTGCACCACCATAATTAAGCCCAAATACCTCGAAAATGAGATATA
66 GAAAATA-TAAAAAATATTTTTGCACCACCATAACTAAGCCAAAATACCTCGAAAATGAAATATA
* ** *
62193602 ATAAATAATATTTTTTACAGTTATCCCGGAAAATTAAAATATATATATTTTTTG-GT
130 ATAAATAATATTTTTCACAGTTATCCCAAAAAATTAAAATATATATA-TTTTTGCAT
* * *
62193658 GCACCATACTAAAGCCCAAGTGCCCAAAAATTG-AATATAATAAATCATATTTTTTACAGTTATC
1 -CACCATACTAAAACCCAAGTGCCCAAAAATTGAAATATAATAAATAATA-TTTTTATAGTTATC
*** * *
62193722 CTGAAAATATAAAAAATATTTTTGGTGCACCATACACT-AGCTCAAAATGCCAT-GAACATGAAA
64 CTGAAAATATAAAAAATATTTTTGCACCACCATA-ACTAAGC-CAAAATACC-TCGAAAATGAAA
** * *
62193785 TATAATAAATAATATTTTTCGTAGTTGTCTCAAAAAATTAAAATA-A-ATATTTTTGCAT
126 TATAATAAATAATATTTTTCACAGTTATCCCAAAAAATTAAAATATATATATTTTTGCAT
* * * *
62193843 CACCATACTCAATCCTATA-TGCCCAAAAA-TGAAATATAAAAAATAATAATTTTTATAGTTATC
1 CACCATACTAAAACCCA-AGTGCCCAAAAATTGAAATATAATAAATAAT-ATTTTTATAGTTAT-
* ** * * *** *
62193906 CCGGAAAAT-TAAATCATATTTTTGCACCACCGT-ACTAAAGCTC-AATTGTTTTGAAAATGAAA
63 CCTGAAAATATAAAAAATATTTTTGCACCACCATAACT-AAGC-CAAAATACCTCGAAAATGAAA
* *
62193968 TATAATAAATAATAATTTTT-ACATTTATCCCATAAAATTAAATATATATATAT
126 TATAATAAATAAT-ATTTTTCACAGTTATCCCAAAAAATTAAA-ATATATATAT
62194021 ATATATATAT
Statistics
Matches: 296, Mismatches: 48, Indels: 35
0.78 0.13 0.09
Matches are distributed among these distances:
182 4 0.01
183 44 0.15
184 102 0.34
185 49 0.17
186 34 0.11
187 62 0.21
188 1 0.00
ACGTcount: A:0.44, C:0.15, G:0.08, T:0.33
Consensus pattern (185 bp):
CACCATACTAAAACCCAAGTGCCCAAAAATTGAAATATAATAAATAATATTTTTATAGTTATCCT
GAAAATATAAAAAATATTTTTGCACCACCATAACTAAGCCAAAATACCTCGAAAATGAAATATAA
TAAATAATATTTTTCACAGTTATCCCAAAAAATTAAAATATATATATTTTTGCAT
Found at i:62193981 original size:91 final size:90
Alignment explanation
Indices: 62193474--62194016 Score: 416
Period size: 91 Copynumber: 5.9 Consensus size: 90
62193464 ATAATTGTTA
* * * * * *
62193474 CACCGTACTAAAACCCAAGTGCCCCGAAATTGAAATATAATAAATAATAA-TTTTATA-TTATCT
1 CACCATACTAAAGCCCAAATG-CCCGAAAATGAAATATAATAAATAATAATTTTTACAGTTATCC
* *
62193537 CAAAAAATTAAAAAATATTTTTGCAC
65 CAGAAAATTAAATAATATTTTTGCAC
* * * * *
62193563 CACCATAATTAAGCCCAAATACCTCGAAAATGAGATATAATAAATAATATTTTTTACAGTTATCC
1 CACCATACTAAAGCCCAAATGCC-CGAAAATGAAATATAATAAATAATAATTTTTACAGTTATCC
* ***
62193628 CGGAAAATTAAAATATATATATTTTTTGGTG
65 CAGAAAATT--AA-ATA-ATA-TTTTTGCAC
* * * *
62193659 CACCATACTAAAGCCCAAGTGCCCAAAAATTG-AATATAATAAATCATATTTTTTACAGTTAT-C
1 CACCATACTAAAGCCCAAATGCCCGAAAA-TGAAATATAATAAATAATAATTTTTACAGTTATCC
* * ***
62193722 CTGAAAATATAAAAAATATTTTTGGTG
65 CAGAAAAT-TAAATAATATTTTTGCAC
* * * *
62193749 CACCATAC-ACTAGCTCAAAATGCCATGAACATGAAATATAATAAATAAT-ATTTTT-CGTAGTT
1 CACCATACTA-AAGC-CCAAATGCC-CGAAAATGAAATATAATAAATAATAATTTTTAC--AGTT
* * * *
62193811 GTCTCAAAAAATTAAAATAAATATTTTTGCAT
61 ATCCCAGAAAATT-AAAT-AATATTTTTGCAC
* * * * * * *
62193843 CACCATACTCAATCCTATATGCCCAAAAATGAAATATAAAAAATAATAATTTTTATAGTTATCCC
1 CACCATACTAAAGCCCAAATGCCCGAAAATGAAATATAATAAATAATAATTTTTACAGTTATCCC
* *
62193908 GGAAAATTAAATCATATTTTTGCAC
66 AGAAAATTAAATAATATTTTTGCAC
* * * *** *
62193933 CACCGTACTAAAGCTCAATTGTTTTGAAAATGAAATATAATAAATAATAATTTTTACATTTATCC
1 CACCATACTAAAGCCCAAATG-CCCGAAAATGAAATATAATAAATAATAATTTTTACAGTTATCC
*
62193998 CATAAAATTAAATATATAT
65 CAGAAAATTAAATA-ATAT
62194017 ATATATATAT
Statistics
Matches: 355, Mismatches: 75, Indels: 45
0.75 0.16 0.09
Matches are distributed among these distances:
88 2 0.01
89 39 0.11
90 52 0.15
91 80 0.23
92 62 0.17
93 26 0.07
94 30 0.08
95 37 0.10
96 27 0.08
ACGTcount: A:0.44, C:0.15, G:0.08, T:0.33
Consensus pattern (90 bp):
CACCATACTAAAGCCCAAATGCCCGAAAATGAAATATAATAAATAATAATTTTTACAGTTATCCC
AGAAAATTAAATAATATTTTTGCAC
Found at i:62194315 original size:91 final size:91
Alignment explanation
Indices: 62194220--62194452 Score: 217
Period size: 91 Copynumber: 2.5 Consensus size: 91
62194210 TTTACAACAT
* * * *
62194220 TATACTCAAGACAAAATGCACCAAAAATGAAGTATTATTAATAAATAATTTGTACATTTATCCC-
1 TATACTCAA-ACAAAGTGC-CCAAAAATGAAATATTATTAATAAATAATTTGTACAGTTAACCCA
* * * *
62194284 GAAATTTTAAGAAATATTTTTGA-GCAC
64 AAAAATTAAAAAAATATTTTTGACGCAC
* * * * * *
62194311 TATACT-AAATTCCAAGTGCTCCAAAAATGAAATATAATAAAT-AATATTTTTTATAGTTAACCC
1 TATACTCAAA--CAAAGTGC-CCAAAAATGAAATATTATTAATAAATAATTTGTACAGTTAACCC
*
62194374 AAAAAATTAAAAAAATATTTTTGACGCGC
63 AAAAAATTAAAAAAATATTTTTGACGCAC
62194403 TATACTCAAACACAAGTGCCCTAAAAATGAAATA-TATTAA-ATAATAATTT
1 TATACTCAAACA-AAGTGCCC-AAAAATGAAATATTATTAATA-AATAATTT
62194453 TTATAATTAT
Statistics
Matches: 113, Mismatches: 20, Indels: 17
0.75 0.13 0.11
Matches are distributed among these distances:
89 1 0.01
90 18 0.16
91 57 0.50
92 34 0.30
93 3 0.03
ACGTcount: A:0.46, C:0.13, G:0.08, T:0.32
Consensus pattern (91 bp):
TATACTCAAACAAAGTGCCCAAAAATGAAATATTATTAATAAATAATTTGTACAGTTAACCCAAA
AAATTAAAAAAATATTTTTGACGCAC
Found at i:62194480 original size:92 final size:90
Alignment explanation
Indices: 62194220--62194480 Score: 246
Period size: 92 Copynumber: 2.9 Consensus size: 90
62194210 TTTACAACAT
* * * * *
62194220 TATACTCAAGACA-AAATGCACCAAAAATGAAGTATTATT-AATAAATAATTTGTACATTTATCC
1 TATACTCAA-ACACAAGTGCACCAAAAATGAAATA-TATTAAAT-AATAATTTTTATAATTATCC
62194283 CG-AAATTTTAAGAAATATTTTTGAGCAC
63 CGAAAATTTTAA-AAATATTTTTGAGCAC
* * * * *
62194311 TATACT-AAATTC-CAAGTGCTCCAAAAATGAAATATAATAAATAATATTTTTTATAGTTAACCC
1 TATACTCAAA--CACAAGTGCACCAAAAATGAAATATATTAAATAATAATTTTTATAATTATCCC
* ** *
62194374 AAAAAATTAAAAAAATATTTTTGACGCGC
64 -GAAAATTTTAAAAATATTTTTGA-GCAC
**
62194403 TATACTCAAACACAAGTGC-CCTAAAAATGAAATATATTAAATAATAATTTTTATAATTATCTTG
1 TATACTCAAACACAAGTGCACC-AAAAATGAAATATATTAAATAATAATTTTTATAATTATCCCG
62194467 AAAATTTTTAAAAA
65 AAAA-TTTTAAAAA
62194481 AATATTATTG
Statistics
Matches: 137, Mismatches: 22, Indels: 21
0.76 0.12 0.12
Matches are distributed among these distances:
89 1 0.01
90 21 0.15
91 47 0.34
92 65 0.47
93 3 0.02
ACGTcount: A:0.46, C:0.12, G:0.08, T:0.34
Consensus pattern (90 bp):
TATACTCAAACACAAGTGCACCAAAAATGAAATATATTAAATAATAATTTTTATAATTATCCCGA
AAATTTTAAAAATATTTTTGAGCAC
Found at i:62194960 original size:92 final size:91
Alignment explanation
Indices: 62194751--62195101 Score: 274
Period size: 91 Copynumber: 3.9 Consensus size: 91
62194741 TTTGGGGACC
* * * * * * *
62194751 ATACTCAAGCTCAAGTG-TTCGAAAATAAAATATAATAAA-AATAATTTTTATAGTTATCTCGGA
1 ATACTCAAACCCAAGTGCCTCGAAAATGAAATATAATAAATAATATTTTTTAAAGTTATCT--TA
* * * * *
62194814 AAATTTAAAAAAA-A-ATTAG-GC-ACT
64 AAATATAAAAAAATATTTTTGCACAACA
* * *
62194838 ATACGCAAGCCCAAGTGCCTCAAAAATGAAATATTAA-AAATAAT-TTTTTTAAAGTTATCTTAG
1 ATACTCAAACCCAAGTGCCTCGAAAATGAAATA-TAATAAATAATATTTTTTAAAGTTATCTTA-
62194901 AATATATAAAAAAATATTTTTGCAGCAAC-
64 AA-ATATAAAAAAATATTTTTGCA-CAACA
* ** * *
62194930 ATACTCAAATCCAAGTG-CTCCGAAAATGAAATATAATAAATAATAAATTTTACAGTTATCTCAA
1 ATACTCAAACCCAAGTGCCT-CGAAAATGAAATATAATAAATAATATTTTTTAAAGTTATCTTAA
* ** *
62194994 AAAATTGAAAAATATTTTTGCACGACA
65 AATATAAAAAAATATTTTTGCACAACA
* ***
62195021 ATTCTCTTGCCCAAGTGCCTCGAAAATGAAATATAATAAATAATATTTTTTACAA-TTATCCTTA
1 ATACTCAAACCCAAGTGCCTCGAAAATGAAATATAATAAATAATATTTTTTA-AAGTTAT-CTTA
*
62195085 AAAAATTAAAAAAATAT
64 AAATA-TAAAAAAATAT
62195102 CACCACCACA
Statistics
Matches: 211, Mismatches: 35, Indels: 30
0.76 0.13 0.11
Matches are distributed among these distances:
86 1 0.00
87 17 0.08
88 39 0.18
89 7 0.03
90 6 0.03
91 69 0.33
92 47 0.22
93 25 0.12
ACGTcount: A:0.47, C:0.13, G:0.09, T:0.32
Consensus pattern (91 bp):
ATACTCAAACCCAAGTGCCTCGAAAATGAAATATAATAAATAATATTTTTTAAAGTTATCTTAAA
ATATAAAAAAATATTTTTGCACAACA
Found at i:62195045 original size:91 final size:91
Alignment explanation
Indices: 62194683--62195153 Score: 335
Period size: 88 Copynumber: 5.3 Consensus size: 91
62194673 AAGTGACCAA
* * * * * * * *
62194683 AAAATAAAATGTAATAAATAATA-ATTTTACAGCTATCCTAAAAATTTTAAGAAATATTTTTG-G
1 AAAATGAAATATAATAAATAATATTTTTTACAGTTATCTTAAAAA-ATTAAAAAATATTTTTGCA
* * * *
62194746 GGACCATACTCAAGCTCAAGTG-TTCG
65 GCAACATACTCAAGCCCAAGTGCCTCG
* * * ** * ** *
62194772 AAAATAAAATATAATAAA-AATAATTTTTATAGTTATCTCGGAAAATTTAAAAAA-AAATTAG--
1 AAAATGAAATATAATAAATAATATTTTTTACAGTTATCT-TAAAAAATTAAAAAATATTTTTGCA
* *
62194833 GC-ACTATACGCAAGCCCAAGTGCCTCA
65 GCAAC-ATACTCAAGCCCAAGTGCCTCG
* * *
62194860 AAAATGAAATATTAA-AAATAAT-TTTTTTAAAGTTATCTTAGAATATATAAAAAAATATTTTTG
1 AAAATGAAATA-TAATAAATAATATTTTTTACAGTTATCTTA-AA-AAATTAAAAAATATTTTTG
**
62194923 CAGCAACATACTCAAATCCAAGTG-CTCCG
63 CAGCAACATACTCAAGCCCAAGTGCCT-CG
** * *
62194952 AAAATGAAATATAATAAATAATAAATTTTACAGTTATCTCAAAAAATTGAAAAATATTTTTGCA-
1 AAAATGAAATATAATAAATAATATTTTTTACAGTTATCTTAAAAAATTAAAAAATATTTTTGCAG
* * **
62195016 CGACAATTCTCTTGCCCAAGTGCCTCG
66 CAAC-ATACTCAAGCCCAAGTGCCTCG
* *
62195043 AAAATGAAATATAATAAATAATATTTTTTACAATTATCCTTAAAAAATTAAAAAA-A--TAT-CA
1 AAAATGAAATATAATAAATAATATTTTTTACAGTTAT-CTTAAAAAATTAAAAAATATTTTTGCA
* * * * * **
62195104 CCACCACACTCAAGCCTAACTATCTCG
65 GCAACATACTCAAGCCCAAGTGCCTCG
*
62195131 AAAATGAAATATAACAAATAATA
1 AAAATGAAATATAATAAATAATA
62195154 ATTAGTACAA
Statistics
Matches: 301, Mismatches: 62, Indels: 39
0.75 0.15 0.10
Matches are distributed among these distances:
86 1 0.00
87 16 0.05
88 77 0.26
89 54 0.18
90 11 0.04
91 72 0.24
92 54 0.18
93 16 0.05
ACGTcount: A:0.47, C:0.14, G:0.09, T:0.31
Consensus pattern (91 bp):
AAAATGAAATATAATAAATAATATTTTTTACAGTTATCTTAAAAAATTAAAAAATATTTTTGCAG
CAACATACTCAAGCCCAAGTGCCTCG
Found at i:62196796 original size:13 final size:13
Alignment explanation
Indices: 62196780--62196830 Score: 50
Period size: 13 Copynumber: 3.9 Consensus size: 13
62196770 TTTAAACCAG
62196780 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
*
62196793 ACTTTTCCACAA-C
1 ACTTTT-CAAAAGC
* * *
62196806 ATTTTTTAAAAAC
1 ACTTTTCAAAAGC
62196819 ACTTTTCAAAAG
1 ACTTTTCAAAAG
62196831 TATTACTAAA
Statistics
Matches: 29, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
12 3 0.10
13 22 0.76
14 4 0.14
ACGTcount: A:0.39, C:0.22, G:0.04, T:0.35
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:62197676 original size:2 final size:2
Alignment explanation
Indices: 62197671--62197703 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
62197661 TCTGTTTTAT
62197671 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 T
62197704 TTTAATTACA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:62201089 original size:46 final size:46
Alignment explanation
Indices: 62201036--62201212 Score: 291
Period size: 46 Copynumber: 3.8 Consensus size: 46
62201026 ACATTGCTAT
* *
62201036 AACTCAGTATGGTTTTCTTCACGGAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
*
62201082 AACTCAGTATGGTTTTCTTCATTGAAACACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
* * *
62201128 AACTCAGTATGGTTTTCTTTACTGAAACACCATATCTACTTTTGAC
1 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
*
62201174 AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTAC
1 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTAC
62201213 GTCAATTCAT
Statistics
Matches: 121, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 121 1.00
ACGTcount: A:0.29, C:0.25, G:0.10, T:0.36
Consensus pattern (46 bp):
AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
Found at i:62202452 original size:16 final size:17
Alignment explanation
Indices: 62202406--62202452 Score: 69
Period size: 17 Copynumber: 2.8 Consensus size: 17
62202396 AAATTCTTTT
62202406 TAAATCACAAAATTCAA
1 TAAATCACAAAATTCAA
*
62202423 TAAATCACAAAATTCAC
1 TAAATCACAAAATTCAA
*
62202440 TAATTCA-AAAATT
1 TAAATCACAAAATT
62202453 ATTCTAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
16 6 0.21
17 22 0.79
ACGTcount: A:0.55, C:0.17, G:0.00, T:0.28
Consensus pattern (17 bp):
TAAATCACAAAATTCAA
Found at i:62203523 original size:33 final size:33
Alignment explanation
Indices: 62203473--62203547 Score: 98
Period size: 34 Copynumber: 2.2 Consensus size: 33
62203463 AAACTAATCA
* *
62203473 TCTCTCAAATTTCCTCTC-AATTTCTTCTAAATT
1 TCTCTC-AATTTCCTCTCAAATTCCTTCAAAATT
*
62203506 TCCTCTCAATTTGCTCTCAAATTCCTTCAAAATT
1 T-CTCTCAATTTCCTCTCAAATTCCTTCAAAATT
62203540 TCTCTCAA
1 TCTCTCAA
62203548 ATCCATATTT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
33 18 0.49
34 19 0.51
ACGTcount: A:0.25, C:0.29, G:0.01, T:0.44
Consensus pattern (33 bp):
TCTCTCAATTTCCTCTCAAATTCCTTCAAAATT
Found at i:62203530 original size:22 final size:22
Alignment explanation
Indices: 62203473--62203549 Score: 97
Period size: 22 Copynumber: 3.5 Consensus size: 22
62203463 AAACTAATCA
62203473 TCTCTCAAATTTCCTCTCAATT
1 TCTCTCAAATTTCCTCTCAATT
62203495 TCT-TCTAAATTTCCTCTCAATT
1 TCTCTC-AAATTTCCTCTCAATT
62203517 TGCTCTCAAA-TTCCT-TCAAAATT
1 T-CTCTCAAATTTCCTCTC--AATT
62203540 TCTCTCAAAT
1 TCTCTCAAAT
62203550 CCATATTTAT
Statistics
Matches: 49, Mismatches: 0, Indels: 11
0.82 0.00 0.18
Matches are distributed among these distances:
21 4 0.08
22 33 0.67
23 10 0.20
24 2 0.04
ACGTcount: A:0.26, C:0.29, G:0.01, T:0.44
Consensus pattern (22 bp):
TCTCTCAAATTTCCTCTCAATT
Found at i:62203549 original size:11 final size:11
Alignment explanation
Indices: 62203473--62203549 Score: 72
Period size: 11 Copynumber: 6.9 Consensus size: 11
62203463 AAACTAATCA
62203473 TCTCTCAAATT
1 TCTCTCAAATT
62203484 TCCTCTC-AATT
1 T-CTCTCAAATT
62203495 TCT-TCTAAATT
1 TCTCTC-AAATT
62203506 TCCTCTC-AATT
1 T-CTCTCAAATT
62203517 TGCTCTCAAATT
1 T-CTCTCAAATT
*
62203529 CCT-TCAAAATT
1 TCTCTC-AAATT
62203540 TCTCTCAAAT
1 TCTCTCAAAT
62203550 CCATATTTAT
Statistics
Matches: 55, Mismatches: 3, Indels: 16
0.74 0.04 0.22
Matches are distributed among these distances:
9 2 0.04
10 4 0.07
11 34 0.62
12 13 0.24
13 2 0.04
ACGTcount: A:0.26, C:0.29, G:0.01, T:0.44
Consensus pattern (11 bp):
TCTCTCAAATT
Found at i:62214937 original size:40 final size:40
Alignment explanation
Indices: 62214874--62215093 Score: 160
Period size: 40 Copynumber: 5.5 Consensus size: 40
62214864 AGCTTTACTG
* * *
62214874 GCATTAGCGACGCTTTTTAAAAAATGCCACAATAGATCGA
1 GCATTAGCGGCGCTATTTGAAAAATGCCACAATAGATCGA
* ** ** *
62214914 GCATTAGTGGCGCTATTTGAAAAACACCACTTTAGATTGA
1 GCATTAGCGGCGCTATTTGAAAAATGCCACAATAGATCGA
* * * * * *
62214954 GCATTAGCGACGCT-TTTCAGAAAACGCTGCAAAAAATTTGAGC-A
1 GCATTAGCGGCGCTATTT--GAAAA--ATGC-CACAA-TAGATCGA
*
62214998 GCATTAGCGGCGCT-TTTTAAAAATGCCACAATAGATCGA
1 GCATTAGCGGCGCTATTTGAAAAATGCCACAATAGATCGA
* * * * * *
62215037 GTATTAGTGGTGCTATGTGAAAAACGCCACTATAGATCGA
1 GCATTAGCGGCGCTATTTGAAAAATGCCACAATAGATCGA
62215077 GCATTAGCGGCGC-ATTT
1 GCATTAGCGGCGCTATTT
62215094 CGGAAAACGC
Statistics
Matches: 133, Mismatches: 39, Indels: 17
0.70 0.21 0.09
Matches are distributed among these distances:
38 4 0.03
39 21 0.16
40 77 0.58
41 5 0.04
42 4 0.03
43 1 0.01
44 18 0.14
45 3 0.02
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.26
Consensus pattern (40 bp):
GCATTAGCGGCGCTATTTGAAAAATGCCACAATAGATCGA
Found at i:62215100 original size:123 final size:124
Alignment explanation
Indices: 62214874--62215117 Score: 382
Period size: 123 Copynumber: 2.0 Consensus size: 124
62214864 AGCTTTACTG
*
62214874 GCATTAGCGACGCTTTTTAAAAAATGCCACAATAGATCGAGCATTAGTGGCGCTATTTGAAAAAC
1 GCATTAGCGACGCTTTTTAAAAAATGCCACAATAGATCGAGCATTAGTGGCGCTATGTGAAAAAC
* * * *
62214939 ACCACTTTAGATTGAGCATTAGCGACGCTTTTCAGAAAACGCTGCAAAAAATTTGAGCA
66 ACCACTATAGATCGAGCATTAGCGACGCATTTCAGAAAACGCTACAAAAAATTTGAGCA
* * *
62214998 GCATTAGCGGCGCTTTTT-AAAAATGCCACAATAGATCGAGTATTAGTGGTGCTATGTGAAAAAC
1 GCATTAGCGACGCTTTTTAAAAAATGCCACAATAGATCGAGCATTAGTGGCGCTATGTGAAAAAC
* * *
62215062 GCCACTATAGATCGAGCATTAGCGGCGCATTTCGGAAAACGCTACAAAAAATTTGA
66 ACCACTATAGATCGAGCATTAGCGACGCATTTCAGAAAACGCTACAAAAAATTTGA
62215118 AGGACTTTTA
Statistics
Matches: 109, Mismatches: 11, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
123 92 0.84
124 17 0.16
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.25
Consensus pattern (124 bp):
GCATTAGCGACGCTTTTTAAAAAATGCCACAATAGATCGAGCATTAGTGGCGCTATGTGAAAAAC
ACCACTATAGATCGAGCATTAGCGACGCATTTCAGAAAACGCTACAAAAAATTTGAGCA
Found at i:62216166 original size:9 final size:9
Alignment explanation
Indices: 62216152--62216192 Score: 55
Period size: 9 Copynumber: 4.6 Consensus size: 9
62216142 GTAGTGATTC
62216152 AATTTGGTT
1 AATTTGGTT
62216161 AATTTGGTT
1 AATTTGGTT
* *
62216170 AATTCGGGT
1 AATTTGGTT
*
62216179 AATTCGGTT
1 AATTTGGTT
62216188 AATTT
1 AATTT
62216193 TTAACCAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.24, C:0.05, G:0.22, T:0.49
Consensus pattern (9 bp):
AATTTGGTT
Found at i:62219502 original size:13 final size:13
Alignment explanation
Indices: 62219484--62219509 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
62219474 CCAAAACACT
62219484 AAATATTGAACTC
1 AAATATTGAACTC
62219497 AAATATTGAACTC
1 AAATATTGAACTC
62219510 TAAACCCCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.15, G:0.08, T:0.31
Consensus pattern (13 bp):
AAATATTGAACTC
Found at i:62225332 original size:20 final size:20
Alignment explanation
Indices: 62225307--62225353 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
62225297 ACCCAAATTA
62225307 TTACAAACCCAAAACCTCGC
1 TTACAAACCCAAAACCTCGC
62225327 TTACAAACCCAAAACCTCGC
1 TTACAAACCCAAAACCTCGC
62225347 TTACAAA
1 TTACAAA
62225354 TCACAATAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.43, C:0.36, G:0.04, T:0.17
Consensus pattern (20 bp):
TTACAAACCCAAAACCTCGC
Found at i:62226066 original size:36 final size:36
Alignment explanation
Indices: 62226026--62226097 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
62226016 GTGGAAATCA
62226026 ATTTCTCTATTTTAGTGTTGAAACTTGTTGAATTGG
1 ATTTCTCTATTTTAGTGTTGAAACTTGTTGAATTGG
62226062 ATTTCTCTATTTTAGTGTTGAAACTTGTTGAATTGG
1 ATTTCTCTATTTTAGTGTTGAAACTTGTTGAATTGG
62226098 TTAAAGGGTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.22, C:0.08, G:0.19, T:0.50
Consensus pattern (36 bp):
ATTTCTCTATTTTAGTGTTGAAACTTGTTGAATTGG
Found at i:62227710 original size:30 final size:30
Alignment explanation
Indices: 62227653--62227725 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 30
62227643 TAACTTTTAT
**
62227653 AAATTACAATTTGACCCCCACAATTTCTCA
1 AAATTACAATTTGACCCAAACAATTTCTCA
* * * *
62227683 AAATTACATTTTGACCCAAATATTTTCTCT
1 AAATTACAATTTGACCCAAACAATTTCTCA
*
62227713 AAATTACACTTTG
1 AAATTACAATTTG
62227726 GCCCCAAAAA
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.36, C:0.23, G:0.04, T:0.37
Consensus pattern (30 bp):
AAATTACAATTTGACCCAAACAATTTCTCA
Found at i:62228252 original size:16 final size:16
Alignment explanation
Indices: 62228231--62228284 Score: 63
Period size: 16 Copynumber: 3.2 Consensus size: 16
62228221 GAGGGGAACG
*
62228231 AAAAGAGAAAGAAGAA
1 AAAAGAGAAAAAAGAA
*
62228247 AAAAGAAAAAAAACGAA
1 AAAAGAGAAAAAA-GAA
*
62228264 AAAGAAAGAAAAAAGAA
1 AAA-AGAGAAAAAAGAA
62228281 AAAA
1 AAAA
62228285 ATCTAAAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
16 12 0.38
17 12 0.38
18 8 0.25
ACGTcount: A:0.81, C:0.02, G:0.17, T:0.00
Consensus pattern (16 bp):
AAAAGAGAAAAAAGAA
Found at i:62228282 original size:7 final size:7
Alignment explanation
Indices: 62228230--62228284 Score: 51
Period size: 7 Copynumber: 8.0 Consensus size: 7
62228220 GGAGGGGAAC
*
62228230 GAAAAGA
1 GAAAAAA
*
62228237 GAAAGAA
1 GAAAAAA
62228244 GAAAAAA
1 GAAAAAA
62228251 GAAAAAA
1 GAAAAAA
*
62228258 -AACGAAA
1 GAA-AAAA
*
62228265 -AAGAAA
1 GAAAAAA
62228271 GAAAAAA
1 GAAAAAA
62228278 GAAAAAA
1 GAAAAAA
62228285 ATCTAAAAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
6 6 0.15
7 35 0.85
ACGTcount: A:0.80, C:0.02, G:0.18, T:0.00
Consensus pattern (7 bp):
GAAAAAA
Found at i:62228595 original size:11 final size:11
Alignment explanation
Indices: 62228557--62228609 Score: 56
Period size: 11 Copynumber: 4.7 Consensus size: 11
62228547 CAGCAGAGAG
*
62228557 GAAAAAAA-AG
1 GAAAAAAAGAA
62228567 GAAAAGAAAGAA
1 GAAAA-AAAGAA
62228579 -AAAAAAGACGAA
1 GAAAAAA-A-GAA
62228591 GAAAAAAAGAA
1 GAAAAAAAGAA
62228602 GAAAAAAA
1 GAAAAAAA
62228610 AAAAAGTTCA
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
10 7 0.19
11 19 0.51
12 5 0.14
13 6 0.16
ACGTcount: A:0.79, C:0.02, G:0.19, T:0.00
Consensus pattern (11 bp):
GAAAAAAAGAA
Found at i:62228597 original size:14 final size:13
Alignment explanation
Indices: 62228568--62228611 Score: 54
Period size: 13 Copynumber: 3.3 Consensus size: 13
62228558 AAAAAAAAGG
62228568 AAAAGAA-AGAAAA
1 AAAAGAAGA-AAAA
*
62228581 AAAAGACGAAGAAA
1 AAAAGAAGAA-AAA
62228595 AAAAGAAGAAAAA
1 AAAAGAAGAAAAA
62228608 AAAA
1 AAAA
62228612 AAAGTTCAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 14 0.52
14 13 0.48
ACGTcount: A:0.82, C:0.02, G:0.16, T:0.00
Consensus pattern (13 bp):
AAAAGAAGAAAAA
Found at i:62228612 original size:14 final size:14
Alignment explanation
Indices: 62228568--62228612 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
62228558 AAAAAAAAGG
*
62228568 AAAAGAA-AGAAAA
1 AAAAGAAGAAAAAA
* *
62228581 AAAAGACGAAGAAA
1 AAAAGAAGAAAAAA
62228595 AAAAGAAGAAAAAA
1 AAAAGAAGAAAAAA
62228609 AAAA
1 AAAA
62228613 AAGTTCAATT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
13 6 0.23
14 20 0.77
ACGTcount: A:0.82, C:0.02, G:0.16, T:0.00
Consensus pattern (14 bp):
AAAAGAAGAAAAAA
Found at i:62228613 original size:15 final size:15
Alignment explanation
Indices: 62228557--62228613 Score: 55
Period size: 15 Copynumber: 3.8 Consensus size: 15
62228547 CAGCAGAGAG
*
62228557 GAAAAAAAAGGAA-AA
1 GAAAAAAAA-AAAGAA
*
62228572 GAAAGAAAAAAAAGAC
1 GAAA-AAAAAAAAGAA
*
62228588 G-AAGAAAAAAAGAA
1 GAAAAAAAAAAAGAA
62228602 GAAAAAAAAAAA
1 GAAAAAAAAAAA
62228614 AGTTCAATTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
14 10 0.29
15 17 0.50
16 7 0.21
ACGTcount: A:0.81, C:0.02, G:0.18, T:0.00
Consensus pattern (15 bp):
GAAAAAAAAAAAGAA
Found at i:62228945 original size:21 final size:21
Alignment explanation
Indices: 62228920--62228985 Score: 61
Period size: 22 Copynumber: 3.3 Consensus size: 21
62228910 GAAAATATTC
62228920 AAAAATTTTCGTGTCTTCGAAA
1 AAAAATTTTCGTGTCTTCG-AA
*
62228942 AAAAAATTTCGTGT-TTCG--
1 AAAAATTTTCGTGTCTTCGAA
* *
62228960 --AAATTTTCTTGTCTTCAAA
1 AAAAATTTTCGTGTCTTCGAA
62228979 AAAAATT
1 AAAAATT
62228986 CGTGCTTTCA
Statistics
Matches: 35, Mismatches: 4, Indels: 11
0.70 0.08 0.22
Matches are distributed among these distances:
16 10 0.29
17 3 0.09
21 9 0.26
22 13 0.37
ACGTcount: A:0.38, C:0.12, G:0.11, T:0.39
Consensus pattern (21 bp):
AAAAATTTTCGTGTCTTCGAA
Found at i:62228946 original size:22 final size:21
Alignment explanation
Indices: 62228920--62228962 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
62228910 GAAAATATTC
*
62228920 AAAAATTTTCGTGTCTTCGAAA
1 AAAAAATTTCGTGT-TTCGAAA
62228942 AAAAAATTTCGTGTTTCGAAA
1 AAAAAATTTCGTGTTTCGAAA
62228963 TTTTCTTGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.40, C:0.12, G:0.14, T:0.35
Consensus pattern (21 bp):
AAAAAATTTCGTGTTTCGAAA
Found at i:62228964 original size:38 final size:37
Alignment explanation
Indices: 62228917--62229019 Score: 120
Period size: 37 Copynumber: 2.8 Consensus size: 37
62228907 ATCGAAAATA
62228917 TTCAAAAATTTTCGTGTCTTCGAAAAAAAAATTTCGTG-T
1 TTCAAAAATTTTCGTGTCTTC--AAAAAAAA-TTCGTGCT
* *
62228956 TTC-GAAATTTTCTTGTCTTCAAAAAAAATTCGTGCT
1 TTCAAAAATTTTCGTGTCTTCAAAAAAAATTCGTGCT
* * *
62228992 TTCAAAAATATTCGTGTTTTTAAAAAAA
1 TTCAAAAATTTTCGTGTCTTCAAAAAAA
62229020 TAAGGCTACA
Statistics
Matches: 55, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
35 6 0.11
36 12 0.22
37 19 0.35
38 15 0.27
39 3 0.05
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.40
Consensus pattern (37 bp):
TTCAAAAATTTTCGTGTCTTCAAAAAAAATTCGTGCT
Found at i:62229004 original size:18 final size:18
Alignment explanation
Indices: 62228977--62229020 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
62228967 CTTGTCTTCA
62228977 AAAAAAATTCGTGCTTTC
1 AAAAAAATTCGTGCTTTC
* * *
62228995 AAAAATATTCGTGTTTTT
1 AAAAAAATTCGTGCTTTC
62229013 AAAAAAAT
1 AAAAAAAT
62229021 AAGGCTACAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.45, C:0.09, G:0.09, T:0.36
Consensus pattern (18 bp):
AAAAAAATTCGTGCTTTC
Found at i:62229182 original size:20 final size:20
Alignment explanation
Indices: 62229122--62229224 Score: 69
Period size: 20 Copynumber: 5.4 Consensus size: 20
62229112 ATATAAAAAT
62229122 AAAAAAAATTT-GTG-TTTC
1 AAAAAAAATTTCGTGTTTTC
*
62229140 ---AAAAATTCCAGTG-TTTC
1 AAAAAAAATTTC-GTGTTTTC
*
62229157 -AAAAAATTTTCGTGTTTTC
1 AAAAAAAATTTCGTGTTTTC
* *
62229176 AAAAAAAATTCCCT-TGTTTC
1 AAAAAAAATTTCGTGT-TTTC
* *
62229196 AAAAAAAATCTCGCGTTTTC
1 AAAAAAAATTTCGTGTTTTC
62229216 AAAACAAAA
1 AAAA-AAAA
62229225 ATTCTCATGT
Statistics
Matches: 66, Mismatches: 10, Indels: 15
0.73 0.11 0.16
Matches are distributed among these distances:
15 7 0.11
17 7 0.11
18 3 0.05
19 12 0.18
20 32 0.48
21 5 0.08
ACGTcount: A:0.43, C:0.15, G:0.09, T:0.34
Consensus pattern (20 bp):
AAAAAAAATTTCGTGTTTTC
Found at i:62229183 original size:21 final size:21
Alignment explanation
Indices: 62229157--62229236 Score: 83
Period size: 20 Copynumber: 3.8 Consensus size: 21
62229147 CCAGTGTTTC
*
62229157 AAAAAATTTTCGTGTTTTCAA
1 AAAAAATTCTCGTGTTTTCAA
* *
62229178 AAAAAATTCCCTTG-TTTCAA
1 AAAAAATTCTCGTGTTTTCAA
*
62229198 AAAAAA-TCTCGCGTTTTCAAA
1 AAAAAATTCTCGTGTTTTC-AA
*
62229219 ACAAAAATTCTCATGTTT
1 A-AAAAATTCTCGTGTTT
62229237 CAATCGGATC
Statistics
Matches: 47, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
19 4 0.09
20 16 0.34
21 14 0.30
22 5 0.11
23 8 0.17
ACGTcount: A:0.40, C:0.16, G:0.07, T:0.36
Consensus pattern (21 bp):
AAAAAATTCTCGTGTTTTCAA
Found at i:62231035 original size:9 final size:9
Alignment explanation
Indices: 62231021--62231113 Score: 134
Period size: 9 Copynumber: 10.4 Consensus size: 9
62231011 GTAGTGCTTC
62231021 AATTCGGTT
1 AATTCGGTT
*
62231030 AATTCGGGT
1 AATTCGGTT
62231039 AATTCGGTT
1 AATTCGGTT
*
62231048 AATTCGGGT
1 AATTCGGTT
*
62231057 AATCCGGTT
1 AATTCGGTT
62231066 AATTC-GTT
1 AATTCGGTT
*
62231074 AATTCGGGT
1 AATTCGGTT
62231083 AATTCGGTT
1 AATTCGGTT
*
62231092 AATTCGGGT
1 AATTCGGTT
62231101 AATTCGGTT
1 AATTCGGTT
62231110 AATT
1 AATT
62231114 TTTAACCAAA
Statistics
Matches: 73, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
8 8 0.11
9 65 0.89
ACGTcount: A:0.24, C:0.12, G:0.25, T:0.40
Consensus pattern (9 bp):
AATTCGGTT
Found at i:62231076 original size:44 final size:45
Alignment explanation
Indices: 62231021--62231113 Score: 170
Period size: 44 Copynumber: 2.1 Consensus size: 45
62231011 GTAGTGCTTC
62231021 AATTCGGTTAATTCGGGTAATTCGGTTAATTCGGGTAATCCGGTT
1 AATTCGGTTAATTCGGGTAATTCGGTTAATTCGGGTAATCCGGTT
*
62231066 AATTC-GTTAATTCGGGTAATTCGGTTAATTCGGGTAATTCGGTT
1 AATTCGGTTAATTCGGGTAATTCGGTTAATTCGGGTAATCCGGTT
62231110 AATT
1 AATT
62231114 TTTAACCAAA
Statistics
Matches: 47, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
44 42 0.89
45 5 0.11
ACGTcount: A:0.24, C:0.12, G:0.25, T:0.40
Consensus pattern (45 bp):
AATTCGGTTAATTCGGGTAATTCGGTTAATTCGGGTAATCCGGTT
Found at i:62232665 original size:2 final size:2
Alignment explanation
Indices: 62232658--62232691 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
62232648 CAAATACATC
* *
62232658 AT AT AT AT AT AT AT AT AT AT AT AT TT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
62232692 TACAAATACG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:62238533 original size:5 final size:5
Alignment explanation
Indices: 62238523--62238553 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
62238513 TGAGTATTCG
*
62238523 ATCGA ATCGA ATCGA ATCGA ATCAA ATCGA A
1 ATCGA ATCGA ATCGA ATCGA ATCGA ATCGA A
62238554 AATTTTCGAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.45, C:0.19, G:0.16, T:0.19
Consensus pattern (5 bp):
ATCGA
Found at i:62244629 original size:22 final size:21
Alignment explanation
Indices: 62244594--62244634 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
62244584 TATATTAAAT
* *
62244594 TAAAGTTCATGTATCAAATTAC
1 TAAAGTTAAAGTAT-AAATTAC
62244616 TAAAGTTAAAGTATAAATT
1 TAAAGTTAAAGTATAAATT
62244635 TAACATTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.46, C:0.07, G:0.10, T:0.37
Consensus pattern (21 bp):
TAAAGTTAAAGTATAAATTAC
Found at i:62253102 original size:15 final size:15
Alignment explanation
Indices: 62253082--62253110 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
62253072 AATTACAACA
62253082 ACAACAACAAAAATC
1 ACAACAACAAAAATC
62253097 ACAACAACAAAAAT
1 ACAACAACAAAAAT
62253111 GAAGAACTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.69, C:0.24, G:0.00, T:0.07
Consensus pattern (15 bp):
ACAACAACAAAAATC
Found at i:62254029 original size:11 final size:11
Alignment explanation
Indices: 62254013--62254037 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
62254003 TTACAATTTT
62254013 ATAATTTATAG
1 ATAATTTATAG
62254024 ATAATTTATAG
1 ATAATTTATAG
62254035 ATA
1 ATA
62254038 GATTAAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (11 bp):
ATAATTTATAG
Found at i:62257199 original size:31 final size:31
Alignment explanation
Indices: 62257125--62257184 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
62257115 TTTAATTTAA
* *
62257125 TCAATTTTAGTCCCTATACTTTTTGAATTGG
1 TCAATTTTAGTCCCCAGACTTTTTGAATTGG
62257156 TCAATTTTAGTCCCCAGACTTTTTGAATT
1 TCAATTTTAGTCCCCAGACTTTTTGAATT
62257185 TTGAAGTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.23, C:0.18, G:0.12, T:0.47
Consensus pattern (31 bp):
TCAATTTTAGTCCCCAGACTTTTTGAATTGG
Found at i:62264553 original size:33 final size:33
Alignment explanation
Indices: 62264496--62264558 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
62264486 GGCCGAGGAA
*
62264496 AAAAGCATAAGCCTGGGCCTGGCCCGGCCCGGG
1 AAAAGCATAAGCCCGGGCCTGGCCCGGCCCGGG
*
62264529 AAAATCATAAGCCCGGGCAC-GGCCCGGCCC
1 AAAAGCATAAGCCCGGGC-CTGGCCCGGCCC
62264559 ATTTTTTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
33 26 0.96
34 1 0.04
ACGTcount: A:0.24, C:0.37, G:0.32, T:0.08
Consensus pattern (33 bp):
AAAAGCATAAGCCCGGGCCTGGCCCGGCCCGGG
Found at i:62264606 original size:10 final size:11
Alignment explanation
Indices: 62264584--62264677 Score: 60
Period size: 11 Copynumber: 9.1 Consensus size: 11
62264574 ATTAAAATTT
62264584 TATTTTAAAAA
1 TATTTTAAAAA
62264595 TATTTT-AAAA
1 TATTTTAAAAA
62264605 TA----AAAAA
1 TATTTTAAAAA
* *
62264612 AATTTAAAAAA
1 TATTTTAAAAA
*
62264623 GTATTTAAAAAA
1 -TATTTTAAAAA
62264635 TATTTT--AAA
1 TATTTTAAAAA
**
62264644 -ATTAAAAAAA
1 TATTTTAAAAA
62264654 GTATTTTAAAAA
1 -TATTTTAAAAA
*
62264666 TATTTTTAAAA
1 TATTTTAAAAA
62264677 T
1 T
62264678 TAAAAAATTA
Statistics
Matches: 65, Mismatches: 8, Indels: 20
0.70 0.09 0.22
Matches are distributed among these distances:
7 5 0.08
8 3 0.05
9 3 0.05
10 9 0.14
11 27 0.42
12 18 0.28
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (11 bp):
TATTTTAAAAA
Found at i:62264620 original size:40 final size:41
Alignment explanation
Indices: 62264570--62264658 Score: 117
Period size: 40 Copynumber: 2.2 Consensus size: 41
62264560 TTTTTTTAAT
*** *
62264570 AAATATTAAAATTTTATTTTAAAAATATTTTAAAATAAAAA
1 AAATATTAAAAAAGTATTTAAAAAATATTTTAAAATAAAAA
62264611 AAAT-TTAAAAAAGTATTTAAAAAATATTTTAAAATTAAAAA
1 AAATATTAAAAAAGTATTTAAAAAATATTTTAAAA-TAAAAA
*
62264652 AAGTATT
1 AAATATT
62264659 TTAAAAATAT
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
40 26 0.63
41 13 0.32
42 2 0.05
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (41 bp):
AAATATTAAAAAAGTATTTAAAAAATATTTTAAAATAAAAA
Found at i:62264628 original size:12 final size:11
Alignment explanation
Indices: 62264605--62264670 Score: 57
Period size: 12 Copynumber: 6.1 Consensus size: 11
62264595 TATTTTAAAA
*
62264605 TAAAAAAAATT
1 TAAAAAATATT
62264616 TAAAAAAGTATT
1 TAAAAAA-TATT
62264628 TAAAAAATATT
1 TAAAAAATATT
*
62264639 T--TAAA-ATT
1 TAAAAAATATT
*
62264647 AAAAAAAGTATT
1 TAAAAAA-TATT
*
62264659 TTAAAAATATT
1 TAAAAAATATT
62264670 T
1 T
62264671 TTAAAATTAA
Statistics
Matches: 44, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
8 3 0.07
9 3 0.07
10 3 0.07
11 17 0.39
12 18 0.41
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (11 bp):
TAAAAAATATT
Found at i:62264652 original size:31 final size:32
Alignment explanation
Indices: 62264610--62264684 Score: 125
Period size: 31 Copynumber: 2.4 Consensus size: 32
62264600 TAAAATAAAA
*
62264610 AAAATTTAAAAAAGTATTTAAAAAATA-TTTT
1 AAAATTAAAAAAAGTATTTAAAAAATATTTTT
*
62264641 AAAATTAAAAAAAGTATTTTAAAAATATTTTT
1 AAAATTAAAAAAAGTATTTAAAAAATATTTTT
62264673 AAAATTAAAAAA
1 AAAATTAAAAAA
62264685 TTAAAAATAT
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
31 25 0.61
32 16 0.39
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (32 bp):
AAAATTAAAAAAAGTATTTAAAAAATATTTTT
Found at i:62264662 original size:32 final size:31
Alignment explanation
Indices: 62264610--62264684 Score: 116
Period size: 32 Copynumber: 2.4 Consensus size: 31
62264600 TAAAATAAAA
*
62264610 AAAATTTAAAAAAGTATTTAAAAA-ATATTTT
1 AAAATTAAAAAAAGTATTTAAAAATAT-TTTT
62264641 AAAATTAAAAAAAGTATTTTAAAAATATTTTT
1 AAAATTAAAAAAAGTA-TTTAAAAATATTTTT
62264673 AAAATTAAAAAA
1 AAAATTAAAAAA
62264685 TTAAAAATAT
Statistics
Matches: 41, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
31 15 0.37
32 24 0.59
33 2 0.05
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (31 bp):
AAAATTAAAAAAAGTATTTAAAAATATTTTT
Found at i:62264666 original size:21 final size:19
Alignment explanation
Indices: 62264590--62264664 Score: 73
Period size: 19 Copynumber: 3.8 Consensus size: 19
62264580 ATTTTATTTT
62264590 AAAAATATTTTAAAA-TAA
1 AAAAATATTTTAAAATTAA
* *
62264608 AAAAA-ATTTAAAAAAGTATTTA
1 AAAAATATTT--TAAA--ATTAA
62264630 AAAAATATTTTAAAATTAA
1 AAAAATATTTTAAAATTAA
62264649 AAAAAGTATTTTAAAA
1 AAAAA-TATTTTAAAA
62264665 ATATTTTTAA
Statistics
Matches: 46, Mismatches: 4, Indels: 12
0.74 0.06 0.19
Matches are distributed among these distances:
17 4 0.09
18 5 0.11
19 12 0.26
20 10 0.22
21 4 0.09
22 7 0.15
23 4 0.09
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (19 bp):
AAAAATATTTTAAAATTAA
Found at i:62265659 original size:38 final size:38
Alignment explanation
Indices: 62265602--62265675 Score: 112
Period size: 38 Copynumber: 1.9 Consensus size: 38
62265592 CATGCTATCA
* *
62265602 AAATCAAACGCGATCAATACGAATCAAAATTTTAATTG
1 AAATCAAACGCAATAAATACGAATCAAAATTTTAATTG
* *
62265640 AAATTAAACGCAATAAATACGAATTAAAATTTTAAT
1 AAATCAAACGCAATAAATACGAATCAAAATTTTAAT
62265676 AGATGCAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 32 1.00
ACGTcount: A:0.51, C:0.12, G:0.08, T:0.28
Consensus pattern (38 bp):
AAATCAAACGCAATAAATACGAATCAAAATTTTAATTG
Found at i:62273644 original size:18 final size:18
Alignment explanation
Indices: 62273621--62273657 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
62273611 AAGAAGATGA
62273621 TAGCTTTGTTTTGTTTAT
1 TAGCTTTGTTTTGTTTAT
62273639 TAGCTTTGTTTTGTTTAT
1 TAGCTTTGTTTTGTTTAT
62273657 T
1 T
62273658 TCATTATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.11, C:0.05, G:0.16, T:0.68
Consensus pattern (18 bp):
TAGCTTTGTTTTGTTTAT
Found at i:62274893 original size:30 final size:30
Alignment explanation
Indices: 62274857--62274950 Score: 89
Period size: 30 Copynumber: 3.1 Consensus size: 30
62274847 GTATCTGAGT
*
62274857 TTTGGTTTTAATGTTCAATTTGGTACCTAA
1 TTTGGTTTTAATGTTCAATTTGGTACATAA
* * * ** *
62274887 TTTGGTTTCAATGTTCACTTTAGTATTTGAG
1 TTTGGTTTTAATGTTCAATTTGGTACAT-AA
* * *
62274918 TTTAGCTTTAATGTTTAATTTGGTACATAA
1 TTTGGTTTTAATGTTCAATTTGGTACATAA
62274948 TTT
1 TTT
62274951 TTTCTTTATC
Statistics
Matches: 48, Mismatches: 15, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
30 27 0.56
31 21 0.44
ACGTcount: A:0.23, C:0.09, G:0.16, T:0.52
Consensus pattern (30 bp):
TTTGGTTTTAATGTTCAATTTGGTACATAA
Found at i:62284242 original size:40 final size:41
Alignment explanation
Indices: 62284185--62284275 Score: 123
Period size: 41 Copynumber: 2.2 Consensus size: 41
62284175 ACACACCAGT
* * *
62284185 TTGGCACTCAGTGCCTCATC-AGAT-AATTCGAAGTAATAAA
1 TTGGCACCCAGTACCTCATCGA-ATCAATCCGAAGTAATAAA
*
62284225 TTGGCACCCAGTACCTCATCGAATCAATCCGAAGTAGTAAA
1 TTGGCACCCAGTACCTCATCGAATCAATCCGAAGTAATAAA
62284266 TTGGCACCCA
1 TTGGCACCCA
62284276 ATGTGTCATC
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
40 20 0.44
41 25 0.56
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.24
Consensus pattern (41 bp):
TTGGCACCCAGTACCTCATCGAATCAATCCGAAGTAATAAA
Found at i:62284480 original size:2 final size:2
Alignment explanation
Indices: 62284473--62284514 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
62284463 AATTCATTCA
62284473 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
62284515 CAATTCAAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:62285278 original size:16 final size:16
Alignment explanation
Indices: 62285238--62285280 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
62285228 ATTTCATTTT
*
62285238 TATTTTAATATAAAATA
1 TATTTAAAT-TAAAATA
*
62285255 TA-TTAAATTAACATA
1 TATTTAAATTAAAATA
62285270 TATTTAAATTA
1 TATTTAAATTA
62285281 TGCGGCGTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 8 0.35
16 13 0.57
17 2 0.09
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (16 bp):
TATTTAAATTAAAATA
Found at i:62286848 original size:29 final size:31
Alignment explanation
Indices: 62286801--62286860 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
62286791 AAATCGGGCC
* *
62286801 AAATCAAAATTTCATGTATA-AAATTGCACA
1 AAATCAAAAGTTCATGTATACAAATTACACA
*
62286831 AAATC-AAAGTTCTTGTATACAAATTACACA
1 AAATCAAAAGTTCATGTATACAAATTACACA
62286861 TTAAACTATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 12 0.46
30 14 0.54
ACGTcount: A:0.48, C:0.15, G:0.07, T:0.30
Consensus pattern (31 bp):
AAATCAAAAGTTCATGTATACAAATTACACA
Found at i:62290984 original size:23 final size:22
Alignment explanation
Indices: 62290944--62290995 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
62290934 GCCGAAGTGT
*
62290944 AATTTTATCATTACTAATTTAA
1 AATTTTATAATTACTAATTTAA
*
62290966 AATTTTATAAATTAGTAATTTAA
1 AATTTTAT-AATTACTAATTTAA
62290989 AATTTTA
1 AATTTTA
62290996 GAGTGAACCA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 8 0.30
23 19 0.70
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.50
Consensus pattern (22 bp):
AATTTTATAATTACTAATTTAA
Found at i:62310041 original size:15 final size:15
Alignment explanation
Indices: 62310021--62310053 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
62310011 TTTTTTCAAG
62310021 AAACAT-TAATATTTT
1 AAACATATAA-ATTTT
62310036 AAACATATAAATTTT
1 AAACATATAAATTTT
62310051 AAA
1 AAA
62310054 AAAATCAGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 14 0.82
16 3 0.18
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (15 bp):
AAACATATAAATTTT
Found at i:62310568 original size:2 final size:2
Alignment explanation
Indices: 62310563--62310590 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
62310553 AATAATTTTC
62310563 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
62310591 CAAATGAATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:62310734 original size:31 final size:31
Alignment explanation
Indices: 62310688--62310751 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 31
62310678 TTACTATAAT
*
62310688 TTGGTCAATTCTAGTCTCTTTACTTTTCGAA
1 TTGGTCAATTCTAGTCTCTGTACTTTTCGAA
* * * *
62310719 TTGGTCGATTTTAGTCTCTGTATTTTTTGAA
1 TTGGTCAATTCTAGTCTCTGTACTTTTCGAA
62310750 TT
1 TT
62310752 TCAAAATTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.17, C:0.14, G:0.16, T:0.53
Consensus pattern (31 bp):
TTGGTCAATTCTAGTCTCTGTACTTTTCGAA
Found at i:62313814 original size:2 final size:2
Alignment explanation
Indices: 62313768--62313795 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
62313758 TGTAATTGAG
62313768 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
62313796 GCATGTGTAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:62314343 original size:3 final size:3
Alignment explanation
Indices: 62314335--62314386 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
62314325 CTTTTTTACG
62314335 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
62314383 TTA T
1 TTA T
62314387 ACATGAAATT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:62319650 original size:30 final size:31
Alignment explanation
Indices: 62319610--62319668 Score: 93
Period size: 30 Copynumber: 1.9 Consensus size: 31
62319600 TAAAACAATA
*
62319610 TTATAATAATTTATA-TTAATCGCTATTTAT
1 TTATAATAATTTATATTTAATCACTATTTAT
*
62319640 TTATAGTAATTTATATTTAATCACTATTT
1 TTATAATAATTTATATTTAATCACTATTT
62319669 TCTTTATTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 14 0.54
31 12 0.46
ACGTcount: A:0.36, C:0.07, G:0.03, T:0.54
Consensus pattern (31 bp):
TTATAATAATTTATATTTAATCACTATTTAT
Found at i:62320153 original size:26 final size:25
Alignment explanation
Indices: 62320105--62320153 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 25
62320095 GAGTAAATTG
*
62320105 ATTTTTTCTGTTAAAAATTACATCC
1 ATTTTTTCTGTTAAAAATAACATCC
62320130 ATTTTTAT-TGTTAAAAACTAACAT
1 ATTTTT-TCTGTTAAAAA-TAACAT
62320154 AATTGACAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 15 0.71
26 6 0.29
ACGTcount: A:0.37, C:0.12, G:0.04, T:0.47
Consensus pattern (25 bp):
ATTTTTTCTGTTAAAAATAACATCC
Found at i:62322939 original size:8 final size:8
Alignment explanation
Indices: 62322922--62322950 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
62322912 TTCCTATATT
62322922 TTTC-AAA
1 TTTCAAAA
62322929 TTTCAAAA
1 TTTCAAAA
62322937 TTTCAAAA
1 TTTCAAAA
62322945 TTTCAA
1 TTTCAA
62322951 TCCTAACTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
7 4 0.19
8 17 0.81
ACGTcount: A:0.45, C:0.14, G:0.00, T:0.41
Consensus pattern (8 bp):
TTTCAAAA
Found at i:62332650 original size:177 final size:174
Alignment explanation
Indices: 62332354--62332702 Score: 608
Period size: 177 Copynumber: 2.0 Consensus size: 174
62332344 AAATTATCCA
*
62332354 AAACAACAAAGAATCAAAGTACATCCAAACAAAATATCTACTTTGACATTAATGATACATAGCAA
1 AAACAACAAAGAATCAAAGTACATCCAAACAAAATATCTACTTTGACATTAAGGATACATAGCAA
*
62332419 TAGTATACAAACAGGGGTGAAACCAAGGGACAGGAAGGCCTTCGGTAAATGGAAAATTTGCATTT
66 TAGCATACAAACAGGGGTGAAACCAAGGGACAGGAAGGCCTTCGGTAAATGGAAAATTTGCATTT
62332484 TAGGCCCTCCCAAGAATTAAAATTTCAATTTAAGACCCTTTTAACAG
131 T-GGCCCTCCCAAGAATTAAAATTTCAATTTAAGA--CTTTTAACAG
* *
62332531 AAACAACAAAGAATCAAAGTTCATCCAAACAAAATATCTACTTTGACATTAAGGATACGTAGCAA
1 AAACAACAAAGAATCAAAGTACATCCAAACAAAATATCTACTTTGACATTAAGGATACATAGCAA
* * *
62332596 TAGCATACAAACAGGGGTGAAACCAAGGGACAGGCAGGCCTTTGGTAAATGGAAATTTTGCATTT
66 TAGCATACAAACAGGGGTGAAACCAAGGGACAGGAAGGCCTTCGGTAAATGGAAAATTTGCATTT
62332661 TGGCCCTCCCAAGAATTAAAATTTCAATTTAAGACTTTTAAC
131 TGGCCCTCCCAAGAATTAAAATTTCAATTTAAGACTTTTAAC
62332703 GCAAAATTCA
Statistics
Matches: 165, Mismatches: 7, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
174 8 0.05
176 33 0.20
177 124 0.75
ACGTcount: A:0.41, C:0.18, G:0.16, T:0.24
Consensus pattern (174 bp):
AAACAACAAAGAATCAAAGTACATCCAAACAAAATATCTACTTTGACATTAAGGATACATAGCAA
TAGCATACAAACAGGGGTGAAACCAAGGGACAGGAAGGCCTTCGGTAAATGGAAAATTTGCATTT
TGGCCCTCCCAAGAATTAAAATTTCAATTTAAGACTTTTAACAG
Found at i:62345741 original size:31 final size:31
Alignment explanation
Indices: 62345706--62345766 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
62345696 TATCATCCTA
**
62345706 GTAACTTAAATAAAAACTTTTGAATAGTTCG
1 GTAACTTAAATAAAAACTTTCAAATAGTTCG
*
62345737 GTAACTTAAATAGAAACTTTCAAATAGTTC
1 GTAACTTAAATAAAAACTTTCAAATAGTTC
62345767 ATTTTGTAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.43, C:0.11, G:0.11, T:0.34
Consensus pattern (31 bp):
GTAACTTAAATAAAAACTTTCAAATAGTTCG
Found at i:62353307 original size:16 final size:16
Alignment explanation
Indices: 62353286--62353321 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
62353276 ATCTATTTAT
62353286 TTATGATATTTTAATG
1 TTATGATATTTTAATG
62353302 TTATGATATTTTAATG
1 TTATGATATTTTAATG
62353318 TTAT
1 TTAT
62353322 AAATGATTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.11, T:0.58
Consensus pattern (16 bp):
TTATGATATTTTAATG
Found at i:62354798 original size:5 final size:5
Alignment explanation
Indices: 62354756--62354824 Score: 50
Period size: 5 Copynumber: 12.8 Consensus size: 5
62354746 GACCCTTTCT
* * *
62354756 TTTTC TTTTC TTTTA TTATTA -TTTA TTTCCTT TTTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TT-TTA TTTTA TTT--TA TTTTA TTTTA TTTTA
62354803 TTTTA TTATTA CTATTTA TTTT
1 TTTTA TT-TTA -T-TTTA TTTT
62354825 TTAATATAAA
Statistics
Matches: 54, Mismatches: 3, Indels: 14
0.76 0.04 0.20
Matches are distributed among these distances:
4 3 0.06
5 35 0.65
6 7 0.13
7 8 0.15
8 1 0.02
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.75
Consensus pattern (5 bp):
TTTTA
Found at i:62360774 original size:25 final size:25
Alignment explanation
Indices: 62360745--62360796 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
62360735 ATGTAAAGGC
*
62360745 AAACAAAACCATAACTAATAGTAAA
1 AAACAAAACCATAACTAAAAGTAAA
*
62360770 AAACAAAACCATATCTAAAAGTAAA
1 AAACAAAACCATAACTAAAAGTAAA
62360795 AA
1 AA
62360797 GTAAATTTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.65, C:0.15, G:0.04, T:0.15
Consensus pattern (25 bp):
AAACAAAACCATAACTAAAAGTAAA
Found at i:62364177 original size:21 final size:21
Alignment explanation
Indices: 62364151--62364192 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
62364141 TTATACCCCC
62364151 GCGAGCGAGAAAGAGAGAAAA
1 GCGAGCGAGAAAGAGAGAAAA
62364172 GCGAGCGAGAAAGAGAGAAAA
1 GCGAGCGAGAAAGAGAGAAAA
62364193 ATAAAGAGGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.52, C:0.10, G:0.38, T:0.00
Consensus pattern (21 bp):
GCGAGCGAGAAAGAGAGAAAA
Found at i:62374005 original size:2 final size:2
Alignment explanation
Indices: 62373998--62374028 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
62373988 ACATACATAC
62373998 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
62374029 CATGTCCCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:62377215 original size:17 final size:18
Alignment explanation
Indices: 62377178--62377216 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
62377168 GGTAGTTAAA
62377178 AAATTAATTTTCAAAATT
1 AAATTAATTTTCAAAATT
* *
62377196 AAATTTATTTT-AATATT
1 AAATTAATTTTCAAAATT
62377213 AAAT
1 AAAT
62377217 AAATCTCCCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (18 bp):
AAATTAATTTTCAAAATT
Found at i:62378498 original size:20 final size:20
Alignment explanation
Indices: 62378473--62378513 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
62378463 ATGGAAATTA
62378473 AGATTTTGATATAAATGTCG
1 AGATTTTGATATAAATGTCG
62378493 AGATTTTGATATAAATGTCG
1 AGATTTTGATATAAATGTCG
62378513 A
1 A
62378514 ATATGGGTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.37, C:0.05, G:0.20, T:0.39
Consensus pattern (20 bp):
AGATTTTGATATAAATGTCG
Found at i:62390470 original size:19 final size:20
Alignment explanation
Indices: 62390432--62390471 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
62390422 TGGTGGACTT
* *
62390432 TTTTGAATTATTTTATTTTA
1 TTTTAAATTATTTTAATTTA
62390452 TTTTAAATT-TTTTAATTTA
1 TTTTAAATTATTTTAATTTA
62390471 T
1 T
62390472 AATTAAATAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.70
Consensus pattern (20 bp):
TTTTAAATTATTTTAATTTA
Found at i:62400962 original size:6 final size:6
Alignment explanation
Indices: 62400951--62400984 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
62400941 TAAATGAATA
*
62400951 ATAATG ATAATG ATAATG ATAATG ATAATA ATAA
1 ATAATG ATAATG ATAATG ATAATG ATAATG ATAA
62400985 CTATAGGATT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.56, C:0.00, G:0.12, T:0.32
Consensus pattern (6 bp):
ATAATG
Found at i:62404564 original size:29 final size:29
Alignment explanation
Indices: 62404505--62404563 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
62404495 TTTGGCTTAA
*
62404505 TGTGTAATTTTATACGTAAACTTTGATTT
1 TGTGTAATTTTATACATAAACTTTGATTT
* *
62404534 TGTGTAATTTTATATATGAAATTTTGATTT
1 TGTGTAATTTTATACAT-AAACTTTGATTT
62404564 GATCCAATTC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 15 0.58
30 11 0.42
ACGTcount: A:0.29, C:0.03, G:0.14, T:0.54
Consensus pattern (29 bp):
TGTGTAATTTTATACATAAACTTTGATTT
Found at i:62411736 original size:42 final size:42
Alignment explanation
Indices: 62411677--62411812 Score: 159
Period size: 42 Copynumber: 3.2 Consensus size: 42
62411667 AGTCTCACAG
* *
62411677 TTAATCCCGCCTTAATTAGGATTTACCTTTTTAACTTTTCAT
1 TTAATCCCACCTCAATTAGGATTTACCTTTTTAACTTTTCAT
* * *
62411719 TTAATCCCACCTCAATTAAGAATTATCTTTTTAACTTTTCAT
1 TTAATCCCACCTCAATTAGGATTTACCTTTTTAACTTTTCAT
**
62411761 TTAATCCCATCC-CAATTAGGATTTATCTTCTTTTT-TTTTTTCAT
1 TTAATCCCA-CCTCAATTAGGATTTA-C--CTTTTTAACTTTTCAT
62411805 TTAATCCC
1 TTAATCCC
62411813 TCTTTGCTAC
Statistics
Matches: 80, Mismatches: 10, Indels: 6
0.83 0.10 0.06
Matches are distributed among these distances:
42 57 0.71
43 2 0.03
44 15 0.19
45 6 0.08
ACGTcount: A:0.25, C:0.22, G:0.04, T:0.49
Consensus pattern (42 bp):
TTAATCCCACCTCAATTAGGATTTACCTTTTTAACTTTTCAT
Found at i:62414382 original size:38 final size:40
Alignment explanation
Indices: 62414322--62414424 Score: 122
Period size: 41 Copynumber: 2.6 Consensus size: 40
62414312 CCCCACAATT
* * *
62414322 AATCCCACTTCAATTAGGATTTATTTTTTTAGC-TTT-TC
1 AATCCCACCTCAATTAGGATTTATTCTTTTAACTTTTATC
* *
62414360 AATCTCACCTCAATTAGGATTTA-TCTTTTAACTTTTTAATT
1 AATCCCACCTCAATTAGGATTTATTCTTTTAAC-TTTT-ATC
62414401 AATCCCACCTCAATTAGGATTTAT
1 AATCCCACCTCAATTAGGATTTAT
62414425 ATAAGCTTTT
Statistics
Matches: 54, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
37 7 0.13
38 21 0.39
39 3 0.06
41 23 0.43
ACGTcount: A:0.28, C:0.19, G:0.07, T:0.46
Consensus pattern (40 bp):
AATCCCACCTCAATTAGGATTTATTCTTTTAACTTTTATC
Found at i:62416228 original size:29 final size:30
Alignment explanation
Indices: 62416194--62416266 Score: 94
Period size: 29 Copynumber: 2.5 Consensus size: 30
62416184 ATGGGGACTA
* *
62416194 GATCAAATTAGTCCCTCTATTATT-AAAAG
1 GATCAAATTAGTCCCTATAATATTAAAAAG
* *
62416223 GATCAATTTAGTCCTTATAATATTAAAAAG
1 GATCAAATTAGTCCCTATAATATTAAAAAG
*
62416253 GATCAAATAAGTCC
1 GATCAAATTAGTCC
62416267 AAATTGTAAC
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
29 20 0.54
30 17 0.46
ACGTcount: A:0.41, C:0.15, G:0.11, T:0.33
Consensus pattern (30 bp):
GATCAAATTAGTCCCTATAATATTAAAAAG
Found at i:62416907 original size:22 final size:22
Alignment explanation
Indices: 62416890--62416961 Score: 117
Period size: 22 Copynumber: 3.3 Consensus size: 22
62416880 GAACTAAACC
62416890 CTCATGGCTAACGTACTAAGCT
1 CTCATGGCTAACGTACTAAGCT
62416912 CTCATGGCTAACGTACTAAGCT
1 CTCATGGCTAACGTACTAAGCT
** *
62416934 CTCATGTTTCACGTACTAAGCT
1 CTCATGGCTAACGTACTAAGCT
62416956 CTCATG
1 CTCATG
62416962 TTTGAGGGAT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 47 1.00
ACGTcount: A:0.25, C:0.28, G:0.17, T:0.31
Consensus pattern (22 bp):
CTCATGGCTAACGTACTAAGCT
Found at i:62426031 original size:29 final size:28
Alignment explanation
Indices: 62425999--62426067 Score: 70
Period size: 29 Copynumber: 2.4 Consensus size: 28
62425989 TGTTTTATAA
62425999 TTAATTATAAATATAAA-AATAATTTTATT
1 TTAATTATAAATATAAATAA-AA-TTTATT
* *
62426028 TTAATAATTAAATTTAAATAAAATTTATT
1 TTAATTA-TAAATATAAATAAAATTTATT
*
62426057 TTTATTA-AAAT
1 TTAATTATAAAT
62426068 TTTAAACAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
27 4 0.12
29 17 0.50
30 11 0.32
31 2 0.06
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (28 bp):
TTAATTATAAATATAAATAAAATTTATT
Found at i:62426496 original size:4 final size:4
Alignment explanation
Indices: 62426489--62426520 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
62426479 CTTGCTTGAA
62426489 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT
62426521 CTTAAATATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TTAT
Found at i:62428587 original size:18 final size:19
Alignment explanation
Indices: 62428556--62428592 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
62428546 AATTAGATTT
*
62428556 TTTATATTTTTATTCTTGA
1 TTTATATTTATATTCTTGA
62428575 TTTA-ATTTATATTCTTGA
1 TTTATATTTATATTCTTGA
62428593 GTCAGTAACG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.24, C:0.05, G:0.05, T:0.65
Consensus pattern (19 bp):
TTTATATTTATATTCTTGA
Found at i:62433733 original size:22 final size:22
Alignment explanation
Indices: 62433708--62433799 Score: 112
Period size: 22 Copynumber: 4.2 Consensus size: 22
62433698 AAATTCAATA
* *
62433708 TCAATTTCTTTCAAAAATTCTC
1 TCAATTCCCTTCAAAAATTCTC
* *
62433730 TCAATTCCTTTCAAAATTTCTC
1 TCAATTCCCTTCAAAAATTCTC
* *
62433752 TCAATTCCCTTCAAAATTTCTA
1 TCAATTCCCTTCAAAAATTCTC
* *
62433774 TCAATTTCCTTCCAAAATTCTC
1 TCAATTCCCTTCAAAAATTCTC
62433796 TCAA
1 TCAA
62433800 ACTCTCAAAT
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 62 1.00
ACGTcount: A:0.30, C:0.27, G:0.00, T:0.42
Consensus pattern (22 bp):
TCAATTCCCTTCAAAAATTCTC
Found at i:62433815 original size:52 final size:51
Alignment explanation
Indices: 62433749--62433851 Score: 129
Period size: 52 Copynumber: 2.0 Consensus size: 51
62433739 TTCAAAATTT
* * *
62433749 CTCTCAATTCCCTT-CAAAATTTCTATCAATTTCCTTCCAAAATTCTCTCAAA
1 CTCTCAATTCCCTTCCAAAA-TCCTATCAATTTCCTTCAAAAAATCTC-CAAA
*
62433801 CTCTCAAATT-CCTTCCAAAATCCTCTCAATTTCCTTCAAAAAATCTCCAAA
1 CTCTC-AATTCCCTTCCAAAATCCTATCAATTTCCTTCAAAAAATCTCCAAA
62433852 TTCATATTAA
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
51 4 0.09
52 32 0.71
53 9 0.20
ACGTcount: A:0.33, C:0.32, G:0.00, T:0.35
Consensus pattern (51 bp):
CTCTCAATTCCCTTCCAAAATCCTATCAATTTCCTTCAAAAAATCTCCAAA
Found at i:62433840 original size:21 final size:22
Alignment explanation
Indices: 62433801--62433854 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
62433791 TTCTCTCAAA
62433801 CTCTCAAATTCCTTCCAAAATC
1 CTCTCAAATTCCTTCCAAAATC
* *
62433823 CTCTCAATTTCCTTCAAAAAAT-
1 CTCTCAAATTCCTTC-CAAAATC
62433845 CTC-CAAATTC
1 CTCTCAAATTC
62433855 ATATTAAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 6 0.21
22 17 0.61
23 5 0.18
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (22 bp):
CTCTCAAATTCCTTCCAAAATC
Found at i:62433928 original size:28 final size:29
Alignment explanation
Indices: 62433884--62433938 Score: 94
Period size: 28 Copynumber: 1.9 Consensus size: 29
62433874 ATTAAATTTC
62433884 ATTTTTTTAAGAAAATTTTAAAATTTTTT
1 ATTTTTTTAAGAAAATTTTAAAATTTTTT
*
62433913 ATTTTTTTAA-ATAATTTTAAAATTTT
1 ATTTTTTTAAGAAAATTTTAAAATTTT
62433939 AATATTTTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 15 0.60
29 10 0.40
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (29 bp):
ATTTTTTTAAGAAAATTTTAAAATTTTTT
Found at i:62433946 original size:28 final size:29
Alignment explanation
Indices: 62433884--62433946 Score: 92
Period size: 29 Copynumber: 2.2 Consensus size: 29
62433874 ATTAAATTTC
*
62433884 ATTTTTTTAAGAAAATTTTAAAATTTTTT
1 ATTTTTTTAAGAAAATTTTAAAATTTTAT
*
62433913 ATTTTTTTAA-ATAATTTTAAAATTTTAAT
1 ATTTTTTTAAGAAAATTTTAAAATTTT-AT
62433942 ATTTT
1 ATTTT
62433947 CAACAATGGC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
28 15 0.48
29 16 0.52
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (29 bp):
ATTTTTTTAAGAAAATTTTAAAATTTTAT
Found at i:62445419 original size:60 final size:60
Alignment explanation
Indices: 62445326--62445455 Score: 251
Period size: 60 Copynumber: 2.1 Consensus size: 60
62445316 TATTCAATGG
62445326 TAATATTATTAGAGCCCCCTAATCTTTTATGGAATTCTTTGAAGAATTCCCATGCAAATT
1 TAATATTATTAGAGCCCCCTAATCTTTTATGGAATTCTTTGAAGAATTCCCATGCAAATT
62445386 TAATATTATTAGAGCCCCCTAATCTTTTATGGAATTCTTTGAAGAATTCCCATGCAAATT
1 TAATATTATTAGAGCCCCCTAATCTTTTATGGAATTCTTTGAAGAATTCCCATGCAAATT
62445446 TACATATTAT
1 TA-ATATTAT
62445456 ACCATGCCCC
Statistics
Matches: 69, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
60 62 0.90
61 7 0.10
ACGTcount: A:0.32, C:0.18, G:0.11, T:0.39
Consensus pattern (60 bp):
TAATATTATTAGAGCCCCCTAATCTTTTATGGAATTCTTTGAAGAATTCCCATGCAAATT
Found at i:62450697 original size:16 final size:15
Alignment explanation
Indices: 62450676--62450705 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
62450666 TTTTAACTTC
62450676 CTTTTTTTTCTTTTTT
1 CTTTTTTTT-TTTTTT
62450692 CTTTTTTTTTTTTT
1 CTTTTTTTTTTTTT
62450706 CCATTTTCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (15 bp):
CTTTTTTTTTTTTTT
Found at i:62450712 original size:16 final size:16
Alignment explanation
Indices: 62450673--62450717 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 16
62450663 TTCTTTTAAC
62450673 TTCCTTTTTTTTCTTT
1 TTCCTTTTTTTTCTTT
*
62450689 TTTCTTTTTTTT-TTT
1 TTCCTTTTTTTTCTTT
* *
62450704 TTCCATTTTCTTCT
1 TTCCTTTTTTTTCT
62450718 ACTTCCCCCT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
15 12 0.50
16 12 0.50
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (16 bp):
TTCCTTTTTTTTCTTT
Found at i:62451115 original size:2 final size:2
Alignment explanation
Indices: 62451108--62451132 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
62451098 GCAATAAGTT
62451108 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
62451133 TAATATTTGT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.