Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 ID=Chr02-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: 62769430
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1067035 characters in sequence are not A, C, G, or T
File 139 of 206
Found at i:42486692 original size:19 final size:18
Alignment explanation
Indices: 42486665--42486711 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 18
42486655 ATATTAATGT
42486665 TAAAA-TTTATTATTAAAA
1 TAAAATTTTATTATT-AAA
*
42486683 TAAAATTTTAATATTAAA
1 TAAAATTTTATTATTAAA
42486701 T--AATTTTATTA
1 TAAAATTTTATTA
42486712 AATAATGAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
16 9 0.35
18 9 0.35
19 8 0.31
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TAAAATTTTATTATTAAA
Found at i:42486703 original size:18 final size:18
Alignment explanation
Indices: 42486647--42486700 Score: 56
Period size: 19 Copynumber: 2.9 Consensus size: 18
42486637 CTAAAAAATT
**
42486647 TAAAA-TTAATATTAATGT
1 TAAAATTTAATATTAA-AA
*
42486665 TAAAATTTATTATTAAAA
1 TAAAATTTAATATTAAAA
42486683 TAAAATTTTAATATTAAA
1 TAAAA-TTTAATATTAAA
42486701 TAATTTTATT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
18 10 0.33
19 20 0.67
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (18 bp):
TAAAATTTAATATTAAAA
Found at i:42490573 original size:103 final size:103
Alignment explanation
Indices: 42490458--42490665 Score: 407
Period size: 103 Copynumber: 2.0 Consensus size: 103
42490448 AAATAATATT
42490458 TATTTTGAGAAATGAAAAACATGTATTGGGTTGGATTAAATTATAAAGTGTAGGATTAAAATTCC
1 TATTTTGAGAAATGAAAAACATGTATTGGGTTGGATTAAATTATAAAGTGTAGGATTAAAATTCC
42490523 AAGAAGTACATATAATTGGACTTAATACATGAGAAACC
66 AAGAAGTACATATAATTGGACTTAATACATGAGAAACC
*
42490561 TATTTTGAGAAATGAAAAACATGTATTGGGTTGGATTAAATTATAAAGTGTAGGGTTAAAATTCC
1 TATTTTGAGAAATGAAAAACATGTATTGGGTTGGATTAAATTATAAAGTGTAGGATTAAAATTCC
42490626 AAGAAGTACATATAATTGGACTTAATACATGAGAAACC
66 AAGAAGTACATATAATTGGACTTAATACATGAGAAACC
42490664 TA
1 TA
42490666 AAACCCCTCA
Statistics
Matches: 104, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
103 104 1.00
ACGTcount: A:0.42, C:0.08, G:0.19, T:0.31
Consensus pattern (103 bp):
TATTTTGAGAAATGAAAAACATGTATTGGGTTGGATTAAATTATAAAGTGTAGGATTAAAATTCC
AAGAAGTACATATAATTGGACTTAATACATGAGAAACC
Found at i:42492023 original size:17 final size:18
Alignment explanation
Indices: 42491996--42492032 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
42491986 AAGAGTCTAT
*
42491996 ATAAGCCATAATATGGAA
1 ATAAGCCATAATATGAAA
42492014 ATAA-CCATAATATGAAA
1 ATAAGCCATAATATGAAA
42492031 AT
1 AT
42492033 TGAAAATTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.54, C:0.11, G:0.11, T:0.24
Consensus pattern (18 bp):
ATAAGCCATAATATGAAA
Found at i:42492547 original size:23 final size:23
Alignment explanation
Indices: 42492512--42492598 Score: 84
Period size: 23 Copynumber: 3.8 Consensus size: 23
42492502 CACAGGGGAC
*
42492512 TTCTATTACTAGTACTTTGGTAA
1 TTCTATTACTAGTACTTCGGTAA
* * *
42492535 TTTTATTATTAGTACTTCGGTAC
1 TTCTATTACTAGTACTTCGGTAA
* * **
42492558 TTCTATTACTAGCACTGCGGTGC
1 TTCTATTACTAGTACTTCGGTAA
* *
42492581 TTCTGTTACTAGAACTTC
1 TTCTATTACTAGTACTTC
42492599 AGTATGATAT
Statistics
Matches: 52, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 52 1.00
ACGTcount: A:0.22, C:0.18, G:0.15, T:0.45
Consensus pattern (23 bp):
TTCTATTACTAGTACTTCGGTAA
Found at i:42494231 original size:55 final size:55
Alignment explanation
Indices: 42494172--42494349 Score: 268
Period size: 55 Copynumber: 3.2 Consensus size: 55
42494162 TTATCGCCAA
* * * *
42494172 AAGGCCATTCATTCAAGAATTTGCCATAAAAGTTACTCTTTTCAGAATTCACCAC
1 AAGGCCATTCATTCAAGAGTTTGCCACAAAGGCTACTCTTTTCAGAATTCACCAC
*
42494227 AAGGCCATTCATTCAAGAGTTTTCCACAAAGGCTACAT-TTTTCAGAATTCACCAC
1 AAGGCCATTCATTCAAGAGTTTGCCACAAAGGCTAC-TCTTTTCAGAATTCACCAC
*
42494282 AAGGCCAATCATTCAAGAGTTTGCCACAAAGGCTACTCTTTTCAGAATTCACCAC
1 AAGGCCATTCATTCAAGAGTTTGCCACAAAGGCTACTCTTTTCAGAATTCACCAC
*
42494337 AAGGGCGATTCAT
1 AA-GGCCATTCAT
42494350 AAGAGTGCGC
Statistics
Matches: 111, Mismatches: 9, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
54 1 0.01
55 101 0.91
56 9 0.08
ACGTcount: A:0.33, C:0.25, G:0.14, T:0.28
Consensus pattern (55 bp):
AAGGCCATTCATTCAAGAGTTTGCCACAAAGGCTACTCTTTTCAGAATTCACCAC
Found at i:42494259 original size:28 final size:27
Alignment explanation
Indices: 42494222--42494310 Score: 83
Period size: 27 Copynumber: 3.3 Consensus size: 27
42494212 TTCAGAATTC
42494222 ACCACAAGGCCATTCATTCAAGAGTTT
1 ACCACAAGGCCATTCATTCAAGAGTTT
* * * *
42494249 TCCACAAAGGCTACATT-TTTC-AGAATTC
1 ACCAC-AAGGC--CATTCATTCAAGAGTTT
*
42494277 ACCACAAGGCCAATCATTCAAGAGTTT
1 ACCACAAGGCCATTCATTCAAGAGTTT
*
42494304 GCCACAA
1 ACCACAA
42494311 AGGCTACTCT
Statistics
Matches: 47, Mismatches: 10, Indels: 10
0.70 0.15 0.15
Matches are distributed among these distances:
25 3 0.06
26 3 0.06
27 20 0.43
28 14 0.30
29 3 0.06
30 4 0.09
ACGTcount: A:0.35, C:0.27, G:0.13, T:0.25
Consensus pattern (27 bp):
ACCACAAGGCCATTCATTCAAGAGTTT
Found at i:42494336 original size:28 final size:28
Alignment explanation
Indices: 42494205--42494338 Score: 98
Period size: 28 Copynumber: 4.9 Consensus size: 28
42494195 CCATAAAAGT
42494205 TACTCTTTTCAGAATTCACCAC-AAGGC
1 TACTCTTTTCAGAATTCACCACAAAGGC
* * * * **
42494232 CATTC-ATTCAAGAGTTTTCCACAAAGGC
1 TACTCTTTTC-AGAATTCACCACAAAGGC
42494260 TACAT-TTTTCAGAATTCACCAC-AAGGC
1 TAC-TCTTTTCAGAATTCACCACAAAGGC
* * * * **
42494287 CAATC-ATTCAAGAGTTTGCCACAAAGGC
1 TACTCTTTTC-AGAATTCACCACAAAGGC
42494315 TACTCTTTTCAGAATTCACCACAA
1 TACTCTTTTCAGAATTCACCACAA
42494339 GGGCGATTCA
Statistics
Matches: 75, Mismatches: 24, Indels: 15
0.66 0.21 0.13
Matches are distributed among these distances:
26 7 0.09
27 27 0.36
28 34 0.45
29 7 0.09
ACGTcount: A:0.33, C:0.27, G:0.12, T:0.28
Consensus pattern (28 bp):
TACTCTTTTCAGAATTCACCACAAAGGC
Found at i:42513639 original size:39 final size:39
Alignment explanation
Indices: 42513599--42513851 Score: 364
Period size: 39 Copynumber: 6.5 Consensus size: 39
42513589 GTTCACTTTT
* * *
42513599 AAGCATATATCACATTACACATATAATCACATAACATTT
1 AAGCATATATCACAATACTCATATAATCACATAACATTC
* *
42513638 AAGCATATATCACAATACTCATATAATTACATAACGTTC
1 AAGCATATATCACAATACTCATATAATCACATAACATTC
* *
42513677 AAGCACATATCGCAATACTCATATAATCACATAACATTC
1 AAGCATATATCACAATACTCATATAATCACATAACATTC
* *
42513716 AAGAATATATCGCAATACTCATATAATCACATAACATTC
1 AAGCATATATCACAATACTCATATAATCACATAACATTC
* *
42513755 AAGCATATATCACAATACTCATATAATCATATAAAATTC
1 AAGCATATATCACAATACTCATATAATCACATAACATTC
* * *
42513794 AAGCATATA-CTACAATTCTTATATAATCATATAACATTC
1 AAGCATATATC-ACAATACTCATATAATCACATAACATTC
42513833 AAGCATATATCACAATACT
1 AAGCATATATCACAATACT
42513852 TAAAAACATG
Statistics
Matches: 193, Mismatches: 19, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
38 1 0.01
39 191 0.99
40 1 0.01
ACGTcount: A:0.45, C:0.21, G:0.04, T:0.30
Consensus pattern (39 bp):
AAGCATATATCACAATACTCATATAATCACATAACATTC
Found at i:42520974 original size:2 final size:2
Alignment explanation
Indices: 42520967--42520993 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
42520957 GACCAATTGA
42520967 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 A
42520994 ATTAGAGCTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:42529257 original size:18 final size:17
Alignment explanation
Indices: 42529225--42529258 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
42529215 TATTTAATTA
*
42529225 ATTTTTTATGTTTTATG
1 ATTTTTTAGGTTTTATG
42529242 ATTTTTTAGGTGTTTAT
1 ATTTTTTAGGT-TTTAT
42529259 AAGCATAGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.18, C:0.00, G:0.15, T:0.68
Consensus pattern (17 bp):
ATTTTTTAGGTTTTATG
Found at i:42535780 original size:22 final size:22
Alignment explanation
Indices: 42535752--42535794 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
42535742 TAAGATAAAA
42535752 AAAATAT-AATCACATACATATG
1 AAAATATCAATCACAT-CATATG
*
42535774 AAAATATCAATCTCATCATAT
1 AAAATATCAATCACATCATAT
42535795 CAATCATCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.51, C:0.16, G:0.02, T:0.30
Consensus pattern (22 bp):
AAAATATCAATCACATCATATG
Found at i:42547547 original size:13 final size:14
Alignment explanation
Indices: 42547519--42547552 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
42547509 AAGTGTTATG
42547519 GAAAAGTACTTTTT
1 GAAAAGTACTTTTT
*
42547533 GAGAAGTAC-TTTT
1 GAAAAGTACTTTTT
42547546 GAAAAGT
1 GAAAAGT
42547553 TTGGTTTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.38, C:0.06, G:0.21, T:0.35
Consensus pattern (14 bp):
GAAAAGTACTTTTT
Found at i:42559783 original size:19 final size:19
Alignment explanation
Indices: 42559761--42559800 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
42559751 TTTTTAATCA
*
42559761 AATATACTTTTTTATTTTT
1 AATATACTATTTTATTTTT
* *
42559780 AATATGCTATTTTCTTTTT
1 AATATACTATTTTATTTTT
42559799 AA
1 AA
42559801 AATATGTTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.28, C:0.07, G:0.03, T:0.62
Consensus pattern (19 bp):
AATATACTATTTTATTTTT
Found at i:42561419 original size:390 final size:391
Alignment explanation
Indices: 42560674--42561443 Score: 1073
Period size: 390 Copynumber: 2.0 Consensus size: 391
42560664 ATTATGCACC
* *
42560674 AAAACATGTAACATGCATGCCTAGTTACCTTTTTCCTCAGATCCATCGATGTTGGGGTGTGACAC
1 AAAACAGGTAACATGCATGCCTAGTTACCCTTTTCCTCAGATCCATCGATGTTGGGGTGTGACAC
*
42560739 ATTTATGGCGAGTCAGGGGGCAGAAAGCATACAATGACCTAAAAAATCAAGTGATTTATCTGAGG
66 ATTTATGGCGAGTCAGGGGGCAGAAAGCATACAATGACCTAAAAAATCAAGTGATTCATCTGAGG
** * * *
42560804 GTAATGTAGCCAAGGAGGAATAGAAAGAAGACAAAGTAAGAGAGGAGGACGATGATGAGGCTAAA
131 ACAACGTAGCCAAGGAGGAATAGAAAGAAGACAAAGCAAGAGAGGAGGACGATGACGAGGCTAAA
* * * * *
42560869 GAAGATGACGACTTCAAGCCCTATCATGATTATATATAAGATGTGTTTGAGCTTGCACAACCATC
196 GAAGATGACAACTTCAAGCCCTATCACGATGATATATAAGATGTGTTCGAGCTCGCACAACCATC
** * * *
42560934 CACGGGGGCCCTTGTCATTCGTAAACTGAGCGATCGACTCAAACTGTCTTACAAAAGGTCGATCG
261 CACGGGGGCCCTCATCATCCGTAAACTGAGCGACCGACTCAAACTATCTTACAAAAGGTCGATCG
* **
42560999 TCAAGGGAAAAGTCAAAGGAATAACAAGATCGAGTGAGAGTCCTGGGGATGCTCAAGGGCAAAGT
326 TCAAGGGAAAAGTCAAAGAAATAACAAGATCGAGTGAGAGTCCCAGGGATGCTCAAGGGCAAAGT
42561064 T
391 T
* *
42561065 AAAACAGGTAACAT-CATGCCTAGTTACCCTTTTGCTCGGATTCGC-T-GATGTTGGGGTGTGAC
1 AAAACAGGTAACATGCATGCCTAGTTACCCTTTTCCTCAGA-TC-CATCGATGTTGGGGTGTGAC
* * * **
42561127 ACATTTATGGCGAGTCAGGGGGCAGAAAGCATACAATGGCCTGACAAATTGAGTGATTCATCTGA
64 ACATTTATGGCGAGTCAGGGGGCAGAAAGCATACAATGACCTAAAAAATCAAGTGATTCATCTGA
* * * ** * *
42561192 GGACAACGTATCCTAGGAGGAATAGAAAGAATATGAAGCAGGAGAGGAGGATGATGACGAGGCT-
129 GGACAACGTAGCCAAGGAGGAATAGAAAGAAGACAAAGCAAGAGAGGAGGACGATGACGAGGCTA
* ** * * *
42561256 ACGAAGGATGACAACTTTGAGCCCTATCACGATGATCTATAAGATGTGTTCGTGCTCGTACAACC
194 AAGAA-GATGACAACTTCAAGCCCTATCACGATGATATATAAGATGTGTTCGAGCTCGCACAACC
* *
42561321 ATCCACGGGGG-CCTCCATCATCCGTAAACTGAGCGACCGACTCAGATTATCTTACAAAAGGTCG
258 ATCCACGGGGGCCCT-CATCATCCGTAAACTGAGCGACCGACTCAAACTATCTTACAAAAGGTCG
*
42561385 ATCGTCAAGGGAAAAGTCAAAGAAATAGCAAGATCGAGTGAGAGTCCCAGGGATGCTCA
322 ATCGTCAAGGGAAAAGTCAAAGAAATAACAAGATCGAGTGAGAGTCCCAGGGATGCTCA
42561444 GGATTAGTTA
Statistics
Matches: 331, Mismatches: 44, Indels: 9
0.86 0.11 0.02
Matches are distributed among these distances:
389 7 0.02
390 307 0.93
391 16 0.05
392 1 0.00
ACGTcount: A:0.33, C:0.19, G:0.26, T:0.22
Consensus pattern (391 bp):
AAAACAGGTAACATGCATGCCTAGTTACCCTTTTCCTCAGATCCATCGATGTTGGGGTGTGACAC
ATTTATGGCGAGTCAGGGGGCAGAAAGCATACAATGACCTAAAAAATCAAGTGATTCATCTGAGG
ACAACGTAGCCAAGGAGGAATAGAAAGAAGACAAAGCAAGAGAGGAGGACGATGACGAGGCTAAA
GAAGATGACAACTTCAAGCCCTATCACGATGATATATAAGATGTGTTCGAGCTCGCACAACCATC
CACGGGGGCCCTCATCATCCGTAAACTGAGCGACCGACTCAAACTATCTTACAAAAGGTCGATCG
TCAAGGGAAAAGTCAAAGAAATAACAAGATCGAGTGAGAGTCCCAGGGATGCTCAAGGGCAAAGT
T
Found at i:42563680 original size:9 final size:9
Alignment explanation
Indices: 42563666--42563695 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
42563656 TGTACACAGG
*
42563666 TTTAATTTA
1 TTTAATTAA
42563675 TTTAATTAA
1 TTTAATTAA
42563684 TTTAATTAA
1 TTTAATTAA
42563693 TTT
1 TTT
42563696 TGATATTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (9 bp):
TTTAATTAA
Found at i:42563712 original size:9 final size:9
Alignment explanation
Indices: 42563666--42563716 Score: 50
Period size: 9 Copynumber: 5.3 Consensus size: 9
42563656 TGTACACAGG
42563666 TTTAATT-T
1 TTTAATTAT
*
42563674 ATTTAATTAA
1 -TTTAATTAT
42563684 TTTAATTAAT
1 TTTAATT-AT
42563694 TTTGATATTAT
1 TTT-A-ATTAT
42563705 TTTAATTAT
1 TTTAATTAT
42563714 TTT
1 TTT
42563717 TTTAACTTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
9 22 0.61
10 5 0.14
11 6 0.17
12 3 0.08
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (9 bp):
TTTAATTAT
Found at i:42563735 original size:15 final size:14
Alignment explanation
Indices: 42563698--42563749 Score: 63
Period size: 15 Copynumber: 3.6 Consensus size: 14
42563688 ATTAATTTTG
42563698 ATATTATTTTAA-TT
1 ATATT-TTTTAACTT
42563712 AT-TTTTTTAACTT
1 ATATTTTTTAACTT
42563725 ATATATTTTTAACTGT
1 ATAT-TTTTTAACT-T
42563741 ATATTTTTT
1 ATATTTTTT
42563750 TGTTATTTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
12 6 0.18
13 6 0.18
14 3 0.09
15 14 0.41
16 5 0.15
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.65
Consensus pattern (14 bp):
ATATTTTTTAACTT
Found at i:42576465 original size:17 final size:18
Alignment explanation
Indices: 42576443--42576476 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
42576433 TCACTATTGT
42576443 TATTATAGATAG-AAAAC
1 TATTATAGATAGTAAAAC
*
42576460 TATTATTGATAGTAAAA
1 TATTATAGATAGTAAAA
42576477 ATAAATATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.50, C:0.03, G:0.12, T:0.35
Consensus pattern (18 bp):
TATTATAGATAGTAAAAC
Found at i:42596526 original size:11 final size:11
Alignment explanation
Indices: 42596512--42596552 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
42596502 TGTTTTCTCT
42596512 CTATTTTGCTA
1 CTATTTTGCTA
*
42596523 CTATTTTACTA
1 CTATTTTGCTA
* *
42596534 TTATGTTGCTA
1 CTATTTTGCTA
42596545 CTATTTTG
1 CTATTTTG
42596553 TTGTTATTGT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.20, C:0.15, G:0.10, T:0.56
Consensus pattern (11 bp):
CTATTTTGCTA
Found at i:42597004 original size:27 final size:27
Alignment explanation
Indices: 42596966--42597020 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
42596956 TCATTCAATC
* *
42596966 ATTATACATTAAAACATAAAATTTAAA
1 ATTACACATTAAAACACAAAATTTAAA
* *
42596993 ATTACACATTAAAATACAAATTTTAAA
1 ATTACACATTAAAACACAAAATTTAAA
42597020 A
1 A
42597021 ATTTATAAAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.58, C:0.09, G:0.00, T:0.33
Consensus pattern (27 bp):
ATTACACATTAAAACACAAAATTTAAA
Found at i:42597962 original size:7 final size:7
Alignment explanation
Indices: 42597950--42597974 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
42597940 TGGTCTCTTC
42597950 TTTTTCT
1 TTTTTCT
42597957 TTTTTCT
1 TTTTTCT
42597964 TTTTTCT
1 TTTTTCT
42597971 TTTT
1 TTTT
42597975 AAGAATGACG
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:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTCT
Found at i:42598629 original size:126 final size:126
Alignment explanation
Indices: 42598440--42598772 Score: 567
Period size: 126 Copynumber: 2.6 Consensus size: 126
42598430 TTTTAAGTCG
* * *
42598440 CGCCCACGTGTACGCGCTTTTGCTACAGTAGGTCCTGGAAAAATAATTTCGAGTTGACGTTTCTG
1 CGCCCTCGTGGACGCGCTTTTGCTACAATAGGTCCTGGAAAAATAATTTCGAGTTGACGTTTCTG
*
42598505 AGCAAATAGTATAAAACAACGCTGCAAGCAGGATGCTATTTGAGAAGAATTTGTGAAATTA
66 AGCAAATAGTATAAAACAACGCTGCAAGCAGGATGCTATTTGAGAAGAATTTGTGAAATCA
*
42598566 CGCCCTCGTGGACACGCTTTTGCTACAATAGGTCCTGGAAAAATAATTTCGAGTTGACGTTTCTG
1 CGCCCTCGTGGACGCGCTTTTGCTACAATAGGTCCTGGAAAAATAATTTCGAGTTGACGTTTCTG
* * *
42598631 AGTAAATAGTATAAAACAACGCTGCAAGCAGGATGGTATTTGAGAAGAATTTGTGAAATCG
66 AGCAAATAGTATAAAACAACGCTGCAAGCAGGATGCTATTTGAGAAGAATTTGTGAAATCA
* *
42598692 CGCCCTCGTGGACGCGCTTTTGCTACAATAGGTCCTGGAAAAATAATTTTGACTTGACGTTTCTG
1 CGCCCTCGTGGACGCGCTTTTGCTACAATAGGTCCTGGAAAAATAATTTCGAGTTGACGTTTCTG
*
42598757 AGCAAACAGTATAAAA
66 AGCAAATAGTATAAAA
42598773 TCGCTTCTAA
Statistics
Matches: 194, Mismatches: 13, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
126 194 1.00
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.28
Consensus pattern (126 bp):
CGCCCTCGTGGACGCGCTTTTGCTACAATAGGTCCTGGAAAAATAATTTCGAGTTGACGTTTCTG
AGCAAATAGTATAAAACAACGCTGCAAGCAGGATGCTATTTGAGAAGAATTTGTGAAATCA
Found at i:42599466 original size:22 final size:22
Alignment explanation
Indices: 42599372--42599803 Score: 333
Period size: 22 Copynumber: 19.0 Consensus size: 22
42599362 TCAAATTATA
*
42599372 TTTAAGTTAAGGG-TAAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
*
42599393 TTTAAGTTAAGTG-TTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* * *
42599414 TTTTATTTAAGGG-TTACGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* *
42599435 TTAAAGTTAAGGGTTTAGGTTT
1 TTTAAGTTAAGGGTTTAGGGTT
* **
42599457 TTTAATTTAAGGG-TTACAGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* *
42599478 TTAAAGTAAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
*
42599500 TTTAAGTTAAGGG-TTACGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* *
42599521 TTAAAGTTAAGGG-TTAGGATT
1 TTTAAGTTAAGGGTTTAGGGTT
* *
42599542 TTTAGGTTAAGGGGTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
42599564 TTTAAGTTAAGGGTTAGGGTTAGGGTT
1 TTTAAGTTAAGGG-T----TTAGGGTT
* * *
42599591 TTTAGGTTAAGGGGTTAAGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* *
42599613 TTTAGGTTAAGGGGTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
42599635 TTTAAGTTAAGGGTTAGGGTTAGGGTT
1 TTTAAGTTAAGGG-T----TTAGGGTT
* * *
42599662 TTTAGGTTAAGGGGTTAGGGGT
1 TTTAAGTTAAGGGTTTAGGGTT
* *
42599684 TTTAAGTTAACGGTTAGGGTTGGGGTT
1 TTTAAGTTAA--G---GGTTTAGGGTT
*
42599711 TTTAGGTTAA-GGTGTTAGGGTT
1 TTTAAGTTAAGGGT-TTAGGGTT
42599733 TTTAAGTTAAGGGTTAGGGTTAGGGTT
1 TTTAAGTTAAGGG-T----TTAGGGTT
* *
42599760 TTTAGGTTAA-GGTGTTATGGTT
1 TTTAAGTTAAGGGT-TTAGGGTT
42599782 TTTAAGTTAAGGG-TTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
42599803 T
1 T
42599804 GCCAATTAAA
Statistics
Matches: 334, Mismatches: 52, Indels: 50
0.77 0.12 0.11
Matches are distributed among these distances:
21 107 0.32
22 142 0.43
23 4 0.01
24 2 0.01
25 1 0.00
26 2 0.01
27 76 0.23
ACGTcount: A:0.23, C:0.01, G:0.34, T:0.43
Consensus pattern (22 bp):
TTTAAGTTAAGGGTTTAGGGTT
Found at i:42599467 original size:43 final size:43
Alignment explanation
Indices: 42599372--42599655 Score: 311
Period size: 43 Copynumber: 6.5 Consensus size: 43
42599362 TCAAATTATA
* * * *
42599372 TTTAAGTTAAGGGTAAGGGTTTTTAAGTTAAGTG-TTAGGGTT
1 TTTAAGTTAAGGGTTACGGTTTTAAAGTTAAGGGTTTAGGGTT
* * *
42599414 TTTTATTTAAGGGTTACGGTTTTAAAGTTAAGGGTTTAGGTTT
1 TTTAAGTTAAGGGTTACGGTTTTAAAGTTAAGGGTTTAGGGTT
* * *
42599457 TTTAATTTAAGGGTTACAGTTTTAAAGTAAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTACGGTTTTAAAGTTAAGGGTTTAGGGTT
*
42599500 TTTAAGTTAAGGGTTACGGTTTTAAAGTTAAGGG-TTAGGATT
1 TTTAAGTTAAGGGTTACGGTTTTAAAGTTAAGGGTTTAGGGTT
* * *
42599542 TTTAGGTTAAGGGGTTAGGGTTTTTAAGTTAAGGGTTAGGGTTAGGGTT
1 TTTAAGTTAA-GGGTTACGGTTTTAAAGTTAAGGG-T----TTAGGGTT
* * * * *
42599591 TTTAGGTTAAGGGGTTAAGGTTTTTAGGTTAAGGGGTTAGGGTT
1 TTTAAGTTAA-GGGTTACGGTTTTAAAGTTAAGGGTTTAGGGTT
*
42599635 TTTAAGTTAAGGGTTAGGGTT
1 TTTAAGTTAAGGGTTACGGTT
42599656 AGGGTTTTTA
Statistics
Matches: 210, Mismatches: 24, Indels: 15
0.84 0.10 0.06
Matches are distributed among these distances:
42 44 0.21
43 109 0.52
44 17 0.08
49 40 0.19
ACGTcount: A:0.25, C:0.01, G:0.32, T:0.43
Consensus pattern (43 bp):
TTTAAGTTAAGGGTTACGGTTTTAAAGTTAAGGGTTTAGGGTT
Found at i:42599583 original size:49 final size:50
Alignment explanation
Indices: 42599530--42599634 Score: 176
Period size: 49 Copynumber: 2.1 Consensus size: 50
42599520 TTTAAAGTTA
*
42599530 AGGGTTAGGATTTTTAGGTTAAGGGGTTAGGGTTTTTAAGTTAA-GGGTT
1 AGGGTTAGGATTTTTAGGTTAAGGGGTTAAGGTTTTTAAGTTAAGGGGTT
* *
42599579 AGGGTTAGGGTTTTTAGGTTAAGGGGTTAAGGTTTTTAGGTTAAGGGGTT
1 AGGGTTAGGATTTTTAGGTTAAGGGGTTAAGGTTTTTAAGTTAAGGGGTT
42599629 AGGGTT
1 AGGGTT
42599635 TTTAAGTTAA
Statistics
Matches: 52, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
49 41 0.79
50 11 0.21
ACGTcount: A:0.21, C:0.00, G:0.39, T:0.40
Consensus pattern (50 bp):
AGGGTTAGGATTTTTAGGTTAAGGGGTTAAGGTTTTTAAGTTAAGGGGTT
Found at i:42599615 original size:71 final size:71
Alignment explanation
Indices: 42599509--42599802 Score: 332
Period size: 71 Copynumber: 4.1 Consensus size: 71
42599499 TTTTAAGTTA
* *
42599509 AGGGTTACGGTTTTAAAGTTAA-GGGTT-AGGATTTTTAGGTTAAGGGGTTAGGGTTTTTAAGTT
1 AGGGTTAGGGTTTTTAAGTTAAGGGGTTAAGG-TTTTTAGGTTAAGGGGTTAGGGTTTTTAAGTT
42599572 AAGGGTT
65 AAGGGTT
*
42599579 AGGGTTAGGGTTTTTAGGTTAAGGGGTTAAGGTTTTTAGGTTAAGGGGTTAGGGTTTTTAAGTTA
1 AGGGTTAGGGTTTTTAAGTTAAGGGGTTAAGGTTTTTAGGTTAAGGGGTTAGGGTTTTTAAGTTA
42599644 AGGGTT
66 AGGGTT
* * * * *
42599650 AGGGTTAGGGTTTTTAGGTTAAGGGGTTAGGGGTTTTAAGTTAACGGTTAGGGTTGGGGTTTTTA
1 AGGGTTAGGGTTTTTAAGTTAAGGGGTTAAGGTTTTTAGGTTAA--G---GGGTTAGGGTTTTTA
*
42599715 GGTTAA-GG-T
61 AGTTAAGGGTT
* * *
42599724 ---GTTAGGGTTTTTAAGTTAAGGGTTAGGGTTAGGGTTTTTAGGTTAAGGTGTTATGGTTTTTA
1 AGGGTTAGGGTTTTTAAGTTAA--G---GGGTTAAGGTTTTTAGGTTAAGGGGTTAGGGTTTTTA
42599786 AGTTAAGGGTT
61 AGTTAAGGGTT
42599797 AGGGTT
1 AGGGTT
42599803 TGCCAATTAA
Statistics
Matches: 192, Mismatches: 15, Indels: 28
0.82 0.06 0.12
Matches are distributed among these distances:
70 19 0.10
71 120 0.62
72 5 0.03
73 3 0.02
74 2 0.01
75 2 0.01
76 41 0.21
ACGTcount: A:0.21, C:0.01, G:0.37, T:0.41
Consensus pattern (71 bp):
AGGGTTAGGGTTTTTAAGTTAAGGGGTTAAGGTTTTTAGGTTAAGGGGTTAGGGTTTTTAAGTTA
AGGGTT
Found at i:42599655 original size:49 final size:49
Alignment explanation
Indices: 42599602--42599802 Score: 339
Period size: 49 Copynumber: 4.1 Consensus size: 49
42599592 TTAGGTTAAG
*
42599602 GGGTTAAGGTTTTTAGGTTAAGGGGTTAGGGTTTTTAAGTTAAGGGTTA
1 GGGTTAGGGTTTTTAGGTTAAGGGGTTAGGGTTTTTAAGTTAAGGGTTA
* *
42599651 GGGTTAGGGTTTTTAGGTTAAGGGGTTAGGGGTTTTAAGTTAACGGTTA
1 GGGTTAGGGTTTTTAGGTTAAGGGGTTAGGGTTTTTAAGTTAAGGGTTA
* *
42599700 GGGTTGGGGTTTTTAGGTTAAGGTGTTAGGGTTTTTAAGTTAAGGGTTA
1 GGGTTAGGGTTTTTAGGTTAAGGGGTTAGGGTTTTTAAGTTAAGGGTTA
* *
42599749 GGGTTAGGGTTTTTAGGTTAAGGTGTTATGGTTTTTAAGTTAAGGGTTA
1 GGGTTAGGGTTTTTAGGTTAAGGGGTTAGGGTTTTTAAGTTAAGGGTTA
42599798 GGGTT
1 GGGTT
42599803 TGCCAATTAA
Statistics
Matches: 143, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 143 1.00
ACGTcount: A:0.20, C:0.00, G:0.38, T:0.42
Consensus pattern (49 bp):
GGGTTAGGGTTTTTAGGTTAAGGGGTTAGGGTTTTTAAGTTAAGGGTTA
Found at i:42600366 original size:18 final size:18
Alignment explanation
Indices: 42600340--42600382 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
42600330 GACTCGGAAA
* *
42600340 AGGAAACATATAAGGGTT
1 AGGAAACATAAAAGGGCT
*
42600358 AGGATACATAAAAGGGCT
1 AGGAAACATAAAAGGGCT
42600376 AGGAAAC
1 AGGAAAC
42600383 GCACCTGTCA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.47, C:0.09, G:0.28, T:0.16
Consensus pattern (18 bp):
AGGAAACATAAAAGGGCT
Found at i:42601636 original size:328 final size:328
Alignment explanation
Indices: 42601039--42601695 Score: 1305
Period size: 328 Copynumber: 2.0 Consensus size: 328
42601029 TAATACTAAA
42601039 TACTAAATACCAATCGACTAGCGAATGATGGAAATATCAATTTTATTTAATACTTACATGTGCTT
1 TACTAAATACCAATCGACTAGCGAATGATGGAAATATCAATTTTATTTAATACTTACATGTGCTT
42601104 CCGACTGTTGGTCTAATAGAAGTCGTATATCTTCAAGAGAGGTAGGTAATCGAGTATGACTTGCC
66 CCGACTGTTGGTCTAATAGAAGTCGTATATCTTCAAGAGAGGTAGGTAATCGAGTATGACTTGCC
42601169 GGATGGTTCCACCTAATTAAATAAATTTTTAGCATACTTTTATTTCTAAAAATCTACATAATAAT
131 GGATGGTTCCACCTAATTAAATAAATTTTTAGCATACTTTTATTTCTAAAAATCTACATAATAAT
42601234 TGTAAAATATAATATAAAATTTACCTCGTTATGAGTGGAAATGTATATGGGTGGTCCACTCGAGG
196 TGTAAAATATAATATAAAATTTACCTCGTTATGAGTGGAAATGTATATGGGTGGTCCACTCGAGG
42601299 ACGTAGAAATGGAAAGCGAAACTGTGCCCATGACTGCAGTAGTGACAGGCAACCTTCGATTTTTG
261 ACGTAGAAATGGAAAGCGAAACTGTGCCCATGACTGCAGTAGTGACAGGCAACCTTCGATTTTTG
42601364 CTT
326 CTT
*
42601367 TACTAAATACCAATCTACTAGCGAATGATGGAAATATCAATTTTATTTAATACTTACATGTGCTT
1 TACTAAATACCAATCGACTAGCGAATGATGGAAATATCAATTTTATTTAATACTTACATGTGCTT
42601432 CCGACTGTTGGTCTAATAGAAGTCGTATATCTTCAAGAGAGGTAGGTAATCGAGTATGACTTGCC
66 CCGACTGTTGGTCTAATAGAAGTCGTATATCTTCAAGAGAGGTAGGTAATCGAGTATGACTTGCC
42601497 GGATGGTTCCACCTAATTAAATAAATTTTTAGCATACTTTTATTTCTAAAAATCTACATAATAAT
131 GGATGGTTCCACCTAATTAAATAAATTTTTAGCATACTTTTATTTCTAAAAATCTACATAATAAT
42601562 TGTAAAATATAATATAAAATTTACCTCGTTATGAGTGGAAATGTATATGGGTGGTCCACTCGAGG
196 TGTAAAATATAATATAAAATTTACCTCGTTATGAGTGGAAATGTATATGGGTGGTCCACTCGAGG
42601627 ACGTAGAAATGGAAAGCGAAACTGTGCCCATGACTGCAGTAGTGACAGGCAACCTTCGATTTTTG
261 ACGTAGAAATGGAAAGCGAAACTGTGCCCATGACTGCAGTAGTGACAGGCAACCTTCGATTTTTG
42601692 CTT
326 CTT
42601695 T
1 T
42601696 CCTCGGTCGC
Statistics
Matches: 328, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
328 328 1.00
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.33
Consensus pattern (328 bp):
TACTAAATACCAATCGACTAGCGAATGATGGAAATATCAATTTTATTTAATACTTACATGTGCTT
CCGACTGTTGGTCTAATAGAAGTCGTATATCTTCAAGAGAGGTAGGTAATCGAGTATGACTTGCC
GGATGGTTCCACCTAATTAAATAAATTTTTAGCATACTTTTATTTCTAAAAATCTACATAATAAT
TGTAAAATATAATATAAAATTTACCTCGTTATGAGTGGAAATGTATATGGGTGGTCCACTCGAGG
ACGTAGAAATGGAAAGCGAAACTGTGCCCATGACTGCAGTAGTGACAGGCAACCTTCGATTTTTG
CTT
Found at i:42602584 original size:11 final size:11
Alignment explanation
Indices: 42602570--42602635 Score: 66
Period size: 11 Copynumber: 5.9 Consensus size: 11
42602560 TTAAATATGG
42602570 ATTTGAGAGAA
1 ATTTGAGAGAA
*
42602581 ATTTG-GAAGGA
1 ATTTGAG-AGAA
42602592 ATTTGAGAGCAA
1 ATTTGAGAG-AA
42602604 A-TTGAGAGGAA
1 ATTTGAGA-GAA
42602615 A-TTGAGAGAAA
1 ATTTGAGAG-AA
42602626 ATTTGAGAGA
1 ATTTGAGAGA
42602636 GGATTAGTTT
Statistics
Matches: 47, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
10 2 0.04
11 34 0.72
12 11 0.23
ACGTcount: A:0.44, C:0.02, G:0.30, T:0.24
Consensus pattern (11 bp):
ATTTGAGAGAA
Found at i:42602592 original size:51 final size:51
Alignment explanation
Indices: 42602511--42602610 Score: 148
Period size: 51 Copynumber: 2.0 Consensus size: 51
42602501 AAATATTTAA
42602511 AAATAGGGATTTAAGAGAAATTTAAGAGGAACTTGAGAGCAAATTGAGATT
1 AAATAGGGATTTAAGAGAAATTTAAGAGGAACTTGAGAGCAAATTGAGATT
* * * *
42602562 AAATATGGATTTGAGAGAAATTT-GGAAGGAATTTGAGAGCAAATTGAGA
1 AAATAGGGATTTAAGAGAAATTTAAG-AGGAACTTGAGAGCAAATTGAGA
42602611 GGAAATTGAG
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
50 1 0.02
51 43 0.98
ACGTcount: A:0.44, C:0.03, G:0.27, T:0.26
Consensus pattern (51 bp):
AAATAGGGATTTAAGAGAAATTTAAGAGGAACTTGAGAGCAAATTGAGATT
Found at i:42602595 original size:22 final size:24
Alignment explanation
Indices: 42602570--42602638 Score: 83
Period size: 22 Copynumber: 3.0 Consensus size: 24
42602560 TTAAATATGG
42602570 ATTTGAGAG-AAATTTGGA-AGGA
1 ATTTGAGAGAAAATTTGGAGAGGA
*
42602592 ATTTGAGAGCAAA-TT-GAGAGGA
1 ATTTGAGAGAAAATTTGGAGAGGA
*
42602614 AATTGAGAGAAAATTTGAGAGAGGA
1 ATTTGAGAGAAAATTTG-GAGAGGA
42602639 TTAGTTTGTG
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
21 2 0.05
22 26 0.65
23 5 0.12
25 7 0.17
ACGTcount: A:0.43, C:0.01, G:0.32, T:0.23
Consensus pattern (24 bp):
ATTTGAGAGAAAATTTGGAGAGGA
Found at i:42604152 original size:25 final size:24
Alignment explanation
Indices: 42604116--42604162 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 24
42604106 CACAATTAAA
*
42604116 TAATCAATATTTATTTAAATAAAAT
1 TAATCAATATTTATGT-AATAAAAT
42604141 TAAT-AATAATTTATGTAATAAA
1 TAATCAAT-ATTTATGTAATAAA
42604163 TAAATTGATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 9 0.45
25 11 0.55
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (24 bp):
TAATCAATATTTATGTAATAAAAT
Found at i:42606387 original size:14 final size:14
Alignment explanation
Indices: 42606368--42606394 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
42606358 GTGGTCTAGT
42606368 TGAACTGAACCGAG
1 TGAACTGAACCGAG
42606382 TGAACTGAACCGA
1 TGAACTGAACCGA
42606395 CCAAGAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.22, G:0.26, T:0.15
Consensus pattern (14 bp):
TGAACTGAACCGAG
Found at i:42617663 original size:16 final size:16
Alignment explanation
Indices: 42617633--42617677 Score: 67
Period size: 15 Copynumber: 2.9 Consensus size: 16
42617623 ATTGGATTGA
42617633 GAAAA-TTATTTAATT
1 GAAAATTTATTTAATT
*
42617648 GAAAATTTAATTAATT
1 GAAAATTTATTTAATT
42617664 -AAAATTTATTTAAT
1 GAAAATTTATTTAAT
42617678 AAGTAATATT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
15 18 0.67
16 9 0.33
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (16 bp):
GAAAATTTATTTAATT
Found at i:42617690 original size:18 final size:19
Alignment explanation
Indices: 42617652--42617692 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
42617642 TTAATTGAAA
*
42617652 ATTTAATTAATTAAAATTT
1 ATTTAATTAAGTAAAATTT
*
42617671 ATTTAA-TAAGTAATATTT
1 ATTTAATTAAGTAAAATTT
42617689 ATTT
1 ATTT
42617693 TGGGAAATTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (19 bp):
ATTTAATTAAGTAAAATTT
Found at i:42621568 original size:11 final size:11
Alignment explanation
Indices: 42621552--42621577 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
42621542 CACAAGAGTC
42621552 GTTCTTTTAGA
1 GTTCTTTTAGA
42621563 GTTCTTTTAGA
1 GTTCTTTTAGA
42621574 GTTC
1 GTTC
42621578 GTGACAAAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.15, C:0.12, G:0.19, T:0.54
Consensus pattern (11 bp):
GTTCTTTTAGA
Found at i:42621659 original size:14 final size:14
Alignment explanation
Indices: 42621640--42621671 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
42621630 TTACCGCAAA
42621640 AGTTATTCTTTCAG
1 AGTTATTCTTTCAG
42621654 AGTTATTCTTTCAG
1 AGTTATTCTTTCAG
42621668 AGTT
1 AGTT
42621672 CGCCACAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.22, C:0.12, G:0.16, T:0.50
Consensus pattern (14 bp):
AGTTATTCTTTCAG
Found at i:42629184 original size:36 final size:36
Alignment explanation
Indices: 42629136--42629206 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 36
42629126 ATCAAAGGCT
*
42629136 ATAATTAAAAGCTGTATACAATTAGAACTCTAAGAC
1 ATAATTAAAAGCTGTATACAATTAAAACTCTAAGAC
*
42629172 ATAATTAGAAGCTGTATACAATTAAAACTCTAAGA
1 ATAATTAAAAGCTGTATACAATTAAAACTCTAAGA
42629207 TTAAATAATC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.48, C:0.13, G:0.11, T:0.28
Consensus pattern (36 bp):
ATAATTAAAAGCTGTATACAATTAAAACTCTAAGAC
Found at i:42633702 original size:36 final size:36
Alignment explanation
Indices: 42633654--42633722 Score: 120
Period size: 36 Copynumber: 1.9 Consensus size: 36
42633644 ATCAAAGGCT
*
42633654 ATAATTAAAAGCTGTATACAATTAGAACTCTAAGAC
1 ATAATTAAAAGCTGTATACAATTAAAACTCTAAGAC
*
42633690 ATAATTAGAAGCTGTATACAATTAAAACTCTAA
1 ATAATTAAAAGCTGTATACAATTAAAACTCTAA
42633723 TATTAAATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.48, C:0.13, G:0.10, T:0.29
Consensus pattern (36 bp):
ATAATTAAAAGCTGTATACAATTAAAACTCTAAGAC
Found at i:42638153 original size:3 final size:3
Alignment explanation
Indices: 42638145--42638169 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
42638135 ATTAATCTCC
42638145 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
42638170 GGATTTTAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:42639629 original size:16 final size:16
Alignment explanation
Indices: 42639608--42639639 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
42639598 TTTTCTCTGC
*
42639608 TGTTTTTCCTCCTCTA
1 TGTTTTTCCTCATCTA
42639624 TGTTTTTCCTCATCTA
1 TGTTTTTCCTCATCTA
42639640 CTTTCTTGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.09, C:0.28, G:0.06, T:0.56
Consensus pattern (16 bp):
TGTTTTTCCTCATCTA
Found at i:42646301 original size:14 final size:14
Alignment explanation
Indices: 42646278--42646317 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
42646268 ACAGAAAAGT
*
42646278 AAAACATTTTCCAG
1 AAAACATTTTACAG
* *
42646292 AAATCATTTTACGG
1 AAAACATTTTACAG
42646306 AAAACATTTTAC
1 AAAACATTTTAC
42646318 TGCCAATCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:42646303 original size:34 final size:35
Alignment explanation
Indices: 42646243--42646309 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
42646233 CAAACACCAG
* *
42646243 AAAATATTTTCCAGTAAGTCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
42646278 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
42646310 CATTTTACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 16 0.55
35 13 0.45
ACGTcount: A:0.45, C:0.13, G:0.10, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:42646665 original size:27 final size:29
Alignment explanation
Indices: 42646635--42646693 Score: 95
Period size: 27 Copynumber: 2.1 Consensus size: 29
42646625 GTGTCCTGCA
42646635 GTTAGGGTTTTGG-GTTATT-GGTTTAGG
1 GTTAGGGTTTTGGTGTTATTAGGTTTAGG
*
42646662 GTTAGGGTTTTGGTGTTTTTAGGTTTAGG
1 GTTAGGGTTTTGGTGTTATTAGGTTTAGG
42646691 GTT
1 GTT
42646694 TTAGAGAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
27 13 0.45
28 5 0.17
29 11 0.38
ACGTcount: A:0.10, C:0.00, G:0.39, T:0.51
Consensus pattern (29 bp):
GTTAGGGTTTTGGTGTTATTAGGTTTAGG
Found at i:42646830 original size:95 final size:95
Alignment explanation
Indices: 42646751--42647023 Score: 363
Period size: 94 Copynumber: 2.9 Consensus size: 95
42646741 GTTTGCCAAT
* * * *
42646751 TAAATTAATTATAAATTTTTCAAAATT-GAATTA-GGTTTCGTGTTTATTGTTTTTTAAGAAAAA
1 TAAATTAATTATAAATTTTTAAAAATTAG-ATTAGGGTTTAGTGTTTA-GGGTTTTTAAGAAAAA
* *
42646814 AGTAATTAAATTAGGGTTTAGGGTTACTTGAG
64 ACTAAATAAATTAGGGTTTAGGGTTACTTGAG
* * * * * *
42646846 TAATTTAATTA-AATTTTTTAAAAATTAGATTAGGGTTTAGAGTTAAGGGTTTTTATGAAAAAAT
1 TAAATTAATTATAAATTTTTAAAAATTAGATTAGGGTTTAGTGTTTAGGGTTTTTAAGAAAAAAC
*
42646910 TAAATAAATTAGGGTTCAGGGTTACTTGAG
66 TAAATAAATTAGGGTTTAGGGTTACTTGAG
*
42646940 TAAATTAATTATAAATTTTTAAAAAATTAGATTAGGGTTTAGTGTTTAGGGTTTTTAAGTAAAAA
1 TAAATTAATTATAAATTTTT-AAAAATTAGATTAGGGTTTAGTGTTTAGGGTTTTTAAGAAAAAA
42647005 CTCAAATAAATTAGGGTTT
65 CT-AAATAAATTAGGGTTT
42647024 GAGGTTTAGG
Statistics
Matches: 153, Mismatches: 20, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
94 69 0.45
95 28 0.18
96 41 0.27
97 15 0.10
ACGTcount: A:0.38, C:0.03, G:0.17, T:0.42
Consensus pattern (95 bp):
TAAATTAATTATAAATTTTTAAAAATTAGATTAGGGTTTAGTGTTTAGGGTTTTTAAGAAAAAAC
TAAATAAATTAGGGTTTAGGGTTACTTGAG
Found at i:42650231 original size:13 final size:13
Alignment explanation
Indices: 42650212--42650245 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
42650202 AATTTTTACG
42650212 ATTTAAAAA-AAA
1 ATTTAAAAATAAA
42650224 ATTTTAAAAATAAA
1 A-TTTAAAAATAAA
42650238 ATTTAAAA
1 ATTTAAAA
42650246 TTTTTTTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 1 0.05
13 15 0.75
14 4 0.20
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
ATTTAAAAATAAA
Found at i:42667191 original size:69 final size:68
Alignment explanation
Indices: 42667117--42667367 Score: 243
Period size: 69 Copynumber: 3.6 Consensus size: 68
42667107 TTCACAAGTA
* ** * *
42667117 AAGAGCCGCAACCTCAAAAATAGTTAATAAGAGCAAAACTCCCAACTGTCATATTAAAGCTCGCA
1 AAGAGCCGCAACCTCAAAAACAGTTAGCAAGAGCAAAGCTCCCAACTGTCATATT-AAGATCGCA
42667182 GGCG
65 GGCG
* * * * * *
42667186 AAGAGCCGCAACCTCCAACACAGTTAGCGAGAGCAAAGCTCCCAACTATCATATTAAGAATTGTA
1 AAGAGCCGCAACCTCAAAAACAGTTAGCAAGAGCAAAGCTCCCAACTGTCATATTAAG-ATCGCA
*
42667251 GGTG
65 GGCG
* * * * * *
42667255 AAAAGCCGCAGCCCCTAAAAA-AGTTAGCAAGAGCAAAGCTCCCAACTGTCAAATTTAGGGTCGC
1 AAGAGCCGCAACCTC-AAAAACAGTTAGCAAGAGCAAAGCTCCCAACTGTCATA-TTAAGATCGC
*
42667319 AAGCG
64 AGGCG
* * * **
42667324 AAGAGCCGTAACCTCCAAAACAATTAGTGAGAGCAAAGCTCCCA
1 AAGAGCCGCAACCTCAAAAACAGTTAGCAAGAGCAAAGCTCCCA
42667368 GCCTTACCAT
Statistics
Matches: 144, Mismatches: 34, Indels: 8
0.77 0.18 0.04
Matches are distributed among these distances:
68 7 0.05
69 130 0.90
70 7 0.05
ACGTcount: A:0.39, C:0.25, G:0.20, T:0.16
Consensus pattern (68 bp):
AAGAGCCGCAACCTCAAAAACAGTTAGCAAGAGCAAAGCTCCCAACTGTCATATTAAGATCGCAG
GCG
Found at i:42667559 original size:57 final size:57
Alignment explanation
Indices: 42667404--42667583 Score: 202
Period size: 57 Copynumber: 3.1 Consensus size: 57
42667394 AATATAAAAC
** *
42667404 ATTTTCCAAGGATATAAAGTAGCTT-GAGGATTTACATTCCCAGCTTTATTATTTTAGAAA
1 ATTTTCCAAGGATA-AAAAAAG-TTCGA-GATTCACATTCCCAGC-TTATTATTTTAGAAA
* * *
42667464 ATTTTTCAAGGATAAAAAAAGTTCGCGTATTCATATTCCCAGCTTATTATTTTAGAAA
1 ATTTTCCAAGGATAAAAAAAGTTCGAG-ATTCACATTCCCAGCTTATTATTTTAGAAA
* * * *
42667522 ATTTTCCAAGGAT-AAAAAATTTTGTAGATTCACATTCCCAACTTATTATTTTACAAA
1 ATTTTCCAAGGATAAAAAAAGTTCG-AGATTCACATTCCCAGCTTATTATTTTAGAAA
42667579 ATTTT
1 ATTTT
42667584 GTAGATCCAC
Statistics
Matches: 104, Mismatches: 13, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
57 41 0.39
58 31 0.30
59 19 0.18
60 13 0.12
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.39
Consensus pattern (57 bp):
ATTTTCCAAGGATAAAAAAAGTTCGAGATTCACATTCCCAGCTTATTATTTTAGAAA
Found at i:42667595 original size:39 final size:39
Alignment explanation
Indices: 42667537--42667622 Score: 136
Period size: 39 Copynumber: 2.2 Consensus size: 39
42667527 CCAAGGATAA
*
42667537 AAAATTTTGTAGATTCACATTCCCAACTTATTATTTTAC
1 AAAATTTTGTAGATCCACATTCCCAACTTATTATTTTAC
* * *
42667576 AAAATTTTGTAGATCCACATTCTCAGCTTATTATTTTAG
1 AAAATTTTGTAGATCCACATTCCCAACTTATTATTTTAC
42667615 AAAATTTT
1 AAAATTTT
42667623 CTCAAGTACA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 43 1.00
ACGTcount: A:0.34, C:0.15, G:0.07, T:0.44
Consensus pattern (39 bp):
AAAATTTTGTAGATCCACATTCCCAACTTATTATTTTAC
Found at i:42672072 original size:80 final size:82
Alignment explanation
Indices: 42671964--42672131 Score: 225
Period size: 80 Copynumber: 2.1 Consensus size: 82
42671954 TGAGTTCCAA
* * * * *
42671964 AATATATATTTTTTAATTATATTTAAAGTTGA-TCTTATTTTTAAATTAATTTTTAAATATGATT
1 AATATATATTTTTTAATTATATTCAAAG-TGAGTATCATTTTTAAATTAAATTTTAAATATAATT
42672028 AAGT-GAATCCTATTTGT
65 AAGTGGAATCCTATTTGT
*
42672045 AATATATA-TTTTTAATTATATTCAAAGTGAGTATCATTTTTAAGTTAAATTTTAAATATAATTA
1 AATATATATTTTTTAATTATATTCAAAGTGAGTATCATTTTTAAATTAAATTTTAAATATAATTA
** *
42672109 AGTGGGGTCCTATTTTT
66 AGTGGAATCCTATTTGT
42672126 AATATA
1 AATATA
42672132 AATACATAAC
Statistics
Matches: 76, Mismatches: 9, Indels: 4
0.85 0.10 0.04
Matches are distributed among these distances:
79 3 0.04
80 49 0.64
81 24 0.32
ACGTcount: A:0.37, C:0.04, G:0.09, T:0.50
Consensus pattern (82 bp):
AATATATATTTTTTAATTATATTCAAAGTGAGTATCATTTTTAAATTAAATTTTAAATATAATTA
AGTGGAATCCTATTTGT
Found at i:42672097 original size:41 final size:38
Alignment explanation
Indices: 42671973--42672097 Score: 94
Period size: 40 Copynumber: 3.1 Consensus size: 38
42671963 AAATATATAT
* *
42671973 TTTTTAATTATATTTAAAGTTGATCTTATTTTTAAATT-AA
1 TTTTTAATTATA-TTAAAG-TGATATCATTTTT-AATTAAA
* * *
42672013 TTTTTAAATATGATT-AAGTGA-ATCCTATTTGTAATATATA
1 TTTTTAATTAT-ATTAAAGTGATAT-C-ATTTTTAAT-TAAA
42672053 TTTTTAATTATATTCAAAGTGAGTATCATTTTTAAGTTAAA
1 TTTTTAATTATATT-AAAGTGA-TATCATTTTTAA-TTAAA
42672094 TTTT
1 TTTT
42672098 AAATATAATT
Statistics
Matches: 67, Mismatches: 8, Indels: 19
0.71 0.09 0.20
Matches are distributed among these distances:
37 1 0.01
38 6 0.09
39 12 0.18
40 23 0.34
41 21 0.31
42 2 0.03
43 2 0.03
ACGTcount: A:0.35, C:0.04, G:0.08, T:0.53
Consensus pattern (38 bp):
TTTTTAATTATATTAAAGTGATATCATTTTTAATTAAA
Found at i:42672134 original size:40 final size:39
Alignment explanation
Indices: 42671999--42672134 Score: 109
Period size: 41 Copynumber: 3.4 Consensus size: 39
42671989 AAGTTGATCT
* * *
42671999 TATTTTTAA-ATTAATTTTTAAATATGATTAAGTGAATCC
1 TATTTTTAATA-TAAATTTTAAATATAATTAAGTGAGTCC
* * * *
42672038 TATTTGTAATATATATTTTTAAT-TATATTCAAAGTGAGT-A
1 TATTTTTAATATAAATTTTAAATATA-ATT--AAGTGAGTCC
*
42672078 TCATTTTTAAGT-TAAATTTTAAATATAATTAAGTGGGGTCC
1 T-ATTTTTAA-TATAAATTTTAAATATAATTAAGT-GAGTCC
42672119 TATTTTTAATATAAAT
1 TATTTTTAATATAAAT
42672135 ACATAACATA
Statistics
Matches: 75, Mismatches: 12, Indels: 19
0.71 0.11 0.18
Matches are distributed among these distances:
38 1 0.01
39 25 0.33
40 18 0.24
41 28 0.37
42 3 0.04
ACGTcount: A:0.38, C:0.04, G:0.10, T:0.49
Consensus pattern (39 bp):
TATTTTTAATATAAATTTTAAATATAATTAAGTGAGTCC
Found at i:42673223 original size:21 final size:21
Alignment explanation
Indices: 42673184--42673223 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
42673174 TATAAATATT
**
42673184 TTTAAAAAATATATTAATAAA
1 TTTAAAAAATATAAAAATAAA
*
42673205 TTTAAAATATATAAAAATA
1 TTTAAAAAATATAAAAATA
42673224 CATAAAATTT
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:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
TTTAAAAAATATAAAAATAAA
Found at i:42673259 original size:21 final size:21
Alignment explanation
Indices: 42673233--42673272 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
42673223 ACATAAAATT
42673233 TTTAAAATTTATAGTAATAAA
1 TTTAAAATTTATAGTAATAAA
* *
42673254 TTTAAATTTTATATTAATA
1 TTTAAAATTTATAGTAATA
42673273 TTAACATTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (21 bp):
TTTAAAATTTATAGTAATAAA
Found at i:42677909 original size:39 final size:40
Alignment explanation
Indices: 42677830--42677918 Score: 103
Period size: 39 Copynumber: 2.2 Consensus size: 40
42677820 AAAAATTATA
* * * *
42677830 TTTAATACAATAAAACTTTTATTATATTTATTTGT-GTTT
1 TTTAATATAATAAAACTTTTATTACATTTATTGGTATTTT
42677869 TTTAATATAATAAAA-TATTTATTACATTTA-TGGTAATTTT
1 TTTAATATAATAAAACT-TTTATTACATTTATTGGT-ATTTT
42677909 TTTAATATAA
1 TTTAATATAA
42677919 ATTGTAACAC
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
38 4 0.09
39 26 0.60
40 13 0.30
ACGTcount: A:0.38, C:0.03, G:0.04, T:0.54
Consensus pattern (40 bp):
TTTAATATAATAAAACTTTTATTACATTTATTGGTATTTT
Found at i:42698409 original size:25 final size:25
Alignment explanation
Indices: 42698355--42698409 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
42698345 AAATATTAAA
*
42698355 TTTAATTTAATATTAAGATAATCAC
1 TTTAATTTAATATTAAGAAAATCAC
*
42698380 TTTAATATTAA-ATTAATAAAAT-AC
1 TTTAAT-TTAATATTAAGAAAATCAC
42698404 TATTAA
1 T-TTAA
42698410 GATAAGTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
24 3 0.12
25 19 0.73
26 4 0.15
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (25 bp):
TTTAATTTAATATTAAGAAAATCAC
Found at i:42698454 original size:68 final size:71
Alignment explanation
Indices: 42698313--42698457 Score: 163
Period size: 68 Copynumber: 2.1 Consensus size: 71
42698303 TATTAAATCT
* * *
42698313 TATTAAATTAATAGAATATTTATCTAGAAGATAAATATTAAATTTAATTTAATATTAAGATAATC
1 TATTAAATTAATAAAATATCTATCTA-AAGATAAATATTAAATTAAATTTAATATTAAGATAATC
***
42698378 ACTTTAA
65 AAAATAA
* * *
42698385 TATTAAATTAATAAAATA-CTAT-T-AAGATAAGTATTAAATTAAATTTAATATTAA-ATCTATT
1 TATTAAATTAATAAAATATCTATCTAAAGATAAATATTAAATTAAATTTAATATTAAGAT-AATC
42698446 AAAATAA
65 AAAATAA
42698453 TATTA
1 TATTA
42698458 TTTTTGGAAT
Statistics
Matches: 63, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
67 2 0.03
68 40 0.63
70 1 0.02
71 3 0.05
72 17 0.27
ACGTcount: A:0.51, C:0.03, G:0.04, T:0.41
Consensus pattern (71 bp):
TATTAAATTAATAAAATATCTATCTAAAGATAAATATTAAATTAAATTTAATATTAAGATAATCA
AAATAA
Found at i:42721324 original size:5 final size:5
Alignment explanation
Indices: 42721309--42721346 Score: 67
Period size: 5 Copynumber: 7.4 Consensus size: 5
42721299 CTATGACTAG
42721309 TTATAT TTATT TTATT TTATT TTATT TTATT TTATT TT
1 TTAT-T TTATT TTATT TTATT TTATT TTATT TTATT TT
42721347 TATGAGTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 28 0.88
6 4 0.12
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
TTATT
Found at i:42725207 original size:19 final size:20
Alignment explanation
Indices: 42725164--42725218 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
42725154 GGTCATATGG
42725164 CCAGGCCGTGTGACATCGCC
1 CCAGGCCGTGTGACATCGCC
42725184 CCAGGCCGTGTGACATCG-C
1 CCAGGCCGTGTGACATCGCC
*
42725203 CCAGGCCGTGTAACAT
1 CCAGGCCGTGTGACAT
42725219 TCAAACAAGG
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 16 0.47
20 18 0.53
ACGTcount: A:0.18, C:0.36, G:0.29, T:0.16
Consensus pattern (20 bp):
CCAGGCCGTGTGACATCGCC
Found at i:42729185 original size:10 final size:9
Alignment explanation
Indices: 42729170--42729207 Score: 51
Period size: 10 Copynumber: 4.1 Consensus size: 9
42729160 GTAATTAAAC
42729170 TAATTAATCT
1 TAATTAAT-T
42729180 TAATTAATT
1 TAATTAATT
42729189 TAACTTAA-T
1 TAA-TTAATT
42729198 TAATTAATT
1 TAATTAATT
42729207 T
1 T
42729208 TTAATCTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
8 4 0.15
9 10 0.38
10 12 0.46
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (9 bp):
TAATTAATT
Found at i:42729195 original size:14 final size:15
Alignment explanation
Indices: 42729173--42729202 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
42729163 ATTAAACTAA
42729173 TTAATCTTAATTAAT
1 TTAATCTTAATTAAT
42729188 TTAA-CTTAATTAAT
1 TTAATCTTAATTAAT
42729202 T
1 T
42729203 AATTTTTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (15 bp):
TTAATCTTAATTAAT
Found at i:42730052 original size:22 final size:22
Alignment explanation
Indices: 42730026--42730072 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
42730016 ATTTGAGCGC
42730026 AATAAATCAATCATCATAAAAT
1 AATAAATCAATCATCATAAAAT
*
42730048 AATAAATCAATCATGATAAAAT
1 AATAAATCAATCATCATAAAAT
42730070 AAT
1 AAT
42730073 TTAATATAAA
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:0.60, C:0.11, G:0.02, T:0.28
Consensus pattern (22 bp):
AATAAATCAATCATCATAAAAT
Found at i:42730625 original size:5 final size:5
Alignment explanation
Indices: 42730615--42730653 Score: 78
Period size: 5 Copynumber: 7.8 Consensus size: 5
42730605 TTACTTGAGT
42730615 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATA
42730654 CTAATTTTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 34 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
TATAA
Found at i:42738471 original size:72 final size:72
Alignment explanation
Indices: 42738016--42738901 Score: 688
Period size: 72 Copynumber: 12.3 Consensus size: 72
42738006 TCATAAAAAA
* * * * * *
42738016 CCCAAACAGTTAGCGAGAGTTAAAAGCTTCCAGCTATCATTATTAAGGCTCGCAGGTTCAATACC
1 CCCAAACAGTTAGCGAGAGTTAAAAGCTCCCAACTGTCATTATTAAGGCTCACAGGTTTAAAACC
*
42738081 ACAACCC
66 GCAACCC
** * * * * * * * * **
42738088 CTTAAATATTTAGCGAGAGTTAAAAACTCCTAGCAGTC-TTCATTCAGACTCGTAGGTTTAAAAC
1 CCCAAACAGTTAGCGAGAGTTAAAAGCTCCCAACTGTCATT-ATTAAGGCTCACAGGTTTAAAAC
* *
42738152 CACAACCA
65 CGCAACCC
* * * *
42738160 CCCAAACAGTTAGCGAGAGTTAAAAGCTCTCAACTGTCATTGTTAAGGCTCGCAGGTTTACAACC
1 CCCAAACAGTTAGCGAGAGTTAAAAGCTCCCAACTGTCATTATTAAGGCTCACAGGTTTAAAACC
*
42738225 ACAA-CC
66 GCAACCC
* * * * * **
42738231 CCCAAATAGTTAGCGAGAGTTAAAAGCTCCCAGCTATCATCATTAAGGCTCGCAGGTTTAAAATT
1 CCCAAACAGTTAGCGAGAGTTAAAAGCTCCCAACTGTCATTATTAAGGCTCACAGGTTTAAAACC
*
42738296 GC-AGCC
66 GCAACCC
* * * * * * *
42738302 CCCAAACAATTAGCGAGATTTAAAAGCTCTCAAATGTCATTATTAAAGCTCAC-GAGATTAAAAT
1 CCCAAACAGTTAGCGAGAGTTAAAAGCTCCCAACTGTCATTATTAAGGCTCACAG-GTTTAAAAC
**
42738366 CGCAGTCC
65 CGCAACCC
* * * * * *
42738374 CTCAAACAGTTAGCGAGAGTTAAAAGCTCCCAACTGTTATTATTAAAGCTCGCAGGTTCAATACC
1 CCCAAACAGTTAGCGAGAGTTAAAAGCTCCCAACTGTCATTATTAAGGCTCACAGGTTTAAAACC
42738439 GCAACCC
66 GCAACCC
* * * * * ** * *
42738446 CCCAAATAGTTAGCGAAAGTTAAAAGCTCCTAACTATCATCATTAAATCTCTCAGGTTTAAAGCC
1 CCCAAACAGTTAGCGAGAGTTAAAAGCTCCCAACTGTCATTATTAAGGCTCACAGGTTTAAAACC
* *
42738511 GTAGCCC
66 GCAACCC
** * ** * * ** * *
42738518 CTTAAATAGTTAATGAGAGTTAAAAACTCCCAATTGTCATTATTAAGGCTCACTTGATTAAAACT
1 CCCAAACAGTTAGCGAGAGTTAAAAGCTCCCAACTGTCATTATTAAGGCTCACAGGTTTAAAACC
*
42738583 G-TACCC
66 GCAACCC
* * * * * * **
42738589 CCTCAAATAGTTGGTGAGAGTTAAAAGCTCCCAGCTGTTATTATTAAAGCTCACAGGTTTAAGGC
1 CC-CAAACAGTTAGCGAGAGTTAAAAGCTCCCAACTGTCATTATTAAGGCTCACAGGTTTAAAAC
* *
42738654 TGCAGCCC
65 CGCAACCC
* * * * * ** *
42738662 TCCAAGCAGTTAGCGAGAGTTAAAAGCTCCTAACTATCATCATTAAGGCTCACAGAATTAAAATC
1 CCCAAACAGTTAGCGAGAGTTAAAAGCTCCCAACTGTCATTATTAAGGCTCACAGGTTTAAAACC
* *
42738727 GCAGCTC
66 GCAACCC
* * * * * * * *
42738734 TCCAAATAGTTAGCGAGAGTTAAAAGCTCTCAGCTGTTATTATTAAGGCTTACAGGTTCAATACC
1 CCCAAACAGTTAGCGAGAGTTAAAAGCTCCCAACTGTCATTATTAAGGCTCACAGGTTTAAAACC
*
42738799 GCAGCCC
66 GCAACCC
* * * * ** *
42738806 TCCAAACAGTTAACGAGAGTTAAAAGCTCTCAGA-TGTCATCATTAAGGCTCGTAGCTTTAAAAC
1 CCCAAACAGTTAGCGAGAGTTAAAAGCTCCCA-ACTGTCATTATTAAGGCTCACAGGTTTAAAAC
* *
42738870 TGTAA-CC
65 CGCAACCC
*
42738877 CCCAAACAGTCAGCGAGAGTTAAAA
1 CCCAAACAGTTAGCGAGAGTTAAAA
42738902 ACTCTCAGAT
Statistics
Matches: 638, Mismatches: 167, Indels: 19
0.77 0.20 0.02
Matches are distributed among these distances:
70 2 0.00
71 143 0.22
72 486 0.76
73 7 0.01
ACGTcount: A:0.34, C:0.23, G:0.17, T:0.25
Consensus pattern (72 bp):
CCCAAACAGTTAGCGAGAGTTAAAAGCTCCCAACTGTCATTATTAAGGCTCACAGGTTTAAAACC
GCAACCC
Found at i:42739316 original size:27 final size:26
Alignment explanation
Indices: 42739245--42739337 Score: 89
Period size: 27 Copynumber: 3.5 Consensus size: 26
42739235 TTGGTCCGCT
* *
42739245 TTGTCATTCTCAGCAAGAAGGGCCACA
1 TTGTCATTCTCA-CAGGAGGGGCCACA
* *
42739272 TTATCATTCTCAATAGGAGGGGCCACA
1 TTGTCATTCTC-ACAGGAGGGGCCACA
*
42739299 TTGTCATTCTCGACAGGAGGGGTCA-A
1 TTGTCATTCTC-ACAGGAGGGGCCACA
*
42739325 GCTGTCATTCTCA
1 -TTGTCATTCTCA
42739338 ACTGGGTCCT
Statistics
Matches: 55, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
26 2 0.04
27 52 0.95
28 1 0.02
ACGTcount: A:0.26, C:0.24, G:0.24, T:0.27
Consensus pattern (26 bp):
TTGTCATTCTCACAGGAGGGGCCACA
Found at i:42741486 original size:132 final size:132
Alignment explanation
Indices: 42741247--42741487 Score: 293
Period size: 132 Copynumber: 1.8 Consensus size: 132
42741237 CGATATGAAA
* * * * *
42741247 ATTCCAATAACGAAAAAATCTCAACGATCAGATCCATGCAAGCACGATCTACCCATACATGTGGC
1 ATTCCAATAACCAAAAAATCTCAACGACCAGATCCATGCAAGCACGATCCACCCATACAAGTGAC
* * * * * *
42741312 AAGGTAGGCGTTAGGTTCTAATAACTCGCAGCGTACCCAACAAGTTGCATTTAAACTCAACATGA
66 AAGGCAGACGTCAGGTTCTAACAACTCGCAACATACCCAACAAGTTGCATTTAAACTCAACATGA
42741377 TG
131 TG
* * * * * * *
42741379 ATTCCAATAACCAAAGAGTCTCAGCGGCCAGATTCATGCGAGCATGATCCACCCATACAAGTGAC
1 ATTCCAATAACCAAAAAATCTCAACGACCAGATCCATGCAAGCACGATCCACCCATACAAGTGAC
* * *
42741444 AAGGCAGACGTCATGTTCTAACAGCTCGCAACATACCTAACAAG
66 AAGGCAGACGTCAGGTTCTAACAACTCGCAACATACCCAACAAG
42741488 CCACACTTAA
Statistics
Matches: 88, Mismatches: 21, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
132 88 1.00
ACGTcount: A:0.35, C:0.26, G:0.18, T:0.21
Consensus pattern (132 bp):
ATTCCAATAACCAAAAAATCTCAACGACCAGATCCATGCAAGCACGATCCACCCATACAAGTGAC
AAGGCAGACGTCAGGTTCTAACAACTCGCAACATACCCAACAAGTTGCATTTAAACTCAACATGA
TG
Found at i:42742701 original size:29 final size:28
Alignment explanation
Indices: 42742657--42742730 Score: 78
Period size: 29 Copynumber: 2.5 Consensus size: 28
42742647 ACTGTTAAAA
42742657 TTATTTTTTTAAATTTAAATATATTA-TAATG
1 TTATTTTTTT--ATTTAAATA-ATTATTAA-G
*
42742688 TTATTTTTTTATTTACATAATTATTAAG
1 TTATTTTTTTATTTAAATAATTATTAAG
*
42742716 TGAATTTTTTTATTT
1 T-TATTTTTTTATTT
42742731 TAAAATCTCA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
28 6 0.15
29 23 0.59
31 10 0.26
ACGTcount: A:0.32, C:0.01, G:0.04, T:0.62
Consensus pattern (28 bp):
TTATTTTTTTATTTAAATAATTATTAAG
Found at i:42744567 original size:17 final size:17
Alignment explanation
Indices: 42744545--42744577 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
42744535 TATAATATAA
42744545 TATAAATAAATTTTTAG
1 TATAAATAAATTTTTAG
42744562 TATAAATAAATTTTTA
1 TATAAATAAATTTTTA
42744578 TAATTTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (17 bp):
TATAAATAAATTTTTAG
Found at i:42744635 original size:24 final size:25
Alignment explanation
Indices: 42744606--42744652 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
42744596 TAACATAATT
*
42744606 ATATTTTGTTATTTAATT-TATAAA
1 ATATTTTGATATTTAATTATATAAA
42744630 ATATTTTGATATTTAATTATATA
1 ATATTTTGATATTTAATTATATA
42744653 TACATTTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 17 0.81
25 4 0.19
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.57
Consensus pattern (25 bp):
ATATTTTGATATTTAATTATATAAA
Found at i:42744659 original size:24 final size:24
Alignment explanation
Indices: 42744608--42744660 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
42744598 ACATAATTAT
* *
42744608 ATTTTGTTATTTAATTTATAAAAT
1 ATTTTGATATTTAATTTATAAAAC
*
42744632 ATTTTGATATTTAA-TTATATATAC
1 ATTTTGATATTTAATTTATA-AAAC
42744656 ATTTT
1 ATTTT
42744661 AACTTAACGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 5 0.20
24 20 0.80
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.58
Consensus pattern (24 bp):
ATTTTGATATTTAATTTATAAAAC
Found at i:42745424 original size:28 final size:27
Alignment explanation
Indices: 42745379--42745456 Score: 88
Period size: 26 Copynumber: 2.9 Consensus size: 27
42745369 TAAGTTGTTT
42745379 ATATATAAAATTTT-AATAAATAAAAA
1 ATATATAAAATTTTAAATAAATAAAAA
*
42745405 ATATATAAAATTATTAAATAATATAAATA
1 ATATATAAAATT-TTAAATAA-ATAAAAA
* * *
42745434 TTTTTTAAAATTTTAAA-AAATAA
1 ATATATAAAATTTTAAATAAATAA
42745457 TATGGATGTG
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
26 16 0.36
27 4 0.09
28 10 0.22
29 15 0.33
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (27 bp):
ATATATAAAATTTTAAATAAATAAAAA
Found at i:42748670 original size:19 final size:20
Alignment explanation
Indices: 42748621--42748673 Score: 56
Period size: 19 Copynumber: 2.7 Consensus size: 20
42748611 TGATGTTGGT
42748621 GATATTTTTATTAATTAATTA
1 GATA-TTTTATTAATTAATTA
** *
42748642 GATA-AATATTATTTAATTA
1 GATATTTTATTAATTAATTA
42748661 -ATATTTTATTAAT
1 GATATTTTATTAAT
42748674 ATTTTTAGTA
Statistics
Matches: 25, Mismatches: 6, Indels: 4
0.71 0.17 0.11
Matches are distributed among these distances:
18 3 0.12
19 18 0.72
21 4 0.16
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.55
Consensus pattern (20 bp):
GATATTTTATTAATTAATTA
Found at i:42748678 original size:11 final size:11
Alignment explanation
Indices: 42748651--42748694 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
42748641 AGATAAATAT
*
42748651 TATTTAATTAA
1 TATTTTATTAA
42748662 TATTTTATTAA
1 TATTTTATTAA
* *
42748673 TATTTTTAGTAT
1 TA-TTTTATTAA
42748685 TATTTTATTA
1 TATTTTATTA
42748695 CTAAATGATT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
11 19 0.68
12 9 0.32
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:42754066 original size:6 final size:6
Alignment explanation
Indices: 42754055--42754091 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
42754045 TTTATATAAT
42754055 TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA T
1 TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA T
42754092 TTGCTAACGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
TATTTA
Found at i:42754068 original size:18 final size:18
Alignment explanation
Indices: 42754045--42754087 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
42754035 GTCTTATTTG
42754045 TTTATATA-ATTATTTATA
1 TTTATATATA-TATTTATA
*
42754063 TTTATATTTATATTTATA
1 TTTATATATATATTTATA
42754081 TTTATAT
1 TTTATAT
42754088 TTATTTGCTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 22 0.96
19 1 0.04
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
TTTATATATATATTTATA
Found at i:42755269 original size:18 final size:20
Alignment explanation
Indices: 42755246--42755290 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
42755236 AAAAATATTT
42755246 AAAATTTT-AAAATA-AAAA
1 AAAATTTTAAAAATATAAAA
*
42755264 ATAATTTTAAAAATATAAAA
1 AAAATTTTAAAAATATAAAA
42755284 AAAATTT
1 AAAATTT
42755291 AAATTTTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 7 0.30
19 6 0.26
20 10 0.43
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
AAAATTTTAAAAATATAAAA
Found at i:42755282 original size:26 final size:24
Alignment explanation
Indices: 42755212--42755287 Score: 84
Period size: 24 Copynumber: 3.1 Consensus size: 24
42755202 AATATATTTT
*
42755212 AAAAATATATAAAATTATGAAAAT-
1 AAAAATATTTAAAATTAT-AAAATA
*
42755236 AAAAATATTTAAAATTTTAAAATA
1 AAAAATATTTAAAATTATAAAATA
*
42755260 AAAAATAATTTTAAAAATATAAAA-A
1 AAAAAT-A-TTTAAAATTATAAAATA
42755285 AAA
1 AAA
42755288 TTTAAATTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
23 5 0.11
24 22 0.49
25 5 0.11
26 13 0.29
ACGTcount: A:0.68, C:0.00, G:0.01, T:0.30
Consensus pattern (24 bp):
AAAAATATTTAAAATTATAAAATA
Found at i:42755291 original size:19 final size:18
Alignment explanation
Indices: 42755246--42755293 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
42755236 AAAAATATTT
*
42755246 AAAATTTTAAAATAAAAA
1 AAAATTTAAAAATAAAAA
*
42755264 ATAATTTTAAAAATATAAAA
1 A-AAATTTAAAAATA-AAAA
42755284 AAAATTTAAA
1 AAAATTTAAA
42755294 TTTTAATGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
18 1 0.04
19 19 0.76
20 5 0.20
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
AAAATTTAAAAATAAAAA
Found at i:42755467 original size:17 final size:18
Alignment explanation
Indices: 42755445--42755485 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
42755435 GTTGAGCCAA
42755445 TTTTTATATTT-ATAATT
1 TTTTTATATTTAATAATT
*
42755462 TTTTTATTTTTAATAATT
1 TTTTTATATTTAATAATT
*
42755480 TATTTA
1 TTTTTA
42755486 CTTTGCATTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 10 0.48
18 11 0.52
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTTTATATTTAATAATT
Found at i:42755777 original size:15 final size:16
Alignment explanation
Indices: 42755750--42755779 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
42755740 AAATAAAAAA
42755750 AATTATATTAATATTT
1 AATTATATTAATATTT
42755766 AATTAT-TTAATATT
1 AATTATATTAATATT
42755780 ATTTTATCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
AATTATATTAATATTT
Found at i:42756824 original size:24 final size:25
Alignment explanation
Indices: 42756775--42756824 Score: 59
Period size: 24 Copynumber: 2.0 Consensus size: 25
42756765 ACCCTTCTCA
* *
42756775 TCTCTTCACTTCTCTCTCATTTTTC
1 TCTCTTCACTTCCCTCTCATTGTTC
42756800 TCTCTTCA-TTCCCT-TCCATTGTTC
1 TCTCTTCACTTCCCTCT-CATTGTTC
42756824 T
1 T
42756825 TCATTTTCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
23 1 0.05
24 13 0.59
25 8 0.36
ACGTcount: A:0.08, C:0.36, G:0.02, T:0.54
Consensus pattern (25 bp):
TCTCTTCACTTCCCTCTCATTGTTC
Found at i:42764567 original size:24 final size:23
Alignment explanation
Indices: 42764540--42764590 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 23
42764530 TTTTCTCCAA
*
42764540 AATTTT-AATTTTATTTAATTAATT
1 AATTTTCAA-TTTATTGAATT-ATT
42764564 AATTTTTCAATTTATTGAATTATT
1 AA-TTTTCAATTTATTGAATTATT
42764588 AAT
1 AAT
42764591 ATTTTATGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
23 1 0.04
24 7 0.29
25 14 0.58
26 2 0.08
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (23 bp):
AATTTTCAATTTATTGAATTATT
Found at i:42772622 original size:4 final size:4
Alignment explanation
Indices: 42772613--42772683 Score: 51
Period size: 4 Copynumber: 18.0 Consensus size: 4
42772603 TGTCTTTCTC
**
42772613 CTTT CTTT CTTT CCCT -TTT C-TT -TTT CTTT CTTT C-TT CTTT CTGTTT
1 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT C--TTT
* *
42772659 CATTT CTAT CTTT TTTT CTTT CTTT
1 C-TTT CTTT CTTT CTTT CTTT CTTT
42772684 TTATTACTTA
Statistics
Matches: 52, Mismatches: 9, Indels: 12
0.71 0.12 0.16
Matches are distributed among these distances:
3 8 0.15
4 36 0.69
5 4 0.08
6 4 0.08
ACGTcount: A:0.03, C:0.24, G:0.01, T:0.72
Consensus pattern (4 bp):
CTTT
Found at i:42772653 original size:21 final size:21
Alignment explanation
Indices: 42772605--42772683 Score: 65
Period size: 21 Copynumber: 3.7 Consensus size: 21
42772595 CCTAGCCTTG
*
42772605 TCTTTCTCCTTTCTTTCTTTC-
1 TCTTTCT-TTTTCTTTCTTTCT
*
42772626 CCTTTTCTTTTTCTTTCTTTCT
1 TC-TTTCTTTTTCTTTCTTTCT
* *
42772648 TCTTTCTGTTTCATTTCTATCT
1 TCTTTCTTTTTC-TTTCTTTCT
42772670 T-TTT-TTCTTTCTTT
1 TCTTTCTT-TTTCTTT
42772684 TTATTACTTA
Statistics
Matches: 48, Mismatches: 6, Indels: 9
0.76 0.10 0.14
Matches are distributed among these distances:
20 4 0.08
21 29 0.60
22 15 0.31
ACGTcount: A:0.03, C:0.25, G:0.01, T:0.71
Consensus pattern (21 bp):
TCTTTCTTTTTCTTTCTTTCT
Found at i:42772664 original size:11 final size:10
Alignment explanation
Indices: 42772614--42772685 Score: 53
Period size: 11 Copynumber: 7.3 Consensus size: 10
42772604 GTCTTTCTCC
42772614 TTTCTTTCTT
1 TTTCTTTCTT
**
42772624 TCCCTTTTCTT
1 TTTC-TTTCTT
42772635 TTTCTTTCTT
1 TTTCTTTCTT
*
42772645 TCTTCTTTCTG
1 T-TTCTTTCTT
42772656 TTTCATTTC--
1 TTTC-TTTCTT
*
42772665 TATC-TT-TT
1 TTTCTTTCTT
42772673 TTTCTTTCTT
1 TTTCTTTCTT
42772683 TTT
1 TTT
42772686 ATTACTTATT
Statistics
Matches: 48, Mismatches: 7, Indels: 14
0.70 0.10 0.20
Matches are distributed among these distances:
7 2 0.04
8 3 0.06
9 5 0.10
10 17 0.35
11 21 0.44
ACGTcount: A:0.03, C:0.22, G:0.01, T:0.74
Consensus pattern (10 bp):
TTTCTTTCTT
Found at i:42772759 original size:20 final size:20
Alignment explanation
Indices: 42772697--42772760 Score: 62
Period size: 20 Copynumber: 3.2 Consensus size: 20
42772687 TTACTTATTT
*
42772697 TATTATAAAATAAT-ATATA
1 TATTATAATATAATAATATA
42772716 TACTTAATAAT-TAATAAT-TAA
1 TA-TT-ATAATATAATAATAT-A
*
42772737 TATTATAATATTATAATATA
1 TATTATAATATAATAATATA
42772757 TATT
1 TATT
42772761 TTAACTTTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 11
0.74 0.04 0.22
Matches are distributed among these distances:
19 7 0.19
20 20 0.54
21 10 0.27
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (20 bp):
TATTATAATATAATAATATA
Found at i:42779418 original size:41 final size:39
Alignment explanation
Indices: 42779295--42779430 Score: 134
Period size: 37 Copynumber: 3.5 Consensus size: 39
42779285 ACCAGTTTGG
* * * *
42779295 CACCCAATGCCTCATC-AGATAATTTGAAGTAATAATTTGA
1 CACCCAGTGCCTCATCGA-ATAAATCGAAG-AATAAATTGA
* ** *
42779335 CACCCAGTGTCTCATCGGCTAAATCGAAG--TAAATTGG
1 CACCCAGTGCCTCATCGAATAAATCGAAGAATAAATTGA
42779372 CACCCAGTGCCTCATCGAATAAATCCGAAGCAATAAATTGA
1 CACCCAGTGCCTCATCGAATAAAT-CGAAG-AATAAATTGA
*
42779413 CACCCAGTGTCTCATCGA
1 CACCCAGTGCCTCATCGA
42779431 CTCAAAGTTG
Statistics
Matches: 78, Mismatches: 13, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
37 27 0.35
38 5 0.06
40 22 0.28
41 24 0.31
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.24
Consensus pattern (39 bp):
CACCCAGTGCCTCATCGAATAAATCGAAGAATAAATTGA
Found at i:42780321 original size:22 final size:22
Alignment explanation
Indices: 42780282--42780350 Score: 70
Period size: 22 Copynumber: 3.1 Consensus size: 22
42780272 CTCCTTCTCC
**
42780282 TTTCTTTCTTTCCCCTTTTCTT
1 TTTCTTTCTTTCTTCTTTTCTT
*
42780304 TTTCTTTCTTTCTTC-TTTCTG
1 TTTCTTTCTTTCTTCTTTTCTT
*
42780325 TTTCATTTCTATCTT-TCTTTCTT
1 TTTC-TTTCTTTCTTCT-TTTCTT
42780348 TTT
1 TTT
42780351 ATTACTTATT
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
21 9 0.23
22 22 0.56
23 8 0.21
ACGTcount: A:0.03, C:0.25, G:0.01, T:0.71
Consensus pattern (22 bp):
TTTCTTTCTTTCTTCTTTTCTT
Found at i:42782915 original size:29 final size:29
Alignment explanation
Indices: 42782843--42782916 Score: 105
Period size: 29 Copynumber: 2.6 Consensus size: 29
42782833 GTTCTTGATA
* *
42782843 TATTTTTTTAGAACTCATCTCGTCAAAAT
1 TATTTTTTCAGAACCCATCTCGTCAAAAT
*
42782872 TATTTTTTC-GAAACCCATCTTGTCAAAAT
1 TATTTTTTCAG-AACCCATCTCGTCAAAAT
42782901 TATTTTTTCAGAACCC
1 TATTTTTTCAGAACCC
42782917 TTGAACACTA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
28 1 0.03
29 38 0.95
30 1 0.03
ACGTcount: A:0.30, C:0.20, G:0.07, T:0.43
Consensus pattern (29 bp):
TATTTTTTCAGAACCCATCTCGTCAAAAT
Found at i:42783042 original size:41 final size:41
Alignment explanation
Indices: 42782987--42783094 Score: 114
Period size: 41 Copynumber: 2.6 Consensus size: 41
42782977 AAAACCTTAA
*
42782987 TTAATAAA-CACTAAACCCTAATTGAAAC-CATAAACACTAAT
1 TTAATAAATC-CTAAACCCTAATTAAAACAC-TAAACACTAAT
* * *
42783028 TTATTAAATCCTAAACCCTAATTAAAATACTAAACATTAAT
1 TTAATAAATCCTAAACCCTAATTAAAACACTAAACACTAAT
* *
42783069 TTAATAAA-CTATAAACCCTAGTTAAA
1 TTAATAAATC-CTAAACCCTAATTAAA
42783095 CAATTAAAAC
Statistics
Matches: 57, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
40 1 0.02
41 54 0.95
42 2 0.04
ACGTcount: A:0.50, C:0.19, G:0.02, T:0.30
Consensus pattern (41 bp):
TTAATAAATCCTAAACCCTAATTAAAACACTAAACACTAAT
Found at i:42783060 original size:19 final size:19
Alignment explanation
Indices: 42782996--42783062 Score: 55
Period size: 19 Copynumber: 3.4 Consensus size: 19
42782986 ATTAATAAAC
*
42782996 ACTAAACCCTAATTGAAA-
1 ACTAAACCCTAATTAAAAT
* *
42783014 CCATAAACACTAATTTATTAAAT
1 AC-TAAACCCTAA-TTA--AAAT
*
42783037 CCTAAACCCTAATTAAAAT
1 ACTAAACCCTAATTAAAAT
42783056 ACTAAAC
1 ACTAAAC
42783063 ATTAATTTAA
Statistics
Matches: 39, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
18 1 0.03
19 19 0.49
20 2 0.05
21 3 0.08
22 12 0.31
23 2 0.05
ACGTcount: A:0.49, C:0.22, G:0.01, T:0.27
Consensus pattern (19 bp):
ACTAAACCCTAATTAAAAT
Found at i:42783248 original size:40 final size:38
Alignment explanation
Indices: 42783163--42783256 Score: 125
Period size: 40 Copynumber: 2.4 Consensus size: 38
42783153 GTGCGTTGAC
* *
42783163 CTGGACGCATTTTACTGGTCAGGGGAAAAGGCGCTGAG
1 CTGGACGCACTTTACTGGTCAGGGGAAAAAGCGCTGAG
* * *
42783201 TTAGACGCACTTTATTGGTCAGAGGGAAAAAAGCGCTGAG
1 CTGGACGCACTTTACTGGTCAG-GGG-AAAAAGCGCTGAG
42783241 CTGGACGCACTTTACT
1 CTGGACGCACTTTACT
42783257 AATTTCCCCC
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
38 18 0.39
39 3 0.07
40 25 0.54
ACGTcount: A:0.27, C:0.19, G:0.31, T:0.23
Consensus pattern (38 bp):
CTGGACGCACTTTACTGGTCAGGGGAAAAAGCGCTGAG
Found at i:42792152 original size:3 final size:3
Alignment explanation
Indices: 42792144--42792181 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
42792134 AACTAGTTTT
42792144 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
42792182 TGGGCTCAAT
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:42793237 original size:16 final size:16
Alignment explanation
Indices: 42793212--42793245 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
42793202 AACATAATAT
*
42793212 ATTATTAATCAATAAA
1 ATTATAAATCAATAAA
*
42793228 ATTATAAATCTATAAA
1 ATTATAAATCAATAAA
42793244 AT
1 AT
42793246 CGTTGAATAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (16 bp):
ATTATAAATCAATAAA
Found at i:42796949 original size:12 final size:12
Alignment explanation
Indices: 42796932--42796957 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
42796922 ATTTTTTATT
42796932 TCATAATCACTA
1 TCATAATCACTA
42796944 TCATAATCACTA
1 TCATAATCACTA
42796956 TC
1 TC
42796958 GTAAACATAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.27, G:0.00, T:0.35
Consensus pattern (12 bp):
TCATAATCACTA
Found at i:42801649 original size:13 final size:11
Alignment explanation
Indices: 42801620--42801646 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
42801610 AAGAAAAATA
42801620 TTTTTGGAATT
1 TTTTTGGAATT
42801631 TTTTTGGAATT
1 TTTTTGGAATT
42801642 TTTTT
1 TTTTT
42801647 TTGAAAAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.15, C:0.00, G:0.15, T:0.70
Consensus pattern (11 bp):
TTTTTGGAATT
Found at i:42807176 original size:41 final size:40
Alignment explanation
Indices: 42807131--42807408 Score: 170
Period size: 41 Copynumber: 6.7 Consensus size: 40
42807121 TACTCGGTGA
*
42807131 AATCAGCACTTAGCAACCACCTTATATTCAGTGATACGGGG
1 AATCAGCACTTAGCAACC-CCTTATATTCAGTGATTCGGGG
* * * * *
42807172 AATCAACACATAGCAACCCCTTTCACAATTAAG-GATACGGTGG
1 AATCAGCACTTAGCAACCCC-TT-A-TATTCAGTGATTCGG-GG
* * * * * *
42807215 AATCAACACTTAGAAACCACCTTTAGATTCAATAATTCAGGG
1 AATCAGCACTTAGCAACC-CC-TTATATTCAGTGATTCGGGG
* * *
42807257 AATCTGCACTTAACAACCCCTT-TGTGATCAGTGATTCGGGG
1 AATCAGCACTTAGCAACCCCTTATAT--TCAGTGATTCGGGG
* * * * *
42807298 AATCTGCACTTAGCAACCCCTTTTCAATCAATGATTCGGTG
1 AATCAGCACTTAGCAACCCCTTAT-ATTCAGTGATTCGGGG
* * *
42807339 AATCTA-CACTTAGCAA-CCCTTTTTTGATCAGTGATTCAGGG
1 AATC-AGCACTTAGCAACCCCTTATAT--TCAGTGATTCGGGG
* *
42807380 AATCTA-CACTTAGAAACCCCTTACATTCA
1 AATC-AGCACTTAGCAACCCCTTATATTCA
42807409 ATGAATCTCG
Statistics
Matches: 187, Mismatches: 36, Indels: 29
0.74 0.14 0.12
Matches are distributed among these distances:
39 1 0.01
40 14 0.07
41 104 0.56
42 35 0.19
43 28 0.15
44 5 0.03
ACGTcount: A:0.32, C:0.25, G:0.15, T:0.28
Consensus pattern (40 bp):
AATCAGCACTTAGCAACCCCTTATATTCAGTGATTCGGGG
Found at i:42807349 original size:82 final size:82
Alignment explanation
Indices: 42807213--42807401 Score: 245
Period size: 82 Copynumber: 2.3 Consensus size: 82
42807203 AGGATACGGT
* ** * *
42807213 GGAATCAACACTTAGAAACCACCTTTAGATTCAATAATTCAGGGAATCTGCACTTAACAACCCCT
1 GGAATCTACACTTAGAAACC-CCTTTTCAATCAATAATTCAGGGAATCTACACTTAACAACCCCT
*
42807278 TTGTGATCAGTGATTCGG
65 TTGTGATCAGTGATTCAG
* * * * *
42807296 GGAATCTGCACTTAGCAACCCCTTTTCAATCAATGATTC-GGTGAATCTACACTTAGCAACCCTT
1 GGAATCTACACTTAGAAACCCCTTTTCAATCAATAATTCAGG-GAATCTACACTTAACAACCCCT
*
42807360 TTTTGATCAGTGATTCAG
65 TTGTGATCAGTGATTCAG
42807378 GGAATCTACACTTAGAAACCCCTT
1 GGAATCTACACTTAGAAACCCCTT
42807402 ACATTCAATG
Statistics
Matches: 91, Mismatches: 14, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
81 2 0.02
82 72 0.79
83 17 0.19
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.30
Consensus pattern (82 bp):
GGAATCTACACTTAGAAACCCCTTTTCAATCAATAATTCAGGGAATCTACACTTAACAACCCCTT
TGTGATCAGTGATTCAG
Found at i:42807486 original size:19 final size:20
Alignment explanation
Indices: 42807449--42807486 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
42807439 TGGGAACCTT
*
42807449 CTTTTACAACATTTTACCAA
1 CTTTTACAACATTTAACCAA
*
42807469 CTTTTTCAA-ATTTAACCA
1 CTTTTACAACATTTAACCA
42807487 CATTTTTGTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.34, C:0.24, G:0.00, T:0.42
Consensus pattern (20 bp):
CTTTTACAACATTTAACCAA
Found at i:42811711 original size:16 final size:17
Alignment explanation
Indices: 42811680--42811712 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
42811670 TACCCAACTT
*
42811680 GTCAAATTCTCCAAATC
1 GTCAAATTCCCCAAATC
42811697 GTCAAA-TCCCCAAATC
1 GTCAAATTCCCCAAATC
42811713 CATAACATCC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.36, C:0.33, G:0.06, T:0.24
Consensus pattern (17 bp):
GTCAAATTCCCCAAATC
Found at i:42812192 original size:117 final size:117
Alignment explanation
Indices: 42811981--42812292 Score: 502
Period size: 117 Copynumber: 2.7 Consensus size: 117
42811971 TGGTTTGTTC
*
42811981 GTTATTTGTGATTTATTATTGCAATTTCAGTGTCGCAATGTAGGGTTTGTTTTGTCGATTTGTGA
1 GTTATTTGTGATTTATTATTGCAATTTCAGTGCCGCAATGTAGGGTTTGTTTTGTCGATTTGTGA
* * * *
42812046 TGCGATAGTGGTCTCGATGTTGTTGATAAAGCTGTTGTTAAAATTGTAGATG
66 TGCGATAGTGGTCCCAATGTTGTTGATAAAGATATTGTTAAAATTGTAGATG
* *
42812098 GTTAATTGTGATTTATTATTGCAATTTCAATG-CGACAATGTAGGGTTTGTTTTGTCGATTTGTG
1 GTTATTTGTGATTTATTATTGCAATTTCAGTGCCG-CAATGTAGGGTTTGTTTTGTCGATTTGTG
*
42812162 ATGCGACAGTGGTCCCAATGTTGTTGATAAAGATATTGTTAAAATTGTAGATG
65 ATGCGATAGTGGTCCCAATGTTGTTGATAAAGATATTGTTAAAATTGTAGATG
* * *
42812215 GTTATTTTTGATTTATTATTGCAATTTTAGTGCCGCAATGTA-GGTTTGTTTTGTCAATTTGTGA
1 GTTATTTGTGATTTATTATTGCAATTTCAGTGCCGCAATGTAGGGTTTGTTTTGTCGATTTGTGA
42812279 TGCGATAGTGGTCC
66 TGCGATAGTGGTCC
42812293 TGTTGTTGTT
Statistics
Matches: 180, Mismatches: 13, Indels: 5
0.91 0.07 0.03
Matches are distributed among these distances:
116 36 0.20
117 142 0.79
118 2 0.01
ACGTcount: A:0.23, C:0.09, G:0.25, T:0.44
Consensus pattern (117 bp):
GTTATTTGTGATTTATTATTGCAATTTCAGTGCCGCAATGTAGGGTTTGTTTTGTCGATTTGTGA
TGCGATAGTGGTCCCAATGTTGTTGATAAAGATATTGTTAAAATTGTAGATG
Found at i:42812865 original size:32 final size:33
Alignment explanation
Indices: 42812810--42812886 Score: 90
Period size: 32 Copynumber: 2.4 Consensus size: 33
42812800 GTTGACTGCT
*
42812810 TGGG-AGGGTGATGTTAAATGGGTAGAAGTTT-A
1 TGGGAAGGGTGATGATAAATGGGTAGAA-TTTAA
*
42812842 TGGGAAGGGTGATGATGAA-GGGTAGAATTTAA
1 TGGGAAGGGTGATGATAAATGGGTAGAATTTAA
42812874 TGGTGAA-GGTGAT
1 TGG-GAAGGGTGAT
42812887 CTGGAAAGGG
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
31 3 0.08
32 22 0.55
33 15 0.38
ACGTcount: A:0.30, C:0.00, G:0.42, T:0.29
Consensus pattern (33 bp):
TGGGAAGGGTGATGATAAATGGGTAGAATTTAA
Found at i:42822863 original size:24 final size:23
Alignment explanation
Indices: 42822836--42822921 Score: 82
Period size: 24 Copynumber: 3.6 Consensus size: 23
42822826 TTCGAGTCTC
*
42822836 TGTATTTAGTAGGATTTGAGCCGG
1 TGTATTTAGCAGG-TTTGAGCCGG
* *
42822860 TGTATTTAGCAGGCTTCGAGCTGG
1 TGTATTTAGCAGG-TTTGAGCCGG
* *
42822884 TGTATTTAGCAGGCTTCATGCCGG
1 TGTATTTAGCAGGTTTGA-GCCGG
* *
42822908 TGTGTTTAGTAGGT
1 TGTATTTAGCAGGT
42822922 ACTGTGTACT
Statistics
Matches: 50, Mismatches: 11, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
23 2 0.04
24 48 0.96
ACGTcount: A:0.17, C:0.13, G:0.33, T:0.37
Consensus pattern (23 bp):
TGTATTTAGCAGGTTTGAGCCGG
Found at i:42822907 original size:48 final size:48
Alignment explanation
Indices: 42822821--42822916 Score: 115
Period size: 48 Copynumber: 2.0 Consensus size: 48
42822811 AACTAAGTAC
* * *
42822821 CAGGCTTCGAGTCTCTGTATTTAGTAGGATTTGAGCCGGTGTATTTAG
1 CAGGCTTCGAGTCTCTGTATTTAGCAGGACTTCAGCCGGTGTATTTAG
* *
42822869 CAGGCTTCGAG-CTGGTGTATTTAGCAGG-CTTCATGCCGGTGTGTTTAG
1 CAGGCTTCGAGTCT-CTGTATTTAGCAGGACTTCA-GCCGGTGTATTTAG
42822917 TAGGTACTGT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
47 5 0.12
48 36 0.88
ACGTcount: A:0.17, C:0.17, G:0.31, T:0.35
Consensus pattern (48 bp):
CAGGCTTCGAGTCTCTGTATTTAGCAGGACTTCAGCCGGTGTATTTAG
Found at i:42830191 original size:69 final size:69
Alignment explanation
Indices: 42830050--42830184 Score: 243
Period size: 69 Copynumber: 2.0 Consensus size: 69
42830040 TACCTTCATA
*
42830050 AAGTGCCATTCAAAAATCCTGGAATCGTATTCCATTTGTAAAAGTGTGCAATTTGACGATCAATT
1 AAGTGCCATTCAAAAATCCTGGAATCGTATTCCATTTGTAAAAGTGTGCAATTTAACGATCAATT
42830115 GCAT
66 GCAT
* *
42830119 AAGTGCCATTCAAAAATCTTGGAATCGTATTCCATTTGTAGAAGTGTGCAATTTAACGATCAATT
1 AAGTGCCATTCAAAAATCCTGGAATCGTATTCCATTTGTAAAAGTGTGCAATTTAACGATCAATT
42830184 G
66 G
42830185 TGTAAGTCTC
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
69 63 1.00
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Consensus pattern (69 bp):
AAGTGCCATTCAAAAATCCTGGAATCGTATTCCATTTGTAAAAGTGTGCAATTTAACGATCAATT
GCAT
Found at i:42832903 original size:13 final size:13
Alignment explanation
Indices: 42832885--42832909 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42832875 AAGTGCGAGC
42832885 CTGTTGAAGACAT
1 CTGTTGAAGACAT
42832898 CTGTTGAAGACA
1 CTGTTGAAGACA
42832910 ATATGCAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.28
Consensus pattern (13 bp):
CTGTTGAAGACAT
Found at i:42835816 original size:24 final size:25
Alignment explanation
Indices: 42835779--42835826 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
42835769 TTAAATCTTT
**
42835779 GATTTTTAAATTTAAGTTTTAATTA
1 GATTTTTAAATTTAAAATTTAATTA
*
42835804 GATTTTT-ATTTTAAAATTTAATT
1 GATTTTTAAATTTAAAATTTAATT
42835827 CTTATGTTCC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.58
Consensus pattern (25 bp):
GATTTTTAAATTTAAAATTTAATTA
Found at i:42835821 original size:31 final size:33
Alignment explanation
Indices: 42835762--42835824 Score: 85
Period size: 31 Copynumber: 2.0 Consensus size: 33
42835752 AAATTTCATT
*
42835762 TTTTAAATTAAATCTTTGATTTTTAAATTTAAG
1 TTTTAAATTAAATCTTTGATTTTAAAATTTAAG
* *
42835795 TTTT-AATTAGAT-TTTTATTTTAAAATTTAA
1 TTTTAAATTAAATCTTTGATTTTAAAATTTAA
42835825 TTCTTATGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 16 0.59
32 7 0.26
33 4 0.15
ACGTcount: A:0.37, C:0.02, G:0.05, T:0.57
Consensus pattern (33 bp):
TTTTAAATTAAATCTTTGATTTTAAAATTTAAG
Found at i:42838104 original size:8 final size:8
Alignment explanation
Indices: 42838081--42838117 Score: 56
Period size: 8 Copynumber: 4.5 Consensus size: 8
42838071 CGGAGACGAC
42838081 GGTGATGGT
1 GGTGA-GGT
*
42838090 AGTGAGGT
1 GGTGAGGT
42838098 GGTGAGGT
1 GGTGAGGT
42838106 GGTGAGGT
1 GGTGAGGT
42838114 GGTG
1 GGTG
42838118 GTTTGGTGGC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
8 22 0.85
9 4 0.15
ACGTcount: A:0.14, C:0.00, G:0.59, T:0.27
Consensus pattern (8 bp):
GGTGAGGT
Found at i:42843334 original size:20 final size:20
Alignment explanation
Indices: 42843311--42843363 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
42843301 AATGTGCAAG
*
42843311 CAGGGGCACCGTAGTGTGA-A
1 CAGGGGCACCGAAGTGT-ATA
*
42843331 CAGGGACACCGAAGTGTATA
1 CAGGGGCACCGAAGTGTATA
*
42843351 CAAGGGCACCGAA
1 CAGGGGCACCGAA
42843364 ATGCAAATCC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 1 0.04
20 27 0.96
ACGTcount: A:0.32, C:0.23, G:0.34, T:0.11
Consensus pattern (20 bp):
CAGGGGCACCGAAGTGTATA
Found at i:42843604 original size:21 final size:21
Alignment explanation
Indices: 42843579--42843619 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
42843569 TATGTATTTA
*
42843579 TACAATTTACTAGCAACAATT
1 TACAATTTACCAGCAACAATT
42843600 TACAATTTACCAGCAACAAT
1 TACAATTTACCAGCAACAAT
42843620 AACTTATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.44, C:0.22, G:0.05, T:0.29
Consensus pattern (21 bp):
TACAATTTACCAGCAACAATT
Found at i:42845989 original size:18 final size:18
Alignment explanation
Indices: 42845962--42845996 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
42845952 TGCCAATTTA
*
42845962 TGAAACTGTGATGTTGTG
1 TGAAACTGTGATATTGTG
*
42845980 TGAAATTGTGATATTGT
1 TGAAACTGTGATATTGT
42845997 TTCTGTGATG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.03, G:0.29, T:0.43
Consensus pattern (18 bp):
TGAAACTGTGATATTGTG
Found at i:42848755 original size:10 final size:10
Alignment explanation
Indices: 42848740--42848773 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
42848730 AAATACTTTA
*
42848740 TATATTATAT
1 TATATTATAG
42848750 TATATTATAG
1 TATATTATAG
*
42848760 TATAGTATAG
1 TATATTATAG
42848770 TATA
1 TATA
42848774 CATAACCCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (10 bp):
TATATTATAG
Found at i:42848848 original size:57 final size:57
Alignment explanation
Indices: 42848780--42848897 Score: 236
Period size: 57 Copynumber: 2.1 Consensus size: 57
42848770 TATACATAAC
42848780 CCATGCATAAATAGAAAAGAAATTTTAAGATTTTAACTTTTGAATTCTTTATGTTTT
1 CCATGCATAAATAGAAAAGAAATTTTAAGATTTTAACTTTTGAATTCTTTATGTTTT
42848837 CCATGCATAAATAGAAAAGAAATTTTAAGATTTTAACTTTTGAATTCTTTATGTTTT
1 CCATGCATAAATAGAAAAGAAATTTTAAGATTTTAACTTTTGAATTCTTTATGTTTT
42848894 CCAT
1 CCAT
42848898 TGTGACTTTC
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 61 1.00
ACGTcount: A:0.36, C:0.10, G:0.10, T:0.43
Consensus pattern (57 bp):
CCATGCATAAATAGAAAAGAAATTTTAAGATTTTAACTTTTGAATTCTTTATGTTTT
Found at i:42848993 original size:19 final size:18
Alignment explanation
Indices: 42848947--42848995 Score: 52
Period size: 17 Copynumber: 2.8 Consensus size: 18
42848937 ATTACTTTTG
42848947 AAAAA-TAAT-TTTTAGA
1 AAAAATTAATATTTTAGA
42848963 AAATAATT--TATTTTATGA
1 AAA-AATTAATATTTTA-GA
42848981 AAAAATTAATATTTT
1 AAAAATTAATATTTT
42848996 TTGGTGTTCG
Statistics
Matches: 27, Mismatches: 0, Indels: 9
0.75 0.00 0.25
Matches are distributed among these distances:
16 4 0.15
17 11 0.41
18 6 0.22
19 6 0.22
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (18 bp):
AAAAATTAATATTTTAGA
Found at i:42849425 original size:23 final size:23
Alignment explanation
Indices: 42849399--42849451 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
42849389 AAACTAAACA
*
42849399 TTATTTAAAAAAAATACTCATAT
1 TTATATAAAAAAAATACTCATAT
** *
42849422 TTATATAATTAAAATATTCATAT
1 TTATATAAAAAAAATACTCATAT
*
42849445 TTTTATA
1 TTATATA
42849452 CTAGATTAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (23 bp):
TTATATAAAAAAAATACTCATAT
Found at i:42849857 original size:17 final size:18
Alignment explanation
Indices: 42849835--42849879 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
42849825 ACATTTACTA
42849835 TTAAT-ATATTTATAATT
1 TTAATAATATTTATAATT
*
42849852 TTAATAGATATTTATTA-T
1 TTAATA-ATATTTATAATT
42849870 TTAA-AATATT
1 TTAATAATATT
42849880 AATATTGAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 5 0.20
17 6 0.24
18 5 0.20
19 9 0.36
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (18 bp):
TTAATAATATTTATAATT
Found at i:42849945 original size:16 final size:16
Alignment explanation
Indices: 42849914--42849950 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
42849904 ATATGATGAA
42849914 TATTATTTAAAATTAT
1 TATTATTTAAAATTAT
42849930 TATT-TTTAAAATTTAT
1 TATTATTTAAAA-TTAT
42849946 TATTA
1 TATTA
42849951 AAATAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTATTTAAAATTAT
Done.