Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold52
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: 1774672
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.32
Warning! 127110 characters in sequence are not A, C, G, or T
File 5 of 9
Found at i:955673 original size:102 final size:101
Alignment explanation
Indices: 955530--955748 Score: 339
Period size: 102 Copynumber: 2.2 Consensus size: 101
955520 AAGTGGGAGA
** * * * *
955530 ATTGTTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTTG
1 ATTGTTGATTAAATGGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTA
955595 CCATTGATGACTAAATGGGAGATTTGGTAGCTTACC
66 CCATTGATGACTAAATGGGAGATTTGGTAGCTTACC
955631 ATTGTTGATTAAATGAGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTT
1 ATTGTTGATTAAATG-GAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTT
* * * *
955696 ACCATTGTTGACTAAATGGTAGATTTGGTAGGTTGCC
65 ACCATTGATGACTAAATGGGAGATTTGGTAGCTTACC
955733 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
955749 TGGTTTTTAC
Statistics
Matches: 107, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
101 16 0.15
102 91 0.85
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.40
Consensus pattern (101 bp):
ATTGTTGATTAAATGGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTA
CCATTGATGACTAAATGGGAGATTTGGTAGCTTACC
Found at i:956968 original size:29 final size:29
Alignment explanation
Indices: 956926--957003 Score: 93
Period size: 29 Copynumber: 2.7 Consensus size: 29
956916 TTGGTAAAAA
* * *
956926 TTTTCAAAAGTTATGATTGATAAATATAAC
1 TTTT-AAAAATTATGAATGACAAATATAAC
*
956956 TTTTAAAAATTATGAATGACAAATATAAT
1 TTTTAAAAATTATGAATGACAAATATAAC
**
956985 TTTTAAAAGGTATGAATGA
1 TTTTAAAAATTATGAATGA
957004 ATAACATGTA
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
29 38 0.90
30 4 0.10
ACGTcount: A:0.46, C:0.04, G:0.12, T:0.38
Consensus pattern (29 bp):
TTTTAAAAATTATGAATGACAAATATAAC
Found at i:957323 original size:14 final size:15
Alignment explanation
Indices: 957306--957337 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
957296 ATATTTTAAT
957306 TATTTTATAT-ATTA
1 TATTTTATATAATTA
957320 TA-TTTATATAATTA
1 TATTTTATATAATTA
957334 TATT
1 TATT
957338 AAAAATGATC
Statistics
Matches: 16, Mismatches: 0, Indels: 3
0.84 0.00 0.16
Matches are distributed among these distances:
13 7 0.44
14 8 0.50
15 1 0.06
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TATTTTATATAATTA
Found at i:959754 original size:17 final size:18
Alignment explanation
Indices: 959734--959783 Score: 50
Period size: 20 Copynumber: 2.8 Consensus size: 18
959724 GAGTCCATGG
959734 CAATA-AAATTAATAAGT
1 CAATAGAAATTAATAAGT
*
959751 CAATTAAGAAATTAACAAGT
1 CAA-T-AGAAATTAATAAGT
*
959771 CAA-ATAAATTAAT
1 CAATAGAAATTAAT
959784 TTCTTTGGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
17 11 0.41
18 1 0.04
19 1 0.04
20 14 0.52
ACGTcount: A:0.58, C:0.08, G:0.06, T:0.28
Consensus pattern (18 bp):
CAATAGAAATTAATAAGT
Found at i:960642 original size:34 final size:33
Alignment explanation
Indices: 960604--960754 Score: 167
Period size: 34 Copynumber: 4.5 Consensus size: 33
960594 ATCTTTTAGT
*
960604 CATTTAGTCAACAATGGTAAACCACCAAATCAC
1 CATTTAGTCAACAATGGCAAACCACCAAATCAC
* * * * *
960637 GCATTTAATTAATAATGGCAAACCACAAAATTAC
1 -CATTTAGTCAACAATGGCAAACCACCAAATCAC
* * *
960671 CTATTTAATCAACAATGGTAAATCACCAAATCAC
1 C-ATTTAGTCAACAATGGCAAACCACCAAATCAC
* *
960705 CTATTTAGTCAACAATGACAAGCCACCAAATCACC
1 C-ATTTAGTCAACAATGGCAAACCACCAAATCA-C
960740 CATTTAGTCAACAAT
1 CATTTAGTCAACAAT
960755 TCTCCTACTT
Statistics
Matches: 98, Mismatches: 17, Indels: 4
0.82 0.14 0.03
Matches are distributed among these distances:
33 1 0.01
34 95 0.97
35 2 0.02
ACGTcount: A:0.43, C:0.25, G:0.08, T:0.25
Consensus pattern (33 bp):
CATTTAGTCAACAATGGCAAACCACCAAATCAC
Found at i:960686 original size:68 final size:68
Alignment explanation
Indices: 960604--960754 Score: 196
Period size: 68 Copynumber: 2.2 Consensus size: 68
960594 ATCTTTTAGT
* * *
960604 CATTTAGTCAACAATGGTAAACCACCAAATCACGC-ATTTAATTAATAATGGCAAACCACAAAAT
1 CATTTAGTCAACAATGGTAAACCACCAAATCAC-CTATTTAATCAACAATGACAAACCACAAAAT
*
960668 TACC
65 CACC
* * * * * *
960672 TATTTAATCAACAATGGTAAATCACCAAATCACCTATTTAGTCAACAATGACAAGCCACCAAATC
1 CATTTAGTCAACAATGGTAAACCACCAAATCACCTATTTAATCAACAATGACAAACCACAAAATC
960737 ACC
66 ACC
960740 CATTTAGTCAACAAT
1 CATTTAGTCAACAAT
960755 TCTCCTACTT
Statistics
Matches: 70, Mismatches: 12, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
67 1 0.01
68 69 0.99
ACGTcount: A:0.43, C:0.25, G:0.08, T:0.25
Consensus pattern (68 bp):
CATTTAGTCAACAATGGTAAACCACCAAATCACCTATTTAATCAACAATGACAAACCACAAAATC
ACC
Found at i:965251 original size:34 final size:34
Alignment explanation
Indices: 965212--965325 Score: 192
Period size: 34 Copynumber: 3.4 Consensus size: 34
965202 TATCTTTTAG
* * *
965212 CCATTTAGTCAACAATGGTAAACCATCAAATCAA
1 CCATTTAGTCAACAATGATAAACCACCAAATCAC
*
965246 CCATTTAGTCAACAATGATAAACCACCAAATGAC
1 CCATTTAGTCAACAATGATAAACCACCAAATCAC
965280 CCATTTAGTCAACAATGATAAACCACCAAATCAC
1 CCATTTAGTCAACAATGATAAACCACCAAATCAC
965314 CCATTTAGTCAA
1 CCATTTAGTCAA
965326 TAAAAAATTG
Statistics
Matches: 75, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 75 1.00
ACGTcount: A:0.43, C:0.26, G:0.08, T:0.23
Consensus pattern (34 bp):
CCATTTAGTCAACAATGATAAACCACCAAATCAC
Found at i:966327 original size:27 final size:27
Alignment explanation
Indices: 966281--966333 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
966271 TTATGTAACC
*
966281 TAAAATTTTTGTATTATATTTTATTTA
1 TAAAATTTTTGTATTATATTTAATTTA
966308 TAAATATTTTTG-A-TATTATTTAATTT
1 TAAA-ATTTTTGTATTA-TATTTAATTT
966334 CTTAAAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
26 2 0.09
27 14 0.61
28 7 0.30
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (27 bp):
TAAAATTTTTGTATTATATTTAATTTA
Found at i:966537 original size:3 final size:3
Alignment explanation
Indices: 966529--966557 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
966519 GTTGTTAACG
966529 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
966558 TAGCATTATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:968434 original size:2 final size:2
Alignment explanation
Indices: 968427--968454 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
968417 TCAATGCATT
968427 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
968455 ATGTACATTA
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):
TA
Found at i:968513 original size:31 final size:29
Alignment explanation
Indices: 968477--968551 Score: 82
Period size: 31 Copynumber: 2.6 Consensus size: 29
968467 CATTGACGGA
* *
968477 TATATGATTAATTAATTAATTAATTAAAAT
1 TATATGATTAATTAA-AAAATAATTAAAAT
*
968507 CTATATGTATTGATTAAAAAATAATTAAAAT
1 -TATATG-ATTAATTAAAAAATAATTAAAAT
968538 T-TAT-ATTAATTAAA
1 TATATGATTAATTAAA
968552 TTTAAAACAA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
27 9 0.23
29 3 0.08
30 1 0.03
31 18 0.46
32 8 0.21
ACGTcount: A:0.51, C:0.01, G:0.04, T:0.44
Consensus pattern (29 bp):
TATATGATTAATTAAAAAATAATTAAAAT
Found at i:969813 original size:29 final size:29
Alignment explanation
Indices: 969780--969863 Score: 82
Period size: 29 Copynumber: 2.9 Consensus size: 29
969770 GTTAATTAAT
969780 ATTTTTAAAGTTTATAAATGATAAATAAA
1 ATTTTTAAAGTTTATAAATGATAAATAAA
* * * **
969809 ATTTTTAAAGGTTATGAATGGCT-AATGCA
1 ATTTTTAAAGTTTATAAAT-GATAAATAAA
969838 ATTTTTCAAAGTTT-TAAATGAATAAA
1 ATTTTT-AAAGTTTATAAATG-ATAAA
969864 ATGTAATTTT
Statistics
Matches: 43, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
28 1 0.02
29 32 0.74
30 10 0.23
ACGTcount: A:0.44, C:0.04, G:0.12, T:0.40
Consensus pattern (29 bp):
ATTTTTAAAGTTTATAAATGATAAATAAA
Found at i:972328 original size:2 final size:2
Alignment explanation
Indices: 972321--972350 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
972311 AAAATCTAAA
972321 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
972351 GTATGGATTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:973181 original size:19 final size:20
Alignment explanation
Indices: 973149--973186 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
973139 ACGTCTTATT
973149 TTTTATTAGATTT-GTTTAG
1 TTTTATTAGATTTGGTTTAG
973168 TTTTA-TAGATTTTGGTTTA
1 TTTTATTAGA-TTTGGTTTA
973187 TTGCAAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 4 0.24
19 8 0.47
20 5 0.29
ACGTcount: A:0.21, C:0.00, G:0.16, T:0.63
Consensus pattern (20 bp):
TTTTATTAGATTTGGTTTAG
Found at i:973713 original size:2 final size:2
Alignment explanation
Indices: 973692--973736 Score: 63
Period size: 2 Copynumber: 22.5 Consensus size: 2
973682 ATTTGTAAAT
* * *
973692 TA TA TA TG TA TA TG TG TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
973734 TA T
1 TA T
973737 CTTAGATTAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (2 bp):
TA
Found at i:974538 original size:20 final size:20
Alignment explanation
Indices: 974504--974574 Score: 81
Period size: 20 Copynumber: 3.6 Consensus size: 20
974494 CTTTATAAGT
*
974504 AATTACATA-AAATATTACA
1 AATTACATATAAATATTAAA
**
974523 AATTACATATAAATATTATT
1 AATTACATATAAATATTAAA
* *
974543 AGTTTCATATAAATATTAAA
1 AATTACATATAAATATTAAA
*
974563 AATTATATATAA
1 AATTACATATAA
974575 GCTTTTTTTT
Statistics
Matches: 42, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 9 0.21
20 33 0.79
ACGTcount: A:0.54, C:0.06, G:0.01, T:0.39
Consensus pattern (20 bp):
AATTACATATAAATATTAAA
Found at i:975812 original size:11 final size:10
Alignment explanation
Indices: 975785--975867 Score: 50
Period size: 10 Copynumber: 8.6 Consensus size: 10
975775 TCTCATGTTC
* *
975785 ATATATTTTT
1 ATATATTATA
975795 ATATATTATA
1 ATATATTATA
975805 ATTATATT-TA
1 A-TATATTATA
*
975815 AAATATTAT-
1 ATATATTATA
975824 ATAT-TTAT-
1 ATATATTATA
* *
975832 ATAAATTTTA
1 ATATATTATA
975842 ATATATTAATA
1 ATATATT-ATA
* *
975853 AT-TTTTATC
1 ATATATTATA
975862 ATATAT
1 ATATAT
975868 ATTTTAATAA
Statistics
Matches: 56, Mismatches: 11, Indels: 12
0.71 0.14 0.15
Matches are distributed among these distances:
8 7 0.12
9 15 0.27
10 24 0.43
11 10 0.18
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.55
Consensus pattern (10 bp):
ATATATTATA
Found at i:975859 original size:18 final size:20
Alignment explanation
Indices: 975785--975848 Score: 55
Period size: 19 Copynumber: 3.4 Consensus size: 20
975775 TCTCATGTTC
* * *
975785 ATATATTTTTATATATTATA
1 ATATATTTATATAAATTTTA
*
975805 AT-TATATT-TA-AAATATT-
1 ATATAT-TTATATAAATTTTA
975822 ATATATTTATATAAATTTTA
1 ATATATTTATATAAATTTTA
975842 ATATATT
1 ATATATT
975849 AATAATTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 10
0.71 0.08 0.20
Matches are distributed among these distances:
17 4 0.11
18 9 0.26
19 11 0.31
20 11 0.31
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
ATATATTTATATAAATTTTA
Found at i:975915 original size:19 final size:21
Alignment explanation
Indices: 975888--975943 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 21
975878 ATTCATACAT
975888 TTATTTTATATT-TATGTTAA
1 TTATTTTATATTATATGTTAA
*
975908 TT-TTTTATATTATATTTTAA
1 TTATTTTATATTATATGTTAA
975928 TTATTTTTTATATTAT
1 TTA--TTTTATATTAT
975944 CTTTTTAGCT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
19 9 0.29
20 11 0.35
23 11 0.35
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.70
Consensus pattern (21 bp):
TTATTTTATATTATATGTTAA
Found at i:975942 original size:12 final size:12
Alignment explanation
Indices: 975907--975950 Score: 63
Period size: 12 Copynumber: 3.7 Consensus size: 12
975897 ATTTATGTTA
975907 ATTTTTTATATT
1 ATTTTTTATATT
*
975919 ATATTTTA-ATT
1 ATTTTTTATATT
975930 ATTTTTTATATT
1 ATTTTTTATATT
975942 ATCTTTTTA
1 AT-TTTTTA
975951 GCTTGTAACC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
11 10 0.36
12 12 0.43
13 6 0.21
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.70
Consensus pattern (12 bp):
ATTTTTTATATT
Found at i:976354 original size:22 final size:23
Alignment explanation
Indices: 976320--976367 Score: 73
Period size: 22 Copynumber: 2.1 Consensus size: 23
976310 TCCCTAAAAA
976320 TTTTAAGAGTAATTTTTTT-ATC
1 TTTTAAGAGTAATTTTTTTCATC
976342 TTTT-AGAGATAATTTTTTTCATC
1 TTTTAAGAG-TAATTTTTTTCATC
976365 TTT
1 TTT
976368 AATGCCTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
21 4 0.17
22 14 0.58
23 6 0.25
ACGTcount: A:0.25, C:0.06, G:0.08, T:0.60
Consensus pattern (23 bp):
TTTTAAGAGTAATTTTTTTCATC
Found at i:978536 original size:67 final size:69
Alignment explanation
Indices: 978413--978555 Score: 166
Period size: 67 Copynumber: 2.1 Consensus size: 69
978403 TTAAAAATTA
* * * ** * *
978413 CATAT-AAATATTACTTTTACATATAATTACATATAACATGATTAATTTCACGTAAACATTA-TA
1 CATATAAAATATTACCTTTAAATATAATTACATAAAACATGACAAATTACACATAAACATTATTA
978476 AGTT
66 AGTT
* * *
978480 -ATATAAAATATTACCTTTAAATGTAATTACATAAAACATTACAAATTACATATAAACATTATTA
1 CATATAAAATATTACCTTTAAATATAATTACATAAAACATGACAAATTACACATAAACATTATTA
*
978544 ATTT
66 AGTT
978548 CATATAAA
1 CATATAAA
978556 TATCAAAAAT
Statistics
Matches: 62, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
66 4 0.06
67 46 0.74
68 5 0.08
69 7 0.11
ACGTcount: A:0.48, C:0.11, G:0.03, T:0.38
Consensus pattern (69 bp):
CATATAAAATATTACCTTTAAATATAATTACATAAAACATGACAAATTACACATAAACATTATTA
AGTT
Found at i:978538 original size:20 final size:20
Alignment explanation
Indices: 978504--978555 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
978494 CTTTAAATGT
978504 AATTACATA-AAACATTACA
1 AATTACATATAAACATTACA
**
978523 AATTACATATAAACATTATT
1 AATTACATATAAACATTACA
*
978543 AATTTCATATAAA
1 AATTACATATAAA
978556 TATCAAAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 9 0.31
20 20 0.69
ACGTcount: A:0.54, C:0.12, G:0.00, T:0.35
Consensus pattern (20 bp):
AATTACATATAAACATTACA
Found at i:979830 original size:20 final size:20
Alignment explanation
Indices: 979791--979830 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
979781 ATATTTTTAC
*
979791 ATATTATAAATATATCTAAA
1 ATATTATAAATATATATAAA
* *
979811 ATATTATATATTTATATAAA
1 ATATTATAAATATATATAAA
979831 TTTTAATATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (20 bp):
ATATTATAAATATATATAAA
Found at i:979906 original size:13 final size:12
Alignment explanation
Indices: 979890--979943 Score: 56
Period size: 13 Copynumber: 4.3 Consensus size: 12
979880 TTATTTCATG
979890 TTTATATTAATTT
1 TTTATATT-ATTT
* *
979903 TTTACATTATAT
1 TTTATATTATTT
979915 TTTA-ATTATTT
1 TTTATATTATTT
979926 TTTCATATTATCTT
1 TTT-ATATTAT-TT
979940 TTTA
1 TTTA
979944 ACGTGTAACT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
11 9 0.26
12 8 0.23
13 13 0.37
14 5 0.14
ACGTcount: A:0.28, C:0.06, G:0.00, T:0.67
Consensus pattern (12 bp):
TTTATATTATTT
Found at i:980675 original size:20 final size:22
Alignment explanation
Indices: 980629--980676 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 22
980619 TTATGTATTT
**
980629 ATATTATAATCGTATATTTTATC
1 ATATTATAATC-TATATTTTAAA
980652 ATATTATAAT-TATA-TTTAAA
1 ATATTATAATCTATATTTTAAA
980672 ATATT
1 ATATT
980677 TTATATTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 9 0.39
21 4 0.17
23 10 0.43
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.52
Consensus pattern (22 bp):
ATATTATAATCTATATTTTAAA
Found at i:980766 original size:13 final size:13
Alignment explanation
Indices: 980748--980772 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
980738 TATATCATAT
980748 TATATTATATTTG
1 TATATTATATTTG
980761 TATATTATATTT
1 TATATTATATTT
980773 AAAATTATTA
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:0.00, G:0.04, T:0.64
Consensus pattern (13 bp):
TATATTATATTTG
Found at i:981181 original size:26 final size:28
Alignment explanation
Indices: 981123--981180 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
981113 TATGTAATGT
* *
981123 AAAATTTTTATATTATATTTATTTATAA
1 AAAATTTTAATATTATAATTATTTATAA
981151 AAAATTTTAATATTATTAATT-TTT-TAA
1 AAAATTTTAATATTA-TAATTATTTATAA
981178 AAA
1 AAA
981181 TATTATTGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
27 6 0.22
28 17 0.63
29 4 0.15
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (28 bp):
AAAATTTTAATATTATAATTATTTATAA
Found at i:983581 original size:12 final size:12
Alignment explanation
Indices: 983564--983588 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
983554 TGTATCTTTA
983564 AGAAGAGAAGAG
1 AGAAGAGAAGAG
983576 AGAAGAGAAGAG
1 AGAAGAGAAGAG
983588 A
1 A
983589 AGAGAAGGGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (12 bp):
AGAAGAGAAGAG
Found at i:986876 original size:29 final size:29
Alignment explanation
Indices: 986823--986878 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
986813 ATATATTAAA
* *
986823 AATTACATATAAACATTATATTTACATGT
1 AATTACATATAAACATAATAATTACATGT
986852 AATTACATA-AAACATAAATAATTACAT
1 AATTACATATAAACAT-AATAATTACAT
986879 ATACACATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 6 0.25
29 18 0.75
ACGTcount: A:0.52, C:0.11, G:0.02, T:0.36
Consensus pattern (29 bp):
AATTACATATAAACATAATAATTACATGT
Found at i:986960 original size:20 final size:20
Alignment explanation
Indices: 986919--986970 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
986909 CTTTAAATGT
* *
986919 AATTATATA-AAAAATTACA
1 AATTACATATAAAAATTAAA
*
986938 AATTACATATAAATATTAAA
1 AATTACATATAAAAATTAAA
986958 AATTACATATAAA
1 AATTACATATAAA
986971 CTTTTCTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 8 0.28
20 21 0.72
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.33
Consensus pattern (20 bp):
AATTACATATAAAAATTAAA
Found at i:986962 original size:67 final size:68
Alignment explanation
Indices: 986797--986971 Score: 185
Period size: 67 Copynumber: 2.6 Consensus size: 68
986787 CTATTATTGC
* * * * *
986797 AATTACATA-TACGTATATATATTAAAAATTACATATAAACATTATATTTACATGTAATTACATA
1 AATTACAAATTACATATAAATATTAAAAATTACATATAAACATTACATTTAAATGTAATTACATA
986861 AAA
66 AAA
* * * * ** * * * *
986864 CA-TAAATAATTACATATACACATTATGAATTATATA-AAATATTACCTTTAAATGTAATTATAT
1 AATTACA-AATTACATATAAATATTAAAAATTACATATAAACATTACATTTAAATGTAATTACAT
986927 AAAA
65 AAAA
986931 AATTACAAATTACATATAAATATTAAAAATTACATATAAAC
1 AATTACAAATTACATATAAATATTAAAAATTACATATAAAC
986972 TTTTCTTTGA
Statistics
Matches: 82, Mismatches: 22, Indels: 7
0.74 0.20 0.06
Matches are distributed among these distances:
66 3 0.04
67 53 0.65
68 26 0.32
ACGTcount: A:0.53, C:0.09, G:0.02, T:0.36
Consensus pattern (68 bp):
AATTACAAATTACATATAAATATTAAAAATTACATATAAACATTACATTTAAATGTAATTACATA
AAA
Found at i:991936 original size:28 final size:27
Alignment explanation
Indices: 991889--991958 Score: 72
Period size: 27 Copynumber: 2.6 Consensus size: 27
991879 AAACAAGCCT
*
991889 CCATATTTGACAAATCCAAAGGA-AACCA
1 CCATTTTTGACAAATCCAAA--ATAACCA
991917 CCATTTTTGACAAA-CACAAAATAACCA
1 CCATTTTTGACAAATC-CAAAATAACCA
* *
991944 CTATTTTTAACAAAT
1 CCATTTTTGACAAAT
991959 AAATGGGTGG
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
26 1 0.03
27 18 0.50
28 17 0.47
ACGTcount: A:0.46, C:0.23, G:0.06, T:0.26
Consensus pattern (27 bp):
CCATTTTTGACAAATCCAAAATAACCA
Found at i:993155 original size:20 final size:20
Alignment explanation
Indices: 993116--993155 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
993106 ATATTTTTAC
*
993116 ATATTATAATTATATTTAAA
1 ATATTATAATTATATATAAA
993136 ATATTATATATT-TATATAAA
1 ATATTATA-ATTATATATAAA
993156 TTTTAATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 15 0.83
21 3 0.17
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
ATATTATAATTATATATAAA
Found at i:993218 original size:11 final size:11
Alignment explanation
Indices: 993202--993262 Score: 56
Period size: 11 Copynumber: 5.5 Consensus size: 11
993192 AATAAATTCG
993202 TATATTTATTT
1 TATATTTATTT
*
993213 TATATTTATGT
1 TATATTTATTT
993224 TA-ATTT-TTT
1 TATATTTATTT
*
993233 TGTATTGTATTT
1 TATATT-TATTT
993245 TAATTATTT-TTT
1 T-A-TATTTATTT
993257 TATATT
1 TATATT
993263 ATCTTTTTAG
Statistics
Matches: 41, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
9 3 0.07
10 11 0.27
11 14 0.34
12 8 0.20
13 1 0.02
14 4 0.10
ACGTcount: A:0.25, C:0.00, G:0.05, T:0.70
Consensus pattern (11 bp):
TATATTTATTT
Found at i:993247 original size:21 final size:20
Alignment explanation
Indices: 993205--993255 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 20
993195 AAATTCGTAT
993205 ATTTATTTTATATTTATGTTA
1 ATTT-TTTTATATTTATGTTA
* *
993226 ATTTTTTTGTATTGTATTTTA
1 ATTTTTTTATATT-TATGTTA
993247 ATTATTTTT
1 ATT-TTTTT
993256 TTATATTATC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 8 0.31
21 13 0.50
22 5 0.19
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.71
Consensus pattern (20 bp):
ATTTTTTTATATTTATGTTA
Found at i:995800 original size:29 final size:28
Alignment explanation
Indices: 995747--995806 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 28
995737 ATATGTTAAA
*
995747 AATTACATATAAATATTACCTTTACATAT
1 AATTACATATAAATATTA-CATTACATAT
995776 AATTACATATAACATGATTA-ATTACATAT
1 AATTACATATAA-AT-ATTACATTACATAT
995805 AA
1 AA
995807 ACATTATAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
29 22 0.79
30 2 0.07
31 4 0.14
ACGTcount: A:0.48, C:0.12, G:0.02, T:0.38
Consensus pattern (28 bp):
AATTACATATAAATATTACATTACATAT
Found at i:995835 original size:67 final size:69
Alignment explanation
Indices: 995752--995894 Score: 202
Period size: 67 Copynumber: 2.1 Consensus size: 69
995742 TTAAAAATTA
* * **
995752 CATAT-AAATATTACCTTTACATATAATTACATATAACATGATTAATTACATATAAACATTA-TA
1 CATATAAAATATTACCTTTAAATATAATTACATAAAACATGACAAATTACATATAAACATTATTA
995815 AGTT
66 AGTT
* *
995819 -ATATAAAATATTACCTTTAAATGTAATTACATAAAACATTACAAATTACATATAAACATTATTA
1 CATATAAAATATTACCTTTAAATATAATTACATAAAACATGACAAATTACATATAAACATTATTA
*
995883 ATTT
66 AGTT
995887 CATATAAA
1 CATATAAA
995895 TATCAAAAAT
Statistics
Matches: 66, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
66 4 0.06
67 50 0.76
68 5 0.08
69 7 0.11
ACGTcount: A:0.49, C:0.11, G:0.02, T:0.38
Consensus pattern (69 bp):
CATATAAAATATTACCTTTAAATATAATTACATAAAACATGACAAATTACATATAAACATTATTA
AGTT
Found at i:995877 original size:20 final size:20
Alignment explanation
Indices: 995843--995894 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
995833 CTTTAAATGT
995843 AATTACATA-AAACATTACA
1 AATTACATATAAACATTACA
**
995862 AATTACATATAAACATTATT
1 AATTACATATAAACATTACA
*
995882 AATTTCATATAAA
1 AATTACATATAAA
995895 TATCAAAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 9 0.31
20 20 0.69
ACGTcount: A:0.54, C:0.12, G:0.00, T:0.35
Consensus pattern (20 bp):
AATTACATATAAACATTACA
Found at i:997169 original size:20 final size:20
Alignment explanation
Indices: 997130--997169 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
997120 ATATTTTTAC
*
997130 ATATTATAAATATATCTAAA
1 ATATTATAAATATATATAAA
* *
997150 ATATTATATATTTATATAAA
1 ATATTATAAATATATATAAA
997170 TTTTAATATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (20 bp):
ATATTATAAATATATATAAA
Found at i:997265 original size:24 final size:26
Alignment explanation
Indices: 997229--997281 Score: 67
Period size: 24 Copynumber: 2.1 Consensus size: 26
997219 TTATTTCATG
997229 TTTATATTAATTTTTT-ACTATTATAT
1 TTTATATTAATTTTTTCA-TATTATAT
*
997255 TTTA-ATT-ATTTTTTCATATTATCT
1 TTTATATTAATTTTTTCATATTATAT
997279 TTT
1 TTT
997282 TAACGTGTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
24 17 0.68
25 4 0.16
26 4 0.16
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.68
Consensus pattern (26 bp):
TTTATATTAATTTTTTCATATTATAT
Found at i:998005 original size:20 final size:22
Alignment explanation
Indices: 997959--998006 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 22
997949 TTATGTATTT
**
997959 ATATTATAATCATATATTTTATG
1 ATATTATAAT-ATATATTTTAAA
997982 ATATTATAAT-TATA-TTTAAA
1 ATATTATAATATATATTTTAAA
998002 ATATT
1 ATATT
998007 TTATATTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 9 0.39
21 4 0.17
23 10 0.43
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (22 bp):
ATATTATAATATATATTTTAAA
Found at i:998513 original size:26 final size:28
Alignment explanation
Indices: 998455--998512 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
998445 TATGTAATGT
* *
998455 AAAATTTTTATATTATATTTATTTATAA
1 AAAATTTTAATATTATAATTATTTATAA
998483 AAAATTTTAATATTATTAATT-TTT-TAA
1 AAAATTTTAATATTA-TAATTATTTATAA
998510 AAA
1 AAA
998513 TATTATTGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
27 6 0.22
28 17 0.63
29 4 0.15
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (28 bp):
AAAATTTTAATATTATAATTATTTATAA
Found at i:1002264 original size:50 final size:50
Alignment explanation
Indices: 1002138--1002320 Score: 312
Period size: 50 Copynumber: 3.6 Consensus size: 50
1002128 ATGGCCACAT
* * *
1002138 TTGTCAAAGGTCGGTGAAGAATCGTTAACAATAATGGCCACCTCTCTCCA
1 TTGTCAAAGGTTGGTGAAGAATCGTCAACAATAATGGCCACCTCTCTCTA
*
1002188 TTTGTCAAAGGTTGGTGAAGAATCGTCAACAATTATGGCCACCTCTCTCTA
1 -TTGTCAAAGGTTGGTGAAGAATCGTCAACAATAATGGCCACCTCTCTCTA
*
1002239 TTGTCAAAGGTTGGTGAAGAATCGTCAACAATAATGGCCACCTCTCTTTA
1 TTGTCAAAGGTTGGTGAAGAATCGTCAACAATAATGGCCACCTCTCTCTA
1002289 TTGTCAAAGGTTGGTGAAGAATCGTCAACAAT
1 TTGTCAAAGGTTGGTGAAGAATCGTCAACAAT
1002321 TACGATAAAT
Statistics
Matches: 126, Mismatches: 6, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
50 80 0.63
51 46 0.37
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Consensus pattern (50 bp):
TTGTCAAAGGTTGGTGAAGAATCGTCAACAATAATGGCCACCTCTCTCTA
Found at i:1006855 original size:101 final size:100
Alignment explanation
Indices: 1006736--1006917 Score: 328
Period size: 101 Copynumber: 1.8 Consensus size: 100
1006726 GCCACATTTG
* **
1006736 TCAAAGGTTGGTGAAGAATCGTCAACAATAATGGCCACCTCTCTCTATTTGTCAAAGGTTGGTGA
1 TCAAAGATTGGTGAAGAATCGTCAACAATAATGGCCACCTCTCTCTA-TTGTCAAAGGTTAATGA
1006801 AGAATCGTCAACAATTATGGCCACCTCTCTCTATTA
65 AGAATCGTCAACAATTATGGCCACCTCTCTCTATTA
1006837 TCAAAGATTGGTGAAGAATCGTCAACAATAATGGCCACCTCTCTCTATTGTCAAAGGTTAATGAA
1 TCAAAGATTGGTGAAGAATCGTCAACAATAATGGCCACCTCTCTCTATTGTCAAAGGTTAATGAA
1006902 GAATCGTCAACAATTA
66 GAATCGTCAACAATTA
1006918 CGACAAATTT
Statistics
Matches: 78, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
100 32 0.41
101 46 0.59
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (100 bp):
TCAAAGATTGGTGAAGAATCGTCAACAATAATGGCCACCTCTCTCTATTGTCAAAGGTTAATGAA
GAATCGTCAACAATTATGGCCACCTCTCTCTATTA
Found at i:1006862 original size:50 final size:50
Alignment explanation
Indices: 1006733--1006915 Score: 312
Period size: 50 Copynumber: 3.6 Consensus size: 50
1006723 ATGGCCACAT
1006733 TTGTCAAAGGTTGGTGAAGAATCGTCAACAATAATGGCCACCTCTCTCTA
1 TTGTCAAAGGTTGGTGAAGAATCGTCAACAATAATGGCCACCTCTCTCTA
*
1006783 TTTGTCAAAGGTTGGTGAAGAATCGTCAACAATTATGGCCACCTCTCTCTA
1 -TTGTCAAAGGTTGGTGAAGAATCGTCAACAATAATGGCCACCTCTCTCTA
* *
1006834 TTATCAAAGATTGGTGAAGAATCGTCAACAATAATGGCCACCTCTCTCTA
1 TTGTCAAAGGTTGGTGAAGAATCGTCAACAATAATGGCCACCTCTCTCTA
**
1006884 TTGTCAAAGGTTAATGAAGAATCGTCAACAAT
1 TTGTCAAAGGTTGGTGAAGAATCGTCAACAAT
1006916 TACGACAAAT
Statistics
Matches: 124, Mismatches: 8, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
50 75 0.60
51 49 0.40
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29
Consensus pattern (50 bp):
TTGTCAAAGGTTGGTGAAGAATCGTCAACAATAATGGCCACCTCTCTCTA
Found at i:1007095 original size:18 final size:18
Alignment explanation
Indices: 1007041--1007096 Score: 51
Period size: 20 Copynumber: 2.9 Consensus size: 18
1007031 CTTATAATAA
1007041 TATAAAATTAA-ATTAATTT
1 TATAAAATTAATATT--TTT
* *
1007060 TATATATTTATATAATTTTT
1 TATAAAATTA-AT-ATTTTT
1007080 TATAAAATTAATATTTT
1 TATAAAATTAATATTTT
1007097 AACAAATTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
18 5 0.17
19 10 0.33
20 12 0.40
22 3 0.10
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TATAAAATTAATATTTTT
Found at i:1007111 original size:17 final size:17
Alignment explanation
Indices: 1007072--1007111 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
1007062 TATATTTATA
1007072 TAATT-TTTTATAAAAT
1 TAATTATTTTATAAAAT
1007088 TAA-TATTTTA-ACAAAT
1 TAATTATTTTATA-AAAT
1007104 TAATTATT
1 TAATTATT
1007112 AGATTTAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 2 0.10
16 15 0.71
17 4 0.19
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (17 bp):
TAATTATTTTATAAAAT
Found at i:1007521 original size:2 final size:2
Alignment explanation
Indices: 1007514--1007540 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1007504 ATAATCTATG
1007514 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
1007541 AAAGCATAAA
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:1009263 original size:29 final size:29
Alignment explanation
Indices: 1009210--1009265 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
1009200 ATATGTTAAA
* *
1009210 AATTACATATAAACAATATATTTACATGT
1 AATTACATATAAACAAAATAATTACATGT
1009239 AATTACATA-AAACATAAATAATTACAT
1 AATTACATATAAACA-AAATAATTACAT
1009266 ATACACATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 5 0.21
29 19 0.79
ACGTcount: A:0.54, C:0.11, G:0.02, T:0.34
Consensus pattern (29 bp):
AATTACATATAAACAAAATAATTACATGT
Found at i:1009347 original size:20 final size:20
Alignment explanation
Indices: 1009306--1009357 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
1009296 CGTTAAATGT
* *
1009306 AATTATATA-AAAAATTACA
1 AATTACATATAAAAATTAAA
*
1009325 AATTACATATAAATATTAAA
1 AATTACATATAAAAATTAAA
1009345 AATTACATATAAA
1 AATTACATATAAA
1009358 CTTTTCTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 8 0.28
20 21 0.72
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.33
Consensus pattern (20 bp):
AATTACATATAAAAATTAAA
Found at i:1012158 original size:3 final size:3
Alignment explanation
Indices: 1012150--1012196 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
1012140 ATTGTTAACG
1012150 TTA TTA TTA 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 TTA TTA TTA TT
1012197 TTAGCATTGT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1013214 original size:17 final size:18
Alignment explanation
Indices: 1013194--1013243 Score: 50
Period size: 20 Copynumber: 2.8 Consensus size: 18
1013184 GAGTCCTTGA
1013194 CAATA-AAATTAATAAGT
1 CAATAGAAATTAATAAGT
*
1013211 CAATTAAGAAATTAACAAGT
1 CAA-T-AGAAATTAATAAGT
*
1013231 CAA-ATAAATTAAT
1 CAATAGAAATTAAT
1013244 TTCTTTGGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
17 11 0.41
18 1 0.04
19 1 0.04
20 14 0.52
ACGTcount: A:0.58, C:0.08, G:0.06, T:0.28
Consensus pattern (18 bp):
CAATAGAAATTAATAAGT
Found at i:1014625 original size:18 final size:18
Alignment explanation
Indices: 1014602--1014636 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
1014592 AATTGTGTAG
1014602 GTTTGGGTTTTGTTTTAA
1 GTTTGGGTTTTGTTTTAA
1014620 GTTTGGGTTTTGTTTTA
1 GTTTGGGTTTTGTTTTA
1014637 GATTTTAAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.09, C:0.00, G:0.29, T:0.63
Consensus pattern (18 bp):
GTTTGGGTTTTGTTTTAA
Found at i:1015029 original size:10 final size:11
Alignment explanation
Indices: 1014999--1015054 Score: 50
Period size: 10 Copynumber: 5.5 Consensus size: 11
1014989 TATTATTAAA
1014999 ATATT-ATTTT
1 ATATTAATTTT
1015009 ATATTAATTTT
1 ATATTAATTTT
*
1015020 ATA-TATTTTT
1 ATATTAATTTT
*
1015030 A-ATTAAATTT
1 ATATTAATTTT
*
1015040 A-AGTAATTTT
1 ATATTAATTTT
1015050 -TATTA
1 ATATTA
1015055 TAAAATAATA
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 1 0.03
10 28 0.76
11 8 0.22
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (11 bp):
ATATTAATTTT
Found at i:1017836 original size:2 final size:2
Alignment explanation
Indices: 1017831--1017857 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1017821 CTCTCATTTC
1017831 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
1017858 GAGAGAGAGA
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:1019130 original size:27 final size:27
Alignment explanation
Indices: 1019082--1019187 Score: 83
Period size: 27 Copynumber: 3.9 Consensus size: 27
1019072 TCATATATTT
* * *
1019082 TTATATATTATAATTATA-TTTAAAGTG
1 TTATATATT-TATTTAAATTTTAAAGTA
1019109 TTATATATTTATTTAAATTTTAATA-TA
1 TTATATATTTATTTAAATTTTAA-AGTA
* * *
1019136 TTA-ATAATTCTTATCATATATTTAAAGTA
1 TTATATATTTATT-T-AAAT-TTTAAAGTA
*
1019165 TTATATATTTATTAAAATTTTAA
1 TTATATATTTATTTAAATTTTAA
1019188 TAAGTTCATA
Statistics
Matches: 62, Mismatches: 10, Indels: 14
0.72 0.12 0.16
Matches are distributed among these distances:
26 13 0.21
27 24 0.39
28 8 0.13
29 10 0.16
30 7 0.11
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.54
Consensus pattern (27 bp):
TTATATATTTATTTAAATTTTAAAGTA
Found at i:1019134 original size:20 final size:18
Alignment explanation
Indices: 1019098--1019186 Score: 58
Period size: 20 Copynumber: 4.7 Consensus size: 18
1019088 ATTATAATTA
*
1019098 TATTTAAAGTGTTATATATT
1 TATTTAAA-TTTTATATA-T
1019118 TATTTAAATTTTA-ATA-
1 TATTTAAATTTTATATAT
*
1019134 TATTAATAATTCTTATCATA-
1 TATTTA-AATT-TTAT-ATAT
*
1019154 TATTTAAAGTATTATATATT
1 TATTTAAA-TTTTATATA-T
*
1019174 TATTAAAATTTTA
1 TATTTAAATTTTA
1019187 ATAAGTTCAT
Statistics
Matches: 56, Mismatches: 6, Indels: 15
0.73 0.08 0.19
Matches are distributed among these distances:
16 5 0.09
17 4 0.07
18 9 0.16
19 14 0.25
20 24 0.43
ACGTcount: A:0.40, C:0.02, G:0.03, T:0.54
Consensus pattern (18 bp):
TATTTAAATTTTATATAT
Found at i:1019997 original size:16 final size:16
Alignment explanation
Indices: 1019945--1019997 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
1019935 TTTAAGATTT
*
1019945 TTTATATTTATATAAAT
1 TTTATATTT-TATAAAA
* *
1019962 TTTGATATATTA-ATAA
1 TTT-ATATTTTATAAAA
1019978 TTTATATTTTATAAAA
1 TTTATATTTTATAAAA
1019994 TTTA
1 TTTA
1019998 AAAATATATT
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
15 7 0.24
16 12 0.41
17 5 0.17
18 5 0.17
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (16 bp):
TTTATATTTTATAAAA
Found at i:1024203 original size:2 final size:2
Alignment explanation
Indices: 1024192--1024234 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
1024182 ATAAGTAAAC
1024192 CT CT CT -T CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1024233 CT
1 CT
1024235 ATATATATAT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
CT
Found at i:1025020 original size:28 final size:28
Alignment explanation
Indices: 1024959--1025013 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
1024949 TATCGTAATT
* * *
1024959 TAATTATTTTATATTTATTATATTTATA
1 TAATTATTTTAAAATTATTAAATTTATA
1024987 TAATTATTTTAAAATTATTAAATTTAT
1 TAATTATTTTAAAATTATTAAATTTAT
1025014 TAAATTAGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (28 bp):
TAATTATTTTAAAATTATTAAATTTATA
Found at i:1026109 original size:2 final size:2
Alignment explanation
Indices: 1026102--1026146 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1026092 TGGCTCAGCA
1026102 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
1026144 AT A
1 AT A
1026147 CTTAGCTAGC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1026296 original size:19 final size:19
Alignment explanation
Indices: 1026251--1026294 Score: 65
Period size: 18 Copynumber: 2.4 Consensus size: 19
1026241 TTAAAATCTT
*
1026251 TTAAA-TTAAAAAATTTTA
1 TTAAATTTAAAAAATTTAA
1026269 TTAAATTTAAAAAA-TTAA
1 TTAAATTTAAAAAATTTAA
1026287 TTAAATTT
1 TTAAATTT
1026295 TATATAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 16 0.67
19 8 0.33
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
TTAAATTTAAAAAATTTAA
Found at i:1027384 original size:17 final size:17
Alignment explanation
Indices: 1027362--1027437 Score: 68
Period size: 17 Copynumber: 4.5 Consensus size: 17
1027352 GATATATATT
* * *
1027362 AATTAAATTTATTTATG
1 AATTAAATTAAATTATA
1027379 AATTAAATTAAATTATA
1 AATTAAATTAAATTATA
*
1027396 AATTAAA--AAATTTTA
1 AATTAAATTAAATTATA
1027411 AATTTAAATTTAAATTA-A
1 AA-TTAAA-TTAAATTATA
*
1027429 AATTTAATT
1 AATTAAATT
1027438 TGATTCAATA
Statistics
Matches: 49, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
15 9 0.18
16 7 0.14
17 25 0.51
18 3 0.06
19 5 0.10
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (17 bp):
AATTAAATTAAATTATA
Found at i:1027433 original size:18 final size:18
Alignment explanation
Indices: 1027410--1027456 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 18
1027400 AAAAAATTTT
1027410 AAATTTAAATTTAAATT-A
1 AAATTTAAATTT-AATTCA
*
1027428 AAATTT-AATTTGATTCA
1 AAATTTAAATTTAATTCA
1027445 ATAATTTAAATT
1 A-AATTTAAATT
1027457 ATTATTTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 3 0.12
17 7 0.28
18 11 0.44
19 4 0.16
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (18 bp):
AAATTTAAATTTAATTCA
Found at i:1027437 original size:11 final size:12
Alignment explanation
Indices: 1027381--1027435 Score: 58
Period size: 12 Copynumber: 4.3 Consensus size: 12
1027371 TATTTATGAA
1027381 TTAAATT-AAAT
1 TTAAATTAAAAT
1027392 TATAAATTAAAAAATT
1 T-TAAATT--AAAA-T
*
1027408 TTAAATTTAAAT
1 TTAAATTAAAAT
1027420 TTAAATTAAAAT
1 TTAAATTAAAAT
1027432 TTAA
1 TTAA
1027436 TTTGATTCAA
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
11 1 0.03
12 22 0.59
13 3 0.08
15 9 0.24
16 2 0.05
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
TTAAATTAAAAT
Found at i:1027521 original size:30 final size:31
Alignment explanation
Indices: 1027462--1027528 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
1027452 AAATTATTAT
* *
1027462 TTAAATTTTATTAAAATAAAATATTTTATAA
1 TTAAATTTAAATAAAATAAAATATTTTATAA
**
1027493 TTAAATTTAAATAAAATATTAT-TTTTATAA
1 TTAAATTTAAATAAAATAAAATATTTTATAA
1027523 TTAAAT
1 TTAAAT
1027529 AGTGATCTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 14 0.44
31 18 0.56
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (31 bp):
TTAAATTTAAATAAAATAAAATATTTTATAA
Found at i:1027859 original size:5 final size:5
Alignment explanation
Indices: 1027811--1027855 Score: 63
Period size: 5 Copynumber: 9.0 Consensus size: 5
1027801 TAATCTCTAG
* * *
1027811 GAAGA GAAGG GAAGA GAAGA GAAGA GAAGA GAAGA AAAGA AAAGA
1 GAAGA GAAGA GAAGA GAAGA GAAGA GAAGA GAAGA GAAGA GAAGA
1027856 AAAGTGAGGG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
5 37 1.00
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (5 bp):
GAAGA
Found at i:1031244 original size:34 final size:35
Alignment explanation
Indices: 1031201--1031270 Score: 124
Period size: 35 Copynumber: 2.0 Consensus size: 35
1031191 TTGAATTGCT
*
1031201 GCAGAAACCAAC-AAAGAGGTTGGTTTCAAACTTG
1 GCAGAAACCAACAAAAGAGGCTGGTTTCAAACTTG
1031235 GCAGAAACCAACAAAAGAGGCTGGTTTCAAACTTG
1 GCAGAAACCAACAAAAGAGGCTGGTTTCAAACTTG
1031270 G
1 G
1031271 AATGTTGCAA
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
34 12 0.35
35 22 0.65
ACGTcount: A:0.39, C:0.19, G:0.24, T:0.19
Consensus pattern (35 bp):
GCAGAAACCAACAAAAGAGGCTGGTTTCAAACTTG
Found at i:1033771 original size:18 final size:18
Alignment explanation
Indices: 1033733--1033773 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
1033723 TTCAATTATA
**
1033733 AAATTTTAAAATTTAAAT
1 AAATTTTAAAACATAAAT
*
1033751 AAATTTTAAAACATAATT
1 AAATTTTAAAACATAAAT
1033769 AAATT
1 AAATT
1033774 AATTTGATTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (18 bp):
AAATTTTAAAACATAAAT
Found at i:1034031 original size:14 final size:13
Alignment explanation
Indices: 1033994--1034045 Score: 70
Period size: 14 Copynumber: 4.0 Consensus size: 13
1033984 ATATCAACCC
1033994 AAATTAATAAATT
1 AAATTAATAAATT
* *
1034007 AATTTTA-AAATT
1 AAATTAATAAATT
1034019 AAATTAATTAAATT
1 AAATTAA-TAAATT
1034033 AAATTAATAAATT
1 AAATTAATAAATT
1034046 TTGATTGATT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
12 10 0.30
13 11 0.33
14 12 0.36
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
AAATTAATAAATT
Found at i:1035644 original size:16 final size:14
Alignment explanation
Indices: 1035613--1035640 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1035603 TTAATTATAA
1035613 AATATATAAATATT
1 AATATATAAATATT
1035627 AATATATAAATATT
1 AATATATAAATATT
1035641 TTAAAAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
AATATATAAATATT
Found at i:1040068 original size:14 final size:14
Alignment explanation
Indices: 1040041--1040083 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
1040031 TATCCGATAT
* *
1040041 ATATTTAAACATGA
1 ATATTAAAATATGA
1040055 ATATTAAAATATGA
1 ATATTAAAATATGA
1040069 AT-TTAAATATATGA
1 ATATTAAA-ATATGA
1040083 A
1 A
1040084 AACCTTAGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
13 5 0.19
14 21 0.81
ACGTcount: A:0.53, C:0.02, G:0.07, T:0.37
Consensus pattern (14 bp):
ATATTAAAATATGA
Found at i:1045466 original size:61 final size:61
Alignment explanation
Indices: 1045329--1045477 Score: 162
Period size: 61 Copynumber: 2.4 Consensus size: 61
1045319 ATTTTTTTTC
* * * *
1045329 ATTATATATTATATTTTAATA-ATTTATATATTTATTTTAAATTTTTATATAGTATTATGTT
1 ATTATATA-TATATTTTAAAATATTTATATATTTATTATAAATTTTAATATAGTATAATGTT
* * *
1045390 ATTACATATATATTTTAACATATTT-TATATTTA-TATAAATTTTAATATATTTATAAT-TCGT
1 ATTATATATATATTTTAAAATATTTATATATTTATTATAAATTTTAATATA-GTATAATGT--T
*
1045451 ATTATATATAAATTTTAAAATATTTAT
1 ATTATATATATATTTTAAAATATTTAT
1045478 GTAATTATAT
Statistics
Matches: 74, Mismatches: 9, Indels: 9
0.80 0.10 0.10
Matches are distributed among these distances:
59 15 0.20
60 24 0.32
61 34 0.46
62 1 0.01
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (61 bp):
ATTATATATATATTTTAAAATATTTATATATTTATTATAAATTTTAATATAGTATAATGTT
Found at i:1045473 original size:16 final size:16
Alignment explanation
Indices: 1045411--1045473 Score: 54
Period size: 17 Copynumber: 3.8 Consensus size: 16
1045401 ATTTTAACAT
*
1045411 ATTTTATATTTATATAA
1 ATTTTA-ATATATATAA
*
1045428 ATTTTAATATATTTATA
1 ATTTTAATATATATA-A
* *
1045445 ATTCGTATTATATATAA
1 ATT-TTAATATATATAA
*
1045462 ATTTTAAAATAT
1 ATTTTAATATAT
1045474 TTATGTAATT
Statistics
Matches: 36, Mismatches: 8, Indels: 5
0.73 0.16 0.10
Matches are distributed among these distances:
16 13 0.36
17 14 0.39
18 9 0.25
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (16 bp):
ATTTTAATATATATAA
Found at i:1045505 original size:21 final size:21
Alignment explanation
Indices: 1045479--1045535 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
1045469 AATATTTATG
1045479 TAATTATATTTTATCTTATTT
1 TAATTATATTTTATCTTATTT
* *
1045500 TAATTATTTTTATATCATATTT
1 TAATTATATTT-TATCTTATTT
*
1045522 TTA-TA-ATTTTATCT
1 TAATTATATTTTATCT
1045536 AATATTATCA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
19 4 0.13
20 3 0.10
21 12 0.40
22 11 0.37
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (21 bp):
TAATTATATTTTATCTTATTT
Found at i:1045520 original size:22 final size:21
Alignment explanation
Indices: 1045479--1045531 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 21
1045469 AATATTTATG
* *
1045479 TAATTATATTTTATCTTATTT
1 TAATTATTTTTTATCATATTT
1045500 TAATTATTTTTATATCATATTT
1 TAATTATTTTT-TATCATATTT
* *
1045522 TTATAATTTT
1 TAATTATTTT
1045532 ATCTAATATT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
21 10 0.37
22 17 0.63
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (21 bp):
TAATTATTTTTTATCATATTT
Found at i:1045947 original size:2 final size:2
Alignment explanation
Indices: 1045940--1045967 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1045930 AATATAACAA
1045940 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
1045968 GAGGCTAACA
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:1047183 original size:21 final size:22
Alignment explanation
Indices: 1047148--1047197 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
1047138 AATTTGATAT
1047148 TAAT-ATTTATAATTAAATAAA
1 TAATAATTTATAATTAAATAAA
*
1047169 -AATTAATTT-TAATTAATTAAA
1 TAA-TAATTTATAATTAAATAAA
1047190 TAATAATT
1 TAATAATT
1047198 CAATAAAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
20 2 0.08
21 17 0.68
22 6 0.24
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
TAATAATTTATAATTAAATAAA
Found at i:1047470 original size:18 final size:15
Alignment explanation
Indices: 1047426--1047463 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
1047416 TTTTTAAAAA
1047426 ATATTATTTAAATTT
1 ATATTATTTAAATTT
*
1047441 ATATCATTTAAATTT
1 ATATTATTTAAATTT
*
1047456 ATTTTATT
1 ATATTATT
1047464 ATTTAAAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.61
Consensus pattern (15 bp):
ATATTATTTAAATTT
Found at i:1048062 original size:2 final size:2
Alignment explanation
Indices: 1048055--1048081 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1048045 AGTAAGATCA
1048055 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
1048082 AATTAAAAAG
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:1050889 original size:16 final size:16
Alignment explanation
Indices: 1050868--1050930 Score: 51
Period size: 16 Copynumber: 3.8 Consensus size: 16
1050858 TAAAATATGA
1050868 TATAAAATATAAATATT
1 TATAAAATATAAA-ATT
1050885 T-TAAAATTTATAAAA--
1 TATAAAA--TATAAAATT
*
1050900 TATAAATATTTTAAAATT
1 TATAAA-A-TATAAAATT
1050918 TATAAAATATAAA
1 TATAAAATATAAA
1050931 TTATTAACTT
Statistics
Matches: 38, Mismatches: 2, Indels: 13
0.72 0.04 0.25
Matches are distributed among these distances:
15 1 0.03
16 21 0.55
17 4 0.11
18 12 0.32
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TATAAAATATAAAATT
Found at i:1050899 original size:25 final size:25
Alignment explanation
Indices: 1050868--1050931 Score: 128
Period size: 25 Copynumber: 2.6 Consensus size: 25
1050858 TAAAATATGA
1050868 TATAAAATATAAATATTTTAAAATT
1 TATAAAATATAAATATTTTAAAATT
1050893 TATAAAATATAAATATTTTAAAATT
1 TATAAAATATAAATATTTTAAAATT
1050918 TATAAAATATAAAT
1 TATAAAATATAAAT
1050932 TATTAACTTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (25 bp):
TATAAAATATAAATATTTTAAAATT
Found at i:1050965 original size:8 final size:8
Alignment explanation
Indices: 1050868--1050983 Score: 60
Period size: 9 Copynumber: 13.8 Consensus size: 8
1050858 TAAAATATGA
1050868 TATAAAA-
1 TATAAAAT
1050875 TATAAATAT
1 TATAAA-AT
*
1050884 TTTAAAATT
1 TATAAAA-T
1050893 TATAAAA-
1 TATAAAAT
1050900 TATAAATAT
1 TATAAA-AT
*
1050909 TTTAAAATT
1 TATAAAA-T
1050918 TATAAAA-
1 TATAAAAT
1050925 TAT-AAAT
1 TATAAAAT
* *
1050932 TATTAACT
1 TATAAAAT
1050940 TATTAAAATTT
1 TA-TAAAA--T
1050951 TAAATAAAAT
1 T--ATAAAAT
*
1050961 TATAATAT
1 TATAAAAT
*
1050969 AATAAAAT
1 TATAAAAT
1050977 ATATAAA
1 -TATAAA
1050984 TATAATAGGA
Statistics
Matches: 84, Mismatches: 11, Indels: 26
0.69 0.09 0.21
Matches are distributed among these distances:
6 3 0.04
7 18 0.21
8 21 0.25
9 32 0.38
10 2 0.02
11 2 0.02
12 5 0.06
13 1 0.01
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (8 bp):
TATAAAAT
Found at i:1052002 original size:18 final size:18
Alignment explanation
Indices: 1051839--1052026 Score: 111
Period size: 18 Copynumber: 10.4 Consensus size: 18
1051829 CAGAAACCGC
1051839 ACCTGGAGCATGACTTGA
1 ACCTGGAGCATGACTTGA
* * *
1051857 ACTTGGAGCA-GAATCCGA
1 ACCTGGAGCATGACT-TGA
1051875 ACCTGGAG-ACTGACTTGA
1 ACCTGGAGCA-TGACTTGA
** * *
1051893 ATTTGGAGCA-GAATCCGA
1 ACCTGGAGCATGACT-TGA
1051911 ACCTGGAG-ACTGACTTGA
1 ACCTGGAGCA-TGACTTGA
* * *
1051929 ACTTGGAGCA-GAATCCGA
1 ACCTGGAGCATGACT-TGA
*
1051947 ACCTGGACCATGACTTGA
1 ACCTGGAGCATGACTTGA
* * *
1051965 ACTTGGAGCA-GAATCCGA
1 ACCTGGAGCATGACT-TGA
1051983 ACCTGGAGCATGACTTGA
1 ACCTGGAGCATGACTTGA
* *
1052001 A-CTCGGAGCATAACATGA
1 ACCT-GGAGCATGACTTGA
*
1052019 ACTTGGAG
1 ACCTGGAG
1052027 GAGAATTCGG
Statistics
Matches: 125, Mismatches: 31, Indels: 28
0.68 0.17 0.15
Matches are distributed among these distances:
17 16 0.13
18 94 0.75
19 15 0.12
ACGTcount: A:0.31, C:0.22, G:0.27, T:0.20
Consensus pattern (18 bp):
ACCTGGAGCATGACTTGA
Found at i:1052026 original size:36 final size:36
Alignment explanation
Indices: 1051784--1052010 Score: 332
Period size: 36 Copynumber: 6.3 Consensus size: 36
1051774 AGAACCCGAA
* * ** *
1051784 AACTTGGAGCAGAATCTGGACCTGGAGCACAACCTG
1 AACTTGGAGCAGAATCCGAACCTGGAGCATGACTTG
* *
1051820 AACTTGGAGCAGAAACCGCACCTGGAGCATGACTTG
1 AACTTGGAGCAGAATCCGAACCTGGAGCATGACTTG
1051856 AACTTGGAGCAGAATCCGAACCTGGAG-ACTGACTTG
1 AACTTGGAGCAGAATCCGAACCTGGAGCA-TGACTTG
*
1051892 AATTTGGAGCAGAATCCGAACCTGGAG-ACTGACTTG
1 AACTTGGAGCAGAATCCGAACCTGGAGCA-TGACTTG
*
1051928 AACTTGGAGCAGAATCCGAACCTGGACCATGACTTG
1 AACTTGGAGCAGAATCCGAACCTGGAGCATGACTTG
1051964 AACTTGGAGCAGAATCCGAACCTGGAGCATGACTTG
1 AACTTGGAGCAGAATCCGAACCTGGAGCATGACTTG
*
1052000 AACTCGGAGCA
1 AACTTGGAGCA
1052011 TAACATGAAC
Statistics
Matches: 176, Mismatches: 13, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
35 1 0.01
36 174 0.99
37 1 0.01
ACGTcount: A:0.31, C:0.23, G:0.27, T:0.19
Consensus pattern (36 bp):
AACTTGGAGCAGAATCCGAACCTGGAGCATGACTTG
Found at i:1052986 original size:27 final size:27
Alignment explanation
Indices: 1052948--1053001 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
1052938 GAAGGATGTC
1052948 ATTTAAAAGATTTGAGTAATTAAAGAA
1 ATTTAAAAGATTTGAGTAATTAAAGAA
* *
1052975 ATTTTAAAGATTTGAGTAATTGAAGAA
1 ATTTAAAAGATTTGAGTAATTAAAGAA
1053002 GACTGTAAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.17, T:0.35
Consensus pattern (27 bp):
ATTTAAAAGATTTGAGTAATTAAAGAA
Found at i:1057368 original size:10 final size:10
Alignment explanation
Indices: 1057313--1057396 Score: 57
Period size: 10 Copynumber: 8.4 Consensus size: 10
1057303 ACTATATTGG
*
1057313 ATAATATTAA
1 ATAATATTAT
1057323 ATAATATTAT
1 ATAATATTAT
* *
1057333 ATAAATATAAA
1 AT-AATATTAT
**
1057344 ATAATTAAAAT
1 ATAA-TATTAT
1057355 ATAATATTAT
1 ATAATATTAT
1057365 ATAA-A-TAT
1 ATAATATTAT
*
1057373 ATTAATATTTT
1 A-TAATATTAT
*
1057384 AAAAT-TTAT
1 ATAATATTAT
1057393 ATAA
1 ATAA
1057397 CGTAAATTAT
Statistics
Matches: 58, Mismatches: 11, Indels: 11
0.73 0.14 0.14
Matches are distributed among these distances:
8 4 0.07
9 10 0.17
10 25 0.43
11 19 0.33
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (10 bp):
ATAATATTAT
Found at i:1057368 original size:21 final size:20
Alignment explanation
Indices: 1057313--1057368 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 20
1057303 ACTATATTGG
**
1057313 ATAATATTAAATAATATTAT
1 ATAATATTAAATAATAAAAT
*
1057333 ATAAATATAAAATAATTAAAAT
1 AT-AATATTAAATAA-TAAAAT
*
1057355 ATAATATTATATAA
1 ATAATATTAAATAA
1057369 ATATATTAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
20 2 0.07
21 21 0.72
22 6 0.21
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
ATAATATTAAATAATAAAAT
Found at i:1057370 original size:16 final size:16
Alignment explanation
Indices: 1057323--1057373 Score: 68
Period size: 16 Copynumber: 3.2 Consensus size: 16
1057313 ATAATATTAA
1057323 ATAATATTATATAAAT
1 ATAATATTATATAAAT
* *
1057339 ATAAAATAAT-TAAAAT
1 ATAATATTATAT-AAAT
1057355 ATAATATTATATAAAT
1 ATAATATTATATAAAT
1057371 ATA
1 ATA
1057374 TTAATATTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 1 0.03
16 27 0.93
17 1 0.03
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
ATAATATTATATAAAT
Found at i:1058153 original size:18 final size:19
Alignment explanation
Indices: 1058119--1058154 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1058109 TGGTAAAGTT
1058119 AAATAATAAATATAATAAA
1 AAATAATAAATATAATAAA
*
1058138 AAATATTAAA-ATAATAA
1 AAATAATAAATATAATAA
1058155 TATAATAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (19 bp):
AAATAATAAATATAATAAA
Found at i:1058534 original size:28 final size:28
Alignment explanation
Indices: 1058503--1058567 Score: 85
Period size: 28 Copynumber: 2.3 Consensus size: 28
1058493 AAATATATAA
***
1058503 AAAGTAATATATTTTTTAAAAATTTAAT
1 AAAGTAATATATTAAGTAAAAATTTAAT
*
1058531 AAAGTAATATATTAAGTAAAAATTTCAT
1 AAAGTAATATATTAAGTAAAAATTTAAT
*
1058559 AAAATAATA
1 AAAGTAATA
1058568 AATAAATAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.55, C:0.02, G:0.05, T:0.38
Consensus pattern (28 bp):
AAAGTAATATATTAAGTAAAAATTTAAT
Found at i:1058785 original size:3 final size:3
Alignment explanation
Indices: 1058779--1058828 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
1058769 TTCTAAGGTT
1058779 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
1058827 TT
1 TT
1058829 TATTTTAGGA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1060584 original size:24 final size:25
Alignment explanation
Indices: 1060556--1060629 Score: 76
Period size: 29 Copynumber: 2.8 Consensus size: 25
1060546 TGATGTTTAA
1060556 AATATTATATATTTATATAAATTTT
1 AATATTATATATTTATATAAATTTT
* *
1060581 ATATTAATTATTTGTATTATATAAATTTT
1 A-A-T-ATTATATAT-TTATATAAATTTT
*
1060610 AATATATATATATATATATA
1 AATAT-TATATATTTATATA
1060630 TATGTATATA
Statistics
Matches: 39, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
25 1 0.03
26 9 0.23
27 7 0.18
28 8 0.21
29 14 0.36
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (25 bp):
AATATTATATATTTATATAAATTTT
Found at i:1060616 original size:2 final size:2
Alignment explanation
Indices: 1060611--1060640 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1060601 ATAAATTTTA
*
1060611 AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1060641 GGTGCTAGGC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1061855 original size:20 final size:21
Alignment explanation
Indices: 1061814--1061863 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 21
1061804 ATTTAATTTT
*
1061814 TAAAT-TAAAATTAATAAATA
1 TAAATATAATATTAATAAATA
*
1061834 TAAATATAATATTAAT-ACTA
1 TAAATATAATATTAATAAATA
*
1061854 TATATATAAT
1 TAAATATAAT
1061864 TATTTAAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 17 0.65
21 9 0.35
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAATATAATATTAATAAATA
Found at i:1062164 original size:19 final size:20
Alignment explanation
Indices: 1062129--1062167 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
1062119 TAGATAACTG
*
1062129 TTAATATATACTTTTTATTT
1 TTAATAAATACTTTTTATTT
1062149 TTAATAAATA-TTTTTATTT
1 TTAATAAATACTTTTTATTT
1062168 ACTTAATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (20 bp):
TTAATAAATACTTTTTATTT
Found at i:1062333 original size:33 final size:33
Alignment explanation
Indices: 1062265--1062337 Score: 87
Period size: 33 Copynumber: 2.2 Consensus size: 33
1062255 ACATTTATCT
* *
1062265 ATAAATATATATAATTTTTTAAAAATTCATAAA
1 ATAAATATAAATAATTTTTTAAAAATTAATAAA
*
1062298 ATAAATATTAAATAATTTTTTTTAAAA-TAAT-AA
1 ATAAATA-TAAATAA-TTTTTTAAAAATTAATAAA
1062331 ATAAATA
1 ATAAATA
1062338 ATTTTTTTCA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
33 16 0.46
34 9 0.26
35 10 0.29
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.42
Consensus pattern (33 bp):
ATAAATATAAATAATTTTTTAAAAATTAATAAA
Found at i:1062546 original size:3 final size:3
Alignment explanation
Indices: 1062538--1062572 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
1062528 GTCTTCTCCT
1062538 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1062573 TAGGATAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1063972 original size:13 final size:14
Alignment explanation
Indices: 1063954--1063987 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
1063944 ACTTTTAATT
1063954 TTATTAAA-TTATA
1 TTATTAAATTTATA
*
1063967 TTATTAAATTTTTA
1 TTATTAAATTTATA
1063981 TTATTAA
1 TTATTAA
1063988 TAAATTAAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 8 0.42
14 11 0.58
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TTATTAAATTTATA
Found at i:1064604 original size:280 final size:280
Alignment explanation
Indices: 1064103--1064893 Score: 1555
Period size: 280 Copynumber: 2.8 Consensus size: 280
1064093 TATCACTATG
*
1064103 CATATCGAGATAATTTTTTCTTTAAAATTATTTATCAAAGTTAACATGAGTAATTTAATTTGTTA
1 CATATCGAGATAGTTTTTTCTTTAAAATTATTTATCAAAGTTAACATGAGTAATTTAATTTGTTA
1064168 CTAATAAAAATTTAGTAATATAACTTGATAAAATTAATCGTGTATAAAAATTATGCTAAATTCAA
66 CTAATAAAAATTTAGTAATATAACTTGATAAAATTAATCGTGTATAAAAATTATGCTAAATTCAA
*
1064233 GAACTCAAAATTTAAATTATCCATAAAAATTAAAAAATATTTTATATTAATAATTTAAATTAAAA
131 GAACTCAAAATTTAAATTATCCATAAAAATTTAAAAATATTTTATATTAATAATTTAAATTAAAA
1064298 AATATTTTTTATTACTAAAATTGACTCAAATTAAAATTATTTATCCATATCGAGATAGTTTTTTA
196 AATATTTTTTATTACTAAAATTGACTCAAATTAAAATTATTTATCCATATCGAGATAGTTTTTTA
1064363 AATTAATAATTTAAATTATC
261 AATTAATAATTTAAATTATC
1064383 CATATCGAGATAGTTTTTTCTTTAAAATTATTTATCAAAGTTAACATGAGTAATTTAATTTGTTA
1 CATATCGAGATAGTTTTTTCTTTAAAATTATTTATCAAAGTTAACATGAGTAATTTAATTTGTTA
1064448 CTAATAAAAATTTAGTAATATAACTTGATAAAATTAATCGTGTATAAAAATTATGCTAAATTCAA
66 CTAATAAAAATTTAGTAATATAACTTGATAAAATTAATCGTGTATAAAAATTATGCTAAATTCAA
1064513 GAACTCAAAATTTAAATTATCCATAAAAATTTAAAAATATTTTATATTAATAATTTAAATTAAAA
131 GAACTCAAAATTTAAATTATCCATAAAAATTTAAAAATATTTTATATTAATAATTTAAATTAAAA
1064578 AATATTTTTTATTACTAAAATTGACTCAAATTAAAATTATTTATCCATATCGAGATAGTTTTTTA
196 AATATTTTTTATTACTAAAATTGACTCAAATTAAAATTATTTATCCATATCGAGATAGTTTTTTA
1064643 AATTAATAATTTAAATTATC
261 AATTAATAATTTAAATTATC
1064663 CATATCGAGATAGTTTTTTCTTTAAAATTATTTATCAAAGTTAACATGAGTAATTTAATTTGTTA
1 CATATCGAGATAGTTTTTTCTTTAAAATTATTTATCAAAGTTAACATGAGTAATTTAATTTGTTA
*
1064728 CTAATAAAAATTTAGTAATATAACTTGATAAAATTAATCGTGTATAAAAATTATGTTAAATTCAA
66 CTAATAAAAATTTAGTAATATAACTTGATAAAATTAATCGTGTATAAAAATTATGCTAAATTCAA
1064793 GAACTCAAAATTTAAATTATCCATAAAAATTTAAAAATATTTTATATTAATAATTTAAATTAAAA
131 GAACTCAAAATTTAAATTATCCATAAAAATTTAAAAATATTTTATATTAATAATTTAAATTAAAA
1064858 AATATTTTTTATTACTAAAATTGACTCAAATTAAAA
196 AATATTTTTTATTACTAAAATTGACTCAAATTAAAA
1064894 AAATATATCC
Statistics
Matches: 508, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
280 508 1.00
ACGTcount: A:0.45, C:0.07, G:0.06, T:0.41
Consensus pattern (280 bp):
CATATCGAGATAGTTTTTTCTTTAAAATTATTTATCAAAGTTAACATGAGTAATTTAATTTGTTA
CTAATAAAAATTTAGTAATATAACTTGATAAAATTAATCGTGTATAAAAATTATGCTAAATTCAA
GAACTCAAAATTTAAATTATCCATAAAAATTTAAAAATATTTTATATTAATAATTTAAATTAAAA
AATATTTTTTATTACTAAAATTGACTCAAATTAAAATTATTTATCCATATCGAGATAGTTTTTTA
AATTAATAATTTAAATTATC
Found at i:1068772 original size:23 final size:24
Alignment explanation
Indices: 1068717--1068772 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 24
1068707 ACATAATATA
* *
1068717 ATAAATTAATAAATAGATTATAAT
1 ATAAATTCATAAATAAATTATAAT
* *
1068741 ATTATTTCATAAA-AAATTATAAT
1 ATAAATTCATAAATAAATTATAAT
*
1068764 GTAAATTCA
1 ATAAATTCA
1068773 AGAGTTATCA
Statistics
Matches: 25, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
23 15 0.60
24 10 0.40
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.39
Consensus pattern (24 bp):
ATAAATTCATAAATAAATTATAAT
Found at i:1084810 original size:12 final size:12
Alignment explanation
Indices: 1084793--1084833 Score: 64
Period size: 12 Copynumber: 3.4 Consensus size: 12
1084783 GAGTCTTGCA
* *
1084793 CATGCATACATT
1 CATGCATCCATC
1084805 CATGCATCCATC
1 CATGCATCCATC
1084817 CATGCATCCATC
1 CATGCATCCATC
1084829 CATGC
1 CATGC
1084834 TTGCACTGCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.27, C:0.37, G:0.10, T:0.27
Consensus pattern (12 bp):
CATGCATCCATC
Found at i:1085937 original size:35 final size:35
Alignment explanation
Indices: 1085838--1085943 Score: 105
Period size: 33 Copynumber: 3.1 Consensus size: 35
1085828 CGGACTAGTT
* *
1085838 TAAAATTTATTTTATTATTAAAAATAAT-ATTTAAA
1 TAAAAATTATTTTATTA-TATAAATAATAATTTAAA
* * *
1085873 -AAAATAATATTAATATT-TAT-AATTA-AATTTAAA
1 TAAAA-ATTATT-TTATTATATAAATAATAATTTAAA
1085906 TAAAAATTATTTTATTATATAAATAATAATTTAAA
1 TAAAAATTATTTTATTATATAAATAATAATTTAAA
1085941 TAA
1 TAA
1085944 GGTCAAGTTA
Statistics
Matches: 56, Mismatches: 8, Indels: 14
0.72 0.10 0.18
Matches are distributed among these distances:
32 4 0.07
33 19 0.34
34 14 0.25
35 15 0.27
36 4 0.07
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (35 bp):
TAAAAATTATTTTATTATATAAATAATAATTTAAA
Found at i:1086374 original size:22 final size:22
Alignment explanation
Indices: 1086348--1086389 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
1086338 AAATTTTATT
1086348 TAAAT-TTAATTATAAAAATATA
1 TAAATATTAA-TATAAAAATATA
1086370 TAAATATTAATATAAAAATA
1 TAAATATTAATATAAAAATA
1086390 ATTTTTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
TAAATATTAATATAAAAATATA
Found at i:1087015 original size:22 final size:22
Alignment explanation
Indices: 1086990--1087031 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1086980 TATTTGTATT
*
1086990 TAAAT-TTAATTATAATAATATA
1 TAAATATTAA-TATAAAAATATA
1087012 TAAATATTAATATAAAAATA
1 TAAATATTAATATAAAAATA
1087032 ATTTATTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
TAAATATTAATATAAAAATATA
Found at i:1089239 original size:3 final size:3
Alignment explanation
Indices: 1089233--1089263 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
1089223 ATCATCAACT
1089233 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1089264 AAAAGATTAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1089935 original size:21 final size:21
Alignment explanation
Indices: 1089911--1089950 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1089901 ATAAATTTTT
1089911 TATTTAAAT-TTAATTATAATA
1 TATTTAAATATTAA-TATAATA
*
1089932 TATTTATATATTAATATAA
1 TATTTAAATATTAATATAA
1089951 AAATAATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
TATTTAAATATTAATATAATA
Found at i:1090831 original size:21 final size:21
Alignment explanation
Indices: 1090805--1090846 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
1090795 AGACTTGACC
1090805 TGGCTTAATTCAAGTTTAGGT
1 TGGCTTAATTCAAGTTTAGGT
1090826 TGGCTTAATTCAAGTTTAGGT
1 TGGCTTAATTCAAGTTTAGGT
1090847 AAAAAAATTA
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:0.24, C:0.10, G:0.24, T:0.43
Consensus pattern (21 bp):
TGGCTTAATTCAAGTTTAGGT
Found at i:1091407 original size:17 final size:17
Alignment explanation
Indices: 1091381--1091422 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
1091371 TCAGATTTAA
*
1091381 AAATAAATATT-ATATAT
1 AAATATATATTCA-ATAT
1091398 AAATATATATTCAATAT
1 AAATATATATTCAATAT
*
1091415 GAATATAT
1 AAATATAT
1091423 TTAAATTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 21 0.95
18 1 0.05
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (17 bp):
AAATATATATTCAATAT
Found at i:1092152 original size:21 final size:23
Alignment explanation
Indices: 1092108--1092153 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 23
1092098 AAAATAATTT
* *
1092108 AAATAATTTAATTAAATTCAATA
1 AAATAATATAATTAAATGCAATA
1092131 AAATAATAT-ATT-AATGCAATA
1 AAATAATATAATTAAATGCAATA
1092152 AA
1 AA
1092154 CTTTTCTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 10 0.48
22 3 0.14
23 8 0.38
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (23 bp):
AAATAATATAATTAAATGCAATA
Found at i:1092488 original size:13 final size:15
Alignment explanation
Indices: 1092457--1092487 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
1092447 AATAAAATTT
1092457 AAATATTAATAAAAA
1 AAATATTAATAAAAA
1092472 AAATATT-ATAAAAA
1 AAATATTAATAAAAA
1092486 AA
1 AA
1092488 TTTTTATTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.56
15 7 0.44
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (15 bp):
AAATATTAATAAAAA
Found at i:1094959 original size:2 final size:2
Alignment explanation
Indices: 1094952--1094982 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1094942 GATTTAACAA
1094952 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1094983 AGCAAACATC
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1095087 original size:2 final size:2
Alignment explanation
Indices: 1095080--1095116 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1095070 TGTATTGTAT
1095080 TA TA TA TA TA TA 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 TA TA TA TA TA TA T
1095117 CACTCGATAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1098917 original size:4 final size:4
Alignment explanation
Indices: 1098908--1098951 Score: 52
Period size: 4 Copynumber: 10.8 Consensus size: 4
1098898 TAGCTACTAT
* * *
1098908 ATAC ATAC ATAAC ATAT ATAT ATAT ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC AT-AC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1098952 TATATATATA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
4 33 0.89
5 4 0.11
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (4 bp):
ATAC
Found at i:1098926 original size:2 final size:2
Alignment explanation
Indices: 1098921--1098966 Score: 56
Period size: 2 Copynumber: 23.0 Consensus size: 2
1098911 CATACATAAC
* * * *
1098921 AT AT AT AT AT AT AT AC AT AC AT AC AT AC 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
1098963 AT AT
1 AT AT
1098967 TCAATAGTAC
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (2 bp):
AT
Found at i:1098931 original size:21 final size:20
Alignment explanation
Indices: 1098905--1098955 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
1098895 AAATAGCTAC
* *
1098905 TATATACATACATAACATATA
1 TATATATATACAT-ACATACA
1098926 TATATATATACATACATACA
1 TATATATATACATACATACA
*
1098946 TACATATATA
1 TATATATATA
1098956 TATATATATA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 15 0.56
21 12 0.44
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (20 bp):
TATATATATACATACATACA
Found at i:1099262 original size:21 final size:20
Alignment explanation
Indices: 1099238--1099276 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
1099228 ATCCACCGCC
*
1099238 ATATAATTTTCTTTTTTAAAA
1 ATATAATTTT-TATTTTAAAA
1099259 ATATAATTTTTATTTTAA
1 ATATAATTTTTATTTTAA
1099277 CCAGTAGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (20 bp):
ATATAATTTTTATTTTAAAA
Found at i:1099483 original size:19 final size:19
Alignment explanation
Indices: 1099459--1099495 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1099449 AAAAATATAT
*
1099459 TTTTTATAATATTTTAAAG
1 TTTTTATAATAATTTAAAG
*
1099478 TTTTTATATTAATTTAAA
1 TTTTTATAATAATTTAAA
1099496 AATAAAATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (19 bp):
TTTTTATAATAATTTAAAG
Found at i:1099666 original size:16 final size:16
Alignment explanation
Indices: 1099633--1099671 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
1099623 TATGATTAAT
1099633 ATTTAAATTAAATATTA
1 ATTT-AATTAAATATTA
* *
1099650 ATTTAATTTAATTTTA
1 ATTTAATTAAATATTA
1099666 ATTTAA
1 ATTTAA
1099672 ATATTAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 16 0.80
17 4 0.20
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
ATTTAATTAAATATTA
Done.