Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold202
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: 2706578
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 499 characters in sequence are not A, C, G, or T
File 10 of 16
Found at i:1669477 original size:3 final size:3
Alignment explanation
Indices: 1669469--1669498 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
1669459 TGAAAAAGAT
*
1669469 GGA GGA GGA GGA GGA GGA GGA GCA GGA GGA
1 GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA
1669499 AGCACATCCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.33, C:0.03, G:0.63, T:0.00
Consensus pattern (3 bp):
GGA
Found at i:1669968 original size:16 final size:16
Alignment explanation
Indices: 1669947--1669980 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1669937 ATAGATAGTG
1669947 ATTTATATACATATAT
1 ATTTATATACATATAT
*
1669963 ATTTATATATATATAT
1 ATTTATATACATATAT
1669979 AT
1 AT
1669981 GCATAGTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (16 bp):
ATTTATATACATATAT
Found at i:1672863 original size:16 final size:16
Alignment explanation
Indices: 1672842--1672875 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1672832 ATAGATAGTG
1672842 ATTTATATACATATAT
1 ATTTATATACATATAT
*
1672858 ATTTATATATATATAT
1 ATTTATATACATATAT
1672874 AT
1 AT
1672876 GCATAGTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (16 bp):
ATTTATATACATATAT
Found at i:1673543 original size:16 final size:17
Alignment explanation
Indices: 1673520--1673559 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
1673510 TGTGAGTGTG
1673520 ATTATAATTTAATATTA
1 ATTATAATTTAATATTA
* *
1673537 A-TATAATTTTATGTTA
1 ATTATAATTTAATATTA
1673553 ATTATAA
1 ATTATAA
1673560 GAATTAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 14 0.70
17 6 0.30
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
ATTATAATTTAATATTA
Found at i:1674697 original size:26 final size:23
Alignment explanation
Indices: 1674648--1674697 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 23
1674638 TATACGATAC
*
1674648 AAATATAATATGAAAAATAATTA
1 AAATATAATATGAAAAAAAATTA
1674671 AAATATAATATGACATAAAAAAATTA
1 AAATATAATATG--A-AAAAAAATTA
1674697 A
1 A
1674698 CAAGACACAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 12 0.52
25 1 0.04
26 10 0.43
ACGTcount: A:0.66, C:0.02, G:0.04, T:0.28
Consensus pattern (23 bp):
AAATATAATATGAAAAAAAATTA
Found at i:1675168 original size:29 final size:29
Alignment explanation
Indices: 1675136--1675191 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
1675126 TTTGCACATG
* * *
1675136 CAAATAAATTTTTAACTTTTAATTTATAC
1 CAAATAAACTCTTAAATTTTAATTTATAC
1675165 CAAATAAACTCTTAAATTTTAATTTAT
1 CAAATAAACTCTTAAATTTTAATTTAT
1675192 TTTTATATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.43, C:0.11, G:0.00, T:0.46
Consensus pattern (29 bp):
CAAATAAACTCTTAAATTTTAATTTATAC
Found at i:1675819 original size:15 final size:16
Alignment explanation
Indices: 1675783--1675816 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
1675773 TTTAAACTTG
1675783 AAATTATTCAAATTTA
1 AAATTATTCAAATTTA
1675799 AAATTA-TCGAAATTTA
1 AAATTATTC-AAATTTA
1675815 AA
1 AA
1675817 TTAAGCATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 2 0.12
16 15 0.88
ACGTcount: A:0.53, C:0.06, G:0.03, T:0.38
Consensus pattern (16 bp):
AAATTATTCAAATTTA
Found at i:1683064 original size:20 final size:20
Alignment explanation
Indices: 1683039--1683080 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
1683029 TGGTCCCTTA
*
1683039 TTAGGTGATCTGTTGTGAGT
1 TTAGGTAATCTGTTGTGAGT
1683059 TTAGGTAATCTGTTGTGAGT
1 TTAGGTAATCTGTTGTGAGT
1683079 TT
1 TT
1683081 TGTAATTATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.17, C:0.05, G:0.31, T:0.48
Consensus pattern (20 bp):
TTAGGTAATCTGTTGTGAGT
Found at i:1683483 original size:2 final size:2
Alignment explanation
Indices: 1683478--1683508 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1683468 ATTCAAATTA
1683478 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1683509 ACAGCAAGGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1684425 original size:2 final size:2
Alignment explanation
Indices: 1684418--1684447 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1684408 GAAATACTAC
1684418 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
1684448 TTAGGTTTGA
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:1684599 original size:2 final size:2
Alignment explanation
Indices: 1684592--1684619 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1684582 GTTGGATGGC
1684592 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
1684620 GAATTATTCT
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:1687216 original size:3 final size:3
Alignment explanation
Indices: 1687208--1687238 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
1687198 CTTGGCTTCT
1687208 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1687239 AAAGTTAAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1688921 original size:21 final size:22
Alignment explanation
Indices: 1688897--1688943 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
1688887 TCAAGTTCAG
* * *
1688897 ATTAATTTATAAAT-TTATATT
1 ATTAATTCACAAATATTATAAT
1688918 ATT-ATTCACAAATATTATAAT
1 ATTAATTCACAAATATTATAAT
1688939 ATTAA
1 ATTAA
1688944 AAAATTATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
20 8 0.38
21 12 0.57
22 1 0.05
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (22 bp):
ATTAATTCACAAATATTATAAT
Found at i:1690815 original size:2 final size:2
Alignment explanation
Indices: 1690808--1690833 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1690798 ATGATGATGA
1690808 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
1690834 GCATGGAGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1692344 original size:22 final size:22
Alignment explanation
Indices: 1692316--1692357 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
1692306 TATTATTGTT
1692316 TAAATA-TAATTATAAAGATATA
1 TAAATATTAA-TATAAAGATATA
1692338 TAAATATTAATATAAAGATA
1 TAAATATTAATATAAAGATA
1692358 ATACTTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 16 0.84
23 3 0.16
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.36
Consensus pattern (22 bp):
TAAATATTAATATAAAGATATA
Found at i:1694590 original size:2 final size:2
Alignment explanation
Indices: 1694583--1694617 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1694573 GAATATTTTA
1694583 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1694618 GCTTTGAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1695416 original size:20 final size:20
Alignment explanation
Indices: 1695387--1695425 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1695377 TAAATATCTT
1695387 AATTTCATTTTAATATTATA
1 AATTTCATTTTAATATTATA
* *
1695407 AATTTTATTTTAATTTTAT
1 AATTTCATTTTAATATTAT
1695426 GTAATTTTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (20 bp):
AATTTCATTTTAATATTATA
Found at i:1695618 original size:2 final size:2
Alignment explanation
Indices: 1695575--1695603 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1695565 TTTATCAAAG
1695575 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1695604 GAAAGAACTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1699188 original size:2 final size:2
Alignment explanation
Indices: 1699183--1699212 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1699173 CTAAAAAAGC
1699183 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
1699213 TTAATACATG
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:1701874 original size:33 final size:31
Alignment explanation
Indices: 1701837--1701905 Score: 75
Period size: 33 Copynumber: 2.2 Consensus size: 31
1701827 TTTTAGATCT
* *
1701837 ATTTTGTAATTAAACTTTGATTTTTTTTGATAA
1 ATTTTATAACTAAACTTTGATTTTTTTT-A-AA
* * *
1701870 ATTTTATCACTCAATTTTGATTTTTTTTAAA
1 ATTTTATAACTAAACTTTGATTTTTTTTAAA
1701901 ATTTT
1 ATTTT
1701906 TCCATTCAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
31 7 0.23
32 1 0.03
33 23 0.74
ACGTcount: A:0.29, C:0.06, G:0.06, T:0.59
Consensus pattern (31 bp):
ATTTTATAACTAAACTTTGATTTTTTTTAAA
Found at i:1701923 original size:32 final size:33
Alignment explanation
Indices: 1701854--1701925 Score: 87
Period size: 31 Copynumber: 2.2 Consensus size: 33
1701844 AATTAAACTT
*
1701854 TGATTTTTTTTGATAAATTTTATCACTCAATTT
1 TGATTTTTTTTGATAAATTTTATCACTCAATTA
*
1701887 TGATTTTTTTT-A-AAATTTT-TCCATTCAATTAA
1 TGATTTTTTTTGATAAATTTTAT-CACTCAATT-A
1701919 TGATTTT
1 TGATTTT
1701926 AGTTCGGATA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
30 1 0.03
31 15 0.43
32 8 0.23
33 11 0.31
ACGTcount: A:0.28, C:0.08, G:0.06, T:0.58
Consensus pattern (33 bp):
TGATTTTTTTTGATAAATTTTATCACTCAATTA
Found at i:1704453 original size:22 final size:22
Alignment explanation
Indices: 1704388--1704441 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
1704378 TTAGTTTGAG
*
1704388 TAAATTAAATTTAAA-TATTTA
1 TAAATTTAATTTAAATTATTTA
1704409 -AATATTTAATTTAAATTATTTA
1 TAA-ATTTAATTTAAATTATTTA
1704431 TAAATTTAATT
1 TAAATTTAATT
1704442 AAAGTTTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
20 2 0.07
21 11 0.38
22 14 0.48
23 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
TAAATTTAATTTAAATTATTTA
Found at i:1705276 original size:26 final size:27
Alignment explanation
Indices: 1705236--1705288 Score: 90
Period size: 26 Copynumber: 2.0 Consensus size: 27
1705226 ATTTCGATAA
1705236 TAAATAAATAATAAATAAATTTAAATTT
1 TAAATAAAT-ATAAATAAATTTAAATTT
1705264 TAAATAAAT-TAAATAAATTTAAATT
1 TAAATAAATATAAATAAATTTAAATT
1705289 CAAATATTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 16 0.64
28 9 0.36
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (27 bp):
TAAATAAATATAAATAAATTTAAATTT
Found at i:1705287 original size:32 final size:29
Alignment explanation
Indices: 1705236--1705299 Score: 76
Period size: 32 Copynumber: 2.1 Consensus size: 29
1705226 ATTTCGATAA
*
1705236 TAAATAAATAATAAATAAATTTAAAT-TT
1 TAAATAAATAATAAATAAATTCAAATATT
1705264 TAAATAAATTAAATAAATTTAAATTCAAATATT
1 TAAATAAA-T-AATAAA--TAAATTCAAATATT
1705297 TAA
1 TAA
1705300 TCCGTTATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
28 8 0.27
29 1 0.03
30 6 0.20
32 10 0.33
33 5 0.17
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (29 bp):
TAAATAAATAATAAATAAATTCAAATATT
Found at i:1705674 original size:14 final size:12
Alignment explanation
Indices: 1705647--1705682 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
1705637 TGTCAAATAC
1705647 AAATACTTAAAA
1 AAATACTTAAAA
1705659 AAATACTTAAAA
1 AAATACTTAAAA
*
1705671 AAA-AATTAAAA
1 AAATACTTAAAA
1705682 A
1 A
1705683 GTGAGAGCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 8 0.35
12 15 0.65
ACGTcount: A:0.72, C:0.06, G:0.00, T:0.22
Consensus pattern (12 bp):
AAATACTTAAAA
Found at i:1713707 original size:29 final size:29
Alignment explanation
Indices: 1713653--1713708 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
1713643 ATATTATTTT
*
1713653 TTAATTTTAAATAAATTATTAAAATAAAA
1 TTAATTTTAAATAAATTATCAAAATAAAA
* * *
1713682 TTAATTTTAAATTATTTATCAGAATAA
1 TTAATTTTAAATAAATTATCAAAATAA
1713709 TACTGTTTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (29 bp):
TTAATTTTAAATAAATTATCAAAATAAAA
Found at i:1713911 original size:30 final size:30
Alignment explanation
Indices: 1713877--1713945 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 30
1713867 ATTTAACAAT
*
1713877 AAGATTTAAATTATTTAAAAATAAAATAAA
1 AAGATTTAAATTATATAAAAATAAAATAAA
* *
1713907 AAGATTT-AATTATATCAAATTAAAATAAA
1 AAGATTTAAATTATATAAAAATAAAATAAA
1713936 AA-A-TTAAATT
1 AAGATTTAAATT
1713946 CATTAATTCA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
27 2 0.06
28 5 0.14
29 21 0.60
30 7 0.20
ACGTcount: A:0.61, C:0.01, G:0.03, T:0.35
Consensus pattern (30 bp):
AAGATTTAAATTATATAAAAATAAAATAAA
Found at i:1714957 original size:27 final size:26
Alignment explanation
Indices: 1714863--1714965 Score: 77
Period size: 27 Copynumber: 4.0 Consensus size: 26
1714853 ATTTTACAAT
* *
1714863 AAAATTAATCACAAATTTTGACAAAC
1 AAAAGTAATCACAATTTTTGACAAAC
* * * *
1714889 AATA-T-GTCACTATTTTTGACAAATA
1 AAAAGTAATCACAATTTTTGACAAA-C
* **
1714914 AAAAG-AAACTATTATTTTTGACAAAC
1 AAAAGTAATC-ACAATTTTTGACAAAC
1714940 ATAAAGTAATCACAATTTTTGACAAA
1 A-AAAGTAATCACAATTTTTGACAAA
1714966 TAATGAGTGG
Statistics
Matches: 58, Mismatches: 13, Indels: 11
0.71 0.16 0.13
Matches are distributed among these distances:
24 15 0.26
25 4 0.07
26 5 0.09
27 31 0.53
28 3 0.05
ACGTcount: A:0.49, C:0.13, G:0.07, T:0.32
Consensus pattern (26 bp):
AAAAGTAATCACAATTTTTGACAAAC
Found at i:1716394 original size:16 final size:16
Alignment explanation
Indices: 1716375--1716418 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
1716365 TATTCACAAA
1716375 TATAAATTTTTAAAAT
1 TATAAATTTTTAAAAT
* *
1716391 TATAAATATTTAATAT
1 TATAAATTTTTAAAAT
1716407 T-TAAAATTTTTA
1 TAT-AAATTTTTA
1716419 TTCAAAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 1 0.04
16 23 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TATAAATTTTTAAAAT
Found at i:1716447 original size:17 final size:17
Alignment explanation
Indices: 1716427--1716459 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1716417 TATTCAAAAA
1716427 AAATATA-AATATATTAG
1 AAATATATAAT-TATTAG
1716444 AAATATATAATTATTA
1 AAATATATAATTATTA
1716460 TTGATTAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (17 bp):
AAATATATAATTATTAG
Found at i:1719626 original size:37 final size:37
Alignment explanation
Indices: 1719576--1719657 Score: 119
Period size: 37 Copynumber: 2.2 Consensus size: 37
1719566 AATATGACTA
* *
1719576 AACTTAATAAACTCAAATGTTAAACTTAATTGATCTG
1 AACTTAATAAACTCAAATATTAAACTTAATTAATCTG
* *
1719613 AACTTAATTAACTCAAGTATTAAACTTAATTAATCTG
1 AACTTAATAAACTCAAATATTAAACTTAATTAATCTG
1719650 AACCTTAA
1 AA-CTTAA
1719658 ATGATTCGAA
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
37 35 0.88
38 5 0.12
ACGTcount: A:0.44, C:0.15, G:0.06, T:0.35
Consensus pattern (37 bp):
AACTTAATAAACTCAAATATTAAACTTAATTAATCTG
Found at i:1719789 original size:47 final size:47
Alignment explanation
Indices: 1719712--1719805 Score: 109
Period size: 47 Copynumber: 2.0 Consensus size: 47
1719702 TAAACTCAGT
* * *
1719712 TGACTTGAATTCGAATGATTTAAAACTAAAATAACTCAAATTCAAAA
1 TGACTTGAACTCGAATGACTTAAAACTAAAATAACTCAAACTCAAAA
* * * *
1719759 TGACTTGAACT-GAAATGACTTGAAATTAAAATGATTCAAACTCAAAA
1 TGACTTGAACTCG-AATGACTTAAAACTAAAATAACTCAAACTCAAAA
1719806 ATAAATTAAA
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
46 1 0.03
47 38 0.97
ACGTcount: A:0.48, C:0.13, G:0.11, T:0.29
Consensus pattern (47 bp):
TGACTTGAACTCGAATGACTTAAAACTAAAATAACTCAAACTCAAAA
Found at i:1720187 original size:9 final size:9
Alignment explanation
Indices: 1720173--1720225 Score: 72
Period size: 9 Copynumber: 6.0 Consensus size: 9
1720163 TCTTTAATTT
1720173 TTAATTTAA
1 TTAATTTAA
1720182 TTAATTTAA
1 TTAATTTAA
1720191 TTAATTTAA
1 TTAATTTAA
*
1720200 TTAATATAA
1 TTAATTTAA
*
1720209 TTGA-TTAA
1 TTAATTTAA
*
1720217 TTTATTTAA
1 TTAATTTAA
1720226 ATAAAATTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
8 6 0.15
9 33 0.85
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (9 bp):
TTAATTTAA
Found at i:1720902 original size:3 final size:3
Alignment explanation
Indices: 1720894--1720920 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1720884 GCAGCGAACA
1720894 AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG
1720921 GGAAGATATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:1722237 original size:2 final size:2
Alignment explanation
Indices: 1722230--1722264 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1722220 GCTTTTAAAT
1722230 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 T
1722265 TATTGACATG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1722425 original size:20 final size:20
Alignment explanation
Indices: 1722393--1722431 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
1722383 TTTTTTACTA
1722393 AAATTTAATTATAAAAATAT
1 AAATTTAATTATAAAAATAT
1722413 AAATATTAA-TATAAAAATA
1 AAAT-TTAATTATAAAAATA
1722432 ATTTTTTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
AAATTTAATTATAAAAATAT
Found at i:1729937 original size:23 final size:22
Alignment explanation
Indices: 1729910--1729952 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
1729900 CCCTAATGCA
1729910 TTTTTCTTCCTTTTTCCTTTTTT
1 TTTTTCTTCC-TTTTCCTTTTTT
*
1729933 TTTTTTTTCCTTTTCCTTTT
1 TTTTTCTTCCTTTTCCTTTT
1729953 GCAAGTTCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (22 bp):
TTTTTCTTCCTTTTCCTTTTTT
Found at i:1730225 original size:27 final size:27
Alignment explanation
Indices: 1730187--1730263 Score: 129
Period size: 27 Copynumber: 2.9 Consensus size: 27
1730177 AACAAGGCTT
1730187 ACACAGTATGACTCATGAAATTGTTTG
1 ACACAGTATGACTCATGAAATTGTTTG
1730214 ACACAGTATGACTCATGAAATTGTTTG
1 ACACAGTATGACTCATGAAATTGTTTG
* *
1730241 ACACAATATGACT-TTGAAATTGT
1 ACACAGTATGACTCATGAAATTGT
1730264 AAAACAAACG
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
26 9 0.19
27 39 0.81
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.34
Consensus pattern (27 bp):
ACACAGTATGACTCATGAAATTGTTTG
Found at i:1732469 original size:96 final size:95
Alignment explanation
Indices: 1732273--1732472 Score: 215
Period size: 97 Copynumber: 2.1 Consensus size: 95
1732263 TGTAATCTTT
* * * *
1732273 GTTTCAAACTATTGCAAGCACTTAAGAAAAAGTTTACCCTTGTTTCCTATCCAATACTCCACAAA
1 GTTTCAAACAATTGCAAGCACTCAAGAAAAAGTTCACCCATGTTTCCTATCCAATACTCCACAAA
* * *** *
1732338 ATCCAAATAAATTCACATTTTTGTAATCTTT
66 ATCCAAATAAAATCACATGTTAACAATC-TA
* * * * *
1732369 GTTTCAAACAATTGCAAGCTCTCAAGAAAAAGGTTCACTCATGTTTCCTA-CTGAATACTTCATA
1 GTTTCAAACAATTGCAAGCACTCAAGAAAAA-GTTCACCCATGTTTCCTATC-CAATACTCCACA
1732433 AAATCCAAATAAAATCACATGTTAACAATGC-A
64 AAATCCAAATAAAATCACATGTTAACAAT-CTA
1732465 GTTTCAAA
1 GTTTCAAA
1732473 GATGTAGATT
Statistics
Matches: 86, Mismatches: 15, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
96 37 0.43
97 48 0.56
98 1 0.01
ACGTcount: A:0.38, C:0.21, G:0.09, T:0.32
Consensus pattern (95 bp):
GTTTCAAACAATTGCAAGCACTCAAGAAAAAGTTCACCCATGTTTCCTATCCAATACTCCACAAA
ATCCAAATAAAATCACATGTTAACAATCTA
Found at i:1735032 original size:2 final size:2
Alignment explanation
Indices: 1735025--1735051 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1735015 ACAAAGAGCA
1735025 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 A
1735052 AATAAATTGC
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1736009 original size:19 final size:19
Alignment explanation
Indices: 1735985--1736022 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
1735975 TCGTGCACGA
*
1735985 CACAACCATTTCCTTATAT
1 CACAACCATTTCCATATAT
1736004 CACAACCATTTCCATATAT
1 CACAACCATTTCCATATAT
1736023 TTGCATACTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.34, C:0.32, G:0.00, T:0.34
Consensus pattern (19 bp):
CACAACCATTTCCATATAT
Found at i:1737108 original size:82 final size:82
Alignment explanation
Indices: 1736971--1737134 Score: 301
Period size: 82 Copynumber: 2.0 Consensus size: 82
1736961 TTTCAAAGAA
* *
1736971 CATCAATTTGGCTTGCAAGACCAAGTTACTAGCATTCCTAGTTCTCAACTAAAGTTGCTCAATCC
1 CATCAATCTGGCTTGCAAGACCAAGTTACAAGCATTCCTAGTTCTCAACTAAAGTTGCTCAATCC
1737036 TTTATCCATTTATGGGG
66 TTTATCCATTTATGGGG
*
1737053 CATCAATCTGGCTTGCAAGACCAAGTTACAAGTATTCCTAGTTCTCAACTAAAGTTGCTCAATCC
1 CATCAATCTGGCTTGCAAGACCAAGTTACAAGCATTCCTAGTTCTCAACTAAAGTTGCTCAATCC
1737118 TTTATCCATTTATGGGG
66 TTTATCCATTTATGGGG
1737135 TTGATTACGA
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
82 79 1.00
ACGTcount: A:0.27, C:0.23, G:0.16, T:0.34
Consensus pattern (82 bp):
CATCAATCTGGCTTGCAAGACCAAGTTACAAGCATTCCTAGTTCTCAACTAAAGTTGCTCAATCC
TTTATCCATTTATGGGG
Found at i:1740462 original size:26 final size:27
Alignment explanation
Indices: 1740411--1740468 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 27
1740401 GACACGAAAA
* *
1740411 GATTT-TAAATTTGAATATCTTAATTT
1 GATTTATAAATTTAAATATATTAATTT
1740437 GATTTATAAATTTAAATATATT-ATTT
1 GATTTATAAATTTAAATATATTAATTT
1740463 -ATTTAT
1 GATTTAT
1740469 TAAAAATTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 6 0.21
26 9 0.31
27 14 0.48
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.55
Consensus pattern (27 bp):
GATTTATAAATTTAAATATATTAATTT
Found at i:1740481 original size:29 final size:29
Alignment explanation
Indices: 1740444--1740518 Score: 75
Period size: 29 Copynumber: 2.6 Consensus size: 29
1740434 TTTGATTTAT
1740444 AAATT-TAAATATATTATTTATT-TATTAA
1 AAATTATAAATATATTATTT-TTATATTAA
*
1740472 AAATTATAAA-AAATTTATTTTTATATTAA
1 AAATTATAAATATA-TTATTTTTATATTAA
* * *
1740501 TATTTATATATATATTAT
1 AAATTATAAATATATTAT
1740519 AATTAAATTT
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
28 9 0.24
29 27 0.71
30 2 0.05
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (29 bp):
AAATTATAAATATATTATTTTTATATTAA
Found at i:1744054 original size:20 final size:20
Alignment explanation
Indices: 1744012--1744070 Score: 56
Period size: 20 Copynumber: 3.1 Consensus size: 20
1744002 ATTTTTATGT
*
1744012 AATTATTTA-TT-ATATT-T
1 AATTATTTATTTAATATTAA
1744029 AA-TATTTATTTAATATTAA
1 AATTATTTATTTAATATTAA
*
1744048 AATTATTT-TTAAATAATTAA
1 AATTATTTATTTAAT-ATTAA
1744068 AAT
1 AAT
1744071 CTCATTTAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
16 6 0.17
17 4 0.11
18 5 0.14
19 7 0.20
20 13 0.37
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
AATTATTTATTTAATATTAA
Found at i:1748111 original size:2 final size:2
Alignment explanation
Indices: 1748104--1748138 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1748094 GCATACACAA
1748104 AG AG 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 AG AG A
1748139 CCTTCAGCTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1748657 original size:2 final size:2
Alignment explanation
Indices: 1748646--1748767 Score: 120
Period size: 2 Copynumber: 61.5 Consensus size: 2
1748636 CAATGAGATT
* * * * *
1748646 TA TA TA -A TA TA TA TT TA TA TA TA TA TA TA TA TG TA TG TG TG
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * *
1748687 TA TA TG CA TA TA TA TT TA TA TA TA AA TA TG TA TA TA CA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
1748729 CA TA TA CA 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 TA T
1748768 GGGACTGGAT
Statistics
Matches: 97, Mismatches: 22, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
1 1 0.01
2 96 0.99
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1751682 original size:8 final size:9
Alignment explanation
Indices: 1751666--1751705 Score: 50
Period size: 9 Copynumber: 4.8 Consensus size: 9
1751656 TAATGTGATG
1751666 TTAATTTAA
1 TTAATTTAA
1751675 TT-ATTTAA
1 TTAATTTAA
1751683 TTAATTTAA
1 TTAATTTAA
*
1751692 --AAATTAA
1 TTAATTTAA
1751699 TTAATTT
1 TTAATTT
1751706 TATAATACTA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
7 6 0.23
8 8 0.31
9 12 0.46
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (9 bp):
TTAATTTAA
Found at i:1752010 original size:16 final size:16
Alignment explanation
Indices: 1751985--1752015 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1751975 TTTACTTAAA
*
1751985 AGATTTAAAAAATAAT
1 AGATTCAAAAAATAAT
1752001 AGATTCAAAAAATAA
1 AGATTCAAAAAATAA
1752016 ATTTAAACAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.65, C:0.03, G:0.06, T:0.26
Consensus pattern (16 bp):
AGATTCAAAAAATAAT
Found at i:1752041 original size:22 final size:22
Alignment explanation
Indices: 1752016--1752059 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1752006 CAAAAAATAA
1752016 ATTTAAACAAAAAAAT-AAATTT
1 ATTTAAA-AAAAAAATCAAATTT
*
1752038 ATTTAAAAAATAAATCAAATTT
1 ATTTAAAAAAAAAATCAAATTT
1752060 TGAGTACATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (22 bp):
ATTTAAAAAAAAAATCAAATTT
Found at i:1752045 original size:18 final size:17
Alignment explanation
Indices: 1752006--1752052 Score: 58
Period size: 18 Copynumber: 2.7 Consensus size: 17
1751996 ATAATAGATT
1752006 CAAAAAATAAATTTAAA
1 CAAAAAATAAATTTAAA
**
1752023 CAAAAAAATAAATTTATT
1 C-AAAAAATAAATTTAAA
*
1752041 TAAAAAATAAAT
1 CAAAAAATAAAT
1752053 CAAATTTTGA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
17 12 0.46
18 14 0.54
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.28
Consensus pattern (17 bp):
CAAAAAATAAATTTAAA
Found at i:1752059 original size:18 final size:17
Alignment explanation
Indices: 1751987--1752059 Score: 51
Period size: 18 Copynumber: 4.2 Consensus size: 17
1751977 TACTTAAAAG
*
1751987 ATTTAAAAAAT-AATAG
1 ATTTAAAAAATAAATAA
*
1752003 ATTCAAAAAATAAATTTAA
1 ATTTAAAAAATAAA--TAA
** **
1752022 A-CAAAAAAATAAATTT
1 ATTTAAAAAATAAATAA
1752038 ATTTAAAAAATAAATCAA
1 ATTTAAAAAATAAAT-AA
1752056 ATTT
1 ATTT
1752060 TGAGTACATT
Statistics
Matches: 42, Mismatches: 10, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
16 12 0.29
17 13 0.31
18 14 0.33
19 3 0.07
ACGTcount: A:0.63, C:0.04, G:0.01, T:0.32
Consensus pattern (17 bp):
ATTTAAAAAATAAATAA
Found at i:1753360 original size:20 final size:20
Alignment explanation
Indices: 1753332--1753369 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1753322 TTGGTTTGTA
1753332 CAAAGTTTTGA-TTTTTTTTT
1 CAAAGTTTT-ACTTTTTTTTT
*
1753352 CAAATTTTTACTTTTTTT
1 CAAAGTTTTACTTTTTTT
1753370 ATTTTTAAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 1 0.06
20 15 0.94
ACGTcount: A:0.21, C:0.08, G:0.05, T:0.66
Consensus pattern (20 bp):
CAAAGTTTTACTTTTTTTTT
Found at i:1753527 original size:26 final size:26
Alignment explanation
Indices: 1753473--1753529 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
1753463 AATTAATTAT
*
1753473 AATTTACTATATTTTAAATATTTCTA
1 AATTTACTATATTTTAAATATTTCAA
*
1753499 AATTTACTA-ATTTATTTAATATTT-AA
1 AATTTACTATA-TT-TTAAATATTTCAA
1753525 AATTT
1 AATTT
1753530 TAAATATTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
25 1 0.04
26 17 0.63
27 9 0.33
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.54
Consensus pattern (26 bp):
AATTTACTATATTTTAAATATTTCAA
Found at i:1753537 original size:16 final size:17
Alignment explanation
Indices: 1753516--1753551 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
1753506 TAATTTATTT
1753516 AATATTTA-AAATTTTA
1 AATATTTATAAATTTTA
*
1753532 AATATTTATAATTTTTA
1 AATATTTATAAATTTTA
1753549 AAT
1 AAT
1753552 TTATATTTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
AATATTTATAAATTTTA
Found at i:1753569 original size:43 final size:42
Alignment explanation
Indices: 1753483--1753570 Score: 97
Period size: 43 Copynumber: 2.0 Consensus size: 42
1753473 AATTTACTAT
* * *
1753483 ATTTTAAATATTTCTAAATTTACTAATTTATTTAATATTTAAA
1 ATTTTAAATATTTATAAATTTAC-AATTTATTTAACATATAAA
* *
1753526 ATTTTAAATATTTATAATTTTTA-AATTTATATTTACATATAAA
1 ATTTTAAATATTTATAA-ATTTACAATTTAT-TTAACATATAAA
1753569 AT
1 AT
1753571 ATAACATATA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
42 7 0.18
43 27 0.71
44 4 0.11
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.53
Consensus pattern (42 bp):
ATTTTAAATATTTATAAATTTACAATTTATTTAACATATAAA
Found at i:1753893 original size:17 final size:17
Alignment explanation
Indices: 1753869--1753915 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
1753859 GAATATTATT
*
1753869 ATTA-TAATAATAAATA
1 ATTATTAATAAAAAATA
1753885 ATTATTAATAAAAAATA
1 ATTATTAATAAAAAATA
*
1753902 TTTATGTAA-AAAAA
1 ATTAT-TAATAAAAA
1753916 GATTTTATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
16 4 0.15
17 20 0.74
18 3 0.11
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (17 bp):
ATTATTAATAAAAAATA
Found at i:1754162 original size:24 final size:24
Alignment explanation
Indices: 1754135--1754198 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 24
1754125 TGTGAGAAAG
*
1754135 TTATAATTTAAAATATATAATTTT
1 TTATAATTTAAAATATATAATTAT
*
1754159 TTAT-A-TTAAAA-GTATAATTAT
1 TTATAATTTAAAATATATAATTAT
*
1754180 TT-TAATATATAAATATATA
1 TTATAATTTA-AAATATATA
1754199 TTAAAATATT
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
20 1 0.03
21 11 0.34
22 8 0.25
23 4 0.12
24 8 0.25
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (24 bp):
TTATAATTTAAAATATATAATTAT
Found at i:1754201 original size:23 final size:22
Alignment explanation
Indices: 1754145--1754198 Score: 67
Period size: 21 Copynumber: 2.4 Consensus size: 22
1754135 TTATAATTTA
1754145 AAATATATAATT-TTTTATATT
1 AAATATATAATTATTTTATATT
1754166 AAA-AGTATAATTATTTTAATATAT
1 AAATA-TATAATTATTTT-ATAT-T
1754190 AAATATATA
1 AAATATATA
1754199 TTAAAATATT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
20 1 0.04
21 10 0.36
22 4 0.14
23 4 0.14
24 8 0.29
25 1 0.04
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (22 bp):
AAATATATAATTATTTTATATT
Found at i:1754491 original size:36 final size:37
Alignment explanation
Indices: 1754449--1754540 Score: 105
Period size: 37 Copynumber: 2.4 Consensus size: 37
1754439 TAGAAAAAAA
*
1754449 TATATTTTATTTATGTTTTTTACATATTTATAA-TAT
1 TATATTTTATTTATGTTTTTTACATATTAATAATTAT
* **
1754485 TATATTTTTATATAAATTTTTTACATATTAATAATTTAT
1 TATA-TTTTATTTATGTTTTTTACATATTAATAA-TTAT
*
1754524 TTTATTTTATTTTATGT
1 TATATTTTA-TTTATGT
1754541 ATATTTATAT
Statistics
Matches: 44, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
36 4 0.09
37 25 0.57
38 5 0.11
39 10 0.23
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (37 bp):
TATATTTTATTTATGTTTTTTACATATTAATAATTAT
Found at i:1755079 original size:20 final size:19
Alignment explanation
Indices: 1755051--1755089 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
1755041 TTTTATTCAT
*
1755051 AATGGGAGAGAAAGAAAAAA
1 AATGAGAGAGAAA-AAAAAA
1755071 AATGAGAGAGAAAAAAAAA
1 AATGAGAGAGAAAAAAAAA
1755090 GAAAGACAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.69, C:0.00, G:0.26, T:0.05
Consensus pattern (19 bp):
AATGAGAGAGAAAAAAAAA
Found at i:1755082 original size:16 final size:16
Alignment explanation
Indices: 1755058--1755088 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1755048 CATAATGGGA
1755058 GAGAAAGAAAAAAAAT
1 GAGAAAGAAAAAAAAT
*
1755074 GAGAGAGAAAAAAAA
1 GAGAAAGAAAAAAAA
1755089 AGAAAGACAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.74, C:0.00, G:0.23, T:0.03
Consensus pattern (16 bp):
GAGAAAGAAAAAAAAT
Found at i:1755408 original size:23 final size:23
Alignment explanation
Indices: 1755372--1755438 Score: 75
Period size: 23 Copynumber: 2.9 Consensus size: 23
1755362 TATTCGTGTA
* *
1755372 TTTATATTGCGTTTATATTATTT
1 TTTATGTTGAGTTTATATTATTT
*
1755395 TTTATGTTGTGTTT-TATT-TTT
1 TTTATGTTGAGTTTATATTATTT
1755416 TATATATGTTGAGTTTATATTAT
1 T-T-TATGTTGAGTTTATATTAT
1755439 ATCTTAATTC
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
21 4 0.11
22 5 0.14
23 23 0.62
24 4 0.11
25 1 0.03
ACGTcount: A:0.21, C:0.01, G:0.12, T:0.66
Consensus pattern (23 bp):
TTTATGTTGAGTTTATATTATTT
Found at i:1755612 original size:10 final size:10
Alignment explanation
Indices: 1755597--1755621 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1755587 GTCAAAAATA
1755597 TTATAAATTT
1 TTATAAATTT
1755607 TTATAAATTT
1 TTATAAATTT
1755617 TTATA
1 TTATA
1755622 TTTCAATAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (10 bp):
TTATAAATTT
Found at i:1755962 original size:8 final size:8
Alignment explanation
Indices: 1755949--1756006 Score: 53
Period size: 8 Copynumber: 6.8 Consensus size: 8
1755939 TTTTTTATAA
1755949 ATATTTAT
1 ATATTTAT
1755957 ATATTTAT
1 ATATTTAT
*
1755965 ATATTTTTT
1 ATA-TTTAT
*
1755974 ATGTTTAT
1 ATATTTAT
*
1755982 ATTATTTTT
1 A-TATTTAT
1755991 ATATTATATT
1 ATATT-TA-T
1756001 ATATTT
1 ATATTT
1756007 TAATTATTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
8 20 0.50
9 14 0.35
10 6 0.15
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (8 bp):
ATATTTAT
Found at i:1755963 original size:18 final size:18
Alignment explanation
Indices: 1755942--1755995 Score: 58
Period size: 17 Copynumber: 3.1 Consensus size: 18
1755932 TAATTTATTT
*
1755942 TTTATAAATATTTATATA
1 TTTATAAATATTTTTATA
* *
1755960 TTTATATAT-TTTTTATG
1 TTTATAAATATTTTTATA
*
1755977 TTTAT-ATTATTTTTATA
1 TTTATAAATATTTTTATA
1755994 TT
1 TT
1755996 ATATTATATT
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
16 1 0.03
17 20 0.69
18 8 0.28
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (18 bp):
TTTATAAATATTTTTATA
Found at i:1755970 original size:16 final size:16
Alignment explanation
Indices: 1755949--1756007 Score: 64
Period size: 17 Copynumber: 3.4 Consensus size: 16
1755939 TTTTTTATAA
*
1755949 ATATTTATATATTTAT
1 ATATTTTTATATTTAT
*
1755965 ATATTTTTTATGTTTAT
1 ATA-TTTTTATATTTAT
1755982 ATTATTTTTATATTATATT
1 A-TATTTTTATATT-TA-T
1756001 ATATTTT
1 ATATTTT
1756008 AATTATTTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
16 3 0.08
17 21 0.58
18 10 0.28
19 2 0.06
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.68
Consensus pattern (16 bp):
ATATTTTTATATTTAT
Found at i:1755991 original size:28 final size:26
Alignment explanation
Indices: 1755960--1756033 Score: 76
Period size: 28 Copynumber: 2.6 Consensus size: 26
1755950 TATTTATATA
* *
1755960 TTTATATATTTTTTATGTTTATATTATT
1 TTTATATATATTATAT-TTTA-ATTATT
1755988 TTTATATTATATTATATTTTAATTATTT
1 TTTATA-TATATTATATTTTAATTA-TT
1756016 TTTATAATATATTTATAT
1 TTTAT-ATATA-TTATAT
1756034 CCTATCTCAA
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
27 4 0.10
28 21 0.52
29 15 0.38
ACGTcount: A:0.31, C:0.00, G:0.01, T:0.68
Consensus pattern (26 bp):
TTTATATATATTATATTTTAATTATT
Found at i:1756031 original size:18 final size:18
Alignment explanation
Indices: 1755929--1756031 Score: 63
Period size: 18 Copynumber: 5.7 Consensus size: 18
1755919 ATTTATACAC
1755929 TAATA-ATTTATTTTTTA
1 TAATATATTTATTTTTTA
*
1755946 TAA-ATATTTATATATTTA
1 TAATATATTTAT-TTTTTA
1755964 T-ATAT-TTT-TTATGTTTA
1 TAATATATTTATT-T-TTTA
* *
1755981 TATTATTTTTATATTATATTA
1 TAATATATTTAT-TT-T-TTA
* * *
1756002 TATTTTAATTATTTTTTA
1 TAATATATTTATTTTTTA
1756020 TAATATATTTAT
1 TAATATATTTAT
1756032 ATCCTATCTC
Statistics
Matches: 66, Mismatches: 10, Indels: 19
0.69 0.11 0.20
Matches are distributed among these distances:
15 1 0.02
16 2 0.03
17 18 0.27
18 23 0.35
19 4 0.06
20 5 0.08
21 13 0.20
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.65
Consensus pattern (18 bp):
TAATATATTTATTTTTTA
Found at i:1756106 original size:13 final size:14
Alignment explanation
Indices: 1756076--1756151 Score: 68
Period size: 14 Copynumber: 5.4 Consensus size: 14
1756066 TTTTTATATA
*
1756076 ATTAAATTTTAATT
1 ATTAAATTTTATTT
1756090 -TTAAA-TTTATTT
1 ATTAAATTTTATTT
*
1756102 ATTAAATATTT-TTA
1 ATTAAAT-TTTATTT
* *
1756116 AATAAATTTTATTA
1 ATTAAATTTTATTT
1756130 ATTATAATTTTATTT
1 ATTA-AATTTTATTT
1756145 AATTAAA
1 -ATTAAA
1756152 AATTTTATAA
Statistics
Matches: 51, Mismatches: 5, Indels: 11
0.76 0.07 0.16
Matches are distributed among these distances:
12 6 0.12
13 13 0.25
14 14 0.27
15 14 0.27
16 4 0.08
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
ATTAAATTTTATTT
Found at i:1756858 original size:24 final size:24
Alignment explanation
Indices: 1756831--1756879 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
1756821 AATATAACTA
1756831 AGGATTTCTCTGGGTTCTTTCATT
1 AGGATTTCTCTGGGTTCTTTCATT
1756855 AGGATTTCTCTGGGTTCTTTCATT
1 AGGATTTCTCTGGGTTCTTTCATT
1756879 A
1 A
1756880 CCAAGAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.14, C:0.16, G:0.20, T:0.49
Consensus pattern (24 bp):
AGGATTTCTCTGGGTTCTTTCATT
Found at i:1757566 original size:6 final size:6
Alignment explanation
Indices: 1757555--1757580 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
1757545 GCAAAAGTGC
1757555 AGTGGA AGTGGA AGTGGA AGTGGA AG
1 AGTGGA AGTGGA AGTGGA AGTGGA AG
1757581 ATGAAGCATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.50, T:0.15
Consensus pattern (6 bp):
AGTGGA
Found at i:1757965 original size:29 final size:29
Alignment explanation
Indices: 1757932--1757987 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
1757922 ATCGTGAAAG
* *
1757932 AAATATTTTAGTTTTTATGCTATTAAATT
1 AAATATTTTAATTTTTATACTATTAAATT
*
1757961 AAATATTTTAATTTTTATACTTTTAAA
1 AAATATTTTAATTTTTATACTATTAAA
1757988 ATTATAGTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.55
Consensus pattern (29 bp):
AAATATTTTAATTTTTATACTATTAAATT
Found at i:1758794 original size:101 final size:101
Alignment explanation
Indices: 1758617--1758819 Score: 372
Period size: 101 Copynumber: 2.0 Consensus size: 101
1758607 TTGCCTCTTA
*
1758617 TCCCTTTCAAGTTTGTTAGGCTTTTCATCTTAAATTGTCTATGGATTTATATTCATGTTGAGCCT
1 TCCCTTTCAAGTTTGTTAGGCTTTACATCTTAAATTGTCTATGGATTTATATTCATGTTGAGCCT
1758682 CTATTCCTATTTCTAATTGGTTTGAGGTTGGATGCT
66 CTATTCCTATTTCTAATTGGTTTGAGGTTGGATGCT
1758718 TCCCTTTCAAGTTTGTTAGGCTTTACATCTTAAATTGTCTAT-GATTTTATATTCATGTTGAGCC
1 TCCCTTTCAAGTTTGTTAGGCTTTACATCTTAAATTGTCTATGGA-TTTATATTCATGTTGAGCC
*
1758782 TCTATTCTTATTTCTAATTGGTTTGAGGTTGGATGCT
65 TCTATTCCTATTTCTAATTGGTTTGAGGTTGGATGCT
1758819 T
1 T
1758820 AACATGATCT
Statistics
Matches: 99, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
100 2 0.02
101 97 0.98
ACGTcount: A:0.19, C:0.15, G:0.17, T:0.48
Consensus pattern (101 bp):
TCCCTTTCAAGTTTGTTAGGCTTTACATCTTAAATTGTCTATGGATTTATATTCATGTTGAGCCT
CTATTCCTATTTCTAATTGGTTTGAGGTTGGATGCT
Found at i:1763886 original size:19 final size:20
Alignment explanation
Indices: 1763864--1763902 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
1763854 AATCGAGATA
*
1763864 AAAAATAAAA-AATTGATTT
1 AAAAATAAAATAAGTGATTT
1763883 AAAAATAAAATAAGTGATTT
1 AAAAATAAAATAAGTGATTT
1763903 TTTTTTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.62, C:0.00, G:0.08, T:0.31
Consensus pattern (20 bp):
AAAAATAAAATAAGTGATTT
Found at i:1765541 original size:20 final size:19
Alignment explanation
Indices: 1765499--1765552 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 19
1765489 GTTTGGGACA
1765499 ATGTATCGATACAATTCTTC
1 ATGTATCGATACAATTC-TC
1765519 ATGTATCGATACAATGTGC-C
1 ATGTATCGATACAAT-T-CTC
*
1765539 ATGTATTGATACAA
1 ATGTATCGATACAA
1765553 ACAGTGGTAG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 29 0.94
21 1 0.03
22 1 0.03
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (19 bp):
ATGTATCGATACAATTCTC
Found at i:1767575 original size:13 final size:13
Alignment explanation
Indices: 1767557--1767583 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1767547 ACATTATGCT
1767557 TTGTATCGATACA
1 TTGTATCGATACA
1767570 TTGTATCGATACA
1 TTGTATCGATACA
1767583 T
1 T
1767584 GCTCACTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1767615 original size:20 final size:19
Alignment explanation
Indices: 1767567--1767623 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
1767557 TTGTATCGAT
1767567 ACATTGTATCGATACATGC
1 ACATTGTATCGATACATGC
* * *
1767586 TCACTGTATCGATACATGG
1 ACATTGTATCGATACATGC
1767605 ACAATTGTATCGATACATG
1 AC-ATTGTATCGATACATG
1767624 AGATTGGCAG
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 17 0.53
20 15 0.47
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32
Consensus pattern (19 bp):
ACATTGTATCGATACATGC
Found at i:1767689 original size:63 final size:63
Alignment explanation
Indices: 1767590--1767748 Score: 284
Period size: 63 Copynumber: 2.5 Consensus size: 63
1767580 ACATGCTCAC
1767590 TGTATCGATACAT-GGACAATTGTATCGATACATGAGATTGGCAGTAGCTACCCTATCACTATT
1 TGTATCGATACATGGGACAA-TGTATCGATACATGAGATTGGCAGTAGCTACCCTATCACTATT
*
1767653 TGTATCGATACATGGGACAATGTATCGATACATGAGATTGGTAGTAGCTACCCTATCACTATT
1 TGTATCGATACATGGGACAATGTATCGATACATGAGATTGGCAGTAGCTACCCTATCACTATT
*
1767716 TGTATCGATACATGGGACAATATATCGATACAT
1 TGTATCGATACATGGGACAATGTATCGATACAT
1767749 TGTATCGATA
Statistics
Matches: 93, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
63 87 0.94
64 6 0.06
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.31
Consensus pattern (63 bp):
TGTATCGATACATGGGACAATGTATCGATACATGAGATTGGCAGTAGCTACCCTATCACTATT
Found at i:1767756 original size:13 final size:13
Alignment explanation
Indices: 1767738--1767838 Score: 63
Period size: 13 Copynumber: 9.0 Consensus size: 13
1767728 TGGGACAATA
1767738 TATCGATACATTG
1 TATCGATACATTG
1767751 TATCGATACA-TG
1 TATCGATACATTG
*
1767763 -A-GGA-A-ATTG
1 TATCGATACATTG
1767772 TATCGATACATTG
1 TATCGATACATTG
*
1767785 ----G--ACAATG
1 TATCGATACATTG
1767792 TATCGATACATTG
1 TATCGATACATTG
1767805 TATCGATACA-TG
1 TATCGATACATTG
*
1767817 -A-GGA-A-ATTG
1 TATCGATACATTG
1767826 TATCGATACATTG
1 TATCGATACATTG
1767839 CTTGTAATGG
Statistics
Matches: 66, Mismatches: 6, Indels: 32
0.63 0.06 0.31
Matches are distributed among these distances:
7 5 0.08
8 2 0.03
9 7 0.11
10 6 0.09
11 7 0.11
12 6 0.09
13 33 0.50
ACGTcount: A:0.35, C:0.13, G:0.20, T:0.33
Consensus pattern (13 bp):
TATCGATACATTG
Found at i:1767757 original size:33 final size:34
Alignment explanation
Indices: 1767715--1767784 Score: 108
Period size: 33 Copynumber: 2.1 Consensus size: 34
1767705 CTATCACTAT
1767715 TTGTATCGATACATG-GGACAA-TATATCGATACA
1 TTGTATCGATACATGAGGA-AATTATATCGATACA
*
1767748 TTGTATCGATACATGAGGAAATTGTATCGATACA
1 TTGTATCGATACATGAGGAAATTATATCGATACA
1767782 TTG
1 TTG
1767785 GACAATGTAT
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
33 17 0.50
34 17 0.50
ACGTcount: A:0.34, C:0.13, G:0.20, T:0.33
Consensus pattern (34 bp):
TTGTATCGATACATGAGGAAATTATATCGATACA
Found at i:1767795 original size:20 final size:20
Alignment explanation
Indices: 1767747--1767838 Score: 83
Period size: 21 Copynumber: 4.8 Consensus size: 20
1767737 ATATCGATAC
*
1767747 ATTGTATCGATACATGAGGAA
1 ATTGTATCGATACAT-TGGAA
1767768 ATTGTATCGATACATTGGACA
1 ATTGTATCGATACATTGGA-A
1767789 A-TGTATCGATAC-------
1 ATTGTATCGATACATTGGAA
*
1767801 ATTGTATCGATACATGAGGAA
1 ATTGTATCGATACAT-TGGAA
1767822 ATTGTATCGATACATTG
1 ATTGTATCGATACATTG
1767839 CTTGTAATGG
Statistics
Matches: 59, Mismatches: 2, Indels: 21
0.72 0.02 0.26
Matches are distributed among these distances:
12 1 0.02
13 11 0.19
20 15 0.25
21 32 0.54
ACGTcount: A:0.35, C:0.12, G:0.21, T:0.33
Consensus pattern (20 bp):
ATTGTATCGATACATTGGAA
Found at i:1767797 original size:54 final size:54
Alignment explanation
Indices: 1767715--1767838 Score: 230
Period size: 54 Copynumber: 2.3 Consensus size: 54
1767705 CTATCACTAT
*
1767715 TTGTATCGATACATGGGACAATATATCGATACATTGTATCGATACATGAGGAAA
1 TTGTATCGATACATTGGACAATATATCGATACATTGTATCGATACATGAGGAAA
*
1767769 TTGTATCGATACATTGGACAATGTATCGATACATTGTATCGATACATGAGGAAA
1 TTGTATCGATACATTGGACAATATATCGATACATTGTATCGATACATGAGGAAA
1767823 TTGTATCGATACATTG
1 TTGTATCGATACATTG
1767839 CTTGTAATGG
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
54 68 1.00
ACGTcount: A:0.35, C:0.13, G:0.20, T:0.32
Consensus pattern (54 bp):
TTGTATCGATACATTGGACAATATATCGATACATTGTATCGATACATGAGGAAA
Found at i:1770888 original size:16 final size:16
Alignment explanation
Indices: 1770863--1770900 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
1770853 TTTTATCAAC
*
1770863 ATTTTCTCTATTAAAA
1 ATTTTGTCTATTAAAA
*
1770879 CTTTTGTCTATTAAAA
1 ATTTTGTCTATTAAAA
1770895 ATTTTG
1 ATTTTG
1770901 AAAGCCTTTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.32, C:0.11, G:0.05, T:0.53
Consensus pattern (16 bp):
ATTTTGTCTATTAAAA
Found at i:1774179 original size:15 final size:15
Alignment explanation
Indices: 1774161--1774195 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
1774151 CGAGTCAACT
1774161 TCATCATTATCATCA
1 TCATCATTATCATCA
*
1774176 TCATCATTATCTTCA
1 TCATCATTATCATCA
1774191 TCATC
1 TCATC
1774196 TTTGATGGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.29, C:0.29, G:0.00, T:0.43
Consensus pattern (15 bp):
TCATCATTATCATCA
Found at i:1776084 original size:20 final size:20
Alignment explanation
Indices: 1776056--1776130 Score: 78
Period size: 20 Copynumber: 3.8 Consensus size: 20
1776046 TTTTACCCTG
1776056 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
1776076 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * * *
1776096 ATGTACCGATATATTCTGCA
1 ATGTATCGATACATTTTTCA
1776116 ATGTATCGATACATT
1 ATGTATCGATACATT
1776131 ATGTCTTTTT
Statistics
Matches: 41, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.39
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:1776123 original size:40 final size:39
Alignment explanation
Indices: 1776056--1776133 Score: 102
Period size: 40 Copynumber: 2.0 Consensus size: 39
1776046 TTTTACCCTG
* * *
1776056 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTACCGATACATTCTGCAATATATCGATACAT-TATGA
* *
1776096 ATGTACCGATATATTCTGCAATGTATCGATACATTATG
1 ATGTACCGATACATTCTGCAATATATCGATACATTATG
1776134 TCTTTTTACC
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
39 4 0.12
40 29 0.88
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.38
Consensus pattern (39 bp):
ATGTACCGATACATTCTGCAATATATCGATACATTATGA
Found at i:1790134 original size:21 final size:19
Alignment explanation
Indices: 1790108--1790173 Score: 87
Period size: 19 Copynumber: 3.3 Consensus size: 19
1790098 CTTTACACCC
*
1790108 AAAAAAAAAAACAAAACAAA
1 AAAAAAAAAAAAAAAAC-AA
1790128 ACAAAAAAAAAAAAAAACAA
1 A-AAAAAAAAAAAAAAACAA
*
1790148 AAAAACAAAAAAAAAACAA
1 AAAAAAAAAAAAAAAACAA
1790167 GAAAAAA
1 -AAAAAA
1790174 TAGCAAAAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
19 17 0.41
20 9 0.22
21 15 0.37
ACGTcount: A:0.89, C:0.09, G:0.02, T:0.00
Consensus pattern (19 bp):
AAAAAAAAAAAAAAAACAA
Found at i:1790135 original size:24 final size:24
Alignment explanation
Indices: 1790108--1790163 Score: 94
Period size: 24 Copynumber: 2.2 Consensus size: 24
1790098 CTTTACACCC
1790108 AAAAAAAAAAACAAAACAAAACAAAA
1 AAAAAAAAAAAC-AAA-AAAACAAAA
1790134 AAAAAAAAAAACAAAAAAACAAAA
1 AAAAAAAAAAACAAAAAAACAAAA
1790158 AAAAAA
1 AAAAAA
1790164 CAAGAAAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
24 15 0.50
25 3 0.10
26 12 0.40
ACGTcount: A:0.91, C:0.09, G:0.00, T:0.00
Consensus pattern (24 bp):
AAAAAAAAAAACAAAAAAACAAAA
Found at i:1790173 original size:24 final size:23
Alignment explanation
Indices: 1790108--1790184 Score: 91
Period size: 24 Copynumber: 3.3 Consensus size: 23
1790098 CTTTACACCC
* *
1790108 AAAAAAAAAAACAAAACAAAACA
1 AAAAAAAAAAAAAAAAAAAAACA
1790131 AAAAAAAAAAAAAACAAAAAAACA
1 AAAAAAAAAAAAAA-AAAAAAACA
* * *
1790155 AAAAAAAAACAAGAAAAAATAGCA
1 AAAAAAAAA-AAAAAAAAAAAACA
1790179 AAAAAA
1 AAAAAA
1790185 TAGAAGGGTC
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
23 13 0.28
24 30 0.64
25 4 0.09
ACGTcount: A:0.87, C:0.09, G:0.03, T:0.01
Consensus pattern (23 bp):
AAAAAAAAAAAAAAAAAAAAACA
Found at i:1790184 original size:1 final size:1
Alignment explanation
Indices: 1790108--1790173 Score: 69
Period size: 1 Copynumber: 66.0 Consensus size: 1
1790098 CTTTACACCC
* * * * * * *
1790108 AAAAAAAAAAACAAAACAAAACAAAAAAAAAAAAAAACAAAAAAACAAAAAAAAAACAAGAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1790173 A
1 A
1790174 TAGCAAAAAA
Statistics
Matches: 51, Mismatches: 14, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
1 51 1.00
ACGTcount: A:0.89, C:0.09, G:0.02, T:0.00
Consensus pattern (1 bp):
A
Found at i:1791443 original size:29 final size:29
Alignment explanation
Indices: 1791401--1792519 Score: 1431
Period size: 28 Copynumber: 38.9 Consensus size: 29
1791391 ATGTTTATCT
1791401 CTTTCAAAGCCCACAAGTCAGTGGCACTC
1 CTTTCAAAGCCCACAAGTCAGTGGCACTC
*
1791430 CTTTCAAAGCCCACAAGTCAGTGGCACTA
1 CTTTCAAAGCCCACAAGTCAGTGGCACTC
* * *
1791459 TTTTCAAAGCCCACAAATCAGTGGCACTT
1 CTTTCAAAGCCCACAAGTCAGTGGCACTC
* *
1791488 TTTTTAAAGCCCACAAGTCAGTGGCAC-C
1 CTTTCAAAGCCCACAAGTCAGTGGCACTC
*
1791516 CTTTCAAAGCCCACAAATCAGTGGCACTC
1 CTTTCAAAGCCCACAAGTCAGTGGCACTC
* *
1791545 TTTTCAAAGCCCACAAGTTAGTGGCACTC
1 CTTTCAAAGCCCACAAGTCAGTGGCACTC
* *
1791574 TTTTCAAAGCCCACAAATCAGTGGCACTC
1 CTTTCAAAGCCCACAAGTCAGTGGCACTC
1791603 CTTTCAAAGCCCACAAGTCAGTGGCAC-C
1 CTTTCAAAGCCCACAAGTCAGTGGCACTC
*
1791631 CTTTCAAAGCCCACAAATCAGTGGCACTC
1 CTTTCAAAGCCCACAAGTCAGTGGCACTC
*
1791660 TTTTCAAAGCCCACAAGTCAGTGGCAC-C
1 CTTTCAAAGCCCACAAGTCAGTGGCACTC
*
1791688 CTTTTAAAGCCCACAAGTCAGTGGCAC-C
1 CTTTCAAAGCCCACAAGTCAGTGGCACTC
*
1791716 CTTTTAAAGCCCACAAGTCAGTGGCACTC
1 CTTTCAAAGCCCACAAGTCAGTGGCACTC
* *
1791745 TTTTCAAAGCCCACAAATCAGTGGCACTC
1 CTTTCAAAGCCCACAAGTCAGTGGCACTC
* * *
1791774 TTTTCAAAGCACACAAATCAGTGGCACTC
1 CTTTCAAAGCCCACAAGTCAGTGGCACTC
* *
1791803 TTTTCAAAGCACACAAGTCAGTGGCAC-C
1 CTTTCAAAGCCCACAAGTCAGTGGCACTC
*
1791831 CTTTTAAAGCCCACAAGTCAGTGGCACTC
1 CTTTCAAAGCCCACAAGTCAGTGGCACTC
1791860 CTTTCAAAGCCCACAAGTCAGTGGCACTC
1 CTTTCAAAGCCCACAAGTCAGTGGCACTC
* * *
1791889 TTTTCAAAGCCCATAAATCAGTGGCACTC
1 CTTTCAAAGCCCACAAGTCAGTGGCACTC
* *
1791918 TTTTCAAAGCCCATAAGTCAGTGGCAC-C
1 CTTTCAAAGCCCACAAGTCAGTGGCACTC
* *
1791946 CTTTCGAAGCCCACAAGTTAGTGGCAC-C
1 CTTTCAAAGCCCACAAGTCAGTGGCACTC
*
1791974 CTTTCAGAGCCCACAAGTCAGTGGCAC-C
1 CTTTCAAAGCCCACAAGTCAGTGGCACTC
*
1792002 CTTTCGAAGCCCACAAGTCAGTGGCAC-C
1 CTTTCAAAGCCCACAAGTCAGTGGCACTC
1792030 CTTTCAAAGCCCACAAGTCAGTGGCAC-C
1 CTTTCAAAGCCCACAAGTCAGTGGCACTC
1792058 CTTTCAAAGCCCACAAGTCAGTGGCAC-C
1 CTTTCAAAGCCCACAAGTCAGTGGCACTC
* *
1792086 CTTGCGAAGCCCACAAGTCAGTGGCACT-
1 CTTTCAAAGCCCACAAGTCAGTGGCACTC
1792114 CTTTCAAAGCCCACAAGTCAGTGGCAC-C
1 CTTTCAAAGCCCACAAGTCAGTGGCACTC
1792142 CTTTCAAAGCCCACACAAGTCAGTGGCACTC
1 CTTTCAAAG-CC-CACAAGTCAGTGGCACTC
*
1792173 CTTTTAAAGCCCACGCAAGTCAGTGGCACAT-
1 CTTTCAAAGCCCA--CAAGTCAGTGGCAC-TC
*
1792204 -TTTCAAAGCCCACGAGTCAGTGGCACT-
1 CTTTCAAAGCCCACAAGTCAGTGGCACTC
1792231 CTTTCAAAGCCCACAAGTCAGTGGCAC-C
1 CTTTCAAAGCCCACAAGTCAGTGGCACTC
* * *
1792259 CTTTC-AAGCACACGAGTCAGTGGTAC-C
1 CTTTCAAAGCCCACAAGTCAGTGGCACTC
* *
1792286 TTTTCAAAGCCCACGAGTCAGTGGCAC-C
1 CTTTCAAAGCCCACAAGTCAGTGGCACTC
* *
1792314 TTTTCAAAGCCCACGAGTCAGTGGCACT-
1 CTTTCAAAGCCCACAAGTCAGTGGCACTC
1792342 CTTTCAAAGCCCACAAGTCAGTGGCA-TC
1 CTTTCAAAGCCCACAAGTCAGTGGCACTC
** *
1792370 CTTTCAAAGCCCATGAGTCAGTGGCA-TT
1 CTTTCAAAGCCCACAAGTCAGTGGCACTC
* *
1792398 ATTTCAAAGCCCACGCAAGTGAGTGGCAC-C
1 CTTTCAAAGCCCA--CAAGTCAGTGGCACTC
* **
1792428 CTTTTAAAGCCCACGCAAGTCAGTAACACTC
1 CTTTCAAAGCCCA--CAAGTCAGTGGCACTC
* * * *
1792459 TTTTCAAAGCCCACATGTGTCAGTGACAACTT
1 CTTTCAAAGCCCACA--AGTCAGTGGC-ACTC
* *
1792491 TTTTCAAAGCCTACACAAGTTAGTGGCAC
1 CTTTCAAAGCC--CACAAGTCAGTGGCAC
1792520 ATTTTTTTGA
Statistics
Matches: 982, Mismatches: 82, Indels: 50
0.88 0.07 0.04
Matches are distributed among these distances:
27 25 0.03
28 471 0.48
29 352 0.36
30 63 0.06
31 45 0.05
32 22 0.02
34 4 0.00
ACGTcount: A:0.29, C:0.31, G:0.18, T:0.22
Consensus pattern (29 bp):
CTTTCAAAGCCCACAAGTCAGTGGCACTC
Found at i:1791612 original size:115 final size:114
Alignment explanation
Indices: 1791401--1792519 Score: 1502
Period size: 115 Copynumber: 9.7 Consensus size: 114
1791391 ATGTTTATCT
* *
1791401 CTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTATTTTCAA
1 CTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAA
* ** *
1791466 AGCCCACAAATCAGTGGCACTTTTTTTAAAGCCCACAAGTCAGTGGCACC
66 AGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCACC
* *
1791516 CTTTCAAAGCCCACAAATCAGTGGCACTCTTTTCAAAGCCCACAAGTTAGTGGCACTCTTTTCAA
1 CTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAA
*
1791581 AGCCCACAAATCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACC
66 AGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCACC
* *
1791631 CTTTCAAAGCCCACAAATCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTT-AA
1 CTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAA
*
1791695 AGCCCACAAGTCAGTGGCACCCTTTTAAAGCCCACAAGTCAGTGGCACTC
66 AGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCAC-C
* * * *
1791745 TTTTCAAAGCCCACAAATCAGTGGCACTCTTTTCAAAGCACACAAATCAGTGGCACTCTTTTCAA
1 CTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAA
* *
1791810 AGCACACAAGTCAGTGGCACCCTTTTAAAGCCCACAAGTCAGTGGCACTC
66 AGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCAC-C
* *
1791860 CTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCATAAATCAGTGGCACTCTTTTCAA
1 CTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAA
* * *
1791925 AGCCCATAAGTCAGTGGCACCCTTTCGAAGCCCACAAGTTAGTGGCACC
66 AGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACC
* * * *
1791974 CTTTCAGAGCCCACAAGTCAGTGGCAC-CCTTTCGAAGCCCACAAGTCAGTGGCAC-CCTTTCAA
1 CTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAA
1792037 AGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACC
66 AGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACC
* * *
1792086 CTTGCGAAGCCCACAAGTCAGTGGCACTC-TTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAA
1 CTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAA
* *
1792149 AGCCCACACAAGTCAGTGGCACTCCTTTTAAAGCCCACGCAAGTCAGTGGCACA
66 AG-CC-CACAAGTCAGTGGCAC-CCTTTCAAAGCCCA--CAAGTCAGTGGCACC
* * *
1792203 TTTTCAAAGCCCACGAGTCAGTGGCACTC-TTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTC-A
1 CTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAA
* * * * *
1792265 AGCACACGAGTCAGTGGTACCTTTTCAAAGCCCACGAGTCAGTGGCACC
66 AGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACC
* * *
1792314 TTTTCAAAGCCCACGAGTCAGTGGCACTC-TTTCAAAGCCCACAAGTCAGTGGCA-TCCTTTCAA
1 CTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAA
** *** *
1792377 AGCCCATGAGTCAGTGGCATTATTTCAAAGCCCACGCAAGTGAGTGGCACC
66 AGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCA--CAAGTCAGTGGCACC
* ** * * *
1792428 CTTTTAAAGCCCACGCAAGTCAGTAACACTCTTTTCAAAGCCCACATGTGTCAGTGACAACTTTT
1 CTTTCAAAGCCCA--CAAGTCAGTGGCACTCTTTTCAAAGCCCACA--AGTCAGTGGC-ACTCTT
*
1792493 TTCAAAGCCTACACAAGTTAGTGGCAC
61 TTCAAAGCC--CACAAGTCAGTGGCAC
1792520 ATTTTTTTGA
Statistics
Matches: 911, Mismatches: 72, Indels: 34
0.90 0.07 0.03
Matches are distributed among these distances:
111 73 0.08
112 141 0.15
113 66 0.07
114 161 0.18
115 337 0.37
116 16 0.02
117 85 0.09
119 8 0.01
120 1 0.00
121 11 0.01
123 12 0.01
ACGTcount: A:0.29, C:0.31, G:0.18, T:0.22
Consensus pattern (114 bp):
CTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAA
AGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACC
Found at i:1793108 original size:20 final size:20
Alignment explanation
Indices: 1793080--1793154 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
1793070 TTTTACCCTG
1793080 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
1793100 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
1793120 ATGTATCGATATATTCTGCA
1 ATGTATCGATACATTTTTCA
1793140 ATGTATCGATACATT
1 ATGTATCGATACATT
1793155 ATGTCTTTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:1793147 original size:40 final size:39
Alignment explanation
Indices: 1793080--1793157 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
1793070 TTTTACCCTG
* *
1793080 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTGCAATATATCGATACAT-TATGA
* *
1793120 ATGTATCGATATATTCTGCAATGTATCGATACATTATG
1 ATGTATCGATACATTCTGCAATATATCGATACATTATG
1793158 TCTTTTTACC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.33, C:0.13, G:0.14, T:0.40
Consensus pattern (39 bp):
ATGTATCGATACATTCTGCAATATATCGATACATTATGA
Found at i:1796926 original size:22 final size:21
Alignment explanation
Indices: 1796888--1796931 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 21
1796878 AATTTTTATT
1796888 TAAATTTAATTATAAAATATA
1 TAAATTTAATTATAAAATATA
1796909 TAAATATTAA-TATAAAAATATA
1 TAAAT-TTAATTAT-AAAATATA
1796931 T
1 T
1796932 TTTTTAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
TAAATTTAATTATAAAATATA
Found at i:1797102 original size:19 final size:18
Alignment explanation
Indices: 1797080--1797182 Score: 71
Period size: 15 Copynumber: 6.1 Consensus size: 18
1797070 TTATCTAATA
1797080 ATTTATATATTTATATTAT
1 ATTTATATATTT-TATTAT
1797099 ATTTATATATTTTATTAT
1 ATTTATATATTTTATTAT
**
1797117 -TTTATA-ATTAAATT-T
1 ATTTATATATTTTATTAT
*
1797132 A-TAATAT-TTTTATT-T
1 ATTTATATATTTTATTAT
* *
1797147 A--TATAAATTTTAATAT
1 ATTTATATATTTTATTAT
*
1797163 ATTAATA-ATTTATATTAT
1 ATTTATATATTT-TATTAT
1797181 AT
1 AT
1797183 AAATTTTAAT
Statistics
Matches: 67, Mismatches: 10, Indels: 15
0.73 0.11 0.16
Matches are distributed among these distances:
14 3 0.04
15 18 0.27
16 8 0.12
17 10 0.15
18 16 0.24
19 12 0.18
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
ATTTATATATTTTATTAT
Found at i:1797194 original size:15 final size:15
Alignment explanation
Indices: 1797139--1797195 Score: 62
Period size: 15 Copynumber: 3.7 Consensus size: 15
1797129 TTTATAATAT
*
1797139 TTTTATTTATATAAA
1 TTTTAATTATATAAA
1797154 TTTTAA-TATATTAATA
1 TTTTAATTATA-TAA-A
*
1797170 ATTTATATTATATAAA
1 TTTTA-ATTATATAAA
1797186 TTTTAATTAT
1 TTTTAATTAT
1797196 TTTATGTTGG
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
14 4 0.11
15 13 0.37
16 10 0.29
17 4 0.11
18 4 0.11
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TTTTAATTATATAAA
Found at i:1797196 original size:18 final size:18
Alignment explanation
Indices: 1797145--1797196 Score: 60
Period size: 16 Copynumber: 3.1 Consensus size: 18
1797135 ATATTTTTAT
1797145 TTATATAAATTTTAATATA
1 TTATATAAATTTTAAT-TA
1797164 TTA-AT-AA-TTT-A-TA
1 TTATATAAATTTTAATTA
1797177 TTATATAAATTTTAATTA
1 TTATATAAATTTTAATTA
1797195 TT
1 TT
1797197 TTATGTTGGG
Statistics
Matches: 28, Mismatches: 0, Indels: 11
0.72 0.00 0.28
Matches are distributed among these distances:
13 5 0.18
14 2 0.07
15 3 0.11
16 6 0.21
17 3 0.11
18 6 0.21
19 3 0.11
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TTATATAAATTTTAATTA
Found at i:1799805 original size:1 final size:1
Alignment explanation
Indices: 1799801--1799827 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
1799791 ATTTTTTTTT
1799801 GGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGG
1799828 AGGTTTGCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:1800933 original size:23 final size:22
Alignment explanation
Indices: 1800907--1800954 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
1800897 CTGGATCGAA
1800907 AATCAAATCAATAAAATTAATTT
1 AATCAAATCAATAAAATT-ATTT
** *
1800930 AATCAAATGTATCAAATTATTT
1 AATCAAATCAATAAAATTATTT
1800952 AAT
1 AAT
1800955 AAAAAATTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 7 0.32
23 15 0.68
ACGTcount: A:0.52, C:0.08, G:0.02, T:0.38
Consensus pattern (22 bp):
AATCAAATCAATAAAATTATTT
Found at i:1800977 original size:21 final size:20
Alignment explanation
Indices: 1800953--1800992 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
1800943 AAATTATTTA
1800953 ATAAAAAATTTAAAATATTAC
1 ATAAAAAATTT-AAATATTAC
* *
1800974 ATAAATAATTTTAATATTA
1 ATAAAAAATTTAAATATTA
1800993 AATATAGTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (20 bp):
ATAAAAAATTTAAATATTAC
Found at i:1801037 original size:21 final size:20
Alignment explanation
Indices: 1801007--1801056 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
1800997 TAGTAAATAT
*
1801007 TTAAAAAATATATAAATTTAA
1 TTAAATAATATA-AAATTTAA
**
1801028 TTAAATAATATAATTTTTAA
1 TTAAATAATATAAAATTTAA
1801048 TATAAATAA
1 T-TAAATAA
1801057 ATCAAATATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 7 0.28
21 18 0.72
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
TTAAATAATATAAAATTTAA
Found at i:1801529 original size:21 final size:22
Alignment explanation
Indices: 1801505--1801551 Score: 71
Period size: 21 Copynumber: 2.2 Consensus size: 22
1801495 TACGTTTTTA
1801505 ATATTAATT-TTATTTAAAAAT
1 ATATTAATTATTATTTAAAAAT
*
1801526 ATA-TAATTATTTTTTAAAAAT
1 ATATTAATTATTATTTAAAAAT
1801547 ATATT
1 ATATT
1801552 TATATAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 5 0.22
21 17 0.74
22 1 0.04
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
ATATTAATTATTATTTAAAAAT
Found at i:1802709 original size:20 final size:20
Alignment explanation
Indices: 1802684--1802741 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
1802674 ACTTTAATAG
* *
1802684 TATTAATATTTTTAATATTT
1 TATTAATAATATTAATATTT
*
1802704 TATTAATAATATTAATTTTT
1 TATTAATAATATTAATATTT
* *
1802724 TAAATATTAATATTAATA
1 T-ATTAATAATATTAATA
1802742 AAATAATATC
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
20 18 0.58
21 13 0.42
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
TATTAATAATATTAATATTT
Found at i:1802716 original size:29 final size:31
Alignment explanation
Indices: 1802677--1802750 Score: 93
Period size: 29 Copynumber: 2.5 Consensus size: 31
1802667 TACCACTACT
* *
1802677 TTAATAGTATTAATATTTTT-AATATT-TTA
1 TTAATAATATTAATATTTTTAAATATTAATA
1802706 TTAATAATATTAAT-TTTTTAAATATTAATA
1 TTAATAATATTAATATTTTTAAATATTAATA
*
1802736 TTAATAA-AATAATAT
1 TTAATAATATTAATAT
1802751 CAAACTATAC
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
28 5 0.13
29 24 0.62
30 10 0.26
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (31 bp):
TTAATAATATTAATATTTTTAAATATTAATA
Found at i:1804076 original size:15 final size:15
Alignment explanation
Indices: 1804056--1804088 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1804046 CTGGGTAAAT
1804056 AGGTGGTGGATGCAC
1 AGGTGGTGGATGCAC
*
1804071 AGGTGGTGGATGGAC
1 AGGTGGTGGATGCAC
1804086 AGG
1 AGG
1804089 ATCAGTGGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.21, C:0.09, G:0.52, T:0.18
Consensus pattern (15 bp):
AGGTGGTGGATGCAC
Found at i:1808248 original size:17 final size:17
Alignment explanation
Indices: 1808226--1808264 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
1808216 GATGATATTG
1808226 ATAATAAAAAAATTAA-T
1 ATAATAAAAAAA-TAATT
*
1808243 ATAATAAAATAATAATT
1 ATAATAAAAAAATAATT
1808260 ATAAT
1 ATAAT
1808265 GTTACACTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 3 0.15
17 17 0.85
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
ATAATAAAAAAATAATT
Found at i:1808813 original size:2 final size:2
Alignment explanation
Indices: 1808806--1808865 Score: 51
Period size: 2 Copynumber: 33.0 Consensus size: 2
1808796 CCATATCGTG
*
1808806 TA TA TA TA TA TA TA TA TA TA TA T- TA TA -A T- TA TA TT TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
1808844 GA TA T- TA T- TA TA TA TT TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA
1808866 AATTTTGACA
Statistics
Matches: 47, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
1 6 0.13
2 41 0.87
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (2 bp):
TA
Found at i:1808945 original size:17 final size:17
Alignment explanation
Indices: 1808925--1808969 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
1808915 ATATTTAAAA
*
1808925 TATATTTTATTATTTTT
1 TATATTTTATTATATTT
*
1808942 TATATCTTATTATATTT
1 TATATTTTATTATATTT
1808959 TACT-TTTTATT
1 TA-TATTTTATT
1808970 TTAACCATCT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 23 0.96
18 1 0.04
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.71
Consensus pattern (17 bp):
TATATTTTATTATATTT
Found at i:1809338 original size:33 final size:34
Alignment explanation
Indices: 1809267--1809338 Score: 80
Period size: 32 Copynumber: 2.2 Consensus size: 34
1809257 ATAAGTATAT
* * *
1809267 TTTTAAAATTTATATCATATAAATTATTAACATA
1 TTTTAAAATTAATATAATATAAATTATTAAAATA
1809301 --TTAAAATTAATATAAATATAAA-TA-TAAAATA
1 TTTTAAAATTAATAT-AATATAAATTATTAAAATA
1809332 TTTTAAA
1 TTTTAAA
1809339 CATATGAATG
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
31 6 0.19
32 14 0.44
33 12 0.38
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (34 bp):
TTTTAAAATTAATATAATATAAATTATTAAAATA
Found at i:1809440 original size:19 final size:19
Alignment explanation
Indices: 1809394--1809443 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
1809384 ATTCAAATCA
1809394 ATAACTATTCTATATATTCAT
1 ATAA-TATT-TATATATTCAT
* **
1809415 ATTATATTTATATATTTTT
1 ATAATATTTATATATTCAT
1809434 ATAATATTTA
1 ATAATATTTA
1809444 AAATGCTACG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 18 0.72
20 4 0.16
21 3 0.12
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (19 bp):
ATAATATTTATATATTCAT
Found at i:1809503 original size:11 final size:11
Alignment explanation
Indices: 1809487--1809541 Score: 55
Period size: 11 Copynumber: 5.3 Consensus size: 11
1809477 ATAATTATAA
1809487 ATTTATATTAT
1 ATTTATATTAT
1809498 ATTTATATTAT
1 ATTTATATTAT
* *
1809509 A-TCATACTAT
1 ATTTATATTAT
1809519 ATATTATA-TAT
1 AT-TTATATTAT
1809530 -TTTA-ATTAT
1 ATTTATATTAT
1809539 ATT
1 ATT
1809542 CGAAATTGTG
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
8 1 0.03
9 6 0.16
10 11 0.30
11 15 0.41
12 4 0.11
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (11 bp):
ATTTATATTAT
Found at i:1810195 original size:19 final size:20
Alignment explanation
Indices: 1810160--1810197 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
1810150 CGATATATTT
1810160 AATAAATATAAAAATAATAA
1 AATAAATATAAAAATAATAA
*
1810180 AATAAA-ATAAATATAATA
1 AATAAATATAAAAATAATA
1810198 TTTTTAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (20 bp):
AATAAATATAAAAATAATAA
Found at i:1810237 original size:13 final size:13
Alignment explanation
Indices: 1810212--1810252 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 13
1810202 TAAATATTAC
1810212 TAATATGATATATT
1 TAATAT-ATATATT
1810226 TAATATATATA--
1 TAATATATATATT
*
1810237 TAATATTTATATT
1 TAATATATATATT
1810250 TAA
1 TAA
1810253 AATGCATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
11 10 0.42
13 8 0.33
14 6 0.25
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (13 bp):
TAATATATATATT
Found at i:1811249 original size:15 final size:15
Alignment explanation
Indices: 1811231--1811290 Score: 93
Period size: 15 Copynumber: 4.0 Consensus size: 15
1811221 AAATCATTAG
1811231 AATTTAAATTATTTT
1 AATTTAAATTATTTT
*
1811246 AATTTTAATTATTTT
1 AATTTAAATTATTTT
* *
1811261 AATTTGAATTAATTT
1 AATTTAAATTATTTT
1811276 AATTTAAATTATTTT
1 AATTTAAATTATTTT
1811291 GAACTCAAAG
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 40 1.00
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (15 bp):
AATTTAAATTATTTT
Found at i:1813210 original size:16 final size:16
Alignment explanation
Indices: 1813189--1813219 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1813179 GATGATCACG
*
1813189 AAATTTAAATCAAATT
1 AAATTTAAATAAAATT
1813205 AAATTTAAATAAAAT
1 AAATTTAAATAAAAT
1813220 ATTAATAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.35
Consensus pattern (16 bp):
AAATTTAAATAAAATT
Found at i:1813965 original size:15 final size:16
Alignment explanation
Indices: 1813937--1813987 Score: 59
Period size: 15 Copynumber: 3.2 Consensus size: 16
1813927 ATTTATATTT
*
1813937 TATTAATATAAATTAA
1 TATTTATATAAATTAA
* *
1813953 T-TTTATTTAAATTAT
1 TATTTATATAAATTAA
1813968 TATTTATATAATATTAA
1 TATTTATATAA-ATTAA
1813985 TAT
1 TAT
1813988 AAAATAATAA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
15 12 0.43
16 9 0.32
17 7 0.25
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TATTTATATAAATTAA
Found at i:1815193 original size:11 final size:11
Alignment explanation
Indices: 1815166--1815199 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
1815156 TATATTTAAT
1815166 TATTAAAAATTA
1 TATTAAAAA-TA
*
1815178 AATTAAAAATA
1 TATTAAAAATA
1815189 TATTAAAAATA
1 TATTAAAAATA
1815200 AAAATATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 12 0.60
12 8 0.40
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
TATTAAAAATA
Found at i:1815210 original size:22 final size:23
Alignment explanation
Indices: 1815162--1815212 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
1815152 ACAATATATT
* *
1815162 TAAT-TATTAAAAATTAAATTAA
1 TAATATATTAAAAATAAAAATAA
*
1815184 AAATATATTAAAAATAAAAAT-A
1 TAATATATTAAAAATAAAAATAA
1815206 TAATATA
1 TAATATA
1815213 AATAGATTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
22 10 0.42
23 14 0.58
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (23 bp):
TAATATATTAAAAATAAAAATAA
Done.