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 6 of 16
Found at i:951601 original size:13 final size:13
Alignment explanation
Indices: 951569--951601 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
951559 ATCGATACAT
*
951569 GATACAATGTATC
1 GATACATTGTATC
951582 GATACATTGTATC
1 GATACATTGTATC
951595 GATACAT
1 GATACAT
951602 GAAGAAATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.33
Consensus pattern (13 bp):
GATACATTGTATC
Found at i:951611 original size:33 final size:33
Alignment explanation
Indices: 951555--951619 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
951545 CTATCACTAT
*
951555 TTGTATCGATACATGATACAATGTATCGATACA
1 TTGTATCGATACATGATAAAATGTATCGATACA
*
951588 TTGTATCGATACATGA-AGAAATGTATTGATAC
1 TTGTATCGATACATGATA-AAATGTATCGATAC
951620 CTAGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 1 0.03
33 28 0.97
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.34
Consensus pattern (33 bp):
TTGTATCGATACATGATAAAATGTATCGATACA
Found at i:952625 original size:7 final size:7
Alignment explanation
Indices: 952613--952653 Score: 82
Period size: 7 Copynumber: 5.9 Consensus size: 7
952603 ATCAATCGAT
952613 TTTTAAA
1 TTTTAAA
952620 TTTTAAA
1 TTTTAAA
952627 TTTTAAA
1 TTTTAAA
952634 TTTTAAA
1 TTTTAAA
952641 TTTTAAA
1 TTTTAAA
952648 TTTTAA
1 TTTTAA
952654 TTCCAAAATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 34 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (7 bp):
TTTTAAA
Found at i:952662 original size:21 final size:21
Alignment explanation
Indices: 952617--952662 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
952607 ATCGATTTTT
**
952617 AAATTTTAAATTTTAAATTTT
1 AAATTTTAAATTTTAAATTCA
952638 AAATTTTAAATTTT-AATTCCA
1 AAATTTTAAATTTTAAATT-CA
952659 AAAT
1 AAAT
952663 AGTTGTAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 4 0.18
21 18 0.82
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (21 bp):
AAATTTTAAATTTTAAATTCA
Found at i:958982 original size:22 final size:22
Alignment explanation
Indices: 958954--958999 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
958944 ATTCTTAATG
*
958954 TTTTTGTGCTAA-AGTTTGTTCA
1 TTTTTGTGC-AAGACTTTGTTCA
958976 TTTTTGTGCAAGACTTTGTTCA
1 TTTTTGTGCAAGACTTTGTTCA
958998 TT
1 TT
959000 CCATTTTTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 2 0.09
22 20 0.91
ACGTcount: A:0.17, C:0.11, G:0.17, T:0.54
Consensus pattern (22 bp):
TTTTTGTGCAAGACTTTGTTCA
Found at i:960533 original size:14 final size:14
Alignment explanation
Indices: 960514--960566 Score: 70
Period size: 14 Copynumber: 3.8 Consensus size: 14
960504 TTCATTTAAA
960514 TAAAAAATATATTT
1 TAAAAAATATATTT
*
960528 TAAAAAATATTTTT
1 TAAAAAATATATTT
** *
960542 TAATTAATTTATTT
1 TAAAAAATATATTT
960556 TAAAAAATATA
1 TAAAAAATATA
960567 AAAAATATTA
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
14 31 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
TAAAAAATATATTT
Found at i:960692 original size:15 final size:16
Alignment explanation
Indices: 960672--960701 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
960662 ACAATTTGTT
960672 AAATATAAA-AATTAA
1 AAATATAAATAATTAA
960687 AAATATAAATAATTA
1 AAATATAAATAATTA
960702 TAAAGGTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
AAATATAAATAATTAA
Found at i:960773 original size:25 final size:26
Alignment explanation
Indices: 960745--960807 Score: 67
Period size: 25 Copynumber: 2.4 Consensus size: 26
960735 TAATTTCTTC
*
960745 TTTAATTTATTTATATCTAAA-TTAT
1 TTTAATTTATTTATACCTAAATTTAT
* *
960770 TTTAA-TTAGTTTTTACCTAAATTTGT
1 TTTAATTTA-TTTATACCTAAATTTAT
960796 TTTAATTATATT
1 TTTAATT-TATT
960808 GTTTAGTTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
24 3 0.10
25 15 0.48
26 8 0.26
27 3 0.10
28 2 0.06
ACGTcount: A:0.32, C:0.05, G:0.03, T:0.60
Consensus pattern (26 bp):
TTTAATTTATTTATACCTAAATTTAT
Found at i:962145 original size:21 final size:21
Alignment explanation
Indices: 962116--962161 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
962106 GAAAGAGGAA
* * *
962116 GAGGTGGCTCCTCAGCCAAAT
1 GAGGAGGCTCCGCAGCAAAAT
*
962137 GAGGAGGCTTCGCAGCAAAAT
1 GAGGAGGCTCCGCAGCAAAAT
962158 GAGG
1 GAGG
962162 TTAACAAACA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.28, C:0.22, G:0.35, T:0.15
Consensus pattern (21 bp):
GAGGAGGCTCCGCAGCAAAAT
Found at i:970315 original size:18 final size:19
Alignment explanation
Indices: 970277--970314 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
970267 TACATATATT
970277 ATTATATATAATACATAAA
1 ATTATATATAATACATAAA
970296 ATTAT-TATAACTACATAAA
1 ATTATATATAA-TACATAAA
970315 TATCTTACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.55, C:0.08, G:0.00, T:0.37
Consensus pattern (19 bp):
ATTATATATAATACATAAA
Found at i:970600 original size:17 final size:18
Alignment explanation
Indices: 970578--970617 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
970568 CTACTATGTA
970578 ATAAAAAATAATA-TTAC
1 ATAAAAAATAATAGTTAC
* *
970595 ATAAAATATTATAGTTAC
1 ATAAAAAATAATAGTTAC
970613 ATAAA
1 ATAAA
970618 TGTTATTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.60, C:0.05, G:0.03, T:0.33
Consensus pattern (18 bp):
ATAAAAAATAATAGTTAC
Found at i:971929 original size:20 final size:20
Alignment explanation
Indices: 971893--971955 Score: 74
Period size: 20 Copynumber: 3.1 Consensus size: 20
971883 GTATGTAAAA
*
971893 AATTATATATAAACATTATCG
1 AATTACATAT-AACATTATCG
*
971914 AATTACATATAACATTAT-A
1 AATTACATATAACATTATCG
*
971933 AATTTACATAAAACATTATCG
1 AA-TTACATATAACATTATCG
971954 AA
1 AA
971956 ACTATAATGT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
19 2 0.06
20 23 0.64
21 11 0.31
ACGTcount: A:0.51, C:0.11, G:0.03, T:0.35
Consensus pattern (20 bp):
AATTACATATAACATTATCG
Found at i:973054 original size:18 final size:19
Alignment explanation
Indices: 973031--973066 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
973021 AAATAATCAA
973031 AATTTACATAAA-TATTAT
1 AATTTACATAAATTATTAT
973049 AATTTACATAAATTATTA
1 AATTTACATAAATTATTA
973067 GAGTGTAGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (19 bp):
AATTTACATAAATTATTAT
Found at i:973430 original size:19 final size:21
Alignment explanation
Indices: 973402--973463 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 21
973392 AAATATATTA
*
973402 TATTAATAAAATTT-AA-TTT
1 TATTATTAAAATTTAAATTTT
973421 TATTATT-AAATTTAAATTTT
1 TATTATTAAAATTTAAATTTT
973441 TCATTACTTAAAATATTATAATT
1 T-ATTA-TTAAAAT-TTA-AATT
973464 AAAGATTATT
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
18 6 0.17
19 8 0.23
20 4 0.11
21 4 0.11
22 2 0.06
23 4 0.11
24 3 0.09
25 4 0.11
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (21 bp):
TATTATTAAAATTTAAATTTT
Found at i:976793 original size:13 final size:13
Alignment explanation
Indices: 976775--976799 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
976765 CAAAGATTAG
976775 TGTATCGATACAA
1 TGTATCGATACAA
976788 TGTATCGATACA
1 TGTATCGATACA
976800 TTTGAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:976866 original size:19 final size:18
Alignment explanation
Indices: 976842--976937 Score: 77
Period size: 19 Copynumber: 5.7 Consensus size: 18
976832 TAGCTTACAT
976842 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
976861 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
*
976874 TGTATCAATACAATACTTA
1 TGTATCGATACAA-ACTTA
976893 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
976906 TGTATCGATACAACACTTTA
1 TGTATCGATACAA-AC-TTA
976926 TGTATCGATACA
1 TGTATCGATACA
976938 TTTGGACAAA
Statistics
Matches: 62, Mismatches: 2, Indels: 25
0.70 0.02 0.28
Matches are distributed among these distances:
13 21 0.34
14 2 0.03
16 4 0.06
18 1 0.02
19 22 0.35
20 12 0.19
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.35
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:976878 original size:32 final size:32
Alignment explanation
Indices: 976837--976939 Score: 170
Period size: 32 Copynumber: 3.2 Consensus size: 32
976827 GGCAGTAGCT
976837 TACATTGTATCGATACAAAACTTATGTATCGA
1 TACATTGTATCGATACAAAACTTATGTATCGA
* *
976869 TACATTGTATCAATACAATACTTATGTATCGA
1 TACATTGTATCGATACAAAACTTATGTATCGA
*
976901 TACATTGTATCGATACAACACTTTATGTATCGA
1 TACATTGTATCGATACAAAAC-TTATGTATCGA
976934 TACATT
1 TACATT
976940 TGGACAAAAA
Statistics
Matches: 66, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
32 49 0.74
33 17 0.26
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.37
Consensus pattern (32 bp):
TACATTGTATCGATACAAAACTTATGTATCGA
Found at i:976879 original size:13 final size:13
Alignment explanation
Indices: 976861--976917 Score: 51
Period size: 13 Copynumber: 3.9 Consensus size: 13
976851 ACAAAACTTA
976861 TGTATCGATACAT
1 TGTATCGATACAT
*
976874 TGTATCAATACAATACTT
1 TGTATCGATAC---A--T
976892 ATGTATCGATACAT
1 -TGTATCGATACAT
976906 TGTATCGATACA
1 TGTATCGATACA
976918 ACACTTTATG
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
13 22 0.61
14 1 0.03
16 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.35, C:0.16, G:0.12, T:0.37
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:977288 original size:21 final size:21
Alignment explanation
Indices: 977259--977301 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
977249 GCAGAAGTTT
* *
977259 TATATTTTTTAAT-TTATTAA
1 TATAATTTTTAATATTAGTAA
977279 TATAATTTTTAATATTAGTAA
1 TATAATTTTTAATATTAGTAA
977300 TA
1 TA
977302 AATATATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (21 bp):
TATAATTTTTAATATTAGTAA
Found at i:982674 original size:25 final size:25
Alignment explanation
Indices: 982640--982717 Score: 85
Period size: 22 Copynumber: 3.2 Consensus size: 25
982630 GGCTAAATGA
982640 TAAATATTTAATAATTATTTTTATAT
1 TAAA-ATTTAATAATTATTTTTATAT
982666 TAAAATTT-ATAA--ATTTTTATAAT
1 TAAAATTTAATAATTATTTTTAT-AT
982689 T-AAATTTAAATAATT-TTTTTATTAT
1 TAAAATTT-AATAATTATTTTTA-TAT
982714 TAAA
1 TAAA
982718 TATTAATTCA
Statistics
Matches: 45, Mismatches: 0, Indels: 14
0.76 0.00 0.24
Matches are distributed among these distances:
22 14 0.31
23 3 0.07
24 8 0.18
25 13 0.29
26 7 0.16
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (25 bp):
TAAAATTTAATAATTATTTTTATAT
Found at i:982718 original size:25 final size:24
Alignment explanation
Indices: 982645--982724 Score: 85
Period size: 25 Copynumber: 3.3 Consensus size: 24
982635 AATGATAAAT
982645 ATTTAATAATTATTTTTA-TATTAAA
1 ATTTAATAATT-TTTTTATTATT-AA
* *
982670 ATTT-ATAA-ATTTTTATAATTAA
1 ATTTAATAATTTTTTTATTATTAA
982692 ATTTAAATAATTTTTTTATTATTAA
1 ATTT-AATAATTTTTTTATTATTAA
982717 ATATTAAT
1 AT-TTAAT
982725 TCAAGTAAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
22 12 0.26
23 3 0.07
24 8 0.17
25 21 0.46
26 2 0.04
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (24 bp):
ATTTAATAATTTTTTTATTATTAA
Found at i:983081 original size:24 final size:24
Alignment explanation
Indices: 983056--983102 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
983046 AAATTTTTAA
983056 TTTATACTTAAATAAACTCTTAAAT
1 TTTA-ACTTAAATAAACTCTTAAAT
**
983081 TTTAACTTGTATAAACTCTTAA
1 TTTAACTTAAATAAACTCTTAA
983103 TATAATTCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.40, C:0.13, G:0.02, T:0.45
Consensus pattern (24 bp):
TTTAACTTAAATAAACTCTTAAAT
Found at i:984184 original size:19 final size:18
Alignment explanation
Indices: 984150--984185 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
984140 CAACTTTACT
984150 ATATAGTTATAAATATAG
1 ATATAGTTATAAATATAG
*
984168 ATATAGATTATAGATATA
1 ATATAG-TTATAAATATA
984186 TTTTGAACAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.50, C:0.00, G:0.11, T:0.39
Consensus pattern (18 bp):
ATATAGTTATAAATATAG
Found at i:984537 original size:2 final size:2
Alignment explanation
Indices: 984489--984529 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
984479 GTTAGCTTGC
984489 TA TA 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 TA TA T
984530 GCATATATTG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:984688 original size:2 final size:2
Alignment explanation
Indices: 984683--984734 Score: 95
Period size: 2 Copynumber: 26.0 Consensus size: 2
984673 TGTATATATT
984683 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
*
984725 TA TG TG TG TG
1 TG TG TG TG TG
984735 CATATCACTA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.02, C:0.00, G:0.48, T:0.50
Consensus pattern (2 bp):
TG
Found at i:985687 original size:14 final size:16
Alignment explanation
Indices: 985648--985689 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 16
985638 TAACACTAAT
985648 TCAATAAATTATTAAAAG
1 TCAATAAA--ATTAAAAG
985666 TCAATAAAATTAAAA-
1 TCAATAAAATTAAAAG
985681 T-AATAAAAT
1 TCAATAAAAT
985690 AGAATAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
14 8 0.33
15 1 0.04
16 7 0.29
18 8 0.33
ACGTcount: A:0.62, C:0.05, G:0.02, T:0.31
Consensus pattern (16 bp):
TCAATAAAATTAAAAG
Found at i:986012 original size:24 final size:24
Alignment explanation
Indices: 985965--986013 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
985955 ATTCACTTTT
*
985965 AAAAAAAAAAAAAACTACCCATTTC
1 AAAAAAAAAAAAAACTA-CAATTTC
985990 AAAAAAAAAAAAAACCTA-AATTTC
1 AAAAAAAAAAAAAA-CTACAATTTC
986014 TGTATTTTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 5 0.23
25 14 0.64
26 3 0.14
ACGTcount: A:0.67, C:0.16, G:0.00, T:0.16
Consensus pattern (24 bp):
AAAAAAAAAAAAAACTACAATTTC
Found at i:986325 original size:9 final size:9
Alignment explanation
Indices: 986311--986349 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
986301 CAAAACTCTT
986311 CCTCCCTTC
1 CCTCCCTTC
*
986320 CCTCCCCTC
1 CCTCCCTTC
986329 CCT-CCTTC
1 CCTCCCTTC
986337 CCTTCCCTTC
1 CC-TCCCTTC
986347 CCT
1 CCT
986350 TTCCTAGTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
8 6 0.23
9 13 0.50
10 7 0.27
ACGTcount: A:0.00, C:0.67, G:0.00, T:0.33
Consensus pattern (9 bp):
CCTCCCTTC
Found at i:988517 original size:218 final size:218
Alignment explanation
Indices: 988139--988568 Score: 797
Period size: 218 Copynumber: 2.0 Consensus size: 218
988129 TACATACCTG
*
988139 CAAGAAATAGTGTATTAATTATAAGATAATACAGCTCAATATGAATGTTTATTTCTCTCTTGGTC
1 CAAGAAATAGTGCATTAATTATAAGATAATACAGCTCAATATGAATGTTTATTTCTCTCTTGGTC
*
988204 TAATAAAGATACCATTATGATTCCGGCTCACAGATTTTCATCTGAACAGGAAGCAATAGAAGCTG
66 TAATAAAGATACCATTATGATTCCGGCTCACAGATTTTCATCTGAACAGGAAGCAATAGAAACTG
988269 AAGATGGTTTTAAATCTAAAGCGCTCAGTACTTGAGGCGTTAATCATTTTCATGTAACTATTTCA
131 AAGATGGTTTTAAATCTAAAGCGCTCAGTACTTGAGGCGTTAATCATTTTCATGTAACTATTTCA
988334 AAAGAAGGTTACTAGGCGTTAAC
196 AAAGAAGGTTACTAGGCGTTAAC
*
988357 CAAGAAATAGTGCATTAATTATAAGATAATACAGCTCAATATGAATGTTTCTTTCTCTCTTGGTC
1 CAAGAAATAGTGCATTAATTATAAGATAATACAGCTCAATATGAATGTTTATTTCTCTCTTGGTC
* * * *
988422 TAATAAAGATACCTTTATGATTGCGGCTCACAGATTTTCATCTGGACAGGTAGCAATAGAAACTG
66 TAATAAAGATACCATTATGATTCCGGCTCACAGATTTTCATCTGAACAGGAAGCAATAGAAACTG
988487 AAGATGGTTTTAAATCTAAAGCGCTCAGTACTTGAGGCGTTAATCATTTTCATGTAACTATTTCA
131 AAGATGGTTTTAAATCTAAAGCGCTCAGTACTTGAGGCGTTAATCATTTTCATGTAACTATTTCA
988552 AAAGAAGGTTACTAGGC
196 AAAGAAGGTTACTAGGC
988569 ATCATGATAA
Statistics
Matches: 205, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
218 205 1.00
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33
Consensus pattern (218 bp):
CAAGAAATAGTGCATTAATTATAAGATAATACAGCTCAATATGAATGTTTATTTCTCTCTTGGTC
TAATAAAGATACCATTATGATTCCGGCTCACAGATTTTCATCTGAACAGGAAGCAATAGAAACTG
AAGATGGTTTTAAATCTAAAGCGCTCAGTACTTGAGGCGTTAATCATTTTCATGTAACTATTTCA
AAAGAAGGTTACTAGGCGTTAAC
Found at i:989395 original size:2 final size:2
Alignment explanation
Indices: 989388--989418 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
989378 GGACGCAGCC
989388 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
989419 GACCACAAAA
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:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:991161 original size:3 final size:3
Alignment explanation
Indices: 991153--991186 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
991143 TGATAAATTT
991153 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
991187 ACCTTCAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1004779 original size:32 final size:32
Alignment explanation
Indices: 1004737--1004797 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
1004727 TTTTTATATT
*
1004737 AATATTTATATATTTTTATAA-ATAAATAAAAA
1 AATAATTATAT-TTTTTATAATATAAATAAAAA
1004769 AATAATTATATTTTTTATAATATAAATAA
1 AATAATTATATTTTTTATAATATAAATAA
1004798 TAATTCAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 9 0.33
32 18 0.67
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (32 bp):
AATAATTATATTTTTTATAATATAAATAAAAA
Found at i:1004799 original size:27 final size:31
Alignment explanation
Indices: 1004736--1004802 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 31
1004726 ATTTTTATAT
*
1004736 TAATATTTATATATTTTTATAAATAAATAAAA
1 TAATAATTATATATTTTTATAAAT-AATAAAA
*
1004768 AAATAATTATAT-TTTTTAT-AAT-AT-AAA
1 TAATAATTATATATTTTTATAAATAATAAAA
1004795 TAATAATT
1 TAATAATT
1004803 CAAATCAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
27 10 0.31
28 2 0.06
30 3 0.09
31 7 0.22
32 10 0.31
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (31 bp):
TAATAATTATATATTTTTATAAATAATAAAA
Found at i:1005819 original size:116 final size:116
Alignment explanation
Indices: 1005698--1005907 Score: 296
Period size: 116 Copynumber: 1.8 Consensus size: 116
1005688 TTTTATTTTA
* * * * *
1005698 TTTTTTAACACTCACGTGGAAATTAAGTGGAAAA-CATAGATTCGTGTGTATTTTTTTTAATAAA
1 TTTTTTAACACTCACATGGAAATTAAGGGGAAAACCATAGATTCGTCTATAATTTTTTT-ATAAA
1005762 ACTTATATTCCTTAATTTTTATATAAAAAAAAAGTTAAAAAGAATATTATAT
65 ACTTATATTCCTTAATTTTTATATAAAAAAAAAGTTAAAAAGAATATTATAT
*** * *
1005814 TTTTTTAACACTTTTATGGAAATTTAGGGGAAAACCATAGATTCTTCTATAATTTTTTTATAAAA
1 TTTTTTAACACTCACATGGAAATTAAGGGGAAAACCATAGATTCGTCTATAATTTTTTTATAAAA
* *
1005879 TTTATATTCCTTAGTTTTTATATAAAAAA
66 CTTATATTCCTTAATTTTTATATAAAAAA
1005908 GTAAAAAAAA
Statistics
Matches: 81, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
116 61 0.75
117 20 0.25
ACGTcount: A:0.39, C:0.08, G:0.10, T:0.43
Consensus pattern (116 bp):
TTTTTTAACACTCACATGGAAATTAAGGGGAAAACCATAGATTCGTCTATAATTTTTTTATAAAA
CTTATATTCCTTAATTTTTATATAAAAAAAAAGTTAAAAAGAATATTATAT
Found at i:1008310 original size:36 final size:36
Alignment explanation
Indices: 1008251--1008319 Score: 93
Period size: 36 Copynumber: 1.9 Consensus size: 36
1008241 TGATTTGATA
*
1008251 ATTATTATTTATATTATACAATATAATTATATATAT
1 ATTATTATTTACATTATACAATATAATTATATATAT
* * * *
1008287 ATTATTTTTTACATTTTATAATATATTTATATA
1 ATTATTATTTACATTATACAATATAATTATATA
1008320 ATTTAAAAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 28 1.00
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.57
Consensus pattern (36 bp):
ATTATTATTTACATTATACAATATAATTATATATAT
Found at i:1008371 original size:19 final size:17
Alignment explanation
Indices: 1008336--1008390 Score: 51
Period size: 19 Copynumber: 3.2 Consensus size: 17
1008326 AAATAATTCA
*
1008336 TATTTT-TATTT-ATAT
1 TATTTTATATTTAAAAT
*
1008351 TATTTTATTTTATAATAAT
1 TATTTTATATT-TAA-AAT
*
1008370 TATATTATATTTAAAAT
1 TATTTTATATTTAAAAT
1008387 TATT
1 TATT
1008391 AAATATGTAT
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
15 6 0.19
16 3 0.10
17 7 0.23
18 4 0.13
19 11 0.35
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
TATTTTATATTTAAAAT
Found at i:1008391 original size:20 final size:19
Alignment explanation
Indices: 1008348--1008391 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
1008338 TTTTTATTTA
* *
1008348 TATTATTTTATTTTATAAT
1 TATTATATTATTTTAAAAT
*
1008367 AATTATATTATATTTAAAAT
1 TATTATATTAT-TTTAAAAT
1008387 TATTA
1 TATTA
1008392 AATATGTATT
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
TATTATATTATTTTAAAAT
Found at i:1008736 original size:2 final size:2
Alignment explanation
Indices: 1008693--1008726 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1008683 TTTCCAGTGC
1008693 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
1008727 TTTCCTCTCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1008910 original size:2 final size:2
Alignment explanation
Indices: 1008903--1008937 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1008893 CATCTTCCTT
1008903 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
1008938 TCTTTCTGAA
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:1009108 original size:2 final size:2
Alignment explanation
Indices: 1009103--1009138 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
1009093 AAACACACAC
1009103 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1009139 CATAAATAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1010032 original size:18 final size:17
Alignment explanation
Indices: 1010000--1010036 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
1009990 AAAACCAATT
*
1010000 TAATTATATTTAATATA
1 TAATTACATTTAATATA
1010017 TAATTACATATTAATATA
1 TAATTACAT-TTAATATA
1010035 TA
1 TA
1010037 TTAAAAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (17 bp):
TAATTACATTTAATATA
Found at i:1010079 original size:9 final size:8
Alignment explanation
Indices: 1010065--1010123 Score: 57
Period size: 8 Copynumber: 7.2 Consensus size: 8
1010055 CTAATTTAAT
1010065 TATATTTGA
1 TATATTT-A
1010074 TATA-TTA
1 TATATTTA
1010081 TATATTTA
1 TATATTTA
* *
1010089 TAAATCTA
1 TATATTTA
*
1010097 TATATATA
1 TATATTTA
*
1010105 TATATATA
1 TATATTTA
1010113 TATATATTA
1 TATAT-TTA
1010122 TA
1 TA
1010124 AAGCTCACAC
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
7 5 0.12
8 30 0.70
9 8 0.19
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (8 bp):
TATATTTA
Found at i:1010084 original size:2 final size:2
Alignment explanation
Indices: 1010073--1010123 Score: 61
Period size: 2 Copynumber: 26.5 Consensus size: 2
1010063 ATTATATTTG
* * *
1010073 AT AT AT -T AT AT AT TT AT AA AT CT 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
1010114 AT AT AT -T AT A
1 AT AT AT AT AT A
1010124 AAGCTCACAC
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
1 2 0.05
2 39 0.95
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1010086 original size:16 final size:16
Alignment explanation
Indices: 1010065--1010123 Score: 66
Period size: 16 Copynumber: 3.6 Consensus size: 16
1010055 CTAATTTAAT
1010065 TATATTTGATATAT-TA
1 TATATTT-ATATATATA
* *
1010081 TATATTTATAAATCTA
1 TATATTTATATATATA
*
1010097 TATATATATATATATA
1 TATATTTATATATATA
1010113 TATATATTATA
1 TATAT-TTATA
1010124 AAGCTCACAC
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
15 5 0.14
16 27 0.75
17 4 0.11
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (16 bp):
TATATTTATATATATA
Found at i:1010971 original size:11 final size:11
Alignment explanation
Indices: 1010955--1010980 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1010945 AAAAATAATA
1010955 AAATAATTTTT
1 AAATAATTTTT
1010966 AAATAATTTTT
1 AAATAATTTTT
1010977 AAAT
1 AAAT
1010981 TTAAAATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (11 bp):
AAATAATTTTT
Found at i:1011441 original size:17 final size:16
Alignment explanation
Indices: 1011419--1011458 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
1011409 ATATTTATAT
1011419 TATTTATATTATAATTA
1 TATTTATATTATAA-TA
* *
1011436 TATTTAAATTATTATA
1 TATTTATATTATAATA
1011452 TATTTAT
1 TATTTAT
1011459 GTAAGTTTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 8 0.40
17 12 0.60
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
TATTTATATTATAATA
Found at i:1011499 original size:26 final size:25
Alignment explanation
Indices: 1011470--1011532 Score: 67
Period size: 26 Copynumber: 2.4 Consensus size: 25
1011460 TAAGTTTTAC
*
1011470 ATATTATAATTTGTTGATATAA-ATTT
1 ATATTATAATTT-TT-ATATAATATCT
1011496 ATATTAT-ATTTTTATATAATATCT
1 ATATTATAATTTTTATATAATATCT
1011520 ATATCATATAATT
1 ATAT--TATAATT
1011533 ATGTGTATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
23 6 0.19
24 9 0.28
25 4 0.12
26 10 0.31
27 3 0.09
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.54
Consensus pattern (25 bp):
ATATTATAATTTTTATATAATATCT
Found at i:1011798 original size:18 final size:19
Alignment explanation
Indices: 1011765--1011801 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
1011755 GGAAAAAAAT
*
1011765 TAAATATGATAGTTTATTA
1 TAAATATGATAATTTATTA
1011784 TAAATA-GATAATTTATTA
1 TAAATATGATAATTTATTA
1011802 AACAGAAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (19 bp):
TAAATATGATAATTTATTA
Found at i:1011970 original size:20 final size:20
Alignment explanation
Indices: 1011931--1011968 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1011921 TTTTAATTTA
*
1011931 ATAAAAATAATATATTAAAT
1 ATAAAAATAAAATATTAAAT
1011951 ATAAAAATAAAAT-TTAAA
1 ATAAAAATAAAATATTAAA
1011969 ATCTATACTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (20 bp):
ATAAAAATAAAATATTAAAT
Found at i:1012159 original size:19 final size:19
Alignment explanation
Indices: 1012127--1012165 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
1012117 AAATAACTTC
1012127 TTAAAATCTATCTATTATTT
1 TTAAAATCTATCTATT-TTT
1012147 TTAAAAT-TATCTATTTTT
1 TTAAAATCTATCTATTTTT
1012165 T
1 T
1012166 AAACTATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 4 0.21
19 8 0.42
20 7 0.37
ACGTcount: A:0.33, C:0.08, G:0.00, T:0.59
Consensus pattern (19 bp):
TTAAAATCTATCTATTTTT
Found at i:1012507 original size:2 final size:2
Alignment explanation
Indices: 1012500--1012540 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
1012490 TTCCTTCCAT
*
1012500 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TT TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1012541 ACTTGTCAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.46, G:0.00, T:0.54
Consensus pattern (2 bp):
TC
Found at i:1014127 original size:21 final size:21
Alignment explanation
Indices: 1014103--1014144 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1014093 AAAAGAAAAA
*
1014103 TAAA-AAAATAATTTTTTTTAT
1 TAAATAAAAT-ATTTTATTTAT
*
1014124 TAAATTAAATATTTTATTTAT
1 TAAATAAAATATTTTATTTAT
1014145 AATTTTACTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
TAAATAAAATATTTTATTTAT
Found at i:1016065 original size:22 final size:22
Alignment explanation
Indices: 1016040--1016081 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1016030 GATAAAAAAT
1016040 ATAATAGGAA-AAATATAATACC
1 ATAATAGGAATAAATA-AATACC
*
1016062 ATAATATGAATAAATAAATA
1 ATAATAGGAATAAATAAATA
1016082 TTTTAAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.62, C:0.05, G:0.07, T:0.26
Consensus pattern (22 bp):
ATAATAGGAATAAATAAATACC
Found at i:1030715 original size:13 final size:13
Alignment explanation
Indices: 1030697--1030745 Score: 54
Period size: 13 Copynumber: 4.2 Consensus size: 13
1030687 ACATACAAGA
1030697 TGTATCGATACAT
1 TGTATCGATACAT
1030710 TGTATCGATACA-
1 TGTATCGATACAT
*
1030722 TG-A-CCA-A-AT
1 TGTATCGATACAT
1030731 TGTATCGATACAT
1 TGTATCGATACAT
1030744 TG
1 TG
1030746 GCTTGTAACG
Statistics
Matches: 29, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
8 1 0.03
9 3 0.10
10 3 0.10
11 3 0.10
12 3 0.10
13 16 0.55
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1030740 original size:34 final size:32
Alignment explanation
Indices: 1030677--1030745 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
1030667 CCTTAACTGT
1030677 TTGTATCGATACATACAAGATGTATCGATACA
1 TTGTATCGATACATACAAGATGTATCGATACA
1030709 TTGTATCGATACATGACCAA-ATTGTATCGATACA
1 TTGTATCGATACAT-A-CAAGA-TGTATCGATACA
1030743 TTG
1 TTG
1030746 GCTTGTAACG
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
32 14 0.41
33 2 0.06
34 18 0.53
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (32 bp):
TTGTATCGATACATACAAGATGTATCGATACA
Found at i:1031662 original size:13 final size:13
Alignment explanation
Indices: 1031644--1031670 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1031634 CCATGCTTTG
1031644 TATCGATACATTA
1 TATCGATACATTA
1031657 TATCGATACATTA
1 TATCGATACATTA
1031670 T
1 T
1031671 GCTTTATATC
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:0.37, C:0.15, G:0.07, T:0.41
Consensus pattern (13 bp):
TATCGATACATTA
Found at i:1031673 original size:33 final size:34
Alignment explanation
Indices: 1031636--1031719 Score: 111
Period size: 33 Copynumber: 2.6 Consensus size: 34
1031626 ATACACATCC
*
1031636 ATGCTTTGTATCGATACATTA-TATCGATACATT
1 ATGCTTTGTATCGATACATTAGTATCGATACATG
*
1031669 ATGCTTTATATCGATACA-TAGTATCGATACATG
1 ATGCTTTGTATCGATACATTAGTATCGATACATG
* *
1031702 CT-CATTGTATCGATACAT
1 ATGCTTTGTATCGATACAT
1031720 ATTCAATTGC
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
32 15 0.34
33 29 0.66
ACGTcount: A:0.31, C:0.17, G:0.13, T:0.39
Consensus pattern (34 bp):
ATGCTTTGTATCGATACATTAGTATCGATACATG
Found at i:1031713 original size:19 final size:20
Alignment explanation
Indices: 1031689--1031740 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
1031679 TCGATACATA
1031689 GTATCGATACATGCTC-ATT
1 GTATCGATACATGCTCAATT
**
1031708 GTATCGATACATATTCAATT
1 GTATCGATACATGCTCAATT
*
1031728 GCATCGATACATG
1 GTATCGATACATG
1031741 AAACTGGCAG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 14 0.50
20 14 0.50
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.35
Consensus pattern (20 bp):
GTATCGATACATGCTCAATT
Found at i:1031733 original size:20 final size:19
Alignment explanation
Indices: 1031691--1031739 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
1031681 GATACATAGT
* *
1031691 ATCGATACATGCTCATTGT
1 ATCGATACATACTCATTGC
*
1031710 ATCGATACATATTCAATTGC
1 ATCGATACATACTC-ATTGC
1031730 ATCGATACAT
1 ATCGATACAT
1031740 GAAACTGGCA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 12 0.46
20 14 0.54
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.35
Consensus pattern (19 bp):
ATCGATACATACTCATTGC
Found at i:1036656 original size:30 final size:30
Alignment explanation
Indices: 1036620--1036678 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
1036610 TGTGCTCTTA
1036620 GGCCAAACGAGTACAATCGAGTCTCACTTG
1 GGCCAAACGAGTACAATCGAGTCTCACTTG
*
1036650 GGCCAAACGAGTACAATTGAGTCTCACTT
1 GGCCAAACGAGTACAATCGAGTCTCACTT
1036679 TGCGACAATG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.31, C:0.25, G:0.22, T:0.22
Consensus pattern (30 bp):
GGCCAAACGAGTACAATCGAGTCTCACTTG
Found at i:1037094 original size:9 final size:9
Alignment explanation
Indices: 1037080--1037109 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
1037070 AGTCAACCGT
1037080 TAAAGATGA
1 TAAAGATGA
1037089 TAAAGATGA
1 TAAAGATGA
*
1037098 TAATGATGA
1 TAAAGATGA
1037107 TAA
1 TAA
1037110 TGATAAAGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.53, C:0.00, G:0.20, T:0.27
Consensus pattern (9 bp):
TAAAGATGA
Found at i:1037110 original size:9 final size:9
Alignment explanation
Indices: 1037084--1037113 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
1037074 AACCGTTAAA
*
1037084 GATGATAAA
1 GATGATAAT
1037093 GATGATAAT
1 GATGATAAT
1037102 GATGATAAT
1 GATGATAAT
1037111 GAT
1 GAT
1037114 AAAGTTGACT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.47, C:0.00, G:0.23, T:0.30
Consensus pattern (9 bp):
GATGATAAT
Found at i:1039483 original size:13 final size:13
Alignment explanation
Indices: 1039465--1039490 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1039455 CAATTTTTTG
1039465 TGTATCGATACAT
1 TGTATCGATACAT
1039478 TGTATCGATACAT
1 TGTATCGATACAT
1039491 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1039555 original size:21 final size:20
Alignment explanation
Indices: 1039529--1039605 Score: 91
Period size: 21 Copynumber: 3.8 Consensus size: 20
1039519 CTGCCAAGAA
*
1039529 ATGTATCGATACATATTTTTT
1 ATGTATCGATACAT-TTTTTC
****
1039550 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTTTTTC
1039570 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TTTTTC
1039591 ATGTATCGATACATT
1 ATGTATCGATACATT
1039606 GCAACATGTA
Statistics
Matches: 46, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
20 16 0.35
21 30 0.65
ACGTcount: A:0.30, C:0.16, G:0.12, T:0.43
Consensus pattern (20 bp):
ATGTATCGATACATTTTTTC
Found at i:1039575 original size:20 final size:20
Alignment explanation
Indices: 1039550--1039622 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
1039540 CATATTTTTT
1039550 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
1039570 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
1039591 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
1039611 ATGTATCGATAC
1 ATGTATCGATAC
1039623 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:1039589 original size:41 final size:41
Alignment explanation
Indices: 1039529--1039622 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
1039519 CTGCCAAGAA
*
1039529 ATGTATCGATACATATTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATATTTTTCATGTATCGATACATTGCAAC
*
1039570 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATATTTTTCATGTATCGATACATTGCAAC
1039611 ATGTATCGATAC
1 ATGTATCGATAC
1039623 TTTGAATTGT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.31, C:0.17, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATATTTTTCATGTATCGATACATTGCAAC
Found at i:1040311 original size:40 final size:40
Alignment explanation
Indices: 1040266--1040344 Score: 158
Period size: 40 Copynumber: 2.0 Consensus size: 40
1040256 CTTAATCAAG
1040266 TAATTCATATCAAAATTTATTTGCCCATGCATCTATTCTA
1 TAATTCATATCAAAATTTATTTGCCCATGCATCTATTCTA
1040306 TAATTCATATCAAAATTTATTTGCCCATGCATCTATTCT
1 TAATTCATATCAAAATTTATTTGCCCATGCATCTATTCT
1040345 CTCCCCCTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.32, C:0.20, G:0.05, T:0.43
Consensus pattern (40 bp):
TAATTCATATCAAAATTTATTTGCCCATGCATCTATTCTA
Found at i:1042131 original size:13 final size:13
Alignment explanation
Indices: 1042113--1042150 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
1042103 ATAAACATCC
1042113 TGTATCGATACAG
1 TGTATCGATACAG
*
1042126 TGTATCGATACAT
1 TGTATCGATACAG
1042139 TGTATCGATACA
1 TGTATCGATACA
1042151 AATAAAAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:1044250 original size:15 final size:15
Alignment explanation
Indices: 1044230--1044260 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1044220 ATTTCGTTTG
*
1044230 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
1044245 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
1044260 G
1 G
1044261 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:1046093 original size:21 final size:21
Alignment explanation
Indices: 1046064--1046108 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1046054 AAGTTTTCAT
*
1046064 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
1046084 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
1046106 TTT
1 TTT
1046109 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:1048342 original size:13 final size:13
Alignment explanation
Indices: 1048324--1048349 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1048314 CAATTTTTTG
1048324 TGTATCGATACAT
1 TGTATCGATACAT
1048337 TGTATCGATACAT
1 TGTATCGATACAT
1048350 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1048414 original size:21 final size:21
Alignment explanation
Indices: 1048388--1048463 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
1048378 CTGCCAAGAA
*
1048388 ATGTATCGATACATCTTTTTT
1 ATGTATCGATACATCTTTTTC
****
1048409 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
1048429 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
1048450 ATGTATCGATACAT
1 ATGTATCGATACAT
1048464 TGCAACATGT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:1048434 original size:20 final size:20
Alignment explanation
Indices: 1048409--1048481 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
1048399 CATCTTTTTT
1048409 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
1048429 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
1048450 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
1048470 ATGTATCGATAC
1 ATGTATCGATAC
1048482 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:1048445 original size:41 final size:41
Alignment explanation
Indices: 1048388--1048481 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
1048378 CTGCCAAGAA
*
1048388 ATGTATCGATACATCTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1048429 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1048470 ATGTATCGATAC
1 ATGTATCGATAC
1048482 TTTGAATTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:1050316 original size:3 final size:3
Alignment explanation
Indices: 1050308--1050345 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
1050298 CCAACCATCA
* *
1050308 ATG ATG ATG AAG ATG GTG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
1050346 AAAGTTGACT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.34, C:0.00, G:0.34, T:0.32
Consensus pattern (3 bp):
ATG
Found at i:1055331 original size:12 final size:12
Alignment explanation
Indices: 1055314--1055345 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
1055304 CCTTAGTGAC
1055314 GATTAGTCATAG
1 GATTAGTCATAG
1055326 GATTAGTCATAG
1 GATTAGTCATAG
*
1055338 GAGTAGTC
1 GATTAGTC
1055346 GTATGCTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.31, C:0.09, G:0.28, T:0.31
Consensus pattern (12 bp):
GATTAGTCATAG
Found at i:1055624 original size:43 final size:41
Alignment explanation
Indices: 1055577--1055656 Score: 106
Period size: 43 Copynumber: 1.9 Consensus size: 41
1055567 CATTTTTGCT
1055577 ATAACAAAAAAAAGAAGAAGTATTTTGCAAATAAATTTGGAGG
1 ATAACAAAAAAAAGAAGAAGTA-TTTGC-AATAAATTTGGAGG
*** *
1055620 ATAACAAAAAGGGGGAGAAGTATTTGCAATAAATTTG
1 ATAACAAAAAAAAGAAGAAGTATTTGCAATAAATTTG
1055657 TTTTAGAACT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
41 10 0.30
42 5 0.15
43 18 0.55
ACGTcount: A:0.50, C:0.05, G:0.21, T:0.24
Consensus pattern (41 bp):
ATAACAAAAAAAAGAAGAAGTATTTGCAATAAATTTGGAGG
Found at i:1058016 original size:13 final size:13
Alignment explanation
Indices: 1057997--1058030 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
1057987 TTTTAATTTT
1057997 TTCTTTTTCAAAC
1 TTCTTTTTCAAAC
* *
1058010 TTTTTTTTGAAAC
1 TTCTTTTTCAAAC
1058023 TTCTTTTT
1 TTCTTTTT
1058031 AATTGGGGGG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.18, C:0.15, G:0.03, T:0.65
Consensus pattern (13 bp):
TTCTTTTTCAAAC
Found at i:1059344 original size:31 final size:31
Alignment explanation
Indices: 1059306--1059555 Score: 143
Period size: 31 Copynumber: 7.9 Consensus size: 31
1059296 ATGTGACCTA
*
1059306 GGTGAAACCTTCAGTCGAAAAGATTGACTAG
1 GGTGAAACCTTTAGTCGAAAAGATTGACTAG
* * *
1059337 GGCGAAACCATAATAGTC-AAAGGGA-TGAACTA-
1 GGTGAAACC-T-TTAGTCGAAA-AGATTG-ACTAG
* * *
1059369 GATGGAACCTTTAGTCAAAAAGATT-AGCTAG
1 GGTGAAACCTTTAGTCGAAAAGATTGA-CTAG
* * * *
1059400 GGAGAAACCTTGATAGCCAAAGAAGATGGA-TAG
1 GGTGAAACCTT--TAGTCGAA-AAGATTGACTAG
*
1059433 GGTGAAACCTATTAGTCGAAAAGATTGACCAG
1 GGTGAAACCT-TTAGTCGAAAAGATTGACTAG
* * *
1059465 GGTAAAACATTTAGTCGAAAATATTGACTAG
1 GGTGAAACCTTTAGTCGAAAAGATTGACTAG
* * * * *
1059496 GGTAAAACCATAGTAGT-AAAAAAATATGACTAA
1 GGTGAAACC-T-TTAGTCGAAAAGAT-TGACTAG
** *
1059529 GGCAAAACCTTTAGTCGAAAAAATTGA
1 GGTGAAACCTTTAGTCGAAAAGATTGA
1059556 TCTTATTTGG
Statistics
Matches: 170, Mismatches: 31, Indels: 36
0.72 0.13 0.15
Matches are distributed among these distances:
29 1 0.01
30 10 0.06
31 62 0.36
32 43 0.25
33 47 0.28
34 6 0.04
35 1 0.01
ACGTcount: A:0.42, C:0.13, G:0.23, T:0.22
Consensus pattern (31 bp):
GGTGAAACCTTTAGTCGAAAAGATTGACTAG
Found at i:1059378 original size:63 final size:62
Alignment explanation
Indices: 1059010--1059472 Score: 211
Period size: 63 Copynumber: 7.4 Consensus size: 62
1059000 CCTTAAGCCA
* * * *
1059010 AAAAGATTGTCTAGGGCAAAACCTACAATAGTCAAAGAGGTG-ACTAGGGTGGAACTTTCAATCG
1 AAAAGATTGACTAGGGCAAAACC-ATAATAGTCAAAG-GGTGAACTA-GGTGGAACCTTCAGTCG
* * * * ** *
1059074 AAAAGATTGA--AGGGCAAAACCATAATAGTTGAAAAGGTGATCAAGACGGAACCTTTAGTCG
1 AAAAGATTGACTAGGGCAAAACCATAATAG-TCAAAGGGTGAACTAGGTGGAACCTTCAGTCG
* ** * * * * * **
1059135 AAAAAATTGACTAGGATAAAACAATAATAATCAAAGAGGTGACCAAGGTAGAATTTTCAGTC-
1 AAAAGATTGACTAGGGCAAAACCATAATAGTCAAAG-GGTGAACTAGGTGGAACCTTCAGTCG
* * * * * ** * ** * *** * * * *
1059197 AGAATATTAATTAAGGTGAAACCATAATAGTCAAAAGGATGGCCTGGGCAAAATCGTCAATCA
1 AAAAGATTGACTAGGGCAAAACCATAATAGTC-AAAGGGTGAACTAGGTGGAACCTTCAGTCG
* * * * ** * *
1059260 AAAAGATTGATTGGGGTAAAACCATAATAGTAAAAAATGTGACCTAGGTGAAACCTTCAGTCG
1 AAAAGATTGACTAGGGCAAAACCATAATAGT-CAAAGGGTGAACTAGGTGGAACCTTCAGTCG
* * * *
1059323 AAAAGATTGACTAGGGCGAAACCATAATAGTCAAAGGGATGAACTAGATGGAACCTTTAGTCA
1 AAAAGATTGACTAGGGCAAAACCATAATAGTCAAAGGG-TGAACTAGGTGGAACCTTCAGTCG
* * * * * * *
1059386 AAAAGATT-AGCTAGGG-AGAAACCTTGATAGCCAAAGAAGATGGA-TAGGGTGAAACCTATTAG
1 AAAAGATTGA-CTAGGGCA-AAACCATAATAGTCAAAG--GGTGAACTA-GGTGGAACCT-TCAG
1059448 TCG
60 TCG
* *
1059451 AAAAGATTGACCAGGGTAAAAC
1 AAAAGATTGACTAGGGCAAAAC
1059473 ATTTAGTCGA
Statistics
Matches: 299, Mismatches: 83, Indels: 33
0.72 0.20 0.08
Matches are distributed among these distances:
61 31 0.10
62 65 0.22
63 157 0.53
64 20 0.07
65 24 0.08
66 2 0.01
ACGTcount: A:0.42, C:0.13, G:0.23, T:0.21
Consensus pattern (62 bp):
AAAAGATTGACTAGGGCAAAACCATAATAGTCAAAGGGTGAACTAGGTGGAACCTTCAGTCG
Found at i:1059551 original size:34 final size:34
Alignment explanation
Indices: 1059482--1059551 Score: 79
Period size: 34 Copynumber: 2.1 Consensus size: 34
1059472 CATTTAGTCG
* * *
1059482 AAAATATTGACTAGGGTAAAACCATAGTAGTAAA
1 AAAATATTGACTAAGGCAAAACCATAGTAGAAAA
* *
1059516 AAAATA-TGACTAAGGCAAAACCTTTAGTCGAAAA
1 AAAATATTGACTAAGGCAAAACC-ATAGTAGAAAA
1059550 AA
1 AA
1059552 TTGATCTTAT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
33 14 0.47
34 16 0.53
ACGTcount: A:0.51, C:0.11, G:0.16, T:0.21
Consensus pattern (34 bp):
AAAATATTGACTAAGGCAAAACCATAGTAGAAAA
Found at i:1060549 original size:25 final size:24
Alignment explanation
Indices: 1060520--1060567 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
1060510 TCATTTGTTT
*
1060520 TCTTTTGTTTTTGCTTTGTTTTTTA
1 TCTTTTGTTTTTG-TTTGGTTTTTA
*
1060545 TCTTTTTTTTTTGTTTGGTTTTT
1 TCTTTTGTTTTTGTTTGGTTTTT
1060568 GTTGACGTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 9 0.43
25 12 0.57
ACGTcount: A:0.02, C:0.06, G:0.12, T:0.79
Consensus pattern (24 bp):
TCTTTTGTTTTTGTTTGGTTTTTA
Found at i:1067822 original size:50 final size:50
Alignment explanation
Indices: 1067768--1067880 Score: 142
Period size: 50 Copynumber: 2.3 Consensus size: 50
1067758 TTGAAGAATA
*
1067768 TATCGATACATTTAGG-TCAAAACAC-AAAATATATCAATACAAT-TAAAATG
1 TATCGATACATTT-GGATC-AAAC-CTAAAATATATCAATACAATAAAAAATG
* * *
1067818 TATCGATACATTTGGATCAAACCTAGAATGTATTAATACAATAAAAAATG
1 TATCGATACATTTGGATCAAACCTAAAATATATCAATACAATAAAAAATG
1067868 TATCGATACATTT
1 TATCGATACATTT
1067881 TCCTTTTAGA
Statistics
Matches: 56, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
48 1 0.02
49 21 0.38
50 34 0.61
ACGTcount: A:0.46, C:0.13, G:0.10, T:0.31
Consensus pattern (50 bp):
TATCGATACATTTGGATCAAACCTAAAATATATCAATACAATAAAAAATG
Found at i:1075104 original size:3 final size:3
Alignment explanation
Indices: 1075090--1075162 Score: 130
Period size: 3 Copynumber: 24.7 Consensus size: 3
1075080 TAATTTTAAA
*
1075090 AAT AAT AGT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1075138 AAT AA- AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
1075163 ATTAAATTAG
Statistics
Matches: 67, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
2 2 0.03
3 65 0.97
ACGTcount: A:0.67, C:0.00, G:0.01, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1075325 original size:2 final size:2
Alignment explanation
Indices: 1075320--1075370 Score: 52
Period size: 2 Copynumber: 26.5 Consensus size: 2
1075310 TTAGTAGTTG
* * *
1075320 TA TA TA TA TA TA TA T- TA TA TA GA TA TA TG TG 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
*
1075361 -A CA TA TA TA T
1 TA TA TA TA TA T
1075371 TATCAACATA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
1 2 0.05
2 40 0.95
ACGTcount: A:0.45, C:0.02, G:0.06, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1075339 original size:31 final size:28
Alignment explanation
Indices: 1075299--1075373 Score: 71
Period size: 31 Copynumber: 2.5 Consensus size: 28
1075289 ATTAGTAAAG
*
1075299 TAACGTATATATTAGTA-GTTGTATATATA
1 TAACATATATATTA-TATG-TGTATATATA
* *
1075328 TATATATTATATAGATATATGTGTATATATA
1 TA-ACA-TATATA-TTATATGTGTATATATA
1075359 TAACATATATATTAT
1 TAACATATATATTAT
1075374 CAACATAAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 9
0.73 0.10 0.18
Matches are distributed among these distances:
28 3 0.08
29 8 0.22
30 3 0.08
31 20 0.54
32 3 0.08
ACGTcount: A:0.41, C:0.03, G:0.09, T:0.47
Consensus pattern (28 bp):
TAACATATATATTATATGTGTATATATA
Found at i:1077324 original size:20 final size:21
Alignment explanation
Indices: 1077287--1077326 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
1077277 ATTATAAAAA
*
1077287 TTTAATTAACTTTAAAATTAT
1 TTTAATTAACTCTAAAATTAT
*
1077308 TTTAATT-ACTCTCAAATTA
1 TTTAATTAACTCTAAAATTA
1077327 AATTATATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (21 bp):
TTTAATTAACTCTAAAATTAT
Found at i:1081613 original size:32 final size:32
Alignment explanation
Indices: 1081577--1081638 Score: 124
Period size: 32 Copynumber: 1.9 Consensus size: 32
1081567 AAGAGGTTTG
1081577 CCTTGTTTGCAACAGGTAGTTTTACCTTGCTA
1 CCTTGTTTGCAACAGGTAGTTTTACCTTGCTA
1081609 CCTTGTTTGCAACAGGTAGTTTTACCTTGC
1 CCTTGTTTGCAACAGGTAGTTTTACCTTGC
1081639 CAAGTAAAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.18, C:0.23, G:0.19, T:0.40
Consensus pattern (32 bp):
CCTTGTTTGCAACAGGTAGTTTTACCTTGCTA
Found at i:1082900 original size:61 final size:61
Alignment explanation
Indices: 1082763--1083058 Score: 301
Period size: 61 Copynumber: 4.8 Consensus size: 61
1082753 TTCTTTTTAT
* * *
1082763 CTTAGTGAATGGTCAAATCCTCAAGCCTTC-ATAATATAACGAG-ATAGGTAGCAATCCTTTTGA
1 CTTAGTGAATGGTCAAATCCTCAAGCTTTCGGTAATAT---G-GCA-AGGTAACAATCCTTTTGA
1082826 C
61 C
* * *
1082827 CTTAGTGAATGGTCAAATCCTCAAGCTTTCAGTAATATGGCAAGGTAACAATCCTCTTAAC
1 CTTAGTGAATGGTCAAATCCTCAAGCTTTCGGTAATATGGCAAGGTAACAATCCTTTTGAC
* * ** * **
1082888 CTTAATGAATGGTCAAATCCTCAAGCTTTTGGTAATATTCCGAGGTAGTAATCCTTTTGAC
1 CTTAGTGAATGGTCAAATCCTCAAGCTTTCGGTAATATGGCAAGGTAACAATCCTTTTGAC
* * * * *
1082949 CTTAGTGAATGGTCAAATCCTTAAGCCTTCGGTAAAATGGCAAGATAACAATTCTTTTTTCGAC
1 CTTAGTGAATGGTCAAATCCTCAAGCTTTCGGTAATATGGCAAGGTAACAA-TC-CTTTT-GAC
* * *
1083013 CTCAGTGAATGGTCAAATCCTTAAGTCTTT-GGTAATAAGGCAAGGT
1 CTTAGTGAATGGTCAAATCCTCAAG-CTTTCGGTAATATGGCAAGGT
1083059 GATTTCTCAA
Statistics
Matches: 194, Mismatches: 32, Indels: 12
0.82 0.13 0.05
Matches are distributed among these distances:
61 108 0.56
62 4 0.02
63 4 0.02
64 69 0.36
65 9 0.05
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Consensus pattern (61 bp):
CTTAGTGAATGGTCAAATCCTCAAGCTTTCGGTAATATGGCAAGGTAACAATCCTTTTGAC
Found at i:1082989 original size:122 final size:125
Alignment explanation
Indices: 1082808--1083049 Score: 339
Period size: 122 Copynumber: 2.0 Consensus size: 125
1082798 ATAACGAGAT
* * *
1082808 AGGTAGCAATCCTTTTGACCTTAGTGAATGGTCAAATCCTCAAGCTTTCAGTAATATGGCAAGGT
1 AGGTAGCAATCCTTTTGACCTTAGTGAATGGTCAAATCCTCAAGCCTTCAGTAAAATGGCAAGAT
*
1082873 AACAA-TC-CTCTT-AACCTTAATGAATGGTCAAATCCTCAAG-CTTTTGGTAATATTCCG
66 AACAATTCTCTCTTCAACCTCAATGAATGGTCAAATCCTCAAGTC-TTTGGTAATATTCCG
* * *
1082930 AGGTAGTAATCCTTTTGACCTTAGTGAATGGTCAAATCCTTAAGCCTTCGGTAAAATGGCAAGAT
1 AGGTAGCAATCCTTTTGACCTTAGTGAATGGTCAAATCCTCAAGCCTTCAGTAAAATGGCAAGAT
* * * * *
1082995 AACAATTCTTTTTTCGACCTCAGTGAATGGTCAAATCCTTAAGTCTTTGGTAATA
66 AACAATTCTCTCTTCAACCTCAATGAATGGTCAAATCCTCAAGTCTTTGGTAATA
1083050 AGGCAAGGTG
Statistics
Matches: 104, Mismatches: 12, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
122 64 0.62
123 2 0.02
124 3 0.03
125 34 0.33
126 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Consensus pattern (125 bp):
AGGTAGCAATCCTTTTGACCTTAGTGAATGGTCAAATCCTCAAGCCTTCAGTAAAATGGCAAGAT
AACAATTCTCTCTTCAACCTCAATGAATGGTCAAATCCTCAAGTCTTTGGTAATATTCCG
Found at i:1084119 original size:24 final size:24
Alignment explanation
Indices: 1084092--1084147 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
1084082 TTTGGGACAT
*
1084092 TTTTTTCACTAGCTCCAATGTATC
1 TTTTTTCACTAGCTCCAATGCATC
* * * *
1084116 TTTTTTTACTGGTTCTAATGCATC
1 TTTTTTCACTAGCTCCAATGCATC
1084140 TTTTTTCA
1 TTTTTTCA
1084148 TCGTCAACCA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.18, C:0.20, G:0.09, T:0.54
Consensus pattern (24 bp):
TTTTTTCACTAGCTCCAATGCATC
Found at i:1085235 original size:20 final size:19
Alignment explanation
Indices: 1085192--1085244 Score: 79
Period size: 19 Copynumber: 2.7 Consensus size: 19
1085182 TCATCATGCT
**
1085192 TTGTATCGATACACGCTCA
1 TTGTATCGATACATACTCA
1085211 TTGTATCGATACATACTCAA
1 TTGTATCGATACATACTC-A
1085231 TTGTATCGATACAT
1 TTGTATCGATACAT
1085245 GAAACAAGCA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.52
20 15 0.48
ACGTcount: A:0.30, C:0.21, G:0.13, T:0.36
Consensus pattern (19 bp):
TTGTATCGATACATACTCA
Found at i:1085313 original size:13 final size:13
Alignment explanation
Indices: 1085295--1085320 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1085285 CATGGGACAA
1085295 TGTATCGATACAT
1 TGTATCGATACAT
1085308 TGTATCGATACAT
1 TGTATCGATACAT
1085321 AAGGAATTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1085864 original size:39 final size:39
Alignment explanation
Indices: 1085816--1085939 Score: 221
Period size: 39 Copynumber: 3.2 Consensus size: 39
1085806 AAAAGATAAA
*
1085816 GTGTTGTAAGGTTATACTTTGCCTGAAAGTAATCAATTC
1 GTGTAGTAAGGTTATACTTTGCCTGAAAGTAATCAATTC
1085855 GTGTAGTAAGGTTATACTTTGCCTGAAAGTAATCAATTC
1 GTGTAGTAAGGTTATACTTTGCCTGAAAGTAATCAATTC
* *
1085894 ATGTAATAAGGTTATACTTTGCCTGAAAGTAATCAATTC
1 GTGTAGTAAGGTTATACTTTGCCTGAAAGTAATCAATTC
1085933 GTGTAGT
1 GTGTAGT
1085940 GAATTGTGGT
Statistics
Matches: 80, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 80 1.00
ACGTcount: A:0.31, C:0.12, G:0.20, T:0.37
Consensus pattern (39 bp):
GTGTAGTAAGGTTATACTTTGCCTGAAAGTAATCAATTC
Found at i:1091603 original size:13 final size:13
Alignment explanation
Indices: 1091585--1091624 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
1091575 ACAATCTTCT
1091585 TTGTATCGATACA
1 TTGTATCGATACA
* *
1091598 TTGTATTGATATA
1 TTGTATCGATACA
*
1091611 ATGTATCGATACA
1 TTGTATCGATACA
1091624 T
1 T
1091625 GGGTTACTAT
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.33, C:0.10, G:0.15, T:0.42
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1094105 original size:13 final size:13
Alignment explanation
Indices: 1094087--1094112 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1094077 CTAAGTGAAA
1094087 TGTATCGATACAT
1 TGTATCGATACAT
1094100 TGTATCGATACAT
1 TGTATCGATACAT
1094113 GAGGAATTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1095404 original size:78 final size:77
Alignment explanation
Indices: 1095307--1095536 Score: 202
Period size: 78 Copynumber: 2.9 Consensus size: 77
1095297 CAGTATCCCC
* *
1095307 TCGAAAACAACGGGGTTGGAGTATCCCTGATGCTGAAAATTTGATATTTTAGAAATAAAATCGAT
1 TCGAAAATAAC-GGGTTGGAGTATCCCTGATG-TGAAAATTTGATATTTTAGAAATAAAATCGAG
1095372 ATTGGAGTA-CCTA
64 ATTGGAGTACCCTA
* * *
1095385 TCGAAAATAACAGGGTTGGAGTATCCCCT-ACGGTAGAAAA--TCATATTTTAGAAATAAAATTG
1 TCGAAAATAAC-GGGTTGGAGTAT-CCCTGA-TGT-GAAAATTTGATATTTTAGAAATAAAATCG
* * *
1095447 GGGTTGGAGTATCCCTT
62 AGATTGGAGTA-CCCTA
* * * * *
1095464 TAG-AAATAACGAGGTTAGAGTAT-CCTCGATAGTGAAAATTTGATGTTTTAAAAATAAAATCGG
1 TCGAAAATAACG-GGTTGGAGTATCCCT-GAT-GTGAAAATTTGATATTTTAGAAATAAAATCGA
*
1095527 GGTTGGAGTA
63 GATTGGAGTA
1095537 TCTCTAATGG
Statistics
Matches: 125, Mismatches: 16, Indels: 21
0.77 0.10 0.13
Matches are distributed among these distances:
76 3 0.02
77 34 0.27
78 44 0.35
79 44 0.35
ACGTcount: A:0.36, C:0.11, G:0.23, T:0.30
Consensus pattern (77 bp):
TCGAAAATAACGGGTTGGAGTATCCCTGATGTGAAAATTTGATATTTTAGAAATAAAATCGAGAT
TGGAGTACCCTA
Found at i:1095454 original size:77 final size:78
Alignment explanation
Indices: 1095271--1095461 Score: 199
Period size: 79 Copynumber: 2.4 Consensus size: 78
1095261 GAAAAATTTA
* * * * * *
1095271 ATATTTTGGAGATAAAAATGGTGTTGCAGTATCCCCTCGAAAACAACGGGGTTGGAGTATCCCTG
1 ATATTTTAGAAATAAAATTGGTGTTGGAGTATCCCATCGAAAACAACAGGGTTGGAGTATCCCTG
* *
1095336 ATGCTGAAAATTTG
66 ACGCTGAAAA-TTC
* * * * *
1095350 ATATTTTAGAAATAAAATCGATATTGGAGTA-CCTATCGAAAATAACAGGGTTGGAGTATCCCCT
1 ATATTTTAGAAATAAAATTGGTGTTGGAGTATCCCATCGAAAACAACAGGGTTGGAGTAT-CCCT
*
1095414 -ACGGTAGAAAA-TC
65 GACGCT-GAAAATTC
*
1095427 ATATTTTAGAAATAAAATTGGGGTTGGAGTATCCC
1 ATATTTTAGAAATAAAATTGGTGTTGGAGTATCCC
1095462 TTTAGAAATA
Statistics
Matches: 90, Mismatches: 19, Indels: 7
0.78 0.16 0.06
Matches are distributed among these distances:
77 28 0.31
78 29 0.32
79 33 0.37
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.29
Consensus pattern (78 bp):
ATATTTTAGAAATAAAATTGGTGTTGGAGTATCCCATCGAAAACAACAGGGTTGGAGTATCCCTG
ACGCTGAAAATTC
Found at i:1095611 original size:79 final size:79
Alignment explanation
Indices: 1095525--1095698 Score: 305
Period size: 79 Copynumber: 2.2 Consensus size: 79
1095515 AAATAAAATC
1095525 GGGGTTGGAGTATCTCTAATGGTGGAAAATTGATATTTTGAAAATAGAACCGGGGTTGGAGTATC
1 GGGGTTGGAGTATCTCTAATGGTGGAAAATTGATATTTTGAAAATAGAACCGGGGTTGGAGTATC
1095590 CCCTCAG-AAATAAT
66 CCCT-AGAAAATAAT
1095604 GGGGTTGGAGTATCTCTAATGGTGGAAAATTGATATTTTGAAAATAGAACCGGGGTTGGAGTATC
1 GGGGTTGGAGTATCTCTAATGGTGGAAAATTGATATTTTGAAAATAGAACCGGGGTTGGAGTATC
* *
1095669 CCCTTGAAAATAGT
66 CCCTAGAAAATAAT
*
1095683 GAGGTTGGAGTATCTC
1 GGGGTTGGAGTATCTC
1095699 GATGATTGAA
Statistics
Matches: 91, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
78 1 0.01
79 90 0.99
ACGTcount: A:0.30, C:0.11, G:0.29, T:0.30
Consensus pattern (79 bp):
GGGGTTGGAGTATCTCTAATGGTGGAAAATTGATATTTTGAAAATAGAACCGGGGTTGGAGTATC
CCCTAGAAAATAAT
Found at i:1098068 original size:20 final size:21
Alignment explanation
Indices: 1098041--1098097 Score: 89
Period size: 20 Copynumber: 2.7 Consensus size: 21
1098031 CAAACTAGCC
1098041 AGATGTATCGATACAATAATA
1 AGATGTATCGATACAATAATA
*
1098062 A-ATGTATCGATACAATTATA
1 AGATGTATCGATACAATAATA
1098082 AGTATGTATCGATACA
1 AG-ATGTATCGATACA
1098098 TTTCCTTGGC
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
20 19 0.58
21 1 0.03
22 13 0.39
ACGTcount: A:0.44, C:0.11, G:0.14, T:0.32
Consensus pattern (21 bp):
AGATGTATCGATACAATAATA
Found at i:1098164 original size:13 final size:13
Alignment explanation
Indices: 1098146--1098172 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1098136 ATTTTAGGTA
1098146 TGTATCAATACAT
1 TGTATCAATACAT
1098159 TGTATCAATACAT
1 TGTATCAATACAT
1098172 T
1 T
1098173 TACTGTTTGT
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:0.37, C:0.15, G:0.07, T:0.41
Consensus pattern (13 bp):
TGTATCAATACAT
Found at i:1112581 original size:5 final size:5
Alignment explanation
Indices: 1112571--1112600 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
1112561 TTCTGGTCAT
*
1112571 GAAAA GAAAA GAAAA AAAAA GAAAA GAAAA
1 GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA
1112601 ATTCCACCTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (5 bp):
GAAAA
Found at i:1112592 original size:15 final size:15
Alignment explanation
Indices: 1112572--1112601 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1112562 TCTGGTCATG
1112572 AAAAGAAAAGAAAAA
1 AAAAGAAAAGAAAAA
1112587 AAAAGAAAAGAAAAA
1 AAAAGAAAAGAAAAA
1112602 TTCCACCTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (15 bp):
AAAAGAAAAGAAAAA
Found at i:1113803 original size:32 final size:31
Alignment explanation
Indices: 1113639--1114066 Score: 171
Period size: 32 Copynumber: 12.9 Consensus size: 31
1113629 TTTCTTTTCA
*
1113639 AAGTCCACAACTTTGTGGCAACCTTTTTTTGTT
1 AAGTCCACAACTCTGTGG-AACCTTTTTTT-TT
* ** *
1113672 AAAGTGCACAACTCCATAGCAACCTTTTTTCTGTT
1 -AAGTCCACAACTCTGT-GGAACCTTTTTT-T-TT
* * * **
1113707 AAAGTCGACAACTCTATGGCA-CTTTCCCCTTTT
1 -AAGTCCACAACTCTGTGGAACCTTT--TTTTTT
* **
1113740 AAATCCACAACTCTGT-GACACCTTCCCTTTTT
1 AAGTCCACAACTCTGTGGA-ACCTT-TTTTTTT
*
1113772 AAGTCCACAACTTTGTGGTAACCTTTTTTTTTTTGTT
1 AAGTCCACAACTCTGTGG-AACC----TTTTTTT-TT
* * * * *
1113809 AAAGTCCACAACTCTATGGCACCTTCCTCTCTT
1 -AAGTCCACAACTCTGTGGAACCTT-TTTTTTT
* ** *
1113842 AAGTCCATAACTCCATGGCAACCTTTTTATGTTA
1 AAGTCCACAACTCTGTGG-AACCTTTTT-T-TTT
* * **
1113876 AAGTCCACAACTCCGTGGCACCTTCCCTTTTT
1 AAGTCCACAACTCTGTGGAACCTT-TTTTTTT
* * * *
1113908 AAGTCGATAACTCTATGGTAACCTTTTTCTATT
1 AAGTCCACAACTCTGTGG-AACCTTTTT-TTTT
* *
1113941 AAGGTCCACAACT-TCGTGGCACCTTCTTTTTTC
1 AA-GTCCACAACTCT-GTGGAACCTT-TTTTTTT
* *
1113974 AAGTCCACAACTCTGTGACAACCTTTTTCTGTTA
1 AAGTCCACAACTCTGTG-GAACCTTTTT-T-TTT
* *
1114008 AAGTCTACAACT-TCGTGGCACCTTTCTTTTTT
1 AAGTCCACAACTCT-GTGGAACCTTT-TTTTTT
* * *
1114040 AAGTCCATAACTCTGTGGCACCCTTTT
1 AAGTCCACAACTCTGTGGAACCTTTTT
1114067 AAGTCCACAA
Statistics
Matches: 297, Mismatches: 65, Indels: 67
0.69 0.15 0.16
Matches are distributed among these distances:
31 3 0.01
32 105 0.35
33 65 0.22
34 78 0.26
35 20 0.07
36 3 0.01
37 7 0.02
38 16 0.05
ACGTcount: A:0.23, C:0.27, G:0.12, T:0.37
Consensus pattern (31 bp):
AAGTCCACAACTCTGTGGAACCTTTTTTTTT
Found at i:1113895 original size:66 final size:66
Alignment explanation
Indices: 1113639--1114066 Score: 337
Period size: 66 Copynumber: 6.4 Consensus size: 66
1113629 TTTCTTTTCA
* * * * * * * **
1113639 AAGTCCACAACTTTGTGGCAACCTTTTTTTGTTAAAGTGCACAACTCCATAGCAACCTTTTTTCT
1 AAGTCCATAACTCTATGGCAACCTTTTTCTGTTAAAGTCCACAACTCCGTGGC-ACC-TTCCTCT
*
1113704 GTTA
64 -TTT
* * ** * * *
1113708 AAGTCGACAACTCTATGGC-A-CTTTCCCCTTTTAAA-TCCACAACTCTGTGACACCTTCC-CTT
1 AAGTCCATAACTCTATGGCAACCTTT-TTCTGTTAAAGTCCACAACTCCGTGGCACCTTCCTC-T
1113769 TTT
64 TTT
* * * * * **
1113772 AAGTCCACAACTTTGTGGTAACCTTTTTTTTTTTGTTAAAGTCCACAACTCTATGGCACCTTCCT
1 AAGTCCATAACTCTATGGCAACC----TTTTTCTGTTAAAGTCCACAACTCCGTGGCACCTTCCT
*
1113837 CTCTT
62 CTTTT
* *
1113842 AAGTCCATAACTCCATGGCAACCTTTTTATGTTAAAGTCCACAACTCCGTGGCACCTTCC-CTTT
1 AAGTCCATAACTCTATGGCAACCTTTTTCTGTTAAAGTCCACAACTCCGTGGCACCTTCCTC-TT
1113906 TT
65 TT
* * * * * *
1113908 AAGTCGATAACTCTATGGTAACCTTTTTCTATTAAGGTCCACAACTTCGTGGCACCTT-CTTTTT
1 AAGTCCATAACTCTATGGCAACCTTTTTCTGTTAAAGTCCACAACTCCGTGGCACCTTCCTCTTT
1113972 T
66 T
* * * * * * *
1113973 CAAGTCCACAACTCTGTGACAACCTTTTTCTGTTAAAGTCTACAACTTCGTGGCACCTTTCTTTT
1 -AAGTCCATAACTCTATGGCAACCTTTTTCTGTTAAAGTCCACAACTCCGTGGCACCTTCCTCTT
1114038 TT
65 TT
* *
1114040 AAGTCCATAACTCTGTGGCACCCTTTT
1 AAGTCCATAACTCTATGGCAACCTTTT
1114067 AAGTCCACAA
Statistics
Matches: 291, Mismatches: 54, Indels: 31
0.77 0.14 0.08
Matches are distributed among these distances:
64 18 0.06
65 10 0.03
66 166 0.57
67 22 0.08
68 7 0.02
69 22 0.08
70 45 0.15
71 1 0.00
ACGTcount: A:0.23, C:0.27, G:0.12, T:0.37
Consensus pattern (66 bp):
AAGTCCATAACTCTATGGCAACCTTTTTCTGTTAAAGTCCACAACTCCGTGGCACCTTCCTCTTT
T
Found at i:1114073 original size:27 final size:27
Alignment explanation
Indices: 1114036--1114149 Score: 151
Period size: 27 Copynumber: 4.2 Consensus size: 27
1114026 CACCTTTCTT
*
1114036 TTTTAAGTCCATAACTCTGTGGCACCC
1 TTTTAAGTCCACAACTCTGTGGCACCC
*
1114063 TTTTAAGTCCACAACTTTGTGGCACCC
1 TTTTAAGTCCACAACTCTGTGGCACCC
* *
1114090 TTTTAAG-CTCACAACTCCGCGGCACCC
1 TTTTAAGTC-CACAACTCTGTGGCACCC
*
1114117 TTTTAAGTCCACAACTAC-GTGGCACCT
1 TTTTAAGTCCACAACT-CTGTGGCACCC
1114144 TTTTAA
1 TTTTAA
1114150 AACCCATAAG
Statistics
Matches: 77, Mismatches: 7, Indels: 6
0.86 0.08 0.07
Matches are distributed among these distances:
26 1 0.01
27 74 0.96
28 2 0.03
ACGTcount: A:0.24, C:0.31, G:0.14, T:0.32
Consensus pattern (27 bp):
TTTTAAGTCCACAACTCTGTGGCACCC
Found at i:1114219 original size:32 final size:31
Alignment explanation
Indices: 1114141--1114236 Score: 97
Period size: 32 Copynumber: 3.1 Consensus size: 31
1114131 CTACGTGGCA
* **
1114141 CCTTTTTAAAACC-CATAAGTCAATGGC-AC
1 CCTTTCTAAAACCACATAAGTCGGTGGCAAC
*
1114170 CCTTCTCTAAAGCCCACATAAGTCGGTGGCAAC
1 CCTT-TCTAAA-ACCACATAAGTCGGTGGCAAC
* *
1114203 CCTTTCTAAAATCCACACAAGTCGGTGACAAC
1 CCTTTCTAAAA-CCACATAAGTCGGTGGCAAC
1114235 CC
1 CC
1114237 CCTTCAAAGC
Statistics
Matches: 55, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
29 4 0.07
30 5 0.09
31 2 0.04
32 38 0.69
33 6 0.11
ACGTcount: A:0.31, C:0.32, G:0.14, T:0.23
Consensus pattern (31 bp):
CCTTTCTAAAACCACATAAGTCGGTGGCAAC
Found at i:1114251 original size:32 final size:32
Alignment explanation
Indices: 1114175--1114261 Score: 104
Period size: 32 Copynumber: 2.7 Consensus size: 32
1114165 GGCACCCTTC
* * *
1114175 TCTAAAGCCCACATAAGTCGGTGGCAACCCTT
1 TCTAAAGCCCACACAAGTCGGTGACAACCCCT
**
1114207 TCTAAAATCCACACAAGTCGGTGACAACCCCCT
1 TCTAAAGCCCACACAAGTCGGTGACAA-CCCCT
*
1114240 TC-AAAGCCCACACAAGTTGGTG
1 TCTAAAGCCCACACAAGTCGGTG
1114262 GCATCTTTTT
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
32 40 0.87
33 6 0.13
ACGTcount: A:0.31, C:0.32, G:0.17, T:0.20
Consensus pattern (32 bp):
TCTAAAGCCCACACAAGTCGGTGACAACCCCT
Found at i:1114333 original size:28 final size:28
Alignment explanation
Indices: 1114301--1114376 Score: 116
Period size: 28 Copynumber: 2.7 Consensus size: 28
1114291 TAATCGCTTC
*
1114301 CTTTCATAGCCCACAAGTCAGTGGCACA
1 CTTTCAAAGCCCACAAGTCAGTGGCACA
* *
1114329 TTTTCAAAGCCCACAAGTCAGTGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACA
*
1114357 CTTCCAAAGCCCACAAGTCA
1 CTTTCAAAGCCCACAAGTCA
1114377 TTTCAAAGTC
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 43 1.00
ACGTcount: A:0.30, C:0.34, G:0.16, T:0.20
Consensus pattern (28 bp):
CTTTCAAAGCCCACAAGTCAGTGGCACA
Found at i:1114397 original size:47 final size:47
Alignment explanation
Indices: 1114330--1114423 Score: 134
Period size: 47 Copynumber: 2.0 Consensus size: 47
1114320 AGTGGCACAT
*
1114330 TTTCAAAGCCCACAAGTCAGTGGCACCCTTCCAAAGCCCACAAGTCA
1 TTTCAAAGCCCACAAGTCAGTAGCACCCTTCCAAAGCCCACAAGTCA
* * * **
1114377 TTTCAAAGTCCATAAGTCAGTAGCATCCTTTTAAAGCCCACAAGTCA
1 TTTCAAAGCCCACAAGTCAGTAGCACCCTTCCAAAGCCCACAAGTCA
1114424 GTTGCACCCC
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
47 41 1.00
ACGTcount: A:0.33, C:0.31, G:0.14, T:0.22
Consensus pattern (47 bp):
TTTCAAAGCCCACAAGTCAGTAGCACCCTTCCAAAGCCCACAAGTCA
Found at i:1114422 original size:28 final size:30
Alignment explanation
Indices: 1114377--1114479 Score: 90
Period size: 28 Copynumber: 3.5 Consensus size: 30
1114367 CCACAAGTCA
* * *
1114377 TTTC-AAAGTCCATAAGTCAGTAGCA-TCC
1 TTTCTAAAGCCCACAAGTCAGTAGCACCCC
*
1114405 TTT-TAAAGCCCACAAGTCAGTTGCACCCC
1 TTTCTAAAGCCCACAAGTCAGTAGCACCCC
* *
1114434 TTTCTAAAGCCCACACAAGTCGGTGGCAACCCC
1 TTTCTAAAG-CC-CACAAGTCAGTAGC-ACCCC
1114467 --TCTAAAGCCCACA
1 TTTCTAAAGCCCACA
1114480 CAAGCTGGTA
Statistics
Matches: 63, Mismatches: 6, Indels: 11
0.79 0.08 0.14
Matches are distributed among these distances:
28 21 0.33
29 9 0.14
30 7 0.11
31 9 0.14
32 12 0.19
33 5 0.08
ACGTcount: A:0.30, C:0.33, G:0.15, T:0.22
Consensus pattern (30 bp):
TTTCTAAAGCCCACAAGTCAGTAGCACCCC
Found at i:1114533 original size:30 final size:31
Alignment explanation
Indices: 1114390--1114609 Score: 157
Period size: 32 Copynumber: 7.0 Consensus size: 31
1114380 CAAAGTCCAT
* * *
1114390 AAGTCAGTAGC-ATCCTTTTAAAG-CC-CAC
1 AAGTCGGTAGCAACCCTTCTAAAGCCCACAC
* * *
1114418 AAGTCAGTTGCACCCCTTTCTAAAGCCCACAC
1 AAGTCGGTAGCAACCC-TTCTAAAGCCCACAC
* *
1114450 AAGTCGGTGGCAACCCCTCTAAAGCCCACAC
1 AAGTCGGTAGCAACCCTTCTAAAGCCCACAC
*
1114481 AAG-CTGGTAGCAACCTCTTCTAAAGCTCACAC
1 AAGTC-GGTAGCAACC-CTTCTAAAGCCCACAC
* *
1114513 AAGTCGGT-G-ATGCCCTTCTAAAGCTCACAC
1 AAGTCGGTAGCA-ACCCTTCTAAAGCCCACAC
* * *
1114543 AAGTTGGTGGC-ACCTTTCTCTAAAGCCCACAC
1 AAGTCGGTAGCAACC-CT-TCTAAAGCCCACAC
* * *
1114575 AAGTTGGTGGCAACCTCTTCTCTAAAACCCACAC
1 AAGTCGGTAGCAACC-C-T-TCTAAAGCCCACAC
1114609 A
1 A
1114610 CGTTGGTGGC
Statistics
Matches: 160, Mismatches: 18, Indels: 22
0.80 0.09 0.11
Matches are distributed among these distances:
28 10 0.06
29 2 0.01
30 34 0.21
31 33 0.21
32 60 0.38
33 5 0.03
34 16 0.10
ACGTcount: A:0.29, C:0.33, G:0.16, T:0.22
Consensus pattern (31 bp):
AAGTCGGTAGCAACCCTTCTAAAGCCCACAC
Found at i:1114565 original size:62 final size:62
Alignment explanation
Indices: 1114435--1114609 Score: 192
Period size: 62 Copynumber: 2.7 Consensus size: 62
1114425 TTGCACCCCT
1114435 TTCTAAAGCCCACACAAGTCGGTGGCAACCCCTCTAAAGCCCACACAAGCTGGTAGCAACCTC
1 TTCTAAAGCCCACACAAGTCGGT-GCAACCCCTCTAAAGCCCACACAAGCTGGTAGCAACCTC
* * * * * * *
1114498 TTCTAAAGCTCACACAAGTCGGTG-ATGCCCTTCTAAAGCTCACACAAGTTGGTGGC-ACCTT
1 TTCTAAAGCCCACACAAGTCGGTGCA-ACCCCTCTAAAGCCCACACAAGCTGGTAGCAACCTC
* *
1114559 TCTCTAAAGCCCACACAAGTTGGTGGCAACCTCTTCTCTAAAACCCACACA
1 T-TCTAAAGCCCACACAAGTCGGT-GCAACC-C--CTCTAAAGCCCACACA
1114610 CGTTGGTGGC
Statistics
Matches: 92, Mismatches: 13, Indels: 11
0.79 0.11 0.09
Matches are distributed among these distances:
61 6 0.07
62 46 0.50
63 25 0.27
64 2 0.02
66 13 0.14
ACGTcount: A:0.29, C:0.33, G:0.17, T:0.21
Consensus pattern (62 bp):
TTCTAAAGCCCACACAAGTCGGTGCAACCCCTCTAAAGCCCACACAAGCTGGTAGCAACCTC
Found at i:1114629 original size:34 final size:32
Alignment explanation
Indices: 1114431--1114629 Score: 185
Period size: 32 Copynumber: 6.2 Consensus size: 32
1114421 TCAGTTGCAC
*
1114431 CCCTT-TCTAAAGCCCACACAAGTCGGTGGCAA
1 CCCTTCTCTAAAGCCCACACAAGTTGGTGGC-A
* *
1114463 CCC--CTCTAAAGCCCACACAAGCTGGTAGCA
1 CCCTTCTCTAAAGCCCACACAAGTTGGTGGCA
* * * ***
1114493 ACC-TCTTCTAAAGCTCACACAAGTCGGTGATG
1 CCCTTC-TCTAAAGCCCACACAAGTTGGTGGCA
*
1114525 CCC-T-TCTAAAGCTCACACAAGTTGGTGGCA
1 CCCTTCTCTAAAGCCCACACAAGTTGGTGGCA
*
1114555 CCTTTCTCTAAAGCCCACACAAGTTGGTGGCAA
1 CCCTTCTCTAAAGCCCACACAAGTTGGTGGC-A
* *
1114588 CCTCTTCTCTAAAACCCACACACGTTGGTGGCA
1 CC-CTTCTCTAAAGCCCACACAAGTTGGTGGCA
1114621 TCTCCTTCT
1 -C-CCTTCT
1114630 AAGCCTAATG
Statistics
Matches: 137, Mismatches: 21, Indels: 16
0.79 0.12 0.09
Matches are distributed among these distances:
30 27 0.20
31 24 0.18
32 49 0.36
33 4 0.03
34 32 0.23
35 1 0.01
ACGTcount: A:0.26, C:0.34, G:0.17, T:0.23
Consensus pattern (32 bp):
CCCTTCTCTAAAGCCCACACAAGTTGGTGGCA
Found at i:1114891 original size:113 final size:113
Alignment explanation
Indices: 1114629--1114891 Score: 267
Period size: 113 Copynumber: 2.3 Consensus size: 113
1114619 CATCTCCTTC
* * * * * * *
1114629 TAAGCCTAATGTCGCTGGCCTTGAATCAGTATACTAGTGCCTTTATCATCTTTAAGTCTAATATC
1 TAAGACTAATGTCGCTGACCTTGAATCAGCAAATTGGTGCCTTTAGCATCTTTAAGTCTAATATC
** ** * * * *
1114694 GTTGGCTTTGAATTAGCATATCGGCACCTTTATCATTCTTCTCATCTT
66 ACTACCCTTGAATCAGCATATCGGCACCTTTATCATTCTTCGCATCCT
* ** * * * * *
1114742 TAAGTCTAATGT-TATTAGCTTTGGATCAACAAATTGGTGCCTTTGGCATCTTTAAGTCTAATAT
1 TAAGACTAATGTCGCTGA-CCTTGAATCAGCAAATTGGTGCCTTTAGCATCTTTAAGTCTAATAT
* * *
1114806 CACTACCCTTGAATCAGTATATTGGCACTTTTATCATTCTTCGCATCCT
65 CACTACCCTTGAATCAGCATATCGGCACCTTTATCATTCTTCGCATCCT
*
1114855 TAAGACTAATGTCGCTGACCTTGAATCAGCACATTGG
1 TAAGACTAATGTCGCTGACCTTGAATCAGCAAATTGG
1114892 CACTTTTCTT
Statistics
Matches: 115, Mismatches: 33, Indels: 4
0.76 0.22 0.03
Matches are distributed among these distances:
112 1 0.01
113 112 0.97
114 2 0.02
ACGTcount: A:0.25, C:0.21, G:0.16, T:0.38
Consensus pattern (113 bp):
TAAGACTAATGTCGCTGACCTTGAATCAGCAAATTGGTGCCTTTAGCATCTTTAAGTCTAATATC
ACTACCCTTGAATCAGCATATCGGCACCTTTATCATTCTTCGCATCCT
Found at i:1114919 original size:61 final size:61
Alignment explanation
Indices: 1114787--1114919 Score: 151
Period size: 61 Copynumber: 2.2 Consensus size: 61
1114777 GGTGCCTTTG
* * * * *
1114787 GCATCTTTAAGTCTAATATCACTACCCTTGAATCAGTATATTGGCACTTTTATCATTCTTC
1 GCATCTTTAAGACTAATATCACTACCCTTGAATCAGCACATTGGCACTTTTATCATCCTTA
* * * * *
1114848 GCATCCTTAAGACTAATGTCGCTGA-CCTTGAATCAGCACATTGGCACTTTTCTTATCCTTA
1 GCATCTTTAAGACTAATATCACT-ACCCTTGAATCAGCACATTGGCACTTTTATCATCCTTA
*
1114909 TCATCTTTAAG
1 GCATCTTTAAG
1114920 GCTAGTGTTA
Statistics
Matches: 59, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
61 58 0.98
62 1 0.02
ACGTcount: A:0.26, C:0.24, G:0.12, T:0.38
Consensus pattern (61 bp):
GCATCTTTAAGACTAATATCACTACCCTTGAATCAGCACATTGGCACTTTTATCATCCTTA
Found at i:1119352 original size:13 final size:13
Alignment explanation
Indices: 1119334--1119359 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1119324 CAATTTTTTG
1119334 TGTATCGATACAT
1 TGTATCGATACAT
1119347 TGTATCGATACAT
1 TGTATCGATACAT
1119360 ACTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1119371 original size:32 final size:33
Alignment explanation
Indices: 1119314--1119377 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
1119304 TGCAAGCCAA
**
1119314 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTTGTGTATCGATACAT
1119347 TGTATCGATAC-ATACTTTGTGTATCGATACA
1 TGTATCGATACAATACTTTGTGTATCGATACA
1119378 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (33 bp):
TGTATCGATACAATACTTTGTGTATCGATACAT
Found at i:1120080 original size:39 final size:40
Alignment explanation
Indices: 1120005--1120084 Score: 108
Period size: 39 Copynumber: 2.0 Consensus size: 40
1119995 TTTTCTTTCT
*
1120005 CCCTTAATTAAAGTAATTTTAACAAATTCGTACATTCTCC
1 CCCTTAATTAAAGTAATTTTAACAAATTCATACATTCTCC
* * * *
1120045 CCCTTAA-TAAGGTAATTTTAGCAAATTTATGCATTCTCC
1 CCCTTAATTAAAGTAATTTTAACAAATTCATACATTCTCC
1120084 C
1 C
1120085 TTTTTTTTAA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
39 28 0.80
40 7 0.20
ACGTcount: A:0.33, C:0.23, G:0.07, T:0.38
Consensus pattern (40 bp):
CCCTTAATTAAAGTAATTTTAACAAATTCATACATTCTCC
Found at i:1121481 original size:21 final size:20
Alignment explanation
Indices: 1121452--1121494 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
1121442 GGCTAGTGTG
* *
1121452 GGGACTGCCCGGTTGTGACCT
1 GGGACTG-CCGGTCGCGACCT
*
1121473 GGGAGTGCCGGTCGCGACCT
1 GGGACTGCCGGTCGCGACCT
1121493 GG
1 GG
1121495 TGGTGCTGCC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.09, C:0.28, G:0.44, T:0.19
Consensus pattern (20 bp):
GGGACTGCCGGTCGCGACCT
Done.