Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015127.1 Kokia drynarioides strain JFW-HI SEQ_130171, whole genome shotgun sequence
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: 179612
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.34
Warning! 347 characters in sequence are not A, C, G, or T
Found at i:6966 original size:31 final size:31
Alignment explanation
Indices: 6927--6996 Score: 104
Period size: 31 Copynumber: 2.3 Consensus size: 31
6917 TATTTTTTGG
6927 ATGACCAAAATGAAAGTAACCTAAAAATTGA
1 ATGACCAAAATGAAAGTAACCTAAAAATTGA
* ** *
6958 GTGACCAAAATGAAAGTGCCCTAAAATTTGA
1 ATGACCAAAATGAAAGTAACCTAAAAATTGA
6989 ATGACCAA
1 ATGACCAA
6997 CTAAGTAGTT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.49, C:0.16, G:0.16, T:0.20
Consensus pattern (31 bp):
ATGACCAAAATGAAAGTAACCTAAAAATTGA
Found at i:12191 original size:32 final size:32
Alignment explanation
Indices: 12155--12219 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
12145 AAGGCTAAAC
12155 GTCTTTTGTAGAAGAAAAATATCTTTTTGAAT
1 GTCTTTTGTAGAAGAAAAATATCTTTTTGAAT
12187 GTCTTTTGTAGAAGAAAAATATCTTTTTGAAT
1 GTCTTTTGTAGAAGAAAAATATCTTTTTGAAT
12219 G
1 G
12220 ATTATAATGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.34, C:0.06, G:0.17, T:0.43
Consensus pattern (32 bp):
GTCTTTTGTAGAAGAAAAATATCTTTTTGAAT
Found at i:15769 original size:14 final size:14
Alignment explanation
Indices: 15739--15783 Score: 63
Period size: 14 Copynumber: 3.1 Consensus size: 14
15729 TTAATTCAAA
15739 TTCAACACTTAATTT
1 TTCAACACTT-ATTT
**
15754 TTCAGTACTTATTT
1 TTCAACACTTATTT
15768 TTCAACACTTATTT
1 TTCAACACTTATTT
15782 TT
1 TT
15784 TCAGCATTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
14 18 0.69
15 8 0.31
ACGTcount: A:0.27, C:0.18, G:0.02, T:0.53
Consensus pattern (14 bp):
TTCAACACTTATTT
Found at i:15797 original size:29 final size:29
Alignment explanation
Indices: 15739--15798 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 29
15729 TTAATTCAAA
*
15739 TTCAACACTTAATTTTTCAGTACTTATTT
1 TTCAACACTTAATTTTTCAGCACTTATTT
* * *
15768 TTCAACACTTATTTTTTCAGCATTTTTTT
1 TTCAACACTTAATTTTTCAGCACTTATTT
15797 TT
1 TT
15799 TAATCAAACA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.23, C:0.17, G:0.03, T:0.57
Consensus pattern (29 bp):
TTCAACACTTAATTTTTCAGCACTTATTT
Found at i:15799 original size:15 final size:15
Alignment explanation
Indices: 15739--15786 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
15729 TTAATTCAAA
*
15739 TTCAACACTTAATTT
1 TTCAACACTTATTTT
**
15754 TTCAGTACTTA-TTT
1 TTCAACACTTATTTT
15768 TTCAACACTTATTTT
1 TTCAACACTTATTTT
15783 TTCA
1 TTCA
15787 GCATTTTTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
14 12 0.43
15 16 0.57
ACGTcount: A:0.27, C:0.19, G:0.02, T:0.52
Consensus pattern (15 bp):
TTCAACACTTATTTT
Found at i:24226 original size:17 final size:16
Alignment explanation
Indices: 24186--24253 Score: 63
Period size: 14 Copynumber: 4.4 Consensus size: 16
24176 TTTGTTTAGT
*
24186 TTTATATTATAAT-TA
1 TTTATATTATATTATA
*
24201 TTTAGA-TATA-TATA
1 TTTATATTATATTATA
*
24215 TTTATATTATATTGTA
1 TTTATATTATATTATA
24231 TTTATAAATT-TATTATA
1 TTTAT--ATTATATTATA
24248 TTTATA
1 TTTATA
24254 ATAATAATAA
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
13 1 0.02
14 11 0.25
15 10 0.23
16 8 0.18
17 11 0.25
18 3 0.07
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (16 bp):
TTTATATTATATTATA
Found at i:27448 original size:30 final size:30
Alignment explanation
Indices: 27414--27478 Score: 112
Period size: 30 Copynumber: 2.2 Consensus size: 30
27404 ACTTATTTTA
27414 TTGTTAATTTTGTTATTATTTTAAAGGCAT
1 TTGTTAATTTTGTTATTATTTTAAAGGCAT
**
27444 TTGTTAATTTTGTTATTATTTTTGAGGCAT
1 TTGTTAATTTTGTTATTATTTTAAAGGCAT
27474 TTGTT
1 TTGTT
27479 TGTTAAGTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.22, C:0.03, G:0.15, T:0.60
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAAAGGCAT
Found at i:28704 original size:17 final size:17
Alignment explanation
Indices: 28678--28711 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
28668 AATATTAAGT
*
28678 TTCCCGATTATGACTAA
1 TTCCCAATTATGACTAA
28695 TTCCCAATTATGACTAA
1 TTCCCAATTATGACTAA
28712 GTTTTTGTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.32, C:0.24, G:0.09, T:0.35
Consensus pattern (17 bp):
TTCCCAATTATGACTAA
Found at i:28918 original size:19 final size:20
Alignment explanation
Indices: 28894--28943 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
28884 TTCTAAAAAA
* *
28894 TGAAATTATATATAT-TTTT
1 TGAAATTATAAAAATATTTT
28913 TGAAATTATAAAAATATTTT
1 TGAAATTATAAAAATATTTT
*
28933 TAAAATTATAA
1 TGAAATTATAA
28944 TTATGTTCAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 13 0.48
20 14 0.52
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (20 bp):
TGAAATTATAAAAATATTTT
Found at i:31730 original size:22 final size:22
Alignment explanation
Indices: 31690--31731 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
31680 AATTGATAAT
* *
31690 AAACTTGTATTTTAACATTATC
1 AAACATGTATTTGAACATTATC
*
31712 AAACATGTATTTGATCATTA
1 AAACATGTATTTGAACATTA
31732 AATTTATAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.38, C:0.12, G:0.07, T:0.43
Consensus pattern (22 bp):
AAACATGTATTTGAACATTATC
Found at i:39277 original size:31 final size:31
Alignment explanation
Indices: 39250--39308 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
39240 ATTATATGTG
*
39250 TGAAAATTTTATTGTGATTCAAATATATGCA
1 TGAAAATTTAATTGTGATTCAAATATATGCA
* * *
39281 TGAAACTTTAATTTTGATTCAATTATAT
1 TGAAAATTTAATTGTGATTCAAATATAT
39309 ATATTTAAAG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.37, C:0.07, G:0.10, T:0.46
Consensus pattern (31 bp):
TGAAAATTTAATTGTGATTCAAATATATGCA
Found at i:39489 original size:29 final size:30
Alignment explanation
Indices: 39433--39494 Score: 90
Period size: 29 Copynumber: 2.1 Consensus size: 30
39423 TGAGAATTTG
*
39433 ATAAAATCAAAATTTCATGTATAAAATTAC
1 ATAAAATCAAAATTTCATATATAAAATTAC
* *
39463 ATAAAATCAAAA-TTCATATATATAATTGC
1 ATAAAATCAAAATTTCATATATAAAATTAC
39492 ATA
1 ATA
39495 TTAAACCAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 17 0.59
30 12 0.41
ACGTcount: A:0.53, C:0.10, G:0.03, T:0.34
Consensus pattern (30 bp):
ATAAAATCAAAATTTCATATATAAAATTAC
Found at i:39705 original size:31 final size:29
Alignment explanation
Indices: 39640--39711 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 29
39630 CTCAGGTAAT
*
39640 ATTTTAGTCACTTATGTTAGAAATATAAC
1 ATTTTAGTCACTTATGTTACAAATATAAC
* *
39669 GTTTTAGTCACTTATGTTATCATGATATAAC
1 ATTTTAGTCACTTATGTTA-CA-AATATAAC
*
39700 ATTTTAATCACT
1 ATTTTAGTCACT
39712 GAACGTTAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
29 18 0.50
30 1 0.03
31 17 0.47
ACGTcount: A:0.33, C:0.12, G:0.10, T:0.44
Consensus pattern (29 bp):
ATTTTAGTCACTTATGTTACAAATATAAC
Found at i:39940 original size:14 final size:14
Alignment explanation
Indices: 39903--39931 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
39893 GAAAAGCATG
39903 AAAAAAAAAAGAAA
1 AAAAAAAAAAGAAA
39917 AAAAAAAAAAGAAA
1 AAAAAAAAAAGAAA
39931 A
1 A
39932 GTTAAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAGAAA
Found at i:43627 original size:17 final size:17
Alignment explanation
Indices: 43605--43655 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
43595 CAGTCAAAAT
43605 AAATTTAAGAAAATAAC
1 AAATTTAAGAAAATAAC
**
43622 AAATTT-AGTCAA-AAC
1 AAATTTAAGAAAATAAC
* *
43637 AAAATTAATAAAATAAC
1 AAATTTAAGAAAATAAC
43654 AA
1 AA
43656 TTTTTAATAA
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
15 8 0.31
16 7 0.27
17 11 0.42
ACGTcount: A:0.65, C:0.08, G:0.04, T:0.24
Consensus pattern (17 bp):
AAATTTAAGAAAATAAC
Found at i:43650 original size:32 final size:33
Alignment explanation
Indices: 43580--43655 Score: 102
Period size: 32 Copynumber: 2.3 Consensus size: 33
43570 CCTATTTACT
* *
43580 TAAAATAA-ATAATTTCAGTCAAAATAAATTTAA
1 TAAAATAACA-AATTTCAGTCAAAACAAAATTAA
*
43613 GAAAATAACAAATTT-AGTCAAAACAAAATTAA
1 TAAAATAACAAATTTCAGTCAAAACAAAATTAA
43645 TAAAATAACAA
1 TAAAATAACAA
43656 TTTTTAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
32 25 0.66
33 12 0.32
34 1 0.03
ACGTcount: A:0.62, C:0.08, G:0.04, T:0.26
Consensus pattern (33 bp):
TAAAATAACAAATTTCAGTCAAAACAAAATTAA
Found at i:45635 original size:18 final size:18
Alignment explanation
Indices: 45608--45658 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
45598 GTTTATAGAT
*
45608 ATCCTTGGACTTACAGCA
1 ATCCTAGGACTTACAGCA
* * *
45626 ATCCTCGGACTTGCAGCG
1 ATCCTAGGACTTACAGCA
45644 ATCCTAGGACTTACA
1 ATCCTAGGACTTACA
45659 TCGTTCATCA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.25, C:0.29, G:0.20, T:0.25
Consensus pattern (18 bp):
ATCCTAGGACTTACAGCA
Found at i:46788 original size:300 final size:300
Alignment explanation
Indices: 46246--46843 Score: 1045
Period size: 300 Copynumber: 2.0 Consensus size: 300
46236 ACCAGCATTT
*
46246 GACAATGGAGAGACCTTATCAAAAGAACTAAGATTCATTTCTGTTGACATGTCGATAGAAGCTTC
1 GACAATGGAGAGACCTTATCAAAAGAACTAAGATTCATTTCTGTTGACACGTCGATAGAAGCTTC
* *
46311 CTTGTCCATCGATGATAAGGAGACATCATCAATAGAAATAAGCTTGGAAGAAGCGGATGGCTCGA
66 CTTGTCCATCAATGATAAGGAGACATCATCAATAGAAATAAGCTTAGAAGAAGCGGATGGCTCGA
* * * *
46376 TTTTGGTACTGGCTTGCTCCCAATTGAGTTCCTCAAAGTCATGTTGTTTTAAATCAGTAGATTCC
131 TTTTGGAACTGGCTTGCTCCCAATTGAGTTCCTCAAAGCCATGTTGTTTCAAATCAGCAGATTCC
46441 GCCAGTATAGTCCCAAGAGGCTCAATGATGGCTGATTCTGATTCTGATTGTGAAATGAATATTGA
196 GCCAGTATAGTCCCAAGAGGCTCAATGATGGCTGATTCTGATTCTGATTGTGAAATGAATATTGA
46506 AGGCTTAAGTGCAGAAACAGGATCCATGAATTTCTCTGTC
261 AGGCTTAAGTGCAGAAACAGGATCCATGAATTTCTCTGTC
*
46546 GACAATGGAGAGACCTTATCAACAGAACTAAGATTCATTTCTGTTGACACGTCGATAGAAGCTTC
1 GACAATGGAGAGACCTTATCAAAAGAACTAAGATTCATTTCTGTTGACACGTCGATAGAAGCTTC
*
46611 CTTGTTCATCAATGATAAAGG-GACATCATCAATAGAAATAAGCTTAGAAGAAGCGGATGGCTCG
66 CTTGTCCATCAATGAT-AAGGAGACATCATCAATAGAAATAAGCTTAGAAGAAGCGGATGGCTCG
* *
46675 ATTTTTGAACTGGCTTGCTCCCAATTGAGTTCCTCCAAGCCATGTTGTTTCAAATCAGCAGATTC
130 ATTTTGGAACTGGCTTGCTCCCAATTGAGTTCCTCAAAGCCATGTTGTTTCAAATCAGCAGATTC
* * * *
46740 TGCCGGTATAGTGCCAAGAGGCTTAATGATGGCTGATTCTGATTCTGATTGTGAAATGAATATTG
195 CGCCAGTATAGTCCCAAGAGGCTCAATGATGGCTGATTCTGATTCTGATTGTGAAATGAATATTG
46805 AAGGCTTAAGTGCAGAAACAGGATCCATGAATTTCTCTG
260 AAGGCTTAAGTGCAGAAACAGGATCCATGAATTTCTCTG
46844 AAGCAAAATT
Statistics
Matches: 282, Mismatches: 15, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
300 278 0.99
301 4 0.01
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.29
Consensus pattern (300 bp):
GACAATGGAGAGACCTTATCAAAAGAACTAAGATTCATTTCTGTTGACACGTCGATAGAAGCTTC
CTTGTCCATCAATGATAAGGAGACATCATCAATAGAAATAAGCTTAGAAGAAGCGGATGGCTCGA
TTTTGGAACTGGCTTGCTCCCAATTGAGTTCCTCAAAGCCATGTTGTTTCAAATCAGCAGATTCC
GCCAGTATAGTCCCAAGAGGCTCAATGATGGCTGATTCTGATTCTGATTGTGAAATGAATATTGA
AGGCTTAAGTGCAGAAACAGGATCCATGAATTTCTCTGTC
Found at i:50083 original size:47 final size:47
Alignment explanation
Indices: 50011--50112 Score: 168
Period size: 47 Copynumber: 2.2 Consensus size: 47
50001 TGTGGTGCCC
*
50011 GCATAACCATCGTCAACTAGAGCCCAATTATGCTTTATCCTTTGACA
1 GCATAATCATCGTCAACTAGAGCCCAATTATGCTTTATCCTTTGACA
* * *
50058 GCATAATCATCGTTAACTAGGGCCCAGTTATGCTTTATCCTTTGACA
1 GCATAATCATCGTCAACTAGAGCCCAATTATGCTTTATCCTTTGACA
50105 GCATAATC
1 GCATAATC
50113 TTTGTAAATT
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 51 1.00
ACGTcount: A:0.28, C:0.25, G:0.15, T:0.31
Consensus pattern (47 bp):
GCATAATCATCGTCAACTAGAGCCCAATTATGCTTTATCCTTTGACA
Found at i:59592 original size:86 final size:86
Alignment explanation
Indices: 59447--59620 Score: 330
Period size: 86 Copynumber: 2.0 Consensus size: 86
59437 ATTTATAAAT
**
59447 TTTAGAACGTGCCTAATATTTAATTTCAAATTTTGGAATAAAAAAGATAACTTTGAAATTCATAA
1 TTTAGAACGTGCCTAATATTTAATTTCAAACGTTGGAATAAAAAAGATAACTTTGAAATTCATAA
59512 ACTAACCTCCTCTTCGGTTTA
66 ACTAACCTCCTCTTCGGTTTA
59533 TTTAGAACGTGCCTAATATTTAATTTCAAACGTTGGAATAAAAAAGATAACTTTGAAATTCATAA
1 TTTAGAACGTGCCTAATATTTAATTTCAAACGTTGGAATAAAAAAGATAACTTTGAAATTCATAA
59598 ACTAACCTCCTCTTCGGTTTA
66 ACTAACCTCCTCTTCGGTTTA
59619 TT
1 TT
59621 ATTCTAAAGC
Statistics
Matches: 86, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
86 86 1.00
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.37
Consensus pattern (86 bp):
TTTAGAACGTGCCTAATATTTAATTTCAAACGTTGGAATAAAAAAGATAACTTTGAAATTCATAA
ACTAACCTCCTCTTCGGTTTA
Found at i:65971 original size:9 final size:9
Alignment explanation
Indices: 65957--66021 Score: 60
Period size: 9 Copynumber: 6.8 Consensus size: 9
65947 TATTATTCTA
65957 AATTTTTTT
1 AATTTTTTT
65966 AA-TTTTTT
1 AATTTTTTT
*
65974 AACTTTTTT
1 AATTTTTTT
65983 ATATTTTTTT
1 A-ATTTTTTT
65993 AGAAATTTTTTT
1 ---AATTTTTTT
66005 AATTTTTATT
1 AATTTTT-TT
*
66015 TATTTTT
1 AATTTTT
66022 AAAATATAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 11
0.79 0.03 0.18
Matches are distributed among these distances:
8 8 0.17
9 16 0.33
10 15 0.31
12 8 0.17
13 1 0.02
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.72
Consensus pattern (9 bp):
AATTTTTTT
Found at i:66061 original size:19 final size:19
Alignment explanation
Indices: 66037--66101 Score: 82
Period size: 19 Copynumber: 3.4 Consensus size: 19
66027 ATAAATTTAA
66037 GAATTTTTATAAA-TATTTT
1 GAATTTTTA-AAATTATTTT
66056 GAA-TTTTAAAATTTATTTT
1 GAATTTTTAAAA-TTATTTT
66075 GAATTTTTGAAAATTATTTT
1 GAATTTTT-AAAATTATTTT
66095 -AATTTTT
1 GAATTTTT
66102 TTTTTTTGTA
Statistics
Matches: 42, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
17 3 0.07
18 5 0.12
19 19 0.45
20 11 0.26
21 4 0.10
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.58
Consensus pattern (19 bp):
GAATTTTTAAAATTATTTT
Found at i:68659 original size:13 final size:14
Alignment explanation
Indices: 68641--68669 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
68631 ATTTTTTATC
68641 TAAACTTAT-TTTT
1 TAAACTTATATTTT
68654 TAAACTTATATTTT
1 TAAACTTATATTTT
68668 TA
1 TA
68670 CTCAAATCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.34, C:0.07, G:0.00, T:0.59
Consensus pattern (14 bp):
TAAACTTATATTTT
Found at i:69254 original size:23 final size:23
Alignment explanation
Indices: 69224--69269 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
69214 TTTAACTTTA
69224 AAAAAATTATAATTAAATTATTC
1 AAAAAATTATAATTAAATTATTC
* *
69247 AAAAAATTTTATTTAAATTATTC
1 AAAAAATTATAATTAAATTATTC
69270 TACTGTTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.43
Consensus pattern (23 bp):
AAAAAATTATAATTAAATTATTC
Found at i:70290 original size:21 final size:20
Alignment explanation
Indices: 70266--70308 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
70256 ACAGTTCCTA
70266 AATTTGATAGAAACTACTTTG
1 AATTT-ATAGAAACTACTTTG
* *
70287 AATTTTTAGGAACTACTTTG
1 AATTTATAGAAACTACTTTG
70307 AA
1 AA
70309 AAAACCTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.37, C:0.09, G:0.14, T:0.40
Consensus pattern (20 bp):
AATTTATAGAAACTACTTTG
Found at i:75486 original size:18 final size:18
Alignment explanation
Indices: 75463--75673 Score: 138
Period size: 18 Copynumber: 11.7 Consensus size: 18
75453 AAGTCCACGC
* *
75463 TGTGCTCTAAGTTAGCAT
1 TGTGCTCCAAGTTAGCAA
*
75481 TATGCTCCAAGTT--CATA
1 TGTGCTCCAAGTTAGCA-A
*
75498 TTGTGCTCCAAGTTAACAA
1 -TGTGCTCCAAGTTAGCAA
* * *
75517 TGTGCTCTAAGTTTGCAT
1 TGTGCTCCAAGTTAGCAA
*
75535 TGTGCTCCAAGTTTGCAA
1 TGTGCTCCAAGTTAGCAA
* ** *
75553 TCTGCTGTAAGTTCGCAA
1 TGTGCTCCAAGTTAGCAA
* * * *
75571 TATGCTCCAAATTTGCAT
1 TGTGCTCCAAGTTAGCAA
* * *
75589 TGTGCTCCAATTTTGCCA
1 TGTGCTCCAAGTTAGCAA
* *
75607 TGTGCTCCAATTTTGCAA
1 TGTGCTCCAAGTTAGCAA
* * *
75625 TATGCTCCAAGTTCGCAT
1 TGTGCTCCAAGTTAGCAA
* * * *
75643 TTTGTTCCAAGTTTGCAT
1 TGTGCTCCAAGTTAGCAA
75661 TGTGCTCCAAGTT
1 TGTGCTCCAAGTT
75674 CAAATCATGC
Statistics
Matches: 155, Mismatches: 34, Indels: 8
0.79 0.17 0.04
Matches are distributed among these distances:
16 2 0.01
18 150 0.97
19 1 0.01
20 2 0.01
ACGTcount: A:0.22, C:0.22, G:0.18, T:0.38
Consensus pattern (18 bp):
TGTGCTCCAAGTTAGCAA
Found at i:75565 original size:54 final size:54
Alignment explanation
Indices: 75465--75673 Score: 215
Period size: 54 Copynumber: 3.9 Consensus size: 54
75455 GTCCACGCTG
* * * * *
75465 TGCTCTAAGTTAGCATTATGCTCCAAG-TT-CATATTGTGCTCCAAGTTAACAATG
1 TGCTCCAAGTTTGCATTGTGCTCCAAGTTTGCA-A-TGTGCTCCAAGTTAGCAATA
* * ** *
75519 TGCTCTAAGTTTGCATTGTGCTCCAAGTTTGCAATCTGCTGTAAGTTCGCAATA
1 TGCTCCAAGTTTGCATTGTGCTCCAAGTTTGCAATGTGCTCCAAGTTAGCAATA
* * * * *
75573 TGCTCCAAATTTGCATTGTGCTCCAATTTTGCCATGTGCTCCAATTTTGCAATA
1 TGCTCCAAGTTTGCATTGTGCTCCAAGTTTGCAATGTGCTCCAAGTTAGCAATA
* * * *
75627 TGCTCCAAGTTCGCATTTTGTTCCAAGTTTGCATTGTGCTCCAAGTT
1 TGCTCCAAGTTTGCATTGTGCTCCAAGTTTGCAATGTGCTCCAAGTT
75674 CAAATCATGC
Statistics
Matches: 128, Mismatches: 25, Indels: 4
0.82 0.16 0.03
Matches are distributed among these distances:
54 123 0.96
55 3 0.02
56 2 0.02
ACGTcount: A:0.22, C:0.22, G:0.18, T:0.38
Consensus pattern (54 bp):
TGCTCCAAGTTTGCATTGTGCTCCAAGTTTGCAATGTGCTCCAAGTTAGCAATA
Found at i:80261 original size:3 final size:3
Alignment explanation
Indices: 80253--80279 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
80243 AAAAGAACAC
80253 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
80280 TTTAAAATTT
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:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:80572 original size:6 final size:6
Alignment explanation
Indices: 80563--80594 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
80553 TATATGTATA
80563 TGGGTG TGGGTG TGGGTG TGGGTG TGGGTG TG
1 TGGGTG TGGGTG TGGGTG TGGGTG TGGGTG TG
80595 CAGAAATCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.66, T:0.34
Consensus pattern (6 bp):
TGGGTG
Found at i:81655 original size:2 final size:2
Alignment explanation
Indices: 81648--81679 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
81638 TGAACAATTA
81648 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
81680 TATTAACTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:83661 original size:18 final size:19
Alignment explanation
Indices: 83638--83676 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
83628 TCATTTCTTT
83638 TTATT-AATTTACAATT-TA
1 TTATTAAATTTA-AATTATA
83656 TTATTAAATTTAAATTATA
1 TTATTAAATTTAAATTATA
83675 TT
1 TT
83677 TATATTTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (19 bp):
TTATTAAATTTAAATTATA
Found at i:84147 original size:26 final size:24
Alignment explanation
Indices: 84090--84137 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
84080 TGAAAAGTAT
84090 TAAAAATTTTAAGAAAAAAAATGA
1 TAAAAATTTTAAGAAAAAAAATGA
84114 TAAAAATTTTAAGAAAAAAAATGA
1 TAAAAATTTTAAGAAAAAAAATGA
84138 AATTTCAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.08, T:0.25
Consensus pattern (24 bp):
TAAAAATTTTAAGAAAAAAAATGA
Found at i:84630 original size:31 final size:31
Alignment explanation
Indices: 84594--84698 Score: 146
Period size: 31 Copynumber: 3.5 Consensus size: 31
84584 TAATGTAATT
*
84594 TATGAAAAAATTATACTTTGATCCTCTTAAA
1 TATGAAAAAATTATACTTTAATCCTCTTAAA
84625 TATGAAAAAATTATACTTTAATCCTCTTAAA
1 TATGAAAAAATTATACTTTAATCCTCTTAAA
* *
84656 TATGAAAAAAAT-TA-TTTAATCCCCTTAAA
1 TATGAAAAAATTATACTTTAATCCTCTTAAA
84685 -AT-AATAAAATTATA
1 TATGAA-AAAATTATA
84699 AATCAGTACG
Statistics
Matches: 68, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
27 2 0.03
28 7 0.10
29 16 0.24
30 2 0.03
31 41 0.60
ACGTcount: A:0.48, C:0.11, G:0.04, T:0.37
Consensus pattern (31 bp):
TATGAAAAAATTATACTTTAATCCTCTTAAA
Found at i:87584 original size:127 final size:127
Alignment explanation
Indices: 87206--87585 Score: 706
Period size: 127 Copynumber: 3.0 Consensus size: 127
87196 AGTTAGGTCT
*
87206 TTGTAACGTATTCAACACGCACTTCCATTTGACCTATGTGTTAATTTTTTTAAATAATATTACAC
1 TTGTAACGTATTCAACACGCACTTCCATTTGACCTATGTATTAATTTTTTTAAATAATATTACAC
*
87271 TTATTTAAATTCAGTTAATTACGAAAAACAGAATCGTGGTTAGGTGTAATTTTACGGGTATA
66 TTATTTAAATTCAGTTAATTACGAAAAACAGAATCGTGGTTAGGTGTAATTTTACGGGTGTA
*
87333 TTGTAACGTATTCAACACGCACTTCCATTTGATCTATGTATTAATTTTTTTAAATAATATTACAC
1 TTGTAACGTATTCAACACGCACTTCCATTTGACCTATGTATTAATTTTTTTAAATAATATTACAC
* * *
87398 TTATTTAAATTCAGTTAATTACGAAAAACAAAATCGTGATTAGGTGTAATTCTACGGGTGTA
66 TTATTTAAATTCAGTTAATTACGAAAAACAGAATCGTGGTTAGGTGTAATTTTACGGGTGTA
87460 TTGTAACGTATTCAACACGCACTTCCATTTGACCTATGTATTAATTTTTTTAAATAATATTACAC
1 TTGTAACGTATTCAACACGCACTTCCATTTGACCTATGTATTAATTTTTTTAAATAATATTACAC
87525 TTATTTAAATTCAGTTAATTACGAAAAACAGAATCGTGGTTAGGTGTAATTTTACGGGTGT
66 TTATTTAAATTCAGTTAATTACGAAAAACAGAATCGTGGTTAGGTGTAATTTTACGGGTGT
87586 GCTTACATTA
Statistics
Matches: 243, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
127 243 1.00
ACGTcount: A:0.33, C:0.13, G:0.14, T:0.39
Consensus pattern (127 bp):
TTGTAACGTATTCAACACGCACTTCCATTTGACCTATGTATTAATTTTTTTAAATAATATTACAC
TTATTTAAATTCAGTTAATTACGAAAAACAGAATCGTGGTTAGGTGTAATTTTACGGGTGTA
Found at i:96818 original size:20 final size:21
Alignment explanation
Indices: 96779--96820 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
96769 AACATCTGAA
* *
96779 ATTTTAAGTAATATTATAATT
1 ATTTTAAGTAAAAATATAATT
96800 ATTTTAA-TAAAAATATAATT
1 ATTTTAAGTAAAAATATAATT
96820 A
1 A
96821 CTTCAATTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (21 bp):
ATTTTAAGTAAAAATATAATT
Found at i:96854 original size:17 final size:17
Alignment explanation
Indices: 96794--96854 Score: 52
Period size: 17 Copynumber: 3.4 Consensus size: 17
96784 AAGTAATATT
*
96794 ATAATTATTTTAATAAAAA
1 ATAATTATTTCAAT--AAA
* *
96813 TATAATTACTTCAATTGAA
1 -ATAATTATTTCAA-TAAA
96832 AT-ATTATTTCAATAAA
1 ATAATTATTTCAATAAA
96848 ATAATTA
1 ATAATTA
96855 AATTTTATTC
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
16 5 0.15
17 13 0.38
18 2 0.06
19 2 0.06
20 11 0.32
21 1 0.03
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.43
Consensus pattern (17 bp):
ATAATTATTTCAATAAA
Found at i:100017 original size:23 final size:23
Alignment explanation
Indices: 99991--100104 Score: 151
Period size: 23 Copynumber: 5.0 Consensus size: 23
99981 TTACTATTCA
*
99991 GCACTGTGTGTGCTTACTGATTC
1 GCACTGTGTGTGCTTACTGATTT
* *
100014 GCACTATATGTGCTTACTGATTT
1 GCACTGTGTGTGCTTACTGATTT
*
100037 GTACTGTGTGTGCTTACT-ATTTT
1 GCACTGTGTGTGCTTACTGA-TTT
* *
100060 GCACTGCGTGTGCCTACTGATTT
1 GCACTGTGTGTGCTTACTGATTT
100083 GCACTGTGTGTGCTTACT-ATTT
1 GCACTGTGTGTGCTTACTGATTT
100105 CCCCAGCACT
Statistics
Matches: 78, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
22 5 0.06
23 72 0.92
24 1 0.01
ACGTcount: A:0.15, C:0.19, G:0.23, T:0.43
Consensus pattern (23 bp):
GCACTGTGTGTGCTTACTGATTT
Found at i:101620 original size:17 final size:17
Alignment explanation
Indices: 101603--101635 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
101593 ATAATATTAT
101603 TTTAA-TAAATTTAATA
1 TTTAATTAAATTTAATA
*
101619 TTTAATTTAATTTAATA
1 TTTAATTAAATTTAATA
101636 CTTATATTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TTTAATTAAATTTAATA
Found at i:105339 original size:3 final size:3
Alignment explanation
Indices: 105331--105357 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
105321 GATATTTCAT
105331 TTG TTG TTG TTG TTG TTG TTG TTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG
105358 AAATTGCAGC
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:0.00, C:0.00, G:0.33, T:0.67
Consensus pattern (3 bp):
TTG
Found at i:105391 original size:3 final size:3
Alignment explanation
Indices: 105383--105408 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
105373 CTGCATCTGT
105383 TGC TGC TGC TGC TGC TGC TGC TGC TG
1 TGC TGC TGC TGC TGC TGC TGC TGC TG
105409 ATGATGAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.35, T:0.35
Consensus pattern (3 bp):
TGC
Found at i:106979 original size:20 final size:19
Alignment explanation
Indices: 106954--107002 Score: 66
Period size: 17 Copynumber: 2.6 Consensus size: 19
106944 TGTTTAATAA
106954 AATTTTTAAGAAAACCAATT
1 AATTTTTAA-AAAACCAATT
106974 AATTTTT--AAAACCAATT
1 AATTTTTAAAAAACCAATT
*
106991 ATTTTTTAAAAA
1 AATTTTTAAAAA
107003 TTAATTCATT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 16 0.62
19 3 0.12
20 7 0.27
ACGTcount: A:0.49, C:0.08, G:0.02, T:0.41
Consensus pattern (19 bp):
AATTTTTAAAAAACCAATT
Found at i:106986 original size:17 final size:17
Alignment explanation
Indices: 106964--107001 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
106954 AATTTTTAAG
106964 AAAACCAATTAATTTTT
1 AAAACCAATTAATTTTT
*
106981 AAAACCAATTATTTTTT
1 AAAACCAATTAATTTTT
106998 AAAA
1 AAAA
107002 ATTAATTCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (17 bp):
AAAACCAATTAATTTTT
Found at i:107904 original size:4 final size:4
Alignment explanation
Indices: 107895--107924 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
107885 AAAATTTGGA
107895 TATG TATG TATG TATG TATG TATG TATG TA
1 TATG TATG TATG TATG TATG TATG TATG TA
107925 CAAAATATCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.27, C:0.00, G:0.23, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:114605 original size:20 final size:21
Alignment explanation
Indices: 114580--114621 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
114570 ACAATTAATT
**
114580 AAAATTTTTAAAAAAT-TAAA
1 AAAATTTCAAAAAAATATAAA
114600 AAAATTTCAAAAAAATATAAA
1 AAAATTTCAAAAAAATATAAA
114621 A
1 A
114622 TTATTAACAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (21 bp):
AAAATTTCAAAAAAATATAAA
Found at i:114656 original size:20 final size:19
Alignment explanation
Indices: 114580--114662 Score: 69
Period size: 19 Copynumber: 4.3 Consensus size: 19
114570 ACAATTAATT
*
114580 AAAATTTTTAAAAAATTAA
1 AAAATTTTTAAAAAATTTA
* * *
114599 AAAAATTTCAAAAAA-ATA
1 AAAATTTTTAAAAAATTTA
* **
114617 TAAAATTATTAACATTATTTA
1 -AAAATTTTTAA-AAAATTTA
114638 AAAATTTTGTAAAAAATTTA
1 AAAATTTT-TAAAAAATTTA
114658 AAAAT
1 AAAAT
114663 ATGATAATTT
Statistics
Matches: 47, Mismatches: 13, Indels: 7
0.70 0.19 0.10
Matches are distributed among these distances:
18 1 0.02
19 21 0.45
20 20 0.43
21 5 0.11
ACGTcount: A:0.60, C:0.02, G:0.01, T:0.36
Consensus pattern (19 bp):
AAAATTTTTAAAAAATTTA
Found at i:122181 original size:14 final size:14
Alignment explanation
Indices: 122113--122174 Score: 63
Period size: 14 Copynumber: 4.4 Consensus size: 14
122103 TCAAGTTTAA
122113 GGTTTAAGGGTTTG
1 GGTTTAAGGGTTTG
* * *
122127 GGGTTATGTGGTATG
1 GGTTTAAG-GGTTTG
*
122142 AGTTT-AGGGTTTG
1 GGTTTAAGGGTTTG
122155 GGTTTAAGGGTTTG
1 GGTTTAAGGGTTTG
122169 AGGTTT
1 -GGTTT
122175 GAGGTTTAAG
Statistics
Matches: 37, Mismatches: 8, Indels: 5
0.74 0.16 0.10
Matches are distributed among these distances:
13 9 0.24
14 15 0.41
15 13 0.35
ACGTcount: A:0.15, C:0.00, G:0.42, T:0.44
Consensus pattern (14 bp):
GGTTTAAGGGTTTG
Found at i:122190 original size:42 final size:42
Alignment explanation
Indices: 122113--122195 Score: 114
Period size: 42 Copynumber: 2.0 Consensus size: 42
122103 TCAAGTTTAA
* * *
122113 GGTTTAAGGGTTTGGGGTTATGTGGTATGAGTTTAGGGTTTG
1 GGTTTAAGGGTTTGAGGTTATGAGGTATAAGTTTAGGGTTTG
*
122155 GGTTTAAGGGTTTGAGGTT-TGAGGTTTAAGATTTAGGGTTT
1 GGTTTAAGGGTTTGAGGTTATGAGGTATAAG-TTTAGGGTTT
122196 TATATTTTGG
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
41 8 0.22
42 28 0.78
ACGTcount: A:0.17, C:0.00, G:0.40, T:0.43
Consensus pattern (42 bp):
GGTTTAAGGGTTTGAGGTTATGAGGTATAAGTTTAGGGTTTG
Found at i:124730 original size:10 final size:11
Alignment explanation
Indices: 124701--124727 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
124691 AAGAAATATT
124701 TTTTTTAATAA
1 TTTTTTAATAA
124712 TTTTTTAATAA
1 TTTTTTAATAA
124723 TTTTT
1 TTTTT
124728 AATTTTAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (11 bp):
TTTTTTAATAA
Found at i:124756 original size:39 final size:38
Alignment explanation
Indices: 124702--124777 Score: 102
Period size: 39 Copynumber: 1.9 Consensus size: 38
124692 AGAAATATTT
124702 TTTTTAATAATTTTTTAATAATTTTT-AATTTTAAAAATA
1 TTTTTAATAATTTTTT--TAATTTTTAAATTTTAAAAATA
124741 TTTTT-ATAACTTTTTTTAATTTTTAAAATTTTAAAAA
1 TTTTTAATAA-TTTTTTTAATTTTT-AAATTTTAAAAA
124778 AATAATTAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
37 8 0.24
38 4 0.12
39 22 0.65
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.59
Consensus pattern (38 bp):
TTTTTAATAATTTTTTTAATTTTTAAATTTTAAAAATA
Found at i:128084 original size:39 final size:39
Alignment explanation
Indices: 128024--128844 Score: 878
Period size: 39 Copynumber: 20.8 Consensus size: 39
128014 TATTGTAGTG
*
128024 CAAAATTTATCTGTTCGTATTTTATTTTTAATCCTTTTT
1 CAAAATTTATCTGTTCGTATTTTATTTTTAATCTTTTTT
*
128063 CAAAATTTATTTGTT--T-TTATT-TTTTTAATCTTTTTTTTTT
1 CAAAATTTATCTGTTCGTATT-TTATTTTTAATC----TTTTTT
* * * *
128103 CAAAATATATTTGTTCATATTTTATTTTTAATCTTTTATG
1 CAAAATTTATCTGTTCGTATTTTATTTTTAATCTTTT-TT
* *
128143 CAAAATTTATTTGTTCGTATTTTATTTTTAATGTTTTTTT
1 CAAAATTTATCTGTTCGTATTTTATTTTTAAT-CTTTTTT
* * *
128183 CAAAATTTATCTATTTGTATTTTATTTTTAAATTTTTTTTTT
1 CAAAATTTATCTGTTCGTATTTTATTTTT-AA--TCTTTTTT
* *
128225 CAAAATTTATCTTTTCGTATTTTATTTTTAATCTCTTTT
1 CAAAATTTATCTGTTCGTATTTTATTTTTAATCTTTTTT
* * *
128264 CAAAATTTATTTGTTCGTATCTTATTTTTAATCCTTTTT
1 CAAAATTTATCTGTTCGTATTTTATTTTTAATCTTTTTT
* * * *
128303 CAATATTTATATGTTCGTTTTTTATTTTTAA-CACTTTTT
1 CAAAATTTATCTGTTCGTATTTTATTTTTAATC-TTTTTT
* * *
128342 CAAAAATTATCTATTGGTATTTTATTTTTAATCTTTTTAT
1 CAAAATTTATCTGTTCGTATTTTATTTTTAATCTTTTT-T
*
128382 GCAAAATTTATTTGTTCGTATTTTATTTTTAATAC-TTTTT
1 -CAAAATTTATCTGTTCGTATTTTATTTTTAAT-CTTTTTT
* * * *
128422 CAAAATATATTTTTTCATATTTTA-TTTTAATCTTTTTT
1 CAAAATTTATCTGTTCGTATTTTATTTTTAATCTTTTTT
* * * ** *
128460 CAAAATTTATCTTTTCATATATTATTACTAATCATTTTT
1 CAAAATTTATCTGTTCGTATTTTATTTTTAATCTTTTTT
* *
128499 CAAAATTTATCTGTTTGTATTTTATTTTTAATATTTTTT
1 CAAAATTTATCTGTTCGTATTTTATTTTTAATCTTTTTT
* *
128538 TAAAATTTATCTGTTCATATTTTATTTTTAATCTTTTTT
1 CAAAATTTATCTGTTCGTATTTTATTTTTAATCTTTTTT
**
128577 TTAAATTTATCTGTTCGTATTTTATTTTTAATCTTTTTT
1 CAAAATTTATCTGTTCGTATTTTATTTTTAATCTTTTTT
* *
128616 TAAAATTTATCTGTTCGTATTTTGTTTTTAATCTTTTTTT
1 CAAAATTTATCTGTTCGTATTTTATTTTTAATC-TTTTTT
* *
128656 CAAAATTTATTTGTTTGTATTTTATTTTTAATGC-TTTTT
1 CAAAATTTATCTGTTCGTATTTTATTTTTAAT-CTTTTTT
* * *
128695 CAATATTTATCTATTCATATTTTATTTTTAATAC-TTTTT
1 CAAAATTTATCTGTTCGTATTTTATTTTTAAT-CTTTTTT
128734 CAAAA-TTATCTTTGTT-GATATTTTATTTTTAATCTTTTTTTTT
1 CAAAATTTATC--TGTTCG-TATTTTATTTTTAATC---TTTTTT
* * *
128777 CAAAATTTATCTGTTCCTA-TTT-TTTTAAATATTTTTT
1 CAAAATTTATCTGTTCGTATTTTATTTTTAATCTTTTTT
*
128814 CAAAATTTATCTGTTTGTA-TTTATTTTTAAT
1 CAAAATTTATCTGTTCGTATTTTATTTTTAAT
128845 TTTAATCTTT
Statistics
Matches: 670, Mismatches: 79, Indels: 67
0.82 0.10 0.08
Matches are distributed among these distances:
36 11 0.02
37 30 0.04
38 46 0.07
39 329 0.49
40 139 0.21
41 44 0.07
42 44 0.07
43 22 0.03
44 5 0.01
ACGTcount: A:0.25, C:0.08, G:0.04, T:0.62
Consensus pattern (39 bp):
CAAAATTTATCTGTTCGTATTTTATTTTTAATCTTTTTT
Found at i:128524 original size:196 final size:196
Alignment explanation
Indices: 128024--128870 Score: 878
Period size: 196 Copynumber: 4.3 Consensus size: 196
128014 TATTGTAGTG
* * * * *
128024 CAAAATTTATCTGTTCGTATTTTATTTTTAATC-CTTTTTCAAAATTTATTTGTT--TTTATT-T
1 CAAAATTTATCTTTTCATATTTTAATTTTAATCTTTTTTTCAAAATTTATTTGTTCATATATTAT
* * *
128085 TTTTAATCTTTTTTTTTTCAAAATATATTTGTTCATATTTTATTTTTAAT-CTTTTATGCAAAAT
66 TTTTAATC-----TTTTTCAAAATTTATCTGTTCATATTTTATTTTTAATACTTTT-T-CAAAAA
* * * *
128149 TTATTTGTTCGTATTTTATTTTTAATGTTTTTTTCAAAATTTATCTATTTGTATTTTATTTTTAA
124 TTATCTGTTCGTATTTTATTTTTAATCTTTTTTTCAAAATTTATCTGTTCGTATTTTATTTTT-A
**
128214 ATTTTTTTTTT
188 A--TACTTTTT
* * * * *
128225 CAAAATTTATCTTTTCGTATTTTATTTTTAATC-TCTTTTCAAAATTTATTTGTTCGTATCTTAT
1 CAAAATTTATCTTTTCATATTTTAATTTTAATCTTTTTTTCAAAATTTATTTGTTCATATATTAT
* * * * *
128289 TTTTAATCCTTTTTCAATATTTATATGTTCGTTTTTTATTTTTAACACTTTTTCAAAAATTATCT
66 TTTTAAT-CTTTTTCAAAATTTATCTGTTCATATTTTATTTTTAATACTTTTTCAAAAATTATCT
* * * *
128354 ATTGGTATTTTATTTTTAATCTTTTTATGCAAAATTTATTTGTTCGTATTTTATTTTTAATACTT
130 GTTCGTATTTTATTTTTAATCTTTTT-TTCAAAATTTATCTGTTCGTATTTTATTTTTAATACTT
128419 TTT
194 TTT
* *
128422 CAAAATATATTTTTTCATATTTT-ATTTTAATC-TTTTTTCAAAATTTATCTT-TTCATATATTA
1 CAAAATTTATCTTTTCATATTTTAATTTTAATCTTTTTTTCAAAATTTAT-TTGTTCATATATTA
** ** * * *
128484 TTACTAATCATTTTTCAAAATTTATCTGTTTGTATTTTATTTTTAATATTTTTTTAAAATTTATC
65 TTTTTAATC-TTTTTCAAAATTTATCTGTTCATATTTTATTTTTAATACTTTTTCAAAAATTATC
* *
128549 TGTTCATATTTTATTTTTAATCTTTTTTT-TAAATTTATCTGTTCGTATTTTATTTTTAAT-CTT
129 TGTTCGTATTTTATTTTTAATCTTTTTTTCAAAATTTATCTGTTCGTATTTTATTTTTAATAC-T
128612 TTTT
193 TTTT
* * * ** ** *
128616 TAAAATTTATCTGTTCGTATTTTGTTTTTAATCTTTTTTTCAAAATTTATTTGTTTGTATTTTAT
1 CAAAATTTATCTTTTCATATTTTAATTTTAATCTTTTTTTCAAAATTTATTTGTTCATATATTAT
* *
128681 TTTTAATGCTTTTTCAATATTTATCTATTCATATTTTATTTTTAATACTTTTTC-AAAATTATCT
66 TTTTAAT-CTTTTTCAAAATTTATCTGTTCATATTTTATTTTTAATACTTTTTCAAAAATTATC-
* *
128745 TTGTT-GATATTTTATTTTTAATCTTTTTTTTTCAAAATTTATCTGTTCCTA-TTT-TTTTAAAT
129 -TGTTCG-TATTTTATTTTTAATC--TTTTTTTCAAAATTTATCTGTTCGTATTTTATTTTTAAT
*
128807 ATTTTTT
190 ACTTTTT
*
128814 CAAAATTTATCTGTTTGTATTTATTTTTAATTTTAATCTTTTTTTCAAAATTTATTT
1 CAAAATTTATCT-TTT-CA--TA-TTTTAATTTTAATCTTTTTTTCAAAATTTATTT
128871 TTAATATTGC
Statistics
Matches: 547, Mismatches: 74, Indels: 48
0.82 0.11 0.07
Matches are distributed among these distances:
193 1 0.00
194 52 0.10
195 20 0.04
196 178 0.33
197 49 0.09
198 23 0.04
199 47 0.09
200 75 0.14
201 56 0.10
202 2 0.00
203 35 0.06
204 8 0.01
205 1 0.00
ACGTcount: A:0.25, C:0.08, G:0.04, T:0.62
Consensus pattern (196 bp):
CAAAATTTATCTTTTCATATTTTAATTTTAATCTTTTTTTCAAAATTTATTTGTTCATATATTAT
TTTTAATCTTTTTCAAAATTTATCTGTTCATATTTTATTTTTAATACTTTTTCAAAAATTATCTG
TTCGTATTTTATTTTTAATCTTTTTTTCAAAATTTATCTGTTCGTATTTTATTTTTAATACTTTT
T
Found at i:128571 original size:22 final size:21
Alignment explanation
Indices: 128546--128649 Score: 71
Period size: 18 Copynumber: 5.2 Consensus size: 21
128536 TTTAAAATTT
128546 ATCTGTTCATATTTTATTTTTA
1 ATCTGTTC-TATTTTATTTTTA
**
128568 ATCT-TT-T-TTTTAAATTT-
1 ATCTGTTCTATTTTATTTTTA
128585 ATCTGTTCGTATTTTATTTTTA
1 ATCTGTTC-TATTTTATTTTTA
* **
128607 ATCT-TT-T-TTTAAAATTT-
1 ATCTGTTCTATTTTATTTTTA
*
128624 ATCTGTTCGTATTTTGTTTTTA
1 ATCTGTTC-TATTTTATTTTTA
128646 ATCT
1 ATCT
128650 TTTTTTCAAA
Statistics
Matches: 61, Mismatches: 11, Indels: 20
0.66 0.12 0.22
Matches are distributed among these distances:
17 8 0.13
18 19 0.31
19 2 0.03
20 2 0.03
21 18 0.30
22 12 0.20
ACGTcount: A:0.21, C:0.09, G:0.06, T:0.64
Consensus pattern (21 bp):
ATCTGTTCTATTTTATTTTTA
Found at i:129060 original size:27 final size:28
Alignment explanation
Indices: 128975--129123 Score: 101
Period size: 27 Copynumber: 5.5 Consensus size: 28
128965 TGCTGGGATG
* * * *
128975 ATAAACGCGAGG-TAGTCTGTCGGGACA
1 ATAAACACGAGGAAAGTTTGTCGAGACA
* * * *
129002 GTACACATGAGG-AAGTTTGTCGAGCCA
1 ATAAACACGAGGAAAGTTTGTCGAGACA
* *
129029 GTAAACACG-GGAAAGTTTGTTGAGACA
1 ATAAACACGAGGAAAGTTTGTCGAGACA
* ** * *
129056 ATAAATACG-GGAAAGTTCATTGAGATA
1 ATAAACACGAGGAAAGTTTGTCGAGACA
* * *
129083 GTAAACACGAGG-AAGTTTGCCGAGATA
1 ATAAACACGAGGAAAGTTTGTCGAGACA
129110 ATAAACACGAGGAA
1 ATAAACACGAGGAA
129124 GTCCTCTGGG
Statistics
Matches: 95, Mismatches: 24, Indels: 5
0.77 0.19 0.04
Matches are distributed among these distances:
26 2 0.02
27 90 0.95
28 3 0.03
ACGTcount: A:0.38, C:0.14, G:0.28, T:0.20
Consensus pattern (28 bp):
ATAAACACGAGGAAAGTTTGTCGAGACA
Found at i:129140 original size:27 final size:27
Alignment explanation
Indices: 129084--129170 Score: 79
Period size: 27 Copynumber: 3.2 Consensus size: 27
129074 ATTGAGATAG
* * * *
129084 TAAACACGAGGAAGT-TTGCCGAGATAA
1 TAAACACGAGGAAGTCCT-CTGGGATGA
129111 TAAACACGAGGAAGTCCTCTGGGATGA
1 TAAACACGAGGAAGTCCTCTGGGATGA
* * *
129138 TAAACAC-AGGGAAGTCCACTAGGATGT
1 TAAACACGA-GGAAGTCCTCTGGGATGA
129165 TAAACA
1 TAAACA
129171 TGATTTGAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
26 1 0.02
27 49 0.96
28 1 0.02
ACGTcount: A:0.39, C:0.17, G:0.25, T:0.18
Consensus pattern (27 bp):
TAAACACGAGGAAGTCCTCTGGGATGA
Found at i:152155 original size:17 final size:17
Alignment explanation
Indices: 152129--152162 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
152119 TGTAGGGATT
152129 AAATTGAAGGCAAAAAG
1 AAATTGAAGGCAAAAAG
* *
152146 AAATTTAAGGGAAAAAG
1 AAATTGAAGGCAAAAAG
152163 TATGAATTTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.59, C:0.03, G:0.24, T:0.15
Consensus pattern (17 bp):
AAATTGAAGGCAAAAAG
Found at i:152893 original size:17 final size:17
Alignment explanation
Indices: 152873--152918 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 17
152863 AGCTCATACA
* *
152873 CTTGATGGGCTTGTAGT
1 CTTGATGAGCTCGTAGT
*
152890 CTTGGTGAGCTCGTAGT
1 CTTGATGAGCTCGTAGT
*
152907 CTTGCTGAGCTC
1 CTTGATGAGCTC
152919 ACACTTCACA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.11, C:0.20, G:0.33, T:0.37
Consensus pattern (17 bp):
CTTGATGAGCTCGTAGT
Found at i:158187 original size:63 final size:66
Alignment explanation
Indices: 158091--158254 Score: 225
Period size: 67 Copynumber: 2.6 Consensus size: 66
158081 TTATTTATTT
* *
158091 ATTTATCTATATTCATAAAATAAT-AAT--A-AAATAATAAAACAAAATTAATATTA-TTT-TA-
1 ATTTATTTATATTCATAAAATAATAAATAAATAAATAATAAAACAAAATAAATATTATTTTATAT
158149 C
66 C
* *
158150 ATTTATTTATATTCATACAATAATAAATAAATAAATAATAAAATAAAATAAATATTATTTTATAT
1 ATTTATTTATATTCATAAAATAATAAATAAATAAATAATAAAACAAAATAAATATTATTTTATA-
*
158215 TT
65 TC
158217 ATTTATTTATATTCATAAAATAATAAATAAATAAATAA
1 ATTTATTTATATTCATAAAATAATAAATAAATAAATAA
158255 AAATAATAAG
Statistics
Matches: 91, Mismatches: 6, Indels: 8
0.87 0.06 0.08
Matches are distributed among these distances:
59 22 0.24
60 3 0.03
62 1 0.01
63 23 0.25
64 3 0.03
65 2 0.02
67 37 0.41
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (66 bp):
ATTTATTTATATTCATAAAATAATAAATAAATAAATAATAAAACAAAATAAATATTATTTTATAT
C
Found at i:158829 original size:38 final size:40
Alignment explanation
Indices: 158786--158870 Score: 95
Period size: 39 Copynumber: 2.2 Consensus size: 40
158776 GATTAGATTG
*
158786 CTTCAATATACACT-A-GGTCAAGGTAAGAAATTGGATGGT
1 CTTCAATATAC-CTCATGGTCAAGGTAAGAAATTGGATGAT
* ** *
158825 -TTCAATCTACCTCATGGTCGGGGTAAGAGATTGGATGAT
1 CTTCAATATACCTCATGGTCAAGGTAAGAAATTGGATGAT
158864 CTTCAAT
1 CTTCAAT
158871 TTGTCCTCTG
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
37 2 0.05
38 10 0.26
39 20 0.53
40 6 0.16
ACGTcount: A:0.31, C:0.15, G:0.24, T:0.31
Consensus pattern (40 bp):
CTTCAATATACCTCATGGTCAAGGTAAGAAATTGGATGAT
Found at i:158851 original size:39 final size:38
Alignment explanation
Indices: 158801--159098 Score: 142
Period size: 39 Copynumber: 7.6 Consensus size: 38
158791 ATATACACTA
* * *
158801 GGTCAAGGTAAGAAATTGGATGGTTTCAATCTACCTCAT
1 GGTCAGGGTAAGAAATTGGATGATTTCAATCTGCC-CAT
* * *
158840 GGTCGGGGTAAGAGATTGGATGATCTTCAATTTGTCCTC-T
1 GGTCAGGGTAAGAAATTGGATGAT-TTCAATCTG-CC-CAT
* * *
158880 GGTTAGGGTAA-AAGATTGGATTGCTTT-GATCTGCCCTAT
1 GGTCAGGGTAAGAA-ATTGGA-TGATTTCAATCTGCCC-AT
* * * * * * *
158919 AGTCGGGGTAAGAGATCGGATGATCTTTAATCTACCCTTT
1 GGTCAGGGTAAGAAATTGGATGAT-TTCAATCTGCCC-AT
* * *
158959 GGTTAGGGTAA-AAGATTGTATTG-CTTCAATCTGCCCCAT
1 GGTCAGGGTAAGAA-ATTGGA-TGATTTCAATCTG-CCCAT
* ** **
158998 GGTCGGGGTAAGAAATCAGATGATCTTCAATCTGCCTTTT
1 GGTCAGGGTAAGAAATTGGATGAT-TTCAATCTGCC-CAT
* *
159038 GGTTAGGGTAA-AAGATTGGATTG-CTTCAATCTGTCCCAT
1 GGTCAGGGTAAGAA-ATTGGA-TGATTTCAATCTG-CCCAT
* *
159077 GATCAGGGTAAGAGATTGGATG
1 GGTCAGGGTAAGAAATTGGATG
159099 CTTGTAACTT
Statistics
Matches: 190, Mismatches: 49, Indels: 41
0.68 0.17 0.15
Matches are distributed among these distances:
37 1 0.01
38 9 0.05
39 91 0.48
40 78 0.41
41 11 0.06
ACGTcount: A:0.26, C:0.15, G:0.27, T:0.33
Consensus pattern (38 bp):
GGTCAGGGTAAGAAATTGGATGATTTCAATCTGCCCAT
Found at i:158899 original size:79 final size:77
Alignment explanation
Indices: 158807--159098 Score: 334
Period size: 79 Copynumber: 3.7 Consensus size: 77
158797 ACTAGGTCAA
* * *
158807 GGTAAGAA-ATTGGATGGTTTCAATCTACCTCATGGTCGGGGTAAGAGATTGGATGATCTTCAAT
1 GGTAA-AAGATTGGATGGCTTCAATCTGCC-CATGGTCGGGGTAAGAGATCGGATGATCTTCAAT
* *
158871 TTGTCCTCTGGTTAG
64 CTG-CCTTTGGTTAG
* ** * *
158886 GGTAAAAGATTGGATTGCTTTGATCTGCCCTATAGTCGGGGTAAGAGATCGGATGATCTTTAATC
1 GGTAAAAGATTGGATGGCTTCAATCTGCCC-ATGGTCGGGGTAAGAGATCGGATGATCTTCAATC
*
158951 TACCCTTTGGTTAG
65 T-GCCTTTGGTTAG
* * * *
158965 GGTAAAAGATTGTATTGCTTCAATCTGCCCCATGGTCGGGGTAAGAAATCAGATGATCTTCAATC
1 GGTAAAAGATTGGATGGCTTCAATCTG-CCCATGGTCGGGGTAAGAGATCGGATGATCTTCAATC
159030 TGCCTTTTGGTTAG
65 TGCC-TTTGGTTAG
* * * *
159044 GGTAAAAGATTGGATTGCTTCAATCTGTCCCATGATCAGGGTAAGAGATTGGATG
1 GGTAAAAGATTGGATGGCTTCAATCTG-CCCATGGTCGGGGTAAGAGATCGGATG
159099 CTTGTAACTT
Statistics
Matches: 182, Mismatches: 26, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
78 5 0.03
79 174 0.96
80 3 0.02
ACGTcount: A:0.25, C:0.15, G:0.27, T:0.33
Consensus pattern (77 bp):
GGTAAAAGATTGGATGGCTTCAATCTGCCCATGGTCGGGGTAAGAGATCGGATGATCTTCAATCT
GCCTTTGGTTAG
Found at i:159174 original size:50 final size:50
Alignment explanation
Indices: 159120--159218 Score: 110
Period size: 50 Copynumber: 2.0 Consensus size: 50
159110 GCTCCATTTC
* * * *
159120 AGCTTCAGGAGTATAAGATTC-ATCCTTATGACTTCAATCTGCCCCTCTAT
1 AGCTTCAGGAGAATAAGATTCGCT-ATTACGACTTCAATCTGCCCCTCTAT
* * * *
159170 AGCTTTAGGTGAATGAGATTCGCTATTACGGCTTCAATCTGCCCCTCTA
1 AGCTTCAGGAGAATAAGATTCGCTATTACGACTTCAATCTGCCCCTCTA
159219 CAACTTTAGG
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
50 39 0.98
51 1 0.03
ACGTcount: A:0.24, C:0.25, G:0.17, T:0.33
Consensus pattern (50 bp):
AGCTTCAGGAGAATAAGATTCGCTATTACGACTTCAATCTGCCCCTCTAT
Found at i:161558 original size:15 final size:15
Alignment explanation
Indices: 161538--161571 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
161528 ACCTTTAAGC
161538 CCAAACCCAATTGAA
1 CCAAACCCAATTGAA
*
161553 CCAAACTCAATTGAA
1 CCAAACCCAATTGAA
161568 CCAA
1 CCAA
161572 GTCCAAACCC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.47, C:0.32, G:0.06, T:0.15
Consensus pattern (15 bp):
CCAAACCCAATTGAA
Found at i:161616 original size:14 final size:14
Alignment explanation
Indices: 161597--161651 Score: 69
Period size: 14 Copynumber: 4.0 Consensus size: 14
161587 AAGTCAAACA
161597 GTTGATCGTTGACT
1 GTTGATCGTTGACT
*
161611 GTTGATTGTTGA-T
1 GTTGATCGTTGACT
*
161624 CGTTGATTGTTGACT
1 -GTTGATCGTTGACT
161639 -TTGATCGTTGACT
1 GTTGATCGTTGACT
161652 TTTTTCGAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
13 13 0.35
14 23 0.62
15 1 0.03
ACGTcount: A:0.15, C:0.11, G:0.27, T:0.47
Consensus pattern (14 bp):
GTTGATCGTTGACT
Found at i:161623 original size:21 final size:21
Alignment explanation
Indices: 161597--161651 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
161587 AAGTCAAACA
*
161597 GTTGATCGTTGACTGTTGATT
1 GTTGATCGTTGACTGTTGACT
*
161618 GTTGATCGTTGATTGTTGACT
1 GTTGATCGTTGACTGTTGACT
161639 -TTGATCGTTGACT
1 GTTGATCGTTGACT
161652 TTTTTCGAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
20 12 0.39
21 19 0.61
ACGTcount: A:0.15, C:0.11, G:0.27, T:0.47
Consensus pattern (21 bp):
GTTGATCGTTGACTGTTGACT
Found at i:166358 original size:28 final size:28
Alignment explanation
Indices: 166322--166449 Score: 134
Period size: 28 Copynumber: 4.6 Consensus size: 28
166312 AATAGATTAA
*
166322 CGCTCTACCCGAGCCA-AAAGCAAAATAT
1 CGCTCTACCCGAGCCAGAAA-CATAATAT
*
166350 CGTTCTACCCGAGCCAGAAACATAATAT
1 CGCTCTACCCGAGCCAGAAACATAATAT
* *
166378 CGCTCTATCCGATCCAGAAACATAATAT
1 CGCTCTACCCGAGCCAGAAACATAATAT
* * * * *
166406 CGCTCTATCCGATCCATAAACA-GATCAA
1 CGCTCTACCCGAGCCAGAAACATAAT-AT
*
166434 AGCTCTACCCGAGCCA
1 CGCTCTACCCGAGCCA
166450 TAATTTGAAG
Statistics
Matches: 87, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
27 2 0.02
28 82 0.94
29 3 0.03
ACGTcount: A:0.35, C:0.32, G:0.13, T:0.20
Consensus pattern (28 bp):
CGCTCTACCCGAGCCAGAAACATAATAT
Found at i:167016 original size:68 final size:68
Alignment explanation
Indices: 166932--167067 Score: 272
Period size: 68 Copynumber: 2.0 Consensus size: 68
166922 ATTTTCCTAT
166932 TTAACAACCAAAATTAATAATCTATCATAAAATTCCAAGAATGAACAAAAATCATTAATGACATA
1 TTAACAACCAAAATTAATAATCTATCATAAAATTCCAAGAATGAACAAAAATCATTAATGACATA
166997 ACC
66 ACC
167000 TTAACAACCAAAATTAATAATCTATCATAAAATTCCAAGAATGAACAAAAATCATTAATGACATA
1 TTAACAACCAAAATTAATAATCTATCATAAAATTCCAAGAATGAACAAAAATCATTAATGACATA
167065 ACC
66 ACC
167068 CACCACATTT
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 68 1.00
ACGTcount: A:0.53, C:0.18, G:0.04, T:0.25
Consensus pattern (68 bp):
TTAACAACCAAAATTAATAATCTATCATAAAATTCCAAGAATGAACAAAAATCATTAATGACATA
ACC
Found at i:168130 original size:101 final size:101
Alignment explanation
Indices: 168008--168208 Score: 330
Period size: 101 Copynumber: 2.0 Consensus size: 101
167998 CACATATAAA
* * *
168008 AAGACTCCGTAAATATTTAATAATAATATTTATGGTCCTATATTTTAGAAACGAGGTCCCGATAC
1 AAGACTCCGTAAATATTTAATAAAAATATTTACGGTCCTAAATTTTAGAAACGAGGTCCCGATAC
*
168073 TTCATTTTTTAAAACCACTTGACTTTTGAACCAAAT
66 CTCATTTTTTAAAACCACTTGACTTTTGAACCAAAT
* * *
168109 AAGACTCTGTAAATATTTAATAAAAATATTTACGGTCCTAAATTTTAGAAATGAGGTCTCGATAC
1 AAGACTCCGTAAATATTTAATAAAAATATTTACGGTCCTAAATTTTAGAAACGAGGTCCCGATAC
*
168174 CTCATTTTTTAAAACCACTTGACTTTTGAATCAAA
66 CTCATTTTTTAAAACCACTTGACTTTTGAACCAAA
168209 CCACTTATAA
Statistics
Matches: 92, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
101 92 1.00
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.36
Consensus pattern (101 bp):
AAGACTCCGTAAATATTTAATAAAAATATTTACGGTCCTAAATTTTAGAAACGAGGTCCCGATAC
CTCATTTTTTAAAACCACTTGACTTTTGAACCAAAT
Found at i:168732 original size:81 final size:82
Alignment explanation
Indices: 168576--168732 Score: 178
Period size: 81 Copynumber: 1.9 Consensus size: 82
168566 ATGTTTAACA
* * *
168576 GATTTTATTTCCAAAATGAGAATAAGTAAATAAATTTGTTTTGAGATTTATTTCCACCGTTTAAT
1 GATTTTATTTCCAAAATGAGAATAAGTAAATAAATCTGTTTTGAGATTTATTTCCACCGATTAAC
* *
168641 AGATTTTATTCCAGTTT
66 AAATTATATTCCAGTTT
* * * *
168658 GATTTTATTTCC-AAAT-ATAATAAGTTGACTAAATCTGTTTCTG-GATTTA-TTCTCGCCGATT
1 GATTTTATTTCCAAAATGAGAATAAG-TAAATAAATCTGTTT-TGAGATTTATTTC-CACCGATT
168719 AACAAATTATATTC
63 AACAAATTATATTC
168733 TATATTTGGA
Statistics
Matches: 63, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
80 10 0.16
81 39 0.62
82 14 0.22
ACGTcount: A:0.32, C:0.12, G:0.11, T:0.44
Consensus pattern (82 bp):
GATTTTATTTCCAAAATGAGAATAAGTAAATAAATCTGTTTTGAGATTTATTTCCACCGATTAAC
AAATTATATTCCAGTTT
Found at i:172063 original size:24 final size:24
Alignment explanation
Indices: 172046--172369 Score: 423
Period size: 24 Copynumber: 13.5 Consensus size: 24
172036 GTGGCTTATA
*
172046 AGCATAAACATATAGTGGCTGACG
1 AGCATAAACGTATAGTGGCTGACG
* * *
172070 AGCATAAACATAAAGTGACTGACG
1 AGCATAAACGTATAGTGGCTGACG
*
172094 AGCATAAACGTAAAGTGGCTGACG
1 AGCATAAACGTATAGTGGCTGACG
* * *
172118 ATCATAAACATATAGTGGCTGATG
1 AGCATAAACGTATAGTGGCTGACG
172142 AGCATAAACGTATAGTGGCTGACG
1 AGCATAAACGTATAGTGGCTGACG
* * * *
172166 AGCGTAAATGTATAGTGGCTAATG
1 AGCATAAACGTATAGTGGCTGACG
* *
172190 ATCATAAACGTAAAGTGGCTGACG
1 AGCATAAACGTATAGTGGCTGACG
*
172214 AGCATAAACGTATAGTTGCTGACG
1 AGCATAAACGTATAGTGGCTGACG
* *
172238 AGCATAAACATAAAGTGGCTGACG
1 AGCATAAACGTATAGTGGCTGACG
*
172262 AGCATAAACGTATAGTTGCTGACG
1 AGCATAAACGTATAGTGGCTGACG
* *
172286 AGCATAAACATAAAGTGGCTGACG
1 AGCATAAACGTATAGTGGCTGACG
* * *
172310 AGCATAAATGTAAAGCGGCTGACG
1 AGCATAAACGTATAGTGGCTGACG
*
172334 AGCATAAACGTATAGTGGTTGACG
1 AGCATAAACGTATAGTGGCTGACG
*
172358 AGAATAAACGTA
1 AGCATAAACGTA
172370 ATCGAAACTT
Statistics
Matches: 259, Mismatches: 41, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 259 1.00
ACGTcount: A:0.38, C:0.15, G:0.26, T:0.21
Consensus pattern (24 bp):
AGCATAAACGTATAGTGGCTGACG
Found at i:174706 original size:29 final size:29
Alignment explanation
Indices: 174671--174735 Score: 112
Period size: 29 Copynumber: 2.2 Consensus size: 29
174661 TTTTGTTGTG
*
174671 CACATGGGCTGGCACAAGGTCGTGTGCCA
1 CACATGGGCTGACACAAGGTCGTGTGCCA
*
174700 CACATGGGCTGACACACGGTCGTGTGCCA
1 CACATGGGCTGACACAAGGTCGTGTGCCA
174729 CACATGG
1 CACATGG
174736 CCTAGCCATA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.22, C:0.29, G:0.32, T:0.17
Consensus pattern (29 bp):
CACATGGGCTGACACAAGGTCGTGTGCCA
Found at i:177325 original size:22 final size:24
Alignment explanation
Indices: 177299--177342 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
177289 TTTGTTTTCT
177299 ATTTAATA-AAAAAAT-ATTTATC
1 ATTTAATATAAAAAATAATTTATC
*
177321 ATTTAATATAATAAATAATTTA
1 ATTTAATATAAAAAATAATTTA
177343 AAATTATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 8 0.42
23 6 0.32
24 5 0.26
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (24 bp):
ATTTAATATAAAAAATAATTTATC
Found at i:177620 original size:21 final size:21
Alignment explanation
Indices: 177582--177621 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
177572 ATATTACTGC
*
177582 TATAATATACTATTTCACTTT
1 TATAATATACTATCTCACTTT
177603 TATAATA-ACTAATCTCACT
1 TATAATATACT-ATCTCACT
177622 ATCACTATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.38, C:0.17, G:0.00, T:0.45
Consensus pattern (21 bp):
TATAATATACTATCTCACTTT
Done.