Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001716.1 Hibiscus syriacus cultivar Beakdansim tig00003476_pilon, 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: 117158
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:4003 original size:60 final size:61
Alignment explanation
Indices: 3845--4018 Score: 159
Period size: 60 Copynumber: 2.9 Consensus size: 61
3835 GTCCTTAAAT
* * *
3845 TATGACCTTCATTCTAAATT-ATTCCCTAATCTTTT-AA-ATATTCTAATTTCATCCCTAAAA
1 TATGATCTTCATTCTAAATTGA-TCCCTAAACTTTTGAACAT-TTCTAATTTCATCCCCAAAA
* * * *
3905 TATGAAT-ATCATTCTAAATTTG-T-CCTCATAA-TTCTGAACATTTC-ATTTTCATCCCCAAAC
1 TATG-ATCTTCATTCTAAA-TTGATCCCT-A-AACTTTTGAACATTTCTAATTTCATCCCCAAAA
*
3965 TATGATCTTCATTCTAAATTGATCCCTAAACTTTTGAACATTT-TAATTTTATCC
1 TATGATCTTCATTCTAAATTGATCCCTAAACTTTTGAACATTTCTAATTTCATCC
4019 AACTTATATG
Statistics
Matches: 91, Mismatches: 11, Indels: 24
0.72 0.09 0.19
Matches are distributed among these distances:
59 10 0.11
60 67 0.74
61 12 0.13
62 2 0.02
ACGTcount: A:0.32, C:0.21, G:0.04, T:0.43
Consensus pattern (61 bp):
TATGATCTTCATTCTAAATTGATCCCTAAACTTTTGAACATTTCTAATTTCATCCCCAAAA
Found at i:4257 original size:60 final size:59
Alignment explanation
Indices: 4193--4329 Score: 154
Period size: 60 Copynumber: 2.3 Consensus size: 59
4183 CCAATTCAAC
* *
4193 ATGAGAGTCGTAGTTTAAGGATGAAA-TTGGA-TTGTTCAAAAGTTTAAAGACTAATTT-AGA
1 ATGAG-GTCATAGTTTAAGGATGAAATTTGAACTT-TT-AAAAGTTTAAAGACTAATTTGA-A
* * *
4253 ATGAGGCTCATAGTTTGATGATGAAATTTGAACTTTTAAAAGTTTAAGGACTAATTTGAA
1 ATGAGG-TCATAGTTTAAGGATGAAATTTGAACTTTTAAAAGTTTAAAGACTAATTTGAA
4313 ATGAGGGTCATAGTTTA
1 ATGA-GGTCATAGTTTA
4330 GGGGCATATC
Statistics
Matches: 66, Mismatches: 6, Indels: 10
0.80 0.07 0.12
Matches are distributed among these distances:
59 1 0.02
60 54 0.82
61 9 0.14
62 2 0.03
ACGTcount: A:0.36, C:0.06, G:0.23, T:0.35
Consensus pattern (59 bp):
ATGAGGTCATAGTTTAAGGATGAAATTTGAACTTTTAAAAGTTTAAAGACTAATTTGAA
Found at i:4629 original size:23 final size:25
Alignment explanation
Indices: 4586--4635 Score: 68
Period size: 23 Copynumber: 2.1 Consensus size: 25
4576 TTTTACTATT
4586 TAAATTTATAAAAAAAACTAAA-TA
1 TAAATTTATAAAAAAAACTAAAGTA
* *
4610 TAAATTT-TAAAACAATCTAAAGTA
1 TAAATTTATAAAAAAAACTAAAGTA
4634 TA
1 TA
4636 TTTTACGCAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 12 0.52
24 11 0.48
ACGTcount: A:0.60, C:0.06, G:0.02, T:0.32
Consensus pattern (25 bp):
TAAATTTATAAAAAAAACTAAAGTA
Found at i:4857 original size:21 final size:21
Alignment explanation
Indices: 4816--4859 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
4806 TTAATAAAAA
* *
4816 TATTTAAAATATCATTATTTT
1 TATTTAAAACATAATTATTTT
4837 TATTTAAAACACTAATT-TTTT
1 TATTTAAAACA-TAATTATTTT
4858 TA
1 TA
4860 ATATTTTTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.39, C:0.07, G:0.00, T:0.55
Consensus pattern (21 bp):
TATTTAAAACATAATTATTTT
Found at i:14430 original size:2 final size:2
Alignment explanation
Indices: 14423--14456 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
14413 ACCCAGAAGC
14423 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
14457 TTTATCTTTT
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:17510 original size:13 final size:13
Alignment explanation
Indices: 17492--17516 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17482 CATAGTTAAA
17492 CAGTCTTCATATG
1 CAGTCTTCATATG
17505 CAGTCTTCATAT
1 CAGTCTTCATAT
17517 ACGCGTCTGT
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:0.24, C:0.24, G:0.12, T:0.40
Consensus pattern (13 bp):
CAGTCTTCATATG
Found at i:22045 original size:2 final size:2
Alignment explanation
Indices: 22038--22078 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
22028 AACAATATTA
22038 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
22079 ACACTATTTT
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:29765 original size:163 final size:164
Alignment explanation
Indices: 29452--29765 Score: 420
Period size: 163 Copynumber: 1.9 Consensus size: 164
29442 CTTTACGGAA
* * * *
29452 TTTTTTAATGGTCATTACGTTACGGGCACCTAAAATGTTAACCTTTGTAACGTTAGACATCTGAA
1 TTTTTTAATGGTCATTACATTACGGGCACCTAAAATATTAACCTTTGTAACATTAGACACCTGAA
* ** * * *
29517 TTATTCAAAAAAATAGTTTGGGCACCTATTTGTGAAAAGTGGTTTAGTTTATACACACATTTTAT
66 TGATTCAAAAAAATAGTTTGAACACCTATTTATGAAAAGTGATTTAGTTTAGACACACATTTTAT
*
29582 AGTTAAGCCTTTGAAAAGAGAGGCTTCACGGGGT
131 AATTAAGCCTTTGAAAAGAGAGGCTTCACGGGGT
* *
29616 TTTTTTAAT-GTCTATTACATTGCGGGCACCTAAAATATTAACGTTTGTAACATTAGACACCT-A
1 TTTTTTAATGGTC-ATTACATTACGGGCACCTAAAATATTAACCTTTGTAACATTAGACACCTGA
* * **
29679 GATGATTC-AAAAAATAGTTTGAACACTTATTTATGAAAA-TCGATTTAGTTTAGATACTTATTT
65 -ATGATTCAAAAAAATAGTTTGAACACCTATTTATGAAAAGT-GATTTAGTTTAGACACACATTT
29742 TATAATTAAGCCTTTGAAAAGAGA
128 TATAATTAAGCCTTTGAAAAGAGA
29766 AGTCTTTTAT
Statistics
Matches: 130, Mismatches: 17, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
162 1 0.01
163 71 0.55
164 58 0.45
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.37
Consensus pattern (164 bp):
TTTTTTAATGGTCATTACATTACGGGCACCTAAAATATTAACCTTTGTAACATTAGACACCTGAA
TGATTCAAAAAAATAGTTTGAACACCTATTTATGAAAAGTGATTTAGTTTAGACACACATTTTAT
AATTAAGCCTTTGAAAAGAGAGGCTTCACGGGGT
Found at i:31931 original size:23 final size:24
Alignment explanation
Indices: 31886--31932 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
31876 ATTTTTTCCA
*
31886 TATATTAATATTTGTATGGTGTAT
1 TATATTAATATTTGTATAGTGTAT
* *
31910 TATATTAA-ATTTTTATATTGTAT
1 TATATTAATATTTGTATAGTGTAT
31933 ATTTCATAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (24 bp):
TATATTAATATTTGTATAGTGTAT
Found at i:32474 original size:25 final size:25
Alignment explanation
Indices: 32446--32494 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
32436 TAAACTAATT
32446 TGTGTAGGTATAATTTCGACCCACC
1 TGTGTAGGTATAATTTCGACCCACC
32471 TGTGTAGGTATAATTTCGACCCAC
1 TGTGTAGGTATAATTTCGACCCAC
32495 ATTCTTCATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.33
Consensus pattern (25 bp):
TGTGTAGGTATAATTTCGACCCACC
Found at i:41720 original size:16 final size:16
Alignment explanation
Indices: 41699--41735 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
41689 TTCCTCTATG
*
41699 ATATTGTTCTTTAACA
1 ATATTGTTCCTTAACA
41715 ATATTGTTCCTTAACA
1 ATATTGTTCCTTAACA
41731 ATATT
1 ATATT
41736 CTATAATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.32, C:0.14, G:0.05, T:0.49
Consensus pattern (16 bp):
ATATTGTTCCTTAACA
Found at i:41767 original size:26 final size:26
Alignment explanation
Indices: 41714--41767 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
41704 GTTCTTTAAC
* *
41714 AATATTGTTCCTTAACAATATTCTAT
1 AATATTGTTCCTTAACAATATCCAAT
41740 AATATTGTTCCTTAACAAGT-TCCAAT
1 AATATTGTTCCTTAACAA-TATCCAAT
41766 AA
1 AA
41768 AGCATTTCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 24 0.96
27 1 0.04
ACGTcount: A:0.37, C:0.17, G:0.06, T:0.41
Consensus pattern (26 bp):
AATATTGTTCCTTAACAATATCCAAT
Found at i:47481 original size:21 final size:21
Alignment explanation
Indices: 47439--47481 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
47429 TTTCTGGGCT
* *
47439 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
* *
47460 AGGGGAATCGATCCCCCCTCA
1 AGGGGAATCGATACCCACTCA
47481 A
1 A
47482 ACGAATATGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.30, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:48512 original size:30 final size:30
Alignment explanation
Indices: 48478--48610 Score: 266
Period size: 30 Copynumber: 4.4 Consensus size: 30
48468 GGTTCTTAGA
48478 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
48508 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
48538 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
48568 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
48598 GACCTCTGGATAG
1 GACCTCTGGATAG
48611 GTCCTTCGGA
Statistics
Matches: 103, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 103 1.00
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.32
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGGATCTTTAT
Found at i:54929 original size:29 final size:30
Alignment explanation
Indices: 54871--54938 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 30
54861 GAGAGTAGTT
* *
54871 TGATTGAATCAATTAAAAAGTTTGGTGGTC
1 TGATTGATTCAATTAAAAAGTTCGGTGGTC
*
54901 TGATTGATTCAATT-GAAAGTTCGGTGGTC
1 TGATTGATTCAATTAAAAAGTTCGGTGGTC
**
54930 AAATTGATT
1 TGATTGATT
54939 TTTGACCATA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
29 20 0.61
30 13 0.39
ACGTcount: A:0.31, C:0.07, G:0.24, T:0.38
Consensus pattern (30 bp):
TGATTGATTCAATTAAAAAGTTCGGTGGTC
Found at i:55304 original size:8 final size:9
Alignment explanation
Indices: 55270--55301 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
55260 ACTAGATCCT
*
55270 ATTTTTCAA
1 ATTTTTAAA
55279 ATTTTTAAA
1 ATTTTTAAA
55288 ATTTTTAAA
1 ATTTTTAAA
55297 ATTTT
1 ATTTT
55302 AAATCAATGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (9 bp):
ATTTTTAAA
Found at i:57462 original size:33 final size:33
Alignment explanation
Indices: 57420--57494 Score: 150
Period size: 33 Copynumber: 2.3 Consensus size: 33
57410 AAAGCAGTCA
57420 ATATTTTGTATAGATGTACGGATTCAATTGTAT
1 ATATTTTGTATAGATGTACGGATTCAATTGTAT
57453 ATATTTTGTATAGATGTACGGATTCAATTGTAT
1 ATATTTTGTATAGATGTACGGATTCAATTGTAT
57486 ATATTTTGT
1 ATATTTTGT
57495 TCACTTTAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.29, C:0.05, G:0.17, T:0.48
Consensus pattern (33 bp):
ATATTTTGTATAGATGTACGGATTCAATTGTAT
Found at i:57822 original size:21 final size:22
Alignment explanation
Indices: 57769--57822 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
57759 ATAATTATTT
*
57769 AAAAAATTAAATAAAAATATCAA
1 AAAAAATT-AGTAAAAATATCAA
* *
57792 AAATATTTAGTAAAAA-ATCAA
1 AAAAAATTAGTAAAAATATCAA
57813 AAAAAATTAG
1 AAAAAATTAG
57823 GTTGAATCGG
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 13 0.50
22 7 0.27
23 6 0.23
ACGTcount: A:0.69, C:0.04, G:0.04, T:0.24
Consensus pattern (22 bp):
AAAAAATTAGTAAAAATATCAA
Found at i:60710 original size:25 final size:22
Alignment explanation
Indices: 60662--60711 Score: 55
Period size: 24 Copynumber: 2.2 Consensus size: 22
60652 AAATTATCCG
* *
60662 TTTTAATATTTATACTTTTATT
1 TTTTAATATATATACATTTATT
*
60684 TTTTAATCATATATAACATTTAGT
1 TTTTAAT-ATATAT-ACATTTATT
60708 TTTT
1 TTTT
60712 GTTTCATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 7 0.30
23 5 0.22
24 11 0.48
ACGTcount: A:0.30, C:0.06, G:0.02, T:0.62
Consensus pattern (22 bp):
TTTTAATATATATACATTTATT
Found at i:72065 original size:16 final size:15
Alignment explanation
Indices: 72040--72070 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
72030 GGAAAAAATG
72040 AATAATAAATAATAA
1 AATAATAAATAATAA
72055 AATAGATAAATAATAA
1 AATA-ATAAATAATAA
72071 TAAATAATGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (15 bp):
AATAATAAATAATAA
Found at i:72552 original size:33 final size:33
Alignment explanation
Indices: 72510--72576 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
72500 TTTATGCTTC
72510 AGTTTTAGTGTTTCAATAGGAATCAAATACGTT
1 AGTTTTAGTGTTTCAATAGGAATCAAATACGTT
*
72543 AGTTTTAGTGTTTCAATAGGATTCAAATACGTT
1 AGTTTTAGTGTTTCAATAGGAATCAAATACGTT
72576 A
1 A
72577 TTTATTTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.33, C:0.09, G:0.18, T:0.40
Consensus pattern (33 bp):
AGTTTTAGTGTTTCAATAGGAATCAAATACGTT
Found at i:72644 original size:3 final size:3
Alignment explanation
Indices: 72636--72697 Score: 94
Period size: 3 Copynumber: 21.3 Consensus size: 3
72626 AAACAAAAGA
72636 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA- ATAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT
72684 AAT -AT AAT -AT AAT A
1 AAT AAT AAT AAT AAT A
72698 TTTTTATAGA
Statistics
Matches: 55, Mismatches: 0, Indels: 8
0.87 0.00 0.13
Matches are distributed among these distances:
2 5 0.09
3 49 0.89
4 1 0.02
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:73930 original size:128 final size:126
Alignment explanation
Indices: 73775--74032 Score: 426
Period size: 128 Copynumber: 2.0 Consensus size: 126
73765 TTCAATCTTT
*
73775 ATTATTTATATAATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATTAGG
1 ATTATTTATATAATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGG
* *
73840 ATCTGACATGTGTTAGCACATGATCATGACACGTGTCATTGGTGACACATGTTACCACCTA
66 ATCTGACATGTGTTAACACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTA
*
73901 ATTATTTATATGCTATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCA
1 ATTATTTATAT--AATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCA
* * * *
73966 GGATCTGACATGTGTTAACACATGATCATGATATGTGTTATTGGTGACACATGTCACCTCCTA
64 GGATCTGACATGTGTTAACACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTA
74029 ATTA
1 ATTA
74033 GAAGAAAATT
Statistics
Matches: 122, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
126 11 0.09
128 111 0.91
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (126 bp):
ATTATTTATATAATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGG
ATCTGACATGTGTTAACACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTA
Found at i:74389 original size:28 final size:27
Alignment explanation
Indices: 74358--74420 Score: 63
Period size: 28 Copynumber: 2.3 Consensus size: 27
74348 AGTTGATACA
*
74358 ATATTTTAAAAGAATAAATTTAAGATTT
1 ATATTTTAAAA-AATAAATTTAAGAATT
** * *
74386 ATATATTTTTAAACTAAATTTAATAATT
1 ATAT-TTTAAAAAATAAATTTAAGAATT
74414 ATATTTT
1 ATATTTT
74421 TCATATTTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
27 3 0.10
28 21 0.72
29 5 0.17
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (27 bp):
ATATTTTAAAAAATAAATTTAAGAATT
Found at i:74521 original size:16 final size:18
Alignment explanation
Indices: 74500--74533 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
74490 ATTTCTTATT
74500 AAAAATA-AAAT-ATTCA
1 AAAAATATAAATGATTCA
74516 AAAAATATAAATGATTCA
1 AAAAATATAAATGATTCA
74534 TACATTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (18 bp):
AAAAATATAAATGATTCA
Found at i:74584 original size:16 final size:16
Alignment explanation
Indices: 74563--74598 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
74553 TTTTTTTATT
74563 TATACATCTAAATAAA
1 TATACATCTAAATAAA
* *
74579 TATACATTTATATAAA
1 TATACATCTAAATAAA
74595 TATA
1 TATA
74599 TTTTATTCGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.39
Consensus pattern (16 bp):
TATACATCTAAATAAA
Found at i:74677 original size:21 final size:21
Alignment explanation
Indices: 74653--74695 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
74643 TATTACCTTA
74653 AATTGAAGTATTTTAGAATTT
1 AATTGAAGTATTTTAGAATTT
74674 AATTGAAGTATTTTAGAATTT
1 AATTGAAGTATTTTAGAATTT
74695 A
1 A
74696 GGGTTTAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.40, C:0.00, G:0.14, T:0.47
Consensus pattern (21 bp):
AATTGAAGTATTTTAGAATTT
Found at i:74713 original size:35 final size:35
Alignment explanation
Indices: 74664--74749 Score: 100
Period size: 35 Copynumber: 2.5 Consensus size: 35
74654 ATTGAAGTAT
** * *
74664 TTTAGAATTTAATTGAAGTATTTTAGAATTTAGGG
1 TTTAGAATAAAATTGAAGTACTTTAGAAATTAGGG
* * *
74699 TTTAGAATAAAATTGAATTACTTTGGAAATTGGGG
1 TTTAGAATAAAATTGAAGTACTTTAGAAATTAGGG
*
74734 TTTAGAATGAAATTGA
1 TTTAGAATAAAATTGA
74750 TGACTGTTTT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 43 1.00
ACGTcount: A:0.37, C:0.01, G:0.21, T:0.41
Consensus pattern (35 bp):
TTTAGAATAAAATTGAAGTACTTTAGAAATTAGGG
Found at i:77794 original size:37 final size:36
Alignment explanation
Indices: 77709--77810 Score: 154
Period size: 34 Copynumber: 2.9 Consensus size: 36
77699 TTTCGTCCTA
77709 CTAGGATTCAAACTCCTAAAAATAAGATAGAA-TTT
1 CTAGGATTCAAACTCCTAAAAATAAGATAGAATTTT
* *
77744 -TAGGATTCAAACTCCTAAAGATATGATAGAATTTT
1 CTAGGATTCAAACTCCTAAAAATAAGATAGAATTTT
*
77779 GCTAGGATTCAAACTCCTAAAAATAGGATAGA
1 -CTAGGATTCAAACTCCTAAAAATAAGATAGA
77811 GTTCTACTAT
Statistics
Matches: 60, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
34 29 0.48
35 3 0.05
37 28 0.47
ACGTcount: A:0.43, C:0.14, G:0.15, T:0.28
Consensus pattern (36 bp):
CTAGGATTCAAACTCCTAAAAATAAGATAGAATTTT
Found at i:77830 original size:37 final size:35
Alignment explanation
Indices: 77709--77844 Score: 157
Period size: 37 Copynumber: 3.8 Consensus size: 35
77699 TTTCGTCCTA
*
77709 CTAGGATTCAAACTCCTAAAAATAAGATAGAATTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTT
* *
77744 -TAGGATTCAAACTCCTAAAGATATGATAGAATTTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAA-TTT
*
77779 GCTAGGATTCAAACTCCTAAAAATAGGATAGAGTTCT
1 -CTAGGATTCAAACTCCTAAAAATAGGATAGAATT-T
** * *
77816 ACTATTATTTAAACTCCTAAAGATAGGAT
1 -CTAGGATTCAAACTCCTAAAAATAGGAT
77845 CCACAAGCAC
Statistics
Matches: 87, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
34 29 0.33
35 3 0.03
36 2 0.02
37 53 0.61
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.31
Consensus pattern (35 bp):
CTAGGATTCAAACTCCTAAAAATAGGATAGAATTT
Found at i:78261 original size:2 final size:2
Alignment explanation
Indices: 78256--78308 Score: 97
Period size: 2 Copynumber: 26.5 Consensus size: 2
78246 TTAGTGTTAT
78256 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
78298 TA TT TA TA TA T
1 TA TA TA TA TA T
78309 TTCCTATTTT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:78438 original size:16 final size:18
Alignment explanation
Indices: 78417--78451 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
78407 TTTACTCATT
78417 TATTTAT-CTAT-TTTTA
1 TATTTATCCTATATTTTA
78433 TATTTATCCTATATTTTA
1 TATTTATCCTATATTTTA
78451 T
1 T
78452 GTTTTTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 4 0.24
18 6 0.35
ACGTcount: A:0.26, C:0.09, G:0.00, T:0.66
Consensus pattern (18 bp):
TATTTATCCTATATTTTA
Found at i:81647 original size:16 final size:14
Alignment explanation
Indices: 81621--81717 Score: 63
Period size: 16 Copynumber: 6.4 Consensus size: 14
81611 AGATCCAATC
81621 AAGAACAAAAAAGAA
1 AAGAACAAAAAA-AA
81636 AAGAAGCAAAAAAAA
1 AAGAA-CAAAAAAAA
* *
81651 AACAA-AGAAAAACA
1 AAGAACA-AAAAAAA
81665 AAGAA-AAAAGAGAAA
1 AAGAACAAAA-A-AAA
81680 CAAGAACAAAAGAAAAA
1 -AAGAAC-AAA-AAAAA
*
81697 AAGAGCAAAAATCAAA
1 AAGAACAAAAA--AAA
81713 AAGAA
1 AAGAA
81718 AAAGGGACAA
Statistics
Matches: 66, Mismatches: 6, Indels: 19
0.73 0.07 0.21
Matches are distributed among these distances:
13 4 0.06
14 14 0.21
15 16 0.24
16 24 0.36
17 3 0.05
18 4 0.06
19 1 0.02
ACGTcount: A:0.77, C:0.08, G:0.13, T:0.01
Consensus pattern (14 bp):
AAGAACAAAAAAAA
Found at i:81649 original size:17 final size:15
Alignment explanation
Indices: 81627--81700 Score: 69
Period size: 16 Copynumber: 4.5 Consensus size: 15
81617 AATCAAGAAC
81627 AAAAAAGAAAAGAAGCA
1 AAAAAAGAAAA-AAG-A
81644 AAAAAA-AAACAAAGAA
1 AAAAAAGAAA-AAAG-A
81660 AAACAAAGAAAAAAGA
1 AAA-AAAGAAAAAAGA
*
81676 GAAACAAGAACAAAAGA
1 -AAAAAAGAA-AAAAGA
81693 AAAAAAGA
1 AAAAAAGA
81701 GCAAAAATCA
Statistics
Matches: 49, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
16 23 0.47
17 23 0.47
18 3 0.06
ACGTcount: A:0.80, C:0.07, G:0.14, T:0.00
Consensus pattern (15 bp):
AAAAAAGAAAAAAGA
Found at i:81661 original size:10 final size:10
Alignment explanation
Indices: 81648--81672 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
81638 GAAGCAAAAA
81648 AAAAACAAAG
1 AAAAACAAAG
81658 AAAAACAAAG
1 AAAAACAAAG
81668 AAAAA
1 AAAAA
81673 AGAGAAACAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.84, C:0.08, G:0.08, T:0.00
Consensus pattern (10 bp):
AAAAACAAAG
Found at i:81668 original size:34 final size:33
Alignment explanation
Indices: 81621--81707 Score: 88
Period size: 34 Copynumber: 2.5 Consensus size: 33
81611 AGATCCAATC
81621 AAGAACAAAAAAGAAAAGAAGCA-AAAAAAAAAC-A
1 AAGAA-AAAAAAGAAAA-AAG-AGAAAAAAAAACAA
* *
81655 AAGAAAAACAAAGAAAAAAGAGAAACAAGAACAA
1 AAGAAAAA-AAAGAAAAAAGAGAAAAAAAAACAA
*
81689 AAGAAAAAAAGAGCAAAAA
1 AAGAAAAAAA-AGAAAAAA
81708 TCAAAAAGAA
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
32 1 0.02
33 16 0.35
34 29 0.63
ACGTcount: A:0.78, C:0.08, G:0.14, T:0.00
Consensus pattern (33 bp):
AAGAAAAAAAAGAAAAAAGAGAAAAAAAAACAA
Found at i:81706 original size:8 final size:8
Alignment explanation
Indices: 81627--81700 Score: 62
Period size: 8 Copynumber: 9.0 Consensus size: 8
81617 AATCAAGAAC
81627 AAAAAAGA
1 AAAAAAGA
*
81635 AAAGAAGCA
1 AAAAAAG-A
81644 AAAAAA-A
1 AAAAAAGA
*
81651 AACAAAGA
1 AAAAAAGA
81659 AAAACAA-A
1 AAAA-AAGA
81667 GAAAAAAGA
1 -AAAAAAGA
*
81676 GAAACAAGA
1 -AAAAAAGA
*
81685 ACAAAAGA
1 AAAAAAGA
81693 AAAAAAGA
1 AAAAAAGA
81701 GCAAAAATCA
Statistics
Matches: 53, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
7 6 0.11
8 26 0.49
9 21 0.40
ACGTcount: A:0.80, C:0.07, G:0.14, T:0.00
Consensus pattern (8 bp):
AAAAAAGA
Found at i:82383 original size:22 final size:22
Alignment explanation
Indices: 82358--82406 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
82348 CCATCAATCT
* *
82358 TTTGAGCATCCAATGTCAAACC
1 TTTGAGCATCAAATGCCAAACC
82380 TTTGAGCATCAAATGCCAAACC
1 TTTGAGCATCAAATGCCAAACC
82402 TTTGA
1 TTTGA
82407 CCAAACACAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.33, C:0.24, G:0.14, T:0.29
Consensus pattern (22 bp):
TTTGAGCATCAAATGCCAAACC
Found at i:83380 original size:36 final size:36
Alignment explanation
Indices: 83337--83480 Score: 252
Period size: 36 Copynumber: 4.0 Consensus size: 36
83327 ACTAGAAGAG
83337 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
*
83373 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
* * *
83409 TTTCGTCTATCTTGAGACAGTTTCCCTTGAAATAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
83445 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
83481 ATATTTGAAT
Statistics
Matches: 100, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 100 1.00
ACGTcount: A:0.26, C:0.21, G:0.14, T:0.40
Consensus pattern (36 bp):
TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
Found at i:83380 original size:71 final size:73
Alignment explanation
Indices: 83295--83480 Score: 229
Period size: 72 Copynumber: 2.6 Consensus size: 73
83285 GTTTTTCTTA
* * * * * *
83295 AAACAAGA-TTTGTCTCGCTTGAGACCGTTTTCACTAG-AA-GAGTTTTGTCTCTCTTGAGACAG
1 AAACAA-ATTTTGTCTCTCTTGAGACAGTTTTCACTAGAAACAAATTTCGTCTATCTTGAGACAG
83357 TTTCCCTTG
65 TTTCCCTTG
* *
83366 AAACAAATTTTGTCTCTCTTGAGACAG-TTTCTCTTGAAACAAATTTCGTCTATCTTGAGACAGT
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTTCACTAGAAACAAATTTCGTCTATCTTGAGACAGT
83430 TTCCCTTG
66 TTCCCTTG
* * *
83438 AAATAAATTTTGTCTCTCTTGAGACAG-TTTCCCTTGAAACAAA
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTTCACTAGAAACAAA
83481 ATATTTGAAT
Statistics
Matches: 102, Mismatches: 10, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
70 8 0.08
71 25 0.25
72 69 0.68
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.37
Consensus pattern (73 bp):
AAACAAATTTTGTCTCTCTTGAGACAGTTTTCACTAGAAACAAATTTCGTCTATCTTGAGACAGT
TTCCCTTG
Found at i:83439 original size:72 final size:71
Alignment explanation
Indices: 83338--83618 Score: 290
Period size: 72 Copynumber: 4.0 Consensus size: 71
83328 CTAGAAGAGT
* *
83338 TTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGA
1 TTTGTCTATCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGA
83403 AACAAA
66 AACAAA
*
83409 TTTCGTCTATCTTGAGACAGTTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
1 TTT-GTCTATCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
83474 AAACAAA
65 AAACAAA
* * * * *** * * **
83481 -----ATAT-TTGA-ATATGTTTTCTTTGAAACAAATACCGTTTCCCTTGAGACAGTTTCTTTTG
1 TTTGTCTATCTTGAGACA-GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
* *
83539 GAACTAAGT
65 AAAC-AA-A
* * *
83548 TTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC-AATTTTCGTCTATCTTGAGACAGTTTCCCTTG
1 TTTGTCTATCTTGAGACAGTTTCCCTTGAAACAAATTTT-GTCTCTCTTGAGACAGTTTCCCTTG
83612 AAACAAA
65 AAACAAA
83619 ATCTTTGAAT
Statistics
Matches: 165, Mismatches: 33, Indels: 24
0.74 0.15 0.11
Matches are distributed among these distances:
64 2 0.01
65 43 0.26
66 5 0.03
71 3 0.02
72 72 0.44
73 38 0.23
74 2 0.01
ACGTcount: A:0.26, C:0.20, G:0.14, T:0.40
Consensus pattern (71 bp):
TTTGTCTATCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGA
AACAAA
Found at i:83603 original size:36 final size:36
Alignment explanation
Indices: 83520--83617 Score: 135
Period size: 36 Copynumber: 2.7 Consensus size: 36
83510 TACCGTTTCC
* * *
83520 CTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCT
1 CTTGAGACAGTTTCTCTTGAAAC-AAGTTTTGTCTAT
83557 CTTGAGACAGTTTCTCTTGAAACAA-TTTTCGTCTAT
1 CTTGAGACAGTTTCTCTTGAAACAAGTTTT-GTCTAT
*
83593 CTTGAGACAGTTTCCCTTGAAACAA
1 CTTGAGACAGTTTCTCTTGAAACAA
83618 AATCTTTGAA
Statistics
Matches: 56, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
35 4 0.07
36 31 0.55
37 21 0.38
ACGTcount: A:0.24, C:0.19, G:0.16, T:0.40
Consensus pattern (36 bp):
CTTGAGACAGTTTCTCTTGAAACAAGTTTTGTCTAT
Found at i:83645 original size:138 final size:137
Alignment explanation
Indices: 83377--83681 Score: 396
Period size: 138 Copynumber: 2.2 Consensus size: 137
83367 AACAAATTTT
*
83377 GTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTCGTCTATCTTGAGACAGTTTCCCTTGAAAT
1 GTCTCCCTTGAGACAGTTTCTCTTGAAACAAATTTCGTCTATCTTGAGACAGTTTCCCTTGAAAT
* * * ** *
83442 AAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATATTTGAATATGTTTTCTTTGAAAC
66 AAATTTTGTCTATCTTGAGACAGTTTCCCTTGAAACAAAATATTTGAATATATTTCCCCTAAAAC
83507 AAATACC
131 AAATACC
* * * * * * *
83514 GTTTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAA
1 GTCTCCCTTGAGACAGTTTCTCTTGAAAC-AAATTTCGTCTATCTTGAGACAGTTTCCCTTGAAA
* * *
83579 -CAATTTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATTTATTTCCCCTAAA
65 TAAATTTT-GTCTATCTTGAGACAGTTTCCCTTGAAACAAAATATTTGAATATATTTCCCCTAAA
***
83643 ACAAATTTT
129 ACAAATACC
*
83652 GTCTCCCTTGAGACAGTTACTCTTGAAACA
1 GTCTCCCTTGAGACAGTTTCTCTTGAAACA
83682 CAAAATCTTC
Statistics
Matches: 142, Mismatches: 24, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
137 32 0.23
138 110 0.77
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.39
Consensus pattern (137 bp):
GTCTCCCTTGAGACAGTTTCTCTTGAAACAAATTTCGTCTATCTTGAGACAGTTTCCCTTGAAAT
AAATTTTGTCTATCTTGAGACAGTTTCCCTTGAAACAAAATATTTGAATATATTTCCCCTAAAAC
AAATACC
Found at i:83680 original size:65 final size:65
Alignment explanation
Indices: 83576--83750 Score: 217
Period size: 67 Copynumber: 2.6 Consensus size: 65
83566 GTTTCTCTTG
** * **
83576 AAAC-AATTTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATTTATTTCCCCT
1 AAACAAATTTT-GTCTCCCTTGAGACAGTTTCTCTTGAAACAAAATCTTCAAATTTATTTCCCCT
83640 A
65 A
* *
83641 AAACAAATTTTGTCTCCCTTGAGACAGTTACTCTTGAAACACAAAATCTTCAAATTTATTTCCCT
1 AAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTG-AA-ACAAAATCTTCAAATTTATTTCCCC
83706 TA
64 TA
* * *
83708 AAACATAATTTTGTTTCCCTTGAGACCGTTTCTCATGAAACAA
1 AAACA-AATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAA
83751 CAGATATCTT
Statistics
Matches: 95, Mismatches: 11, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
65 25 0.26
66 12 0.13
67 31 0.33
68 27 0.28
ACGTcount: A:0.33, C:0.22, G:0.09, T:0.37
Consensus pattern (65 bp):
AAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAAATCTTCAAATTTATTTCCCCTA
Found at i:83710 original size:67 final size:67
Alignment explanation
Indices: 83567--83749 Score: 219
Period size: 68 Copynumber: 2.7 Consensus size: 67
83557 CTTGAGACAG
* * ** * **
83567 TTTCTCTTGAAAC-AATTTTCGTCTATCTTGAGACAGTTTCCCTTG-AA-ACAAAATCTTTGAAT
1 TTTCCCTTAAAACAAATTTT-GTCTCCCTTGAGACAGTTTCTCTTGAAACACAAAATCTTCAAAT
83629 TTA
65 TTA
* *
83632 TTTCCCCTAAAACAAATTTTGTCTCCCTTGAGACAGTTACTCTTGAAACACAAAATCTTCAAATT
1 TTTCCCTTAAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAAATCTTCAAATT
83697 TA
66 TA
* * *
83699 TTTCCCTTAAAACATAATTTTGTTTCCCTTGAGACCGTTTCTCATGAAACA
1 TTTCCCTTAAAACA-AATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
83750 ACAGATATCT
Statistics
Matches: 100, Mismatches: 14, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
65 31 0.31
66 8 0.08
67 29 0.29
68 32 0.32
ACGTcount: A:0.31, C:0.22, G:0.09, T:0.38
Consensus pattern (67 bp):
TTTCCCTTAAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAAATCTTCAAATT
TA
Found at i:84508 original size:100 final size:100
Alignment explanation
Indices: 84323--84518 Score: 279
Period size: 100 Copynumber: 1.9 Consensus size: 100
84313 GCCATCCGCG
* * *
84323 ATTTCAACTCCACGACGGAGGATATCGTGGCACTCGAGACAACACAAGTTCAACTTCACAACGAA
1 ATTTCAACTCCACGACGAAGGATATC-TGGAACTCAAGACAACACAAGTTCAACTTCACAACGAA
*
84388 GGGGCCGTTGACTGTCAACAAACAATTTCCCAATCCA
65 GGGGCCGCTGACTGTCAACAAA-AATTTCCCAATCCA
*
84425 ATTTCAACTTCAC-AGCGAAGGATAT-TGGAACTCAAGACAACACAAGTTCAACTTCACAACGAA
1 ATTTCAACTCCACGA-CGAAGGATATCTGGAACTCAAGACAACACAAGTTCAACTTCACAACGAA
** *
84488 GGGGCCGCTGGTTGTTAACAAAAATTTCCCA
65 GGGGCCGCTGACTGTCAACAAAAATTTCCCA
84519 GTATCAGACA
Statistics
Matches: 85, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
99 9 0.11
100 54 0.64
101 1 0.01
102 21 0.25
ACGTcount: A:0.35, C:0.26, G:0.18, T:0.21
Consensus pattern (100 bp):
ATTTCAACTCCACGACGAAGGATATCTGGAACTCAAGACAACACAAGTTCAACTTCACAACGAAG
GGGCCGCTGACTGTCAACAAAAATTTCCCAATCCA
Found at i:84540 original size:65 final size:64
Alignment explanation
Indices: 84459--84681 Score: 301
Period size: 64 Copynumber: 3.5 Consensus size: 64
84449 TTGGAACTCA
*
84459 AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTTAACAAAAATTTCCCAGTATC
1 AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAACAAAAATTTCCCAGT-TC
*
84524 AGACAACACAAGTTCAACTTCACAACGAAGGGGCCACTGGTTGTCAAC-AAAATTTCCCAGTTC
1 AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAACAAAAATTTCCCAGTTC
* * * *
84587 AAGACAGCACAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCAACAAACAACTTCCCAATT
1 -AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAACAAA-AATTTCCC-AGT
84652 TC
63 TC
* * *
84654 AG--AGC-CAATTTCAACTTCACAGCGAAGG
1 AGACAACACAAGTTCAACTTCACAACGAAGG
84682 ATATTGGACT
Statistics
Matches: 145, Mismatches: 9, Indels: 10
0.88 0.05 0.06
Matches are distributed among these distances:
63 23 0.16
64 61 0.42
65 48 0.33
66 9 0.06
67 4 0.03
ACGTcount: A:0.35, C:0.27, G:0.18, T:0.20
Consensus pattern (64 bp):
AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAACAAAAATTTCCCAGTTC
Found at i:84609 original size:64 final size:65
Alignment explanation
Indices: 84456--84638 Score: 307
Period size: 64 Copynumber: 2.8 Consensus size: 65
84446 ATATTGGAAC
*
84456 TCAAGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTTAACAAAAATTTCCCAGT
1 TCAAGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAAC-AAAATTTCCCAGT
84521 A
65 A
*
84522 TC-AGACAACACAAGTTCAACTTCACAACGAAGGGGCCACTGGTTGTCAACAAAATTTCCCAGT-
1 TCAAGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAACAAAATTTCCCAGTA
* *
84585 TCAAGACAGCACAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCAACAAA
1 TCAAGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAACAAA
84639 CAACTTCCCA
Statistics
Matches: 111, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
63 2 0.02
64 61 0.55
65 46 0.41
66 2 0.02
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.19
Consensus pattern (65 bp):
TCAAGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAACAAAATTTCCCAGTA
Found at i:84649 original size:229 final size:230
Alignment explanation
Indices: 84359--84809 Score: 735
Period size: 235 Copynumber: 1.9 Consensus size: 230
84349 GTGGCACTCG
* *
84359 AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGTTGACTGTCAACAAACAATTTCCCAA-T-
1 AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGACTGTCAACAAACAACTTCCCAATTA
84422 CCAATTTCAACTTCACAGCGAAGGATATTGGAACTCAAGACAACACAAGTTCAACTTCACAACGA
66 CCAATTTCAACTTCACAGCGAAGGATATTGG-ACTCAAGACAACACAAGTTCAACTTCACAACGA
* * *
84487 AGGGGCCGCTGGTTGTTAACAAAAATTTCCCAGTATCAGACAACACAAGTTCAACTTCACAACGA
130 AGGGGCCGCTGGTTGTCAACAAAAATTCCCCAGTATAAGACAACACAAGTTCAACTTCACAACGA
*
84552 AGGGGCCACTGGTTGTCAACAAAATTTCCCAGTTCA
195 AGGGGCCACTGGCTGTCAACAAAATTTCCCAGTTCA
* *
84588 AGACAGCACAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCAACAAACAACTTCCCAATTT
1 AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGACTGTCAACAAACAACTTCCCAA-TT
84653 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACA
65 ---A-CCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACA
* *
84718 ACGAAGGGGCCGCTGGTTGTCAACAAAAATTCCCCAGTTTAAGACAGCACAAGTTCAACTTCACA
126 ACGAAGGGGCCGCTGGTTGTCAACAAAAATTCCCCAGTATAAGACAACACAAGTTCAACTTCACA
*
84783 ACGAAGGGGCCGCTGGCTGTCAACAAA
191 ACGAAGGGGCCACTGGCTGTCAACAAA
84810 CAACTTCCCA
Statistics
Matches: 204, Mismatches: 11, Indels: 8
0.91 0.05 0.04
Matches are distributed among these distances:
229 58 0.28
231 1 0.00
235 114 0.56
236 31 0.15
ACGTcount: A:0.35, C:0.26, G:0.18, T:0.20
Consensus pattern (230 bp):
AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGACTGTCAACAAACAACTTCCCAATTA
CCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACGAA
GGGGCCGCTGGTTGTCAACAAAAATTCCCCAGTATAAGACAACACAAGTTCAACTTCACAACGAA
GGGGCCACTGGCTGTCAACAAAATTTCCCAGTTCA
Found at i:84723 original size:170 final size:171
Alignment explanation
Indices: 84524--84859 Score: 620
Period size: 171 Copynumber: 2.0 Consensus size: 171
84514 TCCCAGTATC
*
84524 AGACAACACAAGTTCAACTTCACAACGAAGGGGCCACTGGTTGTCAAC-AAAATTTCCCAGTTCA
1 AGACAACACAAGTTCAACTTCACAACGAAGGGGCCACTGGTTGTCAACAAAAATTCCCCAGTTCA
84588 AGACAGCACAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCAACAAACAACTTCCCAATTT
66 AGACAGCACAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCAACAAACAACTTCCCAATTT
84653 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCA
131 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCA
* *
84694 AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAACAAAAATTCCCCAGTTTA
1 AGACAACACAAGTTCAACTTCACAACGAAGGGGCCACTGGTTGTCAACAAAAATTCCCCAGTTCA
*
84759 AGACAGCACAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCAACAAACAACTTCCCAGTTT
66 AGACAGCACAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCAACAAACAACTTCCCAATTT
*
84824 CAGAGTCAATTTCAACTTCACAGCGAAGGATATTGG
131 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
84860 CCTCGAAACA
Statistics
Matches: 160, Mismatches: 5, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
170 47 0.29
171 113 0.71
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.20
Consensus pattern (171 bp):
AGACAACACAAGTTCAACTTCACAACGAAGGGGCCACTGGTTGTCAACAAAAATTCCCCAGTTCA
AGACAGCACAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCAACAAACAACTTCCCAATTT
CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCA
Found at i:84773 original size:65 final size:66
Alignment explanation
Indices: 84693--84852 Score: 222
Period size: 65 Copynumber: 2.5 Consensus size: 66
84683 TATTGGACTC
* *
84693 AAGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAACAAA-AA-TTCCCCAGT
1 AAGACAGCACAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCAACAAACAACTT-CCCAGT
84756 TT
65 TT
84758 AAGACAGCACAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCAACAAACAACTTCCCAGTT
1 AAGACAGCACAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCAACAAACAACTTCCCAGTT
84823 T
66 T
* * * *
84824 CAG--AG-TCAATTTCAACTTCACAGCGAAGG
1 AAGACAGCACAAGTTCAACTTCACAACGAAGG
84853 ATATTGGCCT
Statistics
Matches: 87, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
63 21 0.24
64 2 0.02
65 50 0.57
66 12 0.14
67 2 0.02
ACGTcount: A:0.34, C:0.27, G:0.19, T:0.19
Consensus pattern (66 bp):
AAGACAGCACAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCAACAAACAACTTCCCAGTT
T
Found at i:84807 original size:106 final size:104
Alignment explanation
Indices: 84588--84789 Score: 264
Period size: 106 Copynumber: 1.9 Consensus size: 104
84578 TCCCAGTTCA
*
84588 AGACAGCACAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCAACAAACAACTTCCCAATTT
1 AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCAACAAACAACTTCCCAATTT
* * * * *
84653 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACT
66 AAGAGCCAAGTTCAACTTCACAACGAAGGACACTGGACT
* *
84692 CAAGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAACAAA-AA-TTCCCCAG
1 --AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCAACAAACAACTT-CCCAA
84755 TTTAAGACAGCACAAGTTCAACTTCACAACGAAGG
63 TTTAAG--AGC-CAAGTTCAACTTCACAACGAAGG
84790 GGCCGCTGGC
Statistics
Matches: 86, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
104 2 0.02
105 11 0.13
106 49 0.57
107 3 0.03
108 21 0.24
ACGTcount: A:0.36, C:0.27, G:0.19, T:0.19
Consensus pattern (104 bp):
AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCAACAAACAACTTCCCAATTT
AAGAGCCAAGTTCAACTTCACAACGAAGGACACTGGACT
Found at i:85414 original size:34 final size:34
Alignment explanation
Indices: 85371--85477 Score: 160
Period size: 34 Copynumber: 3.1 Consensus size: 34
85361 TTCGTCCTAC
85371 TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
1 TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
* *
85405 TAGGATTCAAACTCCTAAAGATATGATAGAATTTT
1 TAGGATTCAAACTCCTAAAAATAGGATAGAA-TTT
*
85440 GCTAGGATTCAAACTCCTAAAAATAGGATAGAGTTT
1 --TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
85476 TA
1 TA
85478 CTATTATTTA
Statistics
Matches: 65, Mismatches: 5, Indels: 6
0.86 0.07 0.08
Matches are distributed among these distances:
34 31 0.48
35 3 0.05
36 3 0.05
37 28 0.43
ACGTcount: A:0.41, C:0.12, G:0.16, T:0.31
Consensus pattern (34 bp):
TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
Found at i:85455 original size:37 final size:36
Alignment explanation
Indices: 85370--85505 Score: 177
Period size: 37 Copynumber: 3.8 Consensus size: 36
85360 TTTCGTCCTA
85370 CTAGGATTCAAACTCCTAAAAATAGGATAGAA-TTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
* *
85405 -TAGGATTCAAACTCCTAAAGATATGATAGAATTTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
*
85440 GCTAGGATTCAAACTCCTAAAAATAGGATAGAGTTTT
1 -CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
** * *
85477 ACTATTATTTAAACTCCTAAAGATAGGAT
1 -CTAGGATTCAAACTCCTAAAAATAGGAT
85506 CCACAAGCAC
Statistics
Matches: 88, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
34 29 0.33
35 3 0.03
37 56 0.64
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.32
Consensus pattern (36 bp):
CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
Found at i:86063 original size:16 final size:18
Alignment explanation
Indices: 86044--86078 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
86034 TTTACTCATT
86044 TATTTAT-CTAT-TTTTA
1 TATTTATCCTATATTTTA
86060 TATTTATCCTATATTTTA
1 TATTTATCCTATATTTTA
86078 T
1 T
86079 GTTTTTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 4 0.24
18 6 0.35
ACGTcount: A:0.26, C:0.09, G:0.00, T:0.66
Consensus pattern (18 bp):
TATTTATCCTATATTTTA
Found at i:86872 original size:23 final size:23
Alignment explanation
Indices: 86828--86874 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
86818 TGATAAACGC
* *
86828 TAAATGAATATGTTCATAAATAT
1 TAAACGAATATGTTCACAAATAT
* *
86851 TAAACGAATATGTTTACGAATAT
1 TAAACGAATATGTTCACAAATAT
86874 T
1 T
86875 GAATAAACGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.45, C:0.06, G:0.11, T:0.38
Consensus pattern (23 bp):
TAAACGAATATGTTCACAAATAT
Found at i:100417 original size:16 final size:18
Alignment explanation
Indices: 100396--100433 Score: 53
Period size: 16 Copynumber: 2.2 Consensus size: 18
100386 AAAATCTATA
100396 AAATTTA-ATATTAA-TC
1 AAATTTACATATTAATTC
100412 AAATTTAGCATATTAATTC
1 AAATTTA-CATATTAATTC
100431 AAA
1 AAA
100434 AATAAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 7 0.37
18 7 0.37
19 5 0.26
ACGTcount: A:0.50, C:0.08, G:0.03, T:0.39
Consensus pattern (18 bp):
AAATTTACATATTAATTC
Found at i:108505 original size:2 final size:2
Alignment explanation
Indices: 108500--108541 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
108490 ATATATCCTT
108500 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
108540 TA
1 TA
108542 ATGAAATTAT
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.05
2 36 0.95
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:109385 original size:13 final size:13
Alignment explanation
Indices: 109367--109410 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
109357 TAAATTCATA
109367 TATATTTATTTTT
1 TATATTTATTTTT
*
109380 TATATTTATTATT
1 TATATTTATTTTT
*
109393 AATAATTTA-TTTT
1 TAT-ATTTATTTTT
109406 TATAT
1 TATAT
109411 GAAATTTTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
12 2 0.08
13 19 0.73
14 5 0.19
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
TATATTTATTTTT
Found at i:110708 original size:2 final size:2
Alignment explanation
Indices: 110701--110735 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
110691 ACCATCCTAG
110701 TA TA TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
110736 GGATTCACAT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:114643 original size:22 final size:22
Alignment explanation
Indices: 114594--114636 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
114584 CTCTGCAACA
114594 AACTCAAAGCCCTTCTTGGAAC
1 AACTCAAAGCCCTTCTTGGAAC
114616 AACTCAAAGCCCTTCTTGGAA
1 AACTCAAAGCCCTTCTTGGAA
114637 TCACTCATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.33, C:0.30, G:0.14, T:0.23
Consensus pattern (22 bp):
AACTCAAAGCCCTTCTTGGAAC
Found at i:116556 original size:4 final size:4
Alignment explanation
Indices: 116547--116578 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
116537 ATTCGCATTC
*
116547 ATGT ATGT ATGT ATGT ATGT ATGC ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
116579 GGTTTTACAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.25, C:0.03, G:0.25, T:0.47
Consensus pattern (4 bp):
ATGT
Done.