Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006792.1 Hibiscus syriacus cultivar Beakdansim tig00017221_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: 105982
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:12590 original size:31 final size:31
Alignment explanation
Indices: 12536--12614 Score: 126
Period size: 31 Copynumber: 2.6 Consensus size: 31
12526 ATGGAGAAAG
12536 TAAAGTTCAGTGACAG-AAAAACCCAATGTAT
1 TAAA-TTCAGTGACAGAAAAAACCCAATGTAT
12567 TAAATTCAGTGACAGAAAAAACCCAATGTAT
1 TAAATTCAGTGACAGAAAAAACCCAATGTAT
*
12598 TAAGTTCAGTGA-AGAAA
1 TAAATTCAGTGACAGAAA
12615 TTGAGAACTT
Statistics
Matches: 46, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
30 16 0.35
31 30 0.65
ACGTcount: A:0.47, C:0.14, G:0.16, T:0.23
Consensus pattern (31 bp):
TAAATTCAGTGACAGAAAAAACCCAATGTAT
Found at i:15503 original size:15 final size:17
Alignment explanation
Indices: 15483--15521 Score: 55
Period size: 15 Copynumber: 2.4 Consensus size: 17
15473 GAATCACATC
15483 AAATTATATTCT-A-AT
1 AAATTATATTCTCATAT
*
15498 AAATTATATTTTCATAT
1 AAATTATATTCTCATAT
15515 AAATTAT
1 AAATTAT
15522 TCTTAAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 11 0.52
16 1 0.05
17 9 0.43
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (17 bp):
AAATTATATTCTCATAT
Found at i:27186 original size:23 final size:23
Alignment explanation
Indices: 27139--27186 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
27129 CCCTACAGGA
*
27139 GGAATCGGTTCACCTTCAAATGG
1 GGAATCGGTTCACCTTCAAAGGG
*
27162 GGAATCGGTT-ACCCTTCAAGGGG
1 GGAATCGGTTCA-CCTTCAAAGGG
27185 GG
1 GG
27187 TATCAATTCC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 1 0.05
23 21 0.95
ACGTcount: A:0.23, C:0.21, G:0.33, T:0.23
Consensus pattern (23 bp):
GGAATCGGTTCACCTTCAAAGGG
Found at i:33111 original size:19 final size:19
Alignment explanation
Indices: 33087--33139 Score: 97
Period size: 19 Copynumber: 2.7 Consensus size: 19
33077 ATAAAAGTAA
33087 GTAGTTAATTAAACTAATT
1 GTAGTTAATTAAACTAATT
33106 GTAGTTAATTAAACTAATT
1 GTAGTTAATTAAACTAATT
33125 GTAGTTAATTCAAAC
1 GTAGTTAATT-AAAC
33140 ACTTTCATTA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 29 0.88
20 4 0.12
ACGTcount: A:0.42, C:0.08, G:0.11, T:0.40
Consensus pattern (19 bp):
GTAGTTAATTAAACTAATT
Found at i:43356 original size:2 final size:2
Alignment explanation
Indices: 43349--43377 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
43339 TAAGAAAATA
43349 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
43378 GTTTTCAGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:43438 original size:19 final size:21
Alignment explanation
Indices: 43367--43544 Score: 78
Period size: 21 Copynumber: 8.8 Consensus size: 21
43357 ATATATATAT
* *
43367 ATATATAATATGT-TTTCAGA
1 ATATATAATATATATTTCAAA
* *
43387 ATATA-ACCATGTATATTTTAAA
1 ATATATA--ATATATATTTCAAA
43409 ATATATAATATATATTTCAAA
1 ATATATAATATATATTTCAAA
**
43430 AT-TAT-ATAT-GCTTTCAAA
1 ATATATAATATATATTTCAAA
* * *
43448 A-A-ATAATAAATATAT--AT
1 ATATATAATATATATTTCAAA
*
43465 ATATAT-ATTTATATTT-AAA
1 ATATATAATATATATTTCAAA
*
43484 AAACTAT-ATATAT-TTTCCCAAA
1 ATA-TATAATATATATTT--CAAA
* *
43506 CTCTAT-ATATATATTTTCAAAA
1 ATATATAATATATA-TTTC-AAA
43528 ATATATAATATATATTT
1 ATATATAATATATATTT
43545 TTAGAAACTA
Statistics
Matches: 116, Mismatches: 24, Indels: 34
0.67 0.14 0.20
Matches are distributed among these distances:
17 4 0.03
18 19 0.16
19 15 0.13
20 16 0.14
21 28 0.24
22 23 0.20
23 11 0.09
ACGTcount: A:0.47, C:0.07, G:0.02, T:0.44
Consensus pattern (21 bp):
ATATATAATATATATTTCAAA
Found at i:43518 original size:23 final size:22
Alignment explanation
Indices: 43463--43545 Score: 73
Period size: 22 Copynumber: 3.8 Consensus size: 22
43453 ATAAATATAT
*
43463 ATATATATATTTATATTT-AAAA
1 ATATATATATATAT-TTTCAAAA
* *
43485 A-ACTATATATAT-TTTCCCAAA
1 ATA-TATATATATATTTTCAAAA
* *
43506 CTCTATATATATATTTTCAAAA
1 ATATATATATATATTTTCAAAA
43528 ATATATAATATATATTTT
1 ATATAT-ATATATATTTT
43546 TAGAAACTAT
Statistics
Matches: 47, Mismatches: 9, Indels: 9
0.72 0.14 0.14
Matches are distributed among these distances:
20 2 0.04
21 14 0.30
22 20 0.43
23 11 0.23
ACGTcount: A:0.45, C:0.08, G:0.00, T:0.47
Consensus pattern (22 bp):
ATATATATATATATTTTCAAAA
Found at i:43526 original size:21 final size:23
Alignment explanation
Indices: 43488--43545 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 23
43478 TTTAAAAAAC
* * *
43488 TATATATATTTTCCCAAACTCTA
1 TATATATATTTTCCAAAAATATA
43511 TATATATATTTT-CAAAAATATA
1 TATATATATTTTCCAAAAATATA
43533 TAATATATATTTT
1 T-ATATATATTTT
43546 TAGAAACTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
22 8 0.26
23 23 0.74
ACGTcount: A:0.41, C:0.10, G:0.00, T:0.48
Consensus pattern (23 bp):
TATATATATTTTCCAAAAATATA
Found at i:44836 original size:21 final size:21
Alignment explanation
Indices: 44794--44836 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
44784 TTTCTGGGCT
*
44794 AGGGGAATCGATACCCATTCA
1 AGGGGAATCGATACCCACTCA
*
44815 AGGGGAATCGATACCCCCTCA
1 AGGGGAATCGATACCCACTCA
44836 A
1 A
44837 ACGAATATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.28, G:0.23, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:44898 original size:18 final size:19
Alignment explanation
Indices: 44863--44900 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
44853 AGAACGCTAG
*
44863 GGGGGAATCGATACCCCCA
1 GGGGGAACCGATACCCCCA
*
44882 GGGGGAACCGATTCCCCCA
1 GGGGGAACCGATACCCCCA
44901 TAATAAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.24, C:0.34, G:0.32, T:0.11
Consensus pattern (19 bp):
GGGGGAACCGATACCCCCA
Found at i:45607 original size:103 final size:103
Alignment explanation
Indices: 45382--45599 Score: 373
Period size: 103 Copynumber: 2.1 Consensus size: 103
45372 GTAGAGGGTC
* *
45382 TATGTGGTCCTTCGGGATATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
45447 TTGATCCTTGGTATATGTATACGATTCTTAAAGAATGA
66 TTGATCCTTGGCATATGTATACGATTCTTAAAGAATGA
* *
45485 TATATGGTCATTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* *
45550 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATACGATTCTTAAAGAATGA
45588 TATGTGGTCCTT
1 TATGTGGTCCTT
45600 ATGGACATTA
Statistics
Matches: 106, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
103 106 1.00
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCTTGGCATATGTATACGATTCTTAAAGAATGA
Found at i:45650 original size:23 final size:23
Alignment explanation
Indices: 45624--45667 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
45614 ATGACACTAC
45624 GGTGCAATTCAACGCGGCACTCT
1 GGTGCAATTCAACGCGGCACTCT
* *
45647 GGTGCAATTCTACGTGGCACT
1 GGTGCAATTCAACGCGGCACT
45668 TAAGTGTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.25
Consensus pattern (23 bp):
GGTGCAATTCAACGCGGCACTCT
Found at i:51764 original size:21 final size:21
Alignment explanation
Indices: 51722--51764 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
51712 TTTCTGGGCT
*
51722 AGGGGAATCGATACCCATTCA
1 AGGGGAATCGATACCCACTCA
*
51743 AGGGGAATCGATACCCCCTCA
1 AGGGGAATCGATACCCACTCA
51764 A
1 A
51765 ACGAATATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.28, G:0.23, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:51827 original size:20 final size:20
Alignment explanation
Indices: 51789--51829 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
51779 CCAGAACGCT
* *
51789 AGGGGGGAATCGATACCCCC
1 AGGGGGGAACCAATACCCCC
*
51809 AGGGGGGAACCAATTCCCCC
1 AGGGGGGAACCAATACCCCC
51829 A
1 A
51830 TAATAAAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.27, C:0.32, G:0.32, T:0.10
Consensus pattern (20 bp):
AGGGGGGAACCAATACCCCC
Found at i:52536 original size:103 final size:103
Alignment explanation
Indices: 52311--52528 Score: 400
Period size: 103 Copynumber: 2.1 Consensus size: 103
52301 GTAGAGGGTC
*
52311 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATATGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATATGTGAAGTCTGGTGAGACACATAC
*
52376 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
* *
52414 TATGTGGTCATTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATATGTGAAGTCTGGTGAGACACATAC
52479 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
52517 TATGTGGTCCTT
1 TATGTGGTCCTT
52529 ATGGACATTA
Statistics
Matches: 110, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 110 1.00
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATATGTGAAGTCTGGTGAGACACATAC
TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:52575 original size:23 final size:23
Alignment explanation
Indices: 52545--52607 Score: 92
Period size: 23 Copynumber: 2.7 Consensus size: 23
52535 ATTATTATAT
52545 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
52568 GGCACTACGGTGCAGTTCTACGT
1 GGCACTACGGTGCAATTCTACGC
52591 GGCACTTA-GGTGCAATT
1 GGCAC-TACGGTGCAATT
52608 ATATGAGTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
23 34 0.94
24 2 0.06
ACGTcount: A:0.21, C:0.25, G:0.29, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:56764 original size:103 final size:103
Alignment explanation
Indices: 56585--56791 Score: 387
Period size: 103 Copynumber: 2.0 Consensus size: 103
56575 CTTCTGCATT
*
56585 TAAAAAGATTTCATCACTTTGTTTAACTCGATCTTCTCATAGTCTTTTCTAGTTTGAAAACTAGT
1 TAAAAAGATTTCATCACTTTGTTTAACTCAATCTTCTCATAGTCTTTTCTAGTTTGAAAACTAGT
56650 GTATTTCTCGGTAATGGACTTCGTGTTATCGATCGTGC
66 GTATTTCTCGGTAATGGACTTCGTGTTATCGATCGTGC
* *
56688 TAAAAAGATTTCATCACTTTGTTTAACTCAATCTTCTCGTAGTCTTTTCTAGTTTGAAAACTCGT
1 TAAAAAGATTTCATCACTTTGTTTAACTCAATCTTCTCATAGTCTTTTCTAGTTTGAAAACTAGT
56753 GTATTTCTCGGTAATGGACTTCGTGTTATCGATCGTGC
66 GTATTTCTCGGTAATGGACTTCGTGTTATCGATCGTGC
56791 T
1 T
56792 TCAAAACTGT
Statistics
Matches: 101, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 101 1.00
ACGTcount: A:0.24, C:0.18, G:0.16, T:0.42
Consensus pattern (103 bp):
TAAAAAGATTTCATCACTTTGTTTAACTCAATCTTCTCATAGTCTTTTCTAGTTTGAAAACTAGT
GTATTTCTCGGTAATGGACTTCGTGTTATCGATCGTGC
Found at i:57421 original size:22 final size:22
Alignment explanation
Indices: 57391--57435 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
57381 AAGAAGATAG
*
57391 TTGAGTGATGATTAATTTAATT
1 TTGAATGATGATTAATTTAATT
57413 TTGAATGATGATTAATTTAATT
1 TTGAATGATGATTAATTTAATT
57435 T
1 T
57436 ACCCATAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.33, C:0.00, G:0.16, T:0.51
Consensus pattern (22 bp):
TTGAATGATGATTAATTTAATT
Found at i:63306 original size:15 final size:16
Alignment explanation
Indices: 63268--63307 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
63258 ACAGAGCCTC
*
63268 TGAATCATTCAGCATT
1 TGAATCATTCAGCACT
*
63284 TGAATCATTCAGCGCT
1 TGAATCATTCAGCACT
63300 T-AATCATT
1 TGAATCATT
63308 ATGAAGTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 7 0.32
16 15 0.68
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.38
Consensus pattern (16 bp):
TGAATCATTCAGCACT
Found at i:63660 original size:15 final size:15
Alignment explanation
Indices: 63616--63662 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
63606 AATTTAATTA
63616 ATATTTTATAAATAT
1 ATATTTTATAAATAT
** *
63631 ATACATTATATATAT
1 ATATTTTATAAATAT
*
63646 ATATTTTAAAAATAT
1 ATATTTTATAAATAT
63661 AT
1 AT
63663 TTAATATTTT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (15 bp):
ATATTTTATAAATAT
Found at i:63661 original size:21 final size:20
Alignment explanation
Indices: 63637--63678 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
63627 ATATATACAT
63637 TATATATATATATTTTAAAAA
1 TATATATA-ATATTTTAAAAA
* *
63658 TATATTTAATATTTTGAAAA
1 TATATATAATATTTTAAAAA
63678 T
1 T
63679 TAAAAAATTA
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:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (20 bp):
TATATATAATATTTTAAAAA
Found at i:63850 original size:24 final size:25
Alignment explanation
Indices: 63823--63872 Score: 84
Period size: 24 Copynumber: 2.0 Consensus size: 25
63813 ATTCAATAAT
63823 TTTATTTTTATAATACG-TTTCTTC
1 TTTATTTTTATAATACGTTTTCTTC
*
63847 TTTATTTTTATAGTACGTTTTCTTC
1 TTTATTTTTATAATACGTTTTCTTC
63872 T
1 T
63873 ATTAAATGTC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 16 0.67
25 8 0.33
ACGTcount: A:0.18, C:0.12, G:0.06, T:0.64
Consensus pattern (25 bp):
TTTATTTTTATAATACGTTTTCTTC
Found at i:64709 original size:20 final size:20
Alignment explanation
Indices: 64686--64723 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
64676 ATTTAAACAC
64686 GTATTCAAG-ATTTTAATTTG
1 GTATT-AAGCATTTTAATTTG
*
64706 GTATTAAGCCTTTTAATT
1 GTATTAAGCATTTTAATT
64724 AAAAAATGTC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.29, C:0.08, G:0.13, T:0.50
Consensus pattern (20 bp):
GTATTAAGCATTTTAATTTG
Found at i:67088 original size:5 final size:5
Alignment explanation
Indices: 67078--67105 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
67068 GTACTGGTAA
67078 TTCCT TTCCT TTCCT TTCCT TTCCT TTC
1 TTCCT TTCCT TTCCT TTCCT TTCCT TTC
67106 GTTGGCATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (5 bp):
TTCCT
Found at i:68031 original size:28 final size:29
Alignment explanation
Indices: 67971--68032 Score: 83
Period size: 28 Copynumber: 2.1 Consensus size: 29
67961 AAAGAATTGC
*
67971 AATTAGAGAATTAAATTGAATAAAATATAA
1 AATTAGAGAATTAAATTG-ATAAAAAATAA
68001 AATT-GAGAGATTAAATTG-TAAAAAATAA
1 AATTAGAGA-ATTAAATTGATAAAAAATAA
68029 AATT
1 AATT
68033 TATACTTAGA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
28 13 0.43
29 4 0.13
30 13 0.43
ACGTcount: A:0.58, C:0.00, G:0.11, T:0.31
Consensus pattern (29 bp):
AATTAGAGAATTAAATTGATAAAAAATAA
Found at i:75952 original size:24 final size:24
Alignment explanation
Indices: 75925--75978 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
75915 GTATTCGAAA
75925 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
75949 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
75973 TTTGAT
1 TTTGAT
75979 GATTTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:78418 original size:20 final size:21
Alignment explanation
Indices: 78393--78466 Score: 109
Period size: 20 Copynumber: 3.7 Consensus size: 21
78383 GACATTCATT
78393 TGACTATCGCAACGC-GAATA
1 TGACTATCGCAACGCGGAATA
*
78413 TGACTATCGCAACACGGAA-A
1 TGACTATCGCAACGCGGAATA
*
78433 TGACTATCGCAATGCGGAAT-
1 TGACTATCGCAACGCGGAATA
78453 TGACTATCGCAACG
1 TGACTATCGCAACG
78467 AGAGAATCGC
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
20 45 0.94
21 3 0.06
ACGTcount: A:0.34, C:0.24, G:0.22, T:0.20
Consensus pattern (21 bp):
TGACTATCGCAACGCGGAATA
Found at i:78481 original size:34 final size:34
Alignment explanation
Indices: 78438--78533 Score: 140
Period size: 33 Copynumber: 2.9 Consensus size: 34
78428 GGAAATGACT
* **
78438 ATCGCAATGCGGAATTGACTATCGCAACGAGAGA
1 ATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
*
78472 ATCGCAATGC-GAAATGAAAATCGCAACGAGTGA
1 ATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
*
78505 ATCGCAATGCGAAAATGAAAATCGCAACG
1 ATCGCAATGCGGAAATGAAAATCGCAACG
78534 CGAATAGTCA
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
33 29 0.52
34 27 0.48
ACGTcount: A:0.41, C:0.20, G:0.24, T:0.16
Consensus pattern (34 bp):
ATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:78529 original size:20 final size:19
Alignment explanation
Indices: 78471--78537 Score: 72
Period size: 20 Copynumber: 3.7 Consensus size: 19
78461 GCAACGAGAG
78471 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
78490 AATCGCAA--CG-AGTG--
1 AATCGCAATGCGAAATGAA
78504 AATCGCAATGCGAAAATGAA
1 AATCGCAATGCG-AAATGAA
*
78524 AATCGCAACGCGAA
1 AATCGCAATGCGAA
78538 TAGTCATTTC
Statistics
Matches: 39, Mismatches: 3, Indels: 12
0.72 0.06 0.22
Matches are distributed among these distances:
14 8 0.21
16 5 0.13
17 2 0.05
18 3 0.08
19 10 0.26
20 11 0.28
ACGTcount: A:0.45, C:0.19, G:0.22, T:0.13
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:78679 original size:14 final size:14
Alignment explanation
Indices: 78660--78696 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
78650 CATCAATTAA
78660 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
78674 ACAAATCATCTTTT
1 ACAAATCAACATTT
78688 ACAAATCAA
1 ACAAATCAA
78697 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:80159 original size:42 final size:42
Alignment explanation
Indices: 80052--80163 Score: 111
Period size: 42 Copynumber: 2.7 Consensus size: 42
80042 TCTAGAATGT
* * *
80052 TGGGAG-GGACCTCTTCAACGATGACAGTGGCCTCTTGAACGG
1 TGGGAGAGG-CCTCTTGAACGATGACAGGGGCCTCTTGAACGA
* * ** *
80094 TGGGAGGGGACTCTTGAGGGATGATAGGGGCCTCTTGAACGA
1 TGGGAGAGGCCTCTTGAACGATGACAGGGGCCTCTTGAACGA
*
80136 TAGGG-GATGCCTCTTGAACGATGACAGG
1 T-GGGAGAGGCCTCTTGAACGATGACAGG
80164 TGAGTCGGGT
Statistics
Matches: 55, Mismatches: 13, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
42 50 0.91
43 5 0.09
ACGTcount: A:0.22, C:0.19, G:0.38, T:0.21
Consensus pattern (42 bp):
TGGGAGAGGCCTCTTGAACGATGACAGGGGCCTCTTGAACGA
Found at i:80666 original size:20 final size:20
Alignment explanation
Indices: 80651--80729 Score: 140
Period size: 20 Copynumber: 4.0 Consensus size: 20
80641 AAATCGTAAC
80651 GCGAAAATGACTATCGCAAT
1 GCGAAAATGACTATCGCAAT
80671 GCGAAAATGACTATCGCAAT
1 GCGAAAATGACTATCGCAAT
80691 GCGAAAATGACTATCGCAAT
1 GCGAAAATGACTATCGCAAT
**
80711 GCGAATTTGACTATCGCAA
1 GCGAAAATGACTATCGCAA
80730 CGAGAGAATC
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 57 1.00
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.22
Consensus pattern (20 bp):
GCGAAAATGACTATCGCAAT
Found at i:80801 original size:20 final size:20
Alignment explanation
Indices: 80776--80913 Score: 138
Period size: 20 Copynumber: 7.5 Consensus size: 20
80766 GATTATTTCG
**
80776 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
*
80796 TTGCGATAGTCATTTTTGCA
1 TTGCGATAGTCATTTTCGCA
*
80816 TTGCGAT--TC--TCTCG--
1 TTGCGATAGTCATTTTCGCA
80830 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
80850 TTGCGAT--TC--TCTCG--
1 TTGCGATAGTCATTTTCGCA
*
80864 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
80884 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
80904 TTGCGATAGT
1 TTGCGATAGT
80914 AAACTATTCT
Statistics
Matches: 97, Mismatches: 9, Indels: 24
0.75 0.07 0.18
Matches are distributed among these distances:
14 14 0.14
16 11 0.11
18 12 0.12
20 60 0.62
ACGTcount: A:0.18, C:0.20, G:0.22, T:0.40
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:80833 original size:54 final size:53
Alignment explanation
Indices: 80760--80913 Score: 175
Period size: 54 Copynumber: 2.9 Consensus size: 53
80750 TTTCATTTCA
* ** **
80760 CATTGCGATTATTTCGTTGCGATAGTCAAATTCGCATTGCGATAGTCATTTTTG
1 CATTGCGATTATCTCGTTGCGATAGTCATTTTCGCATTGCGATAGTC-TCGTTG
* **
80814 CATTGCGATTCTCTCGTTGCGATAGTCATTTTCGCATTGCGATTCTCTCGTTG
1 CATTGCGATTATCTCGTTGCGATAGTCATTTTCGCATTGCGATAGTCTCGTTG
* * *
80867 CGATAGTC-ATTTTCGCGTTGCGATAGTCATTTTCGCATTGCGATAGT
1 C-ATTG-CGATTATCTCGTTGCGATAGTCATTTTCGCATTGCGATAGT
80914 AAACTATTCT
Statistics
Matches: 85, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
53 5 0.06
54 79 0.93
55 1 0.01
ACGTcount: A:0.18, C:0.20, G:0.21, T:0.40
Consensus pattern (53 bp):
CATTGCGATTATCTCGTTGCGATAGTCATTTTCGCATTGCGATAGTCTCGTTG
Found at i:80834 original size:34 final size:34
Alignment explanation
Indices: 80796--80890 Score: 172
Period size: 34 Copynumber: 2.8 Consensus size: 34
80786 CAAATTCGCA
*
80796 TTGCGATAGTCATTTTTGCATTGCGATTCTCTCG
1 TTGCGATAGTCATTTTCGCATTGCGATTCTCTCG
80830 TTGCGATAGTCATTTTCGCATTGCGATTCTCTCG
1 TTGCGATAGTCATTTTCGCATTGCGATTCTCTCG
*
80864 TTGCGATAGTCATTTTCGCGTTGCGAT
1 TTGCGATAGTCATTTTCGCATTGCGAT
80891 AGTCATTTTC
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 59 1.00
ACGTcount: A:0.15, C:0.21, G:0.22, T:0.42
Consensus pattern (34 bp):
TTGCGATAGTCATTTTCGCATTGCGATTCTCTCG
Found at i:82812 original size:20 final size:20
Alignment explanation
Indices: 82789--82875 Score: 86
Period size: 20 Copynumber: 4.4 Consensus size: 20
82779 CCGAAACTTT
82789 AAATCGCAACACGAAAATGA
1 AAATCGCAACACGAAAATGA
*
82809 AAATCGCAACATGAAAATGA
1 AAATCGCAACACGAAAATGA
** * **
82829 CTATCGCAACGCGAATTTGA
1 AAATCGCAACACGAAAATGA
** *
82849 CTATCGCAACGC-AAAATGA
1 AAATCGCAACACGAAAATGA
82868 AAATCGCA
1 AAATCGCA
82876 TTGCGATTCT
Statistics
Matches: 56, Mismatches: 11, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
19 11 0.20
20 45 0.80
ACGTcount: A:0.46, C:0.22, G:0.16, T:0.16
Consensus pattern (20 bp):
AAATCGCAACACGAAAATGA
Found at i:82933 original size:20 final size:20
Alignment explanation
Indices: 82888--82936 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
82878 GCGATTCTCT
82888 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* ** *
82908 CATTGCGATAGTCATTTTTG
1 CGTTGCGATAGTCAAATTCG
82928 CGTTGCGAT
1 CGTTGCGAT
82937 TCACTCGTTG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.37
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:83530 original size:20 final size:20
Alignment explanation
Indices: 83505--83635 Score: 102
Period size: 20 Copynumber: 6.5 Consensus size: 20
83495 GATATATAAA
83505 TCGCATTGCGATAGT-CATAT
1 TCGCATTGCGAT-GTACATAT
* *
83525 TCGCATTGCGATTTACGTAT
1 TCGCATTGCGATGTACATAT
* *
83545 TCGCATTGCGATTTACGTAT
1 TCGCATTGCGATGTACATAT
* * * * *
83565 TCGTATTACGATTTACGTAA
1 TCGCATTGCGATGTACATAT
* *
83585 TCGCATTGCGATTTACGTAT
1 TCGCATTGCGATGTACATAT
* * * *
83605 TCGCATTACGATTTACGTAA
1 TCGCATTGCGATGTACATAT
*
83625 TCACATTGCGA
1 TCGCATTGCGA
83636 ATCTGGAAAC
Statistics
Matches: 98, Mismatches: 12, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
19 1 0.01
20 97 0.99
ACGTcount: A:0.24, C:0.20, G:0.18, T:0.37
Consensus pattern (20 bp):
TCGCATTGCGATGTACATAT
Found at i:83566 original size:40 final size:40
Alignment explanation
Indices: 83503--83635 Score: 196
Period size: 40 Copynumber: 3.3 Consensus size: 40
83493 ACGATATATA
* * *
83503 AATCGCATTGCGATAGT-CATATTCGCATTGCGATTTACGT
1 AATCGCATTGCGAT-TTACGTATTCGCATTACGATTTACGT
* *
83543 ATTCGCATTGCGATTTACGTATTCGTATTACGATTTACGT
1 AATCGCATTGCGATTTACGTATTCGCATTACGATTTACGT
83583 AATCGCATTGCGATTTACGTATTCGCATTACGATTTACGT
1 AATCGCATTGCGATTTACGTATTCGCATTACGATTTACGT
*
83623 AATCACATTGCGA
1 AATCGCATTGCGA
83636 ATCTGGAAAC
Statistics
Matches: 84, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
39 1 0.01
40 83 0.99
ACGTcount: A:0.26, C:0.20, G:0.18, T:0.37
Consensus pattern (40 bp):
AATCGCATTGCGATTTACGTATTCGCATTACGATTTACGT
Found at i:84642 original size:322 final size:316
Alignment explanation
Indices: 84063--84701 Score: 1129
Period size: 322 Copynumber: 2.0 Consensus size: 316
84053 TTTACTTTTT
84063 AATCTGATTTAGAGGGTTAGCGACTGATAATCCTTATGATAATCTGAAAATTTTCTTTTCCTTTC
1 AATCTGATTTAGAGGGTTAGCGACTGATAATCCTTATGATAATCTGAAAATTTTCTTTTCCTTTC
* *
84128 ACTCTGTTACTGAACTGTTCGTAGTAGGGGGAAAAAGAGAGAACCTGTTTTTTTAGGGGATTTGT
66 ACTCTGTTACTGAACTGTTCGTAGTAGGGGAAAAAAGAGAGAACCTGGTTTTTTAGGGGATTTGT
*
84193 TGAAGGGATATGTATATTTTAGGGTTCTAATTTTCTGGTTATTTACAATATTGGGTCTAAGTTCT
131 TGAAGGGATATGTATATTTTAGGGTTCTAATTTTCTGGTTATTTACAATATTGGGTCTAAATTCT
*
84258 TCATTCAAAGCCGTCTCGTTTTTTACTTTCTTGTTGAAAGGATAGAATTGTCATCTTAGATATGT
196 TCATTCAAAGCCGTCTCGTTTTGTACTTTCTTGTTGAAAGGATAGAATTGTCATCTTAGATATGT
84323 GGAGGTCTTGGTCTTCTTAGTTTGTTCTTGTCTGGTTTTGAAGAACTCTAGAAGCA
261 GGAGGTCTTGGTCTTCTTAGTTTGTTCTTGTCTGGTTTTGAAGAACTCTAGAAGCA
* *
84379 AATCTGATTTAGATGGTTAGCGACTGATAATCC-TATGATAATCTGAGAATTTTCTTTTCCTTTC
1 AATCTGATTTAGAGGGTTAGCGACTGATAATCCTTATGATAATCTGAAAATTTTCTTTTCCTTTC
84443 ACTCTGTTACTGAACTGTTCGTAGTAGGGGAAAAAAGAGAGAACCTGGTTTTTTAGAGGG-TTTG
66 ACTCTGTTACTGAACTGTTCGTAGTAGGGGAAAAAAGAGAGAACCTGGTTTTTTAG-GGGATTTG
*
84507 TTGAAGCCTGAAGGGATATGTATATTTTAGGGTTCTAATTTTCTGGTTATTTACGATATTGGGTC
130 -T------TGAAGGGATATGTATATTTTAGGGTTCTAATTTTCTGGTTATTTACAATATTGGGTC
84572 TAAATTCTTCATTCAAAGCCGTCTCGTTTTGTACTTTCTTGTTGAAAGGATAGAATTGTCATCTT
188 TAAATTCTTCATTCAAAGCCGTCTCGTTTTGTACTTTCTTGTTGAAAGGATAGAATTGTCATCTT
84637 AGATATGTGGAGGTCTTGGTCTTCTTAGTTTGTTCTTGTCTGGTTTTGAAGAACTCTAGAAGCA
253 AGATATGTGGAGGTCTTGGTCTTCTTAGTTTGTTCTTGTCTGGTTTTGAAGAACTCTAGAAGCA
84701 A
1 A
84702 CCCTTATATT
Statistics
Matches: 308, Mismatches: 7, Indels: 10
0.95 0.02 0.03
Matches are distributed among these distances:
315 88 0.29
316 36 0.12
322 184 0.60
ACGTcount: A:0.25, C:0.13, G:0.22, T:0.41
Consensus pattern (316 bp):
AATCTGATTTAGAGGGTTAGCGACTGATAATCCTTATGATAATCTGAAAATTTTCTTTTCCTTTC
ACTCTGTTACTGAACTGTTCGTAGTAGGGGAAAAAAGAGAGAACCTGGTTTTTTAGGGGATTTGT
TGAAGGGATATGTATATTTTAGGGTTCTAATTTTCTGGTTATTTACAATATTGGGTCTAAATTCT
TCATTCAAAGCCGTCTCGTTTTGTACTTTCTTGTTGAAAGGATAGAATTGTCATCTTAGATATGT
GGAGGTCTTGGTCTTCTTAGTTTGTTCTTGTCTGGTTTTGAAGAACTCTAGAAGCA
Found at i:86385 original size:96 final size:96
Alignment explanation
Indices: 86219--86412 Score: 273
Period size: 96 Copynumber: 2.0 Consensus size: 96
86209 GCTATCCATG
* * * *
86219 ATAAATCTGCATTTGAACATGATTTTCCTTCGCTTGGTGCTGAAGAAAGACCAGTGGGGTCTGAA
1 ATAAATCTGCATTTGAACATGATTTGCCTTCACTTGGTGCTGAAGAAAGACAACTGGGGTCTGAA
*
86284 ATAGGAAGAATTTCGTCTCCTGGCTTGAGTA
66 ATAGGAAGAATTTCATCTCCTGGCTTGAGTA
* *
86315 ATAAATTTGC-TTTCGAACATGATTTGCCTTCACTTGGTGCTGAAGAAAGACAACTTGGGTCTGA
1 ATAAATCTGCATTT-GAACATGATTTGCCTTCACTTGGTGCTGAAGAAAGACAACTGGGGTCTGA
* * * *
86379 AGTAGGAAGAGTTTCATTTCCTGGTTTGAGTA
65 AATAGGAAGAATTTCATCTCCTGGCTTGAGTA
86411 AT
1 AT
86413 CCTGGGCAGA
Statistics
Matches: 86, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
95 3 0.03
96 83 0.97
ACGTcount: A:0.27, C:0.15, G:0.24, T:0.33
Consensus pattern (96 bp):
ATAAATCTGCATTTGAACATGATTTGCCTTCACTTGGTGCTGAAGAAAGACAACTGGGGTCTGAA
ATAGGAAGAATTTCATCTCCTGGCTTGAGTA
Found at i:90359 original size:18 final size:18
Alignment explanation
Indices: 90334--90385 Score: 65
Period size: 18 Copynumber: 3.1 Consensus size: 18
90324 AATGGAGGCT
90334 CAGCTTGTGATGATGATG
1 CAGCTTGTGATGATGATG
**
90352 GTGCTTGTGATG-T--TG
1 CAGCTTGTGATGATGATG
90367 CAGCTTGTGATGATGATG
1 CAGCTTGTGATGATGATG
90385 C
1 C
90386 TTGTGATGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
15 12 0.44
16 1 0.04
17 1 0.04
18 13 0.48
ACGTcount: A:0.17, C:0.12, G:0.35, T:0.37
Consensus pattern (18 bp):
CAGCTTGTGATGATGATG
Found at i:90380 original size:30 final size:30
Alignment explanation
Indices: 90334--90400 Score: 107
Period size: 30 Copynumber: 2.1 Consensus size: 30
90324 AATGGAGGCT
90334 CAGCTTGTGATGATGATGGTGCTTGTGATGTTG
1 CAGCTTGTGATGATGA---TGCTTGTGATGTTG
90367 CAGCTTGTGATGATGATGCTTGTGATGTTG
1 CAGCTTGTGATGATGATGCTTGTGATGTTG
90397 CAGC
1 CAGC
90401 CTTTGATAGT
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
30 18 0.53
33 16 0.47
ACGTcount: A:0.16, C:0.12, G:0.34, T:0.37
Consensus pattern (30 bp):
CAGCTTGTGATGATGATGCTTGTGATGTTG
Found at i:90407 original size:15 final size:15
Alignment explanation
Indices: 90354--90400 Score: 69
Period size: 15 Copynumber: 3.1 Consensus size: 15
90344 TGATGATGGT
90354 GCTTGTGATGTTGCA
1 GCTTGTGATGTTGCA
*
90369 GCTTGTGATGATG-A
1 GCTTGTGATGTTGCA
90383 TGCTTGTGATGTTGCA
1 -GCTTGTGATGTTGCA
90399 GC
1 GC
90401 CTTTGATAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
14 1 0.04
15 26 0.93
16 1 0.04
ACGTcount: A:0.15, C:0.13, G:0.34, T:0.38
Consensus pattern (15 bp):
GCTTGTGATGTTGCA
Found at i:90622 original size:18 final size:18
Alignment explanation
Indices: 90599--90635 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
90589 ATTAGGTCGC
90599 CTAGGTGGCATGTTGCCT
1 CTAGGTGGCATGTTGCCT
90617 CTAGGTGGCATGTTGCCT
1 CTAGGTGGCATGTTGCCT
90635 C
1 C
90636 CAACTATCCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.11, C:0.24, G:0.32, T:0.32
Consensus pattern (18 bp):
CTAGGTGGCATGTTGCCT
Found at i:94120 original size:23 final size:22
Alignment explanation
Indices: 94070--94123 Score: 81
Period size: 22 Copynumber: 2.4 Consensus size: 22
94060 TGTTTTTATA
94070 TTAAAAAAACCCTAAAAGTATT
1 TTAAAAAAACCCTAAAAGTATT
* *
94092 TCAAAAAATCCCTAAAAGTATTT
1 TTAAAAAAACCCTAAAAGTA-TT
94115 TTAAAAAAA
1 TTAAAAAAA
94124 TTAAAAAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
22 18 0.67
23 9 0.33
ACGTcount: A:0.56, C:0.13, G:0.04, T:0.28
Consensus pattern (22 bp):
TTAAAAAAACCCTAAAAGTATT
Found at i:95441 original size:14 final size:14
Alignment explanation
Indices: 95422--95464 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 14
95412 ATGATTTTAA
95422 AAAATAAATTATAT
1 AAAATAAATTATAT
* *
95436 AAAATAAATTAAAA
1 AAAATAAATTATAT
*
95450 AAAATAAAGTATAT
1 AAAATAAATTATAT
95464 A
1 A
95465 CTTTTATAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (14 bp):
AAAATAAATTATAT
Found at i:95674 original size:28 final size:29
Alignment explanation
Indices: 95642--95703 Score: 90
Period size: 29 Copynumber: 2.2 Consensus size: 29
95632 TCTAAAAGTT
*
95642 ATATT-TTTAGTCAAAATAGGTGCCTAAA
1 ATATTATTTAGTCAAAATAGGTACCTAAA
* *
95670 ATATTATTTAGTCAAAATATGTACTTAAA
1 ATATTATTTAGTCAAAATAGGTACCTAAA
95699 ATATT
1 ATATT
95704 CAATTTTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 5 0.17
29 25 0.83
ACGTcount: A:0.42, C:0.08, G:0.10, T:0.40
Consensus pattern (29 bp):
ATATTATTTAGTCAAAATAGGTACCTAAA
Found at i:96659 original size:3 final size:3
Alignment explanation
Indices: 96651--96682 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
96641 CTTGATTAAT
*
96651 TAA TAA TAA TAA TAA TAA TAA TAA TAG TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
96683 TAGTCAAACC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:99289 original size:28 final size:28
Alignment explanation
Indices: 99250--99325 Score: 100
Period size: 27 Copynumber: 2.7 Consensus size: 28
99240 AAAATCGGCG
* *
99250 TCGGGTCAGGTTTTTTTAAGTTTGATAT
1 TCGGGTCGGGTTTTTTTAAGTGTGATAT
*
99278 TCGGGTCGGG-TTTTTTAAGTGTGCTAT
1 TCGGGTCGGGTTTTTTTAAGTGTGATAT
99305 TCGGGTCGGGTCATTTTTTAA
1 TCGGGTCGGGT--TTTTTTAA
99326 TTCGGGATCG
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
27 25 0.60
28 9 0.21
30 8 0.19
ACGTcount: A:0.14, C:0.11, G:0.29, T:0.46
Consensus pattern (28 bp):
TCGGGTCGGGTTTTTTTAAGTGTGATAT
Found at i:99999 original size:18 final size:16
Alignment explanation
Indices: 99951--99986 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
99941 ATGTTTTAGA
*
99951 TTCAGATTCCAATTCC
1 TTCAGATTCTAATTCC
99967 TTCAGATTCTAATTCC
1 TTCAGATTCTAATTCC
99983 TTCA
1 TTCA
99987 TAGATTTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.25, C:0.28, G:0.06, T:0.42
Consensus pattern (16 bp):
TTCAGATTCTAATTCC
Done.