Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015278.1 Kokia drynarioides strain JFW-HI SEQ_130323, 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: 232779
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 583 characters in sequence are not A, C, G, or T
Found at i:4906 original size:2 final size:2
Alignment explanation
Indices: 4901--4926 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4891 CAATATATTT
4901 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
4927 GAGAGAGAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4931 original size:2 final size:2
Alignment explanation
Indices: 4926--4952 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4916 ATATATATAT
4926 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
4953 TTATTGATCG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:16992 original size:18 final size:17
Alignment explanation
Indices: 16971--17004 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
16961 ATATTTTTTA
*
16971 TATATATAATAGAAAAAG
1 TATAAATAATA-AAAAAG
16989 TATAAATAATAAAAAA
1 TATAAATAATAAAAAA
17005 TTATGTGACT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.68, C:0.00, G:0.06, T:0.26
Consensus pattern (17 bp):
TATAAATAATAAAAAAG
Found at i:20499 original size:22 final size:22
Alignment explanation
Indices: 20474--20519 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
20464 CATTTAATCC
*
20474 TTAAAACAATAGTCTTTTT-ATT
1 TTAAAAAAATA-TCTTTTTCATT
*
20496 TTAAAAAAATATTTTTTTCATT
1 TTAAAAAAATATCTTTTTCATT
20518 TT
1 TT
20520 TTTCCTGTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 6 0.29
22 15 0.71
ACGTcount: A:0.37, C:0.07, G:0.02, T:0.54
Consensus pattern (22 bp):
TTAAAAAAATATCTTTTTCATT
Found at i:25751 original size:3 final size:3
Alignment explanation
Indices: 25743--25768 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
25733 TTCTCAATTT
25743 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
25769 CAAATTTCAC
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:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:28477 original size:19 final size:20
Alignment explanation
Indices: 28445--28485 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
28435 TAAATAACAC
28445 TTTTTATGCATTTTATA-AT
1 TTTTTATGCATTTTATATAT
28464 TTTTTATG-ATTTTTATATAT
1 TTTTTATGCA-TTTTATATAT
28484 TT
1 TT
28486 GACAATTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 1 0.05
19 15 0.75
20 4 0.20
ACGTcount: A:0.24, C:0.02, G:0.05, T:0.68
Consensus pattern (20 bp):
TTTTTATGCATTTTATATAT
Found at i:28485 original size:28 final size:28
Alignment explanation
Indices: 28445--28506 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
28435 TAAATAACAC
* * *
28445 TTTTTATGCATTTTATAATTTTT-TATGA
1 TTTTTATACATTTGACAATTTTTATAT-A
*
28473 TTTTTATATATTTGACAATTTTTATATA
1 TTTTTATACATTTGACAATTTTTATATA
28501 TTTTTA
1 TTTTTA
28507 AAAAAATTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 26 0.90
29 3 0.10
ACGTcount: A:0.27, C:0.03, G:0.05, T:0.65
Consensus pattern (28 bp):
TTTTTATACATTTGACAATTTTTATATA
Found at i:34297 original size:5 final size:5
Alignment explanation
Indices: 34287--34312 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
34277 GTGTATTTAT
34287 ATTCA ATTCA ATTCA ATTCA ATTCA A
1 ATTCA ATTCA ATTCA ATTCA ATTCA A
34313 AGCTTGTTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.19, G:0.00, T:0.38
Consensus pattern (5 bp):
ATTCA
Found at i:36560 original size:20 final size:20
Alignment explanation
Indices: 36535--36575 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
36525 GGTTTGGGAT
36535 AATGCCTCAATCTAGTATTC
1 AATGCCTCAATCTAGTATTC
36555 AATGCCTCAATCTAGTATTC
1 AATGCCTCAATCTAGTATTC
36575 A
1 A
36576 CTTACTGACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.32, C:0.24, G:0.10, T:0.34
Consensus pattern (20 bp):
AATGCCTCAATCTAGTATTC
Found at i:45708 original size:19 final size:17
Alignment explanation
Indices: 45686--45724 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
45676 AACAATAAAT
45686 CTATACTAAATATATAACA
1 CTATACT-AATATA-AACA
*
45705 CTATTCTAATATAAACA
1 CTATACTAATATAAACA
45722 CTA
1 CTA
45725 AAATAATGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 7 0.37
18 6 0.32
19 6 0.32
ACGTcount: A:0.49, C:0.18, G:0.00, T:0.33
Consensus pattern (17 bp):
CTATACTAATATAAACA
Found at i:45800 original size:28 final size:28
Alignment explanation
Indices: 45733--45812 Score: 74
Period size: 28 Copynumber: 2.8 Consensus size: 28
45723 TAAAATAATG
*
45733 TTAAGATAACTATATAAAAATTTTAAATAA
1 TTAAAATAA-TATAT-AAAATTTTAAATAA
* *
45763 ATAAAA-AATATATAAAATTATTAAGT-A
1 TTAAAATAATATATAAAATT-TTAAATAA
*
45790 TTAAAATAATATTATATAATTTT
1 TTAAAATAATA-TATAAAATTTT
45813 TTTAAAAAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
27 12 0.29
28 16 0.38
29 10 0.24
30 4 0.10
ACGTcount: A:0.56, C:0.01, G:0.03, T:0.40
Consensus pattern (28 bp):
TTAAAATAATATATAAAATTTTAAATAA
Found at i:48293 original size:12 final size:12
Alignment explanation
Indices: 48276--48317 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
48266 TTAGCTTAAT
48276 CGAACATGTTCA
1 CGAACATGTTCA
**
48288 CGAACAT-TAAA
1 CGAACATGTTCA
48299 CGAACATGTTCA
1 CGAACATGTTCA
*
48311 TGAACAT
1 CGAACAT
48318 ATAATTGACT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
11 9 0.38
12 15 0.62
ACGTcount: A:0.40, C:0.21, G:0.14, T:0.24
Consensus pattern (12 bp):
CGAACATGTTCA
Found at i:48297 original size:23 final size:23
Alignment explanation
Indices: 48271--48340 Score: 79
Period size: 23 Copynumber: 3.0 Consensus size: 23
48261 TTCATTTAGC
48271 TTAATCGAACATGTTCACGAACA
1 TTAATCGAACATGTTCACGAACA
* *
48294 TTAAACGAACATGTTCATGAACA
1 TTAATCGAACATGTTCACGAACA
* *
48317 TATAATTG-ACTATGTTCACAAACA
1 T-TAATCGAAC-ATGTTCACGAACA
48341 ATGTTAATGA
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
23 24 0.62
24 15 0.38
ACGTcount: A:0.41, C:0.19, G:0.11, T:0.29
Consensus pattern (23 bp):
TTAATCGAACATGTTCACGAACA
Found at i:49287 original size:37 final size:37
Alignment explanation
Indices: 49244--49323 Score: 151
Period size: 37 Copynumber: 2.2 Consensus size: 37
49234 GTAGCCACTA
*
49244 ACAAGGATGCTTGCATAGGTGCAACCATCACCACTGC
1 ACAAGGATGCTTGCACAGGTGCAACCATCACCACTGC
49281 ACAAGGATGCTTGCACAGGTGCAACCATCACCACTGC
1 ACAAGGATGCTTGCACAGGTGCAACCATCACCACTGC
49318 ACAAGG
1 ACAAGG
49324 TCACGTGGGT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 42 1.00
ACGTcount: A:0.31, C:0.30, G:0.23, T:0.16
Consensus pattern (37 bp):
ACAAGGATGCTTGCACAGGTGCAACCATCACCACTGC
Found at i:51370 original size:25 final size:23
Alignment explanation
Indices: 51303--51379 Score: 104
Period size: 23 Copynumber: 3.3 Consensus size: 23
51293 ACGTTAGCGC
*
51303 GCTTACTG-TTCAGCACTATGTGT
1 GCTTACTGTTTC-GCACTGTGTGT
51326 GCTTACTGTTTCGCACTGTGTGT
1 GCTTACTGTTTCGCACTGTGTGT
51349 GCTTACTGTTTCGCACAT-TGTGT
1 GCTTACTGTTTCGCAC-TGTGTGT
*
51372 GCCTACTG
1 GCTTACTG
51380 ATTTGCGCTT
Statistics
Matches: 50, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
23 46 0.92
24 4 0.08
ACGTcount: A:0.13, C:0.23, G:0.23, T:0.40
Consensus pattern (23 bp):
GCTTACTGTTTCGCACTGTGTGT
Found at i:51431 original size:23 final size:23
Alignment explanation
Indices: 51372--51425 Score: 108
Period size: 23 Copynumber: 2.3 Consensus size: 23
51362 CACATTGTGT
51372 GCCTACTGATTTGCGCTTATAGC
1 GCCTACTGATTTGCGCTTATAGC
51395 GCCTACTGATTTGCGCTTATAGC
1 GCCTACTGATTTGCGCTTATAGC
51418 GCCTACTG
1 GCCTACTG
51426 GATTGCACTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.17, C:0.28, G:0.22, T:0.33
Consensus pattern (23 bp):
GCCTACTGATTTGCGCTTATAGC
Found at i:56945 original size:61 final size:61
Alignment explanation
Indices: 56812--57002 Score: 251
Period size: 61 Copynumber: 3.1 Consensus size: 61
56802 TCTTCTTAAG
* * * *
56812 TTGGTACCTGAATTTGACACTTTTTCCTAATCTGGTATCTAAACTTTTTTTTT-ATTCAAT
1 TTGGTACCTGAACTTGACACTTTTTCCTAATTTGGTACCTAAGCTTTTTTTTTGATTCAAT
* * *
56872 TTGGTACCTGAACTTGACACTTTTT-CTGATTTGGTACCTGAGCTTTTTTTTTGGATCCAAT
1 TTGGTACCTGAACTTGACACTTTTTCCTAATTTGGTACCTAAGCTTTTTTTTT-GATTCAAT
* * * **
56933 TTGGTACTTGAACTTGACATTTTTTCCTAACTTGGTACCTAAGCTTTTTTTAAGATTCAAT
1 TTGGTACCTGAACTTGACACTTTTTCCTAATTTGGTACCTAAGCTTTTTTTTTGATTCAAT
56994 TTGGTACCT
1 TTGGTACCT
57003 AAATTTATCA
Statistics
Matches: 112, Mismatches: 16, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
59 22 0.20
60 24 0.21
61 44 0.39
62 22 0.20
ACGTcount: A:0.21, C:0.17, G:0.14, T:0.47
Consensus pattern (61 bp):
TTGGTACCTGAACTTGACACTTTTTCCTAATTTGGTACCTAAGCTTTTTTTTTGATTCAAT
Found at i:70286 original size:96 final size:96
Alignment explanation
Indices: 70112--70296 Score: 277
Period size: 96 Copynumber: 1.9 Consensus size: 96
70102 GTAAAAGATG
** *
70112 TTCGATTATCTCGATTTGAAGAAAGGTTGCACCTAGTAAGTTAAGGCGCAAATTTTCAGAATTGA
1 TTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAAATTTTCAGAATCGA
*
70177 AGATAAGGAAACATTGCCTCGATTAAGGGTT
66 AGATAAAGAAACATTGCCTCGATTAAGGGTT
*
70208 TTCGATTATTTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAAATTTTC-GAAACTC
1 TTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAAATTTTCAG-AA-TC
70272 GAA-ATAAA-AGAACATTGCCTCGATT
64 GAAGATAAAGA-AACATTGCCTCGATT
70297 TTAAAGTTTT
Statistics
Matches: 81, Mismatches: 5, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
95 2 0.02
96 75 0.93
97 4 0.05
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.30
Consensus pattern (96 bp):
TTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAAATTTTCAGAATCGA
AGATAAAGAAACATTGCCTCGATTAAGGGTT
Found at i:70584 original size:28 final size:28
Alignment explanation
Indices: 70508--70595 Score: 76
Period size: 28 Copynumber: 3.1 Consensus size: 28
70498 AAATGAGACT
* *
70508 TTTTGGATACTCGAGGG-CAAAATGGTAA
1 TTTTGGATA-TTGAGGGTAAAAATGGTAA
*
70536 TTTTGGATTATTGGGGGT-AAAATGGTAA
1 TTTTGGA-TATTGAGGGTAAAAATGGTAA
*
70564 TTTTGGA-AGTTCGAGGTTAAAAATGG-AA
1 TTTTGGATA-TT-GAGGGTAAAAATGGTAA
70592 TTTT
1 TTTT
70596 TAGAAGTTTT
Statistics
Matches: 51, Mismatches: 4, Indels: 10
0.78 0.06 0.15
Matches are distributed among these distances:
26 1 0.02
27 2 0.04
28 39 0.76
29 9 0.18
ACGTcount: A:0.31, C:0.05, G:0.28, T:0.36
Consensus pattern (28 bp):
TTTTGGATATTGAGGGTAAAAATGGTAA
Found at i:70596 original size:29 final size:30
Alignment explanation
Indices: 70554--70625 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 30
70544 TATTGGGGGT
* *
70554 AAAATGGTAA-TTTTGGAAG-TTCGAGGTTA
1 AAAATGG-AATTTTTAGAAGTTTCGAGGTCA
* *
70583 AAAATGGAATTTTTAGAAGTTTTGGGGTCA
1 AAAATGGAATTTTTAGAAGTTTCGAGGTCA
70613 AAAATGGAATTTT
1 AAAATGGAATTTT
70626 CGAATAGTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
28 2 0.05
29 15 0.41
30 20 0.54
ACGTcount: A:0.36, C:0.03, G:0.25, T:0.36
Consensus pattern (30 bp):
AAAATGGAATTTTTAGAAGTTTCGAGGTCA
Found at i:71561 original size:56 final size:56
Alignment explanation
Indices: 71476--71585 Score: 136
Period size: 56 Copynumber: 2.0 Consensus size: 56
71466 TTTTTCATCC
* *
71476 TTTCTCTTTCCTTTTTATTTTGTTAAAACCATATC-TAATTTTTTTTTAAAACCCCT
1 TTTCTCTTTCCTTTTTATTTTGTTAAAACCAT-TCTTAAGTTTCTTTTAAAACCCCT
* *
71532 TTTCTCTTTCTTACTTTTA-TTT-TTAAAACCGTTCTTAAGTTTCTTTTAAAACCC
1 TTTCTCTTTCCT--TTTTATTTTGTTAAAACCATTCTTAAGTTTCTTTTAAAACCC
71586 ATTTCTTTAT
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
55 2 0.04
56 37 0.79
57 3 0.06
58 5 0.11
ACGTcount: A:0.23, C:0.20, G:0.03, T:0.55
Consensus pattern (56 bp):
TTTCTCTTTCCTTTTTATTTTGTTAAAACCATTCTTAAGTTTCTTTTAAAACCCCT
Found at i:71844 original size:15 final size:16
Alignment explanation
Indices: 71817--71850 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
71807 TATTATTTAT
71817 TTAATAAATATTATCA
1 TTAATAAATATTATCA
*
71833 TTAATAAA-ATTATTA
1 TTAATAAATATTATCA
71848 TTA
1 TTA
71851 TTATCATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (16 bp):
TTAATAAATATTATCA
Found at i:71852 original size:24 final size:24
Alignment explanation
Indices: 71825--71870 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
71815 ATTTAATAAA
71825 TATTATCATTAATAAAATTATTAT
1 TATTATCATTAATAAAATTATTAT
*
71849 TATTATCATTAATGAAATTATT
1 TATTATCATTAATAAAATTATT
71871 TAATATATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.50
Consensus pattern (24 bp):
TATTATCATTAATAAAATTATTAT
Found at i:71853 original size:18 final size:17
Alignment explanation
Indices: 71805--71853 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
71795 ATTACTATTT
71805 ATTATTATTTATTTAATAA
1 ATTATTA-TTA-TTAATAA
*
71824 A-TATTATCATTAATAAA
1 ATTATTATTATTAAT-AA
71841 ATTATTATTATTA
1 ATTATTATTATTA
71854 TCATTAATGA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 5 0.19
17 5 0.19
18 15 0.58
19 1 0.04
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (17 bp):
ATTATTATTATTAATAA
Found at i:72673 original size:17 final size:18
Alignment explanation
Indices: 72637--72706 Score: 81
Period size: 17 Copynumber: 4.0 Consensus size: 18
72627 TAATAATTTT
* *
72637 TTTAATTTTAAAAATAAA
1 TTTAAATTTAAAATTAAA
*
72655 TTTAAATTT-AGATTAAA
1 TTTAAATTTAAAATTAAA
72672 TTTAAATTTAAAATT-AA
1 TTTAAATTTAAAATTAAA
* *
72689 TTTAAATTCAAATTTAAA
1 TTTAAATTTAAAATTAAA
72707 ATAAATCTAA
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
17 30 0.68
18 14 0.32
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (18 bp):
TTTAAATTTAAAATTAAA
Found at i:72725 original size:7 final size:6
Alignment explanation
Indices: 72637--72723 Score: 81
Period size: 6 Copynumber: 15.0 Consensus size: 6
72627 TAATAATTTT
* ** *
72637 TTTAAT TTTAAA AATAAA TTTAAA TTTAGA -TTAAA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * * *
72684 ATT-AA TTTAAA TTCAAA TTTAAA -ATAAA TCTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
72724 ATAAAATTAA
Statistics
Matches: 64, Mismatches: 14, Indels: 6
0.76 0.17 0.07
Matches are distributed among these distances:
5 12 0.19
6 52 0.81
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.44
Consensus pattern (6 bp):
TTTAAA
Found at i:72734 original size:17 final size:17
Alignment explanation
Indices: 72647--72734 Score: 70
Period size: 17 Copynumber: 4.8 Consensus size: 17
72637 TTTAATTTTA
*
72647 AAAATAAATTTAAATTT
1 AAAATAAAATTAAATTT
* * *
72664 AGATTAAATTTAAATTT
1 AAAATAAAATTAAATTT
72681 AAAATTAATTTAAATTCAAATTT
1 AAAA-T-A---AAATT-AAATTT
72704 AAAAT-AAATCTAAATTT
1 AAAATAAAAT-TAAATTT
72721 AAAATAAAATTAAA
1 AAAATAAAATTAAA
72735 AAGGGCTCGG
Statistics
Matches: 58, Mismatches: 5, Indels: 16
0.73 0.06 0.20
Matches are distributed among these distances:
17 36 0.62
18 6 0.10
19 1 0.02
22 5 0.09
23 10 0.17
ACGTcount: A:0.58, C:0.02, G:0.01, T:0.39
Consensus pattern (17 bp):
AAAATAAAATTAAATTT
Found at i:72734 original size:23 final size:24
Alignment explanation
Indices: 72651--72734 Score: 95
Period size: 23 Copynumber: 3.7 Consensus size: 24
72641 ATTTTAAAAA
* *
72651 TAAATTTAAATTTAGAT-TAAATT
1 TAAATTTAAAATTAAATCTAAATT
*
72674 TAAATTTAAAATT-AATTTAAATT
1 TAAATTTAAAATTAAATCTAAATT
*
72697 CAAATTTAAAA-TAAATCTAAATT
1 TAAATTTAAAATTAAATCTAAATT
*
72720 TAAA-ATAAAATTAAA
1 TAAATTTAAAATTAAA
72735 AAGGGCTCGG
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
22 8 0.15
23 44 0.85
ACGTcount: A:0.56, C:0.02, G:0.01, T:0.40
Consensus pattern (24 bp):
TAAATTTAAAATTAAATCTAAATT
Found at i:73528 original size:207 final size:206
Alignment explanation
Indices: 73055--73646 Score: 744
Period size: 207 Copynumber: 2.9 Consensus size: 206
73045 TGACTTGACT
* * * * * *
73055 TTCTTCTCAGTATCTTACCAGGAAGATGACTGCATCACTTGCTTT-GATCCACTTCTCTGTGT-T
1 TTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTG-TTTCAATCCGCTTCTCTGTATCT
* * *
73118 TCATCAGGAAGGA-GAATTTGGTTCACTTCTCCGTTTCTCATCAGGAAGCTAACCATTTTATTGT
65 T-ATCAGGAA-GACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGT
* * * * * *
73182 TTCGACTTGCTTCTTAGCATCTCATCAGGAAGTTGGGG-TCAAAGATTTGCTCACATCGAGCGTA
128 TTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCAAGCGTA
*
73246 GGTTTGATTTGGCC
193 GGTTTGATTCGGCC
* * ** *
73260 TTCTTCTCAGTATCTCATCAGGAAAATGACCGTATTGCTTGTTTCAATCCGGTTCTCTGTATCTT
1 TTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCGCTTCTCTGTATCTT
* * * * * *
73325 ATCAGTAAGACGAATTTGGTCCACTTGTCAATATCTCATCAAGAAGCTAACCTTTTTATTGCTTC
66 ATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGTTTC
* * * *
73390 GACCTGCTTCTCAATATCTCATCAGGAAGCTGAGGGTTCGAAGATTCGCTCTA-ATCAAGTGTGG
131 GACCTGCTTCTCAGTATCTCATCAGGAAGCTG-GGGTTCGAAGATTTGCTC-ACATCAAGCGTAG
*
73454 GTTTGATTCGGTC
194 GTTTGATTCGGCC
* * *
73467 TTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATTCGCTTATCTGTATCTC
1 TTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCGCTTCTCTGTATCTT
* * *
73532 ATCAGGAAGACGAATTTGGTCTACTTTTTAGTATCTCATCAGGAAGCTAACCATTTTATTGTTTC
66 ATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGTTTC
* *
73597 GCCCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAATATTTGCTC
131 GACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTC
73647 GCTTTGAGTC
Statistics
Matches: 329, Mismatches: 52, Indels: 11
0.84 0.13 0.03
Matches are distributed among these distances:
204 5 0.02
205 127 0.39
206 21 0.06
207 175 0.53
208 1 0.00
ACGTcount: A:0.23, C:0.22, G:0.19, T:0.36
Consensus pattern (206 bp):
TTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCGCTTCTCTGTATCTT
ATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGTTTC
GACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCAAGCGTAGGT
TTGATTCGGCC
Found at i:76487 original size:18 final size:17
Alignment explanation
Indices: 76466--76508 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
76456 TACTAATTAT
76466 TATTAATTATTTAATAAA
1 TATT-ATTATTTAATAAA
*
76484 TATTATCA-TTAATAAA
1 TATTATTATTTAATAAA
76500 -ATTATTATT
1 TATTATTATT
76509 ATTATCATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 6 0.27
16 9 0.41
17 3 0.14
18 4 0.18
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (17 bp):
TATTATTATTTAATAAA
Found at i:76511 original size:24 final size:24
Alignment explanation
Indices: 76484--76529 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
76474 ATTTAATAAA
76484 TATTATCATTAATAAAATTATTAT
1 TATTATCATTAATAAAATTATTAT
*
76508 TATTATCATTAATGAAATTATT
1 TATTATCATTAATAAAATTATT
76530 TAATATATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.50
Consensus pattern (24 bp):
TATTATCATTAATAAAATTATTAT
Found at i:76512 original size:18 final size:17
Alignment explanation
Indices: 76464--76512 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
76454 TTTACTAATT
76464 ATTATTAATTATTTAATAA
1 ATTATT-ATTA-TTAATAA
*
76483 A-TATTATCATTAATAAA
1 ATTATTATTATTAAT-AA
76500 ATTATTATTATTA
1 ATTATTATTATTA
76513 TCATTAATGA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 5 0.19
17 6 0.23
18 14 0.54
19 1 0.04
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (17 bp):
ATTATTATTATTAATAA
Found at i:77313 original size:17 final size:18
Alignment explanation
Indices: 77277--77346 Score: 74
Period size: 17 Copynumber: 4.0 Consensus size: 18
77267 TAATAATTTT
*
77277 TTTAATTTTGAAAA-TAAA
1 TTTAAATTT-AAAATTAAA
*
77295 TTTAAATTT-AGATTAAA
1 TTTAAATTTAAAATTAAA
77312 TTTAAATTTAAAATT-AA
1 TTTAAATTTAAAATTAAA
* *
77329 TTTAAATTCAAATTTAAA
1 TTTAAATTTAAAATTAAA
77347 ATAAATCTAA
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
16 2 0.05
17 28 0.64
18 14 0.32
ACGTcount: A:0.50, C:0.01, G:0.03, T:0.46
Consensus pattern (18 bp):
TTTAAATTTAAAATTAAA
Found at i:77365 original size:7 final size:6
Alignment explanation
Indices: 77291--77363 Score: 80
Period size: 6 Copynumber: 12.7 Consensus size: 6
77281 ATTTTGAAAA
* *
77291 TAAATT TAAATT TAGA-T TAAATT TAAATT TAAAAT T-AATT TAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT
* * *
77337 CAAATT TAAA-A TAAATC TAAATT TAAA
1 TAAATT TAAATT TAAATT TAAATT TAAA
77364 ATAAAATTAA
Statistics
Matches: 55, Mismatches: 9, Indels: 6
0.79 0.13 0.09
Matches are distributed among these distances:
5 12 0.22
6 43 0.78
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.42
Consensus pattern (6 bp):
TAAATT
Found at i:77374 original size:17 final size:17
Alignment explanation
Indices: 77287--77374 Score: 70
Period size: 17 Copynumber: 4.8 Consensus size: 17
77277 TTTAATTTTG
*
77287 AAAATAAATTTAAATTT
1 AAAATAAAATTAAATTT
* * *
77304 AGATTAAATTTAAATTT
1 AAAATAAAATTAAATTT
77321 AAAATTAATTTAAATTCAAATTT
1 AAAA-T-A---AAATT-AAATTT
77344 AAAAT-AAATCTAAATTT
1 AAAATAAAAT-TAAATTT
77361 AAAATAAAATTAAA
1 AAAATAAAATTAAA
77375 AGGTGCCCGG
Statistics
Matches: 58, Mismatches: 5, Indels: 16
0.73 0.06 0.20
Matches are distributed among these distances:
17 36 0.62
18 6 0.10
19 1 0.02
22 5 0.09
23 10 0.17
ACGTcount: A:0.58, C:0.02, G:0.01, T:0.39
Consensus pattern (17 bp):
AAAATAAAATTAAATTT
Found at i:77374 original size:23 final size:24
Alignment explanation
Indices: 77291--77374 Score: 95
Period size: 23 Copynumber: 3.7 Consensus size: 24
77281 ATTTTGAAAA
* *
77291 TAAATTTAAATTTAGAT-TAAATT
1 TAAATTTAAAATTAAATCTAAATT
*
77314 TAAATTTAAAATT-AATTTAAATT
1 TAAATTTAAAATTAAATCTAAATT
*
77337 CAAATTTAAAA-TAAATCTAAATT
1 TAAATTTAAAATTAAATCTAAATT
*
77360 TAAA-ATAAAATTAAA
1 TAAATTTAAAATTAAA
77375 AGGTGCCCGG
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
22 8 0.15
23 44 0.85
ACGTcount: A:0.56, C:0.02, G:0.01, T:0.40
Consensus pattern (24 bp):
TAAATTTAAAATTAAATCTAAATT
Found at i:93051 original size:2 final size:2
Alignment explanation
Indices: 93044--93073 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
93034 GTATGTCTAC
93044 AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
93074 GTTGTGTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:97092 original size:29 final size:27
Alignment explanation
Indices: 97022--97092 Score: 70
Period size: 29 Copynumber: 2.5 Consensus size: 27
97012 ATAGTCTATA
* *
97022 TAATTATAATTTTTAAAGGATTAAATC
1 TAATTTTATTTTTTAAAGGATTAAATC
* * *
97049 AAATTTTTATATTTTAAAGGAGTTAAAGTG
1 TAA-TTTTATTTTTTAAAGGA-TTAAA-TC
97079 TAATTTTATTTTTT
1 TAATTTTATTTTTT
97093 TACTAATTTA
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
27 2 0.06
28 14 0.41
29 15 0.44
30 3 0.09
ACGTcount: A:0.38, C:0.01, G:0.10, T:0.51
Consensus pattern (27 bp):
TAATTTTATTTTTTAAAGGATTAAATC
Found at i:97327 original size:7 final size:7
Alignment explanation
Indices: 97315--97340 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
97305 TATATATTTT
97315 TTTTTAA
1 TTTTTAA
97322 TTTTTAA
1 TTTTTAA
97329 TTTTTAA
1 TTTTTAA
97336 TTTTT
1 TTTTT
97341 TTTGATAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (7 bp):
TTTTTAA
Found at i:98875 original size:88 final size:90
Alignment explanation
Indices: 98719--98927 Score: 264
Period size: 89 Copynumber: 2.3 Consensus size: 90
98709 TAAGTCATTG
* * *
98719 TTTTTTTTCATTCAATTGGGTTCTTGAACTATCAAAATGCATCAAAAAGGCCCTCAAACTTTTTC
1 TTTTTTTGCACTCAATTGGGTACTTGAACTATCAAAATGCATCAAAAA-GCCCTCAAACTTTTTC
* *
98784 AAAAAAAGCTATTAAGCCCCT-A-CA
65 AAAAAAAGCAATTAAACCCCTGATCA
*
98808 TTTTTTTGTACTCAATTGGGTACTTGAAC-ATTCAAAATGCATCAATAAA-CCCTCAAACTTTTT
1 TTTTTTTGCACTCAATTGGGTACTTGAACTA-TCAAAATGCATCAA-AAAGCCCTCAAACTTTTT
* **
98871 CAAAAAAAGCAATTAAATCCCTGATTTT
64 CAAAAAAAGCAATTAAACCCCTGA-TCA
*
98899 TTTTTTTGCACCCAATTGGGTACTTGAAC
1 TTTTTTTGCACTCAATTGGGTACTTGAAC
98928 CACCCCTAAT
Statistics
Matches: 104, Mismatches: 11, Indels: 8
0.85 0.09 0.07
Matches are distributed among these distances:
88 34 0.33
89 40 0.38
90 3 0.03
91 27 0.26
ACGTcount: A:0.33, C:0.20, G:0.11, T:0.36
Consensus pattern (90 bp):
TTTTTTTGCACTCAATTGGGTACTTGAACTATCAAAATGCATCAAAAAGCCCTCAAACTTTTTCA
AAAAAAGCAATTAAACCCCTGATCA
Found at i:98901 original size:89 final size:88
Alignment explanation
Indices: 98697--98927 Score: 274
Period size: 88 Copynumber: 2.6 Consensus size: 88
98687 CAATTAAAAA
** * *
98697 AAAAAAAGCAATTAAGTCATTG-TTTTTTTT-CATTCAATTGGGTTCTTGAACTATCAAAATGCA
1 AAAAAAAGCAATTAAGTCCCTGATTTTTTTTGCACTCAATTGGGTACTTGAACTATCAAAATGCA
98760 TCAAAAAGGCCCTCAAACTTTTTC
66 TCAAAAA-GCCCTCAAACTTTTTC
* * * *
98784 AAAAAAAGCTATTAAGCCCCT-ACATTTTTTTGTACTCAATTGGGTACTTGAAC-ATTCAAAATG
1 AAAAAAAGCAATTAAGTCCCTGA-TTTTTTTTGCACTCAATTGGGTACTTGAACTA-TCAAAATG
98847 CATCAATAAA-CCCTCAAACTTTTTC
64 CATCAA-AAAGCCCTCAAACTTTTTC
* *
98872 AAAAAAAGCAATTAAATCCCTGATTTTTTTTTTTGCACCCAATTGGGTACTTGAAC
1 AAAAAAAGCAATTAAGTCCCTGA---TTTTTTTTGCACTCAATTGGGTACTTGAAC
98928 CACCCCTAAT
Statistics
Matches: 121, Mismatches: 15, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
87 17 0.14
88 41 0.34
89 33 0.27
90 3 0.02
91 27 0.22
ACGTcount: A:0.35, C:0.19, G:0.11, T:0.35
Consensus pattern (88 bp):
AAAAAAAGCAATTAAGTCCCTGATTTTTTTTGCACTCAATTGGGTACTTGAACTATCAAAATGCA
TCAAAAAGCCCTCAAACTTTTTC
Found at i:99014 original size:15 final size:16
Alignment explanation
Indices: 98994--99024 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
98984 GGCAAAATTG
98994 ATAAAAAA-ATAAAAA
1 ATAAAAAATATAAAAA
99009 ATAAAAAATATAAAAA
1 ATAAAAAATATAAAAA
99025 TTATTAATGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (16 bp):
ATAAAAAATATAAAAA
Found at i:99016 original size:14 final size:15
Alignment explanation
Indices: 98997--99025 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
98987 AAAATTGATA
98997 AAAAAATA-AAAAAT
1 AAAAAATATAAAAAT
99011 AAAAAATATAAAAAT
1 AAAAAATATAAAAAT
99026 TATTAATGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (15 bp):
AAAAAATATAAAAAT
Found at i:99109 original size:29 final size:28
Alignment explanation
Indices: 99077--99203 Score: 91
Period size: 29 Copynumber: 4.5 Consensus size: 28
99067 AATTAGAAAA
99077 AAAAAATATAAAATCATAAAAACAATTAT
1 AAAAAATATAAAATCATAAAAA-AATTAT
* *
99106 AAAATATATAGAAAT-ATAGAAAAATTAT
1 AAAAAATATA-AAATCATAAAAAAATTAT
** * *
99134 AAAATTTTATAAAGTCATAAGAAAATTAT
1 AAAA-AATATAAAATCATAAAAAAATTAT
* * *
99163 AGAAAATGT-AAA-CA-AATATAAAATTCCT
1 AAAAAATATAAAATCATAA-A-AAAATT-AT
99191 AAAAAATATAAAA
1 AAAAAATATAAAA
99204 AATTATCGCA
Statistics
Matches: 76, Mismatches: 15, Indels: 14
0.72 0.14 0.13
Matches are distributed among these distances:
25 2 0.03
26 2 0.03
27 8 0.11
28 23 0.30
29 37 0.49
30 4 0.05
ACGTcount: A:0.64, C:0.05, G:0.05, T:0.27
Consensus pattern (28 bp):
AAAAAATATAAAATCATAAAAAAATTAT
Found at i:99441 original size:11 final size:10
Alignment explanation
Indices: 99411--99461 Score: 52
Period size: 10 Copynumber: 5.2 Consensus size: 10
99401 TTTATAAAAG
99411 TTTATAATTT
1 TTTATAATTT
99421 TTTATAATTT
1 TTTATAATTT
*
99431 TTTAATGATTT
1 TTT-ATAATTT
* *
99442 TTAATAA-AT
1 TTTATAATTT
99451 TTTAT-ATTT
1 TTTATAATTT
99460 TT
1 TT
99462 ATTAAAATTA
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
8 1 0.03
9 8 0.24
10 16 0.48
11 8 0.24
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (10 bp):
TTTATAATTT
Found at i:99459 original size:18 final size:19
Alignment explanation
Indices: 99432--99481 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 19
99422 TTATAATTTT
* *
99432 TTAATGATTTTTAATAAAT
1 TTAATAATTTTTAATAAAA
* *
99451 TTTAT-ATTTTTATTAAAA
1 TTAATAATTTTTAATAAAA
99469 TTAATAATTTTTA
1 TTAATAATTTTTA
99482 TTTATTTTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
18 15 0.58
19 11 0.42
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (19 bp):
TTAATAATTTTTAATAAAA
Found at i:99469 original size:19 final size:20
Alignment explanation
Indices: 99399--99483 Score: 63
Period size: 19 Copynumber: 4.4 Consensus size: 20
99389 TTTATAGTTT
*
99399 TTTTTA-TAAAAGTTTATAA
1 TTTTTATTAAAATTTTATAA
** *
99418 TTTTT-TATAATTTTTTAATGA
1 TTTTTAT-TAAAATTTT-ATAA
*
99439 TTTTTAAT-AAATTTTAT-A
1 TTTTTATTAAAATTTTATAA
*
99457 TTTTTATTAAAA-TTAATAA
1 TTTTTATTAAAATTTTATAA
99476 TTTTTATT
1 TTTTTATT
99484 TATTTTTATT
Statistics
Matches: 51, Mismatches: 9, Indels: 12
0.71 0.12 0.17
Matches are distributed among these distances:
18 12 0.24
19 19 0.37
20 11 0.22
21 9 0.18
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.61
Consensus pattern (20 bp):
TTTTTATTAAAATTTTATAA
Found at i:99826 original size:92 final size:86
Alignment explanation
Indices: 99615--99875 Score: 267
Period size: 92 Copynumber: 2.9 Consensus size: 86
99605 TTTTGATTCA
* * *
99615 TTTGATAGTTAAAATACCCAATTGAGTGAAAAAAAT-CAGGAGCTTAATTGC-TTTTTTGAAAAA
1 TTTGAAAGTTCAAGTACCCAATTGAGTGAAAAAAATGCAGG-GCTTAATTGCTTTTTTTGAAAAA
* *
99678 GTTTAAGGGCCTCTTTTATGCAT
65 GTTTGAGGGTCT-TTTTATGCAT
* * *
99701 TTTGAAAGTTCAAGCACCCAATTAATTGCAAAAAAATGGCAAGGGCTTAATTGCTTTTTTTGAAA
1 TTTGAAAGTTCAAGTACCCAATTGAGTG-AAAAAAAT-GC-AGGGCTTAATTGCTTTTTTTGAAA
* *
99766 AGGTTTGAGGGTCTTTTTGAATTCATT
63 AAGTTTGAGGGTCTTTTT--ATGCA-T
** * **
99793 TTTGGCAGTTCAAGTACCCAATTGAGTGTAAAAAGAAAGCAGCGGCTTAATTGCTTTTTTAAAAA
1 TTTGAAAGTTCAAGTACCCAATTGAGTG-AAAAA-AATGCAG-GGCTTAATTGCTTTTTTTGAAA
99858 AAGTTTGAGGGT-TTTTTA
63 AAGTTTGAGGGTCTTTTTA
99876 CACCCTTAAG
Statistics
Matches: 145, Mismatches: 20, Indels: 17
0.80 0.11 0.09
Matches are distributed among these distances:
86 22 0.15
87 8 0.06
89 16 0.11
90 24 0.17
91 11 0.08
92 62 0.43
93 2 0.01
ACGTcount: A:0.33, C:0.11, G:0.20, T:0.36
Consensus pattern (86 bp):
TTTGAAAGTTCAAGTACCCAATTGAGTGAAAAAAATGCAGGGCTTAATTGCTTTTTTTGAAAAAG
TTTGAGGGTCTTTTTATGCAT
Found at i:108418 original size:18 final size:17
Alignment explanation
Indices: 108397--108481 Score: 50
Period size: 20 Copynumber: 4.8 Consensus size: 17
108387 ACATTTTAAA
108397 ATTTTAAATTTTTTATAT
1 ATTTTAAA-TTTTTATAT
108415 ATTTTTTAGAATTTTTATAT
1 A--TTTTA-AATTTTTATAT
* * *
108435 TTTTTAAA---ATATAA
1 ATTTTAAATTTTTATAT
108449 ATTTTAAAATTTTTATAAAT
1 ATTTT-AAATTTTTAT--AT
*
108469 ATTTTGAATTTTT
1 ATTTTAAATTTTT
108482 GAAAATTATT
Statistics
Matches: 51, Mismatches: 7, Indels: 17
0.68 0.09 0.23
Matches are distributed among these distances:
14 8 0.16
15 3 0.06
17 2 0.04
18 9 0.18
19 7 0.14
20 20 0.39
21 2 0.04
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.61
Consensus pattern (17 bp):
ATTTTAAATTTTTATAT
Found at i:108481 original size:20 final size:20
Alignment explanation
Indices: 108433--108503 Score: 63
Period size: 20 Copynumber: 3.4 Consensus size: 20
108423 GAATTTTTAT
*
108433 ATTTTTTAAAATATAAATTTTAA
1 ATTTTTTAAAAT-T--ATTTTGA
*
108456 AATTTTTATAAA-TATTTTGA
1 ATTTTTTA-AAATTATTTTGA
*
108476 ATTTTTGAAAATTATTTTGA
1 ATTTTTTAAAATTATTTTGA
108496 ATTATTTT
1 ATT-TTTT
108504 GTAATTTTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
19 3 0.08
20 23 0.57
21 3 0.08
22 1 0.03
23 7 0.17
24 3 0.08
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.56
Consensus pattern (20 bp):
ATTTTTTAAAATTATTTTGA
Found at i:112048 original size:6 final size:7
Alignment explanation
Indices: 112032--112058 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
112022 TTTACTTCGC
112032 AAAAATA
1 AAAAATA
112039 AAAAATA
1 AAAAATA
112046 AAAAATA
1 AAAAATA
112053 AAAAAT
1 AAAAAT
112059 TATCCATTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (7 bp):
AAAAATA
Found at i:120076 original size:32 final size:32
Alignment explanation
Indices: 120035--120102 Score: 127
Period size: 32 Copynumber: 2.1 Consensus size: 32
120025 TTTCGTTTAT
120035 CTTAAAGTTAAATAAACCAAGTTAACTCTGGA
1 CTTAAAGTTAAATAAACCAAGTTAACTCTGGA
*
120067 CTTAAAGTTAAATAAATCAAGTTAACTCTGGA
1 CTTAAAGTTAAATAAACCAAGTTAACTCTGGA
120099 CTTA
1 CTTA
120103 TCAGATCCTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.43, C:0.15, G:0.12, T:0.31
Consensus pattern (32 bp):
CTTAAAGTTAAATAAACCAAGTTAACTCTGGA
Found at i:120224 original size:23 final size:23
Alignment explanation
Indices: 120198--120260 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
120188 AAGACGAATG
**
120198 CAAAATATGCCACAAAGGCAAAA
1 CAAAATACACCACAAAGGCAAAA
* *
120221 CAAAATACATCACAAAGGCTAAA
1 CAAAATACACCACAAAGGCAAAA
*
120244 CAGAATACACCACAAAG
1 CAAAATACACCACAAAG
120261 ACATCATAAC
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.56, C:0.24, G:0.11, T:0.10
Consensus pattern (23 bp):
CAAAATACACCACAAAGGCAAAA
Found at i:120290 original size:25 final size:25
Alignment explanation
Indices: 120257--120352 Score: 80
Period size: 25 Copynumber: 4.1 Consensus size: 25
120247 AATACACCAC
120257 AAAGACATCATAACGAATACGCCAAA
1 AAAG-CATCATAACGAATACGCCAAA
120283 AAAGCATCATAAC--A-A-G-C--A
1 AAAGCATCATAACGAATACGCCAAA
* * **
120301 AAGGCATCATAATGAATACGCCGCA
1 AAAGCATCATAACGAATACGCCAAA
* *
120326 AAGGCATCATAACGAATACACCAAA
1 AAAGCATCATAACGAATACGCCAAA
120351 AA
1 AA
120353 GGCTCTGTTA
Statistics
Matches: 57, Mismatches: 6, Indels: 15
0.73 0.08 0.19
Matches are distributed among these distances:
18 12 0.21
20 2 0.04
21 2 0.04
22 2 0.04
23 2 0.04
25 33 0.58
26 4 0.07
ACGTcount: A:0.51, C:0.23, G:0.14, T:0.12
Consensus pattern (25 bp):
AAAGCATCATAACGAATACGCCAAA
Found at i:120318 original size:43 final size:43
Alignment explanation
Indices: 120256--120338 Score: 121
Period size: 43 Copynumber: 1.9 Consensus size: 43
120246 GAATACACCA
120256 CAAAGACATCATAACGAATACGCCAAAAAAGCATCATAACAAG
1 CAAAGACATCATAACGAATACGCCAAAAAAGCATCATAACAAG
* * ** *
120299 CAAAGGCATCATAATGAATACGCCGCAAAGGCATCATAAC
1 CAAAGACATCATAACGAATACGCCAAAAAAGCATCATAAC
120339 GAATACACCA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 35 1.00
ACGTcount: A:0.48, C:0.24, G:0.14, T:0.13
Consensus pattern (43 bp):
CAAAGACATCATAACGAATACGCCAAAAAAGCATCATAACAAG
Found at i:123385 original size:26 final size:26
Alignment explanation
Indices: 123355--123405 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
123345 ATCTTTTAAG
*
123355 TAATT-CATATAAATTATTTATAAAAC
1 TAATTACATATAAAATATTT-TAAAAC
*
123381 TAATTATATATAAAATATTTTAAAA
1 TAATTACATATAAAATATTTTAAAA
123406 AATATACAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 10 0.45
27 12 0.55
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (26 bp):
TAATTACATATAAAATATTTTAAAAC
Found at i:124540 original size:2 final size:2
Alignment explanation
Indices: 124535--124581 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
124525 TCATTATAAA
124535 AT AT AT AT AT 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 AT AT AT AT AT
124577 AT AT A
1 AT AT A
124582 CCTCAACTGT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:143414 original size:6 final size:6
Alignment explanation
Indices: 143403--143438 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
143393 GTGTACCAGT
143403 TGTGGG TGTGGG TGTGGG TGTGGG TGTGGG TGTGGG
1 TGTGGG TGTGGG TGTGGG TGTGGG TGTGGG TGTGGG
143439 AGTAAGTGGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.67, T:0.33
Consensus pattern (6 bp):
TGTGGG
Found at i:148694 original size:21 final size:22
Alignment explanation
Indices: 148668--148719 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
148658 GGTTATTGTT
148668 TTTTTGCTGTT-TTTACTATAA
1 TTTTTGCTGTTGTTTACTATAA
* * *
148689 TTTTTGTTGTTGTTTGCTATTA
1 TTTTTGCTGTTGTTTACTATAA
148711 TTTTTGCTG
1 TTTTTGCTG
148720 CTATTTTGGT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
21 10 0.38
22 16 0.62
ACGTcount: A:0.12, C:0.08, G:0.15, T:0.65
Consensus pattern (22 bp):
TTTTTGCTGTTGTTTACTATAA
Found at i:151052 original size:22 final size:22
Alignment explanation
Indices: 151018--151062 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
151008 TGAAAAAATT
* *
151018 AAAATTTTCATATCAATTTTTA
1 AAAATTCTAATATCAATTTTTA
* *
151040 AAAATTCTAATATTATTTTTTA
1 AAAATTCTAATATCAATTTTTA
151062 A
1 A
151063 GAGAGTTTAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.51
Consensus pattern (22 bp):
AAAATTCTAATATCAATTTTTA
Found at i:154069 original size:17 final size:16
Alignment explanation
Indices: 154047--154081 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
154037 AACATAAAAG
154047 GAGAAGAAATAAAGAAA
1 GAGAAGAAA-AAAGAAA
*
154064 GAGAAGAAAGAAGAAA
1 GAGAAGAAAAAAGAAA
154080 GA
1 GA
154082 AAATTTCCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.69, C:0.00, G:0.29, T:0.03
Consensus pattern (16 bp):
GAGAAGAAAAAAGAAA
Found at i:155446 original size:3 final size:3
Alignment explanation
Indices: 155438--155467 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
155428 TGAAAATTAT
155438 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
155468 CAATTCAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:156088 original size:20 final size:21
Alignment explanation
Indices: 156056--156098 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
156046 ATTAATTCGG
*
156056 TTAATTATCCGAT-TTCGAAC
1 TTAATTATCCGATAATCGAAC
156076 TTAATTAAT-CGATAATCGAAC
1 TTAATT-ATCCGATAATCGAAC
156097 TT
1 TT
156099 TCAAAAAATC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.35, C:0.16, G:0.09, T:0.40
Consensus pattern (21 bp):
TTAATTATCCGATAATCGAAC
Found at i:156151 original size:18 final size:19
Alignment explanation
Indices: 156128--156165 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
156118 CCTTCGATCA
*
156128 AATTAAATCGATT-AATCG
1 AATTAAATCAATTCAATCG
156146 AATTAAATCAATTCAATCG
1 AATTAAATCAATTCAATCG
156165 A
1 A
156166 TTGAACCGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.47, C:0.13, G:0.08, T:0.32
Consensus pattern (19 bp):
AATTAAATCAATTCAATCG
Found at i:156183 original size:12 final size:12
Alignment explanation
Indices: 156166--156195 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
156156 ATTCAATCGA
156166 TTGAACCGGAAT
1 TTGAACCGGAAT
156178 TTGAACCGGAAT
1 TTGAACCGGAAT
156190 TTGAAC
1 TTGAAC
156196 ACTTCTATCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (12 bp):
TTGAACCGGAAT
Found at i:160673 original size:6 final size:6
Alignment explanation
Indices: 160662--160696 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
160652 ACCGCAGCTA
*
160662 ACAAGG ACAAGG ACAAGG ACAAGG ATAAGG ACAAG
1 ACAAGG ACAAGG ACAAGG ACAAGG ACAAGG ACAAG
160697 AAGCGTCCGG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.51, C:0.14, G:0.31, T:0.03
Consensus pattern (6 bp):
ACAAGG
Found at i:163675 original size:89 final size:89
Alignment explanation
Indices: 163572--163747 Score: 334
Period size: 89 Copynumber: 2.0 Consensus size: 89
163562 TTTATTAGAC
163572 TACCTCATATGACATGACATATAATTAACATAAAATAAACATGGAAAAAAATGTTAGCTACATTA
1 TACCTCATATGACATGACATATAATTAACATAAAATAAACATGGAAAAAAATGTTAGCTACATTA
163637 ATTTATTAGGACCCTTTTGGATAT
66 ATTTATTAGGACCCTTTTGGATAT
*
163661 TACCTCATATGACATGACATATAATTAACATAAAATAAACATGGGAAAAAATGTTAGCTACATTA
1 TACCTCATATGACATGACATATAATTAACATAAAATAAACATGGAAAAAAATGTTAGCTACATTA
*
163726 ATTTATTAGGACTCTTTTGGAT
66 ATTTATTAGGACCCTTTTGGAT
163748 GGACGTTTAC
Statistics
Matches: 85, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
89 85 1.00
ACGTcount: A:0.42, C:0.13, G:0.12, T:0.33
Consensus pattern (89 bp):
TACCTCATATGACATGACATATAATTAACATAAAATAAACATGGAAAAAAATGTTAGCTACATTA
ATTTATTAGGACCCTTTTGGATAT
Found at i:184766 original size:10 final size:10
Alignment explanation
Indices: 184751--184780 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
184741 GCTTACCTCT
184751 TACATGCATC
1 TACATGCATC
184761 TACATGCATC
1 TACATGCATC
184771 TACATGCATC
1 TACATGCATC
184781 CTGGATTCCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.30, C:0.30, G:0.10, T:0.30
Consensus pattern (10 bp):
TACATGCATC
Found at i:185508 original size:3 final size:3
Alignment explanation
Indices: 185500--185530 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
185490 TTTTCCCTTA
185500 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
185531 GGCATCCCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:189932 original size:7 final size:7
Alignment explanation
Indices: 189922--189964 Score: 52
Period size: 7 Copynumber: 6.1 Consensus size: 7
189912 AATTAATTTT
189922 TAAAAAA
1 TAAAAAA
*
189929 TAAAACAT
1 TAAAA-AA
*
189937 TAAAATA
1 TAAAAAA
189944 TAAAAAA
1 TAAAAAA
189951 T-AAAAA
1 TAAAAAA
189957 TAAAAAA
1 TAAAAAA
189964 T
1 T
189965 TAACTATTGT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
6 6 0.20
7 18 0.60
8 6 0.20
ACGTcount: A:0.77, C:0.02, G:0.00, T:0.21
Consensus pattern (7 bp):
TAAAAAA
Found at i:189939 original size:15 final size:14
Alignment explanation
Indices: 189921--189967 Score: 51
Period size: 15 Copynumber: 3.3 Consensus size: 14
189911 AAATTAATTT
189921 TTAAAAAATAAAACA
1 TTAAAAAATAAAA-A
*
189936 TTAAAATATAAAAA
1 TTAAAAAATAAAAA
*
189950 AT-AAAAATAAAAAA
1 TTAAAAAAT-AAAAA
189964 TTAA
1 TTAA
189968 CTATTGTTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
13 5 0.19
14 8 0.31
15 13 0.50
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.23
Consensus pattern (14 bp):
TTAAAAAATAAAAA
Found at i:189943 original size:13 final size:13
Alignment explanation
Indices: 189925--189967 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
189915 TAATTTTTAA
*
189925 AAAATAAAACATT
1 AAAATAAAAAATT
*
189938 AAAATATAAAAAATA
1 -AAA-ATAAAAAATT
189953 AAAATAAAAAATT
1 AAAATAAAAAATT
189966 AA
1 AA
189968 CTATTGTTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
13 11 0.44
14 6 0.24
15 8 0.32
ACGTcount: A:0.77, C:0.02, G:0.00, T:0.21
Consensus pattern (13 bp):
AAAATAAAAAATT
Found at i:189964 original size:22 final size:22
Alignment explanation
Indices: 189922--189962 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
189912 AATTAATTTT
*
189922 TAAAAAATAAAACATTAAAATA
1 TAAAAAATAAAACATAAAAATA
189944 TAAAAAATAAAA-ATAAAAA
1 TAAAAAATAAAACATAAAAA
189963 ATTAACTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (22 bp):
TAAAAAATAAAACATAAAAATA
Found at i:199816 original size:13 final size:12
Alignment explanation
Indices: 199794--199824 Score: 53
Period size: 13 Copynumber: 2.5 Consensus size: 12
199784 CTTTACCCAC
199794 AAAAAAAAGAAA
1 AAAAAAAAGAAA
199806 AAAAGAAAAGAAA
1 AAAA-AAAAGAAA
199819 AAAAAA
1 AAAAAA
199825 TGAAGCTTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 6 0.33
13 12 0.67
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (12 bp):
AAAAAAAAGAAA
Found at i:200683 original size:16 final size:15
Alignment explanation
Indices: 200656--200697 Score: 50
Period size: 16 Copynumber: 2.8 Consensus size: 15
200646 TCTACGGATC
*
200656 AAAATT-AAATTTTT
1 AAAATTAAAATTTGT
200670 AAAATTCAAAATTTGT
1 AAAATT-AAAATTTGT
*
200686 AACATTAAAATT
1 AAAATTAAAATT
200698 AATCAAATGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 6 0.25
15 6 0.25
16 12 0.50
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.40
Consensus pattern (15 bp):
AAAATTAAAATTTGT
Found at i:201152 original size:15 final size:15
Alignment explanation
Indices: 201124--201167 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
201114 CCAAATAATA
* *
201124 AAATGTAATGAAATG
1 AAATGAAATTAAATG
*
201139 AAATGAAATTAAATT
1 AAATGAAATTAAATG
*
201154 AAATTAAATTAAAT
1 AAATGAAATTAAAT
201168 ATGCAAACAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.59, C:0.00, G:0.09, T:0.32
Consensus pattern (15 bp):
AAATGAAATTAAATG
Found at i:203401 original size:29 final size:29
Alignment explanation
Indices: 203333--203401 Score: 72
Period size: 29 Copynumber: 2.4 Consensus size: 29
203323 CTGAAAATTA
203333 AAAATTTAA-TTTTTGTGTTTGTATTTTT
1 AAAATTTAAGTTTTTGTGTTTGTATTTTT
* * *
203361 ATTAATTT-AGTTTTT-TTTTTTTATATTTT
1 A-AAATTTAAGTTTTTGTGTTTGTAT-TTTT
203390 AAAATTTAAGTT
1 AAAATTTAAGTT
203402 CAACTGTTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
28 14 0.42
29 19 0.58
ACGTcount: A:0.28, C:0.00, G:0.07, T:0.65
Consensus pattern (29 bp):
AAAATTTAAGTTTTTGTGTTTGTATTTTT
Found at i:204741 original size:2 final size:2
Alignment explanation
Indices: 204734--204766 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
204724 AACCCTTCTT
204734 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
204767 CAAGTTGAGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:212404 original size:15 final size:15
Alignment explanation
Indices: 212384--212413 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
212374 TTAAAAACTC
212384 ATAAAAATAATATAA
1 ATAAAAATAATATAA
*
212399 ATAAAATTAATATAA
1 ATAAAAATAATATAA
212414 TTAATCATAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (15 bp):
ATAAAAATAATATAA
Found at i:214021 original size:18 final size:19
Alignment explanation
Indices: 213985--214026 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
213975 ATCTTAAAAG
213985 ATAAAAAAAATTAATAACT
1 ATAAAAAAAATTAATAACT
214004 ATAAAATAAAATT-A-AACT
1 ATAAAA-AAAATTAATAACT
214022 ATAAA
1 ATAAA
214027 CTTTAAAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 9 0.41
19 7 0.32
20 6 0.27
ACGTcount: A:0.69, C:0.05, G:0.00, T:0.26
Consensus pattern (19 bp):
ATAAAAAAAATTAATAACT
Found at i:217256 original size:6 final size:6
Alignment explanation
Indices: 217245--217274 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
217235 TATATAGGGC
217245 AAGGCA AAGGCA AAGGCA AAGGCA AAGGCA
1 AAGGCA AAGGCA AAGGCA AAGGCA AAGGCA
217275 GACCCATCAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.50, C:0.17, G:0.33, T:0.00
Consensus pattern (6 bp):
AAGGCA
Found at i:226455 original size:97 final size:97
Alignment explanation
Indices: 226289--226483 Score: 390
Period size: 97 Copynumber: 2.0 Consensus size: 97
226279 GCGGGATTGA
226289 GTTTCGAAAACAGGAGAAGAACATTCCTCATTGATTCCTATAAACAAAAGCACATCCAGCATGGA
1 GTTTCGAAAACAGGAGAAGAACATTCCTCATTGATTCCTATAAACAAAAGCACATCCAGCATGGA
226354 GTGAGTATTCAAACCACAAGAGGTGCTAACAT
66 GTGAGTATTCAAACCACAAGAGGTGCTAACAT
226386 GTTTCGAAAACAGGAGAAGAACATTCCTCATTGATTCCTATAAACAAAAGCACATCCAGCATGGA
1 GTTTCGAAAACAGGAGAAGAACATTCCTCATTGATTCCTATAAACAAAAGCACATCCAGCATGGA
226451 GTGAGTATTCAAACCACAAGAGGTGCTAACAT
66 GTGAGTATTCAAACCACAAGAGGTGCTAACAT
226483 G
1 G
226484 GATGCCTGAT
Statistics
Matches: 98, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
97 98 1.00
ACGTcount: A:0.39, C:0.21, G:0.19, T:0.22
Consensus pattern (97 bp):
GTTTCGAAAACAGGAGAAGAACATTCCTCATTGATTCCTATAAACAAAAGCACATCCAGCATGGA
GTGAGTATTCAAACCACAAGAGGTGCTAACAT
Found at i:228410 original size:11 final size:11
Alignment explanation
Indices: 228369--228411 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
228359 TGAACAAAAA
*
228369 ATAAAAAATAG
1 ATAATAAATAG
* * *
228380 AAAATAAAAAT
1 ATAATAAATAG
228391 ATAATAAATAG
1 ATAATAAATAG
228402 ATAATAAATA
1 ATAATAAATA
228412 TTTTTTGGAA
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (11 bp):
ATAATAAATAG
Found at i:231023 original size:24 final size:26
Alignment explanation
Indices: 230987--231034 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
230977 AGAGAAATGT
230987 AAATGTGATATATGA-A-ATTATGAG
1 AAATGTGATATATGAGAGATTATGAG
231011 AAATGATGA-ATATGAGAGATTATG
1 AAATG-TGATATATGAGAGATTATG
231035 TCCATGTAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 11 0.52
25 4 0.19
26 6 0.29
ACGTcount: A:0.46, C:0.00, G:0.23, T:0.31
Consensus pattern (26 bp):
AAATGTGATATATGAGAGATTATGAG
Found at i:231135 original size:23 final size:22
Alignment explanation
Indices: 231097--231221 Score: 83
Period size: 23 Copynumber: 5.5 Consensus size: 22
231087 ATGCTAACGC
*
231097 GCTTACTGTTCAGCACTGTGTGT
1 GCTTACTGTT-TGCACTGTGTGT
*
231120 GCTTACTGTTTCGCACCTCT-TGT
1 GCTTACTGTTT-GCA-CTGTGTGT
* * * *
231143 GCCTACTGATTTG-AGCTATTTGC
1 GCTTACTG-TTTGCA-CTGTGTGT
* *
231166 GCCTACTGATTGCACTGTGTGT
1 GCTTACTGTTTGCACTGTGTGT
* * *
231188 GCTTATTGGATTGCACTGTGCGT
1 GCTTACT-GTTTGCACTGTGTGT
231211 GCTTACTGTTT
1 GCTTACTGTTT
231222 CCCCAACACC
Statistics
Matches: 81, Mismatches: 15, Indels: 13
0.74 0.14 0.12
Matches are distributed among these distances:
22 20 0.25
23 55 0.68
24 6 0.07
ACGTcount: A:0.13, C:0.22, G:0.24, T:0.41
Consensus pattern (22 bp):
GCTTACTGTTTGCACTGTGTGT
Done.