Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005295.1 Hibiscus syriacus cultivar Beakdansim tig00011986_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: 83927
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:75 original size:17 final size:17
Alignment explanation
Indices: 53--91 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
43 CACAAAGTGT
53 CAATCAATTTCAAGCTC
1 CAATCAATTTCAAGCTC
70 CAATCAATTTCAAGCTC
1 CAATCAATTTCAAGCTC
87 CAATC
1 CAATC
92 CTTGCAATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.36, C:0.31, G:0.05, T:0.28
Consensus pattern (17 bp):
CAATCAATTTCAAGCTC
Found at i:5505 original size:25 final size:26
Alignment explanation
Indices: 5477--5540 Score: 67
Period size: 26 Copynumber: 2.5 Consensus size: 26
5467 TAGCATATTT
**
5477 AAAAACAATGCTTGAAAA-TAAAATA
1 AAAAACAAAACTTGAAAAGTAAAATA
**
5502 AAAATGAAAACTTGAAAAGTAAAATA
1 AAAAACAAAACTTGAAAAGTAAAATA
* *
5528 AAATAGAAAACTT
1 AAAAACAAAACTT
5541 TAATAAAACT
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
25 14 0.44
26 18 0.56
ACGTcount: A:0.64, C:0.06, G:0.09, T:0.20
Consensus pattern (26 bp):
AAAAACAAAACTTGAAAAGTAAAATA
Found at i:5536 original size:26 final size:25
Alignment explanation
Indices: 5487--5540 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 25
5477 AAAAACAATG
5487 CTTGAAAATAAAATAAAAATGAAAA
1 CTTGAAAATAAAATAAAAATGAAAA
5512 CTTGAAAAGTAAAAT-AAAATAGAAAA
1 CTTGAAAA-TAAAATAAAAAT-GAAAA
5538 CTT
1 CTT
5541 TAATAAAACT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
25 13 0.48
26 14 0.52
ACGTcount: A:0.63, C:0.06, G:0.09, T:0.22
Consensus pattern (25 bp):
CTTGAAAATAAAATAAAAATGAAAA
Found at i:17722 original size:28 final size:27
Alignment explanation
Indices: 17657--17723 Score: 80
Period size: 28 Copynumber: 2.4 Consensus size: 27
17647 GCTTGCTTTC
*
17657 TTTTTTACTTTTCTTATTTTTCTTTTT
1 TTTTTTATTTTTCTTATTTTTCTTTTT
** *
17684 TTTATGAATTTTTCTTTTTTTTCTTTTT
1 TTT-TTTATTTTTCTTATTTTTCTTTTT
17712 TTTTTTCATTTT
1 TTTTTT-ATTTT
17724 GTACTCCAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
27 4 0.12
28 28 0.88
ACGTcount: A:0.09, C:0.09, G:0.01, T:0.81
Consensus pattern (27 bp):
TTTTTTATTTTTCTTATTTTTCTTTTT
Found at i:17723 original size:10 final size:9
Alignment explanation
Indices: 17665--17714 Score: 55
Period size: 9 Copynumber: 5.4 Consensus size: 9
17655 TCTTTTTTAC
*
17665 TTTTCTTAT
1 TTTTCTTTT
17674 TTTTCTTTT
1 TTTTCTTTT
* **
17683 TTTTATGAAT
1 TTTTCT-TTT
17693 TTTTCTTTT
1 TTTTCTTTT
17702 TTTTCTTTT
1 TTTTCTTTT
17711 TTTT
1 TTTT
17715 TTTCATTTTG
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
9 27 0.82
10 6 0.18
ACGTcount: A:0.08, C:0.08, G:0.02, T:0.82
Consensus pattern (9 bp):
TTTTCTTTT
Found at i:18095 original size:20 final size:21
Alignment explanation
Indices: 18058--18096 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
18048 TATGGTCTTG
*
18058 ATGAAGGATGTTGATGATGAA
1 ATGAAGGATGGTGATGATGAA
*
18079 ATGAA-GATGGTGGTGATG
1 ATGAAGGATGGTGATGATG
18097 TTGTATCTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.33, C:0.00, G:0.38, T:0.28
Consensus pattern (21 bp):
ATGAAGGATGGTGATGATGAA
Found at i:21107 original size:3 final size:3
Alignment explanation
Indices: 21099--21197 Score: 144
Period size: 3 Copynumber: 33.0 Consensus size: 3
21089 ATTGATTTAT
* *
21099 TTA TTA TTA TTA TAA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA CTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * *
21147 TAA ATA TTA TTA TTA TTA TTA TTA TTA TAA ATA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
21195 TTA
1 TTA
21198 AATATATATA
Statistics
Matches: 84, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 84 1.00
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:21129 original size:27 final size:27
Alignment explanation
Indices: 21100--21197 Score: 160
Period size: 27 Copynumber: 3.6 Consensus size: 27
21090 TTGATTTATT
* * *
21100 TATTATTATTATAATTATTATTATTAT
1 TATTATTATTATTATTATTATAAATAT
*
21127 TATTATTATTATTATTACTATAAATAT
1 TATTATTATTATTATTATTATAAATAT
21154 TATTATTATTATTATTATTATAAATAT
1 TATTATTATTATTATTATTATAAATAT
21181 TATTATTATTATTATTA
1 TATTATTATTATTATTA
21198 AATATATATA
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 66 1.00
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (27 bp):
TATTATTATTATTATTATTATAAATAT
Found at i:21319 original size:16 final size:16
Alignment explanation
Indices: 21298--21332 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
21288 AGTTAGGGTT
21298 CTCTGCCTCCAGCCGC
1 CTCTGCCTCCAGCCGC
21314 CTCTGCCTCCAGCCGC
1 CTCTGCCTCCAGCCGC
21330 CTC
1 CTC
21333 AGCCAACGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.06, C:0.57, G:0.17, T:0.20
Consensus pattern (16 bp):
CTCTGCCTCCAGCCGC
Found at i:23288 original size:22 final size:21
Alignment explanation
Indices: 23248--23294 Score: 58
Period size: 24 Copynumber: 2.1 Consensus size: 21
23238 TTTATAATCT
23248 TTTTTATATATATACATATTA
1 TTTTTATATATATACATATTA
*
23269 TTTTTATAGTATTTATATATATTA
1 TTTTTATA-TA--TATACATATTA
23293 TT
1 TT
23295 AATATTTCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 8 0.36
22 2 0.09
24 12 0.55
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (21 bp):
TTTTTATATATATACATATTA
Found at i:30594 original size:114 final size:114
Alignment explanation
Indices: 30310--30650 Score: 574
Period size: 114 Copynumber: 3.0 Consensus size: 114
30300 AAGTGCCATG
30310 TGCTCATAGTAGAAATAAGAAGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
1 TGCTCATAGTAGAAATAAGAAGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
*
30375 TGGTTTGGTATGAACCCCAAAAACCAATCATTGGATTTTAAAGATGAATT
66 TGGTTTGGTATGAACCCC-AAAACCAATCATTGGATTTAAAAGATGAATT
30425 TGCTCATAGTAGAAATAAGAAGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
1 TGCTCATAGTAGAAATAAGAAGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
*
30490 TGGTTTGGTATGAACCCCAAAACCAATCATTAGATTTAAAAGATGAATT
66 TGGTTTGGTATGAACCCCAAAACCAATCATTGGATTTAAAAGATGAATT
* *
30539 TGCTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
1 TGCTCATAGTAGAAATAAGAAGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
* * * * * * *
30604 TGATTCGGTAGGAACCCCAGAACCGATCATTGGAATTGAAAGATGAA
66 TGGTTTGGTATGAACCCCAAAACCAATCATTGGATTTAAAAGATGAA
30651 CTGCATGATC
Statistics
Matches: 214, Mismatches: 12, Indels: 1
0.94 0.05 0.00
Matches are distributed among these distances:
114 131 0.61
115 83 0.39
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31
Consensus pattern (114 bp):
TGCTCATAGTAGAAATAAGAAGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
TGGTTTGGTATGAACCCCAAAACCAATCATTGGATTTAAAAGATGAATT
Found at i:37336 original size:9 final size:8
Alignment explanation
Indices: 37324--37391 Score: 68
Period size: 9 Copynumber: 8.4 Consensus size: 8
37314 TTTTTGGCTC
37324 TTTTTTGT
1 TTTTTTGT
*
37332 TTTTTTGCC
1 TTTTTTG-T
37341 TTTTTT-T
1 TTTTTTGT
*
37348 TTTTTTGCC
1 TTTTTTG-T
*
37357 TTTTTTGCC
1 TTTTTTG-T
37366 TTTTTTGT
1 TTTTTTGT
37374 TTTTTTGT
1 TTTTTTGT
37382 TTTTTT-T
1 TTTTTTGT
37389 TTT
1 TTT
37392 AAAAAAATAG
Statistics
Matches: 53, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
7 10 0.19
8 21 0.40
9 22 0.42
ACGTcount: A:0.00, C:0.09, G:0.09, T:0.82
Consensus pattern (8 bp):
TTTTTTGT
Found at i:37344 original size:16 final size:16
Alignment explanation
Indices: 37325--37387 Score: 72
Period size: 16 Copynumber: 3.8 Consensus size: 16
37315 TTTTGGCTCT
37325 TTTTTGTTTTTTTGCC
1 TTTTTGTTTTTTTGCC
*
37341 TTTTTTTTTTTTTGCC
1 TTTTTGTTTTTTTGCC
* **
37357 TTTTTTGCCTTTTTTGTT
1 -TTTTTG-TTTTTTTGCC
37375 TTTTTGTTTTTTT
1 TTTTTGTTTTTTT
37388 TTTTAAAAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
16 21 0.54
17 11 0.28
18 7 0.18
ACGTcount: A:0.00, C:0.10, G:0.10, T:0.81
Consensus pattern (16 bp):
TTTTTGTTTTTTTGCC
Found at i:37352 original size:25 final size:24
Alignment explanation
Indices: 37324--37387 Score: 92
Period size: 25 Copynumber: 2.6 Consensus size: 24
37314 TTTTTGGCTC
*
37324 TTTTTTGTTTTTTTGCCTTTTTTT
1 TTTTTTGTTTTTTTGCCTTTTTGT
*
37348 TTTTTTGCCTTTTTTGCCTTTTTTGT
1 TTTTTTG-TTTTTTTGCC-TTTTTGT
37374 TTTTTTGTTTTTTT
1 TTTTTTGTTTTTTT
37388 TTTTAAAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
24 7 0.20
25 15 0.43
26 13 0.37
ACGTcount: A:0.00, C:0.09, G:0.09, T:0.81
Consensus pattern (24 bp):
TTTTTTGTTTTTTTGCCTTTTTGT
Found at i:37387 original size:42 final size:43
Alignment explanation
Indices: 37307--37391 Score: 131
Period size: 42 Copynumber: 2.0 Consensus size: 43
37297 TTTTTTGAAA
*
37307 TTTTGGCTTTTTGGCTCTTTTTTGTTTTTTTGCCTTTTTTTTT
1 TTTTGCCTTTTTGGCTCTTTTTTGTTTTTTTGCCTTTTTTTTT
*
37350 TTTTGCCTTTTTTGC-CTTTTTTGTTTTTTTG--TTTTTTTTT
1 TTTTGCCTTTTTGGCTCTTTTTTGTTTTTTTGCCTTTTTTTTT
37390 TT
1 TT
37392 AAAAAAATAG
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
40 11 0.28
42 16 0.40
43 13 0.32
ACGTcount: A:0.00, C:0.11, G:0.12, T:0.78
Consensus pattern (43 bp):
TTTTGCCTTTTTGGCTCTTTTTTGTTTTTTTGCCTTTTTTTTT
Found at i:41002 original size:22 final size:22
Alignment explanation
Indices: 40971--41028 Score: 89
Period size: 22 Copynumber: 2.6 Consensus size: 22
40961 TACATCTACA
*
40971 CTTTTCAAAGATGATAGATTCC
1 CTTTTCAAAGATGACAGATTCC
* *
40993 CTTTTTAAAGATGACAGATTCT
1 CTTTTCAAAGATGACAGATTCC
41015 CTTTTCAAAGATGA
1 CTTTTCAAAGATGA
41029 AAGCTTTATC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.38
Consensus pattern (22 bp):
CTTTTCAAAGATGACAGATTCC
Found at i:41768 original size:113 final size:113
Alignment explanation
Indices: 41431--42107 Score: 1031
Period size: 113 Copynumber: 6.0 Consensus size: 113
41421 TAGCAAAGAT
* * *
41431 TCAAATCTATCATTTGATGGATTGA-CATTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTG
1 TCAAATCCATCATTTGATGGA-TCATCTTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTG
* * *
41495 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGT
65 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
** * * * * * *
41544 TTGAATTCATCATTTGATGGATCAACATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCGTCAT
1 TCAAATCCATCATTTGATGGATCATCTTTTCCAGAG-AAAGTTCATAATAAGAAGAA--C-TCAT
41608 CTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
62 CTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
41660 TCAAATCCATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGA
1 TCAAATCCATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGA
41725 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* *
41773 TCAAATCCATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCCTAATAAGAATAACTCATCTGA
1 TCAAATCCATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGA
41838 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* *
41886 TCAAATCCATCATTTGATGGATCGTCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGA
*
41951 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTAC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * * * *
41999 -CTGAATTCATCAATTGATGGATTATCTTTTCCAGAG-AAGTTCATAATGAGAAGAACTCATCTG
1 TC-AAATCCATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTG
* *
42062 AAGAAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAA-CTTTT
65 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT
42108 CGCATAATTC
Statistics
Matches: 524, Mismatches: 33, Indels: 16
0.91 0.06 0.03
Matches are distributed among these distances:
111 5 0.01
112 70 0.13
113 347 0.66
114 1 0.00
115 1 0.00
116 99 0.19
117 1 0.00
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.30
Consensus pattern (113 bp):
TCAAATCCATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGA
AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
Found at i:42450 original size:3 final size:3
Alignment explanation
Indices: 42442--42540 Score: 135
Period size: 3 Copynumber: 33.0 Consensus size: 3
42432 ATTGATTTAT
* * * *
42442 TTA TTA TTA TTA TAA TTA TAA TTA TTA TTA TTA TTA TTA TTA CTA TAA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
42490 ATA TTA TTA TTA TTA TTA TAA ATA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
42538 TTA
1 TTA
42541 AATATATATA
Statistics
Matches: 82, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 82 1.00
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:42672 original size:16 final size:16
Alignment explanation
Indices: 42653--42693 Score: 82
Period size: 16 Copynumber: 2.6 Consensus size: 16
42643 CTCTAACCCT
42653 AGCCGCCTCTGCCTCC
1 AGCCGCCTCTGCCTCC
42669 AGCCGCCTCTGCCTCC
1 AGCCGCCTCTGCCTCC
42685 AGCCGCCTC
1 AGCCGCCTC
42694 AGACAACGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.07, C:0.56, G:0.20, T:0.17
Consensus pattern (16 bp):
AGCCGCCTCTGCCTCC
Found at i:44869 original size:41 final size:43
Alignment explanation
Indices: 44801--44895 Score: 133
Period size: 42 Copynumber: 2.3 Consensus size: 43
44791 CGGAGCTAAC
44801 TGAT-ATGCTATTCCGCCAGATGCTGTTTCTAG-TTGGCTACG
1 TGATGATGCTATTCCGCCAGATGCTGTTTCTAGTTTGGCTACG
* * *
44842 TGATGATGCTATTCC-CCTGATGCTGTTTTTAGTTTTGCTACG
1 TGATGATGCTATTCCGCCAGATGCTGTTTCTAGTTTGGCTACG
*
44884 AGATGATGCTAT
1 TGATGATGCTAT
44896 AAGAGTGCTA
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
41 19 0.40
42 29 0.60
ACGTcount: A:0.18, C:0.19, G:0.23, T:0.40
Consensus pattern (43 bp):
TGATGATGCTATTCCGCCAGATGCTGTTTCTAGTTTGGCTACG
Found at i:50371 original size:17 final size:17
Alignment explanation
Indices: 50329--50371 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
50319 AGATTTTTTT
* *
50329 AAAAAAAATTTGAGTTG
1 AAAAAATATTTGAGGTG
**
50346 AAATCATATTTGAGGTG
1 AAAAAATATTTGAGGTG
50363 AAAAAATAT
1 AAAAAATAT
50372 GATCGATTAA
Statistics
Matches: 20, Mismatches: 6, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.51, C:0.02, G:0.16, T:0.30
Consensus pattern (17 bp):
AAAAAATATTTGAGGTG
Found at i:50477 original size:2 final size:2
Alignment explanation
Indices: 50436--50463 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
50426 GTGATAACTA
50436 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
50464 TATGTTTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:50481 original size:24 final size:25
Alignment explanation
Indices: 50445--50495 Score: 77
Period size: 24 Copynumber: 2.0 Consensus size: 25
50435 AATATATATA
50445 TATATATATATATATATATTATGTTTT
1 TATATATATAT-TATA-ATTATGTTTT
50472 TATATA-ATATTATAATTATGTTTT
1 TATATATATATTATAATTATGTTTT
50496 ATTTTGTAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
24 10 0.42
25 4 0.17
26 4 0.17
27 6 0.25
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (25 bp):
TATATATATATTATAATTATGTTTT
Found at i:50576 original size:18 final size:19
Alignment explanation
Indices: 50553--50589 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
50543 CACTGTATAA
50553 AACCC-TTTAGTTTTACAC
1 AACCCTTTTAGTTTTACAC
50571 AACCCTTTTAGTTTTACAC
1 AACCCTTTTAGTTTTACAC
50590 TTTTTTTAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.27, C:0.27, G:0.05, T:0.41
Consensus pattern (19 bp):
AACCCTTTTAGTTTTACAC
Found at i:50768 original size:2 final size:2
Alignment explanation
Indices: 50761--50785 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
50751 AACTTATCTC
50761 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 A
50786 AGTCTAATTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:51226 original size:20 final size:20
Alignment explanation
Indices: 51179--51532 Score: 293
Period size: 20 Copynumber: 17.2 Consensus size: 20
51169 AATGACCAAC
* *
51179 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATTTAG
*
51198 AAAACCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
* * **
51218 AAAAGCGCAACGTTGA-AAAG
1 AAAATCGCAACG-CGATTTAG
* **
51238 AAGATCGCAACGCGATCTTCC
1 AAAATCGCAACGCGAT-TTAG
*
51259 AAGAATCGCAACGCGATTCAG
1 AA-AATCGCAACGCGATTTAG
*
51280 AAAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTTAG
**
51300 AAAATCGCAACGCGATCTTCC
1 AAAATCGCAACGCGAT-TTAG
*
51321 AAGAATCGCAACGCGATTAAG
1 AA-AATCGCAACGCGATTTAG
*
51342 AAAATCGCAACGCGATTCCA-
1 AAAATCGCAACGCGATT-TAG
* *
51362 AGAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTTAG
*
51382 AAAATCGCAACGCGATTCCA-
1 AAAATCGCAACGCGATT-TAG
* **
51402 AGAATCGCAACGCGATCTTCC
1 AAAATCGCAACGCGAT-TTAG
*
51423 AAGAATCGCAACGCGATTAAG
1 AA-AATCGCAACGCGATTTAG
**
51444 AAAATCGCAACGCGATCTTCC
1 AAAATCGCAACGCGAT-TTAG
*
51465 AAGAATCGCAACGCGATTCAG
1 AA-AATCGCAACGCGATTTAG
* **
51486 TAAATCGCAACGCGATCTTCC
1 AAAATCGCAACGCGAT-TTAG
*
51507 AAGAATCGCAACGCGATTAAG
1 AA-AATCGCAACGCGATTTAG
51528 AAAAT
1 AAAAT
51533 GAGTAAATTC
Statistics
Matches: 268, Mismatches: 50, Indels: 33
0.76 0.14 0.09
Matches are distributed among these distances:
19 19 0.07
20 150 0.56
21 30 0.11
22 69 0.26
ACGTcount: A:0.39, C:0.26, G:0.19, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTAG
Found at i:51282 original size:62 final size:62
Alignment explanation
Indices: 51179--51532 Score: 309
Period size: 62 Copynumber: 5.8 Consensus size: 62
51169 AATGACCAAC
* * * * *
51179 AAAATCGCAACGCGAT-AT-CAA-AACCGCAACGCGATTTAGAAAAGCGCAACGTTGA-AAAG
1 AAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTAAGAAAATCGCAACG-CGATAAAG
* * **
51238 AAGATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTCAGAAAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTAAGAAAATCGCAACGCGATAAAG
*
51300 AAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTAAGAAAATCGCAACGCGATTCCAAG
1 AAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTAAGAAAATCGCAACGCGA-T-AAAG
*** ****
51364 --AATCGCAACGCGAT-TAAGAA-AATCGCAACGCGATTCCAAG--AATCGCAACGCGATCTTCC
1 AAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATT--AAGAAAATCGCAACGCGAT-AAAG
*** *** **
51423 AAGAATCGCAACGCGAT-TAAGAA-AATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTCAG
1 AA-AATCGCAACGCGATCTTCCAAGAATCGCAACGCGAT-TAAGAA-AATCGCAACGCGATAAAG
*
51486 TAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTAAGAAAAT
1 AAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTAAGAAAAT
51533 GAGTAAATTC
Statistics
Matches: 246, Mismatches: 32, Indels: 31
0.80 0.10 0.10
Matches are distributed among these distances:
59 17 0.07
60 29 0.12
61 8 0.03
62 152 0.62
63 10 0.04
64 30 0.12
ACGTcount: A:0.39, C:0.26, G:0.19, T:0.16
Consensus pattern (62 bp):
AAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTAAGAAAATCGCAACGCGATAAAG
Found at i:51287 original size:42 final size:42
Alignment explanation
Indices: 51236--51532 Score: 344
Period size: 42 Copynumber: 7.2 Consensus size: 42
51226 AACGTTGAAA
*
51236 AGAAGATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTC
1 AGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTC
*
51278 AGAAAATCGCAACGCGA--TT-CAGAAAATCGCAACGCGATCTTCC
1 AGAAAATCGCAACGCGATCTTCCA-AGAATCGCAACGCGA--TT-C
* ***
51321 A-AGAATCGCAACGCGAT-TAAGAA-AATCGCAACGCGATTCC
1 AGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATT-C
* ***
51361 A-AGAATCGCAACGCGAT-TAAGAA-AATCGCAACGCGATTCC
1 AGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATT-C
* *
51401 A-AGAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTA
1 AGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTC
51442 AGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTC
1 AGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTC
* *
51484 AGTAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTA
1 AGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTC
51526 AGAAAAT
1 AGAAAAT
51533 GAGTAAATTC
Statistics
Matches: 232, Mismatches: 14, Indels: 18
0.88 0.05 0.07
Matches are distributed among these distances:
39 2 0.01
40 77 0.33
41 4 0.02
42 144 0.62
43 4 0.02
44 1 0.00
ACGTcount: A:0.38, C:0.26, G:0.20, T:0.16
Consensus pattern (42 bp):
AGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTC
Found at i:51654 original size:5 final size:5
Alignment explanation
Indices: 51632--51681 Score: 82
Period size: 5 Copynumber: 9.6 Consensus size: 5
51622 CGTATTACCA
51632 CGACC ACGACC ACGACC CGACC CGACC CGACC CGACC CGACC CGACC CGA
1 CGACC -CGACC -CGACC CGACC CGACC CGACC CGACC CGACC CGACC CGA
51682 GACGAGACGG
Statistics
Matches: 44, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 33 0.75
6 11 0.25
ACGTcount: A:0.24, C:0.56, G:0.20, T:0.00
Consensus pattern (5 bp):
CGACC
Found at i:52207 original size:6 final size:6
Alignment explanation
Indices: 52172--52289 Score: 183
Period size: 6 Copynumber: 20.5 Consensus size: 6
52162 TCTCGTCTCG
* *
52172 GGTCG- GGTCG- GGTCG- GGTCG- GGTCG- GGTCGG GGTCGG GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
52215 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
52263 GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGT
52290 AATACGTGTC
Statistics
Matches: 111, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
5 25 0.23
6 86 0.77
ACGTcount: A:0.00, C:0.17, G:0.54, T:0.29
Consensus pattern (6 bp):
GGTCGT
Found at i:52410 original size:20 final size:20
Alignment explanation
Indices: 52385--52694 Score: 272
Period size: 20 Copynumber: 15.2 Consensus size: 20
52375 GAATTTACTC
52385 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCG
52405 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCG
52425 A--TTCTTGGAATCGCGTTGCG
1 ATTTTCTT--AATCGCGTTGCG
*
52445 ATTTTCTGAATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCG
52465 A--TTCTTGGAATCGCGTTGCG
1 ATTTTCTT--AATCGCGTTGCG
52485 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCG
***
52505 ATTATTGGAAGATCGCGTTGCG
1 ATT-TTCTTA-ATCGCGTTGCG
52527 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCG
*
52547 ATTTTCTGAATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCG
***
52567 ATTCTTGGAAGATCGCGTTGCG
1 ATT-TTCTTA-ATCGCGTTGCG
* * *
52589 ATTTTATGAATCGCATTGCG
1 ATTTTCTTAATCGCGTTGCG
*** *
52609 ATTCTTGGAAGATCGTGTTGCG
1 ATT-TTCTTA-ATCGCGTTGCG
* * *
52631 ATCTTCTT-TTCAACGTTGCG
1 ATTTTCTTAATC-GCGTTGCG
* *
52651 CTTTTCTAAATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCG
* **
52671 GTTTTGAT-ATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCG
52690 ATTTT
1 ATTTT
52695 GTTGGTCATT
Statistics
Matches: 236, Mismatches: 38, Indels: 33
0.77 0.12 0.11
Matches are distributed among these distances:
18 9 0.04
19 17 0.07
20 143 0.61
21 19 0.08
22 48 0.20
ACGTcount: A:0.16, C:0.19, G:0.25, T:0.40
Consensus pattern (20 bp):
ATTTTCTTAATCGCGTTGCG
Found at i:52441 original size:40 final size:39
Alignment explanation
Indices: 52393--52694 Score: 300
Period size: 40 Copynumber: 7.4 Consensus size: 39
52383 TCATTTTCTT
*
52393 AATCGCGTTGCGATTTTCTTAATCGCGTTGCGATTCTTGG
1 AATCGCGTTGCGATTTTCTAAATCGCGTTGCGATT-TTGG
*
52433 AATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTCTTGG
1 AATCGCGTTGCGATTTTCTAAATCGCGTTGCGATT-TTGG
*
52473 AATCGCGTTGCGATTTTCTTAATCGCGTTGCGATTATTGG
1 AATCGCGTTGCGATTTTCTAAATCGCGTTGCGATT-TTGG
* *
52513 AAGATCGCGTTGCGATTTTCTTAATCGCGTTGCGATTTTCTG
1 -A-ATCGCGTTGCGATTTTCTAAATCGCGTTGCGATTTT-GG
** *
52555 AATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTTTATG
1 AATCGCGTTGCGATT-TTCTAA-ATCGCGTTGCGATTTT-GG
* ** * * **
52597 AATCGCATTGCGATTCTTGGAAGATCGTGTTGCGATCTTCT
1 AATCGCGTTGCGATT-TTCTAA-ATCGCGTTGCGATTTTGG
** * * *
52638 TTTCAACGTTGCGCTTTTCTAAATCGCGTTGCGGTTTT-G
1 AATC-GCGTTGCGATTTTCTAAATCGCGTTGCGATTTTGG
52677 ATATCGCGTTGCGATTTT
1 A-ATCGCGTTGCGATTTT
52695 GTTGGTCATT
Statistics
Matches: 227, Mismatches: 28, Indels: 15
0.84 0.10 0.06
Matches are distributed among these distances:
39 11 0.05
40 106 0.47
41 13 0.06
42 97 0.43
ACGTcount: A:0.17, C:0.19, G:0.25, T:0.39
Consensus pattern (39 bp):
AATCGCGTTGCGATTTTCTAAATCGCGTTGCGATTTTGG
Found at i:52539 original size:62 final size:61
Alignment explanation
Indices: 52394--52611 Score: 286
Period size: 62 Copynumber: 3.6 Consensus size: 61
52384 CATTTTCTTA
*
52394 ATCGCGTTGCGATTTTCTTAATCGCGTTGCGA--TTCTTGGAATCGCGTTGCGATTTTCTG-A-
1 ATCGCGTTGCGATTTTCTTAATCGCGTTGCGATTTTCTT--AATCGCGTTGCGATTTT-GGAAG
52454 ATCGCGTTGCGA--TTCTTGGAATCGCGTTGCGATTTTCTTAATCGCGTTGCGATTATTGGAAG
1 ATCGCGTTGCGATTTTCTT--AATCGCGTTGCGATTTTCTTAATCGCGTTGCGATT-TTGGAAG
*
52516 ATCGCGTTGCGATTTTCTTAATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTCTTGGAAG
1 ATCGCGTTGCGATTTTCTTAATCGCGTTGCGATTTTCTTAATCGCGTTGCGATT-TTGGAAG
* * *
52578 ATCGCGTTGCGATTTTATGAATCGCATTGCGATT
1 ATCGCGTTGCGATTTTCTTAATCGCGTTGCGATT
52612 CTTGGAAGAT
Statistics
Matches: 143, Mismatches: 6, Indels: 16
0.87 0.04 0.10
Matches are distributed among these distances:
58 5 0.03
60 41 0.29
61 3 0.02
62 89 0.62
64 5 0.03
ACGTcount: A:0.17, C:0.19, G:0.26, T:0.39
Consensus pattern (61 bp):
ATCGCGTTGCGATTTTCTTAATCGCGTTGCGATTTTCTTAATCGCGTTGCGATTTTGGAAG
Found at i:52650 original size:42 final size:40
Alignment explanation
Indices: 52536--52632 Score: 122
Period size: 42 Copynumber: 2.3 Consensus size: 40
52526 GATTTTCTTA
* *
52536 ATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTCTTGGAAG
1 ATCGCGTTGCGATTTTATCAAT--CGTTGCGATTCTTGGAAG
*
52578 ATCGCGTTGCGATTTTATGAATCGCATTGCGATTCTTGGAAG
1 ATCGCGTTGCGATTTTATCAATCG--TTGCGATTCTTGGAAG
*
52620 ATCGTGTTGCGAT
1 ATCGCGTTGCGAT
52633 CTTCTTTTCA
Statistics
Matches: 51, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
40 2 0.04
42 49 0.96
ACGTcount: A:0.19, C:0.18, G:0.28, T:0.36
Consensus pattern (40 bp):
ATCGCGTTGCGATTTTATCAATCGTTGCGATTCTTGGAAG
Found at i:52948 original size:6 final size:6
Alignment explanation
Indices: 52937--52962 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
52927 TGGGGGATGC
52937 CCTTTG CCTTTG CCTTTG CCTTTG CC
1 CCTTTG CCTTTG CCTTTG CCTTTG CC
52963 CTCTTGTGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.38, G:0.15, T:0.46
Consensus pattern (6 bp):
CCTTTG
Found at i:55978 original size:29 final size:30
Alignment explanation
Indices: 55914--55976 Score: 94
Period size: 30 Copynumber: 2.2 Consensus size: 30
55904 ATATAACTTT
*
55914 ATTTTATATTTTAGTCCCTAAACTTTTACA
1 ATTTTATATTTTAGTCCCTAAACTTTCACA
*
55944 ACTTTATATTTTAGT-CCTAAACTTTCA-A
1 ATTTTATATTTTAGTCCCTAAACTTTCACA
55972 ATTTT
1 ATTTT
55977 TACATTCCAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
28 5 0.17
29 11 0.37
30 14 0.47
ACGTcount: A:0.30, C:0.16, G:0.03, T:0.51
Consensus pattern (30 bp):
ATTTTATATTTTAGTCCCTAAACTTTCACA
Found at i:56007 original size:13 final size:13
Alignment explanation
Indices: 55991--56015 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
55981 TTCCAATCAC
55991 TAGTCCCAAAATT
1 TAGTCCCAAAATT
56004 TAGTCCCAAAAT
1 TAGTCCCAAAAT
56016 ATCAAATTTA
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:0.40, C:0.24, G:0.08, T:0.28
Consensus pattern (13 bp):
TAGTCCCAAAATT
Found at i:57138 original size:30 final size:30
Alignment explanation
Indices: 57107--57228 Score: 187
Period size: 30 Copynumber: 4.1 Consensus size: 30
57097 TGTTCAATAT
* * *
57107 ATATTTTAACTTAAATTCATAACATTTTAT
1 ATATCTTAACTTAAATTCATAACATTATAA
57137 ATATCTT--CTTAAATTCATAACATTATAA
1 ATATCTTAACTTAAATTCATAACATTATAA
57165 ATATCTTAACTTAAATTCATAACATTATAA
1 ATATCTTAACTTAAATTCATAACATTATAA
57195 ATATCTTAACTTAAATTCATAAC-TTATTAA
1 ATATCTTAACTTAAATTCATAACATTA-TAA
57225 ATAT
1 ATAT
57229 ATTTTGTGCT
Statistics
Matches: 86, Mismatches: 3, Indels: 6
0.91 0.03 0.06
Matches are distributed among these distances:
28 26 0.30
29 3 0.03
30 57 0.66
ACGTcount: A:0.43, C:0.12, G:0.00, T:0.44
Consensus pattern (30 bp):
ATATCTTAACTTAAATTCATAACATTATAA
Found at i:57182 original size:58 final size:59
Alignment explanation
Indices: 57107--57228 Score: 185
Period size: 58 Copynumber: 2.1 Consensus size: 59
57097 TGTTCAATAT
* * *
57107 ATATTTTAACTTAAATTCATAACATTTTATATATCTT-CTTAAATTCATAACATTA-TAA
1 ATATCTTAACTTAAATTCATAACATTATAAATATCTTACTTAAATTCATAAC-TTATTAA
57165 ATATCTTAACTTAAATTCATAACATTATAAATATCTTAACTTAAATTCATAACTTATTAA
1 ATATCTTAACTTAAATTCATAACATTATAAATATCTT-ACTTAAATTCATAACTTATTAA
57225 ATAT
1 ATAT
57229 ATTTTGTGCT
Statistics
Matches: 58, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
58 34 0.59
59 3 0.05
60 21 0.36
ACGTcount: A:0.43, C:0.12, G:0.00, T:0.44
Consensus pattern (59 bp):
ATATCTTAACTTAAATTCATAACATTATAAATATCTTACTTAAATTCATAACTTATTAA
Found at i:57226 original size:16 final size:16
Alignment explanation
Indices: 57145--57226 Score: 54
Period size: 16 Copynumber: 5.4 Consensus size: 16
57135 ATATATCTTC
57145 TTAAATTCATAACATTA
1 TTAAATTCATAAC-TTA
*
57162 -TAAATATCTTAAC---
1 TTAAAT-TCATAACTTA
57175 TTAAATTCATAACATTA
1 TTAAATTCATAAC-TTA
*
57192 -TAAATATCTTAAC---
1 TTAAAT-TCATAACTTA
57205 TTAAATTCATAACTTA
1 TTAAATTCATAACTTA
57221 TTAAAT
1 TTAAAT
57227 ATATTTTGTG
Statistics
Matches: 50, Mismatches: 4, Indels: 23
0.65 0.05 0.30
Matches are distributed among these distances:
13 12 0.24
14 10 0.20
16 16 0.32
17 12 0.24
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.41
Consensus pattern (16 bp):
TTAAATTCATAACTTA
Found at i:57260 original size:29 final size:29
Alignment explanation
Indices: 57214--57299 Score: 102
Period size: 30 Copynumber: 2.9 Consensus size: 29
57204 CTTAAATTCA
57214 TAACTTATTAAATATATTTTGTGCTTA-TTT
1 TAACTTA-TAAATATATTTTGT-CTTATTTT
* *
57244 TAACTTAAAAATATATTTTATTCTTATTTT
1 TAACTTATAAATATATTTT-GTCTTATTTT
*
57274 TAACTTATATATATTATTTTGTCTTA
1 TAACTTATAAATA-TATTTTGTCTTA
57300 AGTTAAAAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
29 15 0.31
30 27 0.56
31 6 0.12
ACGTcount: A:0.33, C:0.07, G:0.03, T:0.57
Consensus pattern (29 bp):
TAACTTATAAATATATTTTGTCTTATTTT
Found at i:57383 original size:29 final size:29
Alignment explanation
Indices: 57351--57467 Score: 118
Period size: 29 Copynumber: 4.1 Consensus size: 29
57341 AAAAAAAAAG
57351 TTAAAAATATATTTTATTCCTATTTTAAC
1 TTAAAAATATATTTTATTCCTATTTTAAC
**
57380 TTAAAAATATATTTTA-TCCTTATAGTAAC
1 TTAAAAATATATTTTATTCC-TATTTTAAC
* * *
57409 TTAAAAAATATATGTTTTATTCTTATCTTCAC
1 TT-AAAAATATA--TTTTATTCCTATTTTAAC
57441 TTAAAAATAT-TTTT-TT--TATTTTAAC
1 TTAAAAATATATTTTATTCCTATTTTAAC
57466 TT
1 TT
57468 TACCTTAACA
Statistics
Matches: 75, Mismatches: 8, Indels: 14
0.77 0.08 0.14
Matches are distributed among these distances:
25 9 0.12
27 2 0.03
28 7 0.09
29 25 0.33
30 9 0.12
31 8 0.11
32 13 0.17
33 2 0.03
ACGTcount: A:0.37, C:0.09, G:0.02, T:0.52
Consensus pattern (29 bp):
TTAAAAATATATTTTATTCCTATTTTAAC
Found at i:57434 original size:32 final size:29
Alignment explanation
Indices: 57351--57455 Score: 120
Period size: 29 Copynumber: 3.5 Consensus size: 29
57341 AAAAAAAAAG
* *
57351 TTAAAAATATATTTTATTCCTATTTTAAC
1 TTAAAAATATATTTTATTCTTATATTAAC
* *
57380 TTAAAAATATATTTTATCCTTATAGTAAC
1 TTAAAAATATATTTTATTCTTATATTAAC
* *
57409 TTAAAAAATATATGTTTTATTCTTATCTTCAC
1 TT-AAAAATATA--TTTTATTCTTATATTAAC
*
57441 TTAAAAATATTTTTT
1 TTAAAAATATATTTT
57456 TTATTTTAAC
Statistics
Matches: 64, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
29 31 0.48
30 9 0.14
31 8 0.12
32 16 0.25
ACGTcount: A:0.38, C:0.10, G:0.02, T:0.50
Consensus pattern (29 bp):
TTAAAAATATATTTTATTCTTATATTAAC
Found at i:57551 original size:30 final size:30
Alignment explanation
Indices: 57516--57589 Score: 89
Period size: 30 Copynumber: 2.5 Consensus size: 30
57506 TGTGTGTTTA
*
57516 TTTAAGGTAAGATAATAATAAAATATA-ATT
1 TTTAAGGTAAGATAAAAATAAAATATATA-T
*
57546 TTTAA-GTAAAAATAAAAATAAAATATATAT
1 TTTAAGGT-AAGATAAAAATAAAATATATAT
*
57576 TTTAAGTTAAGATA
1 TTTAAGGTAAGATA
57590 TGAATTTAAG
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
29 2 0.05
30 33 0.89
31 2 0.05
ACGTcount: A:0.55, C:0.00, G:0.08, T:0.36
Consensus pattern (30 bp):
TTTAAGGTAAGATAAAAATAAAATATATAT
Found at i:58055 original size:29 final size:28
Alignment explanation
Indices: 58023--58093 Score: 81
Period size: 29 Copynumber: 2.5 Consensus size: 28
58013 TTTTCCCTAA
* **
58023 ATTTAAATACAAAATAA-AATTTATTAAGT
1 ATTTAAATACAAAACAAGAA-GAATTAA-T
*
58052 ATTTAAATACAATACAAGAAGAATTAAT
1 ATTTAAATACAAAACAAGAAGAATTAAT
58080 ATTTAAATACAAAA
1 ATTTAAATACAAAA
58094 AATTTGTAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
28 14 0.39
29 20 0.56
30 2 0.06
ACGTcount: A:0.58, C:0.06, G:0.04, T:0.32
Consensus pattern (28 bp):
ATTTAAATACAAAACAAGAAGAATTAAT
Found at i:59064 original size:17 final size:17
Alignment explanation
Indices: 59039--59092 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
59029 TTTTATTTTT
* *
59039 AAAATTATTTAAATTTC
1 AAAAATATTAAAATTTC
*
59056 AAAAATATTGAAATATTTT
1 AAAAATATT-AAA-ATTTC
*
59075 AAAAATATAAAAATTTC
1 AAAAATATTAAAATTTC
59092 A
1 A
59093 GTTTTTTAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
17 13 0.43
18 5 0.17
19 12 0.40
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.39
Consensus pattern (17 bp):
AAAAATATTAAAATTTC
Found at i:59142 original size:19 final size:18
Alignment explanation
Indices: 59116--59170 Score: 53
Period size: 19 Copynumber: 3.0 Consensus size: 18
59106 ATTTGCAATT
59116 GTTT-AAAATTATTAAAA
1 GTTTAAAAATTATTAAAA
59133 GTTATAAAAA-TATTTAAAAA
1 GTT-TAAAAATTA-TT-AAAA
59153 GTTTAACAAATT-TTAAAA
1 GTTTAA-AAATTATTAAAA
59171 AAATTATAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 11
0.74 0.00 0.26
Matches are distributed among these distances:
17 3 0.09
18 7 0.22
19 11 0.34
20 10 0.31
21 1 0.03
ACGTcount: A:0.55, C:0.02, G:0.05, T:0.38
Consensus pattern (18 bp):
GTTTAAAAATTATTAAAA
Found at i:59182 original size:19 final size:20
Alignment explanation
Indices: 59129--59185 Score: 55
Period size: 19 Copynumber: 2.9 Consensus size: 20
59119 TAAAATTATT
*
59129 AAAAGTTATAAAAATATTTAA
1 AAAAATTAT-AAAATATTTAA
**
59150 AAAGTTTA-ACAAAT-TTTAA
1 AAAAATTATA-AAATATTTAA
59169 AAAAATTATAAAATATT
1 AAAAATTATAAAATATT
59186 ACAGAATTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
19 16 0.55
20 7 0.24
21 6 0.21
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.35
Consensus pattern (20 bp):
AAAAATTATAAAATATTTAA
Found at i:61555 original size:22 final size:23
Alignment explanation
Indices: 61496--61544 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
61486 TTTTTTATCC
61496 TTAGAAAGTAAAATCTACTTTAA
1 TTAGAAAGTAAAATCTACTTTAA
61519 TTAGAAAGTAAAATCTACTTTAA
1 TTAGAAAGTAAAATCTACTTTAA
61542 TTA
1 TTA
61545 ATTTTAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.47, C:0.08, G:0.08, T:0.37
Consensus pattern (23 bp):
TTAGAAAGTAAAATCTACTTTAA
Found at i:66442 original size:17 final size:19
Alignment explanation
Indices: 66398--66445 Score: 55
Period size: 21 Copynumber: 2.5 Consensus size: 19
66388 TGACGAACAA
66398 TATCGATACTGATGTAAGTGG
1 TATCGATACTGATG--AGTGG
*
66419 TAACGATACTGATG-G-GG
1 TATCGATACTGATGAGTGG
66436 TATCGATACT
1 TATCGATACT
66446 AACAAGGGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
17 11 0.44
18 1 0.04
21 13 0.52
ACGTcount: A:0.29, C:0.12, G:0.27, T:0.31
Consensus pattern (19 bp):
TATCGATACTGATGAGTGG
Found at i:67070 original size:44 final size:44
Alignment explanation
Indices: 67007--67323 Score: 474
Period size: 44 Copynumber: 7.2 Consensus size: 44
66997 AACCGAATTA
*
67007 ATAACTGAAATGCATAATGGTGCATTAAGGCATGAAAGGATTCC
1 ATAACTGAAATGCATAATGGTGCATTAAGGCATGAAAGGATGCC
* * *
67051 ATAACCGAAATTCATAATGGTGCATTAAGGCATGAAAGCATGCC
1 ATAACTGAAATGCATAATGGTGCATTAAGGCATGAAAGGATGCC
*
67095 ATAACTGAAAGGCATAATGGTGCATTAAGGCATGAAAGGATGCC
1 ATAACTGAAATGCATAATGGTGCATTAAGGCATGAAAGGATGCC
* *
67139 ATAACTGAAATGCATAAAGGTGCATTAAGGCATGAAAGAATGCC
1 ATAACTGAAATGCATAATGGTGCATTAAGGCATGAAAGGATGCC
* * *
67183 ATAACTGAAACGCATAATGGTGTATTAAGGTATGAAAGGATGCC
1 ATAACTGAAATGCATAATGGTGCATTAAGGCATGAAAGGATGCC
* *
67227 ATAACTGAAACGCATAATGGTGCATTAAGGCATGAAAGTATGCC
1 ATAACTGAAATGCATAATGGTGCATTAAGGCATGAAAGGATGCC
* * * *
67271 ATAAATGAAATGCATAACGGTGCAGTAAGGCATGAAA-AATGCC
1 ATAACTGAAATGCATAATGGTGCATTAAGGCATGAAAGGATGCC
*
67314 ATAAATGAAA
1 ATAACTGAAA
67324 ATAATAAATG
Statistics
Matches: 249, Mismatches: 24, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
43 15 0.06
44 234 0.94
ACGTcount: A:0.41, C:0.14, G:0.23, T:0.22
Consensus pattern (44 bp):
ATAACTGAAATGCATAATGGTGCATTAAGGCATGAAAGGATGCC
Found at i:73846 original size:22 final size:21
Alignment explanation
Indices: 73771--73848 Score: 54
Period size: 22 Copynumber: 3.7 Consensus size: 21
73761 ACCGAAAGGG
* *
73771 AGTATCGATACCATAATATACT
1 AGTATCGATACCATAGTATA-A
* *
73793 AGTATCGATA-CTTAGGGA-AA
1 AGTATCGATACCATA-GTATAA
*
73813 GGTATC-AGTACCATAGTATAGA
1 AGTATCGA-TACCATAGTATA-A
73835 AGTATCGATACCAT
1 AGTATCGATACCAT
73849 GGTAGGGTAT
Statistics
Matches: 42, Mismatches: 8, Indels: 12
0.68 0.13 0.19
Matches are distributed among these distances:
19 1 0.02
20 9 0.21
21 8 0.19
22 23 0.55
23 1 0.02
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.28
Consensus pattern (21 bp):
AGTATCGATACCATAGTATAA
Found at i:74324 original size:44 final size:44
Alignment explanation
Indices: 74269--74629 Score: 481
Period size: 44 Copynumber: 8.2 Consensus size: 44
74259 AAACGAATTA
*
74269 ATAACTGAAATGCATAATGGTGCATTAAGGGATGAAAGGATGCC
1 ATAACTGAAATGCATAATGGTGCATTAAGGCATGAAAGGATGCC
* * *
74313 ATAACTAAAATGCATAATGTTTCATTAAGGCATGAAAGGATGCC
1 ATAACTGAAATGCATAATGGTGCATTAAGGCATGAAAGGATGCC
* *
74357 ATAAATGAAATGCATAATGGTGCATTAAGGCATGAAATGATGCC
1 ATAACTGAAATGCATAATGGTGCATTAAGGCATGAAAGGATGCC
* * * * *
74401 ATAACTTAAATGCATAATTGTGCATTAAGGCATTAAAGGACGTC
1 ATAACTGAAATGCATAATGGTGCATTAAGGCATGAAAGGATGCC
* *
74445 ATAACTAAAATGCATAATGGTGCATTAAGGCATGAAAGGTTGCC
1 ATAACTGAAATGCATAATGGTGCATTAAGGCATGAAAGGATGCC
* *
74489 ATAACTGAATTGCATAATAGTGCATTAAGGCATGAAAGGATGCC
1 ATAACTGAAATGCATAATGGTGCATTAAGGCATGAAAGGATGCC
* *
74533 ATAAATGAAATACATAATGGTGCATTAAGGCATGAAAGGATGCC
1 ATAACTGAAATGCATAATGGTGCATTAAGGCATGAAAGGATGCC
* * ** * * **
74577 ATAAATGAAATGCTTAACAGTGCAGTAATG-ATGAAAAAATGCC
1 ATAACTGAAATGCATAATGGTGCATTAAGGCATGAAAGGATGCC
*
74620 ATAAATGAAA
1 ATAACTGAAA
74630 ATAATAAATA
Statistics
Matches: 279, Mismatches: 38, Indels: 1
0.88 0.12 0.00
Matches are distributed among these distances:
43 21 0.08
44 258 0.92
ACGTcount: A:0.42, C:0.12, G:0.21, T:0.25
Consensus pattern (44 bp):
ATAACTGAAATGCATAATGGTGCATTAAGGCATGAAAGGATGCC
Found at i:81397 original size:20 final size:20
Alignment explanation
Indices: 81355--81397 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
81345 CAACTAACTT
* ** *
81355 ACATCCATAATATCCTTATA
1 ACATCCAAAATATCCAAAGA
81375 ACATCCAAAATATCCAAAGA
1 ACATCCAAAATATCCAAAGA
81395 ACA
1 ACA
81398 CTTAAAACTA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.49, C:0.26, G:0.02, T:0.23
Consensus pattern (20 bp):
ACATCCAAAATATCCAAAGA
Done.