Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004998.1 Hibiscus syriacus cultivar Beakdansim tig00011219_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: 53966
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Found at i:9599 original size:22 final size:22
Alignment explanation
Indices: 9560--9604 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
9550 ATTTTAAATA
9560 AAATAATTAAATTCATTATTTT
1 AAATAATTAAATTCATTATTTT
*
9582 AAATAGATTGAATT-ATTATTTT
1 AAATA-ATTAAATTCATTATTTT
9604 A
1 A
9605 TTTTTGACCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.49
Consensus pattern (22 bp):
AAATAATTAAATTCATTATTTT
Found at i:10411 original size:23 final size:24
Alignment explanation
Indices: 10385--10429 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
10375 CCCAAAAATA
*
10385 TAATGTT-ATTTTTAATAAAATTT
1 TAATGTTAAATTTTAATAAAATTT
* *
10408 TAATTTTAAATTTTATTAAAAT
1 TAATGTTAAATTTTAATAAAAT
10430 AACGTTTTTG
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 6 0.33
24 12 0.67
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (24 bp):
TAATGTTAAATTTTAATAAAATTT
Found at i:11742 original size:16 final size:17
Alignment explanation
Indices: 11721--11754 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
11711 CCGATGTGTT
11721 ACATTGACTTTT-CAAA
1 ACATTGACTTTTACAAA
11737 ACATTGACTTTTACAAA
1 ACATTGACTTTTACAAA
11754 A
1 A
11755 GAATGAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.41, C:0.18, G:0.06, T:0.35
Consensus pattern (17 bp):
ACATTGACTTTTACAAA
Found at i:13698 original size:10 final size:10
Alignment explanation
Indices: 13685--13714 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
13675 AAATTTACTT
13685 CACTTTAACA
1 CACTTTAACA
13695 CACTTTAACA
1 CACTTTAACA
13705 CACTTTAACA
1 CACTTTAACA
13715 TCCATATTCT
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:0.40, C:0.30, G:0.00, T:0.30
Consensus pattern (10 bp):
CACTTTAACA
Found at i:16216 original size:16 final size:17
Alignment explanation
Indices: 16189--16238 Score: 63
Period size: 16 Copynumber: 3.2 Consensus size: 17
16179 CAGGCTAATA
16189 TAATT-TTAAAAATATT
1 TAATTATTAAAAATATT
*
16205 TAA-TATTTAAAATA-T
1 TAATTATTAAAAATATT
16220 TAATTATTAAAAAT-TT
1 TAATTATTAAAAATATT
16236 TAA
1 TAA
16239 CAATATAGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
15 5 0.17
16 24 0.83
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TAATTATTAAAAATATT
Found at i:17638 original size:29 final size:29
Alignment explanation
Indices: 17603--17684 Score: 128
Period size: 29 Copynumber: 2.8 Consensus size: 29
17593 AAACTAAATT
*
17603 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
* *
17632 GATGTCATTGCTTACATAATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
17661 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
17685 GTTAGGTGAG
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
29 43 0.90
30 5 0.10
ACGTcount: A:0.34, C:0.13, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:22402 original size:29 final size:29
Alignment explanation
Indices: 22367--22448 Score: 128
Period size: 29 Copynumber: 2.8 Consensus size: 29
22357 AAACTAAATT
*
22367 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
* *
22396 GATGTCATTGCTTACATAATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
22425 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
22449 GTTAGGTGAG
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
29 43 0.90
30 5 0.10
ACGTcount: A:0.34, C:0.13, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:25574 original size:42 final size:42
Alignment explanation
Indices: 25528--25679 Score: 114
Period size: 41 Copynumber: 3.7 Consensus size: 42
25518 TAAAAATGCT
*
25528 GCAATAGAGTTGACATATAGCGGCGTTTTTACAACAAACGTC
1 GCAATAGAGTTGACATATAGCGGCGTTTTTACAACAAACGCC
* *** * ** *
25570 GCAATAGTG-TGGTTTATTGCAACGTTTTT-TAACAAACGCC
1 GCAATAGAGTTGACATATAGCGGCGTTTTTACAACAAACGCC
* * * * *
25610 GCAATAGAGTGGTAAAT-TAGCGGCGTTTATACCACAAATGCC
1 GCAATAGAGTTG-ACATATAGCGGCGTTTTTACAACAAACGCC
* * *
25652 GTAATAGA-TTAACATATAGTGGCGTTTT
1 GCAATAGAGTTGACATATAGCGGCGTTTT
25680 AGCCAAAACG
Statistics
Matches: 79, Mismatches: 27, Indels: 9
0.69 0.23 0.08
Matches are distributed among these distances:
40 20 0.25
41 35 0.44
42 24 0.30
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.30
Consensus pattern (42 bp):
GCAATAGAGTTGACATATAGCGGCGTTTTTACAACAAACGCC
Found at i:25678 original size:82 final size:83
Alignment explanation
Indices: 25592--25782 Score: 239
Period size: 82 Copynumber: 2.3 Consensus size: 83
25582 TTTATTGCAA
* *
25592 CGTTTTTTAACAAACGCCGCAATAGAGT-GGTAAATTAGCGGCGTTTATACCACAAATGCCGTAA
1 CGTTTTTTAACAAACGCCGCAATAGA-TCAGTAAATTAGCGGCGTTTATACCACAAATGCCGCAA
25656 TAGATTA-ACATATAGTGG
65 TAGATTACACATATAGTGG
* * *
25674 CG--TTTTAGCCAAAACGCCACAATAGATCAGTAAATTAGCGGTGTTTATACCACAAATGCCGCA
1 CGTTTTTTA-AC-AAACGCCGCAATAGATCAGTAAATTAGCGGCGTTTATACCACAAATGCCGCA
25737 ATAGATTACACATATAGTGG
64 ATAGATTACACATATAGTGG
* *
25757 CATTTATTCTTA-AAACGCCGCAATAG
1 CGTTT-TT-TAACAAACGCCGCAATAG
25783 TGATAATAAA
Statistics
Matches: 92, Mismatches: 9, Indels: 14
0.80 0.08 0.12
Matches are distributed among these distances:
80 5 0.05
81 2 0.02
82 56 0.61
83 12 0.13
84 13 0.14
85 1 0.01
86 2 0.02
87 1 0.01
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.27
Consensus pattern (83 bp):
CGTTTTTTAACAAACGCCGCAATAGATCAGTAAATTAGCGGCGTTTATACCACAAATGCCGCAAT
AGATTACACATATAGTGG
Found at i:25763 original size:42 final size:41
Alignment explanation
Indices: 25601--25763 Score: 140
Period size: 42 Copynumber: 3.9 Consensus size: 41
25591 ACGTTTTTTA
* *
25601 ACAAACGCCGCAATAGAGTGGTAA-AT-TAGCGGCGTTTATACC
1 ACAAATGCCGCAATAGA-T--TAACATATAGTGGCGTTTATACC
*
25643 ACAAATGCCGTAATAGATTAACATATAGTGGCGTTT-TAGCC
1 ACAAATGCCGCAATAGATTAACATATAGTGGCGTTTATA-CC
* * * *
25684 A-AAACGCCACAATAGATCAGTAA-AT-TAGCGGTGTTTATACC
1 ACAAATGCCGCAATAGAT---TAACATATAGTGGCGTTTATACC
*
25725 ACAAATGCCGCAATAGATTACACATATAGTGGCATTTAT
1 ACAAATGCCGCAATAGATTA-ACATATAGTGGCGTTTAT
25764 TCTTAAAACG
Statistics
Matches: 97, Mismatches: 13, Indels: 22
0.73 0.10 0.17
Matches are distributed among these distances:
39 5 0.05
40 18 0.19
41 28 0.29
42 43 0.44
43 3 0.03
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.26
Consensus pattern (41 bp):
ACAAATGCCGCAATAGATTAACATATAGTGGCGTTTATACC
Found at i:25824 original size:41 final size:41
Alignment explanation
Indices: 25768--25887 Score: 168
Period size: 41 Copynumber: 2.9 Consensus size: 41
25758 ATTTATTCTT
* * *
25768 AAAACGCCGCAATAGTGATAATAAATAGTGGCGTTTTTAGA
1 AAAACGCTGCAATAGTGTTAATCAATAGTGGCGTTTTTAGA
* *
25809 CAAACGCTGTAATAGTGTTAATCAATAGTGGCGTTTTTAGA
1 AAAACGCTGCAATAGTGTTAATCAATAGTGGCGTTTTTAGA
* * *
25850 AAAAAGCTGCAATAGTTTTAATCAATAGTGGCTTTTTT
1 AAAACGCTGCAATAGTGTTAATCAATAGTGGCGTTTTT
25888 TTTTTTGTAT
Statistics
Matches: 69, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 69 1.00
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.33
Consensus pattern (41 bp):
AAAACGCTGCAATAGTGTTAATCAATAGTGGCGTTTTTAGA
Found at i:29160 original size:12 final size:11
Alignment explanation
Indices: 29129--29167 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
29119 CAATTCCTTT
29129 ATCTTTTCTTT-
1 ATCTTTT-TTTA
29140 ATCTTTTTTTA
1 ATCTTTTTTTA
29151 ATCTTATTTTTA
1 ATCTT-TTTTTA
29163 ATCTT
1 ATCTT
29168 GTTTCCAGCA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
10 3 0.12
11 12 0.46
12 11 0.42
ACGTcount: A:0.18, C:0.13, G:0.00, T:0.69
Consensus pattern (11 bp):
ATCTTTTTTTA
Found at i:29521 original size:10 final size:10
Alignment explanation
Indices: 29506--29560 Score: 65
Period size: 10 Copynumber: 5.3 Consensus size: 10
29496 TTTCAAAAAC
*
29506 AAAAAATAAA
1 AAAAAACAAA
29516 AAAAAACAAA
1 AAAAAACAAA
**
29526 AAAAGGCAAAA
1 AAAAAAC-AAA
29537 AAAAAACAAAA
1 AAAAAAC-AAA
29548 AAAAAACAAA
1 AAAAAACAAA
29558 AAA
1 AAA
29561 GCCAAAATTT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
10 20 0.51
11 19 0.49
ACGTcount: A:0.87, C:0.07, G:0.04, T:0.02
Consensus pattern (10 bp):
AAAAAACAAA
Found at i:29527 original size:11 final size:11
Alignment explanation
Indices: 29499--29560 Score: 74
Period size: 11 Copynumber: 5.6 Consensus size: 11
29489 CTATTTTTTT
29499 CAAAAACAAAAA
1 CAAAAA-AAAAA
29511 -ATAAAAAAAAA
1 CA-AAAAAAAAA
**
29522 C-AAAAAAAGG
1 CAAAAAAAAAA
29532 CAAAAAAAAAA
1 CAAAAAAAAAA
29543 CAAAAAAAAAA
1 CAAAAAAAAAA
29554 CAAAAAA
1 CAAAAAA
29561 GCCAAAATTT
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
10 8 0.19
11 31 0.72
12 4 0.09
ACGTcount: A:0.85, C:0.10, G:0.03, T:0.02
Consensus pattern (11 bp):
CAAAAAAAAAA
Found at i:29549 original size:32 final size:33
Alignment explanation
Indices: 29499--29560 Score: 101
Period size: 32 Copynumber: 1.9 Consensus size: 33
29489 CTATTTTTTT
29499 CAAAAACAAAAAATAAAAAAAAACAAAAAAAGG
1 CAAAAACAAAAAATAAAAAAAAACAAAAAAAGG
29532 CAAAAA-AAAAACA-AAAAAAAAACAAAAAA
1 CAAAAACAAAAA-ATAAAAAAAAACAAAAAA
29561 GCCAAAATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
32 21 0.75
33 7 0.25
ACGTcount: A:0.85, C:0.10, G:0.03, T:0.02
Consensus pattern (33 bp):
CAAAAACAAAAAATAAAAAAAAACAAAAAAAGG
Found at i:29561 original size:31 final size:33
Alignment explanation
Indices: 29499--29567 Score: 99
Period size: 32 Copynumber: 2.2 Consensus size: 33
29489 CTATTTTTTT
*
29499 CAAAAACAAAAAATAAAAAAAAACAAAAAAAGG
1 CAAAAACAAAAAATAAAAAAAAACAAAAAAAGC
29532 CAAAAA-AAAAACA-AAAAAAAAAC-AAAAAAGC
1 CAAAAACAAAAA-ATAAAAAAAAACAAAAAAAGC
29563 CAAAA
1 CAAAA
29568 TTTCAAAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
31 12 0.35
32 15 0.44
33 7 0.21
ACGTcount: A:0.83, C:0.12, G:0.04, T:0.01
Consensus pattern (33 bp):
CAAAAACAAAAAATAAAAAAAAACAAAAAAAGC
Found at i:29577 original size:1 final size:1
Alignment explanation
Indices: 29500--29560 Score: 50
Period size: 1 Copynumber: 61.0 Consensus size: 1
29490 TATTTTTTTC
* * * *** * *
29500 AAAAACAAAAAATAAAAAAAAACAAAAAAAGGCAAAAAAAAAACAAAAAAAAAACAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
29561 GCCAAAATTT
Statistics
Matches: 47, Mismatches: 13, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
1 47 1.00
ACGTcount: A:0.87, C:0.08, G:0.03, T:0.02
Consensus pattern (1 bp):
A
Found at i:33887 original size:12 final size:12
Alignment explanation
Indices: 33867--33898 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
33857 TATTTTCTTT
33867 ATCTT-TTTTTA
1 ATCTTATTTTTA
33878 ATCTTATTTTTA
1 ATCTTATTTTTA
33890 ATCTTATTT
1 ATCTTATTT
33899 CCAGCACCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 5 0.25
12 15 0.75
ACGTcount: A:0.22, C:0.09, G:0.00, T:0.69
Consensus pattern (12 bp):
ATCTTATTTTTA
Found at i:39579 original size:21 final size:21
Alignment explanation
Indices: 39555--39626 Score: 72
Period size: 21 Copynumber: 3.4 Consensus size: 21
39545 ATGAAGCAAG
* *
39555 GGAAGCAGAGAGAGCAATAGC
1 GGAAGCAGACAGAGCAGTAGC
* * *
39576 GGAAGCAGCCAGAGTAGCAGC
1 GGAAGCAGACAGAGCAGTAGC
* *
39597 GGAAGCAGCCAGAGCAGTAGT
1 GGAAGCAGACAGAGCAGTAGC
*
39618 GAAAGCAGA
1 GGAAGCAGA
39627 GAAAGAAGCA
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.39, C:0.18, G:0.38, T:0.06
Consensus pattern (21 bp):
GGAAGCAGACAGAGCAGTAGC
Found at i:39690 original size:21 final size:21
Alignment explanation
Indices: 39621--39693 Score: 76
Period size: 21 Copynumber: 3.5 Consensus size: 21
39611 CAGTAGTGAA
* * * *
39621 AGCAGAGAAAGAAGCATCGGT
1 AGCACAGAGAGAAGCAACGAT
*
39642 AGCACAAAGAGAAGCAACGAT
1 AGCACAGAGAGAAGCAACGAT
39663 AGCACAGAGAGAAGCAAC-AT
1 AGCACAGAGAGAAGCAACGAT
*
39683 ATCAACAGAGA
1 AGC-ACAGAGA
39694 TGTGAAGAAT
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
20 4 0.09
21 40 0.91
ACGTcount: A:0.49, C:0.18, G:0.26, T:0.07
Consensus pattern (21 bp):
AGCACAGAGAGAAGCAACGAT
Found at i:40135 original size:43 final size:43
Alignment explanation
Indices: 40086--40207 Score: 138
Period size: 43 Copynumber: 2.8 Consensus size: 43
40076 ATTTGTATGG
* * *
40086 AAACGCCACTAAATCTCAATACCTATTACGACATTTTCAATAA
1 AAACGCCGCTAAATCTCAAAACCTATTGCGACATTTTCAATAA
* * * * * *
40129 AAACGCCGCTAATTCTCAACACTTATTGC-ATCGTTTTCGATAC
1 AAACGCCGCTAAATCTCAAAACCTATTGCGA-CATTTTCAATAA
*
40172 AAACGCCGCTAAATCTGAAAACCTATTGCGACATTT
1 AAACGCCGCTAAATCTCAAAACCTATTGCGACATTT
40208 GTGGGAAAAC
Statistics
Matches: 64, Mismatches: 13, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
42 1 0.02
43 62 0.97
44 1 0.02
ACGTcount: A:0.35, C:0.26, G:0.10, T:0.29
Consensus pattern (43 bp):
AAACGCCGCTAAATCTCAAAACCTATTGCGACATTTTCAATAA
Found at i:40251 original size:42 final size:43
Alignment explanation
Indices: 40205--40373 Score: 150
Period size: 43 Copynumber: 4.0 Consensus size: 43
40195 TATTGCGACA
* * *
40205 TTTGT-GGGAAAACACAGCTAAACATCATCACATTCTGCGGCG
1 TTTGTAGGGAAAACGCAGCTAAACATCAACACCTTCTGCGGCG
* * * * * *
40247 TTTGT-GGAAAAATGCCA-CAAAATATCAAAACCTTCTGCGGCT
1 TTTGTAGGGAAAACG-CAGCTAAACATCAACACCTTCTGCGGCG
* * * *
40289 TTTGTAAGTAAAACGCCGCTAAATC-TCAACACCTACTGCGGCG
1 TTTGTAGGGAAAACGCAGCTAAA-CATCAACACCTTCTGCGGCG
*
40332 TTTGTAGGGAAAACGCCGCTAAACATCAACACCTAT-TGCGGC
1 TTTGTAGGGAAAACGCAGCTAAACATCAACACCT-TCTGCGGC
40374 ATTTTTTGAC
Statistics
Matches: 100, Mismatches: 21, Indels: 11
0.76 0.16 0.08
Matches are distributed among these distances:
42 37 0.37
43 63 0.63
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.24
Consensus pattern (43 bp):
TTTGTAGGGAAAACGCAGCTAAACATCAACACCTTCTGCGGCG
Found at i:40329 original size:43 final size:43
Alignment explanation
Indices: 40172--40378 Score: 145
Period size: 43 Copynumber: 4.8 Consensus size: 43
40162 TTTTCGATAC
* * * * * *
40172 AAACGCCGCTAAATCTGAAAACCTATTGCGACATTTGT-GGGA
1 AAACGCCGCTAAATCTCAACACCTACTGCGGCTTTTGTAAGGA
* * * * * *
40214 AAACACAGCTAAA-CATCATCACATTCTGCGGCGTTTGT--GGAA
1 AAACGCCGCTAAATC-TCAACACCTACTGCGGCTTTTGTAAGG-A
* * * * * * *
40256 AAATGCCACAAAATATCAAAACCTTCTGCGGCTTTTGTAAGTA
1 AAACGCCGCTAAATCTCAACACCTACTGCGGCTTTTGTAAGGA
* *
40299 AAACGCCGCTAAATCTCAACACCTACTGCGGCGTTTGTAGGGA
1 AAACGCCGCTAAATCTCAACACCTACTGCGGCTTTTGTAAGGA
*
40342 AAACGCCGCTAAA-CATCAACACCTATTGCGGCATTTT
1 AAACGCCGCTAAATC-TCAACACCTACTGCGGC-TTTT
40379 TTGACAAACG
Statistics
Matches: 126, Mismatches: 32, Indels: 12
0.74 0.19 0.07
Matches are distributed among these distances:
41 3 0.02
42 55 0.44
43 64 0.51
44 4 0.03
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.24
Consensus pattern (43 bp):
AAACGCCGCTAAATCTCAACACCTACTGCGGCTTTTGTAAGGA
Found at i:41700 original size:31 final size:31
Alignment explanation
Indices: 41660--41912 Score: 470
Period size: 31 Copynumber: 8.2 Consensus size: 31
41650 GGTCACAATA
*
41660 TAAATTGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
* *
41691 TAAACTGTTCATATGTGCCTTCAAACATATA
1 TAAACTGTTCATATGTGCCTTTAAACATATG
*
41722 TAAACTGTTCATATGTGGCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
41753 TAAACTGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
41784 TAAACTGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
41815 TAAACTGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
41846 TAAACTGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
41877 TAAACTGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
41908 TAAAC
1 TAAAC
41913 CCTCGACTCT
Statistics
Matches: 215, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 215 1.00
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.38
Consensus pattern (31 bp):
TAAACTGTTCATATGTGCCTTTAAACATATG
Found at i:42594 original size:64 final size:64
Alignment explanation
Indices: 42408--42631 Score: 211
Period size: 64 Copynumber: 3.5 Consensus size: 64
42398 TAATGAAGGT
* * ** * * *
42408 ATGCATCGATGCACTACTGATGCATCGGTGCAAAAAAGGTATTCGATGTA-GTATTATTACTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCAAAAATTGCATTCGATGTATTTATT-TTAATGGG
** * ** *
42472 ATGCATTAATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGT-TTCATTTTTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCAAAAATTGCATTCGATGTATTTA-TTTTAATGGG
* ** **
42536 ATGCATTGATGCACTACTTATGCATCGATGCATGAATTGCATTCGATGTATTTATTTTAA-AAG
1 ATGCATCGATGCACTACTTATGCATCGATGCAAAAATTGCATTCGATGTATTTATTTTAATGGG
** *
42599 AGTGCATCGATGCACTACCAATGCATCGGTGCA
1 A-TGCATCGATGCACTACTTATGCATCGATGCA
42632 CATTCAAACA
Statistics
Matches: 132, Mismatches: 24, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
63 2 0.02
64 125 0.95
65 5 0.04
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.33
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCAAAAATTGCATTCGATGTATTTATTTTAATGGG
Found at i:44735 original size:16 final size:16
Alignment explanation
Indices: 44714--44798 Score: 56
Period size: 16 Copynumber: 5.4 Consensus size: 16
44704 ATAAACTGTT
44714 CATATGTGCCTTTAAA
1 CATATGTGCCTTTAAA
**
44730 CATATGTAAACTGTT---
1 CATATGT-GCCT-TTAAA
44745 CATATGTGCCTTTAAA
1 CATATGTGCCTTTAAA
**
44761 CATATGTAAACTGTT---
1 CATATGT-GCCT-TTAAA
44776 CATATGTGCCTTTAAA
1 CATATGTGCCTTTAAA
44792 CATATGT
1 CATATGT
44799 AAACCGTTCA
Statistics
Matches: 51, Mismatches: 8, Indels: 20
0.65 0.10 0.25
Matches are distributed among these distances:
13 4 0.08
14 4 0.08
15 14 0.27
16 21 0.41
17 4 0.08
18 4 0.08
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.39
Consensus pattern (16 bp):
CATATGTGCCTTTAAA
Found at i:44834 original size:31 final size:31
Alignment explanation
Indices: 44705--44833 Score: 240
Period size: 31 Copynumber: 4.2 Consensus size: 31
44695 GGTCACAATA
44705 TAAACTGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
44736 TAAACTGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
44767 TAAACTGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
* *
44798 TAAACCGTTCATATGTGCATTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
44829 TAAAC
1 TAAAC
44834 CCTCGACTCT
Statistics
Matches: 96, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 96 1.00
ACGTcount: A:0.34, C:0.16, G:0.12, T:0.37
Consensus pattern (31 bp):
TAAACTGTTCATATGTGCCTTTAAACATATG
Found at i:45436 original size:64 final size:65
Alignment explanation
Indices: 45328--45553 Score: 235
Period size: 64 Copynumber: 3.5 Consensus size: 65
45318 TAATGAAGGT
* * ** * **
45328 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAAGGTATTCGATGTAGT-ATTATTGCTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTAGTCATTATTAATGGG
* ** *
45392 ATGCATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGT-TTCATTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTAGTCATTATTAATGGG
* * * * **
45456 ATGCATTGATGCACTACTTATGCATCGATGCATGAATTGCATTCGATGTATTTATT-TTAA-AAG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTAGTCATTATTAATGGG
** *
45519 AGTGCATCGATGCACTACCAATGCATCGGTGCATA
1 A-TGCATCGATGCACTACTTATGCATCGATGCATA
45554 TTCAAACAAT
Statistics
Matches: 136, Mismatches: 23, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
63 3 0.02
64 128 0.94
65 5 0.04
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33
Consensus pattern (65 bp):
ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTAGTCATTATTAATGGG
Found at i:46476 original size:26 final size:26
Alignment explanation
Indices: 46427--46481 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
46417 AATTCATACC
* *
46427 TAATCCAAAGCAATCAATATTAATTA
1 TAATCCAAAGCAAACAATATTAATCA
*
46453 TAATCCAAATCAAACAATGA-TAATCA
1 TAATCCAAAGCAAACAAT-ATTAATCA
46479 TAA
1 TAA
46482 ATTTGAATGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 24 0.96
27 1 0.04
ACGTcount: A:0.53, C:0.16, G:0.04, T:0.27
Consensus pattern (26 bp):
TAATCCAAAGCAAACAATATTAATCA
Found at i:50114 original size:3 final size:3
Alignment explanation
Indices: 50106--50155 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
50096 TTTGAATATG
50106 TTA TTA TTA TTA TTA TTA TTA TTA 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
50154 TT
1 TT
50156 TTGTTATTTT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:51267 original size:23 final size:24
Alignment explanation
Indices: 51241--51292 Score: 70
Period size: 23 Copynumber: 2.2 Consensus size: 24
51231 TTATATTTAG
* *
51241 TAATTGTTTTTAATTTTTAT-CTT
1 TAATTGTTTTTAAATTTAATACTT
*
51264 TAATTTTTTTTAAATTTAATACTT
1 TAATTGTTTTTAAATTTAATACTT
51288 TAATT
1 TAATT
51293 ATTGTTCTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
23 17 0.68
24 8 0.32
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.65
Consensus pattern (24 bp):
TAATTGTTTTTAAATTTAATACTT
Found at i:52863 original size:7 final size:7
Alignment explanation
Indices: 52837--52881 Score: 65
Period size: 7 Copynumber: 6.3 Consensus size: 7
52827 GTACTAACCA
52837 TTTTATT
1 TTTTATT
52844 TTTCT-TAT
1 TTT-TAT-T
52852 TTTTATT
1 TTTTATT
52859 TTTTATT
1 TTTTATT
52866 TTTTATT
1 TTTTATT
52873 TTTTATT
1 TTTTATT
52880 TT
1 TT
52882 GCTCTAACTT
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
7 29 0.83
8 6 0.17
ACGTcount: A:0.13, C:0.02, G:0.00, T:0.84
Consensus pattern (7 bp):
TTTTATT
Done.