Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006828.1 Hibiscus syriacus cultivar Beakdansim tig00017361_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: 65236
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:4137 original size:65 final size:64
Alignment explanation
Indices: 4049--4203 Score: 188
Period size: 65 Copynumber: 2.4 Consensus size: 64
4039 ACACTTGGTG
* * * * * *
4049 TGCATCGGTACACTAATTACATTCGATTTTTCAA-AAGAGCCAGGAGTGCATCGATGCATGG-TA
1 TGCATCGGTACACAAAATGCATTCGATGTTTCAATAA-AACCAAGAGTGCATCGATGCATGGCT-
4112 T
64 T
** *
4113 GTGCATCGGTACGTAAAATGCATTCGATGTTTCAATAAAATCAAGAGTGCATCGATGCATGGCTT
1 -TGCATCGGTACACAAAATGCATTCGATGTTTCAATAAAACCAAGAGTGCATCGATGCATGGCTT
4178 TGCATCGGTACACAAAATGCATTCGA
1 TGCATCGGTACACAAAATGCATTCGA
4204 ATTAGGGTGT
Statistics
Matches: 77, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
64 24 0.31
65 50 0.65
66 3 0.04
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (64 bp):
TGCATCGGTACACAAAATGCATTCGATGTTTCAATAAAACCAAGAGTGCATCGATGCATGGCTT
Found at i:4921 original size:18 final size:20
Alignment explanation
Indices: 4898--4937 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
4888 CTACATTCAA
4898 AAGGA-GTT-CATGTGCATC
1 AAGGAGGTTCCATGTGCATC
4916 AAGGAGGTTGCCATGTGCATC
1 AAGGAGGTT-CCATGTGCATC
4937 A
1 A
4938 TAAAAGCAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 5 0.26
19 3 0.16
21 11 0.58
ACGTcount: A:0.28, C:0.17, G:0.30, T:0.25
Consensus pattern (20 bp):
AAGGAGGTTCCATGTGCATC
Found at i:7692 original size:2 final size:2
Alignment explanation
Indices: 7685--7714 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
7675 CGTTGGTAAG
7685 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
7715 CATACACGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:9459 original size:23 final size:23
Alignment explanation
Indices: 9433--9481 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
9423 ATCTGTGCTC
*
9433 GTTTATTTATTGTTCGTGAACAT
1 GTTTATTTAATGTTCGTGAACAT
* *
9456 GTTTGTTTAATGTTCGTGAACGT
1 GTTTATTTAATGTTCGTGAACAT
9479 GTT
1 GTT
9482 CGTTTATATG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.18, C:0.08, G:0.22, T:0.51
Consensus pattern (23 bp):
GTTTATTTAATGTTCGTGAACAT
Found at i:9500 original size:24 final size:24
Alignment explanation
Indices: 9450--9553 Score: 120
Period size: 24 Copynumber: 4.4 Consensus size: 24
9440 TATTGTTCGT
* * **
9450 GAACATGTTTGTTTA-ATGTTCGT
1 GAACGTGTTCGTTTATATGTTCAC
9473 GAACGTGTTCGTTTATATGTTCAC
1 GAACGTGTTCGTTTATATGTTCAC
*
9497 GAACGTGCTCGTTTATATGTTCAC
1 GAACGTGTTCGTTTATATGTTCAC
* * *
9521 GAACGTGCTCATTTATATGTCCAC
1 GAACGTGTTCGTTTATATGTTCAC
*
9545 GAACTTGTT
1 GAACGTGTT
9554 TGTTATTTAT
Statistics
Matches: 71, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
23 13 0.18
24 58 0.82
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.40
Consensus pattern (24 bp):
GAACGTGTTCGTTTATATGTTCAC
Found at i:10596 original size:31 final size:32
Alignment explanation
Indices: 10483--10606 Score: 83
Period size: 31 Copynumber: 3.9 Consensus size: 32
10473 AAGTTTAGAA
* **
10483 ATTACAAAATAG-TCATT-AAATTTCTCAAACG
1 ATTACAAAA-AGATCATTAAAATTTATCAAATT
* * * * *
10514 GTTACAAAATGATCATTGAACTTTATTAAATT
1 ATTACAAAAAGATCATTAAAATTTATCAAATT
* * **
10546 ATTACAAAATGGTTGTT-AAATTTATCAAATT
1 ATTACAAAAAGATCATTAAAATTTATCAAATT
* * *
10577 TTTACAAAAAGATCCTTAAAACTTATCAAA
1 ATTACAAAAAGATCATTAAAATTTATCAAA
10607 ATTTATCAAT
Statistics
Matches: 71, Mismatches: 19, Indels: 5
0.75 0.20 0.05
Matches are distributed among these distances:
30 1 0.01
31 37 0.52
32 33 0.46
ACGTcount: A:0.44, C:0.12, G:0.07, T:0.36
Consensus pattern (32 bp):
ATTACAAAAAGATCATTAAAATTTATCAAATT
Found at i:10950 original size:29 final size:29
Alignment explanation
Indices: 10906--10964 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
10896 AATTTCGATC
10906 ATCATTTACTCAAGAAAAAAAACCATTCA
1 ATCATTTACTCAAGAAAAAAAACCATTCA
*
10935 ATCATTTACTCTAGAAAAAAAACCATTCA
1 ATCATTTACTCAAGAAAAAAAACCATTCA
10964 A
1 A
10965 CTAGGTTATA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.51, C:0.20, G:0.03, T:0.25
Consensus pattern (29 bp):
ATCATTTACTCAAGAAAAAAAACCATTCA
Found at i:13592 original size:30 final size:30
Alignment explanation
Indices: 13543--13839 Score: 243
Period size: 30 Copynumber: 9.9 Consensus size: 30
13533 TAACATTAAA
* *
13543 AAATATAATTTATTTTTATCTTAACTTATT
1 AAATATATTTTATTCTTATCTTAACTTATT
* * *
13573 AAACATATTTTATCCTTATCTTAA-TTA-A
1 AAATATATTTTATTCTTATCTTAACTTATT
* *
13601 AAATATATTTTAATCTTATCTTAACTTATA
1 AAATATATTTTATTCTTATCTTAACTTATT
* **
13631 AAATATATTTTATTCTTACCTTAACTTAAA
1 AAATATATTTTATTCTTATCTTAACTTATT
* * *
13661 AAATATACTTT-TTATTATATTAACTT-TT
1 AAATATATTTTATTCTTATCTTAACTTATT
* *
13689 GAAAATATATTTTATTTTTATCTTAA-ATATT
1 --AAATATATTTTATTCTTATCTTAACTTATT
* * *
13720 AAATATATTATATTGTTGA-CTTAAATTATT
1 AAATATATTTTATTCTT-ATCTTAACTTATT
* * *
13750 AGATATATTCTATTCTTA-CATTAAATTATT
1 AAATATATTTTATTCTTATC-TTAACTTATT
* **
13780 AAATATGA-TTTATTCTTATCTTAACCTAAA
1 AAATAT-ATTTTATTCTTATCTTAACTTATT
13810 AATATATATTTTATT-TTAATCTTAATCTTA
1 AA-ATATATTTTATTCTT-ATCTTAA-CTTA
13840 ATCTTAATCT
Statistics
Matches: 218, Mismatches: 34, Indels: 28
0.78 0.12 0.10
Matches are distributed among these distances:
28 21 0.10
29 40 0.18
30 123 0.56
31 31 0.14
32 3 0.01
ACGTcount: A:0.38, C:0.09, G:0.02, T:0.51
Consensus pattern (30 bp):
AAATATATTTTATTCTTATCTTAACTTATT
Found at i:13654 original size:119 final size:120
Alignment explanation
Indices: 13531--13804 Score: 299
Period size: 119 Copynumber: 2.3 Consensus size: 120
13521 TAAATTCACA
*
13531 CTTAACATTAAAAAATATAATTTATTTTTATCTTAACTTATT-AAACATATTTTATCCTTATCTT
1 CTTAACATTAAAAAATATAATTTATTATTATCTTAACTT-TTAAAACATATTTTATCCTTATCTT
* * * *
13595 AATTA-AAAATATATTTTAATCTT-ATCTTAACTTATAAAATATATTTTATTCTTAC
65 AAATATAAAATATATTATAATCTTGA-CTTAAATTATAAAATATATTCTATTCTTAC
* * * **
13650 CTTAAC-TTAAAAAATATACTTT-TTATTATATTAACTTTTGAAAATATATTTTATTTTTATCTT
1 CTTAACATTAAAAAATATAATTTATTATTATCTTAACTTTT-AAAACATATTTTATCCTTATCTT
* * * * *
13713 AAATATTAAATATATTATATTGTTGACTTAAATTATTAGATATATTCTATTCTTAC
65 AAATATAAAATATATTATAATCTTGACTTAAATTATAAAATATATTCTATTCTTAC
* ** * *
13769 ATTAA-ATTATTAAATATGATTTATTCTTATCTTAAC
1 CTTAACATTAAAAAATATAATTTATTATTATCTTAAC
13805 CTAAAAATAT
Statistics
Matches: 127, Mismatches: 22, Indels: 11
0.79 0.14 0.07
Matches are distributed among these distances:
116 2 0.02
117 13 0.10
118 38 0.30
119 62 0.49
120 12 0.09
ACGTcount: A:0.39, C:0.09, G:0.02, T:0.50
Consensus pattern (120 bp):
CTTAACATTAAAAAATATAATTTATTATTATCTTAACTTTTAAAACATATTTTATCCTTATCTTA
AATATAAAATATATTATAATCTTGACTTAAATTATAAAATATATTCTATTCTTAC
Found at i:13836 original size:6 final size:6
Alignment explanation
Indices: 13825--13857 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
13815 ATATTTTATT
13825 TTAATC TTAATC TTAATC TTAATC TTAAT- TTAA
1 TTAATC TTAATC TTAATC TTAATC TTAATC TTAA
13858 AATTTTATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.15
6 23 0.85
ACGTcount: A:0.36, C:0.12, G:0.00, T:0.52
Consensus pattern (6 bp):
TTAATC
Found at i:13893 original size:24 final size:24
Alignment explanation
Indices: 13806--13897 Score: 71
Period size: 24 Copynumber: 3.8 Consensus size: 24
13796 TATCTTAACC
13806 TAAAAATATATATTTTATTTTAATCT
1 TAAAAATATAT-TTTTATTTTAAT-T
*** * * *
13832 TAATCTTA-ATCTTAATCTTAATT
1 TAAAAATATATTTTTATTTTAATT
* *
13855 TAAAATTTTATTTTTATTTTAATT
1 TAAAAATATATTTTTATTTTAATT
13879 TAAGAAATATA-TTTTATTT
1 TAA-AAATATATTTTTATTT
13898 GTATCTTAAC
Statistics
Matches: 50, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
23 6 0.12
24 32 0.64
25 7 0.14
26 5 0.10
ACGTcount: A:0.38, C:0.04, G:0.01, T:0.57
Consensus pattern (24 bp):
TAAAAATATATTTTTATTTTAATT
Found at i:13934 original size:31 final size:30
Alignment explanation
Indices: 13859--13937 Score: 79
Period size: 30 Copynumber: 2.6 Consensus size: 30
13849 TTAATTTAAA
* * * *
13859 ATTTTATTTTTATTTTAATTTAAGAAATAT
1 ATTTCATTTTTATCTTAACTGAAGAAATAT
* *
13889 ATTTTATTTGTATCTTAACTGAA-AAATAT
1 ATTTCATTTTTATCTTAACTGAAGAAATAT
13918 ATATCTCATTTTTATCTTAA
1 AT-T-TCATTTTTATCTTAA
13938 TTTTAAAATA
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
29 8 0.20
30 20 0.49
31 13 0.32
ACGTcount: A:0.35, C:0.06, G:0.04, T:0.54
Consensus pattern (30 bp):
ATTTCATTTTTATCTTAACTGAAGAAATAT
Found at i:13946 original size:31 final size:30
Alignment explanation
Indices: 13864--13948 Score: 82
Period size: 31 Copynumber: 2.8 Consensus size: 30
13854 TTAAAATTTT
* * *
13864 ATTTTTATTTTAATTTAAGAA-ATATATTTT
1 ATTTTTATCTTAATTTAA-AATATATATCTC
* **
13894 ATTTGTATCTTAACTGAAAAATATATATCTC
1 ATTTTTATCTTAA-TTTAAAATATATATCTC
13925 ATTTTTATCTTAATTTTAAAATAT
1 ATTTTTATCTTAA-TTTAAAATAT
13949 TATAAAAATT
Statistics
Matches: 43, Mismatches: 10, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
30 13 0.30
31 30 0.70
ACGTcount: A:0.38, C:0.06, G:0.04, T:0.53
Consensus pattern (30 bp):
ATTTTTATCTTAATTTAAAATATATATCTC
Found at i:13998 original size:30 final size:31
Alignment explanation
Indices: 13964--14026 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 31
13954 AAATTAATTT
*
13964 TAAATATTTAAGTTAAAGTAA-AATAAAATA
1 TAAATATTTAAGTTAAAATAAGAATAAAATA
* * *
13994 TAAATTTTTTATTTAAAATAAGAATAAAATA
1 TAAATATTTAAGTTAAAATAAGAATAAAATA
14025 TA
1 TA
14027 TATTCAATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 17 0.61
31 11 0.39
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (31 bp):
TAAATATTTAAGTTAAAATAAGAATAAAATA
Found at i:14963 original size:67 final size:65
Alignment explanation
Indices: 14855--14987 Score: 239
Period size: 67 Copynumber: 2.0 Consensus size: 65
14845 AACATGTGAG
*
14855 TTATGTAAATATAAAACATCAAAATTGATAAGAAATTTTATAACAAAAAATTTATTTTAGTTTAT
1 TTATGTAAATATAAAACAACAAAATTGATAAGAAATTTTAT-A-AAAAAATTTATTTTAGTTTAT
14920 AA
64 AA
14922 TTATGTAAATATAAAACAACAAAATTGATAAGAAATTTTATAAAAAAATTTATTTTAGTTTATAA
1 TTATGTAAATATAAAACAACAAAATTGATAAGAAATTTTATAAAAAAATTTATTTTAGTTTATAA
14987 T
1 T
14988 AAAAATTTGA
Statistics
Matches: 65, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
65 24 0.37
66 1 0.02
67 40 0.62
ACGTcount: A:0.51, C:0.04, G:0.06, T:0.39
Consensus pattern (65 bp):
TTATGTAAATATAAAACAACAAAATTGATAAGAAATTTTATAAAAAAATTTATTTTAGTTTATAA
Found at i:27664 original size:2 final size:2
Alignment explanation
Indices: 27657--27725 Score: 138
Period size: 2 Copynumber: 34.5 Consensus size: 2
27647 TTTTTAAAAC
27657 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
27699 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
27726 CCCCCATCCC
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 67 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:27918 original size:24 final size:24
Alignment explanation
Indices: 27891--27990 Score: 94
Period size: 24 Copynumber: 4.2 Consensus size: 24
27881 GATATCAAAA
*
27891 ATCAAAACATAATTCAGATCAGAT
1 ATCAAAACAGAATTCAGATCAGAT
* * * *
27915 ATCATAACAGAATCCAGTTTAGGA-
1 ATCAAAACAGAATTCAGATCA-GAT
* *
27939 ATCAGAACAGATTTCAGATCAGAT
1 ATCAAAACAGAATTCAGATCAGAT
* * *
27963 GTCAAAACAGAATTCAAATCAGAA
1 ATCAAAACAGAATTCAGATCAGAT
27987 ATCA
1 ATCA
27991 GATAAAATAT
Statistics
Matches: 58, Mismatches: 16, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
23 2 0.03
24 54 0.93
25 2 0.03
ACGTcount: A:0.47, C:0.17, G:0.13, T:0.23
Consensus pattern (24 bp):
ATCAAAACAGAATTCAGATCAGAT
Found at i:27990 original size:48 final size:48
Alignment explanation
Indices: 27884--27992 Score: 119
Period size: 48 Copynumber: 2.3 Consensus size: 48
27874 AAACGGAGAT
* * * * *
27884 ATCAAAAATCAAAACATAATTCAGATCAGATATCATAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
* * * * * *
27932 TTTAGGAATCAGAACAGATTTCAGATCAGATGTCAAAACAGAATTCAA
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
27980 ATCAGAAATCAGA
1 ATCAGAAATCAGA
27993 TAAAATATTC
Statistics
Matches: 47, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.49, C:0.17, G:0.13, T:0.22
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
Found at i:30496 original size:15 final size:15
Alignment explanation
Indices: 30476--30509 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
30466 GGTCAACTCC
30476 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
30491 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
30506 GGTC
1 GGTC
30510 GGGTCGGGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.24, C:0.26, G:0.35, T:0.15
Consensus pattern (15 bp):
GGTCAACGGTCAACG
Found at i:30521 original size:18 final size:18
Alignment explanation
Indices: 30498--30567 Score: 96
Period size: 18 Copynumber: 4.2 Consensus size: 18
30488 ACGGGTCAAC
30498 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
30516 GGTCAA-----CGGGTCG
1 GGTCAACGGGTCGGGTCG
*
30529 GGTAAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
30547 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
30565 GGT
1 GGT
30568 TGTGACCGGT
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
13 12 0.27
18 33 0.73
ACGTcount: A:0.13, C:0.20, G:0.50, T:0.17
Consensus pattern (18 bp):
GGTCAACGGGTCGGGTCG
Found at i:30527 original size:8 final size:7
Alignment explanation
Indices: 30475--30506 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
30465 TGGTCAACTC
30475 CGGTCAA
1 CGGTCAA
30482 CGGTCAA
1 CGGTCAA
30489 CGGGTCAA
1 C-GGTCAA
30497 CGGTCAA
1 CGGTCAA
30504 CGG
1 CGG
30507 GTCGGGTCGG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.25, C:0.28, G:0.34, T:0.12
Consensus pattern (7 bp):
CGGTCAA
Found at i:30563 original size:13 final size:13
Alignment explanation
Indices: 30509--30545 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
30499 GTCAACGGGT
30509 CGGGTCGGGTCAA
1 CGGGTCGGGTCAA
*
30522 CGGGTCGGGTAAA
1 CGGGTCGGGTCAA
30535 CGGGTCGGGTC
1 CGGGTCGGGTC
30546 GGGTCAACGG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.14, C:0.22, G:0.49, T:0.16
Consensus pattern (13 bp):
CGGGTCGGGTCAA
Found at i:32514 original size:2 final size:2
Alignment explanation
Indices: 32507--32539 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
32497 TTTTTAAAAC
32507 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
32540 CCCCCATCCC
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:32727 original size:24 final size:24
Alignment explanation
Indices: 32700--32798 Score: 85
Period size: 24 Copynumber: 4.2 Consensus size: 24
32690 GATATCAAAA
*
32700 ATCAAAACATAATTCAGATCAGAT
1 ATCAAAACAGAATTCAGATCAGAT
* * * *
32724 ATCATAACAGAATCCAGTTTAGGA-
1 ATCAAAACAGAATTCAGATCA-GAT
* *
32748 ATCAGAACAGATTTCAGATCAGAT
1 ATCAAAACAGAATTCAGATCAGAT
* * *
32772 GTC-AAACAGAATTCAAATCAGAA
1 ATCAAAACAGAATTCAGATCAGAT
32795 ATCA
1 ATCA
32799 GATAAATATT
Statistics
Matches: 56, Mismatches: 16, Indels: 6
0.72 0.21 0.08
Matches are distributed among these distances:
23 20 0.36
24 34 0.61
25 2 0.04
ACGTcount: A:0.46, C:0.17, G:0.13, T:0.23
Consensus pattern (24 bp):
ATCAAAACAGAATTCAGATCAGAT
Found at i:35296 original size:7 final size:7
Alignment explanation
Indices: 35284--35322 Score: 60
Period size: 7 Copynumber: 5.3 Consensus size: 7
35274 GGTCAACTCA
35284 GGTCAAC
1 GGTCAAC
35291 GGTCAAC
1 GGTCAAC
35298 GGGTCAAC
1 -GGTCAAC
35306 GGTCAAC
1 GGTCAAC
35313 GGGTCAAC
1 -GGTCAAC
35321 GG
1 GG
35323 GTCGGGTCGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
7 16 0.53
8 14 0.47
ACGTcount: A:0.26, C:0.26, G:0.36, T:0.13
Consensus pattern (7 bp):
GGTCAAC
Found at i:35304 original size:15 final size:15
Alignment explanation
Indices: 35284--35322 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
35274 GGTCAACTCA
35284 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
35299 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
35314 GGTCAACGG
1 GGTCAACGG
35323 GTCGGGTCGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.26, C:0.26, G:0.36, T:0.13
Consensus pattern (15 bp):
GGTCAACGGTCAACG
Found at i:35330 original size:13 final size:13
Alignment explanation
Indices: 35325--35361 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
35315 GTCAACGGGT
*
35325 CGGGTCGGGTCAA
1 CGGGTCGGGTAAA
35338 CGGGTCGGGTAAA
1 CGGGTCGGGTAAA
35351 CGGGTCGGGTA
1 CGGGTCGGGTA
35362 GGGTCAACGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.16, C:0.19, G:0.49, T:0.16
Consensus pattern (13 bp):
CGGGTCGGGTAAA
Found at i:35335 original size:18 final size:18
Alignment explanation
Indices: 35312--35383 Score: 91
Period size: 18 Copynumber: 4.3 Consensus size: 18
35302 CAACGGTCAA
35312 CGGGTCAACGGGTCGGGT
1 CGGGTCAACGGGTCGGGT
35330 CGGGTCAA-----CGGGT
1 CGGGTCAACGGGTCGGGT
*
35343 CGGGTAAACGGGTCGGGT
1 CGGGTCAACGGGTCGGGT
*
35361 AGGGTCAACGGGTCGGGT
1 CGGGTCAACGGGTCGGGT
35379 CGGGT
1 CGGGT
35384 TGTGACCGGT
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
13 12 0.27
18 33 0.73
ACGTcount: A:0.14, C:0.19, G:0.50, T:0.17
Consensus pattern (18 bp):
CGGGTCAACGGGTCGGGT
Found at i:35343 original size:8 final size:8
Alignment explanation
Indices: 35284--35325 Score: 70
Period size: 8 Copynumber: 5.5 Consensus size: 8
35274 GGTCAACTCA
35284 GGTCAAC-
1 GGTCAACG
35291 GGTCAACG
1 GGTCAACG
35299 GGTCAAC-
1 GGTCAACG
35306 GGTCAACG
1 GGTCAACG
35314 GGTCAACG
1 GGTCAACG
35322 GGTC
1 GGTC
35326 GGGTCGGGTC
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
7 14 0.42
8 19 0.58
ACGTcount: A:0.24, C:0.26, G:0.36, T:0.14
Consensus pattern (8 bp):
GGTCAACG
Found at i:35353 original size:31 final size:31
Alignment explanation
Indices: 35312--35378 Score: 116
Period size: 31 Copynumber: 2.2 Consensus size: 31
35302 CAACGGTCAA
* *
35312 CGGGTCAACGGGTCGGGTCGGGTCAACGGGT
1 CGGGTAAACGGGTCGGGTAGGGTCAACGGGT
35343 CGGGTAAACGGGTCGGGTAGGGTCAACGGGT
1 CGGGTAAACGGGTCGGGTAGGGTCAACGGGT
35374 CGGGT
1 CGGGT
35379 CGGGTTGTGA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.15, C:0.19, G:0.49, T:0.16
Consensus pattern (31 bp):
CGGGTAAACGGGTCGGGTAGGGTCAACGGGT
Found at i:38102 original size:21 final size:22
Alignment explanation
Indices: 38056--38112 Score: 62
Period size: 23 Copynumber: 2.6 Consensus size: 22
38046 CTGAAAATTG
*
38056 TTTTACGTAAAATGAATTACATA
1 TTTTATGTAAAATGAATTA-ATA
*
38079 TTTTATGTAAAATTAATT-ATA
1 TTTTATGTAAAATGAATTAATA
* *
38100 TTTTCTGGAAAAT
1 TTTTATGTAAAAT
38113 AGTTTTCGGA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 14 0.47
23 16 0.53
ACGTcount: A:0.40, C:0.05, G:0.09, T:0.46
Consensus pattern (22 bp):
TTTTATGTAAAATGAATTAATA
Found at i:38372 original size:30 final size:27
Alignment explanation
Indices: 38338--38403 Score: 71
Period size: 30 Copynumber: 2.3 Consensus size: 27
38328 CCTTAATTTT
*
38338 AATTAATAGTATT-TTATTAACATAATACTA
1 AATTAATA-TATTAATATTAA-AT-ATA-TA
*
38368 AATTATTATATTAATATTAAATATATA
1 AATTAATATATTAATATTAAATATATA
38395 AATTAATAT
1 AATTAATAT
38404 TACTCATTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
27 10 0.31
28 3 0.09
29 6 0.19
30 13 0.41
ACGTcount: A:0.50, C:0.03, G:0.02, T:0.45
Consensus pattern (27 bp):
AATTAATATATTAATATTAAATATATA
Found at i:38382 original size:19 final size:19
Alignment explanation
Indices: 38360--38402 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
38350 TTTATTAACA
*
38360 TAATACTAAAT-TATTATAT
1 TAATACTAAATATA-TAAAT
*
38379 TAATATTAAATATATAAAT
1 TAATACTAAATATATAAAT
38398 TAATA
1 TAATA
38403 TTACTCATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 19 0.90
20 2 0.10
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (19 bp):
TAATACTAAATATATAAAT
Found at i:38479 original size:47 final size:49
Alignment explanation
Indices: 38411--38503 Score: 120
Period size: 49 Copynumber: 1.9 Consensus size: 49
38401 TATTACTCAT
* *
38411 TATTAATAATTTTAATAATATTA-T-ATTTAATAAAAATAATATATAAA
1 TATTAATAATTTTAATAATATTACTAAATTAAAAAAAATAATATATAAA
* *
38458 TATTAATAA-TTTATTATATATTACTAAATTAAAAAAAATCATATAT
1 TATTAATAATTTTAATA-ATATTACTAAATTAAAAAAAATAATATAT
38504 TATTATAATA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
46 6 0.15
47 15 0.38
48 1 0.03
49 17 0.44
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (49 bp):
TATTAATAATTTTAATAATATTACTAAATTAAAAAAAATAATATATAAA
Found at i:38567 original size:39 final size:38
Alignment explanation
Indices: 38524--38622 Score: 103
Period size: 39 Copynumber: 2.6 Consensus size: 38
38514 TATCTGAGTA
38524 TATATTAATATAATATTAAAAATTTAATATTATTAA-AAT
1 TATATTAATATAATATTAAAAATTTAATA--ATTAATAAT
* * *
38563 TATATT-ATATGTATATTAAATATTTTAATAATTAATATT
1 TATATTAATAT-AATATTAAA-AATTTAATAATTAATAAT
* *
38602 TTTATTAAAATAATATTAAAA
1 TATATTAATATAATATTAAAA
38623 TATTAATTTA
Statistics
Matches: 50, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
38 10 0.20
39 29 0.58
40 11 0.22
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (38 bp):
TATATTAATATAATATTAAAAATTTAATAATTAATAAT
Found at i:38626 original size:19 final size:18
Alignment explanation
Indices: 38604--38656 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 18
38594 TTAATATTTT
38604 TATTAAAATAATATTAAAA
1 TATTAAAATAATATT-AAA
**
38623 TATTAATTTAATATTAAA
1 TATTAAAATAATATTAAA
*
38641 TGTATAAAATAATATT
1 TAT-TAAAATAATATT
38657 TTTTGAGTAC
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
18 5 0.18
19 23 0.82
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (18 bp):
TATTAAAATAATATTAAA
Found at i:38765 original size:18 final size:18
Alignment explanation
Indices: 38738--38774 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
38728 ATACAAAGGA
* *
38738 ATTAGGAAAATGAATTAC
1 ATTAGAAAAATCAATTAC
38756 ATTAGAAAAATCAATTAC
1 ATTAGAAAAATCAATTAC
38774 A
1 A
38775 ACTATCAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.54, C:0.08, G:0.11, T:0.27
Consensus pattern (18 bp):
ATTAGAAAAATCAATTAC
Found at i:48283 original size:35 final size:36
Alignment explanation
Indices: 48226--48294 Score: 131
Period size: 35 Copynumber: 1.9 Consensus size: 36
48216 AGGAGTAGTA
48226 GTTCTAGTTAGCAAAAATTACAAGACTAAAAGAAGC
1 GTTCTAGTTAGCAAAAATTACAAGACTAAAAGAAGC
48262 GTTCTAGTTAG-AAAAATTACAAGACTAAAAGAA
1 GTTCTAGTTAGCAAAAATTACAAGACTAAAAGAA
48295 ACAGTTAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
35 22 0.67
36 11 0.33
ACGTcount: A:0.49, C:0.12, G:0.16, T:0.23
Consensus pattern (36 bp):
GTTCTAGTTAGCAAAAATTACAAGACTAAAAGAAGC
Found at i:52323 original size:3 final size:3
Alignment explanation
Indices: 52315--52344 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
52305 AAAGAGAGAA
52315 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
52345 TCAAAGGGAA
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):
AAT
Found at i:52324 original size:20 final size:19
Alignment explanation
Indices: 52280--52343 Score: 51
Period size: 18 Copynumber: 3.4 Consensus size: 19
52270 AAAAGGTTAG
52280 ATAA-AAAAGAAAAAAATA
1 ATAATAAAAGAAAAAAATA
* *
52298 TTAAATAAAAGAGAGAAAATA
1 AT-AATAAAAGA-AAAAAATA
* * *
52319 ATAATAATA-ATAATAATA
1 ATAATAAAAGAAAAAAATA
52337 ATAATAA
1 ATAATAA
52344 TTCAAAGGGA
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
18 13 0.36
19 3 0.08
20 12 0.33
21 8 0.22
ACGTcount: A:0.72, C:0.00, G:0.06, T:0.22
Consensus pattern (19 bp):
ATAATAAAAGAAAAAAATA
Found at i:52505 original size:27 final size:26
Alignment explanation
Indices: 52457--52511 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 26
52447 GAAATAGGAT
*
52457 AAAAATAAATAAAAAATTTAAACATAA
1 AAAAATAAATAAAAAATATAAA-ATAA
52484 AAAAATAAATAAATAAA-ATAAAATAA
1 AAAAATAAATAAA-AAATATAAAATAA
52510 AA
1 AA
52512 GGGATTAGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 6 0.23
27 17 0.65
28 3 0.12
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (26 bp):
AAAAATAAATAAAAAATATAAAATAA
Found at i:53682 original size:2 final size:2
Alignment explanation
Indices: 53675--53729 Score: 71
Period size: 2 Copynumber: 29.0 Consensus size: 2
53665 CATATAATTA
*
53675 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A- AG AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
53715 AA AT AT AT A- AT AT AT
1 AT AT AT AT AT AT AT AT
53730 GTCACATCAG
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
1 3 0.06
2 44 0.94
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (2 bp):
AT
Found at i:54511 original size:169 final size:167
Alignment explanation
Indices: 54307--54834 Score: 692
Period size: 169 Copynumber: 3.2 Consensus size: 167
54297 TTTGCCTCTG
* * *
54307 AGCTTAGTGTAATCGAACTCGAAGGTCTTTGGTTGGCAGATAGCCATTCTCGACTTAAGCTATGC
1 AGCTGAGTGTAATCGAACTCGAAGGTC-TTGGTTGGCAGATAGCCCTTCTCGACTTAAGTTATGC
* * * *
54372 TACAAATGATGTGCCTTGGAGTTGAGCGTAGTCGAACTCGATGGTCTTTTATTAACAGATAACCC
65 TGCAAATGATGTGCCTTGGAGTTGAGCGTAGTCAAACTCGAAGGTCTTTT-TTGACAGATAACCC
*
54437 TTCTAGCCTTGAGTTATGCTGTAAATGACGTGCCCTCGA
129 TTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGA
* * * *
54476 AGCTGAGTGTAATCAAACTCGAGGGTCTGTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATAC
1 AGCTGAGTGTAATCGAACTCGAAGGTCT-TGGTTGGCAGATAGCCCTTCTCGACTTAAGTTATGC
* * * *
54541 TGCAAATGATATGCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTTGGTGACAAATAACCC
65 TGCAAATGATGTGCCTTGGAGTTGAGCGTAGTCAAACTCGAAGGTCTTTT-TTGACAGATAACCC
54606 TTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGA
129 TTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGA
* *
54645 AGCTGAGTGTAATCGAACTCGAGGGTC-T--TTGGCAGATAGCCCTTCT-TACCTTAAGTTATGC
1 AGCTGAGTGTAATCGAACTCGAAGGTCTTGGTTGGCAGATAGCCCTTCTCGA-CTTAAGTTATGC
* * ** * * * *
54706 TGCAAATGATGCGCCTTTGAGTTGAATGGAATCAAACTCTAAGGTC---TTTGGCAGATAACCCT
65 TGCAAATGATGTGCCTTGGAGTTGAGCGTAGTCAAACTCGAAGGTCTTTTTTGACAGATAACCCT
* **
54768 TCTAGTCTTGAGTTATGCTACAAATGATGTGCCCTCGA
130 TCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGA
*
54806 AGCTGAGTGTAGTCGAACTCGAAGGTCTT
1 AGCTGAGTGTAATCGAACTCGAAGGTCTT
54835 TGTGTTTCAA
Statistics
Matches: 318, Mismatches: 38, Indels: 13
0.86 0.10 0.04
Matches are distributed among these distances:
161 72 0.23
162 2 0.01
164 1 0.00
165 65 0.20
167 1 0.00
168 1 0.00
169 176 0.55
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.30
Consensus pattern (167 bp):
AGCTGAGTGTAATCGAACTCGAAGGTCTTGGTTGGCAGATAGCCCTTCTCGACTTAAGTTATGCT
GCAAATGATGTGCCTTGGAGTTGAGCGTAGTCAAACTCGAAGGTCTTTTTTGACAGATAACCCTT
CTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGA
Found at i:54516 original size:85 final size:85
Alignment explanation
Indices: 54307--54836 Score: 501
Period size: 84 Copynumber: 6.4 Consensus size: 85
54297 TTTGCCTCTG
* * * * * *
54307 AGCTTAGTGTAATCGAACTCGAAGGTCTTTGGTTGGCAGATAGCCATTCTCGACTTAAGCTATGC
1 AGCTGAGTGTAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTAAGTTATGC
* * *
54372 TACAAATGATGTG-CCTTGG
66 TGCAAATGATGTGCCCTCGA
* * * * ** ** *
54391 AGTTGAGCGTAGTCGAACTCGATGGTCTTTTATTAACAGATAACCCTTCTAGCCTTGAGTTATGC
1 AGCTGAGTGTAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTAAGTTATGC
* *
54456 TGTAAATGACGTGCCCTCGA
66 TGCAAATGATGTGCCCTCGA
* * * * * *
54476 AGCTGAGTGTAATCAAACTCGAGGGTCTGTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATAC
1 AGCTGAGTGTAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTAAGTTATGC
* * *
54541 TGCAAATGATATG-CCTTGG
66 TGCAAATGATGTGCCCTCGA
* * * * * *
54560 AGCTGAGCGTAGTCAAACTCGAAGGTCTTTTGG-TGACAAATAACCCTTCTAGCCTTGAGTTATG
1 AGCTGAGTGTAATCGAACTCGAAGGTC-TTTGGTTGGCAGATAACCCTTCTAGCCTTAAGTTATG
*
54624 CTGTAAATGATGTGCCCTCGA
65 CTGCAAATGATGTGCCCTCGA
* *
54645 AGCTGAGTGTAATCGAACTCGAGGGTC--T--TTGGCAGATAGCCCTTCTTA-CCTTAAGTTATG
1 AGCTGAGTGTAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTC-TAGCCTTAAGTTATG
* * *
54705 CTGCAAATGATGCGCCTTTG-
65 CTGCAAATGATGTGCCCTCGA
* * * * * * *
54725 AGTTGAATGGAATCAAACTCTAAGGTC--T--TTGGCAGATAACCCTTCTAGTCTTGAGTTATGC
1 AGCTGAGTGTAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTAAGTTATGC
*
54786 TACAAATGATGTGCCCTCGA
66 TGCAAATGATGTGCCCTCGA
*
54806 AGCTGAGTGTAGTCGAACTCGAAGGTCTTTG
1 AGCTGAGTGTAATCGAACTCGAAGGTCTTTG
54837 TGTTTCAAGA
Statistics
Matches: 352, Mismatches: 84, Indels: 20
0.77 0.18 0.04
Matches are distributed among these distances:
79 2 0.01
80 64 0.18
81 61 0.17
82 3 0.01
83 1 0.00
84 125 0.36
85 96 0.27
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (85 bp):
AGCTGAGTGTAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTAAGTTATGC
TGCAAATGATGTGCCCTCGA
Found at i:54906 original size:33 final size:34
Alignment explanation
Indices: 54833--54953 Score: 183
Period size: 33 Copynumber: 3.5 Consensus size: 34
54823 CTCGAAGGTC
*
54833 TTTGTGTTTCAAGAAAAAC-ATTTTCAAAGGTTTT
1 TTTGTGTTTCAAGAGAAACGA-TTTCAAAGGTTTT
*
54867 TTTGTGTTTCAAGAGAAACGGTTTCAAAGG-TTT
1 TTTGTGTTTCAAGAGAAACGATTTCAAAGGTTTT
54900 TTTGTGTTTCAAGAGAAACGATTTCAAAGGTTTTTT
1 TTTGTGTTTCAAGAGAAACGATTTCAAAGG--TTTT
54936 TTTGTGTTTCAAGAGAAA
1 TTTGTGTTTCAAGAGAAA
54954 TTATCTCCAA
Statistics
Matches: 80, Mismatches: 3, Indels: 6
0.90 0.03 0.07
Matches are distributed among these distances:
33 32 0.40
34 27 0.34
36 21 0.26
ACGTcount: A:0.30, C:0.08, G:0.20, T:0.42
Consensus pattern (34 bp):
TTTGTGTTTCAAGAGAAACGATTTCAAAGGTTTT
Found at i:55215 original size:42 final size:42
Alignment explanation
Indices: 55157--55283 Score: 218
Period size: 43 Copynumber: 3.0 Consensus size: 42
55147 AAAATGTCAC
* *
55157 AAAAGGTCGATATCTATAGAGTCGTTTTTGGAACAAACGCCGT
1 AAAAGGTC-ATATCTATAGCGGCGTTTTTGGAACAAACGCCGT
55200 AAAAGGTCATATCTATAGCGGCGTTTTTTGGAACAAACGCCGT
1 AAAAGGTCATATCTATAGCGGCG-TTTTTGGAACAAACGCCGT
55243 AAAAGGTCATATCTATAGCGGCGTTTTTGGAACAAACGCCG
1 AAAAGGTCATATCTATAGCGGCGTTTTTGGAACAAACGCCG
55284 CTAATTACCT
Statistics
Matches: 81, Mismatches: 2, Indels: 3
0.94 0.02 0.03
Matches are distributed among these distances:
42 31 0.38
43 50 0.62
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.27
Consensus pattern (42 bp):
AAAAGGTCATATCTATAGCGGCGTTTTTGGAACAAACGCCGT
Found at i:58333 original size:41 final size:41
Alignment explanation
Indices: 58269--58649 Score: 228
Period size: 41 Copynumber: 9.2 Consensus size: 41
58259 GCGTTTATTC
* * *
58269 AAAAACG-CACTATAGTATGAGTATTTAGCGGTGTTTGTTG
1 AAAAACGCCACTAAAGTACGAGTATTTAGCGGTGTTTGTTA
* * *
58309 GAAAATGCCACTAAAGTACGAGTATTTAGCGGCATTTTTTGCTT-
1 AAAAACGCCACTAAAGTACGAGTATTTAGCGG---TGTTTG-TTA
* **
58353 -AAAACGCCATTAAAGTATTATGT-TTTAGCGGTGTTTGTTA
1 AAAAACGCCACTAAAGTACGA-GTATTTAGCGGTGTTTGTTA
* * **
58393 AAAAATGCCACTAAAGTACAAGGT-TTTAGCGACGTTTGTCT-
1 AAAAACGCCACTAAAGTACGA-GTATTTAGCGGTGTTTGT-TA
* ** *
58434 AAAAACGCCACGATATATGTAC-CCTA-TT-GCGGTGTTTGTTT
1 AAAAACGCCAC--TA-AAGTACGAGTATTTAGCGGTGTTTGTTA
* * * * * * *
58475 AAAAATGCCACTAAAGAACGATTATATGGCGGCGTTTGTTT
1 AAAAACGCCACTAAAGTACGAGTATTTAGCGGTGTTTGTTA
* * * *
58516 ACAAACGCCACTAAAGTACTGA-TATTTAGTGGTATTTGTCA
1 AAAAACGCCACTAAAGTAC-GAGTATTTAGCGGTGTTTGTTA
* * *
58557 AATAAACGTCACTAAAGTACTGA-TATTTAGCGGTGTTTATCA
1 AA-AAACGCCACTAAAGTAC-GAGTATTTAGCGGTGTTTGTTA
* * * *
58599 AATAAACACCACTAAAGTATGAGT-TTTAGCGGCGTTTGTTG
1 AA-AAACGCCACTAAAGTACGAGTATTTAGCGGTGTTTGTTA
*
58640 AGAAACGCCA
1 AAAAACGCCA
58650 TTAATGTTAC
Statistics
Matches: 267, Mismatches: 54, Indels: 40
0.74 0.15 0.11
Matches are distributed among these distances:
38 4 0.01
39 6 0.02
40 19 0.07
41 139 0.52
42 59 0.22
43 26 0.10
44 12 0.04
45 2 0.01
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.32
Consensus pattern (41 bp):
AAAAACGCCACTAAAGTACGAGTATTTAGCGGTGTTTGTTA
Found at i:58577 original size:42 final size:42
Alignment explanation
Indices: 58518--58630 Score: 158
Period size: 42 Copynumber: 2.7 Consensus size: 42
58508 GTTTGTTTAC
* *
58518 AAACGCCACTAAAGTACTGATATTTAGTGGTATTTGTCAAAT
1 AAACGCCACTAAAGTACTGATATTTAGCGGTATTTATCAAAT
* *
58560 AAACGTCACTAAAGTACTGATATTTAGCGGTGTTTATCAAAT
1 AAACGCCACTAAAGTACTGATATTTAGCGGTATTTATCAAAT
*
58602 AAACACCACTAAAGTA-TGAGT-TTTAGCGG
1 AAACGCCACTAAAGTACTGA-TATTTAGCGG
58631 CGTTTGTTGA
Statistics
Matches: 64, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
41 11 0.17
42 53 0.83
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (42 bp):
AAACGCCACTAAAGTACTGATATTTAGCGGTATTTATCAAAT
Found at i:58867 original size:36 final size:36
Alignment explanation
Indices: 58780--58938 Score: 203
Period size: 37 Copynumber: 4.4 Consensus size: 36
58770 CAAAGGTTGA
* * *
58780 TGTTTCAAGAGAAATTGTCTCTAGAGAGACAGAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACA-AAATT
*
58817 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
58853 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
* * * * **
58890 AGTTCCAAAAGAAACTGTCTCAAGGGAGATGAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
58926 TGTTTCAAG-GAAA
1 TGTTTCAAGAGAAA
58939 ACATATTCAA
Statistics
Matches: 107, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
35 4 0.04
36 45 0.42
37 58 0.54
ACGTcount: A:0.39, C:0.14, G:0.21, T:0.26
Consensus pattern (36 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
Found at i:58904 original size:73 final size:73
Alignment explanation
Indices: 58780--58938 Score: 221
Period size: 73 Copynumber: 2.2 Consensus size: 73
58770 CAAAGGTTGA
* * * * * **
58780 TGTTTCAAGAGAAATTGTCTCTAGAGAGACAGAACTTTGTTTCAAGGGAAACTGTCTCAAGAGAG
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGAGAG
58845 ACAAAATT
66 ACAAAATT
*
58853 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGGAG
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGAGAG
**
58918 ATGAAATT
66 ACAAAATT
58926 TGTTTCAAG-GAAA
1 TGTTTCAAGAGAAA
58939 ACATATTCAA
Statistics
Matches: 76, Mismatches: 10, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
72 4 0.05
73 72 0.95
ACGTcount: A:0.39, C:0.14, G:0.21, T:0.26
Consensus pattern (73 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGAGAG
ACAAAATT
Found at i:59006 original size:29 final size:29
Alignment explanation
Indices: 58924--58998 Score: 132
Period size: 29 Copynumber: 2.6 Consensus size: 29
58914 GGAGATGAAA
58924 TTTGTTTCAAGGAAAACATATTCAAAGAT
1 TTTGTTTCAAGGAAAACATATTCAAAGAT
*
58953 CTTGTTTCAAGGAAAACATATTCAAAGAT
1 TTTGTTTCAAGGAAAACATATTCAAAGAT
*
58982 TTTGTTTCAAGGGAAAC
1 TTTGTTTCAAGGAAAAC
58999 TGTCTCAAGA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.39, C:0.12, G:0.16, T:0.33
Consensus pattern (29 bp):
TTTGTTTCAAGGAAAACATATTCAAAGAT
Found at i:59043 original size:20 final size:21
Alignment explanation
Indices: 59003--59051 Score: 73
Period size: 20 Copynumber: 2.4 Consensus size: 21
58993 GGAAACTGTC
59003 TCAAGAGACACAAAATTTGTT
1 TCAAGAGACACAAAATTTGTT
* *
59024 TCAAGAGAGAC-AACTTTGTT
1 TCAAGAGACACAAAATTTGTT
59044 TCAAGAGA
1 TCAAGAGA
59052 AACTGTCTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 16 0.62
21 10 0.38
ACGTcount: A:0.41, C:0.14, G:0.18, T:0.27
Consensus pattern (21 bp):
TCAAGAGACACAAAATTTGTT
Found at i:59097 original size:37 final size:34
Alignment explanation
Indices: 59019--59106 Score: 88
Period size: 37 Copynumber: 2.5 Consensus size: 34
59009 GACACAAAAT
*
59019 TTGTTTCAAGAGAGACAACTTTGTTTCAAGAGAAA
1 TTGTCTCAAGAGAGACAACTTTGTTT-AAGAGAAA
* *
59054 CTGTCTCAAGAGAGACAAAACTTTGTTT-TGAGTAAA
1 TTGTCTCAAGAGAGAC--AACTTTGTTTAAGAG-AAA
*
59090 TTAGTCTCAAGCGAGAC
1 TT-GTCTCAAGAGAGAC
59107 GACCCCTTAT
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
35 17 0.39
36 4 0.09
37 23 0.52
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.30
Consensus pattern (34 bp):
TTGTCTCAAGAGAGACAACTTTGTTTAAGAGAAA
Found at i:60570 original size:95 final size:95
Alignment explanation
Indices: 60381--60731 Score: 548
Period size: 95 Copynumber: 3.7 Consensus size: 95
60371 GGCTAGTTGA
* * * *
60381 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACATCTTAATA-TCATTG--TATTA
1 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGATTTATTGTATATTA
*
60443 TAATCACCTTTATCAGGCTAGCTGAATATT
66 TAATCACCTTTATCAGGCTAGCTGAATCTT
* *
60473 ATCCATAAAG-AGAGGACGTTTAACCAATTGCTCTAGAGGGACAACTCAAGATTTATTGTATATT
1 ATCCATAAAGCCG-GGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGATTTATTGTATATT
60537 ATAATCACCTTTATCAGGCTAGCTGAATCTT
65 ATAATCACCTTTATCAGGCTAGCTGAATCTT
* * *
60568 ATCTATAAAGCCGGGGCATTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATATTA
1 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGATTTATTGTATATTA
60633 TAATCACCTTTATCAGGCTAGCTGAATCTT
66 TAATCACCTTTATCAGGCTAGCTGAATCTT
* *
60663 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTTTAGAGGGACAACTCAAGTTTTATTGTATATTT
1 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGATTTATTGTATA-TT
60728 ATAA
65 ATAA
60732 AATTATAATG
Statistics
Matches: 237, Mismatches: 16, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
91 1 0.00
92 44 0.19
93 5 0.02
95 180 0.76
96 7 0.03
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (95 bp):
ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGATTTATTGTATATTA
TAATCACCTTTATCAGGCTAGCTGAATCTT
Found at i:65111 original size:3 final size:3
Alignment explanation
Indices: 65103--65156 Score: 108
Period size: 3 Copynumber: 18.0 Consensus size: 3
65093 AGAGAAAATA
65103 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
65151 AAT AAT
1 AAT AAT
65157 TCAAAGGGAA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Done.