Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008484.1 Hibiscus syriacus cultivar Beakdansim tig00111318_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: 688492
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 4
Found at i:636256 original size:20 final size:20
Alignment explanation
Indices: 636219--636288 Score: 104
Period size: 20 Copynumber: 3.5 Consensus size: 20
636209 GAAACTTAAA
636219 ATCGCAACGCGAAAAATGACT
1 ATCGCAACGCG-AAAATGACT
636240 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* **
636260 ATCACAACGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
636280 ATCGCAACG
1 ATCGCAACG
636289 GGATAATCAC
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
20 34 0.76
21 11 0.24
ACGTcount: A:0.39, C:0.26, G:0.19, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:636326 original size:19 final size:19
Alignment explanation
Indices: 636302--636355 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
636292 TAATCACAAT
*
636302 GCGAAATAAAAATTGCAAC
1 GCGAAATAAAAATCGCAAC
**
636321 GCGAAACCAAAATCGCAAC
1 GCGAAATAAAAATCGCAAC
*
636340 ACGAAACT-AAAATCGC
1 GCGAAA-TAAAAATCGC
636356 GTTGCGATTT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.50, C:0.24, G:0.15, T:0.11
Consensus pattern (19 bp):
GCGAAATAAAAATCGCAAC
Found at i:636380 original size:20 final size:20
Alignment explanation
Indices: 636352--636389 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
636342 GAAACTAAAA
*
636352 TCGCGTTGCGATTTTCATTT
1 TCGCATTGCGATTTTCATTT
636372 TCGCATTGCGATTTTCAT
1 TCGCATTGCGATTTTCAT
636390 GTTGCGATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.13, C:0.21, G:0.18, T:0.47
Consensus pattern (20 bp):
TCGCATTGCGATTTTCATTT
Found at i:636427 original size:33 final size:34
Alignment explanation
Indices: 636355--636430 Score: 109
Period size: 33 Copynumber: 2.3 Consensus size: 34
636345 ACTAAAATCG
*
636355 CGTTGCGATTTTCATTTTCGCATTGCGATTTTCA
1 CGTTGCGATTTTCATTTTCGCATTGCGATTATCA
* * *
636389 TGTTGCGATTTTTA-TTTCGCATTGCGATTATCC
1 CGTTGCGATTTTCATTTTCGCATTGCGATTATCA
636422 CGTTGCGAT
1 CGTTGCGAT
636431 AGTCAAATTC
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
33 25 0.68
34 12 0.32
ACGTcount: A:0.14, C:0.20, G:0.20, T:0.46
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTTCGCATTGCGATTATCA
Found at i:636447 original size:20 final size:20
Alignment explanation
Indices: 636422--636470 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
636412 GCGATTATCC
636422 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
**
636442 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
*
636462 CATTGCGAT
1 CGTTGCGAT
636471 TTTAAGTTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:636480 original size:20 final size:20
Alignment explanation
Indices: 636457--636500 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
636447 CGATAGTCAT
636457 TTTCGCATTGCGATTTTAAG
1 TTTCGCATTGCGATTTTAAG
**
636477 TTTCGTGTTGCGATTTTAAG
1 TTTCGCATTGCGATTTTAAG
636497 TTTC
1 TTTC
636501 AGAAACTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.16, C:0.14, G:0.20, T:0.50
Consensus pattern (20 bp):
TTTCGCATTGCGATTTTAAG
Found at i:637008 original size:21 final size:21
Alignment explanation
Indices: 636982--637058 Score: 84
Period size: 21 Copynumber: 3.7 Consensus size: 21
636972 CTCACCTATC
*
636982 ATCGTTCAAGAGGCCTCTCCT
1 ATCGTTCAAGAGGCCCCTCCT
*
637003 ATCGTTCAAGAGGCCCCT-AT
1 ATCGTTCAAGAGGCCCCTCCT
** * *
637023 CATCCCTCAAGAGTCCCCTCCC
1 -ATCGTTCAAGAGGCCCCTCCT
637045 ATCGTTCAAGAGGC
1 ATCGTTCAAGAGGC
637059 GCCTGTCATC
Statistics
Matches: 44, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
20 1 0.02
21 43 0.98
ACGTcount: A:0.22, C:0.36, G:0.18, T:0.23
Consensus pattern (21 bp):
ATCGTTCAAGAGGCCCCTCCT
Found at i:637035 original size:42 final size:42
Alignment explanation
Indices: 636976--637098 Score: 129
Period size: 42 Copynumber: 2.9 Consensus size: 42
636966 GCCCAACTCA
** * *
636976 CCTATCATCGTTCAAGAGGCCTCTCCTATCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGGCCCCTCCCATCGTTCAAGAGGCC
* *
637018 CCTATCATCCCTCAAGAGTCCCCTCCCATCGTTCAAGAGGCG
1 CCTATCATCCCTCAAGAGGCCCCTCCCATCGTTCAAGAGGCC
* ** * * * *
637060 CCTGTCATCATTGAAGAGGTCCCTCCCACCATTCAAGAG
1 CCTATCATCCCTCAAGAGGCCCCTCCCATCGTTCAAGAG
637099 CCCGATTCAC
Statistics
Matches: 67, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 67 1.00
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.24
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGGCCCCTCCCATCGTTCAAGAGGCC
Found at i:637068 original size:21 final size:20
Alignment explanation
Indices: 636980--637083 Score: 82
Period size: 21 Copynumber: 5.0 Consensus size: 20
636970 AACTCACCTA
*
636980 TCATCGTTCAAGAGGCCTCT
1 TCATCGTTCAAGAGGCCCCT
*
637000 CCTATCGTTCAAGAGGCCCCT
1 TC-ATCGTTCAAGAGGCCCCT
** *
637021 ATCATCCCTCAAGAGTCCCCT
1 -TCATCGTTCAAGAGGCCCCT
* *
637042 CCCATCGTTCAAGAGGCGCCT
1 -TCATCGTTCAAGAGGCCCCT
* * *
637063 GTCATCATTGAAGAGGTCCCT
1 -TCATCGTTCAAGAGGCCCCT
637084 CCCACCATTC
Statistics
Matches: 64, Mismatches: 18, Indels: 3
0.75 0.21 0.04
Matches are distributed among these distances:
20 1 0.02
21 62 0.97
22 1 0.02
ACGTcount: A:0.21, C:0.35, G:0.19, T:0.25
Consensus pattern (20 bp):
TCATCGTTCAAGAGGCCCCT
Found at i:638430 original size:14 final size:14
Alignment explanation
Indices: 638411--638447 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
638401 GATTGTTTAA
638411 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
638425 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
638439 TTGATTTGT
1 TTGATTTGT
638448 TTAATTGATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.30, C:0.00, G:0.22, T:0.49
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:638640 original size:20 final size:20
Alignment explanation
Indices: 638567--638640 Score: 78
Period size: 20 Copynumber: 3.7 Consensus size: 20
638557 AGGTACACTT
*
638567 TCGCAACGCTAAA-CTCAAAA
1 TCGCAACGCGAAAGC-CAAAA
* *
638587 TCGCAATGCGAAAGTCAAAA
1 TCGCAACGCGAAAGCCAAAA
**
638607 TCGCAATTCGAAAGCCAAAA
1 TCGCAACGCGAAAGCCAAAA
*
638627 TCGCAACGCAAAAG
1 TCGCAACGCGAAAG
638641 TTAATTCGCG
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.45, C:0.26, G:0.16, T:0.14
Consensus pattern (20 bp):
TCGCAACGCGAAAGCCAAAA
Found at i:638708 original size:20 final size:20
Alignment explanation
Indices: 638679--638887 Score: 162
Period size: 20 Copynumber: 11.1 Consensus size: 20
638669 CTTTGCGATT
*
638679 TTCTCATTGCGATAGTCAAA
1 TTCTCGTTGCGATAGTCAAA
638699 TTCTCGTTGCGATAGTCAAA
1 TTCTCGTTGCGATAGTCAAA
**
638719 TT-TGCGTTGC-A-A-T--TT
1 TTCT-CGTTGCGATAGTCAAA
* *
638734 TTGT-GTTGTGATAGTCAAA
1 TTCTCGTTGCGATAGTCAAA
* *
638753 TTCGCATTGCGATAGTCAAA
1 TTCTCGTTGCGATAGTCAAA
638773 TTCGT-GTTGCGAT--T----
1 TTC-TCGTTGCGATAGTCAAA
*
638787 TT-TGAGTTGCGATAGTCAAA
1 TTCT-CGTTGCGATAGTCAAA
*
638807 TTCGCGTTGCGATAGTCAAA
1 TTCTCGTTGCGATAGTCAAA
638827 TT-TGCGTTGCGATAGTCAAA
1 TTCT-CGTTGCGATAGTCAAA
*
638847 TTCACGTTGCGATAGTCAAA
1 TTCTCGTTGCGATAGTCAAA
* *
638867 TTCGCGTTGCGATATTCAAA
1 TTCTCGTTGCGATAGTCAAA
638887 T
1 T
638888 GAATATGTAA
Statistics
Matches: 151, Mismatches: 18, Indels: 40
0.72 0.09 0.19
Matches are distributed among these distances:
12 1 0.01
14 14 0.09
15 3 0.02
16 3 0.02
17 2 0.01
18 2 0.01
19 4 0.03
20 122 0.81
ACGTcount: A:0.25, C:0.16, G:0.22, T:0.37
Consensus pattern (20 bp):
TTCTCGTTGCGATAGTCAAA
Found at i:638708 original size:54 final size:53
Alignment explanation
Indices: 638643--638887 Score: 249
Period size: 54 Copynumber: 4.4 Consensus size: 53
638633 CGCAAAAGTT
* *
638643 AATTCGCGTTGCGATAGTCTAATACGCTTTGCGATTTTCTCATTGCGATAGTCA
1 AATTCGCGTTGCGATAGTCAAATTCGCTTTGCGATTTT-TCATTGCGATAGTCA
* * * * ** *
638697 AATTCTCGTTGCGATAGTCAAATTTGCGTTGCAATTTTTGTGTTGTGATAGTCA
1 AATTCGCGTTGCGATAGTCAAATTCGCTTTGCGATTTTT-CATTGCGATAGTCA
* *
638751 AATTCGCATTGCGATAGTCAAATTCG-TGTTGCGATTTTTGAGTTGCGATAGTCA
1 AATTCGCGTTGCGATAGTCAAATTCGCT-TTGCGATTTTTCA-TTGCGATAGTCA
* * *
638805 AATTCGCGTTGCGATAGTCAAATTTGCGTTGCGATAGTCAAATTCACGTTGCGATAGTCA
1 AATTCGCGTTGCGATAGTCAAATTCGCTTTGCGAT--T---TTTCA--TTGCGATAGTCA
*
638865 AATTCGCGTTGCGATATTCAAAT
1 AATTCGCGTTGCGATAGTCAAAT
638888 GAATATGTAA
Statistics
Matches: 158, Mismatches: 23, Indels: 14
0.81 0.12 0.07
Matches are distributed among these distances:
53 1 0.01
54 118 0.75
56 1 0.01
59 3 0.02
60 35 0.22
ACGTcount: A:0.24, C:0.17, G:0.22, T:0.37
Consensus pattern (53 bp):
AATTCGCGTTGCGATAGTCAAATTCGCTTTGCGATTTTTCATTGCGATAGTCA
Found at i:638770 original size:74 final size:73
Alignment explanation
Indices: 638683--638876 Score: 212
Period size: 74 Copynumber: 2.6 Consensus size: 73
638673 GCGATTTTCT
* * * *
638683 CATTGCGATAGTCAAATTCTCGTTGCGATAGTCAAATTTGCGTTGCAATTTTTGTGTTGTGATAG
1 CATTGCGATAGTCAAATTCTCGTTGCGATAGTCAAATTTGCGTTGCAA-ATTCGCGTTGCGATAG
638748 TCAAATTCG
65 TCAAATTCG
* *** * *
638757 CATTGCGATAGTCAAATTCGT-GTTGCGAT-TTTTGAGTTGCGATAGTCAAATTCGCGTTGCGAT
1 CATTGCGATAGTCAAATTC-TCGTTGCGATAGTCAAATTTGCG-TTG-CAAATTCGCGTTGCGAT
*
638820 AGTCAAATTTG
63 AGTCAAATTCG
* * *
638831 CGTTGCGATAGTCAAATTCACGTTGCGATAGTCAAATTCGCGTTGC
1 CATTGCGATAGTCAAATTCTCGTTGCGATAGTCAAATTTGCGTTGC
638877 GATATTCAAA
Statistics
Matches: 95, Mismatches: 20, Indels: 11
0.75 0.16 0.09
Matches are distributed among these distances:
73 8 0.08
74 77 0.81
75 10 0.11
ACGTcount: A:0.24, C:0.16, G:0.23, T:0.36
Consensus pattern (73 bp):
CATTGCGATAGTCAAATTCTCGTTGCGATAGTCAAATTTGCGTTGCAAATTCGCGTTGCGATAGT
CAAATTCG
Found at i:638780 original size:40 final size:40
Alignment explanation
Indices: 638683--638887 Score: 186
Period size: 40 Copynumber: 5.4 Consensus size: 40
638673 GCGATTTTCT
638683 CATTGCGATAGTCAAATTC-TCGTTGCGATAGTCAAATTTG
1 CATTGCGATAGTCAAATTCGT-GTTGCGATAGTCAAATTTG
* * * * *
638723 CGTTGC-A-A-T---TTTTGTGTTGTGATAGTCAAATTCG
1 CATTGCGATAGTCAAATTCGTGTTGCGATAGTCAAATTTG
638757 CATTGCGATAGTCAAATTCGTGTTGCGAT--T----TTTG
1 CATTGCGATAGTCAAATTCGTGTTGCGATAGTCAAATTTG
*
638791 -AGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTTG
1 CA-TTGCGATAGTCAAATTCGTGTTGCGATAGTCAAATTTG
* ** *
638831 CGTTGCGATAGTCAAATTCACGTTGCGATAGTCAAATTCG
1 CATTGCGATAGTCAAATTCGTGTTGCGATAGTCAAATTTG
* *
638871 CGTTGCGATATTCAAAT
1 CATTGCGATAGTCAAAT
638888 GAATATGTAA
Statistics
Matches: 135, Mismatches: 15, Indels: 30
0.75 0.08 0.17
Matches are distributed among these distances:
33 1 0.01
34 53 0.39
35 2 0.01
36 2 0.01
37 2 0.01
38 2 0.01
39 1 0.01
40 72 0.53
ACGTcount: A:0.25, C:0.16, G:0.22, T:0.36
Consensus pattern (40 bp):
CATTGCGATAGTCAAATTCGTGTTGCGATAGTCAAATTTG
Found at i:639110 original size:140 final size:140
Alignment explanation
Indices: 638858--639140 Score: 539
Period size: 140 Copynumber: 2.0 Consensus size: 140
638848 TCACGTTGCG
638858 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATATGTAATAAGTGATAACAACTGAACAGATCA
1 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATATGTAATAAGTGATAACAACTGAACAGATCA
*
638923 TAGTAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
638988 AATACACATA
131 AATACACATA
* *
638998 ATAGTCAAATTTGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
1 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATATGTAATAAGTGATAACAACTGAACAGATCA
639063 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
639128 AATACACATA
131 AATACACATA
639138 ATA
1 ATA
639141 CAACGTTTGC
Statistics
Matches: 140, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
140 140 1.00
ACGTcount: A:0.43, C:0.15, G:0.13, T:0.29
Consensus pattern (140 bp):
ATAGTCAAATTCGCGTTGCGATATTCAAATGAATATGTAATAAGTGATAACAACTGAACAGATCA
TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
AATACACATA
Found at i:639221 original size:18 final size:18
Alignment explanation
Indices: 639198--639232 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
639188 AAGCCGGTTG
*
639198 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
639216 TGATTGCGATTTTGATT
1 TGATTGCGATTTTGATT
639233 GCCTTTTTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.03, G:0.26, T:0.54
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:640750 original size:20 final size:20
Alignment explanation
Indices: 640725--640835 Score: 143
Period size: 20 Copynumber: 5.5 Consensus size: 20
640715 TTGAAATTTA
*
640725 GCGTTGCGACAGTCAGAATC
1 GCGTTGCGATAGTCAGAATC
* *
640745 GCGTTGCGTTAGTTAGAATC
1 GCGTTGCGATAGTCAGAATC
640765 GCGTTGCGATAGTCAGAATC
1 GCGTTGCGATAGTCAGAATC
* **
640785 GAGTTGCGATTATGT-ATTATC
1 GCGTTGCGA-TA-GTCAGAATC
640806 GCGTTGCGATAGTCAGAATC
1 GCGTTGCGATAGTCAGAATC
640826 GCGTTGCGAT
1 GCGTTGCGAT
640836 TTACATATTC
Statistics
Matches: 77, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.03
20 59 0.77
21 14 0.18
22 2 0.03
ACGTcount: A:0.23, C:0.18, G:0.30, T:0.30
Consensus pattern (20 bp):
GCGTTGCGATAGTCAGAATC
Found at i:640819 original size:41 final size:41
Alignment explanation
Indices: 640725--640836 Score: 165
Period size: 41 Copynumber: 2.8 Consensus size: 41
640715 TTGAAATTTA
*
640725 GCGTTGCGACAGTCAGAATCGCGTTGCG-TTAGTTAGAATC
1 GCGTTGCGATAGTCAGAATCGCGTTGCGATTAGTTAGAATC
* **
640765 GCGTTGCGATAGTCAGAATCGAGTTGCGATTA-TGTATTATC
1 GCGTTGCGATAGTCAGAATCGCGTTGCGATTAGT-TAGAATC
640806 GCGTTGCGATAGTCAGAATCGCGTTGCGATT
1 GCGTTGCGATAGTCAGAATCGCGTTGCGATT
640837 TACATATTCG
Statistics
Matches: 65, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
40 27 0.42
41 38 0.58
ACGTcount: A:0.22, C:0.18, G:0.29, T:0.30
Consensus pattern (41 bp):
GCGTTGCGATAGTCAGAATCGCGTTGCGATTAGTTAGAATC
Found at i:640966 original size:19 final size:19
Alignment explanation
Indices: 640942--640978 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
640932 TGCGATACTG
* *
640942 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTACGATTTA
640961 GAGATCGCATTACGATTT
1 GAGATCGCATTACGATTT
640979 TATTGGTCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTACGATTTA
Found at i:641147 original size:6 final size:6
Alignment explanation
Indices: 641136--641162 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
641126 CTAGGTCGTG
641136 TTGCCA TTGCCA TTGCCA TTGCCA TTG
1 TTGCCA TTGCCA TTGCCA TTGCCA TTG
641163 TCAAATTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.30, G:0.19, T:0.37
Consensus pattern (6 bp):
TTGCCA
Found at i:641211 original size:6 final size:6
Alignment explanation
Indices: 641200--641251 Score: 104
Period size: 6 Copynumber: 8.7 Consensus size: 6
641190 AAAACCCCCC
641200 AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA
641248 AAAT
1 AAAT
641252 GGAAAAAAAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 46 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
AAATAA
Found at i:650683 original size:21 final size:21
Alignment explanation
Indices: 650646--650724 Score: 131
Period size: 21 Copynumber: 3.7 Consensus size: 21
650636 TTGCCCGTAA
*
650646 GGTACCGAATCCCCCCCAAGAG
1 GGTACCG-ATTCCCCCCAAGAG
650668 GGTACCGATTCCCCCCAAGAG
1 GGTACCGATTCCCCCCAAGAG
650689 GGTACCGATTCCCCCCAAGAG
1 GGTACCGATTCCCCCCAAGAG
*
650710 GGTACTGATTCCCCC
1 GGTACCGATTCCCCC
650725 TTGTTCAACG
Statistics
Matches: 55, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
21 48 0.87
22 7 0.13
ACGTcount: A:0.23, C:0.39, G:0.23, T:0.15
Consensus pattern (21 bp):
GGTACCGATTCCCCCCAAGAG
Found at i:652644 original size:21 final size:21
Alignment explanation
Indices: 652620--652659 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
652610 AAGACTTTAT
652620 TTTCAAAA-TACAAAAATGATA
1 TTTCAAAATTA-AAAAATGATA
652641 TTTCAAAATTAAAAAATGA
1 TTTCAAAATTAAAAAATGA
652660 AAATAGTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.57, C:0.07, G:0.05, T:0.30
Consensus pattern (21 bp):
TTTCAAAATTAAAAAATGATA
Found at i:659034 original size:21 final size:22
Alignment explanation
Indices: 659009--659052 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
658999 GGGCAAATTG
*
659009 CCCAA-AGGGAATCGATTCCCC
1 CCCAAGAGGGAACCGATTCCCC
* *
659030 CCCAAGGGGGCACCGATTCCCC
1 CCCAAGAGGGAACCGATTCCCC
659052 C
1 C
659053 TTAATGGTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.23, C:0.43, G:0.23, T:0.11
Consensus pattern (22 bp):
CCCAAGAGGGAACCGATTCCCC
Found at i:669208 original size:2 final size:2
Alignment explanation
Indices: 669201--669232 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
669191 TGGCAGGTTG
669201 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
669233 GCGTAAATGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:675120 original size:3 final size:3
Alignment explanation
Indices: 675112--675164 Score: 72
Period size: 3 Copynumber: 18.0 Consensus size: 3
675102 AATTATTTTT
* * *
675112 TAA TAA TAA TAA TTA T-A TAA TAA TAA TTA TTA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
675159 TAA TAA
1 TAA TAA
675165 AATGAGTAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
2 2 0.04
3 44 0.96
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:675648 original size:113 final size:114
Alignment explanation
Indices: 675506--676173 Score: 880
Period size: 113 Copynumber: 6.0 Consensus size: 114
675496 ATAGGGTTAT
* ** *
675506 GCAAAAGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * * ** * * *
675571 ATTATGAACTCTCTTCT-GAAAAGTTGATATATCGAGTGATGAATTCGA
66 ATTATGAACTTTCTTCTGGAAAAGCTAATCCATCAAGTGATGGATTTGA
* * *
675619 GCGAAAA-ATTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
1 GC-AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
* * * * *
675683 TATTATGAA-TTTTTTCTGGAGAAGCTGATCCATCAAATGATGGATTTGA
65 CATTATGAACTTTCTTCTGGAAAAGCTAATCCATCAAGTGATGGATTTGA
* * * *
675732 GCAAAAGATTGAACAAATTCTTCTCATTATGAATTTCTTCTTCTTTATTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
*
675797 ATTATGAACTTTC-TCTGGCAAAGCTAATCCATCAAGTGATGGATTTGA
66 ATTATGAACTTTCTTCTGGAAAAGCTAATCCATCAAGTGATGGATTTGA
675845 GCAAAAGGTTGAACAAATTCTTCTCATTATGAA--T-TTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* *
675907 ATTATGAAC-TT-TTCTGGCAAAGATAATCCATCAAGTGATGGATTTGA
66 ATTATGAACTTTCTTCTGGAAAAGCTAATCCATCAAGTGATGGATTTGA
*
675954 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * * **
676019 ATTATGAACTTT-TTCTGGCAAAGCTAATCCATCAAATGATGAATTCAA
66 ATTATGAACTTTCTTCTGGAAAAGCTAATCCATCAAGTGATGGATTTGA
* * * *
676067 ACAAAAGGTTAAACAAAGTCTTCTCA-T-TGAACTTCTTCTTCCTTCTTCATAT--GTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
*
676128 ATTATGAACTTTC-TCTGGAAAAGCTGATCCATCAAGTGATGGATTT
66 ATTATGAACTTTCTTCTGGAAAAGCTAATCCATCAAGTGATGGATTT
676174 AAATCTTTGC
Statistics
Matches: 499, Mismatches: 46, Indels: 24
0.88 0.08 0.04
Matches are distributed among these distances:
109 118 0.24
110 35 0.07
111 25 0.05
112 48 0.10
113 266 0.53
114 7 0.01
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.38
Consensus pattern (114 bp):
GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
ATTATGAACTTTCTTCTGGAAAAGCTAATCCATCAAGTGATGGATTTGA
Found at i:675995 original size:222 final size:223
Alignment explanation
Indices: 675506--676173 Score: 920
Period size: 222 Copynumber: 3.0 Consensus size: 223
675496 ATAGGGTTAT
* ** *
675506 GCAAAAGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCTTTCTTCAGATGAGTTCTTCTC
* * * * ** * *
675571 ATTATGAACTCTCTTCT-GAAAAGTTGATATATCGAGTGATGAATTCGAGCGAAAA-ATTGAACA
66 ATTATGAACTTTC-TCTGGCAAAGCTAATCCATCAAGTGATGAATTCGAGC-AAAAGGTTGAACA
* * * *
675634 AGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAATTTTTTC
129 AATTCTTCTCATTATGAAC-TCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA-CTTTTC
*
675699 TGGAGAAGCTGATCCATCAAATGATGGATTTGA
192 TGGA-AAGCTGATCCATCAAGTGATGGATTTGA
* *
675732 GCAAAAGATTGAACAAATTCTTCTCATTATGAATTTCTTCTTCTTTATTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCTTTCTTCAGATGAGTTCTTCTC
* *
675797 ATTATGAACTTTCTCTGGCAAAGCTAATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAA
66 ATTATGAACTTTCTCTGGCAAAGCTAATCCATCAAGTGATGAATTCGAGCAAAAGGTTGAACAAA
675862 TTCTTCTCATTATGAA-T-TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTCTGGC
131 TTCTTCTCATTATGAACTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTCTGG-
* *
675925 AAAGATAATCCATCAAGTGATGGATTTGA
195 AAAGCTGATCCATCAAGTGATGGATTTGA
*
675954 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCTTTCTTCAGATGAGTTCTTCTC
* * * * *
676019 ATTATGAACTTTTTCTGGCAAAGCTAATCCATCAAATGATGAATTCAAACAAAAGGTTAAACAAA
66 ATTATGAACTTTCTCTGGCAAAGCTAATCCATCAAGTGATGAATTCGAGCAAAAGGTTGAACAAA
* *
676084 GTCTTCTCA-T-TGAACTTCTTCTTCCTTCTTCATAT--GTTCTTCTCATTATGAACTTTCTCTG
131 TTCTTCTCATTATGAAC-TCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTT-TCTG
676145 GAAAAGCTGATCCATCAAGTGATGGATTT
194 G-AAAGCTGATCCATCAAGTGATGGATTT
676174 AAATCTTTGC
Statistics
Matches: 397, Mismatches: 38, Indels: 18
0.88 0.08 0.04
Matches are distributed among these distances:
220 4 0.01
221 22 0.06
222 192 0.48
223 52 0.13
224 1 0.00
225 7 0.02
226 119 0.30
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.38
Consensus pattern (223 bp):
GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCTTTCTTCAGATGAGTTCTTCTC
ATTATGAACTTTCTCTGGCAAAGCTAATCCATCAAGTGATGAATTCGAGCAAAAGGTTGAACAAA
TTCTTCTCATTATGAACTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTCTGGA
AAGCTGATCCATCAAGTGATGGATTTGA
Found at i:677146 original size:114 final size:113
Alignment explanation
Indices: 676857--677165 Score: 536
Period size: 113 Copynumber: 2.8 Consensus size: 113
676847 GATCATGCAG
* * *
676857 TTCATCTTTTAATTCCAATGATTGGTTC--TG-TTCCTACCAAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTCTGTGTTTCATACCAAACCAGATCAGATAACTCAAAGA
676919 ACACTTCCAGAAGATGCTATTGAGTCTCTTATTTCTACTATGACCAAA
66 ACACTTCCAGAAGATGCTATTGAGTCTCTTATTTCTACTATGACCAAA
676967 TTCATCTTTCAAATCCAATGATTGGTTCTGTGTTTCATACCAAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTCTGTGTTTCATACCAAACCAGATCAGATAACTCAAAGA
*
677032 ACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAGC-AA
66 ACACTTCCAGAAGATGCTATTGAGTCT-CTTATTTCTACTATGACCAAA
677080 TTCATCTTTCAAATCCAATGATTGGTTCTGTGGTTTCATACCAAACCAGATCAGATAACTCAAAG
1 TTCATCTTTCAAATCCAATGATTGGTTCTGT-GTTTCATACCAAACCAGATCAGATAACTCAAAG
677145 AACACTTCCAGAAGATGCTAT
65 AACACTTCCAGAAGATGCTAT
677166 GAGCACATTC
Statistics
Matches: 190, Mismatches: 4, Indels: 6
0.95 0.02 0.03
Matches are distributed among these distances:
110 26 0.14
112 2 0.01
113 91 0.48
114 71 0.37
ACGTcount: A:0.32, C:0.22, G:0.13, T:0.32
Consensus pattern (113 bp):
TTCATCTTTCAAATCCAATGATTGGTTCTGTGTTTCATACCAAACCAGATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGAGTCTCTTATTTCTACTATGACCAAA
Found at i:678328 original size:7 final size:7
Alignment explanation
Indices: 678308--678365 Score: 64
Period size: 8 Copynumber: 7.9 Consensus size: 7
678298 GACCCCCCTT
678308 TTTTCTTC
1 TTTT-TTC
678316 TTTTTTC
1 TTTTTTC
*
678323 TCTTTTTT
1 T-TTTTTC
678331 TCTTTTTC
1 T-TTTTTC
678339 -TTTTTC
1 TTTTTTC
678345 TTTTTTTC
1 -TTTTTTC
678353 TTTTTTC
1 TTTTTTC
678360 TTTTTT
1 TTTTTT
678366 TTCTCTTCAA
Statistics
Matches: 45, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
6 6 0.13
7 17 0.38
8 22 0.49
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (7 bp):
TTTTTTC
Found at i:678329 original size:20 final size:19
Alignment explanation
Indices: 678306--678369 Score: 80
Period size: 18 Copynumber: 3.4 Consensus size: 19
678296 TTGACCCCCC
678306 TTTTTTCTTCTTTTTTCTCT
1 TTTTTTCTTCTTTTTTCT-T
678326 TTTTTTCTT-TTTCTTT-TT
1 TTTTTTCTTCTTT-TTTCTT
*
678344 CTTTTT-TTCTTTTTTCTT
1 TTTTTTCTTCTTTTTTCTT
678362 TTTTTTCT
1 TTTTTTCT
678370 CTTCAAGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
17 5 0.13
18 16 0.42
19 5 0.13
20 12 0.32
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (19 bp):
TTTTTTCTTCTTTTTTCTT
Found at i:678342 original size:21 final size:20
Alignment explanation
Indices: 678306--678364 Score: 84
Period size: 20 Copynumber: 2.9 Consensus size: 20
678296 TTGACCCCCC
*
678306 TTTTTTCTTCTTT-TTTCTCT
1 TTTTTTCTT-TTTCTTTTTCT
678326 TTTTTTCTTTTTCTTTTTCT
1 TTTTTTCTTTTTCTTTTTCT
678346 TTTTTTCTTTTTTCTTTTT
1 TTTTTTC-TTTTTCTTTTT
678365 TTTCTCTTCA
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
19 3 0.08
20 22 0.61
21 11 0.31
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (20 bp):
TTTTTTCTTTTTCTTTTTCT
Done.