Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004154.1 Hibiscus syriacus cultivar Beakdansim tig00009084_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: 73713
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Found at i:2156 original size:3 final size:3
Alignment explanation
Indices: 2148--2207 Score: 84
Period size: 3 Copynumber: 19.7 Consensus size: 3
2138 TAAAATTTAA
* * *
2148 TAT TAT TAT TAT TAT TAA AAT TAT TAT TAT TAT TAA TAT ATAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT
2194 TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TA
2208 AAATAAATAA
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
3 47 0.94
4 3 0.06
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:3541 original size:23 final size:23
Alignment explanation
Indices: 3485--3549 Score: 78
Period size: 23 Copynumber: 2.8 Consensus size: 23
3475 ATTTGCAATT
*
3485 TTATTTTATTATTACTTTTGATA
1 TTATTTTATTATTACTTTCGATA
* *
3508 -TATTTAAATTATTACTTTCGTTA
1 TTATTT-TATTATTACTTTCGATA
*
3531 TTATTTTATTATTATTTTC
1 TTATTTTATTATTACTTTC
3550 ATCTTAGTCA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
22 5 0.14
23 25 0.71
24 5 0.14
ACGTcount: A:0.26, C:0.06, G:0.03, T:0.65
Consensus pattern (23 bp):
TTATTTTATTATTACTTTCGATA
Found at i:3544 original size:11 final size:11
Alignment explanation
Indices: 3485--3548 Score: 51
Period size: 11 Copynumber: 5.6 Consensus size: 11
3475 ATTTGCAATT
3485 TTATTTTATTA
1 TTATTTTATTA
3496 TTACTTTTGA-TA
1 TTA-TTTT-ATTA
*
3508 -TATTTAAATTA
1 TTATTT-TATTA
**
3519 TTACTTTCGTTA
1 TTA-TTTTATTA
3531 TTATTTTATTA
1 TTATTTTATTA
3542 TTATTTT
1 TTATTTT
3549 CATCTTAGTC
Statistics
Matches: 42, Mismatches: 5, Indels: 12
0.71 0.08 0.20
Matches are distributed among these distances:
10 4 0.10
11 20 0.48
12 14 0.33
13 4 0.10
ACGTcount: A:0.27, C:0.05, G:0.03, T:0.66
Consensus pattern (11 bp):
TTATTTTATTA
Found at i:3566 original size:2 final size:2
Alignment explanation
Indices: 3559--3602 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
3549 CATCTTAGTC
3559 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
3601 AT
1 AT
3603 GTTTAATAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5186 original size:16 final size:15
Alignment explanation
Indices: 5134--5186 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 15
5124 GGTACTAACC
5134 ATTTTATTTTTTTCTTA
1 ATTTTA-TTTTTTC-TA
* *
5151 TTTTTATTTTTTATA
1 ATTTTATTTTTTCTA
5166 CATTTTATTTTGTTCTA
1 -ATTTTATTTT-TTCTA
5183 ATTT
1 ATTT
5187 GTTTATATTG
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
15 2 0.07
16 19 0.63
17 9 0.30
ACGTcount: A:0.19, C:0.06, G:0.02, T:0.74
Consensus pattern (15 bp):
ATTTTATTTTTTCTA
Found at i:6894 original size:12 final size:12
Alignment explanation
Indices: 6877--6904 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
6867 ACATCTTTGA
6877 ATTTATATTTTC
1 ATTTATATTTTC
6889 ATTTATATTTTC
1 ATTTATATTTTC
6901 ATTT
1 ATTT
6905 TATGTTTGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.25, C:0.07, G:0.00, T:0.68
Consensus pattern (12 bp):
ATTTATATTTTC
Found at i:7936 original size:19 final size:18
Alignment explanation
Indices: 7912--7948 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
7902 AAAGGAATTC
*
7912 GAGAATTTATTGATAAATG
1 GAGAATTAATTGA-AAATG
7931 GAGAATTAATTGAAAATG
1 GAGAATTAATTGAAAATG
7949 TGATCAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.46, C:0.00, G:0.22, T:0.32
Consensus pattern (18 bp):
GAGAATTAATTGAAAATG
Found at i:12219 original size:75 final size:75
Alignment explanation
Indices: 12109--12251 Score: 202
Period size: 75 Copynumber: 1.9 Consensus size: 75
12099 ATTTTTGGGA
**
12109 CATACTGAAAGCCTATTTCAATCAGAAATTGGAATATTAACGT-ATTTTGAACGTTTGTATCAGC
1 CATACTGAAAGCCTATTTCAATCAGAAATAAGAATATTAAC-TCATTTTGAACGTTTGTATCAGC
12173 AAATACTGGAG
65 AAATACTGGAG
* *
12184 CATACTGAAAG-CTCATTTCAATCAG-AATCAAGAATATTGACTCGTTTTGAACGTTTGTATCAG
1 CATACTGAAAGCCT-ATTTCAATCAGAAAT-AAGAATATTAACTCATTTTGAACGTTTGTATCAG
12247 CAAAT
64 CAAAT
12252 GTTAGGGCAT
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
74 6 0.10
75 55 0.90
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (75 bp):
CATACTGAAAGCCTATTTCAATCAGAAATAAGAATATTAACTCATTTTGAACGTTTGTATCAGCA
AATACTGGAG
Found at i:14706 original size:26 final size:26
Alignment explanation
Indices: 14677--14752 Score: 69
Period size: 20 Copynumber: 3.2 Consensus size: 26
14667 GGTCATCTGT
14677 AAGCCCTTCAGTGCATGATGTTTTCA
1 AAGCCCTTCAGTGCATGATGTTTTCA
* *
14703 AAG-CCTTC-GGGTCAT-CTG---T--
1 AAGCCCTTCAGTG-CATGATGTTTTCA
14722 AAGCCCTTCAGTGCATGATGTTTTCA
1 AAGCCCTTCAGTGCATGATGTTTTCA
14748 AAGCC
1 AAGCC
14753 TTTGGGTCAT
Statistics
Matches: 37, Mismatches: 4, Indels: 18
0.63 0.07 0.31
Matches are distributed among these distances:
19 3 0.08
20 8 0.22
21 5 0.14
24 5 0.14
25 8 0.22
26 8 0.22
ACGTcount: A:0.22, C:0.25, G:0.21, T:0.32
Consensus pattern (26 bp):
AAGCCCTTCAGTGCATGATGTTTTCA
Found at i:14953 original size:45 final size:45
Alignment explanation
Indices: 14177--14930 Score: 1206
Period size: 45 Copynumber: 16.8 Consensus size: 45
14167 CTATTTCCCA
** * *
14177 CATCTGTAAAACCTACAGTGCATGATGTTTTTAAAGCCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAGCCTTCGGGT
** *
14222 CATCTGTAAAACCTTCAGTGCATGATGTTTTCAAAGCCTTTGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAGCCTTCGGGT
*
14267 CATCTGTAAGCCCTTTAGTGCATGATGTTTTCAAAGCCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAGCCTTCGGGT
** *
14312 CATCTGTAAAACCTTCAGTGCATGATGTTTTCAAAGCCTTTGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAGCCTTCGGGT
* *
14357 CATCTGTAAGCCCTTCAGTGTATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAGCCTTCGGGT
* * *
14402 CATCTGTAAACCTTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAGCCTTCGGGT
* *
14447 CATCTGTAAGCCTTTTAGTGCATGATGTTTTCAAAGCCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAGCCTTCGGGT
* *
14492 CATCTGTAAGACCTTCAGTGCATGATGCTTTCAAAGCCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAGCCTTCGGGT
14537 CATCTGT-AGCCCTTCAGTGCATGATGTTTTCAAAGCCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAGCCTTCGGGT
*
14581 CATCTGT-AGCCCTTCAGTGCATAATGTTTTCAAAGCCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAGCCTTCGGGT
* *
14625 CATCTGTAAGCCCTTCACTACATGATGTTTTCAAAGCCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAGCCTTCGGGT
14670 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAGCCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAGCCTTCGGGT
*
14715 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAGCCTTTGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAGCCTTCGGGT
* *
14760 CATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAGCCTTCGGGT
*
14805 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAGCCTTCGGGT
* *
14850 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGAGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAGCCTTCGGGT
* * *
14895 AATCTGTAAGACCTACAGTGCATGATGTTTTCAAAG
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAG
14931 ACCTCCAGGC
Statistics
Matches: 664, Mismatches: 44, Indels: 2
0.94 0.06 0.00
Matches are distributed among these distances:
44 85 0.13
45 579 0.87
ACGTcount: A:0.23, C:0.23, G:0.20, T:0.34
Consensus pattern (45 bp):
CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAGCCTTCGGGT
Found at i:15113 original size:3 final size:3
Alignment explanation
Indices: 15105--15179 Score: 105
Period size: 3 Copynumber: 24.3 Consensus size: 3
15095 ATTTTTAAAA
**
15105 ATT ATT ATT ATT ATT ATT ATT ATT ATT AATT ATT AAA ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT ATT ATT
*
15151 ATT ATT AAT ATT ATAT ATT ATT ATT ATT A
1 ATT ATT ATT ATT AT-T ATT ATT ATT ATT A
15180 AAATAAATAA
Statistics
Matches: 64, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
3 58 0.91
4 6 0.09
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:15136 original size:25 final size:25
Alignment explanation
Indices: 15108--15179 Score: 110
Period size: 25 Copynumber: 2.9 Consensus size: 25
15098 TTTAAAAATT
15108 ATTATTATTATTATTATTATTATTA
1 ATTATTATTATTATTATTATTATTA
**
15133 ATTATTAAAATTATTATTATTATTA
1 ATTATTATTATTATTATTATTATTA
15158 A-TATTATATATTATTATTATTA
1 ATTATTAT-TATTATTATTATTA
15180 AAATAAATAA
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
24 5 0.12
25 37 0.88
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (25 bp):
ATTATTATTATTATTATTATTATTA
Found at i:15192 original size:22 final size:22
Alignment explanation
Indices: 15120--15192 Score: 67
Period size: 22 Copynumber: 3.2 Consensus size: 22
15110 TATTATTATT
* *
15120 ATTATTATTATTAATTATTAA-A
1 ATTATTATTATTAA-AATAAATA
* *
15142 ATTATTATTATTATTAATATTATA
1 ATTATTATTATTA-AAATA-AATA
15166 TATTATTATTATTAAAATAAATA
1 -ATTATTATTATTAAAATAAATA
15189 ATTA
1 ATTA
15193 CAAGCCCAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
22 19 0.46
23 4 0.10
24 5 0.12
25 13 0.32
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
ATTATTATTATTAAAATAAATA
Found at i:16527 original size:23 final size:23
Alignment explanation
Indices: 16468--16541 Score: 80
Period size: 23 Copynumber: 3.3 Consensus size: 23
16458 TTTATTTGCA
* *
16468 ATATTATTTTATTATTGCTTTTG
1 ATATTATTTTATTATTACTTTCG
*
16491 ATA-TATTTAAATTATTACTTTCG
1 ATATTATTT-TATTATTACTTTCG
* *
16514 TTATTATTTTATTATTATTTTC-
1 ATATTATTTTATTATTACTTTCG
16536 ATATTA
1 ATATTA
16542 GTCATATATA
Statistics
Matches: 42, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
22 10 0.24
23 27 0.64
24 5 0.12
ACGTcount: A:0.28, C:0.05, G:0.04, T:0.62
Consensus pattern (23 bp):
ATATTATTTTATTATTACTTTCG
Found at i:20858 original size:16 final size:16
Alignment explanation
Indices: 20847--20883 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
20837 TGACCTGATA
20847 TGATATTTACCTGACT
1 TGATATTTACCTGACT
20863 TGATATTTACCTGACT
1 TGATATTTACCTGACT
20879 T-ATAT
1 TGATAT
20884 ATTATCATTG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 4 0.19
16 17 0.81
ACGTcount: A:0.27, C:0.16, G:0.11, T:0.46
Consensus pattern (16 bp):
TGATATTTACCTGACT
Found at i:21044 original size:13 final size:13
Alignment explanation
Indices: 21028--21054 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
21018 GACCTATTAT
21028 ATAAAATTATTTA
1 ATAAAATTATTTA
21041 ATAAAATTATTTA
1 ATAAAATTATTTA
21054 A
1 A
21055 ATGTAAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
ATAAAATTATTTA
Found at i:21064 original size:15 final size:14
Alignment explanation
Indices: 21028--21070 Score: 52
Period size: 13 Copynumber: 3.1 Consensus size: 14
21018 GACCTATTAT
21028 ATAAAATTATTT-A
1 ATAAAATTATTTAA
21041 ATAAAATTATTTAA
1 ATAAAATTATTTAA
* *
21055 ATGTAAATTATATAA
1 AT-AAAATTATTTAA
21070 A
1 A
21071 ACATGATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
13 12 0.46
14 3 0.12
15 11 0.42
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (14 bp):
ATAAAATTATTTAA
Found at i:21120 original size:23 final size:23
Alignment explanation
Indices: 21094--21142 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
21084 TGTAAAGAAA
21094 AAATAATATAGTTTAATTTATAT
1 AAATAATATAGTTTAATTTATAT
* * *
21117 AAATTATGTAGTTTAATTTATGT
1 AAATAATATAGTTTAATTTATAT
21140 AAA
1 AAA
21143 GAAAAAATAA
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:0.45, C:0.00, G:0.08, T:0.47
Consensus pattern (23 bp):
AAATAATATAGTTTAATTTATAT
Found at i:22894 original size:76 final size:76
Alignment explanation
Indices: 22744--22930 Score: 275
Period size: 76 Copynumber: 2.5 Consensus size: 76
22734 CAAAGCCAAA
* * * * **
22744 AATTACAGATTGCTCAGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTGAATGGT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
22809 TTGGCTCCGAG
66 TTGGCTCCGAG
* *
22820 ATTTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACATT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
* *
22885 TTTGTTCCGAG
66 TTGGCTCCGAG
*
22896 AATTCCAGTATGCTCGGAGGGAACCGATTCCCCCC
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCC
22931 CCCCAGGGGT
Statistics
Matches: 99, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
76 99 1.00
ACGTcount: A:0.25, C:0.30, G:0.23, T:0.22
Consensus pattern (76 bp):
AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
TTGGCTCCGAG
Found at i:28774 original size:21 final size:21
Alignment explanation
Indices: 28748--28787 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
28738 CCCCCTTTGA
*
28748 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
28769 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
28788 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:31575 original size:76 final size:77
Alignment explanation
Indices: 31376--31582 Score: 251
Period size: 76 Copynumber: 2.7 Consensus size: 77
31366 CAAAGCCAAA
* * * **
31376 AATTACAGATTGCTC-AGAGGGAACCGATTCCCCCCATAGGAGGAACCGATT-CCCCCCTGAATG
1 AATTCCAGAATGCTCGA-AGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCCTAAACA
31439 GTTTGGCTCCGAG
65 GTTTGGCTCCGAG
* * *
31452 ATTTCCAGAATGCTCGGAGGGAACCGATT-CCCCCATAGGAGGAACCGATTCCCCCCCTAAACAT
1 AATTCCAGAATGCTCGAAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCCTAAACAG
* *
31516 TTTTGTTCCGAG
66 TTTGGCTCCGAG
* ** *
31528 AATTCCAGTATGCTCGAAGGGAACCGATTCCCCCCCCAGG-GGTACCGATTCCCCC
1 AATTCCAGAATGCTCGAAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCC
31583 ATGTTCAACG
Statistics
Matches: 112, Mismatches: 16, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
75 21 0.19
76 83 0.74
77 8 0.07
ACGTcount: A:0.24, C:0.32, G:0.23, T:0.21
Consensus pattern (77 bp):
AATTCCAGAATGCTCGAAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCCTAAACAG
TTTGGCTCCGAG
Found at i:32296 original size:22 final size:21
Alignment explanation
Indices: 32271--32312 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
32261 TCGTCATTCG
*
32271 ATTAACTCAACAACAAGAAATT
1 ATTAAATCAA-AACAAGAAATT
*
32293 ATTAAATGAAAACAAGAAAT
1 ATTAAATCAAAACAAGAAAT
32313 AAATAAGTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.60, C:0.12, G:0.07, T:0.21
Consensus pattern (21 bp):
ATTAAATCAAAACAAGAAATT
Found at i:34373 original size:19 final size:18
Alignment explanation
Indices: 34351--34387 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
34341 GTTTGAATCT
*
34351 AGGTTCAGGTTTTGGGTTC
1 AGGTTCA-GATTTGGGTTC
34370 AGGTTCAGATTTGGGTTC
1 AGGTTCAGATTTGGGTTC
34388 GAGTTTGTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.14, C:0.11, G:0.35, T:0.41
Consensus pattern (18 bp):
AGGTTCAGATTTGGGTTC
Found at i:34406 original size:43 final size:43
Alignment explanation
Indices: 34352--34490 Score: 127
Period size: 43 Copynumber: 3.3 Consensus size: 43
34342 TTTGAATCTA
* *
34352 GGTTCAGGTTTTGGGTTCAGGTTCAGATTTGGGTTCGAGTTTG
1 GGTTCGGGTTTTGGGTTCAGGTTCAGATTCGGGTTCGAGTTTG
* ** * * *
34395 TGTTCGGGTTTTGGGTTTGGGTTCGGGTTCGGGTTCGGGTTTG
1 GGTTCGGGTTTTGGGTTCAGGTTCAGATTCGGGTTCGAGTTTG
* ** * * * *
34438 GGTTCGGG-TTCGGGTTTGGGTTCGGGTTCGGGTTTGGGTTTG
1 GGTTCGGGTTTTGGGTTCAGGTTCAGATTCGGGTTCGAGTTTG
*
34480 GGTTTGGGTTT
1 GGTTCGGGTTT
34491 AGGTTCTAGT
Statistics
Matches: 83, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
42 39 0.47
43 44 0.53
ACGTcount: A:0.04, C:0.09, G:0.45, T:0.43
Consensus pattern (43 bp):
GGTTCGGGTTTTGGGTTCAGGTTCAGATTCGGGTTCGAGTTTG
Found at i:34415 original size:6 final size:6
Alignment explanation
Indices: 34379--34495 Score: 117
Period size: 6 Copynumber: 19.3 Consensus size: 6
34369 CAGGTTCAGA
* * * * * *
34379 TTTGGG TTCGAG TTTGTG TTCGGG TTTTGGG TTTGGG TTCGGG TTCGGG
1 TTTGGG TTTGGG TTTGGG TTTGGG -TTTGGG TTTGGG TTTGGG TTTGGG
* * * * *
34428 TTCGGG TTTGGG TTCGGG TTCGGG TTTGGG TTCGGG TTCGGG TTTGGG
1 TTTGGG TTTGGG TTTGGG TTTGGG TTTGGG TTTGGG TTTGGG TTTGGG
*
34476 TTTGGG TTTGGG TTTAGG TT
1 TTTGGG TTTGGG TTTGGG TT
34496 CTAGTTTAGG
Statistics
Matches: 96, Mismatches: 14, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
6 91 0.95
7 5 0.05
ACGTcount: A:0.02, C:0.08, G:0.46, T:0.44
Consensus pattern (6 bp):
TTTGGG
Found at i:34434 original size:18 final size:18
Alignment explanation
Indices: 34364--34496 Score: 140
Period size: 18 Copynumber: 7.3 Consensus size: 18
34354 TTCAGGTTTT
* * *
34364 GGGTTCAGGTTCAGATTT
1 GGGTTCGGGTTCGGGTTT
* * * *
34382 GGGTTCGAGTTTGTGTTC
1 GGGTTCGGGTTCGGGTTT
* * *
34400 GGGTTTTGGGTTTGGGTTC
1 GGG-TTCGGGTTCGGGTTT
34419 GGGTTCGGGTTCGGGTTT
1 GGGTTCGGGTTCGGGTTT
34437 GGGTTCGGGTTCGGGTTT
1 GGGTTCGGGTTCGGGTTT
34455 GGGTTCGGGTTCGGGTTT
1 GGGTTCGGGTTCGGGTTT
* *
34473 GGGTTTGGGTTTGGGTTT
1 GGGTTCGGGTTCGGGTTT
*
34491 AGGTTC
1 GGGTTC
34497 TAGTTTAGGG
Statistics
Matches: 97, Mismatches: 17, Indels: 2
0.84 0.15 0.02
Matches are distributed among these distances:
18 82 0.85
19 15 0.15
ACGTcount: A:0.04, C:0.09, G:0.45, T:0.42
Consensus pattern (18 bp):
GGGTTCGGGTTCGGGTTT
Found at i:34534 original size:13 final size:13
Alignment explanation
Indices: 34487--34534 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
34477 TTGGGTTTGG
*
34487 GTTTA-GGTTCTA
1 GTTTAGGGTTCAA
34499 GTTTAGGGTTCAA
1 GTTTAGGGTTCAA
*
34512 -TATTAAGGTTCAA
1 GT-TTAGGGTTCAA
34525 GTTTAGGGTT
1 GTTTAGGGTT
34535 TTAGTTAAGG
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
12 6 0.20
13 23 0.77
14 1 0.03
ACGTcount: A:0.23, C:0.06, G:0.27, T:0.44
Consensus pattern (13 bp):
GTTTAGGGTTCAA
Found at i:35306 original size:15 final size:15
Alignment explanation
Indices: 35282--35311 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
35272 AAAACTATTT
*
35282 ATAATTAATATTAAC
1 ATAATCAATATTAAC
35297 ATAATCAATATTAAC
1 ATAATCAATATTAAC
35312 TTATATTAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.53, C:0.10, G:0.00, T:0.37
Consensus pattern (15 bp):
ATAATCAATATTAAC
Found at i:35630 original size:2 final size:2
Alignment explanation
Indices: 35623--35736 Score: 52
Period size: 2 Copynumber: 61.0 Consensus size: 2
35613 TTCTTTAAAC
* *
35623 TA TA TA TA TA TA TA TA TA TA TA T- TC TA TA GA T- TA CT- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
* * * * *
35663 T- TA GT- TA TA CA TA AA TA TA -A TC TA TA -A CA -A TA AA TA TA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
35701 AA TA TA TA GT- TA TA -A T- 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 TA TA TA TA
35737 AATTATGGTT
Statistics
Matches: 85, Mismatches: 13, Indels: 28
0.67 0.10 0.22
Matches are distributed among these distances:
1 11 0.13
2 71 0.84
3 3 0.04
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.45
Consensus pattern (2 bp):
TA
Found at i:35788 original size:21 final size:21
Alignment explanation
Indices: 35764--35816 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
35754 TTAACATTAA
* *
35764 TATAAACTATAGGTTATAAAT
1 TATAAACTATAGATTATAAAG
* * *
35785 TATATACTAAATATTATAAAG
1 TATAAACTATAGATTATAAAG
35806 TATAAACTATA
1 TATAAACTATA
35817 TAGTACACTA
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.51, C:0.06, G:0.06, T:0.38
Consensus pattern (21 bp):
TATAAACTATAGATTATAAAG
Found at i:35898 original size:2 final size:2
Alignment explanation
Indices: 35891--35978 Score: 124
Period size: 2 Copynumber: 44.0 Consensus size: 2
35881 AAATAGATTG
* ** *
35891 TA TA TA TA CA TA TA CTA TA GG TT 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 TA TA TA TA TA TA
35934 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
35975 TA TA
1 TA TA
35979 CATAGTTTAT
Statistics
Matches: 77, Mismatches: 7, Indels: 4
0.88 0.08 0.05
Matches are distributed among these distances:
1 1 0.01
2 74 0.96
3 2 0.03
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:36085 original size:7 final size:7
Alignment explanation
Indices: 36075--36106 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
36065 TATGTATAGT
36075 GTTTAGG
1 GTTTAGG
*
36082 GTTTAAG
1 GTTTAGG
36089 GTTTAGG
1 GTTTAGG
36096 GTTTAGG
1 GTTTAGG
36103 GTTT
1 GTTT
36107 TTATAAACTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.16, C:0.00, G:0.38, T:0.47
Consensus pattern (7 bp):
GTTTAGG
Found at i:36240 original size:27 final size:29
Alignment explanation
Indices: 36179--36240 Score: 76
Period size: 27 Copynumber: 2.2 Consensus size: 29
36169 AGTAATTTAC
*
36179 TTTATATGGTTTATATATATATATATATA
1 TTTATATGGTTTATATATATATATACATA
*
36208 TATATA-GG-TTATATATAT-TATACATA
1 TTTATATGGTTTATATATATATATACATA
36234 GTTTATA
1 -TTTATA
36241 CATACATGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
26 7 0.24
27 15 0.52
28 2 0.07
29 5 0.17
ACGTcount: A:0.39, C:0.02, G:0.08, T:0.52
Consensus pattern (29 bp):
TTTATATGGTTTATATATATATATACATA
Found at i:36451 original size:21 final size:21
Alignment explanation
Indices: 36422--36481 Score: 77
Period size: 21 Copynumber: 2.9 Consensus size: 21
36412 TTATAAATTT
*
36422 TAGGGTTTAGGGTTTATGTAA
1 TAGGATTTAGGGTTTATGTAA
*
36443 TAGGATTTAGGGTTTATGTAT
1 TAGGATTTAGGGTTTATGTAA
* *
36464 TATGA-TTAAGGTTTATGT
1 TAGGATTTAGGGTTTATGT
36482 TTTAGCGTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
20 12 0.34
21 23 0.66
ACGTcount: A:0.25, C:0.00, G:0.28, T:0.47
Consensus pattern (21 bp):
TAGGATTTAGGGTTTATGTAA
Found at i:36650 original size:15 final size:15
Alignment explanation
Indices: 36599--36648 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
36589 TTATACATAC
*
36599 ATATATATATATACT
1 ATATATATATAAACT
*
36614 ATAT-TAATATAAATT
1 ATATAT-ATATAAACT
*
36629 ATA-ATTTATAAACT
1 ATATATATATAAACT
36643 ATATAT
1 ATATAT
36649 TTTATATAGT
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
14 11 0.39
15 17 0.61
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (15 bp):
ATATATATATAAACT
Found at i:36670 original size:4 final size:4
Alignment explanation
Indices: 36661--37946 Score: 1231
Period size: 4 Copynumber: 323.2 Consensus size: 4
36651 TATATAGTTT
* *
36661 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC GTAC ATAC GTAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
* * * * * * * * *
36709 GTAC ATAC GTAC AAAC GTAC ATAC GTAC AAAC GTAC ATAC GTAC AAAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
* * * * * * * * *
36757 GTAC ATAC GTAC AAAC GTAC ATAC GTAC AAAC GTAC ATAC GTAC AAAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
* * * * * *
36805 GTAC ATAC GTAC ATAC GTAC ATAC GTAC ATAC GTAC ATAC GTAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
* * * * * *
36853 GTAC ATAC GTAC ATAC GTAC ATAC GTAC ATAC GTAC ATAC GTAC A-A-
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
* * * * * * * * * *
36899 ATAT ATAT ATAT ATAT ATAT ATAC ATAC ATAC GTAT TTAC GTAT ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
* * * * * * * * *
36947 ATAT GTAT GTAC GTAC GTTAC ATAC AT-- ATAT ATAT ATAC ATAT ATAC
1 ATAC ATAC ATAC ATAC -ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
* * *
36994 ATAC ATAC ATAC ATAC ATAC ATAC ATAT ATAT ATAC ATAC ATAC ATAT
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
* * * * *
37042 ATAC GTAC GTAC GTAC GTAC ATAC ATAC ATAC ATAC ATAC ATAC ATAT
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
* *
37090 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAT ATAC ATGC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
* * * * * * * * *
37138 ATAT ATAG ATAG ATAC ATAC ATAG ATAC ATGC ATAT GTAC GTAC GTAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
* * * * * * *
37186 ATAC ATAC GTAG ATAC ATAA ATAT ATAC GTAC GTAC GTAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
* * * * * * * * * * * *
37234 GTAG ATAT ATAA ATAT ATAC GTAC GTGC GTAC ATAC ATAC GTAG ATAT
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
* * * * * * *
37282 ATAC ATAC ATAC GTAC GTAT GTAC ATAT ATAC ATAC ATAC ATAT ATAT
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
* * * * * *
37330 ATAT ATAT ATAT ATAT ATAC ATAC ATAC ATAT ATAT ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
* * * * *
37378 ATAT ATAC ATAC ATAT ATAT ATAC ATAC ATAC ATAC ATAC ATAT ATGC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
* * *
37426 ATAC ATAT ATAC ATAC ATAC ATAC ATAC ATAC ATAC AAAT ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
37474 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
37522 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
*
37570 ATAC ATAC ATAC ATAC ATAC ATAC AT-- ATAT ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
37616 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
*
37664 ATAC ATAC ATAC ATAC ATAC AAAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
* * * *
37712 ATAC ATAC ATAC ATAC ATAC AAAC ATAC ATAT ATAT ATAT ATAC AT--
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
* * * * * * *
37758 ATAT ATAC ATAC ATAC ATAC ATAC GTA- TTAC GTAT ATAC ATAT GTAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
* * * * * * *
37805 GTAC GTAC GTTAC ATAC ATAT ATAT ATAC ATAT ATAC TTAC ATAC ATAC
1 ATAC ATAC -ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
* * * * * *
37854 ATAC ATAC ATAT ATAT ATAC ATAC ATAC ATAT ATAC GTAC GTAC GTAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
* * * *
37902 GTAC GTAC ATAC ATAC ATAC ATAC ATAT AGAC ATAC ATAC ATAC A
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC A
37947 CACACACACA
Statistics
Matches: 1083, Mismatches: 188, Indels: 22
0.84 0.15 0.02
Matches are distributed among these distances:
2 7 0.01
3 4 0.00
4 1066 0.98
5 6 0.01
ACGTcount: A:0.46, C:0.20, G:0.06, T:0.29
Consensus pattern (4 bp):
ATAC
Found at i:37759 original size:10 final size:10
Alignment explanation
Indices: 37734--37768 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
37724 ATACATACAA
*
37734 ACATACATAT
1 ACATATATAT
*
37744 ATATATATAT
1 ACATATATAT
37754 ACATATATAT
1 ACATATATAT
37764 ACATA
1 ACATA
37769 CATACATACA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.37
Consensus pattern (10 bp):
ACATATATAT
Found at i:37805 original size:23 final size:25
Alignment explanation
Indices: 37767--37828 Score: 74
Period size: 23 Copynumber: 2.6 Consensus size: 25
37757 TATATATACA
* *
37767 TACATACATACATACGTA-TTACG-
1 TACATACATATATACGTACGTACGT
* *
37790 TATATACATATGTACGTACGTACGT
1 TACATACATATATACGTACGTACGT
37815 TACATACATATATA
1 TACATACATATATA
37829 TATACATATA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
23 15 0.48
24 4 0.13
25 12 0.39
ACGTcount: A:0.39, C:0.18, G:0.10, T:0.34
Consensus pattern (25 bp):
TACATACATATATACGTACGTACGT
Found at i:37951 original size:2 final size:2
Alignment explanation
Indices: 37944--37986 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
37934 ATACATACAT
37944 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
37986 A
1 A
37987 TACCTATGTG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:41842 original size:25 final size:25
Alignment explanation
Indices: 41782--41848 Score: 64
Period size: 25 Copynumber: 2.6 Consensus size: 25
41772 TCATTTAATG
*
41782 TTATTATATTATATTATATATTTACA
1 TTATT-TATTATATTATATATATACA
** *
41808 TTATAAATTATATTATATA-ATATA
1 TTATTTATTATATTATATATATACA
*
41832 TGTATTTATTACATTAT
1 T-TATTTATTATATTAT
41849 TGTTCCCATT
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
24 4 0.12
25 25 0.76
26 4 0.12
ACGTcount: A:0.40, C:0.03, G:0.01, T:0.55
Consensus pattern (25 bp):
TTATTTATTATATTATATATATACA
Found at i:42689 original size:14 final size:13
Alignment explanation
Indices: 42670--42706 Score: 56
Period size: 14 Copynumber: 2.7 Consensus size: 13
42660 AATTTAGTCC
42670 TTTTATTTTTACTT
1 TTTTATTTTT-CTT
42684 TTTTATTATTTCTT
1 TTTTATT-TTTCTT
42698 TTTTATTTT
1 TTTTATTTT
42707 ATTTGTTTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 2 0.09
14 17 0.77
15 3 0.14
ACGTcount: A:0.14, C:0.05, G:0.00, T:0.81
Consensus pattern (13 bp):
TTTTATTTTTCTT
Found at i:42732 original size:13 final size:12
Alignment explanation
Indices: 42670--42750 Score: 56
Period size: 12 Copynumber: 6.4 Consensus size: 12
42660 AATTTAGTCC
42670 TTTTATTTTTACTT
1 TTTTA-TTTTA-TT
*
42684 TTTTATTATTTCTT
1 TTTTA-T-TTTATT
42698 TTTTATTTTATT
1 TTTTATTTTATT
* *
42710 TGTT-TGTTATAT
1 TTTTATTTTAT-T
42722 TTTTATTTTATT
1 TTTTATTTTATT
** *
42734 ACTTATTATATT
1 TTTTATTTTATT
42746 TTTTA
1 TTTTA
42751 ATAATTTTTT
Statistics
Matches: 53, Mismatches: 11, Indels: 8
0.74 0.15 0.11
Matches are distributed among these distances:
11 5 0.09
12 25 0.47
13 6 0.11
14 14 0.26
15 3 0.06
ACGTcount: A:0.19, C:0.04, G:0.02, T:0.75
Consensus pattern (12 bp):
TTTTATTTTATT
Found at i:42742 original size:23 final size:22
Alignment explanation
Indices: 42673--42748 Score: 66
Period size: 23 Copynumber: 3.3 Consensus size: 22
42663 TTAGTCCTTT
42673 TATTTTTACTTTT-TTATTATT-
1 TATTTTTA-TTTTATTATTATTA
* * *
42694 TCTTTTTTATTTTATTTGTTTGTTA
1 T-ATTTTTATTTTA-TT-ATTATTA
42719 TATTTTTATTTTATTACTTATTA
1 TATTTTTATTTTATTA-TTATTA
42742 TATTTTT
1 TATTTTT
42749 TAATAATTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
21 5 0.12
22 6 0.14
23 16 0.37
24 15 0.35
25 1 0.02
ACGTcount: A:0.18, C:0.04, G:0.03, T:0.75
Consensus pattern (22 bp):
TATTTTTATTTTATTATTATTA
Found at i:42815 original size:17 final size:17
Alignment explanation
Indices: 42795--42871 Score: 66
Period size: 17 Copynumber: 4.2 Consensus size: 17
42785 TTTTATTTAC
*
42795 TTTTATTATTACTATTA
1 TTTTATTATTATTATTA
* *
42812 TTTTACTATTATTATTT
1 TTTTATTATTATTATTA
42829 TCTTATATATATATATTATTTA
1 T-TT-TAT-TAT-TATTA-TTA
42851 TTTT-TTATTATTTATTA
1 TTTTATTATTA-TTATTA
42868 TTTT
1 TTTT
42872 GTCTTCCTAG
Statistics
Matches: 49, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
17 24 0.49
18 8 0.16
19 3 0.06
20 4 0.08
21 7 0.14
22 3 0.06
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (17 bp):
TTTTATTATTATTATTA
Found at i:42857 original size:7 final size:7
Alignment explanation
Indices: 42781--42870 Score: 60
Period size: 7 Copynumber: 12.7 Consensus size: 7
42771 TATATGTACA
*
42781 TATTTTT
1 TATTTAT
*
42788 TATTTAC
1 TATTTAT
42795 T-TTTAT
1 TATTTAT
42801 TATTACTAT
1 TATT--TAT
*
42810 TATTTTAC
1 TA-TTTAT
42818 TA-TTAT
1 TATTTAT
*
42824 TATTTTCT
1 TA-TTTAT
*
42832 TATATA-
1 TATTTAT
*
42838 TATATAT
1 TATTTAT
42845 TATTTAT
1 TATTTAT
*
42852 TTTTTAT
1 TATTTAT
42859 TATTTAT
1 TATTTAT
42866 TATTT
1 TATTT
42871 TGTCTTCCTA
Statistics
Matches: 65, Mismatches: 11, Indels: 14
0.72 0.12 0.16
Matches are distributed among these distances:
6 16 0.25
7 33 0.51
8 9 0.14
9 5 0.08
10 2 0.03
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (7 bp):
TATTTAT
Found at i:42976 original size:22 final size:23
Alignment explanation
Indices: 42963--43032 Score: 60
Period size: 22 Copynumber: 3.2 Consensus size: 23
42953 TTTATTATTA
42963 TTTTCTTTTATT-TTGT-TT-TT
1 TTTTCTTTTATTCTTGTATTATT
*
42983 TCTTTGTTTTTATTCTTGTATTA-T
1 T-TTT-CTTTTATTCTTGTATTATT
* *
43007 TTTTCTTTTATTGTT-TATTCTT
1 TTTTCTTTTATTCTTGTATTATT
43029 TTTT
1 TTTT
43033 TGTTATGTTA
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
20 1 0.03
21 7 0.17
22 21 0.52
23 7 0.17
24 4 0.10
ACGTcount: A:0.09, C:0.07, G:0.06, T:0.79
Consensus pattern (23 bp):
TTTTCTTTTATTCTTGTATTATT
Found at i:45193 original size:65 final size:64
Alignment explanation
Indices: 45089--45263 Score: 232
Period size: 65 Copynumber: 2.8 Consensus size: 64
45079 CGACACCATG
* *
45089 TACTCGAGATTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAGGCCAATTTGGTGAGACA
1 TACTC-AGATTGGATTTCAACTTCACGACGAAGGATATCCAACTCAAGGCCAATTTGGTGAAACA
* * *
45154 TACTCAAGATTGGATTTCAACTTTATGACGAAGGATATCCAACTCAAAGCCAATTTGGTGAAACA
1 TACTC-AGATTGGATTTCAACTTCACGACGAAGGATATCCAACTCAAGGCCAATTTGGTGAAACA
* * *
45219 -A-T-A-CTTAGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGC
1 TACTCAGATTGGATTTCAACTTCACGACGAAGGATATCCAACTCAAGGC
45264 TCAACTTCAC
Statistics
Matches: 98, Mismatches: 12, Indels: 5
0.85 0.10 0.04
Matches are distributed among these distances:
60 36 0.37
61 1 0.01
63 1 0.01
64 1 0.01
65 59 0.60
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (64 bp):
TACTCAGATTGGATTTCAACTTCACGACGAAGGATATCCAACTCAAGGCCAATTTGGTGAAACA
Found at i:45370 original size:119 final size:117
Alignment explanation
Indices: 45219--45622 Score: 488
Period size: 119 Copynumber: 3.5 Consensus size: 117
45209 TGGTGAAACA
*
45219 ATACTTAGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACAAAGGGG
1 ATACTTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACAAA-GGG
* *
45284 CCATCCACGATTTTAACTTCACGACGAAGGATATCATG-CACAAGCAGGA-ATGC
65 CCATCCACAATTTCAACTTCACGACGAAGGATATCATGCCACAAGCA--ATATGC
* *
45337 A-ACCCTTGGATTTCAACTTCACGACGAATGATATCCAATTCAAGGCTCAACTTCACAATGAAAG
1 ATA--CTTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAA-CAAAG
* * * *
45401 GGCCATCCACTATTTCAACTTCACGACGAAGGATATCGTGCCCACCAGCAATATTC
63 GGCCATCCACAATTTCAACTTCACGACGAAGGATATCATG-CCACAAGCAATATGC
* *
45457 ATATTTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAATGGG
1 ATACTTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAAC-AAAGGG
* * ** *
45522 CCATTCACAATTTCAACTTCACGGCGAAGGATATTGTG-C-CAA-C--TCT--
65 CCATCCACAATTTCAACTTCACGACGAAGGATATCATGCCACAAGCAATATGC
* * *
45568 AGA-TTGGATTTCAACTTCACGATGAAGGATATCCAATTCAAAGCTCAACTTCACA
1 ATACTTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACA
45623 GCGAATGAGC
Statistics
Matches: 257, Mismatches: 21, Indels: 24
0.85 0.07 0.08
Matches are distributed among these distances:
110 50 0.19
111 2 0.01
113 2 0.01
115 1 0.00
116 2 0.01
117 2 0.01
118 1 0.00
119 182 0.71
120 7 0.03
121 8 0.03
ACGTcount: A:0.34, C:0.25, G:0.16, T:0.25
Consensus pattern (117 bp):
ATACTTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACAAAGGGC
CATCCACAATTTCAACTTCACGACGAAGGATATCATGCCACAAGCAATATGC
Found at i:47229 original size:14 final size:13
Alignment explanation
Indices: 47210--47246 Score: 56
Period size: 14 Copynumber: 2.7 Consensus size: 13
47200 AATTTAGTCC
47210 TTTTATTTTTACTT
1 TTTTATTTTT-CTT
47224 TTTTATTATTTCTT
1 TTTTATT-TTTCTT
47238 TTTTATTTT
1 TTTTATTTT
47247 ATTTGTTTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 2 0.09
14 17 0.77
15 3 0.14
ACGTcount: A:0.14, C:0.05, G:0.00, T:0.81
Consensus pattern (13 bp):
TTTTATTTTTCTT
Found at i:47355 original size:3 final size:3
Alignment explanation
Indices: 47347--47417 Score: 54
Period size: 3 Copynumber: 22.7 Consensus size: 3
47337 TTTTATTTAT
* * *
47347 TTA TTA TTA TTA CTA TTA TTA TTA CTA TTA TTA TT- TTC TTA TATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
* *
47392 TAGA TATA TTA TTT TTA TTTA TTA TT
1 T-TA T-TA TTA TTA TTA -TTA TTA TT
47418 TTGTCTTCCT
Statistics
Matches: 56, Mismatches: 9, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
2 2 0.04
3 42 0.75
4 12 0.21
ACGTcount: A:0.31, C:0.04, G:0.01, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:47365 original size:12 final size:12
Alignment explanation
Indices: 47348--47381 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
47338 TTTATTTATT
47348 TATTATTATTAC
1 TATTATTATTAC
47360 TATTATTATTAC
1 TATTATTATTAC
47372 TATTATTATT
1 TATTATTATT
47382 TTCTTATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (12 bp):
TATTATTATTAC
Found at i:47584 original size:15 final size:14
Alignment explanation
Indices: 47547--47585 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
47537 TTCTTTGTTT
*
47547 TTATTCTTGTATTA
1 TTATTCTTTTATTA
*
47561 TTTTTCTTTTATTGA
1 TTATTCTTTTATT-A
47576 TTATTCTTTT
1 TTATTCTTTT
47586 TTTTGTTATG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 11 0.52
15 10 0.48
ACGTcount: A:0.15, C:0.08, G:0.05, T:0.72
Consensus pattern (14 bp):
TTATTCTTTTATTA
Found at i:56007 original size:65 final size:65
Alignment explanation
Indices: 55897--56034 Score: 154
Period size: 65 Copynumber: 2.1 Consensus size: 65
55887 TTTTGTGCAT
* ** ** *
55897 CGATGCACAATCCATGCATCGATGCACTCTTGAATATTTTGAAACATTGAATGTATTTTA-CGTA
1 CGATGCACAATCCATGCATCGATGCACTCATGAATATTTCAAAACATCAAATGTA-ATTAGCGTA
55961 C
65 C
** * *
55962 CGATGCACAGA-CCATGCATCGATGCACTCATGGCTCTTTCAAAACATCAAATGTAATTAGTGTA
1 CGATGCACA-ATCCATGCATCGATGCACTCATGAATATTTCAAAACATCAAATGTAATTAGCGTA
56026 C
65 C
56027 CGATGCAC
1 CGATGCAC
56035 TAAGTCTTAT
Statistics
Matches: 61, Mismatches: 10, Indels: 4
0.81 0.13 0.05
Matches are distributed among these distances:
64 3 0.05
65 57 0.93
66 1 0.02
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.29
Consensus pattern (65 bp):
CGATGCACAATCCATGCATCGATGCACTCATGAATATTTCAAAACATCAAATGTAATTAGCGTAC
Found at i:61849 original size:21 final size:21
Alignment explanation
Indices: 61825--61952 Score: 98
Period size: 21 Copynumber: 6.0 Consensus size: 21
61815 ATGCATCCCT
61825 TGAATGTGCATCGATACACCA
1 TGAATGTGCATCGATACACCA
* * *
61846 TGAAGGTGCACCGATGA-ATTCCT
1 TGAATGTGCATCGAT-ACA--CCA
61869 TGAATGTGCATCGATACACCA
1 TGAATGTGCATCGATACACCA
* * * *
61890 TGAAGGTGCACCGATGCATTCCT
1 TGAATGTGCATCGATACA--CCA
** *
61913 TGAATGTGCATCGATGTACTA
1 TGAATGTGCATCGATACACCA
*
61934 TG-ATGTGCATCGGTACACC
1 TGAATGTGCATCGATACACC
61953 CATCGGGTTT
Statistics
Matches: 82, Mismatches: 19, Indels: 13
0.72 0.17 0.11
Matches are distributed among these distances:
20 13 0.16
21 34 0.41
22 2 0.02
23 33 0.40
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (21 bp):
TGAATGTGCATCGATACACCA
Found at i:61872 original size:44 final size:44
Alignment explanation
Indices: 61786--61927 Score: 216
Period size: 44 Copynumber: 3.2 Consensus size: 44
61776 TTTTATGCTT
* * * *
61786 TGTGCATTGATACACTA-GACA-GTGTACCGATGCATCCCTTGAA
1 TGTGCATCGATACACCATGA-AGGTGCACCGATGCATTCCTTGAA
*
61829 TGTGCATCGATACACCATGAAGGTGCACCGATGAATTCCTTGAA
1 TGTGCATCGATACACCATGAAGGTGCACCGATGCATTCCTTGAA
61873 TGTGCATCGATACACCATGAAGGTGCACCGATGCATTCCTTGAA
1 TGTGCATCGATACACCATGAAGGTGCACCGATGCATTCCTTGAA
61917 TGTGCATCGAT
1 TGTGCATCGAT
61928 GTACTATGAT
Statistics
Matches: 91, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
43 16 0.18
44 75 0.82
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (44 bp):
TGTGCATCGATACACCATGAAGGTGCACCGATGCATTCCTTGAA
Found at i:61877 original size:23 final size:22
Alignment explanation
Indices: 61811--61928 Score: 82
Period size: 23 Copynumber: 5.3 Consensus size: 22
61801 TAGACAGTGT
*
61811 ACCGATGCATCCCTTGAATGTGC
1 ACCGATGAAT-CCTTGAATGTGC
* * *
61834 ATCGAT-ACA-CCATGAAGGTGC
1 ACCGATGA-ATCCTTGAATGTGC
61855 ACCGATGAATTCCTTGAATGTGC
1 ACCGATGAA-TCCTTGAATGTGC
* * *
61878 ATCGAT-ACA-CCATGAAGGTGC
1 ACCGATGA-ATCCTTGAATGTGC
*
61899 ACCGATGCATTCCTTGAATGTGC
1 ACCGATG-AATCCTTGAATGTGC
*
61922 ATCGATG
1 ACCGATG
61929 TACTATGATG
Statistics
Matches: 72, Mismatches: 15, Indels: 16
0.70 0.15 0.16
Matches are distributed among these distances:
21 31 0.43
22 2 0.03
23 39 0.54
ACGTcount: A:0.27, C:0.25, G:0.23, T:0.25
Consensus pattern (22 bp):
ACCGATGAATCCTTGAATGTGC
Found at i:65897 original size:6 final size:6
Alignment explanation
Indices: 65886--65926 Score: 82
Period size: 6 Copynumber: 6.8 Consensus size: 6
65876 TCCGTTTATC
65886 ATCCCT ATCCCT ATCCCT ATCCCT ATCCCT ATCCCT ATCCC
1 ATCCCT ATCCCT ATCCCT ATCCCT ATCCCT ATCCCT ATCCC
65927 GAACTCCGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.17, C:0.51, G:0.00, T:0.32
Consensus pattern (6 bp):
ATCCCT
Found at i:69508 original size:25 final size:25
Alignment explanation
Indices: 69480--69606 Score: 94
Period size: 25 Copynumber: 5.2 Consensus size: 25
69470 AGGATACCTA
69480 GTGTATATGGTGGGCACGACCTTAT
1 GTGTATATGGTGGGCACGACCTTAT
*
69505 GTGTCATATTCGG-GAGG-A-TACC-TA-
1 GTGT-ATA-T-GGTG-GGCACGACCTTAT
69529 GTGTATATGGTGGGCACGACCTTAT
1 GTGTATATGGTGGGCACGACCTTAT
*
69554 GTGTCATATTCGG-GAGG-A-TACC-TA-
1 GTGT-ATA-T-GGTG-GGCACGACCTTAT
69578 GTGTATATGGTGGGCACGACCTTAT
1 GTGTATATGGTGGGCACGACCTTAT
69603 GTGT
1 GTGT
69607 CATAATCGGG
Statistics
Matches: 80, Mismatches: 4, Indels: 36
0.67 0.03 0.30
Matches are distributed among these distances:
21 8 0.10
22 6 0.08
23 12 0.15
24 12 0.15
25 16 0.20
26 12 0.15
27 6 0.08
28 8 0.10
ACGTcount: A:0.21, C:0.16, G:0.31, T:0.31
Consensus pattern (25 bp):
GTGTATATGGTGGGCACGACCTTAT
Found at i:69542 original size:49 final size:49
Alignment explanation
Indices: 69470--69617 Score: 287
Period size: 49 Copynumber: 3.0 Consensus size: 49
69460 AATACACTAA
69470 AGGATACCTAGTGTATATGGTGGGCACGACCTTATGTGTCATATTCGGG
1 AGGATACCTAGTGTATATGGTGGGCACGACCTTATGTGTCATATTCGGG
69519 AGGATACCTAGTGTATATGGTGGGCACGACCTTATGTGTCATATTCGGG
1 AGGATACCTAGTGTATATGGTGGGCACGACCTTATGTGTCATATTCGGG
*
69568 AGGATACCTAGTGTATATGGTGGGCACGACCTTATGTGTCATAATCGGG
1 AGGATACCTAGTGTATATGGTGGGCACGACCTTATGTGTCATATTCGGG
69617 A
1 A
69618 CTGTACTTAA
Statistics
Matches: 98, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
49 98 1.00
ACGTcount: A:0.24, C:0.16, G:0.30, T:0.30
Consensus pattern (49 bp):
AGGATACCTAGTGTATATGGTGGGCACGACCTTATGTGTCATATTCGGG
Found at i:69550 original size:23 final size:23
Alignment explanation
Indices: 69475--69599 Score: 82
Period size: 23 Copynumber: 5.2 Consensus size: 23
69465 ACTAAAGGAT
69475 ACCTAGTGTATATGGTGGGCACG
1 ACCTAGTGTATATGGTGGGCACG
*
69498 ACCTTATGTGTCATATTCGG-GAGG-A-T
1 ACC-TA-GTGT-ATA-T-GGTG-GGCACG
69524 ACCTAGTGTATATGGTGGGCACG
1 ACCTAGTGTATATGGTGGGCACG
*
69547 ACCTTATGTGTCATATTCGG-GAGG-A-T
1 ACC-TA-GTGT-ATA-T-GGTG-GGCACG
69573 ACCTAGTGTATATGGTGGGCACG
1 ACCTAGTGTATATGGTGGGCACG
69596 ACCT
1 ACCT
69600 TATGTGTCAT
Statistics
Matches: 80, Mismatches: 4, Indels: 36
0.67 0.03 0.30
Matches are distributed among these distances:
21 8 0.10
22 6 0.08
23 16 0.20
24 12 0.15
25 12 0.15
26 12 0.15
27 6 0.08
28 8 0.10
ACGTcount: A:0.22, C:0.18, G:0.30, T:0.30
Consensus pattern (23 bp):
ACCTAGTGTATATGGTGGGCACG
Found at i:72736 original size:20 final size:20
Alignment explanation
Indices: 72688--72749 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 20
72678 AAACTTAATC
*
72688 AAAATAATTAAAATAA-ATAT
1 AAAATAATT-TAATAATATAT
72708 AAAAT--TTTAATAATATAT
1 AAAATAATTTAATAATATAT
72726 AAAATAATTT-AT-ATGATAT
1 AAAATAATTTAATAAT-ATAT
72745 AAAAT
1 AAAAT
72750 TAAATCTATA
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
17 5 0.14
18 13 0.35
19 11 0.30
20 8 0.22
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (20 bp):
AAAATAATTTAATAATATAT
Found at i:72808 original size:56 final size:56
Alignment explanation
Indices: 72743--72878 Score: 151
Period size: 55 Copynumber: 2.5 Consensus size: 56
72733 TTTATATGAT
* *
72743 ATAAAATT-AAATCTATAATATAATATTA-AAAATTAATATTTAATTTATTTAAAATA
1 ATAATATTAAAATCTATAATATAATATTATAAAATT-ATATTTAA-TTATTTAAAAAA
* *
72799 TTAATATTAAAAT-TAATATCTATAA-A-TATAAAATTATATTTAATTATTTAAAAAA
1 ATAATATTAAAATCT-ATA-ATATAATATTATAAAATTATATTTAATTATTTAAAAAA
72854 ATAATATTAAAATC-A-AATATAATAT
1 ATAATATTAAAATCTATAATATAATAT
72879 AAATTAAATA
Statistics
Matches: 67, Mismatches: 6, Indels: 16
0.75 0.07 0.18
Matches are distributed among these distances:
52 5 0.07
53 2 0.03
54 1 0.01
55 23 0.34
56 17 0.25
57 14 0.21
58 5 0.07
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (56 bp):
ATAATATTAAAATCTATAATATAATATTATAAAATTATATTTAATTATTTAAAAAA
Done.