Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012988.1 Kokia drynarioides strain JFW-HI SEQ_128006, 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: 90252
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1137 original size:29 final size:28
Alignment explanation
Indices: 1093--1147 Score: 83
Period size: 29 Copynumber: 1.9 Consensus size: 28
1083 CCACTTTTTA
*
1093 TTTTTCTTTTCTTCTTTTTTCCTTTTCT
1 TTTTTCTTTTCTTCTTTTTTCATTTTCT
*
1121 TTTTCTCTTTTTTTCTTTTTTCATTTT
1 TTTT-TCTTTTCTTCTTTTTTCATTTT
1148 TTCATTTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 4 0.17
29 20 0.83
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (28 bp):
TTTTTCTTTTCTTCTTTTTTCATTTTCT
Found at i:1147 original size:8 final size:7
Alignment explanation
Indices: 1093--1163 Score: 72
Period size: 7 Copynumber: 9.7 Consensus size: 7
1083 CCACTTTTTA
1093 TTTTTCT
1 TTTTTCT
1100 TTTCTTCT
1 TTT-TTCT
1108 TTTTTC-
1 TTTTTCT
*
1114 CTTTTCT
1 TTTTTCT
1121 TTTTCTCTT
1 TTTT-TC-T
1130 TTTTTCT
1 TTTTTCT
1137 TTTTTCAT
1 TTTTTC-T
*
1145 TTTTTCA
1 TTTTTCT
*
1152 TTTTTAT
1 TTTTTCT
1159 TTTTT
1 TTTTT
1164 TTTGTTTTTT
Statistics
Matches: 54, Mismatches: 5, Indels: 10
0.78 0.07 0.14
Matches are distributed among these distances:
6 5 0.09
7 26 0.48
8 18 0.33
9 5 0.09
ACGTcount: A:0.04, C:0.15, G:0.00, T:0.80
Consensus pattern (7 bp):
TTTTTCT
Found at i:1163 original size:16 final size:15
Alignment explanation
Indices: 1093--1179 Score: 79
Period size: 15 Copynumber: 5.7 Consensus size: 15
1083 CCACTTTTTA
*
1093 TTTTTCTTTTCTTCT
1 TTTTTCTTTTTTTCT
*
1108 TTTTTC--CTTTTCT
1 TTTTTCTTTTTTTCT
1121 TTTTCTCTTTTTTTCT
1 TTTT-TCTTTTTTTCT
*
1137 TTTTTCATTTTTTCAT
1 TTTTTCTTTTTTTC-T
* *
1153 TTTTATTTTTTTTTGT
1 TTTT-TCTTTTTTTCT
*
1169 TTTTTGTTTTT
1 TTTTTCTTTTT
1180 AAAATTTCTT
Statistics
Matches: 59, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
13 9 0.15
14 2 0.03
15 21 0.36
16 20 0.34
17 7 0.12
ACGTcount: A:0.03, C:0.13, G:0.02, T:0.82
Consensus pattern (15 bp):
TTTTTCTTTTTTTCT
Found at i:5693 original size:30 final size:30
Alignment explanation
Indices: 5657--5713 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
5647 GGTTAAATTT
*
5657 GAATTTTTGAAAACTTT-AGTGGTCAAATCA
1 GAATTTTTGAAAAATTTAAG-GGTCAAATCA
5687 GAATTTTTGAAAAATTTAAGGGTCAAA
1 GAATTTTTGAAAAATTTAAGGGTCAAA
5714 AAATAATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
30 23 0.92
31 2 0.08
ACGTcount: A:0.40, C:0.07, G:0.18, T:0.35
Consensus pattern (30 bp):
GAATTTTTGAAAAATTTAAGGGTCAAATCA
Found at i:5722 original size:30 final size:30
Alignment explanation
Indices: 5657--5723 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
5647 GGTTAAATTT
* **
5657 GAATTTTTGAAAACTTTAGTGGTCAAATCA
1 GAATTTTTGAAAAATTTAGTGGTCAAAAAA
5687 GAATTTTTGAAAAATTTAAG-GGTCAAAAAA
1 GAATTTTTGAAAAATTT-AGTGGTCAAAAAA
*
5717 TAATTTT
1 GAATTTT
5724 AAATTAAAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 30 0.94
31 2 0.06
ACGTcount: A:0.42, C:0.06, G:0.15, T:0.37
Consensus pattern (30 bp):
GAATTTTTGAAAAATTTAGTGGTCAAAAAA
Found at i:8225 original size:51 final size:51
Alignment explanation
Indices: 8107--8293 Score: 225
Period size: 51 Copynumber: 3.6 Consensus size: 51
8097 TTTCATTTAA
* * ** * *
8107 TACTCATGATGACA-TATAGTCAACGGACCTTTTGTTCCATATAGGAATTCATA
1 TACTCACGATGACACT-TAGTCATCGGACC-TTTAATCCATAAAGG-ATTCATT
*
8160 TACTCACGATGACACTGAGTCATCGGACCTTTAATCCATCAAA-GATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCAT-AAAGGATTCATT
* * *
8211 TACTCACGATGACACTTAGTCATTGGACCTTTAATTCGTAAAGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAAGGATTCATT
*
8262 TACTCACGATGACTCTTAGTCATCGGACCTTT
1 TACTCACGATGACACTTAGTCATCGGACCTTT
8294 TCGTTTATAG
Statistics
Matches: 118, Mismatches: 13, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
50 3 0.03
51 79 0.67
52 9 0.08
53 26 0.22
54 1 0.01
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.33
Consensus pattern (51 bp):
TACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAAGGATTCATT
Found at i:9616 original size:39 final size:39
Alignment explanation
Indices: 9571--9685 Score: 124
Period size: 39 Copynumber: 2.9 Consensus size: 39
9561 ACTCTCCCAT
9571 CCCTCTCCCTCTTCCCCACCATCTTTCCCCCTACTCCAA
1 CCCTCTCCCTCTTCCCCACCATCTTTCCCCCTACTCCAA
** * * ** *
9610 TTCTCTCCCTCTCCCCCACCGTCCGTCCCCCTACTCCGA
1 CCCTCTCCCTCTTCCCCACCATCTTTCCCCCTACTCCAA
*
9649 CCCTCTCCCTC-TCCTCCACCATCCTTTTCCTCCTACT
1 CCCTCTCCCTCTTCC-CCACCAT-C-TTTCCCCCTACT
9686 AACCCTATCC
Statistics
Matches: 59, Mismatches: 14, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
38 2 0.03
39 47 0.80
40 1 0.02
41 9 0.15
ACGTcount: A:0.10, C:0.58, G:0.03, T:0.30
Consensus pattern (39 bp):
CCCTCTCCCTCTTCCCCACCATCTTTCCCCCTACTCCAA
Found at i:10830 original size:17 final size:17
Alignment explanation
Indices: 10810--10844 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
10800 AATTTAAACT
*
10810 TAAAAACATAATTAAAA
1 TAAAAAAATAATTAAAA
*
10827 TAAAAAAATAGTTAAAA
1 TAAAAAAATAATTAAAA
10844 T
1 T
10845 TTTTTTGGGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.69, C:0.03, G:0.03, T:0.26
Consensus pattern (17 bp):
TAAAAAAATAATTAAAA
Found at i:11588 original size:216 final size:216
Alignment explanation
Indices: 11113--11742 Score: 944
Period size: 216 Copynumber: 2.9 Consensus size: 216
11103 AGGGAAGGCT
* * * *
11113 AAAGAATAGAGGATTTTGAACTGTGATT-AGGTTCAGGGGAAGGAAAGATTGATGGGTTTGTGTT
1 AAAGAACAGAGGGTTTTGAACTGTGATTGAGTTTTA-GGGAAGGAAAGATTGATGGGTTTGTGTT
* **
11177 CGAAATTTGAACTATGATAACCCATTTGCTATCTATGCAATAATCTCAACCGTATGCAAGAAAAA
65 CGAAATTTGAACTATGATAACCCATTTGCTATCTATGCAAGAATCTCAGTCGTATGCAAGAAAAA
* * *
11242 C-AAATTTTTTTTGGTGTTTGGTTGATGGGAAAATGTAAGAAAATCTGGGAATTTCTTGTTGCTA
130 CAAAATTTTTTTAGGTGTTTGGTTGATGGGAAAATGTAAGAAAATCTGAGAATTTCTTGTTGCTG
11306 AAGAATTTGCACTTGGTTTCCC
195 AAGAATTTGCACTTGGTTTCCC
* * ** * * *
11328 AAAAAACAGAGGGTTTTGAACTGTGATTGGGTCCTGGGGAAGGAAAGATTGATGAGTTTGTGTTT
1 AAAGAACAGAGGGTTTTGAACTGTGATTGAGTTTTAGGGAAGGAAAGATTGATGGGTTTGTGTTC
11393 GAAATTTGAACTATGATAACCCATCTT-CTATCTATGCAAGAATCTCAGTCGTATGCAAGAAAAA
66 GAAATTTGAACTATGATAACCCAT-TTGCTATCTATGCAAGAATCTCAGTCGTATGCAAGAAAAA
** * * * *
11457 CAAAATTTCCTTGGGTGTTTGGTTGATGGGAAAATGTAAGAAAATCTGAAAAATTCTTGTTGTTG
130 CAAAATTTTTTTAGGTGTTTGGTTGATGGGAAAATGTAAGAAAATCTGAGAATTTCTTGTTGCTG
*
11522 AAGAATTTGCACTTGGTTTCTC
195 AAGAATTTGCACTTGGTTTCCC
* *
11544 AAAGAACAGAGGGTTTTGAACTGTGATTGAGTTTTAGAGAAGGAAAAATTGATGGGTTTGTGTTC
1 AAAGAACAGAGGGTTTTGAACTGTGATTGAGTTTTAGGGAAGGAAAGATTGATGGGTTTGTGTTC
* * *
11609 AAAATTTGAACTATGATAACCCATTTGCTATCTATGCAAGAATCTCAGTTGTATGCAAAAAAAAC
66 GAAATTTGAACTATGATAACCCATTTGCTATCTATGCAAGAATCTCAGTCGTATGCAAGAAAAAC
11674 AAAAATTTTTTTAGGTGTTTGG-TGATGGGAAAATGTAAGAAAATCTGAGAATTTCTTGTTGCTG
131 -AAAATTTTTTTAGGTGTTTGGTTGATGGGAAAATGTAAGAAAATCTGAGAATTTCTTGTTGCTG
11738 AAGAA
195 AAGAA
11743 GATGATGAAA
Statistics
Matches: 369, Mismatches: 41, Indels: 9
0.88 0.10 0.02
Matches are distributed among these distances:
215 113 0.31
216 238 0.64
217 18 0.05
ACGTcount: A:0.33, C:0.10, G:0.23, T:0.33
Consensus pattern (216 bp):
AAAGAACAGAGGGTTTTGAACTGTGATTGAGTTTTAGGGAAGGAAAGATTGATGGGTTTGTGTTC
GAAATTTGAACTATGATAACCCATTTGCTATCTATGCAAGAATCTCAGTCGTATGCAAGAAAAAC
AAAATTTTTTTAGGTGTTTGGTTGATGGGAAAATGTAAGAAAATCTGAGAATTTCTTGTTGCTGA
AGAATTTGCACTTGGTTTCCC
Found at i:11800 original size:13 final size:13
Alignment explanation
Indices: 11784--11834 Score: 57
Period size: 13 Copynumber: 3.7 Consensus size: 13
11774 TAATTTTATT
11784 ATTTTAAAAAATA
1 ATTTTAAAAAATA
**
11797 ATTTTAATAATTTTA
1 ATTTTAA-AA-AATA
11812 TATTTTAAAAAATA
1 -ATTTTAAAAAATA
11826 ATTTTAAAA
1 ATTTTAAAA
11835 TAATTTGTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
13 16 0.52
14 4 0.13
15 4 0.13
16 7 0.23
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
ATTTTAAAAAATA
Found at i:11800 original size:29 final size:28
Alignment explanation
Indices: 11762--11829 Score: 109
Period size: 29 Copynumber: 2.4 Consensus size: 28
11752 ATTGGAAATT
*
11762 AAAATTATTTAATAATTTTATTATTTTAA
1 AAAATAATTTAATAATTTTA-TATTTTAA
11791 AAAATAATTTTAATAATTTTATATTTTAA
1 AAAATAA-TTTAATAATTTTATATTTTAA
11820 AAAATAATTT
1 AAAATAATTT
11830 TAAAATAATT
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
28 3 0.08
29 21 0.57
30 13 0.35
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (28 bp):
AAAATAATTTAATAATTTTATATTTTAA
Found at i:11830 original size:29 final size:30
Alignment explanation
Indices: 11769--11832 Score: 121
Period size: 29 Copynumber: 2.2 Consensus size: 30
11759 ATTAAAATTA
11769 TTTAATAATTTTATTATTTTAAAAAATAAT
1 TTTAATAATTTTATTATTTTAAAAAATAAT
11799 TTTAATAATTTTA-TATTTTAAAAAATAAT
1 TTTAATAATTTTATTATTTTAAAAAATAAT
11828 TTTAA
1 TTTAA
11833 AATAATTTGT
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 21 0.62
30 13 0.38
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (30 bp):
TTTAATAATTTTATTATTTTAAAAAATAAT
Found at i:13333 original size:12 final size:11
Alignment explanation
Indices: 13318--13343 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
13308 ACGAAAATGT
13318 AAAAAAAAAAG
1 AAAAAAAAAAG
13329 AAAAAAAAAAG
1 AAAAAAAAAAG
13340 AAAA
1 AAAA
13344 CAACTATTCG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:13713 original size:20 final size:20
Alignment explanation
Indices: 13688--13730 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
13678 TTTTTATATT
*
13688 AATTATTATT-AAATTAATAA
1 AATTATT-TTAAAATTAAAAA
13708 AATTATTTTAAAATTAAAAA
1 AATTATTTTAAAATTAAAAA
13728 AAT
1 AAT
13731 ATATATGAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 2 0.10
20 19 0.90
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
AATTATTTTAAAATTAAAAA
Found at i:26205 original size:31 final size:31
Alignment explanation
Indices: 26169--26237 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 31
26159 AATACATCGA
* * **
26169 TAGTCATTTAACTTTGATTAAAATAACAAAAC
1 TAGTCATTAAACTTTAAAAAAAATAAC-AAAC
26201 -AGTCATTAAACTTTAAAAAAAATAACAAAC
1 TAGTCATTAAACTTTAAAAAAAATAACAAAC
26231 TAGTCAT
1 TAGTCAT
26238 CAGTAATTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
30 4 0.12
31 28 0.88
ACGTcount: A:0.51, C:0.13, G:0.06, T:0.30
Consensus pattern (31 bp):
TAGTCATTAAACTTTAAAAAAAATAACAAAC
Found at i:30699 original size:52 final size:52
Alignment explanation
Indices: 30541--30834 Score: 364
Period size: 52 Copynumber: 5.6 Consensus size: 52
30531 TTTAATTTAA
* * * *
30541 TACTCATGATGACA-TACAGTCATCGGACCTCTTGT--TCCATATAGGAATTCATA
1 TACTCACGATGACACT-TAGTCATCGGACC-CTT-TAATCCATAAAGG-ATTCATT
* * * *
30594 TACTCACGATGACA-TTGAGTCATCGGA-CCTTTAATCTATCATGAATTCATT
1 TACTCACGATGACACTT-AGTCATCGGACCCTTTAATCCATAAAGGATTCATT
*
30645 TACTCACGATGACACTTAGTCATCGAACCCTTTAATCCATAAAGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCCTTTAATCCATAAAGGATTCATT
* *
30697 TACTCACGATGACACTTAGTCATCGGACCCCTTTAATCCGTAAAGGATTCGTT
1 TACTCACGATGACACTTAGTCATCGGA-CCCTTTAATCCATAAAGGATTCATT
* * * *
30750 TACTCACGATGACATTTAGTCATCGGACCCTTTACTCCGTAAAGGATTCGTT
1 TACTCACGATGACACTTAGTCATCGGACCCTTTAATCCATAAAGGATTCATT
30802 TACTCACGATGACACTTAGTCATCGGACCCTTT
1 TACTCACGATGACACTTAGTCATCGGACCCTTT
30835 CGTTTATAGC
Statistics
Matches: 216, Mismatches: 19, Indels: 13
0.87 0.08 0.05
Matches are distributed among these distances:
50 1 0.00
51 32 0.15
52 110 0.51
53 73 0.34
ACGTcount: A:0.28, C:0.25, G:0.15, T:0.32
Consensus pattern (52 bp):
TACTCACGATGACACTTAGTCATCGGACCCTTTAATCCATAAAGGATTCATT
Found at i:30771 original size:105 final size:104
Alignment explanation
Indices: 30541--30831 Score: 365
Period size: 105 Copynumber: 2.8 Consensus size: 104
30531 TTTAATTTAA
* ** * *
30541 TACTCATGATGACATACAGTCATCGGACCTCTTGT-TCCATATAGGAATTCATATACTCACGATG
1 TACTCACGATGACATTTAGTCATCGGACC-CTT-TATCCATAAAGG-ATTCATTTACTCACGATG
* * *
30605 ACA-TTGAGTCATCGGA--CCTTTAATCTATCATGAATTCATT
63 ACACTT-AGTCATCGGACCCCTTTAATCCATAAAGAATTCATT
* *
30645 TACTCACGATGACACTTAGTCATCGAACCCTTTAATCCATAAAGGATTCATTTACTCACGATGAC
1 TACTCACGATGACATTTAGTCATCGGACCCTTT-ATCCATAAAGGATTCATTTACTCACGATGAC
* * *
30710 ACTTAGTCATCGGACCCCTTTAATCCGTAAAGGATTCGTT
65 ACTTAGTCATCGGACCCCTTTAATCCATAAAGAATTCATT
* *
30750 TACTCACGATGACATTTAGTCATCGGACCCTTTACTCCGTAAAGGATTCGTTTACTCACGATGAC
1 TACTCACGATGACATTTAGTCATCGGACCCTTTA-TCCATAAAGGATTCATTTACTCACGATGAC
30815 ACTTAGTCATCGGACCC
65 ACTTAGTCATCGGACCC
30832 TTTCGTTTAT
Statistics
Matches: 164, Mismatches: 17, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
102 1 0.01
103 33 0.20
104 36 0.22
105 94 0.57
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.31
Consensus pattern (104 bp):
TACTCACGATGACATTTAGTCATCGGACCCTTTATCCATAAAGGATTCATTTACTCACGATGACA
CTTAGTCATCGGACCCCTTTAATCCATAAAGAATTCATT
Found at i:33429 original size:23 final size:23
Alignment explanation
Indices: 33398--33448 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
33388 TGTTCATGTT
* *
33398 TGTTTGTTTAATATTTA-TGAACA
1 TGTTCGTTTAA-ATTAATTGAACA
*
33421 TGTTCGTTTAACTTAATTGAACA
1 TGTTCGTTTAAATTAATTGAACA
33444 TGTTC
1 TGTTC
33449 ACGAATATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 3 0.12
23 21 0.88
ACGTcount: A:0.27, C:0.10, G:0.14, T:0.49
Consensus pattern (23 bp):
TGTTCGTTTAAATTAATTGAACA
Found at i:33494 original size:24 final size:23
Alignment explanation
Indices: 33433--33502 Score: 95
Period size: 23 Copynumber: 3.0 Consensus size: 23
33423 TTCGTTTAAC
*
33433 TTAATTGAACATGTTCACGAATA
1 TTAATTGAACATGTTCACGAACA
** *
33456 TTAAACGAACATGTTCATGAACA
1 TTAATTGAACATGTTCACGAACA
33479 TATAATTGAACATGTTCACGAACA
1 T-TAATTGAACATGTTCACGAACA
33503 ATGTTAATGA
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
23 20 0.51
24 19 0.49
ACGTcount: A:0.41, C:0.16, G:0.13, T:0.30
Consensus pattern (23 bp):
TTAATTGAACATGTTCACGAACA
Found at i:33610 original size:12 final size:12
Alignment explanation
Indices: 33593--33640 Score: 53
Period size: 12 Copynumber: 4.0 Consensus size: 12
33583 ATCATTAATA
33593 AATAAACGAG-T
1 AATAAACGAGCT
33604 CAATAAACGAGCT
1 -AATAAACGAGCT
*
33617 AATAAACAAGCT
1 AATAAACGAGCT
**
33629 TTTAAACGAGCT
1 AATAAACGAGCT
33641 TGCTCGTGAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
12 30 0.97
13 1 0.03
ACGTcount: A:0.48, C:0.17, G:0.15, T:0.21
Consensus pattern (12 bp):
AATAAACGAGCT
Found at i:34424 original size:28 final size:28
Alignment explanation
Indices: 34392--34448 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
34382 ATTGAATAAA
34392 TGTGTAAGGTTAATGGTTAATTTGTTAT
1 TGTGTAAGGTTAATGGTTAATTTGTTAT
34420 TGTGTAAGGTTAATGGTTAATTTGTTAT
1 TGTGTAAGGTTAATGGTTAATTTGTTAT
34448 T
1 T
34449 ATATTATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.51
Consensus pattern (28 bp):
TGTGTAAGGTTAATGGTTAATTTGTTAT
Found at i:35641 original size:15 final size:15
Alignment explanation
Indices: 35608--35647 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
35598 ACTGTTTATA
35608 TAAATATTT-ATATT
1 TAAATATTTAATATT
35622 TAAATATTTAATGA-T
1 TAAATATTTAAT-ATT
35637 TAAATATTTAA
1 TAAATATTTAA
35648 AATATAGTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
14 9 0.38
15 14 0.58
16 1 0.04
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (15 bp):
TAAATATTTAATATT
Found at i:38147 original size:30 final size:30
Alignment explanation
Indices: 38113--38442 Score: 355
Period size: 30 Copynumber: 10.9 Consensus size: 30
38103 TATTTTTAAA
* *
38113 AAAAATTATATTTTGATCCCTAAACTTTTC
1 AAAAATTATATTTTGACCCCTTAACTTTTC
*
38143 AAAAATTAAATTTTGA-CCCTTAAACTTTTC
1 AAAAATTATATTTTGACCCCTT-AACTTTTC
* * * *
38173 AAAAATTATAGTTTAACCCCTAAACTTTTG
1 AAAAATTATATTTTGACCCCTTAACTTTTC
* * *
38203 AAAAATTATATTTT-AACACTTAAACTTTTT
1 AAAAATTATATTTTGACCCCTT-AACTTTTC
* *
38233 ATAAATTATATTTTAACCCC-TAGACTTTTC
1 AAAAATTATATTTTGACCCCTTA-ACTTTTC
*
38263 AAAAAAATATATATTTTGACCCCTTAACTTTTT
1 --AAAAAT-TATATTTTGACCCCTTAACTTTTC
* * *
38296 AGAAATTATATTTTGGCCCCTTAACTTTTG
1 AAAAATTATATTTTGACCCCTTAACTTTTC
*
38326 AAAAATTATGTTTTGACCCCTTAACTTTTC
1 AAAAATTATATTTTGACCCCTTAACTTTTC
* *
38356 AAAAAAATATATTTTAACCCCTTAACTTTTC
1 -AAAAATTATATTTTGACCCCTTAACTTTTC
* * * *
38387 -AAAATTATATTTTAACTCTTTAACTTTTT
1 AAAAATTATATTTTGACCCCTTAACTTTTC
38416 AAAAATTATATTTTGA-CCCTTAACTTT
1 AAAAATTATATTTTGACCCCTTAACTTT
38443 GACCCCCCTC
Statistics
Matches: 253, Mismatches: 36, Indels: 23
0.81 0.12 0.07
Matches are distributed among these distances:
29 43 0.17
30 145 0.57
31 39 0.15
32 5 0.02
33 19 0.08
34 2 0.01
ACGTcount: A:0.37, C:0.16, G:0.04, T:0.43
Consensus pattern (30 bp):
AAAAATTATATTTTGACCCCTTAACTTTTC
Found at i:45819 original size:98 final size:98
Alignment explanation
Indices: 45636--46135 Score: 571
Period size: 98 Copynumber: 5.1 Consensus size: 98
45626 ATGAAGATAT
* * *
45636 GAAGGGAAATATTTAAGCCGCAACGGCGAATCCAGTATCACGAAAATACAAAGGGAAAGGTTTAA
1 GAAGGGAAAGATTTAAGCCGCAACGACGAATCCAGTACCACGAAAATACAAAGGGAAAGGTTTAA
* * * *
45701 GTCGCAATGGCA-AACATTGTACCTCCGAAGCAT
66 GTCGCAACGG-AGAACCTTGTACCTCAGAAGCAC
* * *
45734 GAAGGGAATGATTTAAGCCGTAACGACGAATACAGTACCACGAAAATACAAAGGGAAAGGTTTAA
1 GAAGGGAAAGATTTAAGCCGCAACGACGAATCCAGTACCACGAAAATACAAAGGGAAAGGTTTAA
* * *
45799 GTCGTAATGAAGAACCTTGTACCTCAGAAGCAC
66 GTCGCAACGGAGAACCTTGTACCTCAGAAGCAC
* * * * *
45832 GAAGGGAAAGATTTAAGCCACAACGGCAAATCCAGTACCACGAAGAA-ATAAAGGGATAAAGTTT
1 GAAGGGAAAGATTTAAGCCGCAACGACGAATCCAGTACCACGAA-AATACAAAGGGA-AAGGTTT
* * *
45896 AAGTCGCAACGGCGAAGCTTGTACCTCTGAAGCAC
64 AAGTCGCAACGGAGAACCTTGTACCTCAGAAGCAC
* * * * *
45931 GAAGGGAAAGATTTAAGCCGCAAC-AGTGAATCCAATACCACTAAGATATAGAA-GGAAAGGTTT
1 GAAGGGAAAGATTTAAGCCGCAACGA-CGAATCCAGTACCACGAAAATACA-AAGGGAAAGGTTT
* * * *
45994 AAGTCGCAACGGTGAACCTTGTACCTTAAAAGTAC
64 AAGTCGCAACGGAGAACCTTGTACCTCAGAAGCAC
* * * *
46029 GAAGGGAAAGATTTAAGCCGCAAC-AGCGAATCTAGCACCGCGAAGATACAAAGGGAAAGGTTTA
1 GAAGGGAAAGATTTAAGCCGCAACGA-CGAATCCAGTACCACGAAAATACAAAGGGAAAGGTTTA
* *
46093 AGTCGCAACGGTA-AACCTTGTACCTCAGAAACAT
65 AGTCGCAACGG-AGAACCTTGTACCTCAGAAGCAC
46127 GAAGGGAAA
1 GAAGGGAAA
46136 TATAAGCCAC
Statistics
Matches: 342, Mismatches: 52, Indels: 16
0.83 0.13 0.04
Matches are distributed among these distances:
97 3 0.01
98 257 0.75
99 80 0.23
100 2 0.01
ACGTcount: A:0.40, C:0.19, G:0.24, T:0.18
Consensus pattern (98 bp):
GAAGGGAAAGATTTAAGCCGCAACGACGAATCCAGTACCACGAAAATACAAAGGGAAAGGTTTAA
GTCGCAACGGAGAACCTTGTACCTCAGAAGCAC
Found at i:46083 original size:49 final size:49
Alignment explanation
Indices: 45622--46103 Score: 273
Period size: 49 Copynumber: 9.8 Consensus size: 49
45612 TAGGTCTCAT
* ** * *
45622 TACCATGAAGATATGAAGGGAAATATTTAAGCCGCAACGGCGAATCCAG
1 TACCACGAAGATACAAAGGGAAAGATTTAAGCCGCAACGGCGAATCTAG
* * * * * * *
45671 TATCACGAAAATACAAAGGGAAAGGTTTAAGTCGCAATGGC-AAACATTG
1 TACCACGAAGATACAAAGGGAAAGATTTAAGCCGCAACGGCGAATC-TAG
* * * * *
45720 TACCTCCGAAGCAT--GAAGGGAATGATTTAAGCCGTAACGACGAATAC-AG
1 TACC-ACGAAG-ATACAAAGGGAAAGATTTAAGCCGCAACGGCGAAT-CTAG
* * * * * ** * *
45769 TACCACGAAAATACAAAGGGAAAGGTTTAAGTCGTAATGAAGAACCTTG
1 TACCACGAAGATACAAAGGGAAAGATTTAAGCCGCAACGGCGAATCTAG
* * * * * *
45818 TACCTCAGAAG-CACGAAGGGAAAGATTTAAGCCACAACGGCAAATCCAG
1 TACCAC-GAAGATACAAAGGGAAAGATTTAAGCCGCAACGGCGAATCTAG
* * * * *
45867 TACCACGAAGAAATAAAGGGATAA-AGTTTAAGTCGCAACGGCGAAGCTTG
1 TACCACGAAGATACAAAGGGA-AAGA-TTTAAGCCGCAACGGCGAATCTAG
* * * * * * *
45917 TACCTCTGAAG-CACGAAGGGAAAGATTTAAGCCGCAACAGTGAATCCAA
1 TACCAC-GAAGATACAAAGGGAAAGATTTAAGCCGCAACGGCGAATCTAG
* * * * * * *
45966 TACCACTAAGATATAGAA-GGAAAGGTTTAAGTCGCAACGGTGAACCTTG
1 TACCACGAAGATACA-AAGGGAAAGATTTAAGCCGCAACGGCGAATCTAG
* * *
46015 TACCTTA-AAAG-TACGAAGGGAAAGATTTAAGCCGCAACAGCGAATCTAG
1 TACC--ACGAAGATACAAAGGGAAAGATTTAAGCCGCAACGGCGAATCTAG
* * * *
46064 CACCGCGAAGATACAAAGGGAAAGGTTTAAGTCGCAACGG
1 TACCACGAAGATACAAAGGGAAAGATTTAAGCCGCAACGG
46104 TAAACCTTGT
Statistics
Matches: 314, Mismatches: 98, Indels: 42
0.69 0.22 0.09
Matches are distributed among these distances:
47 2 0.01
48 20 0.06
49 237 0.75
50 47 0.15
51 8 0.03
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.18
Consensus pattern (49 bp):
TACCACGAAGATACAAAGGGAAAGATTTAAGCCGCAACGGCGAATCTAG
Found at i:48230 original size:30 final size:30
Alignment explanation
Indices: 48194--48402 Score: 307
Period size: 30 Copynumber: 7.0 Consensus size: 30
48184 CCCTATTTTG
* *
48194 TTCAAAAATTATATTTTGACTCTTAAACTT
1 TTCAAAAATTATATTTTGACCCTTTAACTT
* * *
48224 TTCAAAAATTATATTTTAATGCC-TAAACTT
1 TTCAAAAATTATATTTTGA-CCCTTTAACTT
48254 TTCAAAAATTATATTTTGACCCTTTAACTT
1 TTCAAAAATTATATTTTGACCCTTTAACTT
* *
48284 TTCAAAAATTATATTTTAACCCCTTAACTT
1 TTCAAAAATTATATTTTGACCCTTTAACTT
*
48314 TTCAAAAATTATATTTTAACCCTTTAACTT
1 TTCAAAAATTATATTTTGACCCTTTAACTT
48344 TTCAAAAATTATATTTTGACCCTTTAACTT
1 TTCAAAAATTATATTTTGACCCTTTAACTT
*
48374 TTC-AAAATTATGTTTTGACCC-TTAACTT
1 TTCAAAAATTATATTTTGACCCTTTAACTT
48402 T
1 T
48403 AACCCCCTCT
Statistics
Matches: 166, Mismatches: 11, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
28 8 0.05
29 19 0.11
30 138 0.83
31 1 0.01
ACGTcount: A:0.35, C:0.16, G:0.03, T:0.46
Consensus pattern (30 bp):
TTCAAAAATTATATTTTGACCCTTTAACTT
Found at i:50447 original size:101 final size:101
Alignment explanation
Indices: 50272--50474 Score: 370
Period size: 101 Copynumber: 2.0 Consensus size: 101
50262 CACCAGGTTG
*
50272 TATGTCAGAAGGCATGGCCAAACAATTAGGTAATTTTATTGGGATTTTCTTGGATTATGATGCCG
1 TATGTCAGAAGGCATGGCCAAACAATTAGGTAATTTTATTGGGATTTTCTTGGACTATGATGCCG
50337 CAATTGTTACAAAAGGTGTGAAGAAATTCATGCGCA
66 CAATTGTTACAAAAGGTGTGAAGAAATTCATGCGCA
*
50373 TATGTCAGAAGGCATGGCCAGACAATTAGGTAATTTTATTGGGATTTTCTTGGACTATGATGCCG
1 TATGTCAGAAGGCATGGCCAAACAATTAGGTAATTTTATTGGGATTTTCTTGGACTATGATGCCG
* *
50438 CAATTGTTACAGAAGGTTTGAAGAAATTCATGCGCA
66 CAATTGTTACAAAAGGTGTGAAGAAATTCATGCGCA
50474 T
1 T
50475 CAAAGTCAGA
Statistics
Matches: 98, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
101 98 1.00
ACGTcount: A:0.31, C:0.13, G:0.24, T:0.32
Consensus pattern (101 bp):
TATGTCAGAAGGCATGGCCAAACAATTAGGTAATTTTATTGGGATTTTCTTGGACTATGATGCCG
CAATTGTTACAAAAGGTGTGAAGAAATTCATGCGCA
Found at i:51215 original size:85 final size:85
Alignment explanation
Indices: 51045--51215 Score: 281
Period size: 85 Copynumber: 2.0 Consensus size: 85
51035 TTCTTTAAGA
* * *
51045 AAGGCATAGAAGGAAGTTAGTAGTCACCTTAATTTCCTTGTAGAGCTACTTTGAAGGTTTAAAGT
1 AAGGCATAAAAGGAAGTTAGTAGTCACCTTAA-TTCCTTGTAGAGCTACTTTAAAGGGTTAAAGT
*
51110 GTGTAGGGTTTGAATTAGAAT
65 GTGTAGGGATTGAATTAGAAT
51131 AAGGCATAAAAGGAAGTTAGTAGTCACCTTAA-TCCTTGTAGAGCTCACTTTAAAGGGTTAAAGT
1 AAGGCATAAAAGGAAGTTAGTAGTCACCTTAATTCCTTGTAGAGCT-ACTTTAAAGGGTTAAAGT
51195 GTGTAGGGATTGAATTAGAAT
65 GTGTAGGGATTGAATTAGAAT
51216 TTTAGGGTTT
Statistics
Matches: 80, Mismatches: 4, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
84 13 0.16
85 36 0.45
86 31 0.39
ACGTcount: A:0.33, C:0.10, G:0.25, T:0.32
Consensus pattern (85 bp):
AAGGCATAAAAGGAAGTTAGTAGTCACCTTAATTCCTTGTAGAGCTACTTTAAAGGGTTAAAGTG
TGTAGGGATTGAATTAGAAT
Found at i:52472 original size:23 final size:23
Alignment explanation
Indices: 52367--52474 Score: 110
Period size: 23 Copynumber: 4.7 Consensus size: 23
52357 TTTGGCACAA
* *
52367 TGTGTGCTTATTG-TTCAGCACTG
1 TGTGTGCTTACTGTTTTA-CACTG
* * * *
52390 TGCGCGCTTACTGATTTACACTA
1 TGTGTGCTTACTGTTTTACACTG
* *
52413 TATGTGCTTACTATTTTACACTG
1 TGTGTGCTTACTGTTTTACACTG
* *
52436 TGTGTTCTTACTGTTTTGCACTG
1 TGTGTGCTTACTGTTTTACACTG
52459 TGTGTGCTTACTGTTT
1 TGTGTGCTTACTGTTT
52475 CCCCAGTACT
Statistics
Matches: 68, Mismatches: 16, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
23 65 0.96
24 3 0.04
ACGTcount: A:0.15, C:0.19, G:0.20, T:0.46
Consensus pattern (23 bp):
TGTGTGCTTACTGTTTTACACTG
Found at i:53453 original size:53 final size:53
Alignment explanation
Indices: 53373--53484 Score: 215
Period size: 53 Copynumber: 2.1 Consensus size: 53
53363 CATAATGAAA
53373 AAGAGAGGATGTGTGAACTTGAAGAAATACCTTGTGAAGCTTTAGAGGGTAAG
1 AAGAGAGGATGTGTGAACTTGAAGAAATACCTTGTGAAGCTTTAGAGGGTAAG
*
53426 AAGAGAGGATGTGTGAACTTGAAGAAATACCTTGTGAAGCTTTAGATGGTAAG
1 AAGAGAGGATGTGTGAACTTGAAGAAATACCTTGTGAAGCTTTAGAGGGTAAG
53479 AAGAGA
1 AAGAGA
53485 CAAAATAAAT
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 58 1.00
ACGTcount: A:0.38, C:0.07, G:0.31, T:0.24
Consensus pattern (53 bp):
AAGAGAGGATGTGTGAACTTGAAGAAATACCTTGTGAAGCTTTAGAGGGTAAG
Found at i:55565 original size:37 final size:37
Alignment explanation
Indices: 55508--55585 Score: 129
Period size: 37 Copynumber: 2.1 Consensus size: 37
55498 GCTAAGTTCG
55508 TATTAATTCATTTTACGTGTAGAGGGTTTTTCTAAAT
1 TATTAATTCATTTTACGTGTAGAGGGTTTTTCTAAAT
* * *
55545 TATTTATTCATTTTATGTGTAGAGGGTTTTTCTAGAT
1 TATTAATTCATTTTACGTGTAGAGGGTTTTTCTAAAT
55582 TATT
1 TATT
55586 GAATCTTGCA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.24, C:0.06, G:0.17, T:0.53
Consensus pattern (37 bp):
TATTAATTCATTTTACGTGTAGAGGGTTTTTCTAAAT
Found at i:58418 original size:31 final size:31
Alignment explanation
Indices: 58382--58486 Score: 124
Period size: 31 Copynumber: 3.4 Consensus size: 31
58372 TAATCACATT
* *
58382 AATATTAATTTAATAAAATATTATCTAGATA
1 AATATTAAATTAATAAAATAATATCTAGATA
** * *
58413 AATATTAAATT-A-AATTTAATATCTCATATT
1 AATATTAAATTAATAAAATAATATCT-AGATA
*
58443 AATATTAAATTAATAAAATACTATCTAGATA
1 AATATTAAATTAATAAAATAATATCTAGATA
58474 AATATTAAATTAA
1 AATATTAAATTAA
58487 ATTTAATATT
Statistics
Matches: 60, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
29 9 0.15
30 15 0.25
31 27 0.45
32 9 0.15
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.41
Consensus pattern (31 bp):
AATATTAAATTAATAAAATAATATCTAGATA
Found at i:58456 original size:61 final size:61
Alignment explanation
Indices: 58379--58495 Score: 216
Period size: 61 Copynumber: 1.9 Consensus size: 61
58369 AATTAATCAC
* *
58379 ATTAATATTAATTTAATAAAATATTATCTAGATAAATATTAAATTAAATTTAATATCTCAT
1 ATTAATATTAAATTAATAAAATACTATCTAGATAAATATTAAATTAAATTTAATATCTCAT
58440 ATTAATATTAAATTAATAAAATACTATCTAGATAAATATTAAATTAAATTTAATAT
1 ATTAATATTAAATTAATAAAATACTATCTAGATAAATATTAAATTAAATTTAATAT
58496 TAAATTCATC
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
61 54 1.00
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (61 bp):
ATTAATATTAAATTAATAAAATACTATCTAGATAAATATTAAATTAAATTTAATATCTCAT
Found at i:62146 original size:17 final size:17
Alignment explanation
Indices: 62124--62156 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
62114 GAAACCAAAA
62124 AGTAAAATA-AAAACATT
1 AGTAAAA-ACAAAACATT
62141 AGTAAAAACAAAACAT
1 AGTAAAAACAAAACAT
62157 AATTTGTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 1 0.07
17 14 0.93
ACGTcount: A:0.67, C:0.09, G:0.06, T:0.18
Consensus pattern (17 bp):
AGTAAAAACAAAACATT
Found at i:72071 original size:118 final size:114
Alignment explanation
Indices: 71857--72076 Score: 318
Period size: 113 Copynumber: 1.9 Consensus size: 114
71847 AAGGTCCTTG
*
71857 CATTTTCTTGTTTCAATAAATTACTTAGCTTTTCTTTTCTATCTCTTCATTGATTATCTCTATCG
1 CATTTTCTTGTTTCAATAAATTACCTAGCTTTTCTTTTCTATCTCTTCATTGATTATCTCTATCG
* **
71922 AGAATTTTAATCCTTATCATTTTGGTATCAAAGCAAATCTTTTCTATCT
66 AGAAATCCAATCCTTATCATTTTGGTATCAAAGCAAATCTTTTCTATCT
**
71971 CATTTTCTT-TTTCAATAAATTACCTAGCTTTTCTTTTCTATCTCTTTGTT-ATTATCTCTATTT
1 CATTTTCTTGTTTCAATAAATTACCTAGCTTTTCTTTTCTATCTCTTCATTGATTATCTCTA--T
72034 CTATTGAGAAATCCAATCCTTATCATTTTGGTATCAAAGCAAA
64 C----GAGAAATCCAATCCTTATCATTTTGGTATCAAAGCAAA
72077 ATGACCATCA
Statistics
Matches: 94, Mismatches: 6, Indels: 8
0.87 0.06 0.07
Matches are distributed among these distances:
112 10 0.11
113 38 0.40
114 11 0.12
118 35 0.37
ACGTcount: A:0.25, C:0.19, G:0.07, T:0.49
Consensus pattern (114 bp):
CATTTTCTTGTTTCAATAAATTACCTAGCTTTTCTTTTCTATCTCTTCATTGATTATCTCTATCG
AGAAATCCAATCCTTATCATTTTGGTATCAAAGCAAATCTTTTCTATCT
Found at i:74521 original size:160 final size:157
Alignment explanation
Indices: 74226--74540 Score: 497
Period size: 160 Copynumber: 2.0 Consensus size: 157
74216 GGTCTACTAT
74226 TGGATATTGTGTTTTTGGTGGAAATTTAGTATCATGAATAAGAAGTAGAATGTGGTATTTCTATG
1 TGGATATTGTGTTTTTGGTGGAAATTTAGTATCATGAATAAGAAGTAGAATGTGGTATTTCTATG
* * ** *
74291 GAGTTTGAAACCAGAGATAAGGCTATGGCACAATTTATGTGTGAAGTCATGTGGATATAACATCT
66 GAGGTTGAAACCAGAGATAA-GCTATGGCACAATGTACATGCGAAGTCATGTGGATATAACATCT
*
74356 GTTAATTGAAATTGGATTGAAGCATACA
130 GTTAATTGAAATTGGATTAAAGCATACA
* *
74384 TGGATATTGTGTTTTTGGTGGAAATTTAGTATCATGAATGAGTGAGAAGTAGAATTTTGTATTTC
1 TGGATATTGTGTTTTTGGTGGAAATTTAGTATCATGAAT-A---AGAAGTAGAATGTGGTATTTC
*
74449 TATGGAGGTTGAAACCAGAGATAA-CTATGGCACAATGTGCATGCGAAGTCATGTGGATATAACA
62 TATGGAGGTTGAAACCAGAGATAAGCTATGGCACAATGTACATGCGAAGTCATGTGGATATAACA
74513 TCTGTTAATTGAAATTGGATTAAAGCAT
127 TCTGTTAATTGAAATTGGATTAAAGCAT
74541 TCATCACTAG
Statistics
Matches: 144, Mismatches: 9, Indels: 6
0.91 0.06 0.04
Matches are distributed among these distances:
158 39 0.27
159 1 0.01
160 62 0.43
162 42 0.29
ACGTcount: A:0.33, C:0.08, G:0.25, T:0.35
Consensus pattern (157 bp):
TGGATATTGTGTTTTTGGTGGAAATTTAGTATCATGAATAAGAAGTAGAATGTGGTATTTCTATG
GAGGTTGAAACCAGAGATAAGCTATGGCACAATGTACATGCGAAGTCATGTGGATATAACATCTG
TTAATTGAAATTGGATTAAAGCATACA
Found at i:80306 original size:33 final size:33
Alignment explanation
Indices: 80268--80333 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
80258 TATAACATAT
80268 TGTGAATGAGTATTATGATTAATAACACATTTA
1 TGTGAATGAGTATTATGATTAATAACACATTTA
80301 TGTGAATGAGTATTATGATTAATAACACATTTA
1 TGTGAATGAGTATTATGATTAATAACACATTTA
80334 CGTGGTTAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.39, C:0.06, G:0.15, T:0.39
Consensus pattern (33 bp):
TGTGAATGAGTATTATGATTAATAACACATTTA
Found at i:87406 original size:20 final size:22
Alignment explanation
Indices: 87371--87417 Score: 62
Period size: 20 Copynumber: 2.2 Consensus size: 22
87361 AAATTGTACT
*
87371 TTTTACAAAAATAAAAATATAA
1 TTTTACAAAAATAAAAATAAAA
*
87393 TTTTA-AAAAA-AAAATTAAAA
1 TTTTACAAAAATAAAAATAAAA
87413 TTTTA
1 TTTTA
87418 TCATTTTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 13 0.57
21 5 0.22
22 5 0.22
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (22 bp):
TTTTACAAAAATAAAAATAAAA
Found at i:89006 original size:17 final size:17
Alignment explanation
Indices: 88984--89054 Score: 70
Period size: 17 Copynumber: 4.1 Consensus size: 17
88974 CAAACTCCCT
88984 TTAAATTTATTTTAAAA
1 TTAAATTTATTTTAAAA
* *
89001 TTAAATTTGTTTAAAAA
1 TTAAATTTATTTTAAAA
* **
89018 TTTAAATTTAATTTAAGT
1 -TTAAATTTATTTTAAAA
* *
89036 TTAAAATTATTTTCAAA
1 TTAAATTTATTTTAAAA
89053 TT
1 TT
89055 TAAAATTATC
Statistics
Matches: 41, Mismatches: 12, Indels: 2
0.75 0.22 0.04
Matches are distributed among these distances:
17 29 0.71
18 12 0.29
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.52
Consensus pattern (17 bp):
TTAAATTTATTTTAAAA
Found at i:89024 original size:18 final size:18
Alignment explanation
Indices: 88983--89063 Score: 69
Period size: 17 Copynumber: 4.6 Consensus size: 18
88973 CCAAACTCCC
*
88983 TTTAAATTTATTTTAAAA
1 TTTAAATTTATTTAAAAA
*
89001 -TTAAATTTGTTTAAAAA
1 TTTAAATTTATTTAAAAA
*
89018 TTTAAATTTAATTT--AAG
1 TTTAAATTT-ATTTAAAAA
* **
89035 TTTAAAATTATTTTCAAA
1 TTTAAATTTATTTAAAAA
*
89053 TTTAAAATTAT
1 TTTAAATTTAT
89064 CATAAATTTA
Statistics
Matches: 53, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
16 4 0.08
17 25 0.47
18 21 0.40
19 3 0.06
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.52
Consensus pattern (18 bp):
TTTAAATTTATTTAAAAA
Found at i:89040 original size:35 final size:35
Alignment explanation
Indices: 88983--89058 Score: 89
Period size: 35 Copynumber: 2.2 Consensus size: 35
88973 CCAAACTCCC
* * *
88983 TTTAAATTTATTTTAAAATTAAATTTGTTTAAAAA
1 TTTAAATTTAATTTAAAATTAAAATTATTTAAAAA
** **
89018 TTTAAATTTAATTTAAGTTTAAAATTATTTTCAAA
1 TTTAAATTTAATTTAAAATTAAAATTATTTAAAAA
89053 TTTAAA
1 TTTAAA
89059 ATTATCATAA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (35 bp):
TTTAAATTTAATTTAAAATTAAAATTATTTAAAAA
Found at i:89072 original size:17 final size:18
Alignment explanation
Indices: 89035--89077 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
89025 TTAATTTAAG
**
89035 TTTAAAATTATTTTCAAA
1 TTTAAAATTATCATCAAA
89053 TTTAAAATTATCAT-AAA
1 TTTAAAATTATCATCAAA
89070 TTTAAAAT
1 TTTAAAAT
89078 AAATAAAGCC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 11 0.48
18 12 0.52
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.47
Consensus pattern (18 bp):
TTTAAAATTATCATCAAA
Done.