Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010961.1 Kokia drynarioides strain JFW-HI SEQ_125929, 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: 121531
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Warning! 96 characters in sequence are not A, C, G, or T
Found at i:7121 original size:29 final size:28
Alignment explanation
Indices: 7089--7170 Score: 83
Period size: 29 Copynumber: 2.8 Consensus size: 28
7079 GTTTAGGTTT
* *
7089 TCACAATATAGATTTCAGAATCTAAAGTC
1 TCAC-ATATAGTTTTCACAATCTAAAGTC
* * * *
7118 TCACATAGAAGTTTTCATAATCTAATGTT
1 TCACATA-TAGTTTTCACAATCTAAAGTC
7147 TCACATAATAGTTTTCACAATCTA
1 TCACAT-ATAGTTTTCACAATCTA
7171 TAAACAATAT
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
28 3 0.07
29 40 0.91
30 1 0.02
ACGTcount: A:0.38, C:0.17, G:0.09, T:0.37
Consensus pattern (28 bp):
TCACATATAGTTTTCACAATCTAAAGTC
Found at i:20040 original size:21 final size:21
Alignment explanation
Indices: 19982--20040 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
19972 TCTGTTCTAC
19982 CGATAGAAGTTTGAGTTGTAT
1 CGATAGAAGTTTGAGTTGTAT
* ****
20003 CGGTAGAACCCAGAGTTGTAT
1 CGATAGAAGTTTGAGTTGTAT
*
20024 CGATAGAAGTTTTAGTT
1 CGATAGAAGTTTGAGTT
20041 TTACCAATAG
Statistics
Matches: 27, Mismatches: 11, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.29, C:0.10, G:0.27, T:0.34
Consensus pattern (21 bp):
CGATAGAAGTTTGAGTTGTAT
Found at i:20840 original size:13 final size:12
Alignment explanation
Indices: 20822--20863 Score: 50
Period size: 11 Copynumber: 3.5 Consensus size: 12
20812 CACTCTAAAA
20822 TTTTTCTTTCTTC
1 TTTTTCTTT-TTC
20835 TTTTTCTTTTTC
1 TTTTTCTTTTTC
* *
20847 -TTCTCTATTTC
1 TTTTTCTTTTTC
20858 TTTTTC
1 TTTTTC
20864 GTATTCTCTA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
11 9 0.36
12 7 0.28
13 9 0.36
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTTTCTTTTTC
Found at i:20843 original size:6 final size:6
Alignment explanation
Indices: 20822--20863 Score: 50
Period size: 6 Copynumber: 7.0 Consensus size: 6
20812 CACTCTAAAA
* *
20822 TTTTTC TTTCTTC TTTTTC TTTTTC -TTCTC TATTTC TTTTTC
1 TTTTTC TTT-TTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC
20864 GTATTCTCTA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
5 4 0.13
6 20 0.67
7 6 0.20
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.76
Consensus pattern (6 bp):
TTTTTC
Found at i:20846 original size:19 final size:17
Alignment explanation
Indices: 20828--20863 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
20818 AAAATTTTTC
20828 TTTCTTCT-T-TTTCTT
1 TTTCTTCTCTATTTCTT
20843 TTTCTTCTCTATTTCTT
1 TTTCTTCTCTATTTCTT
20860 TTTC
1 TTTC
20864 GTATTCTCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 8 0.42
16 1 0.05
17 10 0.53
ACGTcount: A:0.03, C:0.22, G:0.00, T:0.75
Consensus pattern (17 bp):
TTTCTTCTCTATTTCTT
Found at i:21438 original size:401 final size:404
Alignment explanation
Indices: 20746--21555 Score: 1430
Period size: 401 Copynumber: 2.0 Consensus size: 404
20736 CATTGAACTC
20746 AATGACAACTCGGTTTTCGATACCTTAAGAGCATTGTTCTTCCACAACCTCATGCTACTGCTGAA
1 AATGACAACTCGGTTTTCGATACCTTAAGAGCATTGTTCTTCCACAACCTCATGCTACTGCTGAA
20811 CCACTCTAAAATTTTTCTTTCTTCTTTTTCTTTTTCTTCTCTATTTCTTTTTCGTATTCTCTACT
66 CCACTCTAAAATTTTTC-TTCTTC--TTTCTTTTTCTTCTCTATTTCTTTTTCGTATTCTCTACT
*
20876 TCCTTTTCTTTTATTGCCCATCTAAGGTTTTAAATTAGGATCGTTTACACAATGGGATGCCATGT
128 TCCTTTTCTTTTATTGCCCATCTAAGGTTTTAAATTAAGATCGTTTACACAATGGGATGCCATGT
*
20941 CACTTTTCCATTACGTCTGTAACGAAAAATAGTTAAAAGAACTAATTTGTTATTTTTCAAAAATT
193 CACTTTTCCATTACGTCTGTAACGAAAAATAGTTAAAAGAACTAATTTGTTATTTTTCAAAAAGT
*
21006 AAATGATTGAATTGAACTCAAAATAATTGTTATTTTATCAATTGCATATTAAAATTGAGTTCAGT
258 AAATGATTGAATTGAACTCAAAATAATTGTTATTTTATCAATTGCATATCAAAATTGAGTTCAGT
21071 GACTGTTGGTATAATTTATCTTAAATAAATAATGAACAACTTTTAATTGAGGATGTGAATTAAAG
323 GACTGTTGGTATAATTTATCTTAAATAAATAATGAACAACTTTTAATTGAGGATGTGAATTAAAG
*
21136 AGTAGAGGTACATATAT
388 AGGAGAGGTACATATAT
* * *
21153 AATGAACAACTCGTTTTTCGATACCTTAAGAGCATTGTTCTTTCACAACCTCATGCTACTGTTGA
1 AATG-ACAACTCGGTTTTCGATACCTTAAGAGCATTGTTCTTCCACAACCTCATGCTACTGCTGA
21218 ACCACTCTAAAATTTTTC-T-TTC-TTCTTTTTCTTCTCTATTTCTTTTTCGTATTCTCTACTTC
65 ACCACTCTAAAATTTTTCTTCTTCTTTCTTTTTCTTCTCTATTTCTTTTTCGTATTCTCTACTTC
*
21280 CTTTTTTTTTATTGCCCATCTAAGGTTTTAAATTAAGATCGTTTACACAATGGGATG-CATGTCA
130 CTTTTCTTTTATTGCCCATCTAAGGTTTTAAATTAAGATCGTTTACACAATGGGATGCCATGTCA
* * * *
21344 CTTTTTCATTACGTCTGTAATGAAAAATAGTTAAAAGAAGTTATTTGTTATTTTTCAAAAAGTAA
195 CTTTTCCATTACGTCTGTAACGAAAAATAGTTAAAAGAACTAATTTGTTATTTTTCAAAAAGTAA
21409 ATGATTGAATTGAACTCAAAATAATTGTTATTTTATCAATTGCATATCAAAATTGAGTTCAGTGA
260 ATGATTGAATTGAACTCAAAATAATTGTTATTTTATCAATTGCATATCAAAATTGAGTTCAGTGA
* *
21474 TTGTTGGTGTAATTTATCTTAAATAAATAATGAACAACTTTTAATTGAGGATGTGAATTAAAGAG
325 CTGTTGGTATAATTTATCTTAAATAAATAATGAACAACTTTTAATTGAGGATGTGAATTAAAGAG
21539 GAGAGGTACATATAT
390 GAGAGGTACATATAT
21554 AA
1 AA
21556 GGAAAATAAA
Statistics
Matches: 388, Mismatches: 14, Indels: 8
0.95 0.03 0.02
Matches are distributed among these distances:
401 210 0.54
402 95 0.24
405 3 0.01
406 1 0.00
407 4 0.01
408 75 0.19
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.41
Consensus pattern (404 bp):
AATGACAACTCGGTTTTCGATACCTTAAGAGCATTGTTCTTCCACAACCTCATGCTACTGCTGAA
CCACTCTAAAATTTTTCTTCTTCTTTCTTTTTCTTCTCTATTTCTTTTTCGTATTCTCTACTTCC
TTTTCTTTTATTGCCCATCTAAGGTTTTAAATTAAGATCGTTTACACAATGGGATGCCATGTCAC
TTTTCCATTACGTCTGTAACGAAAAATAGTTAAAAGAACTAATTTGTTATTTTTCAAAAAGTAAA
TGATTGAATTGAACTCAAAATAATTGTTATTTTATCAATTGCATATCAAAATTGAGTTCAGTGAC
TGTTGGTATAATTTATCTTAAATAAATAATGAACAACTTTTAATTGAGGATGTGAATTAAAGAGG
AGAGGTACATATAT
Found at i:28963 original size:23 final size:23
Alignment explanation
Indices: 28920--28963 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
28910 GAAATTAAAT
**
28920 TATAATTTTTATGATAATAAAAA
1 TATAATTTTTAAAATAATAAAAA
*
28943 TATAATTTTTAAAATATTAAA
1 TATAATTTTTAAAATAATAAA
28964 TCAAAATTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (23 bp):
TATAATTTTTAAAATAATAAAAA
Found at i:30346 original size:45 final size:45
Alignment explanation
Indices: 30297--30383 Score: 165
Period size: 45 Copynumber: 1.9 Consensus size: 45
30287 AAATGAAAAT
*
30297 AAAGAGGAGAGAAAGAAATAGTGTCAAATGGTGGTTTTGGTCATG
1 AAAGAGGAAAGAAAGAAATAGTGTCAAATGGTGGTTTTGGTCATG
30342 AAAGAGGAAAGAAAGAAATAGTGTCAAATGGTGGTTTTGGTC
1 AAAGAGGAAAGAAAGAAATAGTGTCAAATGGTGGTTTTGGTC
30384 CTTTTATTAT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.39, C:0.05, G:0.32, T:0.24
Consensus pattern (45 bp):
AAAGAGGAAAGAAAGAAATAGTGTCAAATGGTGGTTTTGGTCATG
Found at i:32592 original size:9 final size:9
Alignment explanation
Indices: 32578--32630 Score: 50
Period size: 9 Copynumber: 6.8 Consensus size: 9
32568 TATTTAAAAA
32578 AATAATTTT
1 AATAATTTT
32587 AATAATTTT
1 AATAATTTT
32596 -AT-ATTTT
1 AATAATTTT
32603 AA-AA----
1 AATAATTTT
32607 AATAATTTT
1 AATAATTTT
32616 AATAATTTT
1 AATAATTTT
32625 AA-AATT
1 AATAATT
32631 ATTTGCTGAC
Statistics
Matches: 37, Mismatches: 0, Indels: 15
0.71 0.00 0.29
Matches are distributed among these distances:
4 2 0.05
5 2 0.05
7 5 0.14
8 8 0.22
9 20 0.54
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (9 bp):
AATAATTTT
Found at i:32594 original size:22 final size:22
Alignment explanation
Indices: 32535--32587 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
32525 AAAATTATTT
*
32535 AATAATTTTATTATTTCAAAAT
1 AATAATTTTATTATTTCAAAAA
32557 AATAATTTTATTATTT-AAAAA
1 AATAATTTTATTATTTCAAAAA
32578 AATAATTTTA
1 AATAATTTTA
32588 ATAATTTTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 14 0.47
22 16 0.53
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (22 bp):
AATAATTTTATTATTTCAAAAA
Found at i:32601 original size:29 final size:30
Alignment explanation
Indices: 32556--32625 Score: 124
Period size: 29 Copynumber: 2.4 Consensus size: 30
32546 TATTTCAAAA
32556 TAATAATTTTATTATTTAAAAAAATAATTT
1 TAATAATTTTATTATTTAAAAAAATAATTT
*
32586 TAATAATTTTA-TATTTTAAAAAATAATTT
1 TAATAATTTTATTATTTAAAAAAATAATTT
32615 TAATAATTTTA
1 TAATAATTTTA
32626 AAATTATTTG
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
29 28 0.72
30 11 0.28
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (30 bp):
TAATAATTTTATTATTTAAAAAAATAATTT
Found at i:32612 original size:20 final size:22
Alignment explanation
Indices: 32587--32628 Score: 70
Period size: 20 Copynumber: 2.0 Consensus size: 22
32577 AAATAATTTT
32587 AATAATTTT-AT-ATTTTAAAA
1 AATAATTTTAATAATTTTAAAA
32607 AATAATTTTAATAATTTTAAAA
1 AATAATTTTAATAATTTTAAAA
32629 TTATTTGCTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 9 0.45
21 2 0.10
22 9 0.45
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
AATAATTTTAATAATTTTAAAA
Found at i:32629 original size:20 final size:20
Alignment explanation
Indices: 32578--32634 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
32568 TATTTAAAAA
32578 AATAATTTT--AATAATTTT
1 AATAATTTTAAAATAATTTT
32596 -AT-ATTTTAAAAAATAATTTT
1 AATAATTTT--AAAATAATTTT
*
32616 AATAATTTTAAAATTATTT
1 AATAATTTTAAAATAATTT
32635 GCTGACGACA
Statistics
Matches: 32, Mismatches: 1, Indels: 10
0.74 0.02 0.23
Matches are distributed among these distances:
16 5 0.16
17 2 0.06
20 18 0.56
21 2 0.06
22 5 0.16
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
AATAATTTTAAAATAATTTT
Found at i:33186 original size:87 final size:88
Alignment explanation
Indices: 33087--33361 Score: 236
Period size: 91 Copynumber: 3.1 Consensus size: 88
33077 TTAAGAGTGT
* * *
33087 AAAAAACTCTCAAACATTT-AAAAAAAAACAGTTAAG-CTG-TTTTTTTTTTTGCCCTCAGTTGA
1 AAAAAACCCTCAAACATTTCAAAAAAAAACA-TTAAGCCTGTTTTTTTTTTTTGCACTCAATTGA
* *
33149 GTATTTAAACTTTCATAATGCATC
65 GTACTTAAACTTTCAAAATGCATC
* **
33173 AAAAATACCCTCAAACTTTTCAAAAAAAGCCATTAAGCTCCTGTTTTTTTTTTTTGCACTCAATT
1 AAAAA-ACCCTCAAACATTTCAAAAAAAAACATTAAG--CCTGTTTTTTTTTTTTGCACTCAATT
* *
33238 GAGTACTTGAACTTTCAAAATGCATT
63 GAGTACTTAAACTTTCAAAATGCATC
* * * * * * *
33264 AAAAAGCCCCTTAAAC-GTTAAAAAATAATAATAATTAAGCTCTAGCTTTTTTTTTTTACACTCA
1 AAAAA-ACCCTCAAACATTTCAAAAA-AA-AA-CATTAAGC-CT-GTTTTTTTTTTTTGCACTCA
* * *
33328 ATTG-GATACTTGAACTGTCAAAATGTATC
60 ATTGAG-TACTTAAACTTTCAAAATGCATC
33357 AAAAA
1 AAAAA
33362 GATCCTTTGA
Statistics
Matches: 154, Mismatches: 23, Indels: 17
0.79 0.12 0.09
Matches are distributed among these distances:
86 5 0.03
87 17 0.11
88 9 0.06
90 10 0.06
91 57 0.37
92 3 0.02
93 53 0.34
ACGTcount: A:0.38, C:0.17, G:0.09, T:0.36
Consensus pattern (88 bp):
AAAAAACCCTCAAACATTTCAAAAAAAAACATTAAGCCTGTTTTTTTTTTTTGCACTCAATTGAG
TACTTAAACTTTCAAAATGCATC
Found at i:33260 original size:91 final size:93
Alignment explanation
Indices: 33126--33363 Score: 259
Period size: 91 Copynumber: 2.6 Consensus size: 93
33116 AGTTAAGCTG
* * * * * * *
33126 TTTTTTTTTTTGCCCTCAGTTGAGTATTTAAACTTTCATAATGCATCAAAAATACCCTCAAACTT
1 TTTTTTTTTTTGCACTCAATTGAGTACTTGAACTTTCAAAATGCATCAAAAAGACCCTCAAACGT
** * * *
33191 TTCAAAA-AA-AGCCATTAAGCTCCT-GT
66 TAAAAAATAATAACAATTAAGCT-CTAGC
* * *
33217 TTTTTTTTTTTGCACTCAATTGAGTACTTGAACTTTCAAAATGCATTAAAAAGCCCCTTAAACGT
1 TTTTTTTTTTTGCACTCAATTGAGTACTTGAACTTTCAAAATGCATCAAAAAGACCCTCAAACGT
*
33282 TAAAAAATAATAATAATTAAGCTCTAGC
66 TAAAAAATAATAACAATTAAGCTCTAGC
* * *
33310 TTTTTTTTTTTACACTCAATTG-GATACTTGAACTGTCAAAATGTATCAAAAAGA
1 TTTTTTTTTTTGCACTCAATTGAG-TACTTGAACTTTCAAAATGCATCAAAAAGA
33364 TCCTTTGACC
Statistics
Matches: 122, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
91 60 0.49
92 5 0.04
93 57 0.47
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.38
Consensus pattern (93 bp):
TTTTTTTTTTTGCACTCAATTGAGTACTTGAACTTTCAAAATGCATCAAAAAGACCCTCAAACGT
TAAAAAATAATAACAATTAAGCTCTAGC
Found at i:33551 original size:29 final size:29
Alignment explanation
Indices: 33468--33586 Score: 91
Period size: 29 Copynumber: 4.1 Consensus size: 29
33458 ACATGTGGAA
* * *
33468 AAAAAATATAAAAAAAATAAAAA-TCAAT
1 AAAAAATATAAAAATATTAAAAATTTAAT
** * *
33496 AAAAGTTATAAACATTATT-AAATTTTAAT
1 AAAAAATATAAA-AATATTAAAAATTTAAT
*
33525 AAAAAATATAAAAATATTAAAAATTTATT
1 AAAAAATATAAAAATATTAAAAATTTAAT
* * * *
33554 AAAAATTAGAATAATATTATAAAAATT-AT
1 AAAAAATATAAAAATATTA-AAAATTTAAT
33583 AAAA
1 AAAA
33587 TTTTATAAAA
Statistics
Matches: 70, Mismatches: 17, Indels: 7
0.74 0.18 0.07
Matches are distributed among these distances:
28 18 0.26
29 46 0.66
30 6 0.09
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.31
Consensus pattern (29 bp):
AAAAAATATAAAAATATTAAAAATTTAAT
Found at i:33576 original size:20 final size:19
Alignment explanation
Indices: 33527--33598 Score: 71
Period size: 19 Copynumber: 3.8 Consensus size: 19
33517 ATTTTAATAA
33527 AAAATA-TA-AAAATATTA-
1 AAAATATTATAAAA-ATTAG
33544 AAAAT-TTATTAAAAATTAG
1 AAAATATTA-TAAAAATTAG
*
33563 AATAATATTATAAAAATTAT
1 AA-AATATTATAAAAATTAG
*
33583 AAAATTTTATAAAAAT
1 AAAATATTATAAAAAT
33599 CATAAAAAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
17 7 0.15
18 4 0.09
19 19 0.40
20 14 0.30
21 3 0.06
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.36
Consensus pattern (19 bp):
AAAATATTATAAAAATTAG
Found at i:33594 original size:10 final size:9
Alignment explanation
Indices: 33468--33606 Score: 82
Period size: 9 Copynumber: 14.6 Consensus size: 9
33458 ACATGTGGAA
*
33468 AAAAAATAT
1 AAAAATTAT
**
33477 AAAAAAAAT
1 AAAAATTAT
*
33486 AAAAATCAAT
1 AAAAAT-TAT
*
33496 AAAAGTTAT
1 AAAAATTAT
*
33505 AAACATTATT
1 AAAAATTA-T
**
33515 AAATTTTAAT
1 AAAAATT-AT
*
33525 AAAAAATAT
1 AAAAATTAT
33534 AAAAA-TATT
1 AAAAATTA-T
33543 AAAAATTTATT
1 AAAAA-TTA-T
*
33554 AAAAATTAG
1 AAAAATTAT
33563 AATAATATTAT
1 AA-AA-ATTAT
33574 AAAAATTAT
1 AAAAATTAT
*
33583 AAAATTTTAT
1 AAAA-ATTAT
*
33593 AAAAATCAT
1 AAAAATTAT
33602 AAAAA
1 AAAAA
33607 AATTATAACA
Statistics
Matches: 105, Mismatches: 16, Indels: 18
0.76 0.12 0.13
Matches are distributed among these distances:
8 2 0.02
9 53 0.50
10 34 0.32
11 16 0.15
ACGTcount: A:0.65, C:0.02, G:0.01, T:0.32
Consensus pattern (9 bp):
AAAAATTAT
Found at i:33612 original size:20 final size:20
Alignment explanation
Indices: 33515--33614 Score: 78
Period size: 20 Copynumber: 5.0 Consensus size: 20
33505 AAACATTATT
* *
33515 AAATTTTAATAAAAAATATAA
1 AAATTATAA-AAAAATTATAA
* *
33536 AAA-TATTAAAAATTTATTAA
1 AAATTATAAAAAAATTA-TAA
* * *
33556 AAATTAGAATAATATTATAA
1 AAATTATAAAAAAATTATAA
**
33576 AAATTAT-AAAATTTTATAA
1 AAATTATAAAAAAATTATAA
*
33595 AAATCATAAAAAAATTATAA
1 AAATTATAAAAAAATTATAA
33615 CATACATCAA
Statistics
Matches: 61, Mismatches: 15, Indels: 7
0.73 0.18 0.08
Matches are distributed among these distances:
19 22 0.36
20 28 0.46
21 11 0.18
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.35
Consensus pattern (20 bp):
AAATTATAAAAAAATTATAA
Found at i:33845 original size:10 final size:9
Alignment explanation
Indices: 33789--33995 Score: 81
Period size: 9 Copynumber: 22.2 Consensus size: 9
33779 TTTTGATACG
33789 ATAATTTTT
1 ATAATTTTT
33798 ATAATTTTTTT
1 ATAA--TTTTT
*
33809 ATGAA-TTCT
1 AT-AATTTTT
*
33818 ATATTTCTTT
1 ATAATT-TTT
*
33828 ATATTTTTTT
1 ATA-ATTTTT
33838 ATAATTTTCT
1 ATAATTTT-T
*
33848 -TACGA-CTTT
1 ATA--ATTTTT
*
33857 ATAAAGTTTT
1 AT-AATTTTT
33867 ATAATTTTTTT
1 ATAA--TTTTT
* *
33878 CTATATTTCT
1 ATA-ATTTTT
33888 ATATAT-TTT
1 ATA-ATTTTT
33897 ATAATTTTT
1 ATAATTTTT
*
33906 ATGATTTTT
1 ATAATTTTT
*
33915 ATAAAATTTT
1 AT-AATTTTT
*
33925 ACAATTTTT
1 ATAATTTTT
33934 ATAAATTTTT
1 AT-AATTTTT
**
33944 ACGATTTTT
1 ATAATTTTT
33953 AT-ATTTTT
1 ATAATTTTT
33961 AT-ATATTTT
1 ATAAT-TTTT
*
33970 A-AAATTTT
1 ATAATTTTT
*
33978 A-AA-TTTA
1 ATAATTTTT
33985 ATAATTTTT
1 ATAATTTTT
33994 AT
1 AT
33996 TGATATTTAT
Statistics
Matches: 153, Mismatches: 23, Indels: 44
0.70 0.10 0.20
Matches are distributed among these distances:
7 4 0.03
8 22 0.14
9 63 0.41
10 43 0.28
11 18 0.12
12 3 0.02
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.61
Consensus pattern (9 bp):
ATAATTTTT
Found at i:33914 original size:18 final size:18
Alignment explanation
Indices: 33893--33961 Score: 86
Period size: 19 Copynumber: 3.8 Consensus size: 18
33883 TTTCTATATA
*
33893 TTTTATAATTTTTATGAT
1 TTTTATAATTTTTACGAT
* *
33911 TTTTATAAAATTTTACAAT
1 TTTTAT-AATTTTTACGAT
33930 TTTTATAAATTTTTACGAT
1 TTTTAT-AATTTTTACGAT
33949 TTTTAT-ATTTTTA
1 TTTTATAATTTTTA
33962 TATATTTTAA
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
17 7 0.16
18 6 0.13
19 32 0.71
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (18 bp):
TTTTATAATTTTTACGAT
Found at i:33976 original size:18 final size:18
Alignment explanation
Indices: 33882--33977 Score: 65
Period size: 19 Copynumber: 5.3 Consensus size: 18
33872 TTTTTTCTAT
* *
33882 ATTTCTATATATTTTATA
1 ATTTTTATATATTTTAAA
33900 ATTTTTATGAT-TTTTATAA
1 ATTTTTAT-ATATTTTA-AA
* *
33919 AATTTTACA-ATTTTTATAA
1 ATTTTTATATA-TTTTA-AA
* *
33938 ATTTTTACGAT-TTTT-AT
1 ATTTTTA-TATATTTTAAA
33955 ATTTTTATATATTTTAAA
1 ATTTTTATATATTTTAAA
33973 ATTTT
1 ATTTT
33978 AAATTTAATA
Statistics
Matches: 61, Mismatches: 9, Indels: 16
0.71 0.10 0.19
Matches are distributed among these distances:
16 2 0.03
17 12 0.20
18 19 0.31
19 27 0.44
20 1 0.02
ACGTcount: A:0.33, C:0.03, G:0.02, T:0.61
Consensus pattern (18 bp):
ATTTTTATATATTTTAAA
Found at i:34473 original size:20 final size:20
Alignment explanation
Indices: 34448--34487 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
34438 TTAAAAAATT
34448 AATTAAATT-ATTTTTATTAA
1 AATTAAATTAATTTTT-TTAA
*
34468 AATTAATTTAATTTTTTTAA
1 AATTAAATTAATTTTTTTAA
34488 CGAAACCGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
AATTAAATTAATTTTTTTAA
Found at i:34474 original size:24 final size:23
Alignment explanation
Indices: 34442--34486 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
34432 TAGAGATTAA
34442 AAAATTAATTAAATTATTTTTATT
1 AAAATTAATTAAATT-TTTTTATT
*
34466 AAAATTAATTTAATTTTTTTA
1 AAAATTAATTAAATTTTTTTA
34487 ACGAAACCGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
AAAATTAATTAAATTTTTTTATT
Found at i:35925 original size:30 final size:30
Alignment explanation
Indices: 35900--36106 Score: 261
Period size: 30 Copynumber: 6.9 Consensus size: 30
35890 CGATTTTGGT
* *
35900 GAAGTTCAAGGGTTAAAATGTGATTTTTGA
1 GAAGTTTAAGGGTTAAAATGTAATTTTTGA
* ** * *
35930 GAAATTCGAGGGTTAAAATATGATTTTTGA
1 GAAGTTTAAGGGTTAAAATGTAATTTTTGA
*
35960 GAAGTTTGAGGGTTAAAATGTAATTTTTGA
1 GAAGTTTAAGGGTTAAAATGTAATTTTTGA
*
35990 GAAGTTTAAGGGTTAAAATGTAATTTTTTA
1 GAAGTTTAAGGGTTAAAATGTAATTTTTGA
* ** *
36020 AAAGTTTGGGGGTTAAAATGTAACTTTTGA
1 GAAGTTTAAGGGTTAAAATGTAATTTTTGA
* * *
36050 GAAGTTTATGGGTTAAAATATAATTTTTAA
1 GAAGTTTAAGGGTTAAAATGTAATTTTTGA
*
36080 GAAGTTTAAGGGTTAAAATGTGATTTT
1 GAAGTTTAAGGGTTAAAATGTAATTTT
36107 AAGAAAGTTC
Statistics
Matches: 154, Mismatches: 23, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 154 1.00
ACGTcount: A:0.35, C:0.01, G:0.24, T:0.40
Consensus pattern (30 bp):
GAAGTTTAAGGGTTAAAATGTAATTTTTGA
Found at i:36114 original size:90 final size:91
Alignment explanation
Indices: 35900--36121 Score: 308
Period size: 90 Copynumber: 2.5 Consensus size: 91
35890 CGATTTTGGT
* * * * *
35900 GAAGTTCAAGGGTTAAAATGTGATTTTTGAGAAA-TTCGAGGGTTAAAATATGATTTTTGAGAAG
1 GAAGTTTAAGGGTTAAAATGTGATTTTTAAGAAAGTTCGGGGGTTAAAATATAACTTTTGAGAAG
* *
35964 TTTGAGGGTTAAAATGTAATTTTTGA
66 TTTGAGGGTTAAAATATAATTTTTAA
* * * *
35990 GAAGTTTAAGGGTTAAAATGTAATTTTTTA-AAAGTTTGGGGGTTAAAATGTAACTTTTGAGAAG
1 GAAGTTTAAGGGTTAAAATGTGATTTTTAAGAAAGTTCGGGGGTTAAAATATAACTTTTGAGAAG
36054 TTT-ATGGGTTAAAATATAATTTTTAA
66 TTTGA-GGGTTAAAATATAATTTTTAA
36080 GAAGTTTAAGGGTTAAAATGTGA-TTTTAAGAAAGTTCGGGGG
1 GAAGTTTAAGGGTTAAAATGTGATTTTTAAGAAAGTTCGGGGG
36122 CCTTTCGAAC
Statistics
Matches: 116, Mismatches: 13, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
89 9 0.08
90 107 0.92
ACGTcount: A:0.35, C:0.02, G:0.25, T:0.38
Consensus pattern (91 bp):
GAAGTTTAAGGGTTAAAATGTGATTTTTAAGAAAGTTCGGGGGTTAAAATATAACTTTTGAGAAG
TTTGAGGGTTAAAATATAATTTTTAA
Found at i:36977 original size:15 final size:16
Alignment explanation
Indices: 36949--36987 Score: 62
Period size: 15 Copynumber: 2.4 Consensus size: 16
36939 TTTATTTATT
36949 TTTATTTAATTTATGTA
1 TTTA-TTAATTTATGTA
36966 TTTATTAA-TTATGTA
1 TTTATTAATTTATGTA
36981 TTTATTA
1 TTTATTA
36988 TACTTTGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 14 0.64
16 4 0.18
17 4 0.18
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (16 bp):
TTTATTAATTTATGTA
Found at i:37531 original size:26 final size:25
Alignment explanation
Indices: 37492--37544 Score: 88
Period size: 26 Copynumber: 2.1 Consensus size: 25
37482 AGATGGGCAA
*
37492 TTGGGTCATGGGTTTGTAATTGGGC
1 TTGGGTAATGGGTTTGTAATTGGGC
37517 TTGGGTAATTGGGTTTGTAATTGGGC
1 TTGGGTAA-TGGGTTTGTAATTGGGC
37543 TT
1 TT
37545 CACAATTTGT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
25 7 0.27
26 19 0.73
ACGTcount: A:0.13, C:0.06, G:0.38, T:0.43
Consensus pattern (25 bp):
TTGGGTAATGGGTTTGTAATTGGGC
Found at i:37538 original size:12 final size:12
Alignment explanation
Indices: 37500--37541 Score: 57
Period size: 12 Copynumber: 3.3 Consensus size: 12
37490 AATTGGGTCA
37500 TGGGTTTGTAAT
1 TGGGTTTGTAAT
*
37512 TGGGCTTGGGTAAT
1 TGGG-TT-TGTAAT
37526 TGGGTTTGTAAT
1 TGGGTTTGTAAT
37538 TGGG
1 TGGG
37542 CTTCACAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
12 13 0.50
13 4 0.15
14 9 0.35
ACGTcount: A:0.14, C:0.02, G:0.40, T:0.43
Consensus pattern (12 bp):
TGGGTTTGTAAT
Found at i:37590 original size:16 final size:17
Alignment explanation
Indices: 37569--37615 Score: 69
Period size: 17 Copynumber: 2.8 Consensus size: 17
37559 GAACATTCTT
*
37569 TTTAAA-TTCAAATAAA
1 TTTAAATTTAAAATAAA
37585 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
*
37602 TTTAAACTTAAAAT
1 TTTAAATTTAAAAT
37616 TGAGTTCAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
16 6 0.21
17 22 0.79
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.40
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:38285 original size:39 final size:39
Alignment explanation
Indices: 38242--38552 Score: 202
Period size: 39 Copynumber: 8.0 Consensus size: 39
38232 CTTGTCGCGG
* *
38242 GGTAAGAGATTGACTGACGGTGATCTGCCCCAAGCTCGA
1 GGTAAGAGATTGACTGATGGTGATCTGCCCCAGGCTCGA
* * * * * * ***
38281 GGTAAAATATCGAAT-A-GTTACAATCTTTTCCAGGCTCGA
1 GGTAAGAGATTGACTGATGGT--GATCTGCCCCAGGCTCGA
* * * *
38320 GGTAAGAGATTGGCTGATTGTGATCTGCCCCAAGCTCGG
1 GGTAAGAGATTGACTGATGGTGATCTGCCCCAGGCTCGA
* * * ** *
38359 GGTAAAAGATTGGACGGCT-GCAATCTGCCCTAGGCTC-A
1 GGTAAGAGATT-GACTGATGGTGATCTGCCCCAGGCTCGA
** * *
38397 GGGTAAGAGATTGGTTGATGGTGATCTGCCCTAGGCTCGG
1 -GGTAAGAGATTGACTGATGGTGATCTGCCCCAGGCTCGA
* * *
38437 GGTAAGAGATTGGCTGATGGTGATTTGCCCTAGGCTCGA
1 GGTAAGAGATTGACTGATGGTGATCTGCCCCAGGCTCGA
* * ** * *
38476 GGTAAAAGATCGGA-TGACT-GCAATCTGTCCCAGGCTCGG
1 GGTAAGAGAT-TGACTGA-TGGTGATCTGCCCCAGGCTCGA
**
38515 GGTAAGAGATTGACTGATGGTGATCTGCCTTAGGCTCG
1 GGTAAGAGATTGACTGATGGTGATCTGCCCCAGGCTCG
38553 GGATAAAAGA
Statistics
Matches: 201, Mismatches: 59, Indels: 24
0.71 0.21 0.08
Matches are distributed among these distances:
37 2 0.01
38 7 0.03
39 184 0.92
40 7 0.03
41 1 0.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (39 bp):
GGTAAGAGATTGACTGATGGTGATCTGCCCCAGGCTCGA
Found at i:38383 original size:78 final size:78
Alignment explanation
Indices: 38241--38449 Score: 233
Period size: 78 Copynumber: 2.7 Consensus size: 78
38231 CCTTGTCGCG
* * * * * * * *
38241 GGGTAAGAGATTGACTGACGGTGATCTGCCCCAAGCTCGAGGTAAAATATCGAATAGTTACAATC
1 GGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCGGGGTAAAAGATTGGACAGCTACAATC
**
38306 TTTTCC-AGGCTC-
66 -TGCCCTAGGCTCA
* * *
38318 GAGGTAAGAGATTGGCTGATTGTGATCTGCCCCAAGCTCGGGGTAAAAGATTGGACGGCTGCAAT
1 G-GGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCGGGGTAAAAGATTGGACAGCTACAAT
38383 CTGCCCTAGGCTCA
65 CTGCCCTAGGCTCA
* * * *
38397 GGGTAAGAGATTGGTTGATGGTGATCTGCCCTAGGCTCGGGGTAAGAGATTGG
1 GGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCGGGGTAAAAGATTGG
38450 CTGATGGTGA
Statistics
Matches: 111, Mismatches: 18, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
77 4 0.04
78 106 0.95
79 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.32, T:0.25
Consensus pattern (78 bp):
GGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCGGGGTAAAAGATTGGACAGCTACAATC
TGCCCTAGGCTCA
Found at i:38434 original size:117 final size:118
Alignment explanation
Indices: 38312--38760 Score: 471
Period size: 117 Copynumber: 3.8 Consensus size: 118
38302 AATCTTTTCC
* ** * * * *
38312 AGGCTCGAGGTAAGAGATTGGCTGATTGTGATCTGCCCCAAGCTCGGGGTAAAAGATTGGACGGC
1 AGGCTCGGGGTAAGAGATTGGCTGACGGTGATCTGCCCCAGGCTCGGGGTAAAAGATCGGATGAC
* *
38377 TGCAATCTGCCCT-AGGCTCAGGGTAAGAGATTGGTTGATGGTGATCTGCCCT
66 TGCAATCTGCCCTCAAGCTCAGGGTAAGAGATTGGATGATGGTGATCTGCCCT
* * * *
38429 AGGCTCGGGGTAAGAGATTGGCTGATGGTGATTTGCCCTAGGCTCGAGGTAAAAGATCGGATGAC
1 AGGCTCGGGGTAAGAGATTGGCTGACGGTGATCTGCCCCAGGCTCGGGGTAAAAGATCGGATGAC
* * * *
38494 TGCAATCTGTCC-CAGGCTCGGGGTAAGAGATT-GACTGATGGTGATCTGCCTT
66 TGCAATCTGCCCTCAAGCTCAGGGTAAGAGATTGGA-TGATGGTGATCTGCCCT
* * * * * * ** *
38546 AGGCTCGGGATAAAAGATCGGATGGCCGCAATCTTCCCCAGGCTCGGGGTAAAAGATCGGATGA-
1 AGGCTCGGGGTAAGAGATTGGCTGACGGTGATCTGCCCCAGGCTCGGGGTAAAAGATCGGATGAC
* * * * * *
38610 TCGCAATCT-ACGTCAAGCTCAGGGTAAAAGATCGGAT-AGTTGTAATCTGCCCT
66 T-GCAATCTGCCCTCAAGCTCAGGGTAAGAGATTGGATGA-TGGTGATCTGCCCT
* * * * *
38663 AGGCTTGGGGTAAGAGATTGGCTGACGGTGATTTGCCCTAGGCTCAGGGTAAAAGATCGGATGAT
1 AGGCTCGGGGTAAGAGATTGGCTGACGGTGATCTGCCCCAGGCTCGGGGTAAAAGATCGGATGAC
* *
38728 TACAATCTG-CCTCAAGCTCGGGGTAAGAGATTG
66 TGCAATCTGCCCTCAAGCTCAGGGTAAGAGATTG
38761 AAATCTTCAA
Statistics
Matches: 271, Mismatches: 53, Indels: 16
0.80 0.16 0.05
Matches are distributed among these distances:
116 4 0.01
117 264 0.97
118 3 0.01
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.24
Consensus pattern (118 bp):
AGGCTCGGGGTAAGAGATTGGCTGACGGTGATCTGCCCCAGGCTCGGGGTAAAAGATCGGATGAC
TGCAATCTGCCCTCAAGCTCAGGGTAAGAGATTGGATGATGGTGATCTGCCCT
Found at i:38466 original size:78 final size:77
Alignment explanation
Indices: 38312--38760 Score: 386
Period size: 78 Copynumber: 5.8 Consensus size: 77
38302 AATCTTTTCC
* * * ** * * * * *
38312 AGGCTCGAGGTAAGAGATTGGCTGATTGTGATCTGCCCCAAGCTCGGGGTAAAAGATTGGACGGC
1 AGGCTCG-GGTAAAAGATCGGATGATTGCAATCTGCCCTAGGCTCGGGGTAAGAGATTGG-CTGA
**
38377 T-GCAATCTGCCCT
64 TGGTGATCTGCCCT
* * * * **
38390 AGGCTCAGGGTAAGAGATTGGTTGATGGTGATCTGCCCTAGGCTCGGGGTAAGAGATTGGCTGAT
1 AGGCTC-GGGTAAAAGATCGGATGATTGCAATCTGCCCTAGGCTCGGGGTAAGAGATTGGCTGAT
*
38455 GGTGATTTGCCCT
65 GGTGATCTGCCCT
* *
38468 AGGCTCGAGGTAAAAGATCGGATGACTGCAATCTGTCCC-AGGCTCGGGGTAAGAGATTGACTGA
1 AGGCTCG-GGTAAAAGATCGGATGATTGCAATCTG-CCCTAGGCTCGGGGTAAGAGATTGGCTGA
*
38532 TGGTGATCTGCCTT
64 TGGTGATCTGCCCT
*** * * * * *
38546 AGGCTCGGGATAAAAGATCGGATGGCCGCAATCTTCCCCAGGCTCGGGGTAAAAGATCGGATGAT
1 AGGCTCGGG-TAAAAGATCGGATGATTGCAATCTGCCCTAGGCTCGGGGTAAGAGATTGGCTGAT
* ** * *
38611 CGCAATCT-ACGT
65 GGTGATCTGCCCT
* * *
38623 CAAGCTCAGGGTAAAAGATCGGAT-AGTTGTAATCTGCCCTAGGCTTGGGGTAAGAGATTGGCTG
1 -AGGCTC-GGGTAAAAGATCGGATGA-TTGCAATCTGCCCTAGGCTCGGGGTAAGAGATTGGCTG
* *
38687 ACGGTGATTTGCCCT
63 ATGGTGATCTGCCCT
* *
38702 AGGCTCAGGGTAAAAGATCGGATGATTACAATCTG-CCTCAAGCTCGGGGTAAGAGATTG
1 AGGCTC-GGGTAAAAGATCGGATGATTGCAATCTGCCCT-AGGCTCGGGGTAAGAGATTG
38761 AAATCTTCAA
Statistics
Matches: 304, Mismatches: 55, Indels: 24
0.79 0.14 0.06
Matches are distributed among these distances:
77 14 0.05
78 280 0.92
79 10 0.03
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.24
Consensus pattern (77 bp):
AGGCTCGGGTAAAAGATCGGATGATTGCAATCTGCCCTAGGCTCGGGGTAAGAGATTGGCTGATG
GTGATCTGCCCT
Found at i:38674 original size:39 final size:39
Alignment explanation
Indices: 38312--38758 Score: 292
Period size: 39 Copynumber: 11.5 Consensus size: 39
38302 AATCTTTTCC
* * * * * *
38312 AGGCTCGAGGTAAGAGATTGGCTGATTGTGATCTGCCCC
1 AGGCTCGGGGTAAAAGATCGGATGATTGTAATCTGCCCT
* * * ** *
38351 AAGCTCGGGGTAAAAGATTGGACGGCTGCAATCTGCCCT
1 AGGCTCGGGGTAAAAGATCGGATGATTGTAATCTGCCCT
* * * * * *
38390 AGGCTCAGGGTAAGAGATTGGTTGATGGTGATCTGCCCT
1 AGGCTCGGGGTAAAAGATCGGATGATTGTAATCTGCCCT
* * * * * *
38429 AGGCTCGGGGTAAGAGATTGGCTGATGGTGATTTGCCCT
1 AGGCTCGGGGTAAAAGATCGGATGATTGTAATCTGCCCT
* * *
38468 AGGCTCGAGGTAAAAGATCGGATGACTGCAATCTGTCCC-
1 AGGCTCGGGGTAAAAGATCGGATGATTGTAATCTG-CCCT
* * * * *
38507 AGGCTCGGGGTAAGAGAT-TGACTGATGGTGATCTGCCTT
1 AGGCTCGGGGTAAAAGATCGGA-TGATTGTAATCTGCCCT
* *** * * *
38546 AGGCTCGGGATAAAAGATCGGATGGCCGCAATCTTCCCC
1 AGGCTCGGGGTAAAAGATCGGATGATTGTAATCTGCCCT
* * * *
38585 AGGCTCGGGGTAAAAGATCGGATGATCGCAATCT-ACGT
1 AGGCTCGGGGTAAAAGATCGGATGATTGTAATCTGCCCT
* *
38623 CAAGCTCAGGGTAAAAGATCGGAT-AGTTGTAATCTGCCCT
1 -AGGCTCGGGGTAAAAGATCGGATGA-TTGTAATCTGCCCT
* * * * ** * *
38663 AGGCTTGGGGTAAGAGATTGGCTGACGGTGATTTGCCCT
1 AGGCTCGGGGTAAAAGATCGGATGATTGTAATCTGCCCT
* **
38702 AGGCTCAGGGTAAAAGATCGGATGATTACAATCTG-CCT
1 AGGCTCGGGGTAAAAGATCGGATGATTGTAATCTGCCCT
* *
38740 CAAGCTCGGGGTAAGAGAT
1 -AGGCTCGGGGTAAAAGAT
38759 TGAAATCTTC
Statistics
Matches: 312, Mismatches: 87, Indels: 18
0.75 0.21 0.04
Matches are distributed among these distances:
38 9 0.03
39 295 0.95
40 8 0.03
ACGTcount: A:0.25, C:0.19, G:0.32, T:0.24
Consensus pattern (39 bp):
AGGCTCGGGGTAAAAGATCGGATGATTGTAATCTGCCCT
Found at i:39796 original size:41 final size:40
Alignment explanation
Indices: 39751--39829 Score: 95
Period size: 40 Copynumber: 1.9 Consensus size: 40
39741 AACTCAAAAT
* * *
39751 TCCTTCGGTTTCAAGACTCCTTTTATGGGTTGTCATCTCGA
1 TCCTT-GGTTTCAAGACGCCCTTTATGAGTTGTCATCTCGA
** *
39792 TCCTTTTTTTCAAGACGCCCTTTATGAGTTTTCATCTC
1 TCCTTGGTTTCAAGACGCCCTTTATGAGTTGTCATCTC
39830 AATCTCTCTC
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
40 27 0.84
41 5 0.16
ACGTcount: A:0.15, C:0.25, G:0.15, T:0.44
Consensus pattern (40 bp):
TCCTTGGTTTCAAGACGCCCTTTATGAGTTGTCATCTCGA
Found at i:50878 original size:30 final size:30
Alignment explanation
Indices: 50822--50962 Score: 185
Period size: 30 Copynumber: 4.7 Consensus size: 30
50812 GGAGAGCTTG
* * *
50822 GGGTTAAAATGCGA-TTTAGGGAAGTTTGA
1 GGGTTAAAATGTGATTTTTGAGAAGTTTGA
*
50851 GGGTTAAAATGTGATTTTTGAGAAGTTTAA
1 GGGTTAAAATGTGATTTTTGAGAAGTTTGA
* *
50881 GGGTTAAAATGTAATTTTTGAGAAGTTCGA
1 GGGTTAAAATGTGATTTTTGAGAAGTTTGA
* *
50911 GGGTCAAAATGTAATTTTTGAGAAGTTTGA
1 GGGTTAAAATGTGATTTTTGAGAAGTTTGA
* *
50941 GGGTCAAAATGTGACTTTTGAG
1 GGGTTAAAATGTGATTTTTGAG
50963 GTAAAAATGT
Statistics
Matches: 100, Mismatches: 11, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
29 13 0.13
30 87 0.87
ACGTcount: A:0.32, C:0.04, G:0.29, T:0.35
Consensus pattern (30 bp):
GGGTTAAAATGTGATTTTTGAGAAGTTTGA
Found at i:50962 original size:21 final size:21
Alignment explanation
Indices: 50936--50982 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
50926 TTTTGAGAAG
* *
50936 TTTGAGGGTCAAAATGTGACT
1 TTTGAGGGTAAAAATGTAACT
*
50957 TTTGA-GGTAAAAATGTAATT
1 TTTGAGGGTAAAAATGTAACT
50977 TTTGAG
1 TTTGAG
50983 ATGTTTAAGG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
20 17 0.77
21 5 0.23
ACGTcount: A:0.32, C:0.04, G:0.26, T:0.38
Consensus pattern (21 bp):
TTTGAGGGTAAAAATGTAACT
Found at i:51626 original size:10 final size:10
Alignment explanation
Indices: 51599--51633 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
51589 CCGAGCTCTA
*
51599 GTCGCCGTCC
1 GTCGCCATCC
51609 GTCGGCCATCC
1 GTC-GCCATCC
51620 GTCGCCATCC
1 GTCGCCATCC
51630 GTCG
1 GTCG
51634 ACCGTCTGCC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 14 0.61
11 9 0.39
ACGTcount: A:0.06, C:0.46, G:0.29, T:0.20
Consensus pattern (10 bp):
GTCGCCATCC
Found at i:52715 original size:5 final size:5
Alignment explanation
Indices: 52705--52730 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
52695 ATATAATGTG
52705 ATTAA ATTAA ATTAA ATTAA ATTAA A
1 ATTAA ATTAA ATTAA ATTAA ATTAA A
52731 ATGTTATATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
ATTAA
Found at i:55233 original size:81 final size:81
Alignment explanation
Indices: 55098--55260 Score: 326
Period size: 81 Copynumber: 2.0 Consensus size: 81
55088 TTACAATACC
55098 TTTATCGTTTCAGCAAAGATTTAAAGAGAAAGTCCATGATAAAGAATATCATAGGTTTGTTTCTA
1 TTTATCGTTTCAGCAAAGATTTAAAGAGAAAGTCCATGATAAAGAATATCATAGGTTTGTTTCTA
55163 CTTTGAAACAATTGCA
66 CTTTGAAACAATTGCA
55179 TTTATCGTTTCAGCAAAGATTTAAAGAGAAAGTCCATGATAAAGAATATCATAGGTTTGTTTCTA
1 TTTATCGTTTCAGCAAAGATTTAAAGAGAAAGTCCATGATAAAGAATATCATAGGTTTGTTTCTA
55244 CTTTGAAACAATTGCA
66 CTTTGAAACAATTGCA
55260 T
1 T
55261 ATTAATATAC
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
81 82 1.00
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.35
Consensus pattern (81 bp):
TTTATCGTTTCAGCAAAGATTTAAAGAGAAAGTCCATGATAAAGAATATCATAGGTTTGTTTCTA
CTTTGAAACAATTGCA
Found at i:59660 original size:3 final size:3
Alignment explanation
Indices: 59652--59680 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
59642 GCGTAAGGAC
59652 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
59681 TCATGATGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:73834 original size:19 final size:21
Alignment explanation
Indices: 73796--73835 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
73786 GTTGGGGACC
*
73796 TCATTTTATTATTATCACATT
1 TCATTTTATGATTATCACATT
73817 TCATTTT-TGATT-TCACATT
1 TCATTTTATGATTATCACATT
73836 ATTGCTTCGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 7 0.39
20 4 0.22
21 7 0.39
ACGTcount: A:0.25, C:0.15, G:0.03, T:0.57
Consensus pattern (21 bp):
TCATTTTATGATTATCACATT
Found at i:75835 original size:2 final size:2
Alignment explanation
Indices: 75828--75860 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
75818 TTTTATAGCA
75828 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
75861 AAATGACTGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:76473 original size:18 final size:18
Alignment explanation
Indices: 76437--76480 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
76427 AAATACACTA
**
76437 ACAAAT-AAAATGCCGTG
1 ACAAATAAAAATGCAATG
76454 ACAAATAAAAATGCAATG
1 ACAAATAAAAATGCAATG
*
76472 ACAACTAAA
1 ACAAATAAA
76481 TAAAATGCAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 6 0.26
18 17 0.74
ACGTcount: A:0.57, C:0.16, G:0.11, T:0.16
Consensus pattern (18 bp):
ACAAATAAAAATGCAATG
Found at i:83799 original size:47 final size:47
Alignment explanation
Indices: 83744--83849 Score: 196
Period size: 47 Copynumber: 2.3 Consensus size: 47
83734 TATTAATATT
83744 ATTT-GATAATTATTTTCACGATTGAATTCTTTCTTATGCTTGGTTC
1 ATTTGGATAATTATTTTCACGATTGAATTCTTTCTTATGCTTGGTTC
*
83790 ATTTGGATAATTATTTTCACGATTGAATTCTTTCTTATGTTTGGTTC
1 ATTTGGATAATTATTTTCACGATTGAATTCTTTCTTATGCTTGGTTC
83837 ATTTGGATAATTA
1 ATTTGGATAATTA
83850 GAAGCTCATA
Statistics
Matches: 58, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
46 4 0.07
47 54 0.93
ACGTcount: A:0.24, C:0.10, G:0.14, T:0.52
Consensus pattern (47 bp):
ATTTGGATAATTATTTTCACGATTGAATTCTTTCTTATGCTTGGTTC
Found at i:93272 original size:17 final size:17
Alignment explanation
Indices: 93250--93310 Score: 77
Period size: 17 Copynumber: 3.5 Consensus size: 17
93240 TATTAGTAAG
* *
93250 CATTGTCATCGCATTCC
1 CATTGTCATTGCATTTC
*
93267 CATTGTCATTACATTTC
1 CATTGTCATTGCATTTC
*
93284 AATTGTCATTGCATTTC
1 CATTGTCATTGCATTTC
93301 CATTTGTCAT
1 CA-TTGTCAT
93311 GGTATTTTAC
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
17 30 0.81
18 7 0.19
ACGTcount: A:0.21, C:0.25, G:0.10, T:0.44
Consensus pattern (17 bp):
CATTGTCATTGCATTTC
Found at i:96708 original size:18 final size:18
Alignment explanation
Indices: 96685--96726 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
96675 ATAGGTATGC
96685 TCCCTTTCAGATCCAACT
1 TCCCTTTCAGATCCAACT
96703 TCCCTTTCAGATCCAACT
1 TCCCTTTCAGATCCAACT
96721 TCCCTT
1 TCCCTT
96727 AGTTGTACAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.19, C:0.40, G:0.05, T:0.36
Consensus pattern (18 bp):
TCCCTTTCAGATCCAACT
Found at i:98043 original size:33 final size:33
Alignment explanation
Indices: 98006--98072 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
97996 AGTCGATATA
98006 TTGCGTCTTAATATTGTCAGCACAGGAACTAAG
1 TTGCGTCTTAATATTGTCAGCACAGGAACTAAG
98039 TTGCGTCTTAATATTGTCAGCACAGGAACTAAG
1 TTGCGTCTTAATATTGTCAGCACAGGAACTAAG
98072 T
1 T
98073 CTAGAAGCTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.31
Consensus pattern (33 bp):
TTGCGTCTTAATATTGTCAGCACAGGAACTAAG
Found at i:110979 original size:29 final size:25
Alignment explanation
Indices: 110922--110983 Score: 106
Period size: 25 Copynumber: 2.5 Consensus size: 25
110912 GGATGAGTAC
110922 GAATGAATGATTGGAATTACTTCAG
1 GAATGAATGATTGGAATTACTTCAG
*
110947 GAATGAATGATTGGAATTACTTTAG
1 GAATGAATGATTGGAATTACTTCAG
*
110972 TAATGAATGATT
1 GAATGAATGATT
110984 AGTGTTCATG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.37, C:0.05, G:0.23, T:0.35
Consensus pattern (25 bp):
GAATGAATGATTGGAATTACTTCAG
Found at i:111262 original size:6 final size:6
Alignment explanation
Indices: 111232--111281 Score: 59
Period size: 6 Copynumber: 8.5 Consensus size: 6
111222 AGACATTTAA
* *
111232 AAAAAG AAAAA- AAAAAG TAATAAG AAAAAG AAAAAG AGAAAG -AAAAG
1 AAAAAG AAAAAG AAAAAG -AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG
111279 AAA
1 AAA
111282 GAAAATTTTG
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
5 9 0.24
6 23 0.62
7 5 0.14
ACGTcount: A:0.80, C:0.00, G:0.16, T:0.04
Consensus pattern (6 bp):
AAAAAG
Found at i:117934 original size:24 final size:25
Alignment explanation
Indices: 117907--117956 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
117897 AGCACCATAG
117907 AACTAT-GAAAACTATAAATTGTGA
1 AACTATAGAAAACTATAAATTGTGA
* *
117931 AACTATAGGAGACTATAAATTGTGA
1 AACTATAGAAAACTATAAATTGTGA
117956 A
1 A
117957 TAGAAAACTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 6 0.26
25 17 0.74
ACGTcount: A:0.48, C:0.08, G:0.16, T:0.28
Consensus pattern (25 bp):
AACTATAGAAAACTATAAATTGTGA
Found at i:119509 original size:9 final size:9
Alignment explanation
Indices: 119495--119519 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
119485 CCTCATGACA
119495 CTTAAGGAG
1 CTTAAGGAG
119504 CTTAAGGAG
1 CTTAAGGAG
119513 CTTAAGG
1 CTTAAGG
119520 CACAATTACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.32, C:0.12, G:0.32, T:0.24
Consensus pattern (9 bp):
CTTAAGGAG
Found at i:120511 original size:7 final size:7
Alignment explanation
Indices: 120499--120546 Score: 51
Period size: 7 Copynumber: 6.3 Consensus size: 7
120489 GAATATGACC
120499 ATGTGAT
1 ATGTGAT
120506 ATGTGATCCT
1 ATGTGA---T
120516 ATGTGAT
1 ATGTGAT
120523 ATGTGAT
1 ATGTGAT
*
120530 ACGTGATT
1 ATGTGA-T
120538 ATGTGAT
1 ATGTGAT
120545 AT
1 AT
120547 ATGACATTGT
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
7 22 0.63
8 6 0.17
10 7 0.20
ACGTcount: A:0.27, C:0.06, G:0.25, T:0.42
Consensus pattern (7 bp):
ATGTGAT
Found at i:120549 original size:24 final size:23
Alignment explanation
Indices: 120499--120546 Score: 71
Period size: 24 Copynumber: 2.1 Consensus size: 23
120489 GAATATGACC
*
120499 ATGTGATATGTGATCCTATGTGAT
1 ATGTGATACGTGAT-CTATGTGAT
120523 ATGTGATACGTGAT-TATGTGAT
1 ATGTGATACGTGATCTATGTGAT
120545 AT
1 AT
120547 ATGACATTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 10 0.43
24 13 0.57
ACGTcount: A:0.27, C:0.06, G:0.25, T:0.42
Consensus pattern (23 bp):
ATGTGATACGTGATCTATGTGAT
Found at i:120838 original size:5 final size:6
Alignment explanation
Indices: 120811--120839 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
120801 ATCTCAGTCA
120811 AAAATT AAAATT AAAATT AAAA-T AAAATT
1 AAAATT AAAATT AAAATT AAAATT AAAATT
120840 TAATTCCAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.23
6 17 0.77
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (6 bp):
AAAATT
Done.