Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006983.1 Kokia drynarioides strain JFW-HI SEQ_121589, 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: 100753
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:7120 original size:26 final size:25
Alignment explanation
Indices: 7086--7201 Score: 126
Period size: 26 Copynumber: 4.6 Consensus size: 25
7076 TCTTTAGTTA
*
7086 AATATTTAAATATTTGGATTGCTTTT
1 AATAATTAAATATTTGGATTG-TTTT
*
7112 AATAATTAAATATTTGGGTTGTTGTT
1 AATAATTAAATATTTGGATTGTT-TT
* * * * * *
7138 AATAATTAACTAATT-AAATATTTA
1 AATAATTAAATATTTGGATTGTTTT
*
7162 AATATTTAAATATTTGGATTGTTTT
1 AATAATTAAATATTTGGATTGTTTT
7187 AATAATTAAATATTT
1 AATAATTAAATATTT
7202 AATTAAATAT
Statistics
Matches: 71, Mismatches: 17, Indels: 5
0.76 0.18 0.05
Matches are distributed among these distances:
24 13 0.18
25 24 0.34
26 34 0.48
ACGTcount: A:0.39, C:0.02, G:0.09, T:0.50
Consensus pattern (25 bp):
AATAATTAAATATTTGGATTGTTTT
Found at i:7162 original size:8 final size:8
Alignment explanation
Indices: 7151--7176 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
7141 AATTAACTAA
7151 TTAAATAT
1 TTAAATAT
7159 TTAAATAT
1 TTAAATAT
7167 TTAAATAT
1 TTAAATAT
7175 TT
1 TT
7177 GGATTGTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (8 bp):
TTAAATAT
Found at i:7162 original size:16 final size:16
Alignment explanation
Indices: 7138--7267 Score: 59
Period size: 16 Copynumber: 8.2 Consensus size: 16
7128 GGTTGTTGTT
* *
7138 AATAATTAACTAATTA
1 AATAATTAAATATTTA
*
7154 AATATTTAAATATTTA
1 AATAATTAAATATTTA
* * * * *
7170 AATATTTGGATTGTTTT
1 AATAATT-AAATATTTA
7187 AATAATTAAATATTTA
1 AATAATTAAATATTTA
* * *
7203 ATTAA--ATATAATTA
1 AATAATTAAATATTTA
* *
7217 AAAAATTAAATATTTG
1 AATAATTAAATATTTA
* ** *
7233 AGTTGTT-AATAATTA
1 AATAATTAAATATTTA
* *
7248 ACTAATTAAATAATTA
1 AATAATTAAATATTTA
7264 AATA
1 AATA
7268 TTTGAGTTGT
Statistics
Matches: 80, Mismatches: 30, Indels: 8
0.68 0.25 0.07
Matches are distributed among these distances:
14 10 0.12
15 10 0.12
16 49 0.61
17 11 0.14
ACGTcount: A:0.50, C:0.02, G:0.05, T:0.44
Consensus pattern (16 bp):
AATAATTAAATATTTA
Found at i:7162 original size:49 final size:50
Alignment explanation
Indices: 7112--7267 Score: 176
Period size: 50 Copynumber: 3.1 Consensus size: 50
7102 GATTGCTTTT
7112 AATAATTAAATATTTGGGTTGTTGTTAATAATTAACTAATTAAATATTTA
1 AATAATTAAATATTTGGGTTGTTGTTAATAATTAACTAATTAAATATTTA
* * *
7162 AATATTTAAATATTTGGATTGTT-TTAATAATTAAATATTTAATTAAATATAATTA
1 AATAATTAAATATTTGGGTTGTTGTTAATAATT--A-A-CTAATTAAATAT--TTA
* * *
7217 AAAAATTAAATATTT--G-AGTTGTTAATAATTAACTAATTAAATAATTA
1 AATAATTAAATATTTGGGTTGTTGTTAATAATTAACTAATTAAATATTTA
7264 AATA
1 AATA
7268 TTTGAGTTGT
Statistics
Matches: 89, Mismatches: 10, Indels: 17
0.77 0.09 0.15
Matches are distributed among these distances:
47 6 0.07
49 19 0.21
50 22 0.25
51 2 0.02
52 4 0.04
53 20 0.22
55 16 0.18
ACGTcount: A:0.47, C:0.01, G:0.07, T:0.45
Consensus pattern (50 bp):
AATAATTAAATATTTGGGTTGTTGTTAATAATTAACTAATTAAATATTTA
Found at i:7203 original size:8 final size:8
Alignment explanation
Indices: 7187--7267 Score: 51
Period size: 8 Copynumber: 10.5 Consensus size: 8
7177 GGATTGTTTT
7187 AATAATTA
1 AATAATTA
*
7195 AATATTTA
1 AATAATTA
*
7203 ATTAA--A
1 AATAATTA
*
7209 TATAATTA
1 AATAATTA
*
7217 AAAAATTA
1 AATAATTA
* *
7225 AATATTTG
1 AATAATTA
* **
7233 AGTTGTT-
1 AATAATTA
7240 AATAATTA
1 AATAATTA
*
7248 ACTAATTA
1 AATAATTA
7256 AATAATTA
1 AATAATTA
7264 AATA
1 AATA
7268 TTTGAGTTGT
Statistics
Matches: 52, Mismatches: 18, Indels: 6
0.68 0.24 0.08
Matches are distributed among these distances:
6 4 0.08
7 4 0.08
8 44 0.85
ACGTcount: A:0.54, C:0.01, G:0.04, T:0.41
Consensus pattern (8 bp):
AATAATTA
Found at i:7287 original size:26 final size:26
Alignment explanation
Indices: 7256--7319 Score: 110
Period size: 26 Copynumber: 2.5 Consensus size: 26
7246 TAACTAATTA
7256 AATAATTAAATATTTGAGTTGTTTTT
1 AATAATTAAATATTTGAGTTGTTTTT
* *
7282 AGTAATTAAATTTTTGAGTTGTTTTT
1 AATAATTAAATATTTGAGTTGTTTTT
7308 AATAATTAAATA
1 AATAATTAAATA
7320 ATTAAATAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.38, C:0.00, G:0.11, T:0.52
Consensus pattern (26 bp):
AATAATTAAATATTTGAGTTGTTTTT
Found at i:7321 original size:8 final size:8
Alignment explanation
Indices: 7308--7354 Score: 62
Period size: 8 Copynumber: 6.0 Consensus size: 8
7298 AGTTGTTTTT
7308 AATAATTA
1 AATAATTA
7316 AATAATTA
1 AATAATTA
7324 AATAA-TA
1 AATAATTA
*
7331 CAACAATTA
1 -AATAATTA
7340 AATAATTA
1 AATAATTA
7348 AA-AATTA
1 AATAATTA
7355 GAAATGTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
7 7 0.20
8 26 0.74
9 2 0.06
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (8 bp):
AATAATTA
Found at i:7402 original size:34 final size:34
Alignment explanation
Indices: 7335--7402 Score: 93
Period size: 34 Copynumber: 2.0 Consensus size: 34
7325 ATAATACAAC
* *
7335 AATTAAATAATTAAAAATTAGAAATGTTTTTATT
1 AATTAAATAATTAAAAATTACAAATGTTCTTATT
*
7369 AATTAAATAATTAAATATTACAAAT-TTCCTTATT
1 AATTAAATAATTAAAAATTACAAATGTT-CTTATT
7403 TAGATTATGT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
33 2 0.07
34 28 0.93
ACGTcount: A:0.49, C:0.04, G:0.03, T:0.44
Consensus pattern (34 bp):
AATTAAATAATTAAAAATTACAAATGTTCTTATT
Found at i:13341 original size:35 final size:35
Alignment explanation
Indices: 13302--13380 Score: 158
Period size: 35 Copynumber: 2.3 Consensus size: 35
13292 TGGAAGGTAC
13302 GGTACCGAATTATGTAGTTAACCAGTTGGATTCGT
1 GGTACCGAATTATGTAGTTAACCAGTTGGATTCGT
13337 GGTACCGAATTATGTAGTTAACCAGTTGGATTCGT
1 GGTACCGAATTATGTAGTTAACCAGTTGGATTCGT
13372 GGTACCGAA
1 GGTACCGAA
13381 GTGAGAGGGA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 44 1.00
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.32
Consensus pattern (35 bp):
GGTACCGAATTATGTAGTTAACCAGTTGGATTCGT
Found at i:16567 original size:29 final size:27
Alignment explanation
Indices: 16486--16567 Score: 74
Period size: 31 Copynumber: 2.8 Consensus size: 27
16476 CTTGAACCAC
16486 AATCAAAGTTTCATGTGTATAATTGCATAA
1 AATCAAAG-TTCA--TGTATAATTGCATAA
* *
16516 AATTAAAGTTCATGTATCAAATTGCACATTA
1 AATCAAAGTTCATGTAT--AATTG--CATAA
*
16547 AATCAACGTTCATGTATAATT
1 AATCAAAGTTCATGTATAATT
16568 TTGAGATTTA
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
27 5 0.11
29 13 0.30
30 7 0.16
31 19 0.43
ACGTcount: A:0.40, C:0.12, G:0.11, T:0.37
Consensus pattern (27 bp):
AATCAAAGTTCATGTATAATTGCATAA
Found at i:17210 original size:19 final size:18
Alignment explanation
Indices: 17186--17222 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
17176 AAAATAACAA
17186 AAAAATCAATAAAAGTTAT
1 AAAAAT-AATAAAAGTTAT
*
17205 AAAAATTATAAAAGTTAT
1 AAAAATAATAAAAGTTAT
17223 TAAATTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.30
Consensus pattern (18 bp):
AAAAATAATAAAAGTTAT
Found at i:17260 original size:196 final size:203
Alignment explanation
Indices: 17053--17420 Score: 477
Period size: 196 Copynumber: 1.8 Consensus size: 203
17043 GTACTTGAAT
* * * **
17053 TATTAAAATGCATCAAAAAAG-CCTTTTAACTATTAATTTTAACAGTTGACTGTTAAAATTAACT
1 TATTAAAATGCAT-AAAAAAGTCCCTTTAACCATTAATCTTAACAGTTGACCATTAAAATTAACT
* ** * *
17117 -GTCCCTAATTTTTTAAATTAAAGTTATC-CGTGTCACAATCATGGCGTGACATGTGG-CAAAAA
65 AGTCCC-AATTTTTTAAATTAAAGTCATCACGTGTCACAA-CACAGCGGGACAAGTGGACAAAAA
*
17179 -ATAACAAA-AAAA-TCAATAAAAGTTA-T-AAAAATTATAAAAGTTATTAAATTTTAATAAAAA
128 GATAAAAAATAAAAGTCAATAAAAGTTATTGAAAAATTATAAAAGTTATTAAATTTTAATAAAAA
17239 TATAAAAAAAA
193 TATAAAAAAAA
* *
17250 TATT-AAATGCATTAAAAAGTCCCTTTAACCATTAATCTTAACCGTTGACCATTAAAATTAACTA
1 TATTAAAATGCATAAAAAAGTCCCTTTAACCATTAATCTTAACAGTTGACCATTAAAATTAACTA
* * * *
17314 TTTCCAATTTTTTCAATTAAAGTCATCACGTGTCACAACACAGCGGGACAAGTGGAGAAAAATGA
66 GTCCCAATTTTTTAAATTAAAGTCATCACGTGTCACAACACAGCGGGACAAGTGGACAAAAA-GA
17379 TAAAAAATAAAAGTCAATAAAAGTTATTGAAAAATTATAAAA
130 TAAAAAATAAAAGTCAATAAAAGTTATTGAAAAATTATAAAA
17421 TATTTCTTTT
Statistics
Matches: 144, Mismatches: 17, Indels: 14
0.82 0.10 0.08
Matches are distributed among these distances:
195 6 0.04
196 78 0.54
197 22 0.15
199 7 0.05
200 4 0.03
201 13 0.09
202 1 0.01
203 13 0.09
ACGTcount: A:0.46, C:0.12, G:0.10, T:0.31
Consensus pattern (203 bp):
TATTAAAATGCATAAAAAAGTCCCTTTAACCATTAATCTTAACAGTTGACCATTAAAATTAACTA
GTCCCAATTTTTTAAATTAAAGTCATCACGTGTCACAACACAGCGGGACAAGTGGACAAAAAGAT
AAAAAATAAAAGTCAATAAAAGTTATTGAAAAATTATAAAAGTTATTAAATTTTAATAAAAATAT
AAAAAAAA
Found at i:17451 original size:9 final size:9
Alignment explanation
Indices: 17437--17648 Score: 127
Period size: 9 Copynumber: 23.0 Consensus size: 9
17427 TTTTGGTGTG
17437 ATAATTTTT
1 ATAATTTTT
17446 ATAATTTTTT
1 ATAA-TTTTT
17456 ATGAA-TTTT
1 AT-AATTTTT
17465 AT-ATTTCTT
1 ATAATTT-TT
17474 -TACATTTTT
1 ATA-ATTTTT
17483 ATAATTGTTT
1 ATAATT-TTT
*
17493 -TACTATTTT
1 ATAAT-TTTT
*
17502 ATAAAATTTT
1 AT-AATTTTT
17512 ATAATTTTT
1 ATAATTTTT
*
17521 CTATATATTTT
1 ATA-AT-TTTT
17532 AT--TTTTT
1 ATAATTTTT
*
17539 ATTATTTTT
1 ATAATTTTT
*
17548 ATAATTTGTC
1 ATAATTT-TT
*
17558 CTAATTTTT
1 ATAATTTTT
17567 A-ATATTTTT
1 ATA-ATTTTT
17576 AT-ATTTTT
1 ATAATTTTT
* *
17584 ATTAAAATTTA
1 A-T-AATTTTT
*
17595 ATAATTTTA
1 ATAATTTTT
17604 ATAATTTTT
1 ATAATTTTT
17613 ATAATTTTT
1 ATAATTTTT
*
17622 ATTGATTTTT
1 A-TAATTTTT
*
17632 AT-TTTTTT
1 ATAATTTTT
*
17640 ATCATTTTT
1 ATAATTTTT
17649 GTCACATGTC
Statistics
Matches: 162, Mismatches: 18, Indels: 46
0.72 0.08 0.20
Matches are distributed among these distances:
7 7 0.04
8 19 0.12
9 81 0.50
10 42 0.26
11 13 0.08
ACGTcount: A:0.30, C:0.03, G:0.02, T:0.65
Consensus pattern (9 bp):
ATAATTTTT
Found at i:17462 original size:11 final size:10
Alignment explanation
Indices: 17437--17621 Score: 64
Period size: 10 Copynumber: 19.9 Consensus size: 10
17427 TTTTGGTGTG
17437 ATAA-TTTTT
1 ATAATTTTTT
17446 ATAATTTTTT
1 ATAATTTTTT
17456 ATGAA--TTTT
1 AT-AATTTTTT
17465 AT-ATTTCTTT
1 ATAATTT-TTT
*
17475 A-CA-TTTTT
1 ATAATTTTTT
*
17483 ATAATTGTTT
1 ATAATTTTTT
* *
17493 -TACTATTTT
1 ATAATTTTTT
**
17502 ATAAAATTTT
1 ATAATTTTTT
17512 ATAATTTTTCT
1 ATAATTTTT-T
*
17523 AT-A-TATTT
1 ATAATTTTTT
17531 -T-ATTTTTT
1 ATAATTTTTT
*
17539 ATTA-TTTTT
1 ATAATTTTTT
* *
17548 ATAATTTGTC
1 ATAATTTTTT
* *
17558 CTAATTTTTA
1 ATAATTTTTT
17568 AT-A-TTTTT
1 ATAATTTTTT
17576 AT-A-TTTTT
1 ATAATTTTTT
** *
17584 ATTAAAATTTA
1 A-TAATTTTTT
*
17595 ATAA-TTTTA
1 ATAATTTTTT
17604 ATAA-TTTTT
1 ATAATTTTTT
17613 ATAATTTTT
1 ATAATTTTT
17622 ATTGATTTTT
Statistics
Matches: 135, Mismatches: 23, Indels: 35
0.70 0.12 0.18
Matches are distributed among these distances:
7 3 0.02
8 22 0.16
9 50 0.37
10 51 0.38
11 9 0.07
ACGTcount: A:0.31, C:0.03, G:0.02, T:0.64
Consensus pattern (10 bp):
ATAATTTTTT
Found at i:17545 original size:45 final size:45
Alignment explanation
Indices: 17490--17640 Score: 125
Period size: 46 Copynumber: 3.3 Consensus size: 45
17480 TTTATAATTG
* *
17490 TTTTACTATTTTATAAAATTT-T-ATAATTTTTCTATATATTTTAT-T
1 TTTTATTATTTT-TAAAATTTGTCATAATTTTT-AATAT-TTTTATAT
* *
17535 TTTTATTATTTTTATAATTTGTCCTAATTTTTAATATTTTTATAT
1 TTTTATTATTTTTAAAATTTGTCATAATTTTTAATATTTTTATAT
** *
17580 TTTTATTAAAATTTAATAATTT-TAATAATTTTT-ATAATTTTTATTGAT
1 TTTTATT-ATTTTTAA-AATTTGTCATAATTTTTAAT-ATTTTTA-T-AT
17628 TTTTATT-TTTTTA
1 TTTTATTATTTTTA
17641 TCATTTTTGT
Statistics
Matches: 87, Mismatches: 11, Indels: 15
0.77 0.10 0.13
Matches are distributed among these distances:
44 13 0.15
45 26 0.30
46 33 0.38
47 6 0.07
48 9 0.10
ACGTcount: A:0.30, C:0.03, G:0.01, T:0.66
Consensus pattern (45 bp):
TTTTATTATTTTTAAAATTTGTCATAATTTTTAATATTTTTATAT
Found at i:17549 original size:16 final size:17
Alignment explanation
Indices: 17515--17546 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
17505 AAATTTTATA
17515 ATTTTTCTATATATTTT
1 ATTTTTCTATATATTTT
17532 ATTTTT-TAT-TATTTT
1 ATTTTTCTATATATTTT
17547 TATAATTTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 3 0.20
17 6 0.40
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.75
Consensus pattern (17 bp):
ATTTTTCTATATATTTT
Found at i:24023 original size:16 final size:16
Alignment explanation
Indices: 24002--24036 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
23992 CTTGTATCGG
24002 TTTCCATATTACCAAA
1 TTTCCATATTACCAAA
*
24018 TTTCCATATTTCCAAA
1 TTTCCATATTACCAAA
24034 TTT
1 TTT
24037 ACTTATTCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.31, C:0.23, G:0.00, T:0.46
Consensus pattern (16 bp):
TTTCCATATTACCAAA
Found at i:31983 original size:14 final size:14
Alignment explanation
Indices: 31956--31998 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
31946 TTAGTAAATT
31956 TTTTATAATATTATA
1 TTTT-TAATATTATA
*
31971 TTTTTAATTTTATA
1 TTTTTAATATTATA
*
31985 TATTTTAAAATTAT
1 T-TTTTAATATTAT
31999 TGTAGTTTCA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 10 0.42
15 14 0.58
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
TTTTTAATATTATA
Found at i:35184 original size:14 final size:14
Alignment explanation
Indices: 35165--35236 Score: 62
Period size: 14 Copynumber: 5.3 Consensus size: 14
35155 TGTATGTTAA
35165 CAAAATAAAACCAT
1 CAAAATAAAACCAT
*
35179 CAAAAT-AACCCAAT
1 CAAAATAAAACC-AT
*
35193 -AGAATAAAACCAT
1 CAAAATAAAACCAT
*
35206 CAAAAT-AACCCAAT
1 CAAAATAAAACC-AT
*
35220 -AGAATAAAACCAT
1 CAAAATAAAACCAT
35233 CAAA
1 CAAA
35237 TTATCCATCA
Statistics
Matches: 44, Mismatches: 8, Indels: 12
0.69 0.12 0.19
Matches are distributed among these distances:
13 20 0.45
14 24 0.55
ACGTcount: A:0.61, C:0.22, G:0.03, T:0.14
Consensus pattern (14 bp):
CAAAATAAAACCAT
Found at i:35198 original size:27 final size:27
Alignment explanation
Indices: 35168--35236 Score: 138
Period size: 27 Copynumber: 2.6 Consensus size: 27
35158 ATGTTAACAA
35168 AATAAAACCATCAAAATAACCCAATAG
1 AATAAAACCATCAAAATAACCCAATAG
35195 AATAAAACCATCAAAATAACCCAATAG
1 AATAAAACCATCAAAATAACCCAATAG
35222 AATAAAACCATCAAA
1 AATAAAACCATCAAA
35237 TTATCCATCA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.61, C:0.22, G:0.03, T:0.14
Consensus pattern (27 bp):
AATAAAACCATCAAAATAACCCAATAG
Found at i:35229 original size:90 final size:89
Alignment explanation
Indices: 35105--35271 Score: 244
Period size: 90 Copynumber: 1.9 Consensus size: 89
35095 TGTCCATCAA
* * * **
35105 AATACAACCATCAAAATGATCCAACAAAACAAAACCATCAAATTATCCATTGTATGTTAACAAAA
1 AATAAAACCATCAAAATAACCCAACAAAACAAAACCATCAAATTATCCATCATATGTTAACAAAA
35170 TAAAACCATCAAAATAACCCAATAG
66 -AAAACCATCAAAATAACCCAATAG
* * *
35195 AATAAAACCATCAAAATAACCCAATAGAATAAAACCATCAAATTATCCATCATATGTTAACAAAA
1 AATAAAACCATCAAAATAACCCAACAAAACAAAACCATCAAATTATCCATCATATGTTAACAAAA
*
35260 AGAACCATCAAA
66 AAAACCATCAAA
35272 CTTTCCATCG
Statistics
Matches: 68, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
89 11 0.16
90 57 0.84
ACGTcount: A:0.54, C:0.22, G:0.04, T:0.20
Consensus pattern (89 bp):
AATAAAACCATCAAAATAACCCAACAAAACAAAACCATCAAATTATCCATCATATGTTAACAAAA
AAAACCATCAAAATAACCCAATAG
Found at i:53849 original size:70 final size:70
Alignment explanation
Indices: 53736--53867 Score: 192
Period size: 70 Copynumber: 1.9 Consensus size: 70
53726 ACATTTATGA
* ** * * * *
53736 GACTTCTACTGATACAACCTTGACTTTTATCGGTAAAACAAACTCCAGAGAGTAAAGAAGTTGTG
1 GACTTCTACCGATACAACCAAGACTTATATCAGTAAAACAAACTCCAAAGAGCAAAGAAGTTGTG
53801 ATCGG
66 ATCGG
*
53806 GACTTCTACCGCTACAACCAAGACTTATATCAGTAAAACAAACTCCAAAGAGCAAAGAAGTT
1 GACTTCTACCGATACAACCAAGACTTATATCAGTAAAACAAACTCCAAAGAGCAAAGAAGTT
53868 ATGGCCTGAG
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
70 54 1.00
ACGTcount: A:0.39, C:0.21, G:0.17, T:0.23
Consensus pattern (70 bp):
GACTTCTACCGATACAACCAAGACTTATATCAGTAAAACAAACTCCAAAGAGCAAAGAAGTTGTG
ATCGG
Found at i:53961 original size:13 final size:13
Alignment explanation
Indices: 53943--53970 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
53933 GTTCAGCATC
53943 CCCTGCACTTCTA
1 CCCTGCACTTCTA
53956 CCCTGCACTTCTA
1 CCCTGCACTTCTA
53969 CC
1 CC
53971 GATAAGGGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.14, C:0.50, G:0.07, T:0.29
Consensus pattern (13 bp):
CCCTGCACTTCTA
Found at i:58705 original size:16 final size:16
Alignment explanation
Indices: 58684--58716 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
58674 CTTCTATCGG
58684 TAGAAGTGTACAAGTA
1 TAGAAGTGTACAAGTA
*
58700 TAGAAGTGTCCAAGTA
1 TAGAAGTGTACAAGTA
58716 T
1 T
58717 CGGTAGTTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.39, C:0.09, G:0.24, T:0.27
Consensus pattern (16 bp):
TAGAAGTGTACAAGTA
Found at i:68661 original size:18 final size:17
Alignment explanation
Indices: 68634--68667 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
68624 CGTCAACTTA
*
68634 TATTATAAAATTAAAAAT
1 TATTA-AAAAATAAAAAT
68652 TATTAAAAAATAAAAA
1 TATTAAAAAATAAAAA
68668 AATGAAAACT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
TATTAAAAAATAAAAAT
Found at i:68668 original size:18 final size:18
Alignment explanation
Indices: 68634--68668 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
68624 CGTCAACTTA
* *
68634 TATTATAAAATTAAAAAT
1 TATTAAAAAATAAAAAAT
68652 TATTAAAAAATAAAAAA
1 TATTAAAAAATAAAAAA
68669 ATGAAAACTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
TATTAAAAAATAAAAAAT
Found at i:69384 original size:10 final size:9
Alignment explanation
Indices: 69362--69453 Score: 53
Period size: 10 Copynumber: 9.4 Consensus size: 9
69352 ATTTTCTCAT
69362 AAAATATTAA
1 AAAATATT-A
69372 AAAATCATTA
1 AAAAT-ATTA
69382 AAAATATTA
1 AAAATATTA
*
69391 TATAAACTTATAA
1 -A-AAA--TATTA
69404 AAAATA-TA
1 AAAATATTA
69412 AAAA-ATTA
1 AAAATATTA
*
69420 TAAATATTCA
1 AAAATATT-A
*
69430 TAAATATTTA
1 AAAATA-TTA
*
69440 TAAATATTA
1 AAAATATTA
69449 TAAAA
1 -AAAA
69454 ATTGTAAAAT
Statistics
Matches: 68, Mismatches: 4, Indels: 20
0.74 0.04 0.22
Matches are distributed among these distances:
7 1 0.01
8 10 0.15
9 12 0.18
10 29 0.43
11 11 0.16
12 1 0.01
13 4 0.06
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (9 bp):
AAAATATTA
Found at i:69396 original size:32 final size:29
Alignment explanation
Indices: 69360--69421 Score: 72
Period size: 32 Copynumber: 2.0 Consensus size: 29
69350 CAATTTTCTC
69360 ATAAAA-TATTAAAAAATCATTAAAAATATTAT
1 ATAAAATTA-TAAAAAAT-A-TAAAAA-ATTAT
*
69392 ATAAACTTATAAAAAATATAAAAAATTAT
1 ATAAAATTATAAAAAATATAAAAAATTAT
69421 A
1 A
69422 AATATTCATA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
29 6 0.21
30 6 0.21
31 1 0.04
32 13 0.46
33 2 0.07
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (29 bp):
ATAAAATTATAAAAAATATAAAAAATTAT
Found at i:69420 original size:19 final size:19
Alignment explanation
Indices: 69362--69423 Score: 61
Period size: 19 Copynumber: 3.1 Consensus size: 19
69352 ATTTTCTCAT
*
69362 AAAATATTAAAAAATCATTAA
1 AAAATA-TAAAAAATTA-TAA
* *
69383 AAATATTATATAAACTTATAA
1 AAA-A-TATAAAAAATTATAA
69404 AAAATATAAAAAATTATAA
1 AAAATATAAAAAATTATAA
69423 A
1 A
69424 TATTCATAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
19 14 0.41
20 1 0.03
21 9 0.26
22 8 0.24
23 2 0.06
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (19 bp):
AAAATATAAAAAATTATAA
Found at i:69451 original size:39 final size:38
Alignment explanation
Indices: 69363--69566 Score: 108
Period size: 38 Copynumber: 5.4 Consensus size: 38
69353 TTTTCTCATA
* *
69363 AAATATTA-AAAAATCATTAAAAATATTATATAA-ACTTAT
1 AAATATTATAAAAA--ATTATAAATATTATA-AATATTTAT
* *
69402 AAAAAATATAAAAAATTATAAATATTCATAAATATTTAT
1 AAATATTATAAAAAATTATAAATATT-ATAAATATTTAT
* * * *
69441 AAATATTAT-AAAAATTGTAAA-ATTCTTAATAAATTAT
1 AAATATTATAAAAAATTATAAATATTATAAAT-ATTTAT
* * * *
69478 AAA-A--ATAATAAAAGTACAAAGCATTTAAAAATATTTA-
1 AAATATTATAA-AAAATTATAAA-TA-TTATAAATATTTAT
69515 AAAT-TTAT-AAAAATTCCAT-AATAACTTATAAATA-TTAT
1 AAATATTATAAAAAATT--ATAAAT-A-TTATAAATATTTAT
69553 AAATATTATAAAAA
1 AAATATTATAAAAA
69567 CTTAGAAGCA
Statistics
Matches: 125, Mismatches: 22, Indels: 35
0.69 0.12 0.19
Matches are distributed among these distances:
34 2 0.02
35 1 0.01
36 13 0.10
37 22 0.18
38 45 0.36
39 33 0.26
40 9 0.07
ACGTcount: A:0.59, C:0.04, G:0.01, T:0.35
Consensus pattern (38 bp):
AAATATTATAAAAAATTATAAATATTATAAATATTTAT
Found at i:69489 original size:37 final size:38
Alignment explanation
Indices: 69378--69490 Score: 101
Period size: 37 Copynumber: 3.0 Consensus size: 38
69368 TTAAAAAATC
*
69378 ATTAAAAATATT-AT-ATAAACTTATAAAAA-ATATAAAAA
1 ATTATAAATATTCATAATAAA-TTATAAAAATA-AT-AAAA
* * *
69416 ATTATAAATATTCATAA-ATATTTATAAATATTATAAAA
1 ATTATAAATATTCATAATA-AATTATAAAAATAATAAAA
* *
69454 ATTGTAAA-ATTCTTAATAAATTATAAAAATAATAAAA
1 ATTATAAATATTCATAATAAATTATAAAAATAATAAAA
69491 GTACAAAGCA
Statistics
Matches: 61, Mismatches: 9, Indels: 11
0.75 0.11 0.14
Matches are distributed among these distances:
37 23 0.38
38 23 0.38
39 13 0.21
40 2 0.03
ACGTcount: A:0.60, C:0.03, G:0.01, T:0.36
Consensus pattern (38 bp):
ATTATAAATATTCATAATAAATTATAAAAATAATAAAA
Found at i:69525 original size:9 final size:9
Alignment explanation
Indices: 69360--69565 Score: 50
Period size: 10 Copynumber: 21.7 Consensus size: 9
69350 CAATTTTCTC
69360 ATAAAATATT
1 ATAAAAT-TT
*
69370 AAAAAATCATT
1 ATAAAAT--TT
69381 A-AAAATATT
1 ATAAAAT-TT
*
69390 ATATAAACTT
1 ATA-AAATTT
**
69400 ATAAAAAAT
1 ATAAAATTT
*
69409 ATAAAAAATT
1 AT-AAAATTT
*
69419 ATAAATATTC
1 ATAAA-ATTT
69429 ATAAATATTT
1 ATAAA-ATTT
69439 AT-AAATATT
1 ATAAAAT-TT
*
69448 ATAAAAATT
1 ATAAAATTT
*
69457 GTAAAATTCT
1 ATAAAATT-T
*
69467 -TAATAAATT
1 ATAA-AATTT
* *
69476 ATAAAAATA
1 ATAAAATTT
*
69485 ATAAAA-GT
1 ATAAAATTT
*
69493 ACAAAGCATTT
1 ATAAA--ATTT
69504 A-AAAATATT
1 ATAAAAT-TT
69513 -TAAAATTT
1 ATAAAATTT
*
69521 ATAAAAATTCC
1 AT-AAAATT-T
*
69532 ATAATAACTT
1 ATAA-AATTT
69542 AT-AAATATT
1 ATAAAAT-TT
69551 AT-AAATATT
1 ATAAAAT-TT
69560 ATAAAA
1 ATAAAA
69566 ACTTAGAAGC
Statistics
Matches: 154, Mismatches: 21, Indels: 42
0.71 0.10 0.19
Matches are distributed among these distances:
8 12 0.08
9 63 0.41
10 65 0.42
11 14 0.09
ACGTcount: A:0.59, C:0.04, G:0.01, T:0.35
Consensus pattern (9 bp):
ATAAAATTT
Found at i:69548 original size:11 final size:9
Alignment explanation
Indices: 69540--69564 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
69530 CCATAATAAC
69540 TTATAAATA
1 TTATAAATA
69549 TTATAAATA
1 TTATAAATA
69558 TTATAAA
1 TTATAAA
69565 AACTTAGAAG
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:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (9 bp):
TTATAAATA
Found at i:69554 original size:19 final size:18
Alignment explanation
Indices: 69506--69564 Score: 50
Period size: 21 Copynumber: 3.2 Consensus size: 18
69496 AAGCATTTAA
*
69506 AAATATT-TAAAATTTAT
1 AAATATTATAAAACTTAT
*
69523 AAAAATTCCATAATAACTTAT
1 AAATATT--ATAA-AACTTAT
69544 AAATATTATAAATA-TTAT
1 AAATATTATAAA-ACTTAT
69562 AAA
1 AAA
69565 AACTTAGAAG
Statistics
Matches: 34, Mismatches: 3, Indels: 9
0.74 0.07 0.20
Matches are distributed among these distances:
17 6 0.18
18 8 0.24
19 5 0.15
20 3 0.09
21 12 0.35
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (18 bp):
AAATATTATAAAACTTAT
Found at i:69563 original size:28 final size:28
Alignment explanation
Indices: 69515--69570 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
69505 AAAATATTTA
*
69515 AAATTTATAAAAATTCCATAATAACTTAT
1 AAATTTATAAAAATT-CATAAAAACTTAT
*
69544 AAATATTATAAATATT-ATAAAAACTTA
1 AAAT-TTATAAAAATTCATAAAAACTTA
69571 GAAGCAAGCA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 10 0.42
29 4 0.17
30 10 0.42
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (28 bp):
AAATTTATAAAAATTCATAAAAACTTAT
Found at i:69820 original size:30 final size:30
Alignment explanation
Indices: 69779--69846 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
69769 TTATAACTTG
*
69779 TTTTATAATTTA-TTAGAATTTTTTATAGGT
1 TTTTATAATTTATTTAGAA-TTTTTATAAGT
* *
69809 TTTTATGATTTATTTATAATTTTTATAAGT
1 TTTTATAATTTATTTAGAATTTTTATAAGT
*
69839 TTATATAA
1 TTTTATAA
69847 ATTCTATAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
30 27 0.84
31 5 0.16
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.60
Consensus pattern (30 bp):
TTTTATAATTTATTTAGAATTTTTATAAGT
Found at i:69831 original size:20 final size:20
Alignment explanation
Indices: 69779--69877 Score: 71
Period size: 20 Copynumber: 4.9 Consensus size: 20
69769 TTATAACTTG
69779 TTTTATAATTTATTA-GAATT
1 TTTTATAATTT-TTATGAATT
*
69799 TTTTATAGGTTTTTATG-ATT
1 TTTTATA-ATTTTTATGAATT
*
69819 TATTTATAATTTTTAT-AAGT
1 T-TTTATAATTTTTATGAATT
* * *
69839 TTATATAAATTCTAT-AATTT
1 TTTTATAATTTTTATGAA-TT
*
69859 TTTTTTATATTTTTATGAA
1 TTTTATA-ATTTTTATGAA
69878 AGAAAATAAA
Statistics
Matches: 61, Mismatches: 11, Indels: 12
0.73 0.13 0.14
Matches are distributed among these distances:
19 13 0.21
20 30 0.49
21 16 0.26
22 2 0.03
ACGTcount: A:0.31, C:0.01, G:0.06, T:0.62
Consensus pattern (20 bp):
TTTTATAATTTTTATGAATT
Found at i:77797 original size:19 final size:18
Alignment explanation
Indices: 77764--77876 Score: 79
Period size: 19 Copynumber: 6.1 Consensus size: 18
77754 TTAAAAAATC
77764 ATTA-AAAATATTATATAA
1 ATTATAAAA-ATTATATAA
*
77782 ACTTATAAAAATTATAAAAA
1 A-TTATAAAAATTAT-ATAA
*
77802 ATTATAAAAAATTCATAATTA
1 ATTAT-AAAAATT-AT-ATAA
* *
77823 ATTATAAATATTATAAAA
1 ATTATAAAAATTATATAA
* * *
77841 ATTGTAAAATTTTTAATAA
1 ATTATAAAAATTAT-ATAA
77860 ATTAT-AAAATTA-ATAA
1 ATTATAAAAATTATATAA
77876 A
1 A
77877 AATAATAAAA
Statistics
Matches: 75, Mismatches: 14, Indels: 14
0.73 0.14 0.14
Matches are distributed among these distances:
16 5 0.07
18 18 0.24
19 21 0.28
20 21 0.28
21 10 0.13
ACGTcount: A:0.59, C:0.02, G:0.01, T:0.38
Consensus pattern (18 bp):
ATTATAAAAATTATATAA
Found at i:77798 original size:9 final size:9
Alignment explanation
Indices: 77746--77916 Score: 98
Period size: 10 Copynumber: 18.0 Consensus size: 9
77736 CATTTTTCTC
77746 ATAAAATATT
1 ATAAAA-ATT
*
77756 A-AAAAATC
1 ATAAAAATT
77764 ATTAAAAATATT
1 A-T-AAAA-ATT
*
77776 ATATAAACTT
1 ATA-AAAATT
77786 ATAAAAATT
1 ATAAAAATT
77795 ATAAAAAATT
1 AT-AAAAATT
77805 ATAAAAAATT
1 AT-AAAAATT
*
77815 CATAATTAATT
1 -ATAA-AAATT
*
77826 ATAAATATT
1 ATAAAAATT
77835 ATAAAAATT
1 ATAAAAATT
* *
77844 GTAAAATTT
1 ATAAAAATT
*
77853 TTAATAAATT
1 ATAA-AAATT
77863 AT-AAAATT
1 ATAAAAATT
*
77871 AATAAAAATA
1 -ATAAAAATT
77881 AT-AAAATT
1 ATAAAAATT
* *
77889 ACAAAGCATT
1 ATAAA-AATT
77899 -TAAAAATAT
1 ATAAAAAT-T
*
77908 TTAAAAATT
1 ATAAAAATT
77917 TCATAATAAT
Statistics
Matches: 127, Mismatches: 19, Indels: 31
0.72 0.11 0.18
Matches are distributed among these distances:
8 16 0.13
9 44 0.35
10 50 0.39
11 14 0.11
12 3 0.02
ACGTcount: A:0.60, C:0.03, G:0.01, T:0.36
Consensus pattern (9 bp):
ATAAAAATT
Found at i:77863 original size:37 final size:36
Alignment explanation
Indices: 77778--77888 Score: 114
Period size: 37 Copynumber: 2.9 Consensus size: 36
77768 AAAATATTAT
77778 ATAAACTTATAAAAATTATAAAAAATTATAAAAAATTCATA
1 ATAAA-TTAT-AAAATTAT-AAAAATTAT--AAAATTCATA
* * **
77819 ATTAATTATAAATATTATAAAAATTGTAAAATTTTTA
1 ATAAATTATAAA-ATTATAAAAATTATAAAATTCATA
*
77856 ATAAATTATAAAATTAATAAAAATAATAAAATT
1 ATAAATTATAAAATT-ATAAAAATTATAAAATT
77889 ACAAAGCATT
Statistics
Matches: 61, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
36 3 0.05
37 34 0.56
39 11 0.18
40 9 0.15
41 4 0.07
ACGTcount: A:0.60, C:0.02, G:0.01, T:0.37
Consensus pattern (36 bp):
ATAAATTATAAAATTATAAAAATTATAAAATTCATA
Found at i:80294 original size:3 final size:3
Alignment explanation
Indices: 80286--80311 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
80276 CATCCAACAA
80286 TGG TGG TGG TGG TGG TGG TGG TGG TG
1 TGG TGG TGG TGG TGG TGG TGG TGG TG
80312 TCGTCTTAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.65, T:0.35
Consensus pattern (3 bp):
TGG
Found at i:80633 original size:8 final size:8
Alignment explanation
Indices: 80622--80671 Score: 59
Period size: 8 Copynumber: 6.5 Consensus size: 8
80612 GGATATTCAC
80622 ATATACAT
1 ATATACAT
*
80630 ATATATAT
1 ATATACAT
*
80638 ATGTACAT
1 ATATACAT
80646 ATATACAT
1 ATATACAT
80654 ATAT--AT
1 ATATACAT
*
80660 ATGTACAT
1 ATATACAT
80668 ATAT
1 ATAT
80672 GGTAGTATAC
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
6 5 0.15
8 29 0.85
ACGTcount: A:0.46, C:0.08, G:0.04, T:0.42
Consensus pattern (8 bp):
ATATACAT
Found at i:80680 original size:22 final size:22
Alignment explanation
Indices: 80620--80671 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
80610 GTGGATATTC
* *
80620 ACATATACATATATATATATGT
1 ACATATATACATATATATATGT
80642 ACATATATACATATATATATGT
1 ACATATATACATATATATATGT
80664 ACATATAT
1 ACATATAT
80672 GGTAGTATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.46, C:0.10, G:0.04, T:0.40
Consensus pattern (22 bp):
ACATATATACATATATATATGT
Found at i:81339 original size:9 final size:9
Alignment explanation
Indices: 81313--81342 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
81303 TTATAACTAA
*
81313 ATTAATTTA
1 ATTAATTTT
81322 ATTAATTTT
1 ATTAATTTT
81331 ATTAATTTT
1 ATTAATTTT
81340 ATT
1 ATT
81343 TACAATAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (9 bp):
ATTAATTTT
Found at i:87007 original size:36 final size:35
Alignment explanation
Indices: 86960--87036 Score: 111
Period size: 36 Copynumber: 2.2 Consensus size: 35
86950 AAGATAATAT
*
86960 ATTTTGTTTAACTTTACTT-TCAAGCAATTCTCTTAG
1 ATTTTGTTTAACTTGACTTGT-AAGCAA-TCTCTTAG
86996 ATTTTGTTTAACTTGACTTGTAAGCAATCTCTTAG
1 ATTTTGTTTAACTTGACTTGTAAGCAATCTCTTAG
*
87031 AATTTG
1 ATTTTG
87037 GGTCACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
35 13 0.34
36 24 0.63
37 1 0.03
ACGTcount: A:0.26, C:0.14, G:0.12, T:0.48
Consensus pattern (35 bp):
ATTTTGTTTAACTTGACTTGTAAGCAATCTCTTAG
Found at i:92224 original size:15 final size:15
Alignment explanation
Indices: 92204--92234 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
92194 AATATTTTTT
*
92204 TATATAATTTTAAAA
1 TATATAATTCTAAAA
92219 TATATAATTCTAAAA
1 TATATAATTCTAAAA
92234 T
1 T
92235 TCTAAAAATG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (15 bp):
TATATAATTCTAAAA
Found at i:92913 original size:30 final size:28
Alignment explanation
Indices: 92848--92901 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
92838 TTCAAATTTG
*
92848 AAAAGTAAAAAAATTAAATTCCTTAAAAT
1 AAAAGTAAAAAAATTAAATT-CTCAAAAT
*
92877 AAAAGTAAAATAATTAAATT-TCAAA
1 AAAAGTAAAAAAATTAAATTCTCAAA
92902 TGATAAAAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 4 0.17
29 19 0.83
ACGTcount: A:0.63, C:0.06, G:0.04, T:0.28
Consensus pattern (28 bp):
AAAAGTAAAAAAATTAAATTCTCAAAAT
Found at i:93927 original size:31 final size:33
Alignment explanation
Indices: 93856--93928 Score: 78
Period size: 34 Copynumber: 2.2 Consensus size: 33
93846 ACATGTGACA
93856 AAAAATTATAATAAATAAAAATATACAATAATT
1 AAAAATTATAATAAATAAAAATATACAATAATT
* * * * *
93889 ATTAAATTTTAATAAA-AAATATATA-ATTTATT
1 A-AAAATTATAATAAATAAAAATATACAATAATT
93921 AAAAATTA
1 AAAAATTA
93929 GAATTTTTTT
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
31 5 0.16
32 6 0.19
33 9 0.28
34 12 0.38
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (33 bp):
AAAAATTATAATAAATAAAAATATACAATAATT
Found at i:93981 original size:19 final size:19
Alignment explanation
Indices: 93937--93993 Score: 69
Period size: 19 Copynumber: 3.0 Consensus size: 19
93927 TAGAATTTTT
*
93937 TTTTTATAAAAATCGTAAA
1 TTTTTATAAAAATTGTAAA
***
93956 AAGTTATAAAAATTGTAAA
1 TTTTTATAAAAATTGTAAA
*
93975 TTTTTATAAAAATTATAAA
1 TTTTTATAAAAATTGTAAA
93994 AAAATTTATA
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.53, C:0.02, G:0.05, T:0.40
Consensus pattern (19 bp):
TTTTTATAAAAATTGTAAA
Found at i:94240 original size:10 final size:10
Alignment explanation
Indices: 94222--94282 Score: 63
Period size: 10 Copynumber: 6.3 Consensus size: 10
94212 TATAAAATTG
*
94222 TATAAATTTT
1 TATATATTTT
*
94232 TCTATATTTT
1 TATATATTTT
94242 TATATA-TTT
1 TATATATTTT
94251 TATATATTTT
1 TATATATTTT
*
94261 TAT-GATTTT
1 TATATATTTT
* *
94270 TATTTTTTTT
1 TATATATTTT
94280 TAT
1 TAT
94283 TTTTTAATAA
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
9 17 0.40
10 26 0.60
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (10 bp):
TATATATTTT
Found at i:94256 original size:19 final size:19
Alignment explanation
Indices: 94227--94282 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
94217 AATTGTATAA
*
94227 ATTTTTCTATATTTTTAT-
1 ATTTTTATATATTTTTATG
94245 ATATTTTATATATTTTTATG
1 AT-TTTTATATATTTTTATG
* *
94265 ATTTTTATTTTTTTTTAT
1 ATTTTTATATATTTTTAT
94283 TTTTTAATAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
18 2 0.06
19 29 0.88
20 2 0.06
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.73
Consensus pattern (19 bp):
ATTTTTATATATTTTTATG
Found at i:94270 original size:9 final size:8
Alignment explanation
Indices: 94229--94286 Score: 53
Period size: 9 Copynumber: 6.6 Consensus size: 8
94219 TTGTATAAAT
94229 TTTTCTATA
1 TTTT-TATA
94238 TTTTTATATA
1 -TTTT-TATA
94248 TTTTATATA
1 TTTT-TATA
94257 TTTTTATGA
1 TTTTTAT-A
*
94266 TTTTTATT
1 TTTTTATA
*
94274 TTTTTTTA
1 TTTTTATA
94282 TTTTT
1 TTTTT
94287 TAATAAAAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
8 14 0.33
9 21 0.49
10 8 0.19
ACGTcount: A:0.21, C:0.02, G:0.02, T:0.76
Consensus pattern (8 bp):
TTTTTATA
Found at i:94334 original size:29 final size:29
Alignment explanation
Indices: 94274--94348 Score: 80
Period size: 28 Copynumber: 2.6 Consensus size: 29
94264 GATTTTTATT
* * *
94274 TTTTTTTATTTTTTAATAAAAATTAAATA
1 TTTTTATAATTTTTATTAAAAATTAAATA
* *
94303 TTTTTATAGTTTTTATT-AAAATTTAATA
1 TTTTTATAATTTTTATTAAAAATTAAATA
* *
94331 ATTTTATAACTTTTATTA
1 TTTTTATAATTTTTATTA
94349 TTTTTTATTT
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
28 24 0.63
29 14 0.37
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.60
Consensus pattern (29 bp):
TTTTTATAATTTTTATTAAAAATTAAATA
Found at i:96447 original size:35 final size:35
Alignment explanation
Indices: 96382--96532 Score: 167
Period size: 35 Copynumber: 4.3 Consensus size: 35
96372 TGACCTATCT
* *
96382 TTGTGTTTCTAGTCGAGTCGCCACATTCGTCATCC
1 TTGTGTTTCTAGTCGAGTCACCACACTCGTCATCC
* * * *
96417 TTATGTTTCTAGTTGGGTCATCACACTCGTCATCC
1 TTGTGTTTCTAGTCGAGTCACCACACTCGTCATCC
* * *
96452 TTGTGTTTTTGGCCGAGTCACCACACTCGTCATCC
1 TTGTGTTTCTAGTCGAGTCACCACACTCGTCATCC
* * * * *
96487 TTGTGTTTTTGGCCAAGTCACCACACTCGTAATCC
1 TTGTGTTTCTAGTCGAGTCACCACACTCGTCATCC
*
96522 TTGTATTTCTA
1 TTGTGTTTCTA
96533 CCCAGGTCAC
Statistics
Matches: 98, Mismatches: 18, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 98 1.00
ACGTcount: A:0.17, C:0.27, G:0.18, T:0.38
Consensus pattern (35 bp):
TTGTGTTTCTAGTCGAGTCACCACACTCGTCATCC
Found at i:96542 original size:35 final size:35
Alignment explanation
Indices: 96432--96562 Score: 149
Period size: 35 Copynumber: 3.7 Consensus size: 35
96422 TTTCTAGTTG
*
96432 GGTCATCACACTCGTCATCCTTGTGTTTTTGGCC-
1 GGTCACCACACTCGTCATCCTTGTGTTTTTGGCCA
96466 GAGTCACCACACTCGTCATCCTTGTGTTTTTGGCCA
1 G-GTCACCACACTCGTCATCCTTGTGTTTTTGGCCA
* * * * **
96502 AGTCACCACACTCGTAATCCTTGTATTTCTACCCA
1 GGTCACCACACTCGTCATCCTTGTGTTTTTGGCCA
* *
96537 GGTCACCATAC-CTGTCACCCTTGTGT
1 GGTCACCACACTC-GTCATCCTTGTGT
96563 GATGTTCGTG
Statistics
Matches: 82, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
34 2 0.02
35 80 0.98
ACGTcount: A:0.18, C:0.32, G:0.17, T:0.34
Consensus pattern (35 bp):
GGTCACCACACTCGTCATCCTTGTGTTTTTGGCCA
Found at i:97072 original size:36 final size:35
Alignment explanation
Indices: 96981--97073 Score: 89
Period size: 36 Copynumber: 2.6 Consensus size: 35
96971 TTTGCACCGC
* ** *
96981 TTACATTTCATATCGCCAACGAATAGTACACATTTC
1 TTACATTT-ATATCGCCAACAAATAGTACACACCTA
**
97017 TTACATTTTATATTACCAACAAATAGGT-CACACCTA
1 TTACA-TTTATATCGCCAACAAATA-GTACACACCTA
97053 TTACAGTTTATATCGCCAACA
1 TTACA-TTTATATCGCCAACA
97074 TATTGCTTGA
Statistics
Matches: 46, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
36 41 0.89
37 5 0.11
ACGTcount: A:0.35, C:0.24, G:0.08, T:0.33
Consensus pattern (35 bp):
TTACATTTATATCGCCAACAAATAGTACACACCTA
Found at i:99681 original size:29 final size:30
Alignment explanation
Indices: 99638--99983 Score: 320
Period size: 30 Copynumber: 11.7 Consensus size: 30
99628 GGTTAAGGGA
99638 AAAAATGGAATTTTTGGAAGTTTCGAGGTT
1 AAAAATGGAATTTTTGGAAGTTTCGAGGTT
* *
99668 AAAAATGGGATTTTTGGAAG-TTCGAGGGT
1 AAAAATGGAATTTTTGGAAGTTTCGAGGTT
* *
99697 AAAAATGGAATTTTTGGAAGTTT-TAGGGTC
1 AAAAATGGAATTTTTGGAAGTTTCGA-GGTT
* *
99727 AAAAAT-GAGATTTTTGGAAG-TTCGGGGGT
1 AAAAATGGA-ATTTTTGGAAGTTTCGAGGTT
* * *
99756 AAAAATAGAATTTTTTGAAGTTTCG-GAGTC
1 AAAAATGGAATTTTTGGAAGTTTCGAG-GTT
* *
99786 AAAGAAT-GAGATTTTTGGAAGTTT-GGGGAT
1 AAA-AATGGA-ATTTTTGGAAGTTTCGAGGTT
* * *
99816 AAAAACT-AAATTTTTGGAAGTTTTGGGGTT
1 AAAAA-TGGAATTTTTGGAAGTTTCGAGGTT
* *
99846 AAAAATGGGATTTTTGGAAG-TTCGAGGGT
1 AAAAATGGAATTTTTGGAAGTTTCGAGGTT
* ** *
99875 AGAAATATAATTTTTGGAAGTTT-TAGGGTT
1 AAAAATGGAATTTTTGGAAGTTTCGA-GGTT
*
99905 -AAAATGGAATTTTTGGAAGTTT-GAGGGTA
1 AAAAATGGAATTTTTGGAAGTTTCGA-GGTT
* *
99934 AAAAATGGAATTTTTGGAAGTTTTGGGGTT
1 AAAAATGGAATTTTTGGAAGTTTCGAGGTT
*
99964 AAAAATAGAATTTTTGGAAG
1 AAAAATGGAATTTTTGGAAG
99984 GTTTAGGGAC
Statistics
Matches: 262, Mismatches: 37, Indels: 34
0.79 0.11 0.10
Matches are distributed among these distances:
29 115 0.44
30 129 0.49
31 18 0.07
ACGTcount: A:0.34, C:0.02, G:0.28, T:0.36
Consensus pattern (30 bp):
AAAAATGGAATTTTTGGAAGTTTCGAGGTT
Found at i:99716 original size:59 final size:58
Alignment explanation
Indices: 99633--99983 Score: 386
Period size: 59 Copynumber: 5.9 Consensus size: 58
99623 TTGGAGGTTA
*
99633 AGGGAAAAAATGGAATTTTTGGAAGTTTCGAGGTTAAAAATGGGATTTTTGGAAGTTCG
1 AGGGTAAAAATGGAATTTTTGGAAGTTT-GAGGTTAAAAATGGGATTTTTGGAAGTTCG
* * *
99692 AGGGTAAAAATGGAATTTTTGGAAGTTTTAGGGTCAAAAATGAGATTTTTGGAAGTTCG
1 AGGGTAAAAATGGAATTTTTGGAAGTTTGA-GGTTAAAAATGGGATTTTTGGAAGTTCG
* * * * * *
99751 GGGGTAAAAATAGAATTTTTTGAAGTTTCG-GAGTCAAAGAATGAGATTTTTGGAAGTTTG
1 AGGGTAAAAATGGAATTTTTGGAAGTTT-GAG-GTTAAA-AATGGGATTTTTGGAAGTTCG
* *
99811 -GGGATAAAAACT-AAATTTTTGGAAGTTTTGGGGTTAAAAATGGGATTTTTGGAAGTTCG
1 AGGG-TAAAAA-TGGAATTTTTGGAAG-TTTGAGGTTAAAAATGGGATTTTTGGAAGTTCG
* ** * * *
99870 AGGGTAGAAATATAATTTTTGGAAGTTTTAGGGTT-AAAATGGAATTTTTGGAAGTTTG
1 AGGGTAAAAATGGAATTTTTGGAAGTTTGA-GGTTAAAAATGGGATTTTTGGAAGTTCG
* * *
99928 AGGGTAAAAAATGGAATTTTTGGAAGTTTTGGGGTTAAAAATAGAATTTTTGGAAG
1 AGGGT-AAAAATGGAATTTTTGGAAG-TTTGAGGTTAAAAATGGGATTTTTGGAAG
99984 GTTTAGGGAC
Statistics
Matches: 252, Mismatches: 26, Indels: 27
0.83 0.09 0.09
Matches are distributed among these distances:
58 32 0.13
59 148 0.59
60 67 0.27
61 5 0.02
ACGTcount: A:0.34, C:0.02, G:0.29, T:0.35
Consensus pattern (58 bp):
AGGGTAAAAATGGAATTTTTGGAAGTTTGAGGTTAAAAATGGGATTTTTGGAAGTTCG
Found at i:100695 original size:17 final size:17
Alignment explanation
Indices: 100652--100725 Score: 94
Period size: 17 Copynumber: 4.2 Consensus size: 17
100642 TTGAACCTTT
*
100652 TTAATTTTAAATTTAAAT
1 TTAA-TTTAAATTTAAAA
*
100670 TTAAATTTAAATTTAAGA
1 TT-AATTTAAATTTAAAA
100688 TTAATTTAAATTTAAAA
1 TTAATTTAAATTTAAAA
* *
100705 TAAATCTAAATTTAAAA
1 TTAATTTAAATTTAAAA
100722 TTAA
1 TTAA
100726 AAAGGGGCCC
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
17 32 0.65
18 15 0.31
19 2 0.04
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (17 bp):
TTAATTTAAATTTAAAA
Found at i:100716 original size:23 final size:22
Alignment explanation
Indices: 100659--100727 Score: 77
Period size: 23 Copynumber: 3.0 Consensus size: 22
100649 TTTTTAATTT
*
100659 TAAATTTAAATTTAAATTTAAATT
1 TAAA-TTAAATTTAAATTTAAA-A
100683 TAAGATT-AATTTAAATTTAAAA
1 TAA-ATTAAATTTAAATTTAAAA
*
100705 TAAATCTAAATTTAAAATTAAAA
1 TAAAT-TAAATTTAAATTTAAAA
100728 AGGGGCCCGA
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
21 2 0.05
22 4 0.10
23 28 0.70
24 5 0.12
25 1 0.03
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (22 bp):
TAAATTAAATTTAAATTTAAAA
Found at i:100727 original size:6 final size:6
Alignment explanation
Indices: 100651--100726 Score: 86
Period size: 6 Copynumber: 13.0 Consensus size: 6
100641 TTTGAACCTT
*
100651 TTTAAT TTTAAA TTTAAA TTTAAA TTTAAA TTTAAGA -TT-AA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAA-A TTTAAA TTTAAA
* * *
100698 TTTAAA -ATAAA TCTAAA TTTAAA ATTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
100727 AAGGGGCCCG
Statistics
Matches: 61, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
4 1 0.02
5 7 0.11
6 52 0.85
7 1 0.02
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (6 bp):
TTTAAA
Done.