Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032250.1 Gossypioides kirkii chromosome KI_08
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: 39602670
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 500 characters in sequence are not A, C, G, or T
File 116 of 125
Found at i:36037313 original size:22 final size:22
Alignment explanation
Indices: 36037274--36037329 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
36037264 TAAGAAAACT
* *
36037274 ATATAAAAAAATTCAATAAAAA
1 ATATAAAATAATTAAATAAAAA
* **
36037296 ATATAAAATTATTAAATATTAA
1 ATATAAAATAATTAAATAAAAA
36037318 ATATTAAAATAA
1 ATA-TAAAATAA
36037330 AATAAAATAA
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
22 20 0.74
23 7 0.26
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (22 bp):
ATATAAAATAATTAAATAAAAA
Found at i:36047536 original size:18 final size:18
Alignment explanation
Indices: 36047512--36047553 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
36047502 GTGTCACATC
*
36047512 AATAAATAAATTTAAAAA
1 AATAAATAAATTCAAAAA
* *
36047530 TATAAATATATTCAAAAA
1 AATAAATAAATTCAAAAA
36047548 AATAAA
1 AATAAA
36047554 AATTATAGAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (18 bp):
AATAAATAAATTCAAAAA
Found at i:36050136 original size:28 final size:31
Alignment explanation
Indices: 36050074--36050146 Score: 82
Period size: 28 Copynumber: 2.5 Consensus size: 31
36050064 TGCAATTATG
* *
36050074 TTGTTATTAGTTTATTATTATTGTTTAGATA
1 TTGTTAATATTTTATTATTATTGTTTAGATA
*
36050105 TTGTGTAAT-TTTTATT-TTATTG-TTA-ATT
1 TTGT-TAATATTTTATTATTATTGTTTAGATA
36050133 TTGTTAATATTTTA
1 TTGTTAATATTTTA
36050147 GAGGTATTTG
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
27 4 0.11
28 11 0.30
29 3 0.08
30 6 0.16
31 10 0.27
32 3 0.08
ACGTcount: A:0.25, C:0.00, G:0.11, T:0.64
Consensus pattern (31 bp):
TTGTTAATATTTTATTATTATTGTTTAGATA
Found at i:36055223 original size:2 final size:2
Alignment explanation
Indices: 36055216--36055240 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
36055206 TATAAGAAAT
36055216 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
36055241 TTCTATGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:36062644 original size:53 final size:53
Alignment explanation
Indices: 36062564--36062723 Score: 311
Period size: 53 Copynumber: 3.0 Consensus size: 53
36062554 AGAGATCAAG
*
36062564 ACATAAAAGTAATATAAATATAGAAGACTTCAGTTTCATAGTGTCCTTGTAAT
1 ACATAAAAGTAATATAAACATAGAAGACTTCAGTTTCATAGTGTCCTTGTAAT
36062617 ACATAAAAGTAATATAAACATAGAAGACTTCAGTTTCATAGTGTCCTTGTAAT
1 ACATAAAAGTAATATAAACATAGAAGACTTCAGTTTCATAGTGTCCTTGTAAT
36062670 ACATAAAAGTAATATAAACATAGAAGACTTCAGTTTCATAGTGTCCTTGTAAT
1 ACATAAAAGTAATATAAACATAGAAGACTTCAGTTTCATAGTGTCCTTGTAAT
36062723 A
1 A
36062724 ATTAATCAAA
Statistics
Matches: 106, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
53 106 1.00
ACGTcount: A:0.42, C:0.12, G:0.13, T:0.33
Consensus pattern (53 bp):
ACATAAAAGTAATATAAACATAGAAGACTTCAGTTTCATAGTGTCCTTGTAAT
Found at i:36066244 original size:12 final size:12
Alignment explanation
Indices: 36066226--36066256 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
36066216 CTGTGGGTTC
36066226 CTTTTTTTT-TT
1 CTTTTTTTTGTT
36066237 CTTTTTTTTGTT
1 CTTTTTTTTGTT
36066249 CTTTTTTT
1 CTTTTTTT
36066257 CGTTGCTGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 9 0.47
12 10 0.53
ACGTcount: A:0.00, C:0.10, G:0.03, T:0.87
Consensus pattern (12 bp):
CTTTTTTTTGTT
Found at i:36070441 original size:105 final size:105
Alignment explanation
Indices: 36070252--36070443 Score: 249
Period size: 105 Copynumber: 1.8 Consensus size: 105
36070242 TATAGGTAAC
* ** *
36070252 AACATCAGGCTCAATGCCTTGCTTTATCATTGTGTCAACAATATCTTTAGCTTCGGAAAGCATCC
1 AACATCAGGCTCAATGCCATGCTTTATCATTGTGTCAACAATATCTACAGCTTCCGAAAGCATCC
* * *
36070317 CTTCTTTGCAACATGCATCGATACACATATTGTACGTGAT
66 CCTCCTTGCAACATCCATCGATACACATATTGTACGTGAT
* * * * *
36070357 AACATTAGGCTCAATGCCATGCTTTCTCATTGTGTCAACGATTTCTACAGCTTCCGAAATCATCC
1 AACATCAGGCTCAATGCCATGCTTTATCATTGTGTCAACAATATCTACAGCTTCCGAAAGCATCC
* **
36070422 CCTCCTTGTAATGTCCATCGAT
66 CCTCCTTGCAACATCCATCGAT
36070444 CAATGTATTA
Statistics
Matches: 72, Mismatches: 15, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
105 72 1.00
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.33
Consensus pattern (105 bp):
AACATCAGGCTCAATGCCATGCTTTATCATTGTGTCAACAATATCTACAGCTTCCGAAAGCATCC
CCTCCTTGCAACATCCATCGATACACATATTGTACGTGAT
Found at i:36074331 original size:33 final size:33
Alignment explanation
Indices: 36074294--36074356 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
36074284 TAATGACATG
36074294 AAAAA-AATATTGAAATGA-CATTAAATAATTGAT
1 AAAAATAATATTG-AATGAGCATT-AATAATTGAT
*
36074327 AAAAATGATATTGAATGAGCATTAATAATT
1 AAAAATAATATTGAATGAGCATTAATAATT
36074357 AAATTGTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 17 0.63
34 10 0.37
ACGTcount: A:0.54, C:0.03, G:0.11, T:0.32
Consensus pattern (33 bp):
AAAAATAATATTGAATGAGCATTAATAATTGAT
Found at i:36074985 original size:28 final size:27
Alignment explanation
Indices: 36074914--36074990 Score: 70
Period size: 28 Copynumber: 2.9 Consensus size: 27
36074904 TATCGGAGTG
* **
36074914 AAAATTATATAACAAATATATCTATTA
1 AAAATTATATAACAAATATATATAGGA
*
36074941 AAAATTCAAATAA-AAATA-AGTAATAGGA
1 AAAATT-ATATAACAAATATA-T-ATAGGA
36074969 AAAATTATATAACAAAT-TATAT
1 AAAATTATATAACAAATATATAT
36074991 TTTCAGTTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 11
0.71 0.09 0.20
Matches are distributed among these distances:
26 3 0.08
27 18 0.45
28 19 0.47
ACGTcount: A:0.60, C:0.05, G:0.04, T:0.31
Consensus pattern (27 bp):
AAAATTATATAACAAATATATATAGGA
Found at i:36085182 original size:21 final size:21
Alignment explanation
Indices: 36085156--36085197 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
36085146 AACATGAACA
36085156 AATTGATTCACATTCACAAGT
1 AATTGATTCACATTCACAAGT
36085177 AATTGATTCACATTCACAAGT
1 AATTGATTCACATTCACAAGT
36085198 GTCAATCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.38, C:0.19, G:0.10, T:0.33
Consensus pattern (21 bp):
AATTGATTCACATTCACAAGT
Found at i:36087599 original size:3 final size:3
Alignment explanation
Indices: 36087591--36087615 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
36087581 TCCACTCTTA
36087591 TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT T
36087616 TCTGCTCTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:36089008 original size:3 final size:3
Alignment explanation
Indices: 36089000--36089027 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
36088990 CACAATTTTA
36089000 TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT T
36089028 TCTGCTCTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:36113599 original size:19 final size:19
Alignment explanation
Indices: 36113554--36113599 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
36113544 TATAACTTAA
36113554 TTATTTTTTATTATACTTT
1 TTATTTTTTATTATACTTT
*
36113573 TTAGTTTTTTGA-TATATTTT
1 TTA-TTTTTT-ATTATACTTT
36113593 TTATTTT
1 TTATTTT
36113600 GGTCAAAAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 7 0.29
20 16 0.67
21 1 0.04
ACGTcount: A:0.20, C:0.02, G:0.04, T:0.74
Consensus pattern (19 bp):
TTATTTTTTATTATACTTT
Found at i:36115280 original size:29 final size:29
Alignment explanation
Indices: 36115247--36115316 Score: 140
Period size: 29 Copynumber: 2.4 Consensus size: 29
36115237 TTTATACATT
36115247 CATGCAATAATTTTCTTTTCAAAGGCAAA
1 CATGCAATAATTTTCTTTTCAAAGGCAAA
36115276 CATGCAATAATTTTCTTTTCAAAGGCAAA
1 CATGCAATAATTTTCTTTTCAAAGGCAAA
36115305 CATGCAATAATT
1 CATGCAATAATT
36115317 CAATGGTAGT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.39, C:0.17, G:0.10, T:0.34
Consensus pattern (29 bp):
CATGCAATAATTTTCTTTTCAAAGGCAAA
Found at i:36117604 original size:25 final size:24
Alignment explanation
Indices: 36117575--36117623 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
36117565 TTTAAATTGT
* *
36117575 ATATTAATTTTAATATTAAAGAAAA
1 ATATTAATATAAATATTAAA-AAAA
*
36117600 ATATTTATATAAATATTAAAAAAA
1 ATATTAATATAAATATTAAAAAAA
36117624 GAAAAAACTC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 4 0.19
25 17 0.81
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (24 bp):
ATATTAATATAAATATTAAAAAAA
Found at i:36117725 original size:32 final size:32
Alignment explanation
Indices: 36117684--36117747 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
36117674 CTGAATCTCG
36117684 AGCAAAAGAAGCAATGGTAACGAAGGACAAAA
1 AGCAAAAGAAGCAATGGTAACGAAGGACAAAA
36117716 AGCAAAAGAAGCAATGGTAACGAAGGACAAAA
1 AGCAAAAGAAGCAATGGTAACGAAGGACAAAA
36117748 CTGACTAGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.56, C:0.12, G:0.25, T:0.06
Consensus pattern (32 bp):
AGCAAAAGAAGCAATGGTAACGAAGGACAAAA
Found at i:36120099 original size:2 final size:2
Alignment explanation
Indices: 36120092--36120137 Score: 58
Period size: 2 Copynumber: 23.5 Consensus size: 2
36120082 TATAGAAAGC
* * *
36120092 AT AT AT AT AT -T AG CT AT AT AT AC AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
36120133 AT AT A
1 AT AT A
36120138 GAGAGAGAGA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (2 bp):
AT
Found at i:36122679 original size:10 final size:11
Alignment explanation
Indices: 36122664--36122692 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
36122654 ATTAGTCAAA
36122664 TATAAATAT-T
1 TATAAATATAT
36122674 TATAAATATAT
1 TATAAATATAT
36122685 TATAAATA
1 TATAAATA
36122693 AAAAATGCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 9 0.50
11 9 0.50
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (11 bp):
TATAAATATAT
Found at i:36123262 original size:17 final size:17
Alignment explanation
Indices: 36123224--36123263 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
36123214 ATATATATGA
*
36123224 AAAGAAAATAAAGAAGG
1 AAAGAAAATAAAGAAAG
*
36123241 AAAGAAAATGAAGAAAG
1 AAAGAAAATAAAGAAAG
*
36123258 TAAGAA
1 AAAGAA
36123264 GAGGATACTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.70, C:0.00, G:0.23, T:0.07
Consensus pattern (17 bp):
AAAGAAAATAAAGAAAG
Found at i:36126139 original size:21 final size:19
Alignment explanation
Indices: 36126110--36126148 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 19
36126100 CTTCCAAAAA
36126110 TAATATTATAATTTTTTTTTG
1 TAATATTAT--TTTTTTTTTG
*
36126131 TAATTTTATTTTTTTTTT
1 TAATATTATTTTTTTTTT
36126149 ATGATATTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
21 8 0.47
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (19 bp):
TAATATTATTTTTTTTTTG
Found at i:36126831 original size:14 final size:14
Alignment explanation
Indices: 36126800--36126834 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
36126790 TAATGTTTAT
*
36126800 TTATTTTTTTCATA
1 TTATATTTTTCATA
36126814 -TATATTTTTCATA
1 TTATATTTTTCATA
36126827 TTATATTT
1 TTATATTT
36126835 AGATTCAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.69
Consensus pattern (14 bp):
TTATATTTTTCATA
Found at i:36127036 original size:28 final size:27
Alignment explanation
Indices: 36126980--36127063 Score: 69
Period size: 28 Copynumber: 3.0 Consensus size: 27
36126970 TTACTATTGT
* * *
36126980 AATAACTTATATTTTTATAATTTTTAAAA
1 AATAAATTA-ATTTTTATTA-TTTAAAAA
*
36127009 ATTAAATTAATTTTTTATTATTTAAAAA
1 AATAAATTAA-TTTTTATTATTTAAAAA
* * *
36127037 AATAATTTTATTATTATTAATTTAAAA
1 AATAAATTAATTTTTATT-ATTTAAAA
36127064 TTTTAAAAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 5
0.78 0.14 0.09
Matches are distributed among these distances:
27 7 0.16
28 23 0.51
29 15 0.33
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.52
Consensus pattern (27 bp):
AATAAATTAATTTTTATTATTTAAAAA
Found at i:36127670 original size:15 final size:16
Alignment explanation
Indices: 36127640--36127676 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
36127630 ATAATATAAA
36127640 AATAATTTATTATTTT
1 AATAATTTATTATTTT
36127656 AATAATTTA-TATTTT
1 AATAATTTATTATTTT
*
36127671 TATAAT
1 AATAAT
36127677 ATTTAAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 11 0.55
16 9 0.45
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
AATAATTTATTATTTT
Found at i:36127702 original size:30 final size:32
Alignment explanation
Indices: 36127666--36127736 Score: 92
Period size: 30 Copynumber: 2.2 Consensus size: 32
36127656 AATAATTTAT
*
36127666 ATTTTTATAATATTTAAAATATT-AAAT-TAA
1 ATTTTTATAATATTTAAAAAATTAAAATATAA
* *
36127696 ATTTTTATTATTTTTAAAAAATTAAAATATAA
1 ATTTTTATAATATTTAAAAAATTAAAATATAA
36127728 ATTTATTAT
1 ATTT-TTAT
36127737 TATTAATTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
30 20 0.57
31 4 0.11
32 7 0.20
33 4 0.11
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (32 bp):
ATTTTTATAATATTTAAAAAATTAAAATATAA
Found at i:36136315 original size:2 final size:2
Alignment explanation
Indices: 36136308--36136335 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
36136298 AATGTGAATC
36136308 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
36136336 TTGTATTTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:36137786 original size:17 final size:17
Alignment explanation
Indices: 36137764--36137798 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
36137754 AAAGATCTTG
*
36137764 TTTAAAAATGTTTTTAT
1 TTTAAAAATATTTTTAT
36137781 TTTAAAAATATTTTTAT
1 TTTAAAAATATTTTTAT
36137798 T
1 T
36137799 CCAAAAATAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (17 bp):
TTTAAAAATATTTTTAT
Found at i:36137804 original size:17 final size:17
Alignment explanation
Indices: 36137767--36137807 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
36137757 GATCTTGTTT
* **
36137767 AAAAATGTTTTTATTTT
1 AAAAATATTTTTATTCC
36137784 AAAAATATTTTTATTCC
1 AAAAATATTTTTATTCC
36137801 AAAAATA
1 AAAAATA
36137808 CTCATTAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.46, C:0.05, G:0.02, T:0.46
Consensus pattern (17 bp):
AAAAATATTTTTATTCC
Found at i:36139523 original size:29 final size:28
Alignment explanation
Indices: 36139487--36139556 Score: 77
Period size: 28 Copynumber: 2.5 Consensus size: 28
36139477 TTTTTAAATC
* *
36139487 AAATTAAATTTATATTTTATAATTTTAAA
1 AAATTAAATTTATATATTAT-ATTTAAAA
* ** *
36139516 AATTTAAATCAAAATATTATATTTAAAA
1 AAATTAAATTTATATATTATATTTAAAA
36139544 AAATTAAATTTAT
1 AAATTAAATTTAT
36139557 CATTACTAAT
Statistics
Matches: 31, Mismatches: 10, Indels: 1
0.74 0.24 0.02
Matches are distributed among these distances:
28 16 0.52
29 15 0.48
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (28 bp):
AAATTAAATTTATATATTATATTTAAAA
Found at i:36142337 original size:22 final size:22
Alignment explanation
Indices: 36142301--36142342 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
36142291 ATATAATTTA
*
36142301 TTATATTTAGTTTTTATTTTTT
1 TTATATTTAGGTTTTATTTTTT
* *
36142323 TTATATTTTGGTTTTCTTTT
1 TTATATTTAGGTTTTATTTT
36142343 AATTTTTATC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.14, C:0.02, G:0.07, T:0.76
Consensus pattern (22 bp):
TTATATTTAGGTTTTATTTTTT
Found at i:36144597 original size:2 final size:2
Alignment explanation
Indices: 36144590--36144628 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
36144580 GAAATGAAGA
36144590 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
36144629 TACCTCTTCA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:36147629 original size:19 final size:20
Alignment explanation
Indices: 36147605--36147642 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
36147595 ATCAAGGTAA
36147605 ATTATATTATTAT-TAAAAT
1 ATTATATTATTATATAAAAT
*
36147624 ATTATATTTTTATATAAAA
1 ATTATATTATTATATAAAA
36147643 GTAATAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
ATTATATTATTATATAAAAT
Found at i:36147972 original size:19 final size:19
Alignment explanation
Indices: 36147937--36148014 Score: 54
Period size: 20 Copynumber: 4.1 Consensus size: 19
36147927 TGATAAAAAC
*
36147937 TTAATATATTACTTTTTTT
1 TTAATATATTAATTTTTTT
*
36147956 TTAATA-ATTAATATTTTT
1 TTAATATATTAATTTTTTT
* *
36147974 AT-ATATTTTGTAATTTTTTT
1 TTAATA-TAT-TAATTTTTTT
*
36147994 CATTAAT-TTTTAATTTTTTT
1 --TTAATATATTAATTTTTTT
36148014 T
1 T
36148015 AGTTTTGTAC
Statistics
Matches: 47, Mismatches: 6, Indels: 13
0.71 0.09 0.20
Matches are distributed among these distances:
17 3 0.06
18 12 0.26
19 7 0.15
20 19 0.40
21 3 0.06
22 1 0.02
23 2 0.04
ACGTcount: A:0.28, C:0.03, G:0.01, T:0.68
Consensus pattern (19 bp):
TTAATATATTAATTTTTTT
Found at i:36147993 original size:21 final size:20
Alignment explanation
Indices: 36147969--36148015 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 20
36147959 ATAATTAATA
36147969 TTTTTA-TATATTTTGTAATTT
1 TTTTTATTA-ATTTT-TAATTT
*
36147990 TTTTCATTAATTTTTAATTT
1 TTTTTATTAATTTTTAATTT
36148010 TTTTTA
1 TTTTTA
36148016 GTTTTGTACT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 11 0.48
21 10 0.43
22 2 0.09
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.72
Consensus pattern (20 bp):
TTTTTATTAATTTTTAATTT
Found at i:36150461 original size:14 final size:14
Alignment explanation
Indices: 36150444--36150474 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
36150434 ATAATTTTAC
36150444 TATTATATTGTTAT
1 TATTATATTGTTAT
*
36150458 TATTTTATTGTTAT
1 TATTATATTGTTAT
36150472 TAT
1 TAT
36150475 CTGAATATTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (14 bp):
TATTATATTGTTAT
Found at i:36152047 original size:28 final size:28
Alignment explanation
Indices: 36152016--36152075 Score: 86
Period size: 28 Copynumber: 2.1 Consensus size: 28
36152006 AAAACGGGAC
*
36152016 TTTTGGA-TACCCGGGGGCAAAATGGTAA
1 TTTTGGACT-CCCGGGAGCAAAATGGTAA
*
36152044 TTTTGGACTCGCGGGAGCAAAATGGTAA
1 TTTTGGACTCCCGGGAGCAAAATGGTAA
36152072 TTTT
1 TTTT
36152076 CGATGAAATC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 28 0.97
29 1 0.03
ACGTcount: A:0.27, C:0.13, G:0.30, T:0.30
Consensus pattern (28 bp):
TTTTGGACTCCCGGGAGCAAAATGGTAA
Found at i:36152124 original size:58 final size:59
Alignment explanation
Indices: 36152062--36152194 Score: 171
Period size: 59 Copynumber: 2.3 Consensus size: 59
36152052 TCGCGGGAGC
* *
36152062 AAAATGGTAATTTTCGATGAAATCGGGGTC-AAAAGAGAATTTTGGAAAATTCGA-GGGT
1 AAAATGGTAATTTTCGATGAAATCGAGATCGAAAAGAGAATTTTGGAAAATT-GAGGGGT
* * * * * *
36152120 AAAATAGTAATTTTTGGTGAAATCGAGATCGAAAATAGAATTTTGGAAAGTTTAGGGGT
1 AAAATGGTAATTTTCGATGAAATCGAGATCGAAAAGAGAATTTTGGAAAATTGAGGGGT
36152179 AAAATGGTAATTTTCG
1 AAAATGGTAATTTTCG
36152195 GACAATCCAG
Statistics
Matches: 63, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
58 26 0.41
59 37 0.59
ACGTcount: A:0.38, C:0.05, G:0.26, T:0.31
Consensus pattern (59 bp):
AAAATGGTAATTTTCGATGAAATCGAGATCGAAAAGAGAATTTTGGAAAATTGAGGGGT
Found at i:36152146 original size:30 final size:31
Alignment explanation
Indices: 36152061--36152163 Score: 85
Period size: 30 Copynumber: 3.5 Consensus size: 31
36152051 CTCGCGGGAG
* * *
36152061 CAAAATGGTAATTTTCGATGAAATCG-GGGT
1 CAAAATAGTAATTTTTGGTGAAATCGAGGGT
* *
36152091 CAAAAGAG-AA-TTTTGG-AAAATTCGAGGGT
1 CAAAATAGTAATTTTTGGTGAAA-TCGAGGGT
*
36152120 -AAAATAGTAATTTTTGGTGAAATCGA-GAT
1 CAAAATAGTAATTTTTGGTGAAATCGAGGGT
36152149 CGAAAATAG-AATTTT
1 C-AAAATAGTAATTTT
36152164 GGAAAGTTTA
Statistics
Matches: 58, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
27 3 0.05
28 13 0.22
29 10 0.17
30 22 0.38
31 10 0.17
ACGTcount: A:0.40, C:0.07, G:0.23, T:0.30
Consensus pattern (31 bp):
CAAAATAGTAATTTTTGGTGAAATCGAGGGT
Found at i:36154056 original size:6 final size:6
Alignment explanation
Indices: 36154041--36154099 Score: 50
Period size: 6 Copynumber: 9.8 Consensus size: 6
36154031 TTAAATTTGA
* * *
36154041 TTAAAC TTAAAT TTAAA- GTAAAT TTAAAT AAGTAAAT TTAAAT TTAAA-
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT --TTAAAT TTAAAT TTAAAT
*
36154089 ATAAAT TTAAA
1 TTAAAT TTAAA
36154100 ACTCATTTAA
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
5 8 0.19
6 29 0.69
8 5 0.12
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.39
Consensus pattern (6 bp):
TTAAAT
Found at i:36154075 original size:14 final size:14
Alignment explanation
Indices: 36154056--36154083 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
36154046 CTTAAATTTA
36154056 AAGTAAATTTAAAT
1 AAGTAAATTTAAAT
36154070 AAGTAAATTTAAAT
1 AAGTAAATTTAAAT
36154084 TTAAAATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (14 bp):
AAGTAAATTTAAAT
Found at i:36155117 original size:16 final size:17
Alignment explanation
Indices: 36155093--36155126 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
36155083 AAAATTTCTA
36155093 ATTTGTAATTAT-TTAT
1 ATTTGTAATTATCTTAT
*
36155109 ATTTTTAATTATCTTAT
1 ATTTGTAATTATCTTAT
36155126 A
1 A
36155127 ATTTAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (17 bp):
ATTTGTAATTATCTTAT
Found at i:36158412 original size:105 final size:105
Alignment explanation
Indices: 36158101--36158414 Score: 443
Period size: 105 Copynumber: 3.0 Consensus size: 105
36158091 TATAGGTAAC
* * * * * * * *
36158101 AACATCAGGCTCAATGCCTTGCTTTATCATTGTGTCAACGATATCTGTAGCTTCAGAATTCATCC
1 AACATTAGGCTCAATGCCATGCTTTCTCATTGTGTCAAGGATTTCTATAGCTTCCGAAATCATCC
* ** *
36158166 CCTCCTTGCAACATGCATTGATACATATATTTTACGTGAT
66 CCTCCTTGCAATATGCATCAATACATATATTATACGTGAT
*
36158206 AACATTAGGCTCAATGTCATGCTTTCTCATTGTGTCAAGGATTTCTATAGCTTCCGAAATCATCC
1 AACATTAGGCTCAATGCCATGCTTTCTCATTGTGTCAAGGATTTCTATAGCTTCCGAAATCATCC
* *
36158271 CCTCCTTGCAATATGCATCAATACATATACTGTACGTGAT
66 CCTCCTTGCAATATGCATCAATACATATATTATACGTGAT
*
36158311 AACATTAGGCTCAATGCCATGCTTTCTCATTGTGTCAAGGATTTCTACAGCTTCCGAAATCATCC
1 AACATTAGGCTCAATGCCATGCTTTCTCATTGTGTCAAGGATTTCTATAGCTTCCGAAATCATCC
*
36158376 CCTCCTTGCAATGTGCATCAAT-CA-ATGCATTATACGTGA
66 CCTCCTTGCAATATGCATCAATACATAT--ATTATACGTGA
36158415 CAATATCAAG
Statistics
Matches: 188, Mismatches: 19, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
103 2 0.01
104 2 0.01
105 184 0.98
ACGTcount: A:0.27, C:0.25, G:0.15, T:0.34
Consensus pattern (105 bp):
AACATTAGGCTCAATGCCATGCTTTCTCATTGTGTCAAGGATTTCTATAGCTTCCGAAATCATCC
CCTCCTTGCAATATGCATCAATACATATATTATACGTGAT
Found at i:36164989 original size:20 final size:20
Alignment explanation
Indices: 36164964--36165003 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
36164954 ATTTTTCCTT
36164964 ACTTTAAATTAATATATCGA
1 ACTTTAAATTAATATATCGA
36164984 ACTTTAAATTAATATATCGA
1 ACTTTAAATTAATATATCGA
36165004 TGGATTCTCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.45, C:0.10, G:0.05, T:0.40
Consensus pattern (20 bp):
ACTTTAAATTAATATATCGA
Found at i:36168396 original size:9 final size:9
Alignment explanation
Indices: 36168384--36168413 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
36168374 ACCAAAAGCA
36168384 CCGCCTCCG
1 CCGCCTCCG
36168393 CCGCCTCCG
1 CCGCCTCCG
36168402 CCGCCTCCG
1 CCGCCTCCG
36168411 CCG
1 CCG
36168414 TCCCTTCTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.00, C:0.67, G:0.23, T:0.10
Consensus pattern (9 bp):
CCGCCTCCG
Found at i:36177321 original size:146 final size:148
Alignment explanation
Indices: 36177066--36177393 Score: 459
Period size: 146 Copynumber: 2.2 Consensus size: 148
36177056 TATTATCTTG
* * * * * *
36177066 ATTAGAATTTCCCTTTAGCCCTAAAAATGTTGGCAACTTTTATTGGTGGCCATATATTTTTCTTT
1 ATTAGAATTTCCTTTTAGTCCTCAAAATGTTGGCAACCTTTATTGGTGGCCATATATTTTCCCTT
*
36177131 TTCATACACCATTTGTATATGATGTAAGATCCCAAATCCCAAAAGAATGAAAGTGATTT-CC-TA
66 TTCATACACCATTTGTATATGATGTAAGATCCCAAATCCCAAAAGAATAAAAGTGATTTCCCATA
36177194 A-TTCTAATCTTTAGATTA
131 AGTT-TAATCTTTAGATTA
* * *
36177212 ATTATAATTTCCTTTTAGTCCTCAGAATGTTGGCAACCTTTCTTGGTGGCCATAT-TCTTTCCCT
1 ATTAGAATTTCCTTTTAGTCCTCAAAATGTTGGCAACCTTTATTGGTGGCCATATAT-TTTCCCT
* * *
36177276 TTTCATACACCCTTT-TATATGATGTAAGATCCCACATTCCTAAAAGAATAAAAGTGATTTCCCA
65 TTTCATACACCATTTGTATATGATGTAAGATCCCA-AATCCCAAAAGAATAAAAGTGATTTCCC-
*
36177340 ATAAGTTTAATCTTTATATTA
128 ATAAGTTTAATCTTTAGATTA
36177361 ATTAGAATTTCCTTTTAGTCCTCAAAATGTTGG
1 ATTAGAATTTCCTTTTAGTCCTCAAAATGTTGG
36177394 GAAGGTTATA
Statistics
Matches: 160, Mismatches: 16, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
145 20 0.12
146 89 0.56
147 2 0.01
149 47 0.29
150 2 0.01
ACGTcount: A:0.30, C:0.18, G:0.12, T:0.40
Consensus pattern (148 bp):
ATTAGAATTTCCTTTTAGTCCTCAAAATGTTGGCAACCTTTATTGGTGGCCATATATTTTCCCTT
TTCATACACCATTTGTATATGATGTAAGATCCCAAATCCCAAAAGAATAAAAGTGATTTCCCATA
AGTTTAATCTTTAGATTA
Found at i:36180453 original size:28 final size:28
Alignment explanation
Indices: 36180387--36180453 Score: 66
Period size: 28 Copynumber: 2.4 Consensus size: 28
36180377 TTAAATTTAT
* *
36180387 AATGAGAAAATTACATTTAACCCTAAAA
1 AATGATAAATTTACATTTAACCCTAAAA
*
36180415 AAT-ATTAAAATTTA-ATTTAACCCTTTAAA
1 AATGA-T-AAATTTACATTTAACCC-TAAAA
36180444 AATGATAAAT
1 AATGATAAAT
36180454 ATATAAACTA
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
27 1 0.03
28 16 0.50
29 14 0.44
30 1 0.03
ACGTcount: A:0.52, C:0.10, G:0.04, T:0.33
Consensus pattern (28 bp):
AATGATAAATTTACATTTAACCCTAAAA
Found at i:36184312 original size:18 final size:17
Alignment explanation
Indices: 36184289--36184324 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
36184279 TTAAAAATTT
*
36184289 TAAAAATTTAAAATTAAA
1 TAAAAAATTAAAA-TAAA
36184307 TAAAAAATTAAAATAAA
1 TAAAAAATTAAAATAAA
36184324 T
1 T
36184325 TTTTTATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
TAAAAAATTAAAATAAA
Found at i:36199055 original size:23 final size:24
Alignment explanation
Indices: 36199023--36199067 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
36199013 TTTCTTTTCC
36199023 TTTTATTTTTCTGTTCGGTTTTTT
1 TTTTATTTTTCTGTTCGGTTTTTT
*
36199047 TTTTA-TTTTCTGTTGGGTTTT
1 TTTTATTTTTCTGTTCGGTTTT
36199068 GACATGTGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.04, C:0.07, G:0.16, T:0.73
Consensus pattern (24 bp):
TTTTATTTTTCTGTTCGGTTTTTT
Found at i:36209711 original size:21 final size:21
Alignment explanation
Indices: 36209687--36209737 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
36209677 CCATATTGTA
36209687 ACCCATCTGACCACCCATTTG
1 ACCCATCTGACCACCCATTTG
36209708 ACCCATCTGACCACCCATTTG
1 ACCCATCTGACCACCCATTTG
*
36209729 GCCCATCTG
1 ACCCATCTG
36209738 CCCCATATTC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.22, C:0.43, G:0.12, T:0.24
Consensus pattern (21 bp):
ACCCATCTGACCACCCATTTG
Found at i:36210386 original size:24 final size:24
Alignment explanation
Indices: 36210366--36210419 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
36210356 ATCATCATCA
36210366 TCATCATCGAACTCATCATCAAAT
1 TCATCATCGAACTCATCATCAAAT
* *
36210390 TCATCATCGAACTCATCACCAAAC
1 TCATCATCGAACTCATCATCAAAT
36210414 TCATCA
1 TCATCA
36210420 AAATCACAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.37, C:0.33, G:0.04, T:0.26
Consensus pattern (24 bp):
TCATCATCGAACTCATCATCAAAT
Found at i:36210393 original size:12 final size:12
Alignment explanation
Indices: 36210366--36210419 Score: 72
Period size: 12 Copynumber: 4.5 Consensus size: 12
36210356 ATCATCATCA
*
36210366 TCATCATCGAAC
1 TCATCATCAAAC
*
36210378 TCATCATCAAAT
1 TCATCATCAAAC
*
36210390 TCATCATCGAAC
1 TCATCATCAAAC
*
36210402 TCATCACCAAAC
1 TCATCATCAAAC
36210414 TCATCA
1 TCATCA
36210420 AAATCACAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 36 1.00
ACGTcount: A:0.37, C:0.33, G:0.04, T:0.26
Consensus pattern (12 bp):
TCATCATCAAAC
Found at i:36210397 original size:3 final size:3
Alignment explanation
Indices: 36210348--36210386 Score: 53
Period size: 3 Copynumber: 13.0 Consensus size: 3
36210338 AAATTCCCCT
*
36210348 TCA TCA TCA TCA TCA TCA TCA TCA TCGA AC- TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TC-A TCA TCA TCA TCA
36210387 AATTCATCAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 1 0.03
3 29 0.91
4 2 0.06
ACGTcount: A:0.33, C:0.33, G:0.03, T:0.31
Consensus pattern (3 bp):
TCA
Found at i:36211192 original size:12 final size:12
Alignment explanation
Indices: 36211175--36211205 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
36211165 AAGAAAGACA
36211175 AGACAGACAAAG
1 AGACAGACAAAG
*
36211187 AGACAGACAGAG
1 AGACAGACAAAG
36211199 AGACAGA
1 AGACAGA
36211206 AGATGAAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.55, C:0.16, G:0.29, T:0.00
Consensus pattern (12 bp):
AGACAGACAAAG
Found at i:36212709 original size:2 final size:2
Alignment explanation
Indices: 36212702--36212729 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
36212692 CTTGTCAATA
36212702 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
36212730 GTAAAGATGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:36213193 original size:16 final size:16
Alignment explanation
Indices: 36213139--36213193 Score: 78
Period size: 15 Copynumber: 3.6 Consensus size: 16
36213129 TTGGAAAGTA
*
36213139 TAATATTTTCAATATT
1 TAATTTTTTCAATATT
36213155 TAATTTTTT-AATATT
1 TAATTTTTTCAATATT
*
36213170 T-ATCTTTTCAATATT
1 TAATTTTTTCAATATT
36213185 TAATTTTTT
1 TAATTTTTT
36213194 AATTTATCGA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
14 6 0.18
15 14 0.41
16 14 0.41
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.64
Consensus pattern (16 bp):
TAATTTTTTCAATATT
Found at i:36221353 original size:2 final size:2
Alignment explanation
Indices: 36221348--36221380 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
36221338 TTTGGACATG
36221348 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
36221381 TATCTGACCT
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:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:36227454 original size:22 final size:22
Alignment explanation
Indices: 36227425--36227467 Score: 79
Period size: 21 Copynumber: 2.0 Consensus size: 22
36227415 AATTAAATTC
36227425 TTTTAAAAATT-TAAAAATTAT
1 TTTTAAAAATTCTAAAAATTAT
36227446 TTTTAAAAATTCTAAAAATTAT
1 TTTTAAAAATTCTAAAAATTAT
36227468 AAACAAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (22 bp):
TTTTAAAAATTCTAAAAATTAT
Found at i:36227496 original size:21 final size:21
Alignment explanation
Indices: 36227419--36227497 Score: 76
Period size: 21 Copynumber: 3.8 Consensus size: 21
36227409 AAAATCAATT
*
36227419 AAATTCTT-TTAAAAATTTAA
1 AAATTATTATTAAAAATTTAA
*
36227439 AAATTATTTTTAAAAATTCTAA
1 AAATTATTATTAAAAATT-TAA
*
36227461 AAATTA-TA-AACAAAATTTATA
1 AAATTATTATTA-AAAATTTA-A
36227482 AAATT-TTATTAAAAAT
1 AAATTATTATTAAAAAT
36227498 AAAAATACCG
Statistics
Matches: 49, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
20 10 0.20
21 29 0.59
22 10 0.20
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (21 bp):
AAATTATTATTAAAAATTTAA
Found at i:36238417 original size:3 final size:3
Alignment explanation
Indices: 36238409--36238440 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
36238399 TTACCTTCAT
36238409 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
36238441 TTGATTTGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:36239648 original size:17 final size:17
Alignment explanation
Indices: 36239628--36239660 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
36239618 ATATTAACTA
36239628 TAATGATAAATTATATG
1 TAATGATAAATTATATG
*
36239645 TAATGGTAAATTATAT
1 TAATGATAAATTATAT
36239661 TACACTTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.12, T:0.42
Consensus pattern (17 bp):
TAATGATAAATTATATG
Found at i:36251426 original size:19 final size:18
Alignment explanation
Indices: 36251402--36251440 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 18
36251392 GATTCAAATT
36251402 TTTAATAGTAA-TAATCAAA
1 TTTAATA-TAAGTAAT-AAA
36251421 TTTAATATAAGTAATAAA
1 TTTAATATAAGTAATAAA
36251439 TT
1 TT
36251441 GATTTAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.51, C:0.03, G:0.05, T:0.41
Consensus pattern (18 bp):
TTTAATATAAGTAATAAA
Found at i:36261775 original size:16 final size:17
Alignment explanation
Indices: 36261750--36261782 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
36261740 GTAATCTTAT
*
36261750 TTTTATTAA-TTTAAAA
1 TTTTACTAATTTTAAAA
36261766 TTTTACTAATTTTAAAA
1 TTTTACTAATTTTAAAA
36261783 AAATTTAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (17 bp):
TTTTACTAATTTTAAAA
Found at i:36269295 original size:18 final size:18
Alignment explanation
Indices: 36269272--36269306 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
36269262 AACTAACTAA
36269272 TTACATTATAAAAATTGT
1 TTACATTATAAAAATTGT
36269290 TTACATTATAAAAATTG
1 TTACATTATAAAAATTG
36269307 AAGTGTCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.46, C:0.06, G:0.06, T:0.43
Consensus pattern (18 bp):
TTACATTATAAAAATTGT
Found at i:36273998 original size:50 final size:50
Alignment explanation
Indices: 36273923--36274024 Score: 195
Period size: 50 Copynumber: 2.0 Consensus size: 50
36273913 CATTAATTCT
*
36273923 ATGCATATTGATAGATTCAATCCATGCAGTGATTTCTTTAAGAGACTAAA
1 ATGCATATTGATAGATTCAATCCATGCAGTGATTTCTTTAACAGACTAAA
36273973 ATGCATATTGATAGATTCAATCCATGCAGTGATTTCTTTAACAGACTAAA
1 ATGCATATTGATAGATTCAATCCATGCAGTGATTTCTTTAACAGACTAAA
36274023 AT
1 AT
36274025 TGATTAGCAG
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Consensus pattern (50 bp):
ATGCATATTGATAGATTCAATCCATGCAGTGATTTCTTTAACAGACTAAA
Found at i:36277011 original size:18 final size:20
Alignment explanation
Indices: 36276986--36277029 Score: 65
Period size: 19 Copynumber: 2.2 Consensus size: 20
36276976 GATAGGGAAG
36276986 GAAAAAA-AAAAGATTAAA-A
1 GAAAAAACAAAA-ATTAAAGA
36277005 GAAAAAACAAAAATTAAAGA
1 GAAAAAACAAAAATTAAAGA
36277025 GAAAA
1 GAAAA
36277030 TATGGTGAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 13 0.57
20 10 0.43
ACGTcount: A:0.77, C:0.02, G:0.11, T:0.09
Consensus pattern (20 bp):
GAAAAAACAAAAATTAAAGA
Found at i:36293627 original size:29 final size:29
Alignment explanation
Indices: 36293575--36293634 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
36293565 TCTCAAATTG
*
36293575 TTGTTTAATCATTAAATTATTTAATTGTT
1 TTGTTTAATCATTAAATTAGTTAATTGTT
* *
36293604 TTGTTTAAGTCATTCAATT-GTTAATTTTT
1 TTGTTTAA-TCATTAAATTAGTTAATTGTT
36293633 TT
1 TT
36293635 TTTTCAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 18 0.67
30 9 0.33
ACGTcount: A:0.27, C:0.05, G:0.08, T:0.60
Consensus pattern (29 bp):
TTGTTTAATCATTAAATTAGTTAATTGTT
Found at i:36297978 original size:14 final size:15
Alignment explanation
Indices: 36297928--36297977 Score: 52
Period size: 14 Copynumber: 3.4 Consensus size: 15
36297918 AATAAAGAGG
*
36297928 TATATGATGATATA-
1 TATATGATGAAATAT
36297942 TATATGATGAACA-AT
1 TATATGATGAA-ATAT
36297957 GTATATG-TGAAATAT
1 -TATATGATGAAATAT
36297972 TATATG
1 TATATG
36297978 TTTAATTATA
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
14 18 0.58
15 7 0.23
16 6 0.19
ACGTcount: A:0.42, C:0.02, G:0.16, T:0.40
Consensus pattern (15 bp):
TATATGATGAAATAT
Found at i:36298133 original size:6 final size:6
Alignment explanation
Indices: 36298122--36298154 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
36298112 TGATCAAAAT
*
36298122 TGAAAG TGAAAG TGAAAG TGAAAT TGAAAG TGA
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGA
36298155 TATGAATTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.30, T:0.21
Consensus pattern (6 bp):
TGAAAG
Found at i:36305136 original size:22 final size:22
Alignment explanation
Indices: 36305085--36305137 Score: 58
Period size: 20 Copynumber: 2.5 Consensus size: 22
36305075 AATTCTCAAT
*
36305085 ATTTATATT-TTTTATTAACTTA
1 ATTTA-ATTATTTTATTAACTAA
*
36305107 ATTT--TTATTTTGTTAACTAA
1 ATTTAATTATTTTATTAACTAA
36305127 ATTTAATTATT
1 ATTTAATTATT
36305138 AATTTTGTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
19 2 0.08
20 15 0.58
22 9 0.35
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (22 bp):
ATTTAATTATTTTATTAACTAA
Found at i:36308610 original size:69 final size:69
Alignment explanation
Indices: 36308478--36308671 Score: 253
Period size: 69 Copynumber: 2.8 Consensus size: 69
36308468 TTCAAGTAGT
* * * * * * **
36308478 TTAAGGAGATTTGAAGGATCAAGAGACTCGTATCAATCTGATAGTAACACTGGATTAGTTTCAGG
1 TTAAGGAGATTAGAAGAATCAAGAGACTCATATCAATCTGATGGTAACACCGAATTAACTTCAGG
36308543 TAAC
66 TAAC
* * *
36308547 TTAAAGAGATTAGAAGAATCAAGAGACTCATATCAATCTAATGGTAGCACCGAATTAACTTCAGG
1 TTAAGGAGATTAGAAGAATCAAGAGACTCATATCAATCTGATGGTAACACCGAATTAACTTCAGG
*
36308612 TAGC
66 TAAC
* * *
36308616 TTAAGGAAATTAGAAGAATCAAGAGACTCATATGAATATGATGGTAACACCGAATT
1 TTAAGGAGATTAGAAGAATCAAGAGACTCATATCAATCTGATGGTAACACCGAATT
36308672 GTCTACATTT
Statistics
Matches: 107, Mismatches: 18, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
69 107 1.00
ACGTcount: A:0.40, C:0.13, G:0.21, T:0.26
Consensus pattern (69 bp):
TTAAGGAGATTAGAAGAATCAAGAGACTCATATCAATCTGATGGTAACACCGAATTAACTTCAGG
TAAC
Found at i:36310759 original size:69 final size:69
Alignment explanation
Indices: 36310638--36310790 Score: 227
Period size: 69 Copynumber: 2.2 Consensus size: 69
36310628 GATCATAATT
* * *
36310638 AATCTAATGATAGCATCGGATTAATTCAAGATAGCTTAAGGATATTAGAAGAATCAAGAGACTCA
1 AATCTAATGGTAGCATCGGATTAATTCAAGATAGCTTAAGGAGATTAAAAGAATCAAGAGACTCA
36310703 TATC
66 TATC
*
36310707 AATCTAATGGTAGCATCGGATTAACTTC-AGATAGCTTAAGGAGATTAAAAGAATCAAGAGACTT
1 AATCTAATGGTAGCATCGGATTAA-TTCAAGATAGCTTAAGGAGATTAAAAGAATCAAGAGACTC
* *
36310771 GTATG
65 ATATC
*
36310776 AATCTTATGGTAGCA
1 AATCTAATGGTAGCA
36310791 CTAGATCCTT
Statistics
Matches: 76, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
69 73 0.96
70 3 0.04
ACGTcount: A:0.40, C:0.12, G:0.20, T:0.28
Consensus pattern (69 bp):
AATCTAATGGTAGCATCGGATTAATTCAAGATAGCTTAAGGAGATTAAAAGAATCAAGAGACTCA
TATC
Found at i:36311559 original size:48 final size:48
Alignment explanation
Indices: 36311488--36311674 Score: 146
Period size: 48 Copynumber: 3.7 Consensus size: 48
36311478 GTTCTAATGC
**
36311488 GGCATTATTACAATGAAGAACAAGACCCTT-TGTGTGCCAACATCAAAA
1 GGCATTAGCACAA-GAAGAACAAGACCCTTATGTGTGCCAACATCAAAA
* ** * *
36311536 GGCATTAGCACAAGGAAGAACAAGGTCAATTGTGTGCCAATGCCAACATCAGAA
1 GGCATTAGCACAA-GAAGAACAA-GACCCTTATGTG----TGCCAACATCAAAA
* * *
36311590 TGCATTAGCACAAGAATGAACAAGGCCCATTA--TATGCCAACATCAAAA
1 GGCATTAGCACAAGAA-GAACAAGACCC-TTATGTGTGCCAACATCAAAA
* *
36311638 GACATTAGCATACAGAAGAACAAGACCCATTATGTGT
1 GGCATTAGCACA-AGAAGAACAAGACCC-TTATGTGT
36311675 TTTTCATTTT
Statistics
Matches: 109, Mismatches: 19, Indels: 20
0.74 0.13 0.14
Matches are distributed among these distances:
48 56 0.51
49 8 0.07
50 6 0.06
52 1 0.01
53 5 0.05
54 33 0.30
ACGTcount: A:0.41, C:0.21, G:0.19, T:0.20
Consensus pattern (48 bp):
GGCATTAGCACAAGAAGAACAAGACCCTTATGTGTGCCAACATCAAAA
Found at i:36311628 original size:54 final size:54
Alignment explanation
Indices: 36311522--36311629 Score: 146
Period size: 54 Copynumber: 2.0 Consensus size: 54
36311512 ACCCTTTGTG
* * *
36311522 TGCCAACATCAAAAGGCATTAGCACAAGGAAGAACAAGGTCAATTGTGTGCCAA
1 TGCCAACATCAAAAGGCATTAGCACAAGGAAGAACAAGGCCAATTATATGCCAA
* * *
36311576 TGCCAACATCAGAATGCATTAGCACAA-GAATGAACAAGGCCCATTATATGCCAA
1 TGCCAACATCAAAAGGCATTAGCACAAGGAA-GAACAAGGCCAATTATATGCCAA
36311630 CATCAAAAGA
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
53 3 0.06
54 44 0.94
ACGTcount: A:0.41, C:0.22, G:0.19, T:0.18
Consensus pattern (54 bp):
TGCCAACATCAAAAGGCATTAGCACAAGGAAGAACAAGGCCAATTATATGCCAA
Found at i:36312486 original size:21 final size:23
Alignment explanation
Indices: 36312444--36312487 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
36312434 TTAGCGGAAA
*
36312444 TTTGGATTTCAAAAATCAATATT
1 TTTGAATTTCAAAAATCAATATT
*
36312467 TTTGAATTT-AAAATTC-ATATT
1 TTTGAATTTCAAAAATCAATATT
36312488 CTTGTATATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 5 0.26
22 6 0.32
23 8 0.42
ACGTcount: A:0.39, C:0.07, G:0.07, T:0.48
Consensus pattern (23 bp):
TTTGAATTTCAAAAATCAATATT
Found at i:36321770 original size:5 final size:6
Alignment explanation
Indices: 36321753--36321777 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
36321743 TTATAAAATT
36321753 ATAAAA ATAAAA ATAAAA ATAAAA A
1 ATAAAA ATAAAA ATAAAA ATAAAA A
36321778 ATCTGATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
ATAAAA
Found at i:36322339 original size:15 final size:15
Alignment explanation
Indices: 36322304--36322338 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
36322294 CAAGATCAAG
*
36322304 ATTTTTACAACATCC
1 ATTTTTACAACATAC
36322319 ATTTTTACAACA-AC
1 ATTTTTACAACATAC
36322333 ATTTTT
1 ATTTTT
36322339 TTCTTTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 7 0.37
15 12 0.63
ACGTcount: A:0.34, C:0.20, G:0.00, T:0.46
Consensus pattern (15 bp):
ATTTTTACAACATAC
Found at i:36327011 original size:21 final size:21
Alignment explanation
Indices: 36326987--36327030 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
36326977 ACCTCCACGA
*
36326987 CTGCCTCCTCTACCACCACCT
1 CTGCCTCCTCCACCACCACCT
*
36327008 CTGCCTCCTCCACGACCACCT
1 CTGCCTCCTCCACCACCACCT
36327029 CT
1 CT
36327031 TCCACCACCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.14, C:0.57, G:0.07, T:0.23
Consensus pattern (21 bp):
CTGCCTCCTCCACCACCACCT
Found at i:36328593 original size:25 final size:26
Alignment explanation
Indices: 36328536--36328598 Score: 80
Period size: 25 Copynumber: 2.6 Consensus size: 26
36328526 AATTATCTTA
*
36328536 TATTTATA-TTT-TAATTTATTAATG
1 TATTTATATTTTGTAATATATTAATG
*
36328560 -ATTTATATTTTGTAA-ATATTGATG
1 TATTTATATTTTGTAATATATTAATG
36328584 TATTTATATTTTGTA
1 TATTTATATTTTGTA
36328599 GTGTTCAAGT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
23 7 0.21
24 10 0.29
25 17 0.50
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.60
Consensus pattern (26 bp):
TATTTATATTTTGTAATATATTAATG
Found at i:36328726 original size:21 final size:21
Alignment explanation
Indices: 36328676--36328726 Score: 50
Period size: 23 Copynumber: 2.3 Consensus size: 21
36328666 GATATGATCC
*
36328676 AAATTTTTATATATTTAATGGAT
1 AAATTTTTATATATATAAT-G-T
*
36328699 AATTTTTTATATTATATAAT-T
1 AAATTTTTATA-TATATAATGT
36328720 AAATTTT
1 AAATTTT
36328727 AATTTATTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
21 7 0.29
23 10 0.42
24 7 0.29
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (21 bp):
AAATTTTTATATATATAATGT
Found at i:36337049 original size:14 final size:14
Alignment explanation
Indices: 36337026--36337059 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
36337016 TGCAATTTTT
36337026 AAATAATAACAATA
1 AAATAATAACAATA
*
36337040 AAATAGTAACAATA
1 AAATAATAACAATA
*
36337054 TAATAA
1 AAATAA
36337060 CGAAATGGTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.68, C:0.06, G:0.03, T:0.24
Consensus pattern (14 bp):
AAATAATAACAATA
Found at i:36338362 original size:13 final size:14
Alignment explanation
Indices: 36338344--36338372 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
36338334 TTTTAAAAAG
36338344 AATCAA-ATTTTAA
1 AATCAATATTTTAA
36338357 AATCAATATTTTAA
1 AATCAATATTTTAA
36338371 AA
1 AA
36338373 AGAGTTAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (14 bp):
AATCAATATTTTAA
Found at i:36342584 original size:29 final size:29
Alignment explanation
Indices: 36342526--36342589 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
36342516 ATATTCATGA
* *
36342526 AAAATTGATCAAATAAAAAGTTAGTGTAT
1 AAAATTGATAAAATAAAAAGTTAGTATAT
* *
36342555 AAAATTGGATAAAATTAAAATTTA-TATAT
1 AAAATT-GATAAAATAAAAAGTTAGTATAT
36342584 AAAATT
1 AAAATT
36342590 ATACATTATA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 16 0.53
30 14 0.47
ACGTcount: A:0.55, C:0.02, G:0.09, T:0.34
Consensus pattern (29 bp):
AAAATTGATAAAATAAAAAGTTAGTATAT
Found at i:36342598 original size:19 final size:20
Alignment explanation
Indices: 36342563--36342605 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
36342553 ATAAAATTGG
36342563 ATAAAATTAAAATTTAT-AT
1 ATAAAATTAAAATTTATAAT
*
36342582 ATAAAATTATACA-TTATAAT
1 ATAAAATTA-AAATTTATAAT
36342602 ATAA
1 ATAA
36342606 TTTATGTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 13 0.62
20 8 0.38
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (20 bp):
ATAAAATTAAAATTTATAAT
Found at i:36357456 original size:30 final size:30
Alignment explanation
Indices: 36357412--36357472 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 30
36357402 TAAAATTTTT
* *
36357412 ATTTTCCCTTAAAATTTTTATTCTC-TCCC
1 ATTTTCCCCTAAAATTTTTACTCTCATCCC
36357441 ATTTTCTCCCTAAAATTTTTACTCTCATCCC
1 ATTTTC-CCCTAAAATTTTTACTCTCATCCC
36357472 A
1 A
36357473 CCCTCCATCT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 6 0.21
30 17 0.61
31 5 0.18
ACGTcount: A:0.23, C:0.30, G:0.00, T:0.48
Consensus pattern (30 bp):
ATTTTCCCCTAAAATTTTTACTCTCATCCC
Found at i:36357821 original size:32 final size:32
Alignment explanation
Indices: 36357780--36357843 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
36357770 AATTTTATGT
36357780 TAGTATTAATTTCACATTTTATCTTTGAAATA
1 TAGTATTAATTTCACATTTTATCTTTGAAATA
*
36357812 TAGTATTAATTTCATATTTTATCTTTGAAATA
1 TAGTATTAATTTCACATTTTATCTTTGAAATA
36357844 ATTTTTATTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.34, C:0.08, G:0.06, T:0.52
Consensus pattern (32 bp):
TAGTATTAATTTCACATTTTATCTTTGAAATA
Found at i:36359251 original size:17 final size:18
Alignment explanation
Indices: 36359231--36359271 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
36359221 CTAATTTAAC
*
36359231 ATAAATTTAT-TTTAAAA
1 ATAAATATATATTTAAAA
*
36359248 AT-AATATATATTTGAAA
1 ATAAATATATATTTAAAA
36359265 ATAAATA
1 ATAAATA
36359272 CACTCTAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
16 6 0.30
17 10 0.50
18 4 0.20
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.41
Consensus pattern (18 bp):
ATAAATATATATTTAAAA
Found at i:36359365 original size:16 final size:16
Alignment explanation
Indices: 36359344--36359374 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
36359334 TTAAAAATTT
36359344 TCATATATTTATATTA
1 TCATATATTTATATTA
*
36359360 TCATATTTTTATATT
1 TCATATATTTATATT
36359375 TATATTAACT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.61
Consensus pattern (16 bp):
TCATATATTTATATTA
Found at i:36360040 original size:16 final size:16
Alignment explanation
Indices: 36360016--36360047 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
36360006 GTTAAAAGCA
36360016 TTTTGTTTTTCTTTTT
1 TTTTGTTTTTCTTTTT
*
36360032 TTTTTTTTTTCTTTTT
1 TTTTGTTTTTCTTTTT
36360048 GGGATTTTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.00, C:0.06, G:0.03, T:0.91
Consensus pattern (16 bp):
TTTTGTTTTTCTTTTT
Found at i:36375952 original size:35 final size:35
Alignment explanation
Indices: 36375913--36375979 Score: 89
Period size: 35 Copynumber: 1.9 Consensus size: 35
36375903 AATAAAGATT
*
36375913 TTTTTCTCAAAAAATCTCTCTTCCTCGGCAAATTC
1 TTTTTCTCAAAAAATCTCTCTTCCTCCGCAAATTC
** * *
36375948 TTTTTCTCCCAAAATTTCTCTTTCTCCGCAAA
1 TTTTTCTCAAAAAATCTCTCTTCCTCCGCAAA
36375980 GCATAAGATC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 27 1.00
ACGTcount: A:0.24, C:0.30, G:0.04, T:0.42
Consensus pattern (35 bp):
TTTTTCTCAAAAAATCTCTCTTCCTCCGCAAATTC
Found at i:36377729 original size:245 final size:245
Alignment explanation
Indices: 36377299--36377790 Score: 930
Period size: 245 Copynumber: 2.0 Consensus size: 245
36377289 ATCCACCACG
*
36377299 CTCCGCAATTCCAATCCCTACATGGATTAGCTTTGTGCTAGCTTATTCTAGCTTCAGGCCTACAC
1 CTCCGCAATTCCAATCCCTACATGGATTAGCTTTGTGCTAGCTTATTCTAGCTCCAGGCCTACAC
36377364 TACACTACCAATGTCAACATTTATCACATGATTGCAATTAAAAGGCATGACAACTAGCTAACTCT
66 TACACTACCAATGTCAACATTTATCACATGATTGCAATTAAAAGGCATGACAACTAGCTAACTCT
*
36377429 GATACCAATTAATATGGACCTTTGGAGATCCACACCCCAAAAAAGCTAGCGATTGAAACTAAAGA
131 GATACCAATTAATATGGACCTTTGGAGAACCACACCCCAAAAAAGCTAGCGATTGAAACTAAAGA
*
36377494 GCCTATGTCCATATAACCCCTACTAGGAAACCTCATACTTTGCCCCACAC
196 GCCTATATCCATATAACCCCTACTAGGAAACCTCATACTTTGCCCCACAC
36377544 CTCCGCAATTCCAATCCCTACATGGATTAGCTTTGTGCTAGCTTATTCTAGCTCCAGGCCTACAC
1 CTCCGCAATTCCAATCCCTACATGGATTAGCTTTGTGCTAGCTTATTCTAGCTCCAGGCCTACAC
36377609 TACACTACCAATGTCAACATTTATCACATGATTGCAATTAAAAGGCATGACAACTAGCTAACTCT
66 TACACTACCAATGTCAACATTTATCACATGATTGCAATTAAAAGGCATGACAACTAGCTAACTCT
*
36377674 GATACCAATTAATATGGACCTTTGGAGAACCACACCCCAAAAAAGCTAGCGATTGAAACTAGAGA
131 GATACCAATTAATATGGACCTTTGGAGAACCACACCCCAAAAAAGCTAGCGATTGAAACTAAAGA
* *
36377739 GTCTATATCCATATAACCCCTACTAGGAAATCTCATACTTTGCCCCACAC
196 GCCTATATCCATATAACCCCTACTAGGAAACCTCATACTTTGCCCCACAC
36377789 CT
1 CT
36377791 TGCAATTGAG
Statistics
Matches: 241, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
245 241 1.00
ACGTcount: A:0.33, C:0.28, G:0.13, T:0.26
Consensus pattern (245 bp):
CTCCGCAATTCCAATCCCTACATGGATTAGCTTTGTGCTAGCTTATTCTAGCTCCAGGCCTACAC
TACACTACCAATGTCAACATTTATCACATGATTGCAATTAAAAGGCATGACAACTAGCTAACTCT
GATACCAATTAATATGGACCTTTGGAGAACCACACCCCAAAAAAGCTAGCGATTGAAACTAAAGA
GCCTATATCCATATAACCCCTACTAGGAAACCTCATACTTTGCCCCACAC
Found at i:36390320 original size:87 final size:87
Alignment explanation
Indices: 36390200--36390372 Score: 294
Period size: 87 Copynumber: 2.0 Consensus size: 87
36390190 ACTGATTAGA
36390200 GGTCACTCTATTAGATAATCCAGAGGAACTAACA-TCAGAATCACCACTTGGAACTGATAATGAA
1 GGTCACTCTATTAGATAATCCAGAGGAACTAACACT-AGAATCACCACTTGGAACTGATAATGAA
* *
36390264 GGCAACACTTCTGCAGTTCCAGG
65 GGCAACACTTCCGCAATTCCAGG
* *
36390287 GGTCACTCTATTAGATAATCCGGAGGAACTAACACTAGAATCACCACTTGGACCTGATAATGAAG
1 GGTCACTCTATTAGATAATCCAGAGGAACTAACACTAGAATCACCACTTGGAACTGATAATGAAG
36390352 GCAACACTTCCGCAATTCCAG
66 GCAACACTTCCGCAATTCCAG
36390373 TACTTGACCC
Statistics
Matches: 81, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
87 80 0.99
88 1 0.01
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.23
Consensus pattern (87 bp):
GGTCACTCTATTAGATAATCCAGAGGAACTAACACTAGAATCACCACTTGGAACTGATAATGAAG
GCAACACTTCCGCAATTCCAGG
Found at i:36394406 original size:24 final size:23
Alignment explanation
Indices: 36394371--36394446 Score: 75
Period size: 23 Copynumber: 3.3 Consensus size: 23
36394361 TTAACTCATC
36394371 ATATTTTATTTTAGTCAATTTTA
1 ATATTTTATTTTAGTCAATTTTA
* * *
36394394 ATATTTATATTTT-TTGAAATTTCA
1 ATATTT-TATTTTAGT-CAATTTTA
*
36394418 A-ATTTTAACTTTAGTCAATTTTA
1 ATATTTT-ATTTTAGTCAATTTTA
36394441 ATATTT
1 ATATTT
36394447 AAGTTTTTCA
Statistics
Matches: 41, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
22 1 0.02
23 22 0.54
24 18 0.44
ACGTcount: A:0.33, C:0.05, G:0.04, T:0.58
Consensus pattern (23 bp):
ATATTTTATTTTAGTCAATTTTA
Found at i:36394441 original size:47 final size:47
Alignment explanation
Indices: 36394380--36394477 Score: 144
Period size: 47 Copynumber: 2.1 Consensus size: 47
36394370 CATATTTTAT
* *
36394380 TTTAGTCAATTTTAATATTTATATTTTTTGAAATTTCAAA-TTTTAAC
1 TTTAGTCAATTTTAATATTTA-AGTTTTTCAAATTTCAAACTTTTAAC
* *
36394427 TTTAGTCAATTTTAATATTTAAGTTTTTCAATTTTTAAACTTTTAAC
1 TTTAGTCAATTTTAATATTTAAGTTTTTCAAATTTCAAACTTTTAAC
36394474 TTTA
1 TTTA
36394478 ACTTAAATGA
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
46 14 0.30
47 32 0.70
ACGTcount: A:0.33, C:0.07, G:0.04, T:0.56
Consensus pattern (47 bp):
TTTAGTCAATTTTAATATTTAAGTTTTTCAAATTTCAAACTTTTAAC
Found at i:36394447 original size:23 final size:22
Alignment explanation
Indices: 36394375--36394461 Score: 61
Period size: 23 Copynumber: 3.8 Consensus size: 22
36394365 CTCATCATAT
*
36394375 TTTATTTTAGTCAATTTTAATA
1 TTTAATTTAGTCAATTTTAATA
** * *
36394397 TTTATATTTTTTGAAATTTCAA-A
1 TTTA-ATTTAGT-CAATTTTAATA
36394420 TTTTAACTTTAGTCAATTTTAATA
1 -TTTAA-TTTAGTCAATTTTAATA
*
36394444 TTTAAGTTT-TTCAATTTT
1 TTTAA-TTTAGTCAATTTT
36394462 TAAACTTTTA
Statistics
Matches: 49, Mismatches: 11, Indels: 10
0.70 0.16 0.14
Matches are distributed among these distances:
22 12 0.24
23 21 0.43
24 16 0.33
ACGTcount: A:0.31, C:0.06, G:0.05, T:0.59
Consensus pattern (22 bp):
TTTAATTTAGTCAATTTTAATA
Found at i:36418748 original size:150 final size:153
Alignment explanation
Indices: 36418292--36418911 Score: 439
Period size: 152 Copynumber: 4.0 Consensus size: 153
36418282 TACTAATGGA
* * * * *
36418292 AATGGAAAAGCAGG-TCTACCAACAAATCTTAGGCATGATGCTAACAGATTCA-TGTTGAAAATG
1 AATGCAAAAGCAGGCACAACCAACAAATCTCAAGCATGATGCTAACAGATTCACT-TTGAAAA--
* * * ** *
36418355 CCCTGTTAATTGTTAT-ATGCT-ATCGGGTTCATATGGCTAATTT-AAGTTCAATG-TTTCATTG
63 ---TG-T-ATTGTTATAATGCTAAT-GGCTTCATATAGATGCTTTCAAGTTCAATGCTTTCATTA
* * * * * *
36418416 CTTCTATTTCAGTTATACATTGTTTGACGACT
122 CTTCTATTTCAGTTCTAAAATGCTCGATGACT
* * * * ** * *
36418448 AATGAAAACAGAAAGACAAGCACTACCAA-ATAATCTTAGGCATGATGCTAATGGACTCACTCTG
1 AATG----CA-AAAG-CAGGCACAACCAACA-AATCTCAAGCATGATGCTAACAGATTCACTTTG
* * * * *
36418512 AAAATGT-TATGTTAT-ATGCTATTTGG-TTCATATTGCTGCCTTCCGAGTTCAA--CATTTCAT
59 AAAATGTAT-TGTTATAATGCTA-ATGGCTTCATATAGATG-CTTTCAAGTTCAATGC-TTTCAT
*
36418572 TACTTCTATTTCAGTTCTAAAATGCTCAATGACT
120 TACTTCTATTTCAGTTCTAAAATGCTCGATGACT
* * *
36418606 AATGCAAAAGCAGGC-CAAACGAAGAAATCTCAAGCATGATTCTAACAGATTCACTTT-AAAATG
1 AATGCAAAAGCAGGCAC-AACCAACAAATCTCAAGCATGATGCTAACAGATTCACTTTGAAAATG
* * * * *
36418669 TATTGTTAT-ATGCTATATGG-TTCATGTAGCTGTTTTCAAGTTTACT-CTTTCATTACTTCTAT
65 TATTGTTATAATGCTA-ATGGCTTCATATAGATGCTTTCAAGTTCAATGCTTTCATTACTTCTAT
*
36418731 TTCAGTTCTAAAATGCTCGATGGCT
129 TTCAGTTCTAAAATGCTCGATGACT
* * * * * *
36418756 AATGGAAAGGCAGGCACTACCAACAAATCTCAGGCTTGATGCTAACAGATTCACTTTGAAAATTT
1 AATGCAAAAGCAGGCACAACCAACAAATCTCAAGCATGATGCTAACAGATTCACTTTGAAAATGT
* * *
36418821 CTTGTTATAATGCTAATGGCTTCATATGGATGCTTTCAAGTTCAATGC-TTCATTGCTTCTATTT
66 ATTGTTATAATGCTAATGGCTTCATATAGATGCTTTCAAGTTCAATGCTTTCATTACTTCTATTT
* ** *
36418885 CAGCTCTACGATGTTCGATGACT
131 CAGTTCTAAAATGCTCGATGACT
36418908 AATG
1 AATG
36418912 GAAACCAAAA
Statistics
Matches: 376, Mismatches: 63, Indels: 54
0.76 0.13 0.11
Matches are distributed among these distances:
150 93 0.25
151 53 0.14
152 97 0.26
153 6 0.02
154 2 0.01
155 1 0.00
156 25 0.07
157 5 0.01
158 46 0.12
160 1 0.00
161 4 0.01
162 4 0.01
163 38 0.10
164 1 0.00
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.35
Consensus pattern (153 bp):
AATGCAAAAGCAGGCACAACCAACAAATCTCAAGCATGATGCTAACAGATTCACTTTGAAAATGT
ATTGTTATAATGCTAATGGCTTCATATAGATGCTTTCAAGTTCAATGCTTTCATTACTTCTATTT
CAGTTCTAAAATGCTCGATGACT
Found at i:36418903 original size:152 final size:152
Alignment explanation
Indices: 36418292--36419106 Score: 582
Period size: 150 Copynumber: 5.3 Consensus size: 152
36418282 TACTAATGGA
* *
36418292 AATGGAAAAGCAGG-TCTACCAACAAATCTTAGGCATGATGCTAACAGATTCA-TGTTGAAAATG
1 AATGGAAAAGCAGGCACTACCAACAAATCTCAGGCATGATGCTAACAGATTCACT-TTGAAAA--
** ** * *
36418355 CCCTGTTAATTGTTATATGCTATCGGGTTCATATGGCTAATTT-AAGTTCAATGTTTCATTGCTT
63 ---TGTT-ATTGTTATATGCTATATGGTTCATATGGCTGCTTTCAAGTTCAATGCTTCATTACTT
* * * * * *
36418419 CTATTTCAGTTATACATTGTTTGACGACT
124 CTATTTCAGTTCTAAAATGCTCGATGACT
* * * ** * *
36418448 AATGAAAACAGAAAGACAAGCACTACCAA-ATAATCTTAGGCATGATGCTAATGGACTCACTCTG
1 AATG----GA-AAAG-CAGGCACTACCAACA-AATCTCAGGCATGATGCTAACAGATTCACTTTG
* * * * ***
36418512 AAAATGTTA-TGTTATATGCTATTTGGTTCATATTGCTGCCTTCCGAGTTCAACATTTCATTACT
59 AAAATGTTATTGTTATATGCTATATGGTTCATATGGCTG-CTTTCAAGTTCAATGCTTCATTACT
*
36418576 TCTATTTCAGTTCTAAAATGCTCAATGACT
123 TCTATTTCAGTTCTAAAATGCTCGATGACT
* * * * * *
36418606 AATGCAAAAGCAGGC-CAAACGAAGAAATCTCAAGCATGATTCTAACAGATTCACTTT-AAAATG
1 AATGGAAAAGCAGGCAC-TACCAACAAATCTCAGGCATGATGCTAACAGATTCACTTTGAAAATG
* * * * *
36418669 -TATTGTTATATGCTATATGGTTCATGTAGCTGTTTTCAAGTTTACT-CTTTCATTACTTCTATT
65 TTATTGTTATATGCTATATGGTTCATATGGCTGCTTTCAAGTTCAATGC-TTCATTACTTCTATT
*
36418732 TCAGTTCTAAAATGCTCGATGGCT
129 TCAGTTCTAAAATGCTCGATGACT
* *
36418756 AATGGAAAGGCAGGCACTACCAACAAATCTCAGGCTTGATGCTAACAGATTCACTTTGAAAAT-T
1 AATGGAAAAGCAGGCACTACCAACAAATCTCAGGCATGATGCTAACAGATTCACTTTGAAAATGT
* * *
36418820 TCTTGTTATAATGCTA-ATGGCTTCATATGGATGCTTTCAAGTTCAATGCTTCATTGCTTCTATT
66 TATTGTTAT-ATGCTATATGG-TTCATATGGCTGCTTTCAAGTTCAATGCTTCATTACTTCTATT
* ** *
36418884 TCAGCTCTACGATGTTCGATGACT
129 TCAGTTCTAAAATGCTCGATGACT
* * * * * * * *
36418908 AATGGAAACCAAAAAAGCAGGCACTA-CAAAATAATCTTAGTCACGATGTTAA-GGATTCAATCT
1 AATGG-------AAAAGCAGGCACTACCAACA-AATCTCAGGCATGATGCTAACAGATTCACTTT
* ** * * * * *
36418971 GAACATG-TCGT-TTATATGCTATTTGGTTTACATGGCTGGTTTCAAGTTCAATGTTTC-TCTAC
58 GAAAATGTTATTGTTATATGCTATATGGTTCATATGGCTGCTTTCAAGTTCAATGCTTCAT-TAC
* * * *
36419033 TTCTATTGCAGTTCTACAATGTTCAATGACT
122 TTCTATTTCAGTTCTAAAATGCTCGATGACT
* * * * * *
36419064 AATGGAAAGGCAGACAATACCAAGAAAGCTAAGGCATGATGCT
1 AATGGAAAAGCAGGCACTACCAACAAATCTCAGGCATGATGCT
36419107 CAAGTGAAAA
Statistics
Matches: 527, Mismatches: 99, Indels: 73
0.75 0.14 0.10
Matches are distributed among these distances:
149 24 0.05
150 98 0.19
151 51 0.10
152 97 0.18
153 6 0.01
154 2 0.00
155 1 0.00
156 95 0.18
157 10 0.02
158 67 0.13
159 28 0.05
160 1 0.00
161 4 0.01
162 4 0.01
163 38 0.07
164 1 0.00
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Consensus pattern (152 bp):
AATGGAAAAGCAGGCACTACCAACAAATCTCAGGCATGATGCTAACAGATTCACTTTGAAAATGT
TATTGTTATATGCTATATGGTTCATATGGCTGCTTTCAAGTTCAATGCTTCATTACTTCTATTTC
AGTTCTAAAATGCTCGATGACT
Found at i:36432319 original size:25 final size:26
Alignment explanation
Indices: 36432280--36432329 Score: 68
Period size: 25 Copynumber: 1.9 Consensus size: 26
36432270 TTAAAACATT
36432280 AAATTAAATATTTA-TTATTTTTAAA
1 AAATTAAATATTTATTTATTTTTAAA
36432305 AAATTAAA-ATGTTATTTTATTTTTA
1 AAATTAAATAT-TTA-TTTATTTTTA
36432330 TTAATTTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 2 0.09
25 11 0.50
27 9 0.41
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (26 bp):
AAATTAAATATTTATTTATTTTTAAA
Found at i:36433474 original size:20 final size:20
Alignment explanation
Indices: 36433437--36433475 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
36433427 TTTTATAATT
*
36433437 ATTTTTTATAAGTTTTTATG
1 ATTTTTTATAAGTGTTTATG
36433457 ATTTTTTAATAA-TGTTTAT
1 ATTTTTT-ATAAGTGTTTAT
36433476 AAGTTTATAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (20 bp):
ATTTTTTATAAGTGTTTATG
Found at i:36438730 original size:19 final size:18
Alignment explanation
Indices: 36438708--36438751 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
36438698 AAAAAATTAT
36438708 AATTATGTAAAAAATAAAA
1 AATTAT-TAAAAAATAAAA
* *
36438727 AATTCATTAAAAATTGAAA
1 AATT-ATTAAAAAATAAAA
36438746 AATTAT
1 AATTAT
36438752 AATAAACAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 2 0.09
19 18 0.82
20 2 0.09
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.32
Consensus pattern (18 bp):
AATTATTAAAAAATAAAA
Found at i:36439645 original size:20 final size:21
Alignment explanation
Indices: 36439606--36439645 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
36439596 ATAGAATAAA
*
36439606 TTTAGTGTTGCTTGTAAATTG
1 TTTAGTGTTGCGTGTAAATTG
*
36439627 TTTAGTTTTGCGT-TAAATT
1 TTTAGTGTTGCGTGTAAATT
36439646 AATCAAATAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.20, C:0.05, G:0.20, T:0.55
Consensus pattern (21 bp):
TTTAGTGTTGCGTGTAAATTG
Found at i:36440550 original size:31 final size:29
Alignment explanation
Indices: 36440512--36440570 Score: 82
Period size: 31 Copynumber: 2.0 Consensus size: 29
36440502 ATATCAAAAC
*
36440512 TATACATGAACTATGGTTTAATGTGCAATTG
1 TATACATGAACTATGATTT--TGTGCAATTG
*
36440543 TATACATGAACTTTGATTTTGTGCAATT
1 TATACATGAACTATGATTTTGTGCAATT
36440571 TTATTATGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 9 0.35
31 17 0.65
ACGTcount: A:0.31, C:0.10, G:0.17, T:0.42
Consensus pattern (29 bp):
TATACATGAACTATGATTTTGTGCAATTG
Found at i:36441535 original size:20 final size:21
Alignment explanation
Indices: 36441496--36441535 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
36441486 ATAGAATAAA
*
36441496 TTTAGTGTTGCTTGTAAATTG
1 TTTAGTGTTGCGTGTAAATTG
*
36441517 TTTAGTTTTGCGT-TAAATT
1 TTTAGTGTTGCGTGTAAATT
36441536 AATTAAATAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.20, C:0.05, G:0.20, T:0.55
Consensus pattern (21 bp):
TTTAGTGTTGCGTGTAAATTG
Found at i:36445365 original size:2 final size:2
Alignment explanation
Indices: 36445358--36445416 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
36445348 AATGCAAACA
36445358 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
36445400 AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
36445417 AATTGGATCA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:36448104 original size:13 final size:13
Alignment explanation
Indices: 36448086--36448126 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
36448076 TGGTTTGATC
36448086 AACTGATTCTATT
1 AACTGATTCTATT
*
36448099 AACTGATT-TAATC
1 AACTGATTCT-ATT
36448112 AACTGATTCTATT
1 AACTGATTCTATT
36448125 AA
1 AA
36448127 TTGTTTATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
12 1 0.04
13 22 0.92
14 1 0.04
ACGTcount: A:0.37, C:0.15, G:0.07, T:0.41
Consensus pattern (13 bp):
AACTGATTCTATT
Found at i:36456244 original size:3 final size:3
Alignment explanation
Indices: 36456236--36456270 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
36456226 TGAAAAAGTG
36456236 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
36456271 GCTGATTTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:36464195 original size:2 final size:2
Alignment explanation
Indices: 36464188--36464253 Score: 123
Period size: 2 Copynumber: 33.0 Consensus size: 2
36464178 ATCTTAAGAA
36464188 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
36464230 AT AT AT AT AT AT AT TT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT
36464254 CATGTTCAAA
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:36478971 original size:19 final size:19
Alignment explanation
Indices: 36478911--36478971 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 19
36478901 TAGTACTATA
36478911 TATTA-AATAATTATTTAT
1 TATTATAATAATTATTTAT
** *
36478929 TAAAATAATAAATATTGTA-
1 TATTATAATAATTATT-TAT
*
36478948 AATTATAATAATTATTTAT
1 TATTATAATAATTATTTAT
36478967 TATTA
1 TATTA
36478972 ACATAATATT
Statistics
Matches: 32, Mismatches: 8, Indels: 5
0.71 0.18 0.11
Matches are distributed among these distances:
18 5 0.16
19 25 0.78
20 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (19 bp):
TATTATAATAATTATTTAT
Found at i:36480787 original size:32 final size:33
Alignment explanation
Indices: 36480742--36480825 Score: 102
Period size: 32 Copynumber: 2.6 Consensus size: 33
36480732 ATTTTCTTAC
*
36480742 ATATAAATA-TAAATATTAAAATTAAATTATCT
1 ATATAAGTATTAAATATTAAAATTAAATTATCT
*
36480774 -TATATGTATTAAATGA-TAAAATTAAATTATCT
1 ATATAAGTATTAAAT-ATTAAAATTAAATTATCT
* *
36480806 ATTTAAGTTTTAAATATTAA
1 ATATAAGTATTAAATATTAA
36480826 TGGGTATTGA
Statistics
Matches: 43, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
31 6 0.14
32 22 0.51
33 15 0.35
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.44
Consensus pattern (33 bp):
ATATAAGTATTAAATATTAAAATTAAATTATCT
Found at i:36483785 original size:18 final size:16
Alignment explanation
Indices: 36483758--36483800 Score: 50
Period size: 18 Copynumber: 2.6 Consensus size: 16
36483748 TACCAACTCT
* *
36483758 AAATAAATTATCAAAA
1 AAATATATTAACAAAA
36483774 TATAATATATTAACAAAA
1 -A-AATATATTAACAAAA
36483792 AAATATATT
1 AAATATATT
36483801 CTTCAAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 8 0.35
17 2 0.09
18 13 0.57
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.33
Consensus pattern (16 bp):
AAATATATTAACAAAA
Found at i:36484946 original size:35 final size:35
Alignment explanation
Indices: 36484900--36484971 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
36484890 CCCAAATTTA
36484900 AAAAAAAAAAATCAAATTTTCTATTATTTTATTAC
1 AAAAAAAAAAATCAAATTTTCTATTATTTTATTAC
36484935 AAAAAAAAAAATCAAATTTTCTATTATTTTATTAC
1 AAAAAAAAAAATCAAATTTTCTATTATTTTATTAC
36484970 AA
1 AA
36484972 TATTTTTTAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.39
Consensus pattern (35 bp):
AAAAAAAAAAATCAAATTTTCTATTATTTTATTAC
Found at i:36489648 original size:22 final size:21
Alignment explanation
Indices: 36489598--36489674 Score: 59
Period size: 22 Copynumber: 3.5 Consensus size: 21
36489588 TTTTTAACCA
* *
36489598 ATTTCTAA-TTTTAAATGTTT
1 ATTTTTAATTTTTAAATGTAT
36489618 ACTTATTTAATTTTTAAATAGTAT
1 A-TT-TTTAATTTTTAAAT-GTAT
*
36489642 ATTTTTAATTGTTTTAAT-TAT
1 ATTTTTAATT-TTTAAATGTAT
*
36489663 CTTTTTTAATTT
1 -ATTTTTAATTT
36489675 ATTATTTGAA
Statistics
Matches: 47, Mismatches: 4, Indels: 11
0.76 0.06 0.18
Matches are distributed among these distances:
20 1 0.02
21 6 0.13
22 20 0.43
23 16 0.34
24 4 0.09
ACGTcount: A:0.30, C:0.04, G:0.04, T:0.62
Consensus pattern (21 bp):
ATTTTTAATTTTTAAATGTAT
Found at i:36489928 original size:25 final size:26
Alignment explanation
Indices: 36489900--36489948 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
36489890 CTAGTGGGCT
36489900 TAATT-AAATATATAAATTATTTTGG
1 TAATTAAAATATATAAATTATTTTGG
* *
36489925 TAATTAAAATGTATGAATTATTTT
1 TAATTAAAATATATAAATTATTTT
36489949 ACTTAAAGGC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 5 0.24
26 16 0.76
ACGTcount: A:0.43, C:0.00, G:0.08, T:0.49
Consensus pattern (26 bp):
TAATTAAAATATATAAATTATTTTGG
Found at i:36500468 original size:23 final size:24
Alignment explanation
Indices: 36500431--36500490 Score: 86
Period size: 23 Copynumber: 2.5 Consensus size: 24
36500421 CGATTTTTAT
*
36500431 TTTAATATTTAATTTGATATTTCAG
1 TTTAAT-TTTAATTTGATATTTAAG
*
36500456 TTT-TTTTTAATTTGATATTTAAG
1 TTTAATTTTAATTTGATATTTAAG
36500479 TTTAATTTTAAT
1 TTTAATTTTAAT
36500491 ATTTAATTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
23 20 0.65
24 8 0.26
25 3 0.10
ACGTcount: A:0.30, C:0.02, G:0.07, T:0.62
Consensus pattern (24 bp):
TTTAATTTTAATTTGATATTTAAG
Found at i:36500494 original size:19 final size:17
Alignment explanation
Indices: 36500426--36500500 Score: 55
Period size: 19 Copynumber: 4.2 Consensus size: 17
36500416 GTACTCGATT
*
36500426 TTTATTTTAATATTTAA
1 TTTAATTTAATATTTAA
* *
36500443 TTTGATATTTCAGT-TTT-T
1 TTT-A-ATTT-AATATTTAA
*
36500461 TTTAATTTGATATTTAA
1 TTTAATTTAATATTTAA
36500478 GTTTAATTTTAATATTTAA
1 -TTTAA-TTTAATATTTAA
36500497 TTTA
1 TTTA
36500501 GTATTCAAAC
Statistics
Matches: 44, Mismatches: 7, Indels: 13
0.69 0.11 0.20
Matches are distributed among these distances:
15 1 0.02
16 7 0.16
17 4 0.09
18 13 0.30
19 17 0.39
20 2 0.05
ACGTcount: A:0.31, C:0.01, G:0.05, T:0.63
Consensus pattern (17 bp):
TTTAATTTAATATTTAA
Found at i:36500674 original size:18 final size:17
Alignment explanation
Indices: 36500644--36500678 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
36500634 ATTGGGTAAA
*
36500644 AAATTTGATACCAAATT
1 AAATTTGAAACCAAATT
36500661 AAATATTGAAACCAAATT
1 AAAT-TTGAAACCAAATT
36500679 TATGTACTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.51, C:0.11, G:0.06, T:0.31
Consensus pattern (17 bp):
AAATTTGAAACCAAATT
Found at i:36507788 original size:18 final size:18
Alignment explanation
Indices: 36507765--36507840 Score: 91
Period size: 18 Copynumber: 4.2 Consensus size: 18
36507755 TACGTGGACA
*
36507765 TGGAACCCAATGTGAACT
1 TGGAACACAATGTGAACT
36507783 TGGAACACAATGTGAACT
1 TGGAACACAATGTGAACT
36507801 TGGAACACAATGT-AAGCT
1 TGGAACACAATGTGAA-CT
** * *
36507819 TGGTTCACAACGTTAACT
1 TGGAACACAATGTGAACT
36507837 TGGA
1 TGGA
36507841 GCAGAACCTG
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
17 2 0.04
18 47 0.92
19 2 0.04
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.25
Consensus pattern (18 bp):
TGGAACACAATGTGAACT
Found at i:36507805 original size:36 final size:36
Alignment explanation
Indices: 36507756--36507840 Score: 91
Period size: 36 Copynumber: 2.4 Consensus size: 36
36507746 TTAGGGAACT
* * *
36507756 ACGTGGACATGGAACCCAATGTGAA-CTTGGAACACA
1 ACGTGAACTTGGAACACAATGT-AAGCTTGGAACACA
* **
36507792 ATGTGAACTTGGAACACAATGTAAGCTTGGTTCACA
1 ACGTGAACTTGGAACACAATGTAAGCTTGGAACACA
*
36507828 ACGTTAACTTGGA
1 ACGTGAACTTGGA
36507841 GCAGAACCTG
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
35 2 0.05
36 38 0.95
ACGTcount: A:0.34, C:0.19, G:0.24, T:0.24
Consensus pattern (36 bp):
ACGTGAACTTGGAACACAATGTAAGCTTGGAACACA
Found at i:36513455 original size:3 final size:3
Alignment explanation
Indices: 36513447--36513475 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
36513437 AATGACGGCC
36513447 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
36513476 CCATGACTTT
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:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:36514674 original size:29 final size:29
Alignment explanation
Indices: 36514641--36514699 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
36514631 TTGTTTTGAA
*
36514641 TTACATATTAATCACTTATGTTTGAAATG
1 TTACATATTAATCACTTATGATTGAAATG
* *
36514670 TTACATTTTGATCACTTATGATTGAAATG
1 TTACATATTAATCACTTATGATTGAAATG
36514699 T
1 T
36514700 GCAGTGTTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.32, C:0.10, G:0.12, T:0.46
Consensus pattern (29 bp):
TTACATATTAATCACTTATGATTGAAATG
Found at i:36518064 original size:2 final size:2
Alignment explanation
Indices: 36518053--36518084 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
36518043 TTTCAGCATT
36518053 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
36518085 TTATTTATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:36519504 original size:143 final size:143
Alignment explanation
Indices: 36519246--36519513 Score: 475
Period size: 143 Copynumber: 1.9 Consensus size: 143
36519236 AGTTAATTTT
* *
36519246 TGGAGTAAAATTTAAAAGTCAAAATATGCTCTAATTACTTACATTTATTGGACATTTTCAAATCC
1 TGGAGTAAAATTTAAAAGTCAAAATATGCTCTAACTACTTACATTTATTGCACATTTTCAAATCC
36519311 CAATACTTTTATTTTTAAGAATTTAGTGCCTTCTTAACAATGTGCACTTGTCAAGCAATTAATTT
66 CAATACTTTTATTTTTAAGAATTTAGTGCCTTCTTAACAATGTGCACTTGTCAAGCAATTAATTT
36519376 TTGGAGCAAATTA
131 TTGGAGCAAATTA
* * *
36519389 TGGAGTAAAATTTAAAAGTCAAAATATGCTCTAACTATTTATATTCT-TTGCATATTTTCAAATC
1 TGGAGTAAAATTTAAAAGTCAAAATATGCTCTAACTACTTACATT-TATTGCACATTTTCAAATC
36519453 CCAATACTTTTATTTTTAAGAATTTAGTGCCTTCTTAACAATGTGCACTTGTCAAGCAATT
65 CCAATACTTTTATTTTTAAGAATTTAGTGCCTTCTTAACAATGTGCACTTGTCAAGCAATT
36519514 TGGTTGAATA
Statistics
Matches: 119, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
143 118 0.99
144 1 0.01
ACGTcount: A:0.34, C:0.15, G:0.11, T:0.40
Consensus pattern (143 bp):
TGGAGTAAAATTTAAAAGTCAAAATATGCTCTAACTACTTACATTTATTGCACATTTTCAAATCC
CAATACTTTTATTTTTAAGAATTTAGTGCCTTCTTAACAATGTGCACTTGTCAAGCAATTAATTT
TTGGAGCAAATTA
Done.