Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 124041150
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: 124041150
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 335 characters in sequence are not A, C, G, or T
File 35 of 410
Found at i:8736098 original size:15 final size:15
Alignment explanation
Indices: 8736078--8736108 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
8736068 GCAAAAGAAA
8736078 ACAAAAAGGAAAAGG
1 ACAAAAAGGAAAAGG
8736093 ACAAAAAGGAAAAGG
1 ACAAAAAGGAAAAGG
8736108 A
1 A
8736109 GATTTGAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.68, C:0.06, G:0.26, T:0.00
Consensus pattern (15 bp):
ACAAAAAGGAAAAGG
Found at i:8737197 original size:15 final size:16
Alignment explanation
Indices: 8737167--8737205 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
8737157 GAGTTAAAAT
8737167 ATAATTTTATTATTTTA
1 ATAA-TTTATTATTTTA
*
8737184 ATAATTTA-TATTTTT
1 ATAATTTATTATTTTA
8737199 ATAATTT
1 ATAATTT
8737206 TTTAAATGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 13 0.62
16 4 0.19
17 4 0.19
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
ATAATTTATTATTTTA
Found at i:8737659 original size:2 final size:2
Alignment explanation
Indices: 8737647--8737677 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
8737637 TTATGTTTAA
*
8737647 AT AT TT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
8737678 AATTTTAAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:8744829 original size:10 final size:11
Alignment explanation
Indices: 8744803--8744831 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
8744793 AAAAAATATT
8744803 AAAATTATAAA
1 AAAATTATAAA
8744814 AAAATTAT-AA
1 AAAATTATAAA
8744824 AAAATTAT
1 AAAATTAT
8744832 TTTGTTAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (11 bp):
AAAATTATAAA
Found at i:8746557 original size:17 final size:18
Alignment explanation
Indices: 8746535--8746578 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
8746525 AGAAAAAAAT
*
8746535 TTAAAAAT-TAATTTTAA
1 TTAAAAATGTAATATTAA
*
8746552 TTAAAAATGTAATATTAT
1 TTAAAAATGTAATATTAA
8746570 TATAAAAAT
1 T-TAAAAAT
8746579 ATTTATGTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 8 0.35
18 8 0.35
19 7 0.30
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (18 bp):
TTAAAAATGTAATATTAA
Found at i:8746944 original size:2 final size:2
Alignment explanation
Indices: 8746937--8746967 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
8746927 GATAATCAAA
8746937 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
8746968 AATAGAAGTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:8750592 original size:39 final size:39
Alignment explanation
Indices: 8750538--8750794 Score: 379
Period size: 39 Copynumber: 6.5 Consensus size: 39
8750528 TAATGGAAAA
* *
8750538 TTATATCTGGGCTAAGTCCCGAAGGTATTCGTGCTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
8750577 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
* *
8750616 TTATATCCGGGCTAAGTCTCGAAGGCATTCGTACTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
* * *
8750655 TTATATCCGGGCTAAGCCCCGAAGGTATTTGTGCTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
*
8750694 TTATATCCGGGCTAAGCCCCGAAGGCATTCGTGCTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
* * * *
8750733 TTATATCTGGACTAAGCCCCGAAGGCATTCGTGCTGGTA
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
*
8750772 TTATATTCGGGCTTAAAGTCCCG
1 TTATATCCGGGC-T-AAGTCCCG
8750795 CATGCTTTGT
Statistics
Matches: 198, Mismatches: 18, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
39 190 0.96
40 1 0.01
41 7 0.04
ACGTcount: A:0.19, C:0.22, G:0.29, T:0.30
Consensus pattern (39 bp):
TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
Found at i:8754225 original size:15 final size:15
Alignment explanation
Indices: 8754205--8754235 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
8754195 CAATTATGAC
8754205 ATGCAATGTATCTAA
1 ATGCAATGTATCTAA
8754220 ATGCAATGTATCTAA
1 ATGCAATGTATCTAA
8754235 A
1 A
8754236 ACACGTAGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.32
Consensus pattern (15 bp):
ATGCAATGTATCTAA
Found at i:8754615 original size:35 final size:35
Alignment explanation
Indices: 8754569--8754638 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
8754559 AAGTTTAAGA
8754569 ACATTTAGTGAAATTAACCCGATAATATGGTGCAT
1 ACATTTAGTGAAATTAACCCGATAATATGGTGCAT
8754604 ACATTTAGTGAAATTAACCCGATAATATGGTGCAT
1 ACATTTAGTGAAATTAACCCGATAATATGGTGCAT
8754639 TTTTAGTTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.31
Consensus pattern (35 bp):
ACATTTAGTGAAATTAACCCGATAATATGGTGCAT
Found at i:8756321 original size:21 final size:22
Alignment explanation
Indices: 8756295--8756348 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 22
8756285 AACAGCGATG
*
8756295 GCGGTGAAG-TTAGTTACTGTA
1 GCGGTGAAGATTAGATACTGTA
*
8756316 GCGGTG-AGATTGGATACTGTA
1 GCGGTGAAGATTAGATACTGTA
*
8756337 ACGGTGAA-ATTA
1 GCGGTGAAGATTA
8756349 AAAACAATGG
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
20 2 0.07
21 24 0.89
22 1 0.04
ACGTcount: A:0.28, C:0.09, G:0.33, T:0.30
Consensus pattern (22 bp):
GCGGTGAAGATTAGATACTGTA
Found at i:8758397 original size:32 final size:32
Alignment explanation
Indices: 8758360--8758518 Score: 246
Period size: 32 Copynumber: 5.0 Consensus size: 32
8758350 CATAAAAAAT
* * *
8758360 ATCATACATTAGGTTTACATAAAAAAAAGTAG
1 ATCATACATTAGTTTTGCATATAAAAAAGTAG
8758392 ATCATACATTAGTTTTGCATATAAAAAAGTAG
1 ATCATACATTAGTTTTGCATATAAAAAAGTAG
* **
8758424 ATCATACATTAGGTTCACATATAAAAAAGTAG
1 ATCATACATTAGTTTTGCATATAAAAAAGTAG
*
8758456 ATCATACATTAGTTTTGCATATGAAAAAGTAG
1 ATCATACATTAGTTTTGCATATAAAAAAGTAG
*
8758488 ATTATACATTAGTTTTGCATATAAAAAAGTA
1 ATCATACATTAGTTTTGCATATAAAAAAGTA
8758519 ACATAGTTGT
Statistics
Matches: 115, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 115 1.00
ACGTcount: A:0.45, C:0.09, G:0.13, T:0.33
Consensus pattern (32 bp):
ATCATACATTAGTTTTGCATATAAAAAAGTAG
Found at i:8760136 original size:24 final size:27
Alignment explanation
Indices: 8760105--8760166 Score: 78
Period size: 23 Copynumber: 2.4 Consensus size: 27
8760095 AACAATTTAA
8760105 AATAATTAAAAAGAAATTT-AA-TTT-
1 AATAATTAAAAAGAAATTTAAATTTTC
* *
8760129 AATGATT-AAAATAAATTTAAATTTTC
1 AATAATTAAAAAGAAATTTAAATTTTC
8760155 AATAATTAAAAA
1 AATAATTAAAAA
8760167 TATTTATTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
23 10 0.32
24 8 0.26
25 3 0.10
26 6 0.19
27 4 0.13
ACGTcount: A:0.58, C:0.02, G:0.03, T:0.37
Consensus pattern (27 bp):
AATAATTAAAAAGAAATTTAAATTTTC
Found at i:8763098 original size:25 final size:25
Alignment explanation
Indices: 8763070--8763127 Score: 116
Period size: 25 Copynumber: 2.3 Consensus size: 25
8763060 TACAAACTAC
8763070 GAATATGGTAGCAAGAAGAAACAGA
1 GAATATGGTAGCAAGAAGAAACAGA
8763095 GAATATGGTAGCAAGAAGAAACAGA
1 GAATATGGTAGCAAGAAGAAACAGA
8763120 GAATATGG
1 GAATATGG
8763128 GAATGAAAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.50, C:0.07, G:0.29, T:0.14
Consensus pattern (25 bp):
GAATATGGTAGCAAGAAGAAACAGA
Found at i:8764390 original size:15 final size:15
Alignment explanation
Indices: 8764370--8764399 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
8764360 AGTCTGACCA
8764370 CATGTTGTGAATGGT
1 CATGTTGTGAATGGT
8764385 CATGTTGTGAATGGT
1 CATGTTGTGAATGGT
8764400 TGCACGGCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.07, G:0.33, T:0.40
Consensus pattern (15 bp):
CATGTTGTGAATGGT
Found at i:8779227 original size:23 final size:23
Alignment explanation
Indices: 8779188--8779245 Score: 57
Period size: 23 Copynumber: 2.6 Consensus size: 23
8779178 TTTTGAAATG
**
8779188 TATA-TTTTAAACGTTTTATAACA
1 TATATTTTTAAAAATTTTA-AACA
*
8779211 T-TATTTTTAAAAATTTTAAATA
1 TATATTTTTAAAAATTTTAAACA
*
8779233 TATTTTTTTAAAA
1 TATATTTTTAAAA
8779246 TTATTTTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
22 6 0.21
23 23 0.79
ACGTcount: A:0.41, C:0.03, G:0.02, T:0.53
Consensus pattern (23 bp):
TATATTTTTAAAAATTTTAAACA
Found at i:8779253 original size:15 final size:15
Alignment explanation
Indices: 8779224--8779265 Score: 61
Period size: 14 Copynumber: 2.9 Consensus size: 15
8779214 TTTTTAAAAA
*
8779224 TTTTAAATA-TATTT
1 TTTTAAAAATTATTT
8779238 TTTT-AAAATTATTT
1 TTTTAAAAATTATTT
8779252 TTTTAAAAATTATT
1 TTTTAAAAATTATT
8779266 CTTTAATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
13 3 0.12
14 13 0.52
15 9 0.36
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TTTTAAAAATTATTT
Found at i:8779270 original size:14 final size:14
Alignment explanation
Indices: 8779224--8779271 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 14
8779214 TTTTTAAAAA
*
8779224 TTTTAAATA-TATT
1 TTTTAAAAATTATT
*
8779237 TTTTTAAAATTATTT
1 TTTTAAAAATTA-TT
8779252 TTTTAAAAATTATT
1 TTTTAAAAATTATT
*
8779266 CTTTAA
1 TTTTAA
8779272 TTTTGAAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
13 7 0.24
14 9 0.31
15 13 0.45
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (14 bp):
TTTTAAAAATTATT
Found at i:8779706 original size:22 final size:22
Alignment explanation
Indices: 8779672--8779771 Score: 96
Period size: 22 Copynumber: 4.3 Consensus size: 22
8779662 TTTTAAATGT
* * *
8779672 TTTATAATATTAAAAAATTATA
1 TTTAAAATTTTAAAAAATAATA
8779694 TTTAAAATTTTAAAAAATAATA
1 TTTAAAATTTTAAAAAATAATA
8779716 TTT-AAATTAAAAATTAAAAAAT-ATA
1 TTTAAAATT-----TTAAAAAATAATA
8779741 TTTAAAAATTTTAAAAAATAATA
1 TTT-AAAATTTTAAAAAATAATA
8779764 TTATAAAA
1 TT-TAAAA
8779772 CATTTAATGT
Statistics
Matches: 66, Mismatches: 3, Indels: 17
0.77 0.03 0.20
Matches are distributed among these distances:
21 5 0.08
22 31 0.47
23 9 0.14
24 1 0.02
25 6 0.09
26 9 0.14
27 5 0.08
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
TTTAAAATTTTAAAAAATAATA
Found at i:8781334 original size:41 final size:37
Alignment explanation
Indices: 8781232--8781337 Score: 113
Period size: 37 Copynumber: 2.8 Consensus size: 37
8781222 AATCCAAAGT
* * **
8781232 AGTAAATTGACACCCAATGTCTTATCGGTTAAACCGA
1 AGTAAATTGACACCCAGTGTCTCATCGAATAAACCGA
* * *
8781269 AGTAAATTGGCACCTAGTGCCTCATCGAATAAATCCGA
1 AGTAAATTGACACCCAGTGTCTCATCGAATAAA-CCGA
8781307 AGAAATAAATTGACACCCAGTGTCTCATCGA
1 AG---TAAATTGACACCCAGTGTCTCATCGA
8781338 CTCAAAGTTG
Statistics
Matches: 55, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
37 26 0.47
38 6 0.11
41 23 0.42
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.25
Consensus pattern (37 bp):
AGTAAATTGACACCCAGTGTCTCATCGAATAAACCGA
Found at i:8784397 original size:10 final size:10
Alignment explanation
Indices: 8784382--8784411 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
8784372 AAATCTAGAG
8784382 TTTTCTTCAT
1 TTTTCTTCAT
8784392 TTTTCTTCAT
1 TTTTCTTCAT
8784402 TTTTCTTCAT
1 TTTTCTTCAT
8784412 CCTCTCCAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.10, C:0.20, G:0.00, T:0.70
Consensus pattern (10 bp):
TTTTCTTCAT
Found at i:8785289 original size:52 final size:52
Alignment explanation
Indices: 8785224--8785377 Score: 200
Period size: 52 Copynumber: 2.9 Consensus size: 52
8785214 GACAGAAAAT
*
8785224 ATGTGATATGTGTTTCCGTATAAGACCATAGCTAGGCTATGGCATCGGTGCA
1 ATGTGATATGTGTTTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTGCA
* * * * * **
8785276 ATGTGATACGTGTTCCCATATAAGACCATAGTTGGGCTATGACATCGGTGTG
1 ATGTGATATGTGTTTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTGCA
* * *
8785328 ATGTGATAATGTGATTCCGTATAAGACCATATCTGGGATATGGCATCGGT
1 ATGTGAT-ATGTGTTTCCGTATAAGACCATAGCTGGGCTATGGCATCGGT
8785378 ATGATATGTG
Statistics
Matches: 85, Mismatches: 16, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
52 51 0.60
53 34 0.40
ACGTcount: A:0.26, C:0.16, G:0.27, T:0.31
Consensus pattern (52 bp):
ATGTGATATGTGTTTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTGCA
Found at i:8786311 original size:13 final size:13
Alignment explanation
Indices: 8786295--8786329 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
8786285 GCCACATGGG
8786295 TGTGTGCCCAGGC
1 TGTGTGCCCAGGC
*
8786308 TGTGTTCCCAGGC
1 TGTGTGCCCAGGC
*
8786321 CGTGTGCCC
1 TGTGTGCCC
8786330 CTCTGATATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.06, C:0.34, G:0.34, T:0.26
Consensus pattern (13 bp):
TGTGTGCCCAGGC
Found at i:8788233 original size:12 final size:10
Alignment explanation
Indices: 8788209--8788252 Score: 56
Period size: 9 Copynumber: 4.6 Consensus size: 10
8788199 TTCACATCAT
8788209 TCTCTCAAAC
1 TCTCTCAAAC
8788219 TCTCTCAAAC
1 TCTCTCAAAC
* *
8788229 CCTCTC-AAG
1 TCTCTCAAAC
8788238 TCTCTC-AAC
1 TCTCTCAAAC
8788247 TCTCTC
1 TCTCTC
8788253 GTTTTAAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
9 15 0.50
10 15 0.50
ACGTcount: A:0.23, C:0.43, G:0.02, T:0.32
Consensus pattern (10 bp):
TCTCTCAAAC
Found at i:8794470 original size:13 final size:13
Alignment explanation
Indices: 8794422--8794475 Score: 51
Period size: 13 Copynumber: 4.2 Consensus size: 13
8794412 ATTATTTAAG
8794422 TAATAACAATAAT-
1 TAATAAC-ATAATA
*
8794435 T-ATAATATAATA
1 TAATAACATAATA
8794447 TAATATA-ATAATA
1 TAATA-ACATAATA
*
8794460 TAATAACATAAAA
1 TAATAACATAATA
8794473 TAA
1 TAA
8794476 AAGAAATAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
11 5 0.14
12 6 0.17
13 23 0.66
14 1 0.03
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (13 bp):
TAATAACATAATA
Found at i:8794474 original size:18 final size:18
Alignment explanation
Indices: 8794422--8794475 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 18
8794412 ATTATTTAAG
*
8794422 TAATAACAATAATTATAATA
1 TAATAAC-ATAA-AATAATA
*
8794442 TAATATA-ATATAATAATA
1 TAATA-ACATAAAATAATA
8794460 TAATAACATAAAATAA
1 TAATAACATAAAATAA
8794476 AAGAAATAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
17 1 0.03
18 19 0.66
19 3 0.10
20 5 0.17
21 1 0.03
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (18 bp):
TAATAACATAAAATAATA
Found at i:8794510 original size:16 final size:17
Alignment explanation
Indices: 8794436--8794513 Score: 52
Period size: 16 Copynumber: 4.3 Consensus size: 17
8794426 AACAATAATT
8794436 ATAATATAATATAATATAATA
1 ATAA-ATAA-ATAA-ATAA-A
8794457 ATATAATAACATAAAATAAA
1 ATA-AATAA-AT-AAATAAA
* * *
8794477 AGAAATAAA-ACATGAA
1 ATAAATAAATAAATAAA
8794493 ATAAATAAATAAAT-AA
1 ATAAATAAATAAATAAA
8794509 ATAAA
1 ATAAA
8794514 ATAAGAAGAA
Statistics
Matches: 48, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
16 20 0.42
17 3 0.06
18 1 0.02
19 5 0.10
20 3 0.06
21 13 0.27
22 3 0.06
ACGTcount: A:0.69, C:0.03, G:0.03, T:0.26
Consensus pattern (17 bp):
ATAAATAAATAAATAAA
Found at i:8799483 original size:30 final size:30
Alignment explanation
Indices: 8799448--8799509 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
8799438 CTTAATAAGT
8799448 AAATATCTCTAAAATAATAACAAAATTAAC
1 AAATATCTCTAAAATAATAACAAAATTAAC
*
8799478 AAATATCTTTAAAATAATAACAAAATTAAC
1 AAATATCTCTAAAATAATAACAAAATTAAC
8799508 AA
1 AA
8799510 TAAAATAAGT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.61, C:0.11, G:0.00, T:0.27
Consensus pattern (30 bp):
AAATATCTCTAAAATAATAACAAAATTAAC
Found at i:8810431 original size:32 final size:32
Alignment explanation
Indices: 8810395--8810493 Score: 96
Period size: 31 Copynumber: 3.2 Consensus size: 32
8810385 CATTAATGAT
*
8810395 AATTTTCAAAAGATTTAAGAGAATTTAATTAA
1 AATTTTCAAAAGATTTAAGAGAATATAATTAA
** * *
8810427 AATTTTCAAAAGAAATAAAAG-ATATAATGAA
1 AATTTTCAAAAGATTTAAGAGAATATAATTAA
* * **
8810458 ATTTTTCAAAA-ATTTGAG-GAACCTAATTAA
1 AATTTTCAAAAGATTTAAGAGAATATAATTAA
8810488 AATTTT
1 AATTTT
8810494 TTAAAAAGTT
Statistics
Matches: 52, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
29 1 0.02
30 15 0.29
31 18 0.35
32 18 0.35
ACGTcount: A:0.51, C:0.05, G:0.09, T:0.35
Consensus pattern (32 bp):
AATTTTCAAAAGATTTAAGAGAATATAATTAA
Found at i:8810467 original size:31 final size:31
Alignment explanation
Indices: 8810388--8810468 Score: 83
Period size: 32 Copynumber: 2.5 Consensus size: 31
8810378 TTTTTAACAT
** * *
8810388 TAATGATAATTTTCAAAAGATTTAAGAGAATT
1 TAATGA-AATTTTCAAAAGAAATAAAAGAATA
*
8810420 TAATTAAAATTTTCAAAAGAAATAAAAG-ATA
1 TAA-TGAAATTTTCAAAAGAAATAAAAGAATA
8810451 TAATGAAATTTTTCAAAA
1 TAATGAAA-TTTTCAAAA
8810469 ATTTGAGGAA
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
30 4 0.10
31 14 0.34
32 21 0.51
33 2 0.05
ACGTcount: A:0.53, C:0.04, G:0.09, T:0.35
Consensus pattern (31 bp):
TAATGAAATTTTCAAAAGAAATAAAAGAATA
Found at i:8812563 original size:26 final size:25
Alignment explanation
Indices: 8812516--8812568 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 25
8812506 TCAGTGATAC
*
8812516 TTTTTATAATAATTAATATATTTTAA
1 TTTTTAAAATAATTAATATA-TTTAA
*
8812542 TTTTTAAAATTATGTAAT-TATTTAA
1 TTTTTAAAATAAT-TAATATATTTAA
8812567 TT
1 TT
8812569 ATAATTTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 7 0.29
26 13 0.54
27 4 0.17
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (25 bp):
TTTTTAAAATAATTAATATATTTAA
Found at i:8817497 original size:17 final size:17
Alignment explanation
Indices: 8817458--8817497 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
8817448 ATTAGAACTA
*
8817458 AGTTAAGAAAATTATTTT
1 AGTT-AGAAAATTAATTT
8817476 A-TTAGAAAATTAATTT
1 AGTTAGAAAATTAATTT
8817492 AGTTAG
1 AGTTAG
8817498 TTTGATTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 13 0.65
17 6 0.30
18 1 0.05
ACGTcount: A:0.45, C:0.00, G:0.12, T:0.42
Consensus pattern (17 bp):
AGTTAGAAAATTAATTT
Found at i:8818365 original size:29 final size:30
Alignment explanation
Indices: 8818319--8818375 Score: 73
Period size: 29 Copynumber: 1.9 Consensus size: 30
8818309 AGATTTAAGT
*
8818319 TAATAAAATGATCAAATTGCATTTTAACTC
1 TAATAAAATGATCAAATTGAATTTTAACTC
*
8818349 TAATAAAAT-AT-ATAATTTAATTTTAAC
1 TAATAAAATGATCA-AATTGAATTTTAAC
8818376 CCCCAAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 1 0.04
29 14 0.58
30 9 0.38
ACGTcount: A:0.47, C:0.09, G:0.04, T:0.40
Consensus pattern (30 bp):
TAATAAAATGATCAAATTGAATTTTAACTC
Found at i:8826595 original size:17 final size:17
Alignment explanation
Indices: 8826564--8826620 Score: 57
Period size: 17 Copynumber: 3.5 Consensus size: 17
8826554 TAACAGATTT
*
8826564 AAAATATAATATATAATA
1 AAAATAT-ATTTATAATA
*
8826582 AAAATATATTTATAAGA
1 AAAATATATTTATAATA
*
8826599 ATAATA-A-TTAT-ATA
1 AAAATATATTTATAATA
8826613 AAAATATA
1 AAAATATA
8826621 AAATATATTG
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
14 7 0.21
15 5 0.15
16 1 0.03
17 13 0.39
18 7 0.21
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (17 bp):
AAAATATATTTATAATA
Found at i:8829182 original size:205 final size:205
Alignment explanation
Indices: 8828742--8829287 Score: 909
Period size: 205 Copynumber: 2.7 Consensus size: 205
8828732 AAATCTGCTT
* *
8828742 CTTCAATTTGTTCTCTGACAATATAGAGATGCCAAATCATCTTAGATTTGCTTCATCGTAAGCAC
1 CTTCGATTTGTTCTCTGACAATATAGAGATGCCAAATCATCTTAGATTTGCTTCATCGTAAACAC
* *
8828807 GTGAAAGCCAAATCAGCTATGTCTTCGATTTG-TTCCTTGTAAGCACAAGAATGTCAAATCATCT
66 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGCTT-CTTGTAAGCACAAGGATGCCAAATCATCT
**
8828871 TGGATCTTGCTTCAGTGAAATTATCTGAAGGTGAGATCTGCTATGTATCTGCTCCCCGTTAAAGT
130 TGGATC-TGCTTCAGTGAAAACATCTGAAGGTGAGATCTGCTATGTATCTGCTCCCCGTTAAAGT
8828936 GGAGATGCCAGA
194 GGAGATGCCAGA
8828948 CTTCGATTTGTTCTCTGA-AATATAGAGATGCCAAATCATCTTAGATTTGCTTCATCGTAAACAC
1 CTTCGATTTGTTCTCTGACAATATAGAGATGCCAAATCATCTTAGATTTGCTTCATCGTAAACAC
* *
8829012 GTGAAAGCCAAATCAGCTATGTCTTCGATTCGCTTCTTATAAGCACAAGGATGCCAAATCATCTT
66 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGCTTCTTGTAAGCACAAGGATGCCAAATCATCTT
*
8829077 GGATCTGCTTCAGT-ATAAACATCTGAAGGTGAGATCTGCTATGTATCTGCTCCCCGTTGAAGTG
131 GGATCTGCTTCAGTGA-AAACATCTGAAGGTGAGATCTGCTATGTATCTGCTCCCCGTTAAAGTG
8829141 GAGATGCCAGA
195 GAGATGCCAGA
* * * *
8829152 CTTCGATTTGTTCTCTGACATTACAGAGATGCCAAATCATCTTAGATTTGTTTTATCGTAAACAC
1 CTTCGATTTGTTCTCTGACAATATAGAGATGCCAAATCATCTTAGATTTGCTTCATCGTAAACAC
* *
8829217 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATGCCAAACCATCTT
66 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGCTTCTTGTAAGCACAAGGATGCCAAATCATCTT
8829282 GGATCT
131 GGATCT
8829288 TCTTTCAGCC
Statistics
Matches: 320, Mismatches: 17, Indels: 7
0.93 0.05 0.02
Matches are distributed among these distances:
203 1 0.00
204 83 0.26
205 217 0.68
206 19 0.06
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (205 bp):
CTTCGATTTGTTCTCTGACAATATAGAGATGCCAAATCATCTTAGATTTGCTTCATCGTAAACAC
GTGAAAGCCAAATCAGCTATGTCTTCGATTTGCTTCTTGTAAGCACAAGGATGCCAAATCATCTT
GGATCTGCTTCAGTGAAAACATCTGAAGGTGAGATCTGCTATGTATCTGCTCCCCGTTAAAGTGG
AGATGCCAGA
Found at i:8842284 original size:26 final size:26
Alignment explanation
Indices: 8842246--8842407 Score: 279
Period size: 26 Copynumber: 6.2 Consensus size: 26
8842236 TGGTACAAAT
*
8842246 TGATAATAGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
* *
8842272 TGATAATGTGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTTCA
8842298 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
* *
8842324 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTTCA
8842350 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
8842376 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
8842402 TGATAA
1 TGATAA
8842408 GAATATCATG
Statistics
Matches: 127, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 127 1.00
ACGTcount: A:0.33, C:0.05, G:0.25, T:0.38
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTTCA
Found at i:8844461 original size:136 final size:136
Alignment explanation
Indices: 8844193--8844477 Score: 509
Period size: 135 Copynumber: 2.1 Consensus size: 136
8844183 GAGTAGTCTC
8844193 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
1 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
* *
8844258 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTATTGTAATCTGAAAAGGGCTTTGGCCCAGTATCA
66 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACCA
8844323 CTGTTA
131 CTGTTA
*
8844329 CCCAAATGGGCTTGCATATG-TTATTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
1 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
8844393 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
66 TGTTATCTGAATAAGGGGCTAAGGCCCAG-TTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
8844458 ACTGTTA
130 ACTGTTA
**
8844465 CCTGAATGGGCTT
1 CCCAAATGGGCTT
8844478 AGGCCCAATG
Statistics
Matches: 143, Mismatches: 5, Indels: 2
0.95 0.03 0.01
Matches are distributed among these distances:
135 72 0.50
136 71 0.50
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (136 bp):
CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
TGTTATCTGAATAAGGGGCTAAGGCCCAGTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACCA
CTGTTA
Found at i:8849614 original size:2 final size:2
Alignment explanation
Indices: 8849607--8849633 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
8849597 ATAATATTAG
8849607 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
8849634 ATAGTATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:8849914 original size:13 final size:14
Alignment explanation
Indices: 8849896--8849926 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
8849886 ATGTACGAAT
8849896 ATATACATATA-TA
1 ATATACATATATTA
8849909 ATATACATATATTA
1 ATATACATATATTA
8849923 ATAT
1 ATAT
8849927 TAATAATGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.65
14 6 0.35
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (14 bp):
ATATACATATATTA
Found at i:8850026 original size:12 final size:12
Alignment explanation
Indices: 8849988--8850027 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
8849978 TGAAAATAAT
8849988 TAAT-ATATTAA
1 TAATAATATTAA
* *
8849999 TAAAAATACTAA
1 TAATAATATTAA
8850011 TAATAATATTAA
1 TAATAATATTAA
8850023 TAATA
1 TAATA
8850028 TGTAAAAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
11 3 0.12
12 21 0.88
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.38
Consensus pattern (12 bp):
TAATAATATTAA
Found at i:8850522 original size:18 final size:20
Alignment explanation
Indices: 8850498--8850541 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
8850488 GGAAGGGGAA
*
8850498 GGAGAGAAAAGA-GGGAGCGG
1 GGAGAGAAGAGAGGGGAG-GG
8850518 GGAGAGAAGAGAGGGGAGGG
1 GGAGAGAAGAGAGGGGAGGG
8850538 GGAG
1 GGAG
8850542 CTCCGGCCAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 17 0.77
21 5 0.23
ACGTcount: A:0.36, C:0.02, G:0.61, T:0.00
Consensus pattern (20 bp):
GGAGAGAAGAGAGGGGAGGG
Found at i:8850655 original size:12 final size:12
Alignment explanation
Indices: 8850633--8850671 Score: 51
Period size: 13 Copynumber: 3.1 Consensus size: 12
8850623 AGGTAAAAAA
8850633 TCTTATTTTTTAT
1 TCTT-TTTTTTAT
8850646 TCTTTTTTTTAT
1 TCTTTTTTTTAT
*
8850658 TCTGTTATTTTAT
1 TCT-TTTTTTTAT
8850671 T
1 T
8850672 GTATTTCTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 11 0.46
13 13 0.54
ACGTcount: A:0.13, C:0.08, G:0.03, T:0.77
Consensus pattern (12 bp):
TCTTTTTTTTAT
Found at i:8851670 original size:30 final size:30
Alignment explanation
Indices: 8851634--8851733 Score: 148
Period size: 30 Copynumber: 3.3 Consensus size: 30
8851624 CTAGCCTTTG
* *
8851634 CCACCACCACCTCCACTAGCCACAATTGTT
1 CCACCACCACCTCCACTAGCCACACTTGCT
*
8851664 CCACCACCAACTCCACTAGCCACACTTGCT
1 CCACCACCACCTCCACTAGCCACACTTGCT
*
8851694 CCACTACCTA-CTCCACTAGCCACACTTGCT
1 CCACCACC-ACCTCCACTAGCCACACTTGCT
8851724 CCACCACCAC
1 CCACCACCAC
8851734 TTGTACCTAC
Statistics
Matches: 63, Mismatches: 5, Indels: 4
0.88 0.07 0.06
Matches are distributed among these distances:
29 1 0.02
30 61 0.97
31 1 0.02
ACGTcount: A:0.26, C:0.50, G:0.06, T:0.18
Consensus pattern (30 bp):
CCACCACCACCTCCACTAGCCACACTTGCT
Found at i:8851697 original size:18 final size:18
Alignment explanation
Indices: 8851674--8851727 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
8851664 CCACCACCAA
8851674 CTCCACTAGCCACACTTG
1 CTCCACTAGCCACACTTG
*
8851692 CTCCACT----AC-C-TA
1 CTCCACTAGCCACACTTG
8851704 CTCCACTAGCCACACTTG
1 CTCCACTAGCCACACTTG
8851722 CTCCAC
1 CTCCAC
8851728 CACCACTTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 12
0.67 0.05 0.29
Matches are distributed among these distances:
12 8 0.29
13 1 0.04
14 2 0.07
16 2 0.07
17 1 0.04
18 14 0.50
ACGTcount: A:0.22, C:0.48, G:0.07, T:0.22
Consensus pattern (18 bp):
CTCCACTAGCCACACTTG
Found at i:8853993 original size:7 final size:7
Alignment explanation
Indices: 8853981--8854009 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
8853971 TATACAGAAA
8853981 TCACTTG
1 TCACTTG
8853988 TCACTTG
1 TCACTTG
8853995 TCACTTG
1 TCACTTG
8854002 TCACTTG
1 TCACTTG
8854009 T
1 T
8854010 AGCCAAAGCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.14, C:0.28, G:0.14, T:0.45
Consensus pattern (7 bp):
TCACTTG
Found at i:8854065 original size:31 final size:31
Alignment explanation
Indices: 8854015--8854216 Score: 287
Period size: 31 Copynumber: 6.5 Consensus size: 31
8854005 CTTGTAGCCA
* *
8854015 AAGCTACCACTATTAACTGATCAGGTAGCTG
1 AAGCTACCACTTTTCACTGATCAGGTAGCTG
** * * *
8854046 GTGCTCCCATTTTTCACTGATCAGGTAGCCG
1 AAGCTACCACTTTTCACTGATCAGGTAGCTG
* *
8854077 GAGCTACCACTTTTCACTGATCAGGTAGCCG
1 AAGCTACCACTTTTCACTGATCAGGTAGCTG
* *
8854108 AAGCTACCACTTTTCACTGATTAGGTAGCAG
1 AAGCTACCACTTTTCACTGATCAGGTAGCTG
8854139 AAGCTACCACTTTTCACTGATCAGGTAGCTG
1 AAGCTACCACTTTTCACTGATCAGGTAGCTG
**
8854170 AAAATACCACTTTTCACTGATCAGGTAGCTG
1 AAGCTACCACTTTTCACTGATCAGGTAGCTG
8854201 AAGCTACCACTTTTCA
1 AAGCTACCACTTTTCA
8854217 GTTGTCATTT
Statistics
Matches: 152, Mismatches: 19, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 152 1.00
ACGTcount: A:0.27, C:0.26, G:0.19, T:0.29
Consensus pattern (31 bp):
AAGCTACCACTTTTCACTGATCAGGTAGCTG
Found at i:8854285 original size:50 final size:51
Alignment explanation
Indices: 8854194--8854322 Score: 181
Period size: 50 Copynumber: 2.5 Consensus size: 51
8854184 CACTGATCAG
* * * *
8854194 GTAGCTGAAGCTACCACTTTTCAGTTGTCATTTGCCATTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTGTCATTTGCCATTGATCAGATAAGT
*
8854245 GTAGTCGAAGCTATCACTTATCACTT-TCATTTGTCC-TTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTGTCATTTG-CCATTGATCAGATAAGT
*
8854295 GTAGCCGAAGCTATCACTTATCGCTTGT
1 GTAGCCGAAGCTATCACTTATCACTTGT
8854323 TTCCATGGTC
Statistics
Matches: 69, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
50 45 0.65
51 24 0.35
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.36
Consensus pattern (51 bp):
GTAGCCGAAGCTATCACTTATCACTTGTCATTTGCCATTGATCAGATAAGT
Found at i:8856672 original size:8 final size:8
Alignment explanation
Indices: 8856659--8856688 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
8856649 GGAATCAAGA
8856659 ATTTTTTT
1 ATTTTTTT
8856667 ATTTTTTT
1 ATTTTTTT
8856675 ATTTTTTTT
1 A-TTTTTTT
8856684 ATTTT
1 ATTTT
8856689 CCGGACTATC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 13 0.62
9 8 0.38
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (8 bp):
ATTTTTTT
Found at i:8856674 original size:9 final size:9
Alignment explanation
Indices: 8856660--8856688 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
8856650 GAATCAAGAA
8856660 TTTTTTTA-
1 TTTTTTTAT
8856668 TTTTTTTAT
1 TTTTTTTAT
8856677 TTTTTTTAT
1 TTTTTTTAT
8856686 TTT
1 TTT
8856689 CCGGACTATC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 8 0.40
9 12 0.60
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (9 bp):
TTTTTTTAT
Found at i:8862681 original size:20 final size:20
Alignment explanation
Indices: 8862645--8862684 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
8862635 GTTTGAATTT
*
8862645 GGGTTTTAGGTTCAAGTTTG
1 GGGTTTTAGGTTAAAGTTTG
8862665 GGGTTTT-GGTTTAAAGTTTG
1 GGGTTTTAGG-TTAAAGTTTG
8862685 ATGTTCAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 2 0.11
20 16 0.89
ACGTcount: A:0.15, C:0.03, G:0.35, T:0.47
Consensus pattern (20 bp):
GGGTTTTAGGTTAAAGTTTG
Found at i:8865945 original size:17 final size:16
Alignment explanation
Indices: 8865916--8865954 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
8865906 TGTAATCGAC
8865916 TTTTTT-ATAAAAATA
1 TTTTTTAATAAAAATA
*
8865931 TTTTTTAATAGAAAATT
1 TTTTTTAATA-AAAATA
8865948 TTTTTTA
1 TTTTTTA
8865955 GACTAATTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 6 0.29
16 3 0.14
17 12 0.57
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (16 bp):
TTTTTTAATAAAAATA
Found at i:8866788 original size:6 final size:6
Alignment explanation
Indices: 8866772--8866813 Score: 70
Period size: 6 Copynumber: 7.3 Consensus size: 6
8866762 CAGAAAAGAA
8866772 AGGGGG A-GGGG AGGGGG AGGGGG AGGGGG A-GGGG AGGGGG AG
1 AGGGGG AGGGGG AGGGGG AGGGGG AGGGGG AGGGGG AGGGGG AG
8866814 AACCCATTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
5 10 0.29
6 24 0.71
ACGTcount: A:0.19, C:0.00, G:0.81, T:0.00
Consensus pattern (6 bp):
AGGGGG
Found at i:8866788 original size:11 final size:11
Alignment explanation
Indices: 8866772--8866813 Score: 75
Period size: 11 Copynumber: 3.7 Consensus size: 11
8866762 CAGAAAAGAA
8866772 AGGGGGAGGGG
1 AGGGGGAGGGG
8866783 AGGGGGAGGGGG
1 AGGGGGA-GGGG
8866795 AGGGGGAGGGG
1 AGGGGGAGGGG
8866806 AGGGGGAG
1 AGGGGGAG
8866814 AACCCATTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
11 19 0.63
12 11 0.37
ACGTcount: A:0.19, C:0.00, G:0.81, T:0.00
Consensus pattern (11 bp):
AGGGGGAGGGG
Found at i:8866794 original size:17 final size:17
Alignment explanation
Indices: 8866772--8866813 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
8866762 CAGAAAAGAA
8866772 AGGGGGA-GGGGAGGGGG
1 AGGGGGAGGGGGA-GGGG
8866789 AGGGGGAGGGGGAGGGG
1 AGGGGGAGGGGGAGGGG
8866806 AGGGGGAG
1 AGGGGGAG
8866814 AACCCATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 19 0.79
18 5 0.21
ACGTcount: A:0.19, C:0.00, G:0.81, T:0.00
Consensus pattern (17 bp):
AGGGGGAGGGGGAGGGG
Found at i:8872240 original size:11 final size:11
Alignment explanation
Indices: 8872226--8872255 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
8872216 GAGTTTCCAT
8872226 GGAGATGGGAC
1 GGAGATGGGAC
8872237 GGAGATGGGAC
1 GGAGATGGGAC
8872248 GGAGATGG
1 GGAGATGG
8872256 AGCCACCTCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.27, C:0.07, G:0.57, T:0.10
Consensus pattern (11 bp):
GGAGATGGGAC
Found at i:8874678 original size:95 final size:95
Alignment explanation
Indices: 8874515--8874709 Score: 354
Period size: 95 Copynumber: 2.1 Consensus size: 95
8874505 TTGCCTCGTA
*
8874515 AGTTGAAATGATAAAATGGCTACAGAGAAAGATGATTGACTAATACATGAAATAAACTAAAATTC
1 AGTTGAAATGATAAAATGGCTACACAGAAAGATGATTGACTAATACATGAAATAAACTAAAATTC
*
8874580 AGTGCAAATTTAATATGCATTTGTACTTTC
66 AGTGCAAATTTAAGATGCATTTGTACTTTC
*
8874610 AGTTGAAATGATAAAATGGCTACACAGAAAGATGATTGACTAATGCATGAAATAAACTAAAATTC
1 AGTTGAAATGATAAAATGGCTACACAGAAAGATGATTGACTAATACATGAAATAAACTAAAATTC
*
8874675 AGTGCAAATTTAAGATGCGTTTGTACTTTC
66 AGTGCAAATTTAAGATGCATTTGTACTTTC
8874705 AGTTG
1 AGTTG
8874710 CTGTTACTGA
Statistics
Matches: 96, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
95 96 1.00
ACGTcount: A:0.42, C:0.11, G:0.17, T:0.30
Consensus pattern (95 bp):
AGTTGAAATGATAAAATGGCTACACAGAAAGATGATTGACTAATACATGAAATAAACTAAAATTC
AGTGCAAATTTAAGATGCATTTGTACTTTC
Found at i:8877445 original size:31 final size:31
Alignment explanation
Indices: 8877407--8877467 Score: 122
Period size: 31 Copynumber: 2.0 Consensus size: 31
8877397 TCTTCATAAT
8877407 GTTTTAGTTAAGTCCTTAAAGTACCTACATG
1 GTTTTAGTTAAGTCCTTAAAGTACCTACATG
8877438 GTTTTAGTTAAGTCCTTAAAGTACCTACAT
1 GTTTTAGTTAAGTCCTTAAAGTACCTACAT
8877468 TGTATGGGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.30, C:0.16, G:0.15, T:0.39
Consensus pattern (31 bp):
GTTTTAGTTAAGTCCTTAAAGTACCTACATG
Found at i:8878657 original size:20 final size:18
Alignment explanation
Indices: 8878624--8878669 Score: 65
Period size: 20 Copynumber: 2.4 Consensus size: 18
8878614 AAATTATATT
8878624 TTTTATTTTAATTTTTAG
1 TTTTATTTTAATTTTTAG
*
8878642 TTTTAGTTTTAGATTTTTAT
1 TTTTA-TTTTA-ATTTTTAG
8878662 TTTTATTT
1 TTTTATTT
8878670 ATTAAATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 5 0.20
19 8 0.32
20 12 0.48
ACGTcount: A:0.20, C:0.00, G:0.07, T:0.74
Consensus pattern (18 bp):
TTTTATTTTAATTTTTAG
Found at i:8880672 original size:3 final size:3
Alignment explanation
Indices: 8880666--8880706 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
8880656 TCAACTTCTT
* * *
8880666 CAC CAC CAC CAC CAC CAT CAC CAT CAC CCC CAC CAC CAC CA
1 CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CA
8880707 GCAGAGTCAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.32, C:0.63, G:0.00, T:0.05
Consensus pattern (3 bp):
CAC
Found at i:8880752 original size:18 final size:18
Alignment explanation
Indices: 8880665--8880753 Score: 54
Period size: 18 Copynumber: 4.9 Consensus size: 18
8880655 GTCAACTTCT
* *
8880665 TCACCACCACCACCACCA
1 TCACCATCACCGCCACCA
*
8880683 TCACCATCACCCCCACCA
1 TCACCATCACCGCCACCA
* * ** * *
8880701 CCACCAGCAGAGTCAAC-
1 TCACCATCACCGCCACCA
* * *
8880718 TCCATCAACATCGCCACCA
1 T-CACCATCACCGCCACCA
8880737 TCACCATCACCGCCACC
1 TCACCATCACCGCCACC
8880754 GCCACCGTCA
Statistics
Matches: 50, Mismatches: 19, Indels: 4
0.68 0.26 0.05
Matches are distributed among these distances:
18 49 0.98
19 1 0.02
ACGTcount: A:0.30, C:0.54, G:0.06, T:0.10
Consensus pattern (18 bp):
TCACCATCACCGCCACCA
Found at i:8896249 original size:16 final size:18
Alignment explanation
Indices: 8896223--8896259 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
8896213 AGTTAAATAT
8896223 AAATGTAAAAATT-TTAA
1 AAATGTAAAAATTATTAA
8896240 AAAT-TAAAAATTATTAA
1 AAATGTAAAAATTATTAA
8896257 AAA
1 AAA
8896260 AATTTGTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (18 bp):
AAATGTAAAAATTATTAA
Found at i:8898621 original size:57 final size:57
Alignment explanation
Indices: 8898533--8898650 Score: 236
Period size: 57 Copynumber: 2.1 Consensus size: 57
8898523 ATGTTATCTT
8898533 ACTACATTTTACTATTATATTACTTTTATTTTGTTATTATTATTTAGATATTGTATA
1 ACTACATTTTACTATTATATTACTTTTATTTTGTTATTATTATTTAGATATTGTATA
8898590 ACTACATTTTACTATTATATTACTTTTATTTTGTTATTATTATTTAGATATTGTATA
1 ACTACATTTTACTATTATATTACTTTTATTTTGTTATTATTATTTAGATATTGTATA
8898647 ACTA
1 ACTA
8898651 ACTCTTATTT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 61 1.00
ACGTcount: A:0.31, C:0.08, G:0.05, T:0.57
Consensus pattern (57 bp):
ACTACATTTTACTATTATATTACTTTTATTTTGTTATTATTATTTAGATATTGTATA
Found at i:8899291 original size:24 final size:27
Alignment explanation
Indices: 8899243--8899298 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 27
8899233 CAAATAACAT
* *
8899243 AAAACACACATTAATTTTGCTTTAA-A
1 AAAATACACATTAATTTTACTTTAATA
8899269 AAAATACACATTAA-TTTAC-TTAATA
1 AAAATACACATTAATTTTACTTTAATA
8899294 AAAAT
1 AAAAT
8899299 CCAAAGGAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
24 4 0.15
25 10 0.37
26 13 0.48
ACGTcount: A:0.52, C:0.12, G:0.02, T:0.34
Consensus pattern (27 bp):
AAAATACACATTAATTTTACTTTAATA
Found at i:8904725 original size:23 final size:22
Alignment explanation
Indices: 8904683--8904728 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 22
8904673 ATTATTATAG
*
8904683 ATTAATTAAATATAATATATTT
1 ATTAATTAAATATAAAATATTT
8904705 ATTAATTAAA-ATTAAAAATATTT
1 ATTAATTAAATA-T-AAAATATTT
8904728 A
1 A
8904729 ATATATTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 1 0.05
22 11 0.52
23 9 0.43
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
ATTAATTAAATATAAAATATTT
Found at i:8905007 original size:17 final size:17
Alignment explanation
Indices: 8904985--8905020 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
8904975 AAGTAAATAT
*
8904985 AATTATGAGTGAACCTA
1 AATTATGAGTCAACCTA
8905002 AATTATGAGTCAACCTA
1 AATTATGAGTCAACCTA
8905019 AA
1 AA
8905021 ATAGGCTCAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.44, C:0.14, G:0.14, T:0.28
Consensus pattern (17 bp):
AATTATGAGTCAACCTA
Found at i:8908389 original size:21 final size:21
Alignment explanation
Indices: 8908363--8908403 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
8908353 ATCTGCTCAA
* *
8908363 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
8908384 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
8908404 TCGCTTGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:8912482 original size:27 final size:27
Alignment explanation
Indices: 8912434--8912486 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
8912424 AATATTAATA
*
8912434 ATTTATAATAATTAAAATAAAATCAAT
1 ATTTATAATAATTAAAACAAAATCAAT
*
8912461 ATTTATATATAATT-ATACAAAATCAA
1 ATTTATA-ATAATTAAAACAAAATCAA
8912487 CATTAATGTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 17 0.74
28 6 0.26
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.38
Consensus pattern (27 bp):
ATTTATAATAATTAAAACAAAATCAAT
Found at i:8914252 original size:12 final size:13
Alignment explanation
Indices: 8914237--8914265 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
8914227 ATATAAACAT
8914237 AATAA-TAATTGA
1 AATAATTAATTGA
8914249 AATAATTAATTGA
1 AATAATTAATTGA
8914262 AATA
1 AATA
8914266 TTTCACATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.31
13 11 0.69
ACGTcount: A:0.59, C:0.00, G:0.07, T:0.34
Consensus pattern (13 bp):
AATAATTAATTGA
Found at i:8915921 original size:28 final size:28
Alignment explanation
Indices: 8915877--8915962 Score: 145
Period size: 29 Copynumber: 3.0 Consensus size: 28
8915867 TTAAGAAGAT
8915877 TATTTAAAGATGCTAAAATATATTATTAA
1 TATTTAAA-ATGCTAAAATATATTATTAA
8915906 TATTTAAAATGCTAAAATATATTATTAA
1 TATTTAAAATGCTAAAATATATTATTAA
*
8915934 TATTTAAAAATGCTAAAATACATTATTAA
1 TATTT-AAAATGCTAAAATATATTATTAA
8915963 CATAAAATTG
Statistics
Matches: 55, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
28 25 0.45
29 30 0.55
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.41
Consensus pattern (28 bp):
TATTTAAAATGCTAAAATATATTATTAA
Found at i:8916016 original size:26 final size:26
Alignment explanation
Indices: 8915987--8916037 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
8915977 ATTAAATAAT
*
8915987 TTATTAAA-AAAATTATATTAATTATA
1 TTATCAAATAAAATTA-ATTAATTATA
*
8916013 TTATCAAATATAATTAATTAATTAT
1 TTATCAAATAAAATTAATTAATTAT
8916038 GTTTGTATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 16 0.73
27 6 0.27
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (26 bp):
TTATCAAATAAAATTAATTAATTATA
Found at i:8918676 original size:27 final size:28
Alignment explanation
Indices: 8918646--8918715 Score: 97
Period size: 27 Copynumber: 2.5 Consensus size: 28
8918636 ATAGTGAATC
*
8918646 CGCACACTTAGTGCTATAAAATC-AGCT
1 CGCACACTTAGTGCTATAAAATCAAACT
* * *
8918673 CGCACACATAGTGCTATATAATCAAATT
1 CGCACACTTAGTGCTATAAAATCAAACT
8918701 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
8918716 GTACAATTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
27 21 0.57
28 16 0.43
ACGTcount: A:0.33, C:0.26, G:0.14, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATAAAATCAAACT
Found at i:8918787 original size:42 final size:42
Alignment explanation
Indices: 8918723--8918829 Score: 196
Period size: 42 Copynumber: 2.5 Consensus size: 42
8918713 GCTGTACAAT
* *
8918723 TTTAAACCCGCACACGTAGTGCCAATCTTGTCACCGTGTCCA
1 TTTATACCCGCACACTTAGTGCCAATCTTGTCACCGTGTCCA
8918765 TTTATACCCGCACACTTAGTGCCAATCTTGTCACCGTGTCCA
1 TTTATACCCGCACACTTAGTGCCAATCTTGTCACCGTGTCCA
8918807 TTTATACCCGCACACTTAGTGCC
1 TTTATACCCGCACACTTAGTGCC
8918830 GAGACCAATA
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 63 1.00
ACGTcount: A:0.22, C:0.34, G:0.15, T:0.29
Consensus pattern (42 bp):
TTTATACCCGCACACTTAGTGCCAATCTTGTCACCGTGTCCA
Found at i:8925833 original size:27 final size:28
Alignment explanation
Indices: 8925803--8925872 Score: 97
Period size: 27 Copynumber: 2.5 Consensus size: 28
8925793 ATAGTGAATC
*
8925803 CGCACACTTAGTGCTATAAAATC-AGCT
1 CGCACACTTAGTGCTATAAAATCAAACT
* * *
8925830 CGCACACATAGTGCTATATAATCAAATT
1 CGCACACTTAGTGCTATAAAATCAAACT
8925858 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
8925873 GTACAATTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
27 21 0.57
28 16 0.43
ACGTcount: A:0.33, C:0.26, G:0.14, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATAAAATCAAACT
Found at i:8925944 original size:42 final size:42
Alignment explanation
Indices: 8925880--8925986 Score: 196
Period size: 42 Copynumber: 2.5 Consensus size: 42
8925870 GCTGTACAAT
* *
8925880 TTTAAACCCGCACACGTAGTGCCAATCTTGTCACCGTGTCCA
1 TTTATACCCGCACACTTAGTGCCAATCTTGTCACCGTGTCCA
8925922 TTTATACCCGCACACTTAGTGCCAATCTTGTCACCGTGTCCA
1 TTTATACCCGCACACTTAGTGCCAATCTTGTCACCGTGTCCA
8925964 TTTATACCCGCACACTTAGTGCC
1 TTTATACCCGCACACTTAGTGCC
8925987 GAGACCAATA
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 63 1.00
ACGTcount: A:0.22, C:0.34, G:0.15, T:0.29
Consensus pattern (42 bp):
TTTATACCCGCACACTTAGTGCCAATCTTGTCACCGTGTCCA
Found at i:8928815 original size:13 final size:13
Alignment explanation
Indices: 8928797--8928825 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
8928787 TTTACTTACG
8928797 TATTCTCATAAGC
1 TATTCTCATAAGC
8928810 TATTCTCATAAGC
1 TATTCTCATAAGC
8928823 TAT
1 TAT
8928826 GATGAAATGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.31, C:0.21, G:0.07, T:0.41
Consensus pattern (13 bp):
TATTCTCATAAGC
Found at i:8931636 original size:46 final size:44
Alignment explanation
Indices: 8931582--8931758 Score: 176
Period size: 46 Copynumber: 3.9 Consensus size: 44
8931572 ATATTTGGGC
*
8931582 ATCCGAACTCGTTGAGTTGAGACCGAGTTCACTTATGGATGCGA
1 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGA
*** * *
8931626 ATGTCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-GC
1 A--TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGA
*
8931675 ATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA
1 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCG-A
* * * *
8931720 CACCCGAGCTCATTGAGTTTAGTCCGAGTTCACTTATGG
1 -ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
8931759 GCGGGTTACA
Statistics
Matches: 109, Mismatches: 15, Indels: 16
0.78 0.11 0.11
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 1 0.01
46 67 0.61
47 32 0.29
48 1 0.01
49 3 0.03
50 1 0.01
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (44 bp):
ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGA
Found at i:8931738 original size:93 final size:93
Alignment explanation
Indices: 8931579--8931750 Score: 272
Period size: 93 Copynumber: 1.8 Consensus size: 93
8931569 AGGATATTTG
*** *
8931579 GGCATCCGAACTCGTTGAGTTGAGACCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGACCGAGTTCACTTATGGATGCGAACACCCGAACTCATTGAG
8931644 TTGAGTCCGAGTTCGAGAGATGTAACTA
66 TTGAGTCCGAGTTCGAGAGATGTAACTA
* * *
8931672 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACACCCGAGCTCATTGAG
1 GGCATCCGAACTCGTTGAGTTGAGACCGAGTTCACTTATGGATGCGAACACCCGAACTCATTGAG
*
8931737 TTTAGTCCGAGTTC
66 TTGAGTCCGAGTTC
8931751 ACTTATGGGC
Statistics
Matches: 71, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 71 1.00
ACGTcount: A:0.23, C:0.22, G:0.28, T:0.27
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGACCGAGTTCACTTATGGATGCGAACACCCGAACTCATTGAG
TTGAGTCCGAGTTCGAGAGATGTAACTA
Found at i:8934231 original size:4 final size:4
Alignment explanation
Indices: 8934222--8934255 Score: 59
Period size: 4 Copynumber: 8.5 Consensus size: 4
8934212 TTTTAACCCC
*
8934222 TTAT TTAT TTAT TTAT TTAT TTAT TCAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
8934256 TATTATTGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (4 bp):
TTAT
Found at i:8935480 original size:40 final size:37
Alignment explanation
Indices: 8935393--8935524 Score: 146
Period size: 35 Copynumber: 3.6 Consensus size: 37
8935383 GTTTTCCTCA
*
8935393 TTGAAATACCATACCTACATTTTTCAACTCGGTATGG
1 TTGAAATACCATACCTACATTTTTCAACTCAGTATGG
* *
8935430 --GAAATGCCATACCTACATTTTTTAACTCAGTATGG
1 TTGAAATACCATACCTACATTTTTCAACTCAGTATGG
** *
8935465 ATTTGATAATACCATACCTACATTTCACAGCTCAGTATGG
1 --TTGA-AATACCATACCTACATTTTTCAACTCAGTATGG
*
8935505 ATG--ATACCATACCTACATTT
1 TTGAAATACCATACCTACATTT
8935525 CACACTTTTC
Statistics
Matches: 81, Mismatches: 9, Indels: 12
0.79 0.09 0.12
Matches are distributed among these distances:
35 49 0.60
38 2 0.02
39 2 0.02
40 28 0.35
ACGTcount: A:0.32, C:0.22, G:0.12, T:0.34
Consensus pattern (37 bp):
TTGAAATACCATACCTACATTTTTCAACTCAGTATGG
Found at i:8942900 original size:34 final size:35
Alignment explanation
Indices: 8942833--8942961 Score: 136
Period size: 35 Copynumber: 3.6 Consensus size: 35
8942823 TTTCCTCATT
*
8942833 GAAATACCATACCTACATTTTTCAACTCGGTATGG
1 GAAATACCATACCTACATTTTTCAACTCAGTATGG
*
8942868 GAAATGCCATACCTACATTTTT-AACTCAGTATGG
1 GAAATACCATACCTACATTTTTCAACTCAGTATGG
** *
8942902 ATTTGATAATACCATACCTACATTTCACAGCTCAGTAT-G
1 ----GA-AATACCATACCTACATTTTTCAACTCAGTATGG
*
8942941 GATGATACCATACCTACATTT
1 GA-AATACCATACCTACATTT
8942962 CACACTTTTC
Statistics
Matches: 81, Mismatches: 7, Indels: 12
0.81 0.07 0.12
Matches are distributed among these distances:
34 11 0.14
35 41 0.51
38 2 0.02
39 18 0.22
40 9 0.11
ACGTcount: A:0.33, C:0.22, G:0.12, T:0.33
Consensus pattern (35 bp):
GAAATACCATACCTACATTTTTCAACTCAGTATGG
Found at i:8944354 original size:14 final size:14
Alignment explanation
Indices: 8944336--8944377 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
8944326 CTATATTTAA
8944336 AATTATTTATTATT
1 AATTATTTATTATT
*
8944350 CATTATTTA-TATT
1 AATTATTTATTATT
8944363 AAGTTATCTTATTAT
1 AA-TTAT-TTATTAT
8944378 ATATATTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
13 5 0.22
14 12 0.52
15 3 0.13
16 3 0.13
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (14 bp):
AATTATTTATTATT
Found at i:8945148 original size:6 final size:6
Alignment explanation
Indices: 8945149--8945177 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
8945139 CTTATTCTTA
8945149 TTTATT TTTATT TTTATT TTTATT TTTAT
1 TTTATT TTTATT TTTATT TTTATT TTTAT
8945178 CATGTTATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTATT
Found at i:8947697 original size:26 final size:26
Alignment explanation
Indices: 8947668--8947720 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
8947658 ATGCAGGCGT
8947668 TTATCATACAGCATTCAATGAATTGG
1 TTATCATACAGCATTCAATGAATTGG
8947694 TTATCATACAGCATTCAATGAATTGG
1 TTATCATACAGCATTCAATGAATTGG
8947720 T
1 T
8947721 AAATGTAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Consensus pattern (26 bp):
TTATCATACAGCATTCAATGAATTGG
Found at i:8948485 original size:42 final size:42
Alignment explanation
Indices: 8948422--8948509 Score: 167
Period size: 42 Copynumber: 2.1 Consensus size: 42
8948412 TACTAGGATT
8948422 ACAACAATAAATGACAAAGTACTAAAGGGGTAGTTTATTCTA
1 ACAACAATAAATGACAAAGTACTAAAGGGGTAGTTTATTCTA
*
8948464 ACAACAATAAATGACAGAGTACTAAAGGGGTAGTTTATTCTA
1 ACAACAATAAATGACAAAGTACTAAAGGGGTAGTTTATTCTA
8948506 ACAA
1 ACAA
8948510 GATTGCGGGT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.45, C:0.12, G:0.17, T:0.25
Consensus pattern (42 bp):
ACAACAATAAATGACAAAGTACTAAAGGGGTAGTTTATTCTA
Found at i:8956333 original size:21 final size:21
Alignment explanation
Indices: 8956307--8956352 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
8956297 AATAAATTTT
8956307 TTATTTTAAAAAT-CATTAAAA
1 TTATTTT-AAAATGCATTAAAA
*
8956328 TTATTTTAAAATGTATTAAAA
1 TTATTTTAAAATGCATTAAAA
8956349 TTAT
1 TTAT
8956353 AACAAGAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 5 0.22
21 18 0.78
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (21 bp):
TTATTTTAAAATGCATTAAAA
Found at i:8964843 original size:6 final size:6
Alignment explanation
Indices: 8964826--8964856 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
8964816 TGAGGGTAAC
*
8964826 GGTGGA GATGGA GGTGGA GGTGGA GGTGGA G
1 GGTGGA GGTGGA GGTGGA GGTGGA GGTGGA G
8964857 AGAGGGAGGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.19, C:0.00, G:0.65, T:0.16
Consensus pattern (6 bp):
GGTGGA
Found at i:8972016 original size:17 final size:17
Alignment explanation
Indices: 8971994--8972027 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
8971984 AAAACTAATT
8971994 TTTTTAAAAACATTAAC
1 TTTTTAAAAACATTAAC
* *
8972011 TTTTTAATAATATTAAC
1 TTTTTAAAAACATTAAC
8972028 ACCACGGTTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47
Consensus pattern (17 bp):
TTTTTAAAAACATTAAC
Found at i:8972938 original size:107 final size:108
Alignment explanation
Indices: 8972815--8973030 Score: 398
Period size: 107 Copynumber: 2.0 Consensus size: 108
8972805 TAAACAAAAA
8972815 ATTAGTTTAACAAAACAATGATATGTTAAGTTAGAATAAGTTTTAAATAATAAAATTTCAAACAA
1 ATTAGTTTAACAAAACAATGATATGTTAAGTTAGAATAAGTTTTAAATAATAAAATTTCAAACAA
8972880 AATTGTATTAAAATTTTTGTTAATTACTCT-ATAAAATTTTTG
66 AATTGTATTAAAATTTTTGTTAATTACTCTGATAAAATTTTTG
* *
8972922 ATTAGTTTAACAAAACAATGATATGTTAAGTTGGAATAAGTTTTAAATAATAAAATTTCTAACAA
1 ATTAGTTTAACAAAACAATGATATGTTAAGTTAGAATAAGTTTTAAATAATAAAATTTCAAACAA
*
8972987 AATTGTCTTAAAATTTTTGTTAATTACTCTGATAAAATTTTTG
66 AATTGTATTAAAATTTTTGTTAATTACTCTGATAAAATTTTTG
8973030 A
1 A
8973031 CGTGTTTTTT
Statistics
Matches: 105, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
107 92 0.88
108 13 0.12
ACGTcount: A:0.44, C:0.06, G:0.09, T:0.41
Consensus pattern (108 bp):
ATTAGTTTAACAAAACAATGATATGTTAAGTTAGAATAAGTTTTAAATAATAAAATTTCAAACAA
AATTGTATTAAAATTTTTGTTAATTACTCTGATAAAATTTTTG
Found at i:8974000 original size:12 final size:12
Alignment explanation
Indices: 8973985--8974009 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
8973975 AAAATTATAA
8973985 TGTTAATTAGTT
1 TGTTAATTAGTT
8973997 TGTTAATTAGTT
1 TGTTAATTAGTT
8974009 T
1 T
8974010 ATAAAAAAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.00, G:0.16, T:0.60
Consensus pattern (12 bp):
TGTTAATTAGTT
Found at i:8976447 original size:14 final size:14
Alignment explanation
Indices: 8976428--8976458 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
8976418 TTCAGAATTT
*
8976428 AAGATTTAGGGTTC
1 AAGATTGAGGGTTC
8976442 AAGATTGAGGGTTC
1 AAGATTGAGGGTTC
8976456 AAG
1 AAG
8976459 TTAAAAAAAT
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:0.32, C:0.06, G:0.32, T:0.29
Consensus pattern (14 bp):
AAGATTGAGGGTTC
Found at i:8976704 original size:30 final size:30
Alignment explanation
Indices: 8976644--8976705 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 30
8976634 AGCTTCTGTC
**
8976644 TTTATAATTTTTAAAAAATTAAATTAAATT
1 TTTATAATTTTTAAAAAACAAAATTAAATT
* *
8976674 TTTATTATTTTTAAAAGACAAAA-TATAATT
1 TTTATAATTTTTAAAAAACAAAATTA-AATT
8976704 TT
1 TT
8976706 ACTTTTAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 2 0.07
30 25 0.93
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (30 bp):
TTTATAATTTTTAAAAAACAAAATTAAATT
Found at i:8977671 original size:17 final size:18
Alignment explanation
Indices: 8977646--8977689 Score: 56
Period size: 17 Copynumber: 2.5 Consensus size: 18
8977636 CATGAAAATT
*
8977646 AACACATATA-TATAAAA
1 AACAAATATAGTATAAAA
8977663 AACAAATATAGGTATAAAA
1 AACAAATATA-GTATAAAA
8977682 AA-AAATAT
1 AACAAATAT
8977690 TACTCGAGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 9 0.38
18 6 0.25
19 9 0.38
ACGTcount: A:0.66, C:0.07, G:0.05, T:0.23
Consensus pattern (18 bp):
AACAAATATAGTATAAAA
Found at i:8978434 original size:91 final size:89
Alignment explanation
Indices: 8978265--8978495 Score: 286
Period size: 91 Copynumber: 2.6 Consensus size: 89
8978255 ATTAAGGGTG
* * *
8978265 CAAAAA-GCCCTCACAA-TTTTTGAAAAAATGCAATTAAGCCCCTGTTTTTTTTTTTTGCACTCA
1 CAAAAAGGCCCTCA-AACTTTTTCAAAAAAAGCAATTAAGCCCC---TATTTTTTTTTGCACTCA
* *
8978328 TTTGGATACTTGAACTTTTAAAATGTAT
62 ATTGGATACTTGAACTTTCAAAATGTAT
* *
8978356 CAAAAAGGCCCTCAAACCTTTTTTAAAAAAAGCAATTAAGCTCCTAATTTTTTTTTGCACTCAAT
1 CAAAAAGGCCCTCAAA-CTTTTTCAAAAAAAGCAATTAAGCCCCT-ATTTTTTTTTGCACTCAAT
* *
8978421 TGGGTATTTGAACTTTCAAAATGTAT
64 TGGATACTTGAACTTTCAAAATGTAT
* * *
8978447 CAAAAAGACCCTTAAACTTTTTCAGAAAAAGCAATTAAGCCCCTATTTT
1 CAAAAAGGCCCTCAAACTTTTTCAAAAAAAGCAATTAAGCCCCTATTTT
8978496 ATTAAAAATT
Statistics
Matches: 123, Mismatches: 13, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
89 5 0.04
90 26 0.21
91 62 0.50
92 7 0.06
93 23 0.19
ACGTcount: A:0.35, C:0.19, G:0.10, T:0.36
Consensus pattern (89 bp):
CAAAAAGGCCCTCAAACTTTTTCAAAAAAAGCAATTAAGCCCCTATTTTTTTTTGCACTCAATTG
GATACTTGAACTTTCAAAATGTAT
Found at i:8978522 original size:8 final size:8
Alignment explanation
Indices: 8978511--8978594 Score: 60
Period size: 8 Copynumber: 9.5 Consensus size: 8
8978501 AAATTAGAAA
8978511 AAAAATAT
1 AAAAATAT
*
8978519 AAAAATGT
1 AAAAATAT
8978527 AAAAATAT
1 AAAAATAT
*
8978535 AAAAAATTGT
1 -AAAAA-TAT
*
8978545 AAAATTTTAT
1 AAAA--ATAT
8978555 AAAAATAGT
1 AAAAATA-T
8978564 AAAAGATTAT
1 AAAA-A-TAT
*
8978574 AGAAATAT
1 AAAAATAT
8978582 AAAAAATAT
1 -AAAAATAT
8978591 AAAA
1 AAAA
8978595 TTTTATAAAG
Statistics
Matches: 60, Mismatches: 8, Indels: 16
0.71 0.10 0.19
Matches are distributed among these distances:
8 23 0.38
9 22 0.37
10 13 0.22
11 2 0.03
ACGTcount: A:0.67, C:0.00, G:0.06, T:0.27
Consensus pattern (8 bp):
AAAAATAT
Found at i:8978522 original size:9 final size:9
Alignment explanation
Indices: 8978510--8978594 Score: 52
Period size: 9 Copynumber: 9.4 Consensus size: 9
8978500 AAAATTAGAA
8978510 AAAAAATAT
1 AAAAAATAT
*
8978519 -AAAAATGT
1 AAAAAATAT
8978527 -AAAAATAT
1 AAAAAATAT
8978535 AAAAAAT-T
1 AAAAAATAT
* * *
8978543 GTAAAATTTT
1 -AAAAAATAT
8978553 ATAAAAATAGT
1 A-AAAAATA-T
*
8978564 AAAAGAT-T
1 AAAAAATAT
*
8978572 ATAGAAATAT
1 A-AAAAATAT
8978582 AAAAAATAT
1 AAAAAATAT
8978591 AAAA
1 AAAA
8978595 TTTTATAAAG
Statistics
Matches: 58, Mismatches: 11, Indels: 14
0.70 0.13 0.17
Matches are distributed among these distances:
8 17 0.29
9 26 0.45
10 13 0.22
11 2 0.03
ACGTcount: A:0.67, C:0.00, G:0.06, T:0.27
Consensus pattern (9 bp):
AAAAAATAT
Found at i:8978573 original size:19 final size:18
Alignment explanation
Indices: 8978510--8978594 Score: 77
Period size: 19 Copynumber: 4.7 Consensus size: 18
8978500 AAAATTAGAA
*
8978510 AAAAAATATAAAAAT-GT
1 AAAAATTATAAAAATAGT
*
8978527 AAAAA-TATAAAAAATTGT
1 AAAAATTAT-AAAAATAGT
*
8978545 AAAATTTTATAAAAATAGT
1 AAAA-ATTATAAAAATAGT
*
8978564 AAAAGATTATAGAAATA-T
1 AAAA-ATTATAAAAATAGT
*
8978582 AAAAAATATAAAA
1 AAAAATTATAAAA
8978595 TTTTATAAAG
Statistics
Matches: 57, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
16 3 0.05
17 18 0.32
18 11 0.19
19 22 0.39
20 3 0.05
ACGTcount: A:0.67, C:0.00, G:0.06, T:0.27
Consensus pattern (18 bp):
AAAAATTATAAAAATAGT
Found at i:8978619 original size:46 final size:47
Alignment explanation
Indices: 8978528--8978641 Score: 133
Period size: 46 Copynumber: 2.4 Consensus size: 47
8978518 TAAAAATGTA
* *
8978528 AAAATATAAAAAATTGTAAAATTTTATAAAAATAGTAAAAGATTATA-
1 AAAATATAAAAAA-TATAAAATTTTATAAAAATAGTAAAAAATTATAC
* * *
8978575 GAAATATAAAAAATATAAAATTTTAT-AAAGTCGTAAGAAAATTATAC
1 AAAATATAAAAAATATAAAATTTTATAAAAATAGTAA-AAAATTATAC
*
8978622 AAAATGTAAAGAAATATAAA
1 AAAATATAAA-AAATATAAA
8978642 TTTCGTAAAT
Statistics
Matches: 57, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
45 8 0.14
46 20 0.35
47 20 0.35
48 9 0.16
ACGTcount: A:0.61, C:0.02, G:0.08, T:0.29
Consensus pattern (47 bp):
AAAATATAAAAAATATAAAATTTTATAAAAATAGTAAAAAATTATAC
Found at i:8978813 original size:9 final size:9
Alignment explanation
Indices: 8978799--8978852 Score: 56
Period size: 9 Copynumber: 6.0 Consensus size: 9
8978789 CATCAAAATT
8978799 TTTTTATAA
1 TTTTTATAA
8978808 TTTTTATAAA
1 TTTTTAT-AA
* *
8978818 ATTTTACAA
1 TTTTTATAA
*
8978827 TTTTT-TAT
1 TTTTTATAA
*
8978835 TTTTTACAA
1 TTTTTATAA
8978844 TTTTTATAA
1 TTTTTATAA
8978853 AAAAATTCTA
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
8 6 0.17
9 22 0.63
10 7 0.20
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (9 bp):
TTTTTATAA
Found at i:8980638 original size:45 final size:45
Alignment explanation
Indices: 8980544--8980669 Score: 138
Period size: 45 Copynumber: 2.9 Consensus size: 45
8980534 TTTTCTCAAA
* *
8980544 TCACCGGCATT-TCGCC-GTTAGGCTCG-AGGCCCG-ATATCAGT
1 TCACCGGCATTATAGCCTGCTAGGCTCGAAGGCCCGAATATCAGT
8980585 TCACCGGCATTATAGCCTGCTAGGCTCGAAGGCCCGAATAGT-A-T
1 TCACCGGCATTATAGCCTGCTAGGCTCGAAGGCCCGAATA-TCAGT
** * *
8980629 CTCACCGGCATTATAGTTTGCTAAGCTCAAAGGCCCGAATA
1 -TCACCGGCATTATAGCCTGCTAGGCTCGAAGGCCCGAATA
8980670 ATCAAGTCAA
Statistics
Matches: 73, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
41 11 0.15
42 4 0.05
43 9 0.12
44 8 0.11
45 40 0.55
46 1 0.01
ACGTcount: A:0.24, C:0.29, G:0.24, T:0.24
Consensus pattern (45 bp):
TCACCGGCATTATAGCCTGCTAGGCTCGAAGGCCCGAATATCAGT
Found at i:8981076 original size:42 final size:43
Alignment explanation
Indices: 8980985--8981171 Score: 283
Period size: 42 Copynumber: 4.4 Consensus size: 43
8980975 ACATATCATT
* * *
8980985 TCACCGGCATTACGCCTGCTAGGCACAAAGGCCCGAATACACA
1 TCACCGGCACTAAGCCTGCTAGGCACGAAGGCCCGAATACACA
*
8981028 TCACCGGCACGAAGCCTGCTAGGCACGAAGG-CCGAATACACA
1 TCACCGGCACTAAGCCTGCTAGGCACGAAGGCCCGAATACACA
8981070 TCACCGGCACTAAGCCTGCTAGGCACGAAGGCCCGAATACACA
1 TCACCGGCACTAAGCCTGCTAGGCACGAAGGCCCGAATACACA
*
8981113 TCACCGGCACTAAG-CTGCTAGGCACGAAGGCCCGAATATA-A
1 TCACCGGCACTAAGCCTGCTAGGCACGAAGGCCCGAATACACA
* *
8981154 T-ACCAGCACTAGGCCTGC
1 TCACCGGCACTAAGCCTGC
8981172 AGGATTTATC
Statistics
Matches: 134, Mismatches: 8, Indels: 6
0.91 0.05 0.04
Matches are distributed among these distances:
40 10 0.07
41 6 0.04
42 66 0.49
43 52 0.39
ACGTcount: A:0.30, C:0.34, G:0.24, T:0.13
Consensus pattern (43 bp):
TCACCGGCACTAAGCCTGCTAGGCACGAAGGCCCGAATACACA
Found at i:8981148 original size:85 final size:84
Alignment explanation
Indices: 8980985--8981171 Score: 279
Period size: 85 Copynumber: 2.2 Consensus size: 84
8980975 ACATATCATT
* *
8980985 TCACCGGCATTACGCCTGCTAGGCACAAAGGCCCGAATACACATCACCGGCACGAAGCCTGCTAG
1 TCACCGGCACTAAGCCTGCTAGGCACAAAGGCCCGAATACACATCACCGGCACGAAGCCTGCTAG
8981050 GCACGAAGGCCGAATACACA
66 GCACGAAGGCCGAATACA-A
* *
8981070 TCACCGGCACTAAGCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACTAAG-CTGCTAG
1 TCACCGGCACTAAGCCTGCTAGGCACAAAGGCCCGAATACACATCACCGGCACGAAGCCTGCTAG
*
8981134 GCACGAAGGCCCGAATATAA
66 GCACGAAGG-CCGAATACAA
* *
8981154 T-ACCAGCACTAGGCCTGC
1 TCACCGGCACTAAGCCTGC
8981172 AGGATTTATC
Statistics
Matches: 94, Mismatches: 7, Indels: 4
0.90 0.07 0.04
Matches are distributed among these distances:
83 15 0.16
84 18 0.19
85 61 0.65
ACGTcount: A:0.30, C:0.34, G:0.24, T:0.13
Consensus pattern (84 bp):
TCACCGGCACTAAGCCTGCTAGGCACAAAGGCCCGAATACACATCACCGGCACGAAGCCTGCTAG
GCACGAAGGCCGAATACAA
Found at i:8981192 original size:38 final size:38
Alignment explanation
Indices: 8981143--8981226 Score: 123
Period size: 38 Copynumber: 2.2 Consensus size: 38
8981133 GGCACGAAGG
* * *
8981143 CCCGAATATAATACCAGCACTAGGCCTGCAGGATTTAT
1 CCCGAATATAATACCAGCACGAAGCCTGCAGGATTTAA
* *
8981181 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
1 CCCGAATATAATACCAGCACGAAGCCTGCAGGATTTAA
8981219 CCCGAATA
1 CCCGAATA
8981227 CACATCAAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.32, C:0.27, G:0.20, T:0.20
Consensus pattern (38 bp):
CCCGAATATAATACCAGCACGAAGCCTGCAGGATTTAA
Found at i:8994037 original size:8 final size:8
Alignment explanation
Indices: 8994019--8994057 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
8994009 ATAAATATTC
*
8994019 AAAACAAT
1 AAAAAAAT
*
8994027 AAATAAAT
1 AAAAAAAT
8994035 AAAAAAAT
1 AAAAAAAT
8994043 GAAAAAAAT
1 -AAAAAAAT
8994052 AAAAAA
1 AAAAAA
8994058 TGAAAGATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
8 19 0.70
9 8 0.30
ACGTcount: A:0.82, C:0.03, G:0.03, T:0.13
Consensus pattern (8 bp):
AAAAAAAT
Found at i:8994056 original size:16 final size:17
Alignment explanation
Indices: 8994031--8994062 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
8994021 AACAATAAAT
8994031 AAATAAAAAAATGAAAA
1 AAATAAAAAAATGAAAA
8994048 AAAT-AAAAAATGAAA
1 AAATAAAAAAATGAAA
8994063 GATACACACA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.81, C:0.00, G:0.06, T:0.12
Consensus pattern (17 bp):
AAATAAAAAAATGAAAA
Found at i:8999892 original size:3 final size:3
Alignment explanation
Indices: 8999864--8999915 Score: 50
Period size: 3 Copynumber: 17.3 Consensus size: 3
8999854 ATCTAGTCTT
* * * * * *
8999864 TTA TTA CTA TTA TCA TTA TCA TTA TTA TTA TTA TTA CTA CTA TTA TTG
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
8999912 TTA T
1 TTA T
8999916 CATTTTTTTT
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.31, C:0.10, G:0.02, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:9004709 original size:20 final size:20
Alignment explanation
Indices: 9004680--9004720 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
9004670 AACCTGGGCC
9004680 AAGCCCGGCCCGCCCGTATT
1 AAGCCCGGCCCGCCCGTATT
*
9004700 AAGCCTGGCCCGCCCGTATT
1 AAGCCCGGCCCGCCCGTATT
9004720 A
1 A
9004721 TTTTTTATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.17, C:0.41, G:0.24, T:0.17
Consensus pattern (20 bp):
AAGCCCGGCCCGCCCGTATT
Found at i:9004919 original size:30 final size:31
Alignment explanation
Indices: 9004860--9004923 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
9004850 ACTTAACAAG
*
9004860 CAAATGCTTTTAAAATAATAAAAAAAATTAA
1 CAAATGCCTTTAAAATAATAAAAAAAATTAA
*
9004891 CAAATGCCTTTAAAATAAT-AAGAAAATTAA
1 CAAATGCCTTTAAAATAATAAAAAAAATTAA
9004921 CAA
1 CAA
9004924 TAAAATAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 13 0.42
31 18 0.58
ACGTcount: A:0.59, C:0.09, G:0.05, T:0.27
Consensus pattern (31 bp):
CAAATGCCTTTAAAATAATAAAAAAAATTAA
Found at i:9004978 original size:22 final size:22
Alignment explanation
Indices: 9004952--9005000 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
9004942 ATATTCAAAC
9004952 AATAACAATAAAATAGTAGCAA
1 AATAACAATAAAATAGTAGCAA
* * * *
9004974 CATAATAGTAAAATGGTAGCAA
1 AATAACAATAAAATAGTAGCAA
9004996 AATAA
1 AATAA
9005001 GGAGAAAACA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.59, C:0.08, G:0.12, T:0.20
Consensus pattern (22 bp):
AATAACAATAAAATAGTAGCAA
Found at i:9006313 original size:15 final size:15
Alignment explanation
Indices: 9006273--9006305 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
9006263 TAGAGGCAGC
9006273 AAAAAA-AAAAACAA
1 AAAAAACAAAAACAA
9006287 AAAAAACAAAAACAA
1 AAAAAACAAAAACAA
9006302 AAAA
1 AAAA
9006306 TATAAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.91, C:0.09, G:0.00, T:0.00
Consensus pattern (15 bp):
AAAAAACAAAAACAA
Found at i:9015137 original size:15 final size:14
Alignment explanation
Indices: 9015103--9015141 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
9015093 GTTTACCAGT
*
9015103 AAAATGTTTTCCGG
1 AAAATGATTTCCGG
*
9015117 AAAATGATTTCTGG
1 AAAATGATTTCCGG
9015131 AAAAATGATTT
1 -AAAATGATTT
9015142 ACTTTTCTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 12 0.55
15 10 0.45
ACGTcount: A:0.38, C:0.08, G:0.18, T:0.36
Consensus pattern (14 bp):
AAAATGATTTCCGG
Found at i:9015157 original size:20 final size:21
Alignment explanation
Indices: 9015124--9015164 Score: 75
Period size: 20 Copynumber: 2.0 Consensus size: 21
9015114 CGGAAAATGA
9015124 TTTCTGGAAAAATGATTTACT
1 TTTCTGGAAAAATGATTTACT
9015145 TTTCTGG-AAAATGATTTACT
1 TTTCTGGAAAAATGATTTACT
9015165 GAAAATATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.32, C:0.10, G:0.15, T:0.44
Consensus pattern (21 bp):
TTTCTGGAAAAATGATTTACT
Found at i:9015287 original size:20 final size:20
Alignment explanation
Indices: 9015262--9015300 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
9015252 GTTGTTACAT
9015262 ATATTAATAAATTTATATAC
1 ATATTAATAAATTTATATAC
*
9015282 ATATTAATAAATTTTTATA
1 ATATTAATAAATTTATATA
9015301 TTTTAAATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (20 bp):
ATATTAATAAATTTATATAC
Found at i:9019228 original size:16 final size:16
Alignment explanation
Indices: 9019177--9019230 Score: 63
Period size: 16 Copynumber: 3.3 Consensus size: 16
9019167 TCACAGCTCA
*
9019177 CACATTACTACAACTCA
1 CACATTAC-ACAACTCG
* * *
9019194 CACATTACATAGCTTG
1 CACATTACACAACTCG
9019210 CACATTACACAACTCG
1 CACATTACACAACTCG
9019226 CACAT
1 CACAT
9019231 CATTGTAGCT
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
16 22 0.73
17 8 0.27
ACGTcount: A:0.37, C:0.33, G:0.06, T:0.24
Consensus pattern (16 bp):
CACATTACACAACTCG
Found at i:9019240 original size:33 final size:32
Alignment explanation
Indices: 9019171--9019298 Score: 123
Period size: 33 Copynumber: 3.9 Consensus size: 32
9019161 ATATTTTCAC
*
9019171 AGCTCACACATTACTACAACTCACACATTACAT
1 AGCTCACACATTAC-ACAACTCACACATCACAT
** * **
9019204 AGCTTGCACATTACACAACTCGCACATCATTGT
1 AGCTCACACATTACACAACTCACACATCA-CAT
*
9019237 AGCTCACACATTACACAGCTCACACATCAC-T
1 AGCTCACACATTACACAACTCACACATCACAT
* * *
9019268 ATGACTCAAAAATTACACAGCTCACACATCA
1 A-G-CTCACACATTACACAACTCACACATCA
9019299 TTACAACTCG
Statistics
Matches: 79, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
31 2 0.03
32 14 0.18
33 63 0.80
ACGTcount: A:0.38, C:0.33, G:0.07, T:0.23
Consensus pattern (32 bp):
AGCTCACACATTACACAACTCACACATCACAT
Found at i:9020617 original size:8 final size:8
Alignment explanation
Indices: 9020606--9020632 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
9020596 GAGATTGCAT
9020606 GAGAAAGA
1 GAGAAAGA
9020614 GAGAAAGA
1 GAGAAAGA
9020622 GAGAAAGA
1 GAGAAAGA
9020630 GAG
1 GAG
9020633 GGAGAAAGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (8 bp):
GAGAAAGA
Found at i:9021174 original size:40 final size:40
Alignment explanation
Indices: 9021110--9021185 Score: 116
Period size: 40 Copynumber: 1.9 Consensus size: 40
9021100 ATTAGGTACC
* **
9021110 ACTTGGTGTGTAGGGTTGGATGGGTTGATTTTATCCTCAT
1 ACTTGGTGTGTAGGGCTGGATGGGTCAATTTTATCCTCAT
*
9021150 ACTTGGTGTGTAGGGCTGGGTGGGTCAATTTTATCC
1 ACTTGGTGTGTAGGGCTGGATGGGTCAATTTTATCC
9021186 CTTTTGATTG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.14, C:0.12, G:0.34, T:0.39
Consensus pattern (40 bp):
ACTTGGTGTGTAGGGCTGGATGGGTCAATTTTATCCTCAT
Found at i:9023702 original size:42 final size:43
Alignment explanation
Indices: 9023646--9023729 Score: 109
Period size: 42 Copynumber: 2.0 Consensus size: 43
9023636 TCTTACATAT
9023646 AATCAAATATCGATGCC-ACTGCCCCAGACAGGGTCTTACACGG
1 AATCAAATATCGATGCCGA-TGCCCCAGACAGGGTCTTACACGG
* * * *
9023689 AATCAATTA-CGATGCCGATGTCCCTGACATGGTCTTACACG
1 AATCAAATATCGATGCCGATGCCCCAGACAGGGTCTTACACG
9023730 TAAATCATAA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
42 27 0.75
43 9 0.25
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.23
Consensus pattern (43 bp):
AATCAAATATCGATGCCGATGCCCCAGACAGGGTCTTACACGG
Found at i:9023736 original size:43 final size:44
Alignment explanation
Indices: 9023633--9023786 Score: 117
Period size: 43 Copynumber: 3.6 Consensus size: 44
9023623 CGTCCCAGAG
9023633 TGGTCTTACA--TATAATCAAATATCGATGCCACTGCCCCAGACA
1 TGGTCTTACACGTA-AATCAAATATCGATGCCACTGCCCCAGACA
* * * * *
9023676 GGGTCTTACACG-GAATCAATTA-CGATGCCGA-TGTCCCTGACA
1 TGGTCTTACACGTAAATCAAATATCGATGCC-ACTGCCCCAGACA
* * * *
9023718 TGGTCTTACACGTAAATCATAA-GTCGATGCCAACT-TCCTAGACG
1 TGGTCTTACACGTAAATCA-AATATCGATGCC-ACTGCCCCAGACA
* *
9023762 TGGTCTTACACG-AAAACACATATCG
1 TGGTCTTACACGTAAATCAAATATCG
9023787 GGTCCTATGT
Statistics
Matches: 87, Mismatches: 16, Indels: 16
0.73 0.13 0.13
Matches are distributed among these distances:
42 28 0.32
43 31 0.36
44 27 0.31
45 1 0.01
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.25
Consensus pattern (44 bp):
TGGTCTTACACGTAAATCAAATATCGATGCCACTGCCCCAGACA
Found at i:9026039 original size:21 final size:24
Alignment explanation
Indices: 9026015--9026058 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
9026005 TATGTATGAT
9026015 CTGC-TATG-TATAT-AGCATGTG
1 CTGCATATGTTATATGAGCATGTG
*
9026036 CTGCATCTGTTATATGAGCATGT
1 CTGCATATGTTATATGAGCATGT
9026059 ATGATATGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 4 0.21
22 3 0.16
23 5 0.26
24 7 0.37
ACGTcount: A:0.23, C:0.16, G:0.23, T:0.39
Consensus pattern (24 bp):
CTGCATATGTTATATGAGCATGTG
Found at i:9027799 original size:26 final size:26
Alignment explanation
Indices: 9027768--9027828 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 26
9027758 TACCTCCAAC
* *
9027768 AAATTTTGACGATTTTACCACTGGTA
1 AAATTTTGACCATTTTACCACTAGTA
* * *
9027794 AAATTTTGACCTTTTTGCCCCTAGTA
1 AAATTTTGACCATTTTACCACTAGTA
9027820 AAATTTTGA
1 AAATTTTGA
9027829 GAAAATATAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.30, C:0.16, G:0.13, T:0.41
Consensus pattern (26 bp):
AAATTTTGACCATTTTACCACTAGTA
Found at i:9036027 original size:20 final size:20
Alignment explanation
Indices: 9035993--9036034 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
9035983 AACTATTTAA
** *
9035993 ATAATATTATTTGAATAGTT
1 ATAATATTAAATGAATAATT
9036013 ATAATATTAAATGAATAATT
1 ATAATATTAAATGAATAATT
9036033 AT
1 AT
9036035 GTGTTTATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (20 bp):
ATAATATTAAATGAATAATT
Done.