Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007768.1 Hibiscus syriacus cultivar Beakdansim tig00110044_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2539099
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 11
Found at i:1151868 original size:33 final size:33
Alignment explanation
Indices: 1151826--1151890 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 33
1151816 TTACTCAAAG
*
1151826 TGATGTAACCCATGGCATTATCAATGCTTTTTT
1 TGATGTAACCCATGGCATTATCAATGATTTTTT
1151859 TGATGTAACCCATGGCATTATCAATGATTTTT
1 TGATGTAACCCATGGCATTATCAATGATTTTT
1151891 GTACTTACTC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.26, C:0.17, G:0.15, T:0.42
Consensus pattern (33 bp):
TGATGTAACCCATGGCATTATCAATGATTTTTT
Found at i:1160656 original size:18 final size:18
Alignment explanation
Indices: 1160629--1160663 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1160619 CCAGTTTTTC
*
1160629 GCCTGTGTTTGTAACAAT
1 GCCTGCGTTTGTAACAAT
1160647 GCCTGCGTTTGTAACAA
1 GCCTGCGTTTGTAACAA
1160664 GTAATCTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.34
Consensus pattern (18 bp):
GCCTGCGTTTGTAACAAT
Found at i:1166768 original size:31 final size:31
Alignment explanation
Indices: 1166725--1166809 Score: 136
Period size: 31 Copynumber: 2.8 Consensus size: 31
1166715 GTTTTTTAAA
*
1166725 AAAATGAA-AGTTTAAATACTAAAATAGATC
1 AAAATTAATAGTTTAAATACTAAAATAGATC
*
1166755 AAAATTAATAGTTTAAATACTAAAATAGATT
1 AAAATTAATAGTTTAAATACTAAAATAGATC
*
1166786 AAAATTGATAGTTTAAATACTAAA
1 AAAATTAATAGTTTAAATACTAAA
1166810 TGAATAATTT
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
30 7 0.14
31 44 0.86
ACGTcount: A:0.55, C:0.05, G:0.08, T:0.32
Consensus pattern (31 bp):
AAAATTAATAGTTTAAATACTAAAATAGATC
Found at i:1166787 original size:17 final size:17
Alignment explanation
Indices: 1166736--1166788 Score: 58
Period size: 17 Copynumber: 3.3 Consensus size: 17
1166726 AAATGAAAGT
1166736 TTAAATACTAAAATAGA
1 TTAAATACTAAAATAGA
* * *
1166753 TCAAA-A-T-TAATAGT
1 TTAAATACTAAAATAGA
1166767 TTAAATACTAAAATAGA
1 TTAAATACTAAAATAGA
1166784 TTAAA
1 TTAAA
1166789 ATTGATAGTT
Statistics
Matches: 27, Mismatches: 6, Indels: 6
0.69 0.15 0.15
Matches are distributed among these distances:
14 9 0.33
15 2 0.07
16 2 0.07
17 14 0.52
ACGTcount: A:0.57, C:0.06, G:0.06, T:0.32
Consensus pattern (17 bp):
TTAAATACTAAAATAGA
Found at i:1167273 original size:32 final size:31
Alignment explanation
Indices: 1167186--1167273 Score: 77
Period size: 37 Copynumber: 2.6 Consensus size: 31
1167176 TTGTATAATA
*
1167186 TTACAAATTATAAAATATATTTATATATTTTCT
1 TTACAAAAT-TAAAA-ATATTTATATATTTTCT
* *
1167219 TTAAAAAATTAAATTCATAATATTTATATAATTTTTT
1 TTACAAAATT-AA---A-AATATTTATAT-ATTTTCT
1167256 TTACAAAATTAAAAATAT
1 TTACAAAATTAAAAATAT
1167274 ATAAAAAGTT
Statistics
Matches: 45, Mismatches: 4, Indels: 13
0.73 0.06 0.21
Matches are distributed among these distances:
32 6 0.13
33 10 0.22
36 13 0.29
37 16 0.36
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (31 bp):
TTACAAAATTAAAAATATTTATATATTTTCT
Found at i:1171261 original size:9 final size:9
Alignment explanation
Indices: 1171247--1171272 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
1171237 AAGGGAAAAG
1171247 TGACCGGTT
1 TGACCGGTT
1171256 TGACCGGTT
1 TGACCGGTT
1171265 TGACCGGT
1 TGACCGGT
1171273 CACAACCCGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.12, C:0.23, G:0.35, T:0.31
Consensus pattern (9 bp):
TGACCGGTT
Found at i:1171318 original size:31 final size:32
Alignment explanation
Indices: 1171281--1171381 Score: 138
Period size: 31 Copynumber: 3.2 Consensus size: 32
1171271 GTCACAACCC
*
1171281 GACCCGACCCGTTTACCCGACCCGTTGACC-T
1 GACCCGACCCGTTGACCCGACCCGTTGACCTT
1171312 GACCCGACCCGTTGACCCGACCC---GACCTGTT
1 GACCCGACCCGTTGACCCGACCCGTTGACC--TT
1171343 GACCCGACCCGTTGACCCGACCCGTTGACCGTT
1 GACCCGACCCGTTGACCCGACCCGTTGACC-TT
1171376 GACCCG
1 GACCCG
1171382 TTGACCGTTG
Statistics
Matches: 63, Mismatches: 1, Indels: 10
0.85 0.01 0.14
Matches are distributed among these distances:
28 4 0.06
31 46 0.73
33 9 0.14
34 4 0.06
ACGTcount: A:0.16, C:0.45, G:0.23, T:0.17
Consensus pattern (32 bp):
GACCCGACCCGTTGACCCGACCCGTTGACCTT
Found at i:1171359 original size:8 final size:8
Alignment explanation
Indices: 1171348--1171394 Score: 59
Period size: 8 Copynumber: 6.5 Consensus size: 8
1171338 CTGTTGACCC
1171348 GACCCGTT
1 GACCCGTT
1171356 GACCC---
1 GACCCGTT
1171361 GACCCGTT
1 GACCCGTT
1171369 GA-CCGTT
1 GACCCGTT
1171376 GACCCGTT
1 GACCCGTT
1171384 GA-CCGTT
1 GACCCGTT
1171391 GACC
1 GACC
1171395 GGAGTTGACC
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
5 5 0.15
7 14 0.41
8 15 0.44
ACGTcount: A:0.15, C:0.38, G:0.26, T:0.21
Consensus pattern (8 bp):
GACCCGTT
Found at i:1171366 original size:18 final size:18
Alignment explanation
Indices: 1171295--1171353 Score: 100
Period size: 18 Copynumber: 3.3 Consensus size: 18
1171285 CGACCCGTTT
*
1171295 ACCCGACCCGTTGACCTG
1 ACCCGACCCGTTGACCCG
1171313 ACCCGACCCGTTGACCCG
1 ACCCGACCCGTTGACCCG
*
1171331 ACCCGACCTGTTGACCCG
1 ACCCGACCCGTTGACCCG
1171349 ACCCG
1 ACCCG
1171354 TTGACCCGAC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 39 1.00
ACGTcount: A:0.17, C:0.47, G:0.22, T:0.14
Consensus pattern (18 bp):
ACCCGACCCGTTGACCCG
Found at i:1171369 original size:13 final size:13
Alignment explanation
Indices: 1171281--1171387 Score: 91
Period size: 13 Copynumber: 8.3 Consensus size: 13
1171271 GTCACAACCC
1171281 GACCCGACCCGTT
1 GACCCGACCCGTT
*
1171294 TACCCGACCCGTT
1 GACCCGACCCGTT
*
1171307 GACCTGACCC---
1 GACCCGACCCGTT
1171317 GACCCGTTGACCC---
1 GACCC---GACCCGTT
*
1171330 GACCCGACCTGTT
1 GACCCGACCCGTT
1171343 GACCCGACCCGTT
1 GACCCGACCCGTT
1171356 GACCCGACCCGTT
1 GACCCGACCCGTT
*
1171369 GACCGTTGACCCGTT
1 GACC--CGACCCGTT
1171384 GACC
1 GACC
1171388 GTTGACCGGA
Statistics
Matches: 79, Mismatches: 7, Indels: 14
0.79 0.07 0.14
Matches are distributed among these distances:
10 8 0.10
13 59 0.75
15 12 0.15
ACGTcount: A:0.16, C:0.44, G:0.22, T:0.18
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:1171376 original size:7 final size:7
Alignment explanation
Indices: 1171364--1171395 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
1171354 TTGACCCGAC
1171364 CCGTTGA
1 CCGTTGA
1171371 CCGTTGA
1 CCGTTGA
1171378 CCCGTTGA
1 -CCGTTGA
1171386 CCGTTGA
1 CCGTTGA
1171393 CCG
1 CCG
1171396 GAGTTGACCA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.12, C:0.34, G:0.28, T:0.25
Consensus pattern (7 bp):
CCGTTGA
Found at i:1171381 original size:15 final size:15
Alignment explanation
Indices: 1171348--1171394 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
1171338 CTGTTGACCC
*
1171348 GACCCGTTGACC--C
1 GACCCGTTGACCGTT
1171361 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
1171376 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
1171391 GACC
1 GACC
1171395 GGAGTTGACC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 12 0.39
15 19 0.61
ACGTcount: A:0.15, C:0.38, G:0.26, T:0.21
Consensus pattern (15 bp):
GACCCGTTGACCGTT
Found at i:1173643 original size:24 final size:24
Alignment explanation
Indices: 1173547--1173655 Score: 94
Period size: 24 Copynumber: 4.5 Consensus size: 24
1173537 GAATATTTTA
* *
1173547 TCTGATTTCTGATTTGAATTATGT
1 TCTGATATCTGATCTGAATTATGT
* * * *
1173571 TTTGACATCTGATCTGAAATCTGT
1 TCTGATATCTGATCTGAATTATGT
* * * *
1173595 TCTGAT-TCCTAACCTGGATTCTGT
1 TCTGATAT-CTGATCTGAATTATGT
1173619 TCTGATATCTGATCTGAATTATGT
1 TCTGATATCTGATCTGAATTATGT
* *
1173643 TTTGATTTCTGAT
1 TCTGATATCTGAT
1173656 ATCTCGTTTA
Statistics
Matches: 65, Mismatches: 18, Indels: 4
0.75 0.21 0.05
Matches are distributed among these distances:
23 1 0.02
24 63 0.97
25 1 0.02
ACGTcount: A:0.21, C:0.15, G:0.17, T:0.48
Consensus pattern (24 bp):
TCTGATATCTGATCTGAATTATGT
Found at i:1173820 original size:2 final size:2
Alignment explanation
Indices: 1173813--1173853 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1173803 CGGATGGGGG
1173813 TA TA TA TA TA TA TA 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 TA TA TA TA T
1173854 GTTTTAAAAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1175876 original size:309 final size:313
Alignment explanation
Indices: 1175314--1175937 Score: 1143
Period size: 309 Copynumber: 2.0 Consensus size: 313
1175304 GTGTTCGTTG
1175314 TCAACCGAAGAACAAAACCCCTCAAACCTTTCGTCGTAAACTAACCATTCGTTGTGAATTTCAGT
1 TCAACCGAAGAACAAAACCCCTCAAACCTTTCGTCGTAAACTAACCATTCGTTGTGAATTTCAGT
1175379 CGGAAGTATCGTCGTAATAACTCGGTTTTAGTTGGTTTTTTCATCGATCACACGACGATCGGGTC
66 CGGAAGTATCGTCGTAATAACTCGGTTTTAGTTGG-TTTTTCATCGATCACACGACGATCGGGTC
1175444 ATCCGTTTTACGACAACCTCCCGCACCATCGTGTTCCTTGTGCCGTTCCGAGTCCACCGGTGTTC
130 ATCCGTTTTACGACAACCTCCCGCACCATCGTGTTCCTTGTGCCGTTCCGAGTCCACCGGTGTTC
1175509 TCCTTTTTCTCCGGCGGCGGCGGCGCGTTGGGAGGTGAACCGGTCAAACTTCCCGATTTGTTGAA
195 TCCTTTTTCTCCGGCGGCGGCGGCGCGTTGGGAGGTGAACCGGTCAAACTTCCCGATTTGTTGAA
1175574 ATCGAGCTCTCCGCCG-TCAAAAA-TGAACCGAGCTTTGTAAGTATCTCGAAAT
260 ATCGAGCTCTCCGCCGTTCAAAAAGTGAACCGAGCTTTGTAAGTATCTCGAAAT
* *
1175626 TCAACCGAAGAACAAAACCCCTCAAACCTTTCGTCGTAAATCATCACCGTTCGTTGTGAATTTCA
1 TCAACCGAAGAACAAAACCCCTCAAACCTTTCGTCGTAAA-C-TAACCATTCGTTGTGAATTTCA
*
1175691 GTCGGAAGTATCGTCGTAATAACTCGGTTTTAGTTGG-TTTTCATCGAT-TCACGACGATCGGGT
64 GTCGGAAGTATCGTCGTAATAACTCGGTTTTAGTTGGTTTTTCATCGATCACACGACGATCGGGT
1175754 CATCCG-TTTACGAC-ACCTCCCGCACCATCGTGTTCCTTGTGCCGTTCCGAGTCCACCGGTGTT
129 CATCCGTTTTACGACAACCTCCCGCACCATCGTGTTCCTTGTGCCGTTCCGAGTCCACCGGTGTT
1175817 CTCCTTTTTCTCCGGCGGCGGCGGCGCGTTGGGAGGTGAACCGGTCAAACTTCCCGATTTGTTGA
194 CTCCTTTTTCTCCGGCGGCGGCGGCGCGTTGGGAGGTGAACCGGTCAAACTTCCCGATTTGTTGA
1175882 AATCGAGCTCTCCGCCGTTCAAAAATGTGAACCGAGCTTTGTAAGTATCTCGAAAT
259 AATCGAGCTCTCCGCCGTTCAAAAA-GTGAACCGAGCTTTGTAAGTATCTCGAAAT
1175938 CGCTCAAAAT
Statistics
Matches: 304, Mismatches: 3, Indels: 10
0.96 0.01 0.03
Matches are distributed among these distances:
309 131 0.43
310 15 0.05
311 20 0.07
312 80 0.26
313 1 0.00
314 57 0.19
ACGTcount: A:0.22, C:0.27, G:0.22, T:0.29
Consensus pattern (313 bp):
TCAACCGAAGAACAAAACCCCTCAAACCTTTCGTCGTAAACTAACCATTCGTTGTGAATTTCAGT
CGGAAGTATCGTCGTAATAACTCGGTTTTAGTTGGTTTTTCATCGATCACACGACGATCGGGTCA
TCCGTTTTACGACAACCTCCCGCACCATCGTGTTCCTTGTGCCGTTCCGAGTCCACCGGTGTTCT
CCTTTTTCTCCGGCGGCGGCGGCGCGTTGGGAGGTGAACCGGTCAAACTTCCCGATTTGTTGAAA
TCGAGCTCTCCGCCGTTCAAAAAGTGAACCGAGCTTTGTAAGTATCTCGAAAT
Found at i:1176120 original size:31 final size:32
Alignment explanation
Indices: 1176083--1176183 Score: 138
Period size: 31 Copynumber: 3.2 Consensus size: 32
1176073 GTCACAACCC
*
1176083 GACCCGACCCGTTTACCCGACCCGTTGACC-T
1 GACCCGACCCGTTGACCCGACCCGTTGACCTT
1176114 GACCCGACCCGTTGACCCGACCC---GACCTGTT
1 GACCCGACCCGTTGACCCGACCCGTTGACC--TT
1176145 GACCCGACCCGTTGACCCGACCCGTTGACCGTT
1 GACCCGACCCGTTGACCCGACCCGTTGACC-TT
1176178 GACCCG
1 GACCCG
1176184 TTGACCGTTG
Statistics
Matches: 63, Mismatches: 1, Indels: 10
0.85 0.01 0.14
Matches are distributed among these distances:
28 4 0.06
31 46 0.73
33 9 0.14
34 4 0.06
ACGTcount: A:0.16, C:0.45, G:0.23, T:0.17
Consensus pattern (32 bp):
GACCCGACCCGTTGACCCGACCCGTTGACCTT
Found at i:1176161 original size:8 final size:8
Alignment explanation
Indices: 1176150--1176196 Score: 59
Period size: 8 Copynumber: 6.5 Consensus size: 8
1176140 CTGTTGACCC
1176150 GACCCGTT
1 GACCCGTT
1176158 GACCC---
1 GACCCGTT
1176163 GACCCGTT
1 GACCCGTT
1176171 GA-CCGTT
1 GACCCGTT
1176178 GACCCGTT
1 GACCCGTT
1176186 GA-CCGTT
1 GACCCGTT
1176193 GACC
1 GACC
1176197 GGAGTTGACC
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
5 5 0.15
7 14 0.41
8 15 0.44
ACGTcount: A:0.15, C:0.38, G:0.26, T:0.21
Consensus pattern (8 bp):
GACCCGTT
Found at i:1176168 original size:18 final size:18
Alignment explanation
Indices: 1176097--1176155 Score: 100
Period size: 18 Copynumber: 3.3 Consensus size: 18
1176087 CGACCCGTTT
*
1176097 ACCCGACCCGTTGACCTG
1 ACCCGACCCGTTGACCCG
1176115 ACCCGACCCGTTGACCCG
1 ACCCGACCCGTTGACCCG
*
1176133 ACCCGACCTGTTGACCCG
1 ACCCGACCCGTTGACCCG
1176151 ACCCG
1 ACCCG
1176156 TTGACCCGAC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 39 1.00
ACGTcount: A:0.17, C:0.47, G:0.22, T:0.14
Consensus pattern (18 bp):
ACCCGACCCGTTGACCCG
Found at i:1176171 original size:13 final size:13
Alignment explanation
Indices: 1176083--1176189 Score: 91
Period size: 13 Copynumber: 8.3 Consensus size: 13
1176073 GTCACAACCC
1176083 GACCCGACCCGTT
1 GACCCGACCCGTT
*
1176096 TACCCGACCCGTT
1 GACCCGACCCGTT
*
1176109 GACCTGACCC---
1 GACCCGACCCGTT
1176119 GACCCGTTGACCC---
1 GACCC---GACCCGTT
*
1176132 GACCCGACCTGTT
1 GACCCGACCCGTT
1176145 GACCCGACCCGTT
1 GACCCGACCCGTT
1176158 GACCCGACCCGTT
1 GACCCGACCCGTT
*
1176171 GACCGTTGACCCGTT
1 GACC--CGACCCGTT
1176186 GACC
1 GACC
1176190 GTTGACCGGA
Statistics
Matches: 79, Mismatches: 7, Indels: 14
0.79 0.07 0.14
Matches are distributed among these distances:
10 8 0.10
13 59 0.75
15 12 0.15
ACGTcount: A:0.16, C:0.44, G:0.22, T:0.18
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:1176178 original size:7 final size:7
Alignment explanation
Indices: 1176166--1176197 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
1176156 TTGACCCGAC
1176166 CCGTTGA
1 CCGTTGA
1176173 CCGTTGA
1 CCGTTGA
1176180 CCCGTTGA
1 -CCGTTGA
1176188 CCGTTGA
1 CCGTTGA
1176195 CCG
1 CCG
1176198 GAGTTGACCA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.12, C:0.34, G:0.28, T:0.25
Consensus pattern (7 bp):
CCGTTGA
Found at i:1176183 original size:15 final size:15
Alignment explanation
Indices: 1176150--1176196 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
1176140 CTGTTGACCC
*
1176150 GACCCGTTGACC--C
1 GACCCGTTGACCGTT
1176163 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
1176178 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
1176193 GACC
1 GACC
1176197 GGAGTTGACC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 12 0.39
15 19 0.61
ACGTcount: A:0.15, C:0.38, G:0.26, T:0.21
Consensus pattern (15 bp):
GACCCGTTGACCGTT
Found at i:1177465 original size:18 final size:18
Alignment explanation
Indices: 1177439--1177474 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1177429 TCGAAAGGAC
*
1177439 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
1177457 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
1177475 CGGATGGAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:1180842 original size:31 final size:32
Alignment explanation
Indices: 1180807--1180907 Score: 138
Period size: 31 Copynumber: 3.2 Consensus size: 32
1180797 CGGTCAACCC
*
1180807 GACCCGACCCGTTTACCCGACCCGTTGACC-T
1 GACCCGACCCGTTGACCCGACCCGTTGACCTT
1180838 GACCCGACCCGTTGACCCGACCC---GACCTGTT
1 GACCCGACCCGTTGACCCGACCCGTTGACC--TT
1180869 GACCCGACCCGTTGACCCGACCCGTTGACCGTT
1 GACCCGACCCGTTGACCCGACCCGTTGACC-TT
1180902 GACCCG
1 GACCCG
1180908 TTGACCGTTG
Statistics
Matches: 63, Mismatches: 1, Indels: 10
0.85 0.01 0.14
Matches are distributed among these distances:
28 4 0.06
31 46 0.73
33 9 0.14
34 4 0.06
ACGTcount: A:0.16, C:0.45, G:0.23, T:0.17
Consensus pattern (32 bp):
GACCCGACCCGTTGACCCGACCCGTTGACCTT
Found at i:1180885 original size:8 final size:8
Alignment explanation
Indices: 1180874--1180920 Score: 59
Period size: 8 Copynumber: 6.5 Consensus size: 8
1180864 CTGTTGACCC
1180874 GACCCGTT
1 GACCCGTT
1180882 GACCC---
1 GACCCGTT
1180887 GACCCGTT
1 GACCCGTT
1180895 GA-CCGTT
1 GACCCGTT
1180902 GACCCGTT
1 GACCCGTT
1180910 GA-CCGTT
1 GACCCGTT
1180917 GACC
1 GACC
1180921 GGAGTTGACC
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
5 5 0.15
7 14 0.41
8 15 0.44
ACGTcount: A:0.15, C:0.38, G:0.26, T:0.21
Consensus pattern (8 bp):
GACCCGTT
Found at i:1180892 original size:18 final size:18
Alignment explanation
Indices: 1180821--1180879 Score: 100
Period size: 18 Copynumber: 3.3 Consensus size: 18
1180811 CGACCCGTTT
*
1180821 ACCCGACCCGTTGACCTG
1 ACCCGACCCGTTGACCCG
1180839 ACCCGACCCGTTGACCCG
1 ACCCGACCCGTTGACCCG
*
1180857 ACCCGACCTGTTGACCCG
1 ACCCGACCCGTTGACCCG
1180875 ACCCG
1 ACCCG
1180880 TTGACCCGAC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 39 1.00
ACGTcount: A:0.17, C:0.47, G:0.22, T:0.14
Consensus pattern (18 bp):
ACCCGACCCGTTGACCCG
Found at i:1180895 original size:13 final size:13
Alignment explanation
Indices: 1180807--1180913 Score: 91
Period size: 13 Copynumber: 8.3 Consensus size: 13
1180797 CGGTCAACCC
1180807 GACCCGACCCGTT
1 GACCCGACCCGTT
*
1180820 TACCCGACCCGTT
1 GACCCGACCCGTT
*
1180833 GACCTGACCC---
1 GACCCGACCCGTT
1180843 GACCCGTTGACCC---
1 GACCC---GACCCGTT
*
1180856 GACCCGACCTGTT
1 GACCCGACCCGTT
1180869 GACCCGACCCGTT
1 GACCCGACCCGTT
1180882 GACCCGACCCGTT
1 GACCCGACCCGTT
*
1180895 GACCGTTGACCCGTT
1 GACC--CGACCCGTT
1180910 GACC
1 GACC
1180914 GTTGACCGGA
Statistics
Matches: 79, Mismatches: 7, Indels: 14
0.79 0.07 0.14
Matches are distributed among these distances:
10 8 0.10
13 59 0.75
15 12 0.15
ACGTcount: A:0.16, C:0.44, G:0.22, T:0.18
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:1180902 original size:7 final size:7
Alignment explanation
Indices: 1180890--1180921 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
1180880 TTGACCCGAC
1180890 CCGTTGA
1 CCGTTGA
1180897 CCGTTGA
1 CCGTTGA
1180904 CCCGTTGA
1 -CCGTTGA
1180912 CCGTTGA
1 CCGTTGA
1180919 CCG
1 CCG
1180922 GAGTTGACCA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.12, C:0.34, G:0.28, T:0.25
Consensus pattern (7 bp):
CCGTTGA
Found at i:1180907 original size:15 final size:15
Alignment explanation
Indices: 1180874--1180920 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
1180864 CTGTTGACCC
*
1180874 GACCCGTTGACC--C
1 GACCCGTTGACCGTT
1180887 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
1180902 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
1180917 GACC
1 GACC
1180921 GGAGTTGACC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 12 0.39
15 19 0.61
ACGTcount: A:0.15, C:0.38, G:0.26, T:0.21
Consensus pattern (15 bp):
GACCCGTTGACCGTT
Found at i:1182253 original size:18 final size:18
Alignment explanation
Indices: 1182227--1182262 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1182217 TCGAAAGGAC
*
1182227 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
1182245 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
1182263 CGGATGGAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:1183485 original size:24 final size:24
Alignment explanation
Indices: 1183389--1183497 Score: 94
Period size: 24 Copynumber: 4.5 Consensus size: 24
1183379 GAATATTTTA
* *
1183389 TCTGATTTCTGATTTGAATTATGT
1 TCTGATATCTGATCTGAATTATGT
* * * *
1183413 TTTGACATCTGATCTGAAATCTGT
1 TCTGATATCTGATCTGAATTATGT
* * * *
1183437 TCTGAT-TCCTAACCTGGATTCTGT
1 TCTGATAT-CTGATCTGAATTATGT
1183461 TCTGATATCTGATCTGAATTATGT
1 TCTGATATCTGATCTGAATTATGT
* *
1183485 TTTGATTTCTGAT
1 TCTGATATCTGAT
1183498 ATCTCCGTTT
Statistics
Matches: 65, Mismatches: 18, Indels: 4
0.75 0.21 0.05
Matches are distributed among these distances:
23 1 0.02
24 63 0.97
25 1 0.02
ACGTcount: A:0.21, C:0.15, G:0.17, T:0.48
Consensus pattern (24 bp):
TCTGATATCTGATCTGAATTATGT
Found at i:1183665 original size:2 final size:2
Alignment explanation
Indices: 1183658--1183686 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1183648 CGGATGGGGG
1183658 TA 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 T
1183687 GTTTTAAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 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):
TA
Found at i:1189893 original size:2 final size:2
Alignment explanation
Indices: 1189886--1189912 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1189876 TCACTACTTA
1189886 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
1189913 ATCTACACTT
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:1198368 original size:27 final size:23
Alignment explanation
Indices: 1198289--1198349 Score: 122
Period size: 23 Copynumber: 2.7 Consensus size: 23
1198279 AGAATAAAGA
1198289 TAAAAGAGATTTATTTCTTTTAT
1 TAAAAGAGATTTATTTCTTTTAT
1198312 TAAAAGAGATTTATTTCTTTTAT
1 TAAAAGAGATTTATTTCTTTTAT
1198335 TAAAAGAGATTTATT
1 TAAAAGAGATTTATT
1198350 ACGTCTTTTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.38, C:0.03, G:0.10, T:0.49
Consensus pattern (23 bp):
TAAAAGAGATTTATTTCTTTTAT
Found at i:1200446 original size:22 final size:22
Alignment explanation
Indices: 1200418--1200460 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
1200408 ATTAACCAAC
1200418 TTGGTTAAGAATATACAGCGAG
1 TTGGTTAAGAATATACAGCGAG
*
1200440 TTGGTTAAGAATATGCAGCGA
1 TTGGTTAAGAATATACAGCGA
1200461 CCTAGCAATC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.35, C:0.09, G:0.28, T:0.28
Consensus pattern (22 bp):
TTGGTTAAGAATATACAGCGAG
Found at i:1202931 original size:2 final size:2
Alignment explanation
Indices: 1202919--1202957 Score: 69
Period size: 2 Copynumber: 19.0 Consensus size: 2
1202909 CACAGAAGAG
1202919 TA TA CTA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1202958 AAGGAATTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 34 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1204364 original size:58 final size:58
Alignment explanation
Indices: 1204256--1204367 Score: 138
Period size: 58 Copynumber: 1.9 Consensus size: 58
1204246 AGTCCACAAA
*
1204256 TGGTCCCATGACTATAGGATGTTAATTTTTGAGTCCCTTCACTATCAAAAGTTAGAAAC
1 TGGTCCCA-GACTATAGGATGTTAATTTTTGACTCCCTTCACTATCAAAAGTTAGAAAC
* ** *
1204315 TGGTCCCA-ACTGTAGGATGTTGCTTTGTTGACTCCC-TCGACTATTAAAAGTTA
1 TGGTCCCAGACTATAGGATGTTAATTT-TTGACTCCCTTC-ACTATCAAAAGTTA
1204368 TAAAATTGTC
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
57 17 0.37
58 21 0.46
59 8 0.17
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.35
Consensus pattern (58 bp):
TGGTCCCAGACTATAGGATGTTAATTTTTGACTCCCTTCACTATCAAAAGTTAGAAAC
Found at i:1204656 original size:60 final size:60
Alignment explanation
Indices: 1204592--1204708 Score: 171
Period size: 60 Copynumber: 1.9 Consensus size: 60
1204582 ATAGTCAAGT
* *
1204592 GATCATTTTATAACTTTTAATAGTCGAGAGACTCAACAAAGCAACATTCTATAGTTATAG
1 GATCATTTTATAACTTTTAATAGTCGAGACACTCAACAAAGCAACACTCTATAGTTATAG
* * ** *
1204652 GATCATTTTGTAACTTTTGATAGTTTAGACACTCCACAAAGCAACACTCTATAGTTA
1 GATCATTTTATAACTTTTAATAGTCGAGACACTCAACAAAGCAACACTCTATAGTTA
1204709 AGGGACAAAA
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
60 50 1.00
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.34
Consensus pattern (60 bp):
GATCATTTTATAACTTTTAATAGTCGAGACACTCAACAAAGCAACACTCTATAGTTATAG
Found at i:1204728 original size:60 final size:60
Alignment explanation
Indices: 1204602--1204728 Score: 141
Period size: 60 Copynumber: 2.1 Consensus size: 60
1204592 GATCATTTTA
* * ***
1204602 TAACTTTTAATAGTCGAGAGACTCAACAAAGCAACATTCTATAGTTATAGGATCATTTTG
1 TAACTTTTAATAGTCGAGACACTCAACAAAGCAACACTCTATAGTTATAGGATCAAAATG
* ** *
1204662 TAACTTTTGATAGTTTAGACACTCCACAAAGCAACACTCTATAGTTA-AGGGA-CAAAATG
1 TAACTTTTAATAGTCGAGACACTCAACAAAGCAACACTCTATAGTTATA-GGATCAAAATG
1204721 TAGACTTT
1 TA-ACTTT
1204729 ACCCTAAAAA
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
59 7 0.12
60 49 0.88
ACGTcount: A:0.37, C:0.17, G:0.15, T:0.31
Consensus pattern (60 bp):
TAACTTTTAATAGTCGAGACACTCAACAAAGCAACACTCTATAGTTATAGGATCAAAATG
Found at i:1208058 original size:16 final size:16
Alignment explanation
Indices: 1208037--1208075 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
1208027 AATTTCAAAC
*
1208037 AAAATCTCGATATGAA
1 AAAATCTCGATACGAA
1208053 AAAATCTCGATACGAA
1 AAAATCTCGATACGAA
1208069 AAAATCT
1 AAAATCT
1208076 AACTGCAATG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.51, C:0.15, G:0.10, T:0.23
Consensus pattern (16 bp):
AAAATCTCGATACGAA
Found at i:1208690 original size:4 final size:4
Alignment explanation
Indices: 1208652--1208684 Score: 57
Period size: 4 Copynumber: 8.2 Consensus size: 4
1208642 TTCAATGATA
*
1208652 ACAT ATAT ACAT ACAT ACAT ACAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
1208685 TATATAATTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.52, C:0.21, G:0.00, T:0.27
Consensus pattern (4 bp):
ACAT
Found at i:1208815 original size:2 final size:2
Alignment explanation
Indices: 1208810--1208853 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
1208800 AGTGTGTGTG
1208810 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1208852 TA
1 TA
1208854 GTAGTAGTAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1218177 original size:81 final size:80
Alignment explanation
Indices: 1218006--1218170 Score: 240
Period size: 81 Copynumber: 2.0 Consensus size: 80
1217996 ATGATATTGG
* * **
1218006 AAAGAGAAATAATCATTGTTAACTAATTCAGTTTCTTTCAATGCAGCCAAACACAAAGCCAAACT
1 AAAGAGAATTAATCATCGTTAACTAATTCAGTTTCTTTCAATGCAGCCAAACACAAAGAAAAACT
*
1218071 TCACCCATAACAAAT
66 TCACCCAAAACAAAT
** *
1218086 AAAGAGAATTAATCATCGTTAACTAATTTGGCTTTCTTTCAATGCAGCCAAACAGAAAGAAAAAC
1 AAAGAGAATTAATCATCGTTAACTAATTCAG-TTTCTTTCAATGCAGCCAAACACAAAGAAAAAC
*
1218151 TTCACCGAAAACAAAT
65 TTCACCCAAAACAAAT
1218167 AAAG
1 AAAG
1218171 TTAATTATAT
Statistics
Matches: 75, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
80 27 0.36
81 48 0.64
ACGTcount: A:0.45, C:0.20, G:0.11, T:0.24
Consensus pattern (80 bp):
AAAGAGAATTAATCATCGTTAACTAATTCAGTTTCTTTCAATGCAGCCAAACACAAAGAAAAACT
TCACCCAAAACAAAT
Found at i:1222906 original size:19 final size:19
Alignment explanation
Indices: 1222857--1222912 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
1222847 AAAACAGACT
*
1222857 AAAAGTATCGATACTTCTGC
1 AAAAGTATCGATACTT-TAC
* *
1222877 AAAAGTTTCGATACTTTAT
1 AAAAGTATCGATACTTTAC
*
1222896 ATAAGTATCGATACTTT
1 AAAAGTATCGATACTTT
1222913 TAAATATTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
19 16 0.52
20 15 0.48
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (19 bp):
AAAAGTATCGATACTTTAC
Found at i:1224336 original size:18 final size:18
Alignment explanation
Indices: 1224268--1224337 Score: 60
Period size: 18 Copynumber: 4.2 Consensus size: 18
1224258 ACCGGTCACA
*
1224268 ACCCGACCCGACCCGTTG
1 ACCCGATCCGACCCGTTG
* *
1224286 ACCCGATCCAACCCGTTT
1 ACCCGATCCGACCCGTTG
* *
1224304 ACCCG-T----TCTGTTG
1 ACCCGATCCGACCCGTTG
1224317 ACCCGATCCGACCCGTTG
1 ACCCGATCCGACCCGTTG
1224335 ACC
1 ACC
1224338 GTTGACCGTT
Statistics
Matches: 39, Mismatches: 8, Indels: 10
0.68 0.14 0.18
Matches are distributed among these distances:
13 9 0.23
14 1 0.03
17 1 0.03
18 28 0.72
ACGTcount: A:0.17, C:0.44, G:0.19, T:0.20
Consensus pattern (18 bp):
ACCCGATCCGACCCGTTG
Found at i:1226919 original size:12 final size:12
Alignment explanation
Indices: 1226897--1226962 Score: 55
Period size: 12 Copynumber: 5.6 Consensus size: 12
1226887 AATGACCTGA
1226897 ATTT-TGTTCTG
1 ATTTCTGTTCTG
*
1226908 ATTTCTGATCTGG
1 ATTTCTGTTCT-G
*
1226921 A-TTCTGTTTTG
1 ATTTCTGTTCTG
* *
1226932 ATATCTGTTATG
1 ATTTCTGTTCTG
* *
1226944 AATTCTGTTTTG
1 ATTTCTGTTCTG
1226956 ATTTCTG
1 ATTTCTG
1226963 ATATCTTCGT
Statistics
Matches: 43, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
11 6 0.14
12 35 0.81
13 2 0.05
ACGTcount: A:0.15, C:0.11, G:0.18, T:0.56
Consensus pattern (12 bp):
ATTTCTGTTCTG
Found at i:1226928 original size:24 final size:24
Alignment explanation
Indices: 1226856--1226964 Score: 94
Period size: 24 Copynumber: 4.5 Consensus size: 24
1226846 AAATATTTTA
*
1226856 TCTGATTTCCGA-CTTGAATTCTGT
1 TCTGATTTCTGATC-TGAATTCTGT
*** * *
1226880 TCTGATAAATGACCTGAATTTTGT
1 TCTGATTTCTGATCTGAATTCTGT
*
1226904 TCTGATTTCTGATCTGGATTCTGT
1 TCTGATTTCTGATCTGAATTCTGT
* * * *
1226928 TTTGATATCTGTTATGAATTCTGT
1 TCTGATTTCTGATCTGAATTCTGT
*
1226952 TTTGATTTCTGAT
1 TCTGATTTCTGAT
1226965 ATCTTCGTTT
Statistics
Matches: 66, Mismatches: 18, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
24 65 0.98
25 1 0.02
ACGTcount: A:0.19, C:0.14, G:0.17, T:0.50
Consensus pattern (24 bp):
TCTGATTTCTGATCTGAATTCTGT
Found at i:1229898 original size:20 final size:21
Alignment explanation
Indices: 1229846--1229899 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 21
1229836 TAATTAATAT
*
1229846 AAAATAAGATAATTTTCATAAA
1 AAAATAATA-AATTTTCATAAA
*
1229868 AAAATATTAAATTTT-ATAAA
1 AAAATAATAAATTTTCATAAA
**
1229888 AATGTAATAAAT
1 AAAATAATAAAT
1229900 AACTATTATA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
20 14 0.52
21 6 0.22
22 7 0.26
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.35
Consensus pattern (21 bp):
AAAATAATAAATTTTCATAAA
Found at i:1232254 original size:3 final size:3
Alignment explanation
Indices: 1232246--1232277 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
1232236 ATTCTAAAAT
1232246 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1232278 GATGATGATT
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:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:1232427 original size:19 final size:19
Alignment explanation
Indices: 1232403--1232446 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
1232393 AGTTAATTTT
*
1232403 TTATTTTTCATAATCATCA
1 TTATTTTTCATAATCACCA
*
1232422 TTATTTTTTATAATCACCA
1 TTATTTTTCATAATCACCA
1232441 TTATTT
1 TTATTT
1232447 CATAACAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.30, C:0.14, G:0.00, T:0.57
Consensus pattern (19 bp):
TTATTTTTCATAATCACCA
Found at i:1233981 original size:23 final size:24
Alignment explanation
Indices: 1233947--1233991 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
1233937 AAATTAGGGT
1233947 TTTTTAATAT-AATAATATTTTTAA
1 TTTTTAATATAAATAA-ATTTTTAA
1233971 TTTTTAA-ATAAATAAATTTTT
1 TTTTTAATATAAATAAATTTTT
1233992 TGAAATCACC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (24 bp):
TTTTTAATATAAATAAATTTTTAA
Found at i:1233992 original size:24 final size:25
Alignment explanation
Indices: 1233946--1233991 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
1233936 AAAATTAGGG
*
1233946 TTTTTTAATATAATAATATTTTTAA
1 TTTTTAAATATAATAATATTTTTAA
1233971 TTTTTAAATA-AATAA-ATTTTT
1 TTTTTAAATATAATAATATTTTT
1233992 TGAAATCACC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 5 0.25
25 9 0.45
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (25 bp):
TTTTTAAATATAATAATATTTTTAA
Found at i:1234988 original size:3 final size:3
Alignment explanation
Indices: 1234980--1235051 Score: 144
Period size: 3 Copynumber: 24.0 Consensus size: 3
1234970 ATATAAAAAC
1234980 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1235028 ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA
1235052 TGGGTTTAAA
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 69 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1243219 original size:22 final size:22
Alignment explanation
Indices: 1243194--1243262 Score: 92
Period size: 22 Copynumber: 3.3 Consensus size: 22
1243184 GTCAATTGGG
1243194 TTATAAACTGAAAATTAAAATT
1 TTATAAACTGAAAATTAAAATT
*
1243216 TTATAATTCT----ATTAAAATT
1 TTATAA-ACTGAAAATTAAAATT
1243235 TTATAAACTGAAAATTAAAATT
1 TTATAAACTGAAAATTAAAATT
1243257 TTATAA
1 TTATAA
1243263 CTTTTTAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
18 2 0.05
19 15 0.38
22 21 0.52
23 2 0.05
ACGTcount: A:0.51, C:0.04, G:0.03, T:0.42
Consensus pattern (22 bp):
TTATAAACTGAAAATTAAAATT
Found at i:1243846 original size:6 final size:6
Alignment explanation
Indices: 1243836--1243902 Score: 82
Period size: 6 Copynumber: 11.2 Consensus size: 6
1243826 TATGTATACA
* * *
1243836 TATCAT CATCAT TATCAT TATCAT TATCCA- CATCAT TATCAT TATCAA
1 TATCAT TATCAT TATCAT TATCAT TAT-CAT TATCAT TATCAT TATCAT
*
1243884 CATCAT TATCAT TATCAT T
1 TATCAT TATCAT TATCAT T
1243903 CAATGTTCAT
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
5 2 0.04
6 47 0.92
7 2 0.04
ACGTcount: A:0.34, C:0.22, G:0.00, T:0.43
Consensus pattern (6 bp):
TATCAT
Found at i:1244131 original size:23 final size:23
Alignment explanation
Indices: 1244030--1244123 Score: 107
Period size: 23 Copynumber: 4.1 Consensus size: 23
1244020 CATTGAAGTG
1244030 CCACATAGAAATGTCCCGAAGGA
1 CCACATAGAAATGTCCCGAAGGA
* * *
1244053 CCACATAGTACTGTCCCGAATGA
1 CCACATAGAAATGTCCCGAAGGA
* * **
1244076 CCGCATAAAAACATCCCGAAGGA
1 CCACATAGAAATGTCCCGAAGGA
* *
1244099 CCACGTAGAATTGTCCCGAAGGA
1 CCACATAGAAATGTCCCGAAGGA
1244122 CC
1 CC
1244124 GCGTAGAACC
Statistics
Matches: 55, Mismatches: 16, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
23 55 1.00
ACGTcount: A:0.35, C:0.30, G:0.20, T:0.15
Consensus pattern (23 bp):
CCACATAGAAATGTCCCGAAGGA
Found at i:1244301 original size:15 final size:15
Alignment explanation
Indices: 1244281--1244348 Score: 52
Period size: 15 Copynumber: 4.5 Consensus size: 15
1244271 TTTCAGATAT
1244281 TCACATAGTTCAATA
1 TCACATAGTTCAATA
1244296 TCACATAGCTT--ATA
1 TCACATAG-TTCAATA
1244310 TCACAT-GTTCATATA
1 TCACATAGTTCA-ATA
* * **
1244325 TTCACGTAGTCCGGTA
1 -TCACATAGTTCAATA
1244341 TCACATAG
1 TCACATAG
1244349 CTTATATCAT
Statistics
Matches: 42, Mismatches: 5, Indels: 12
0.71 0.08 0.20
Matches are distributed among these distances:
12 2 0.05
13 1 0.02
14 9 0.21
15 18 0.43
16 9 0.21
17 3 0.07
ACGTcount: A:0.32, C:0.22, G:0.12, T:0.34
Consensus pattern (15 bp):
TCACATAGTTCAATA
Found at i:1244326 original size:45 final size:45
Alignment explanation
Indices: 1244272--1244357 Score: 127
Period size: 45 Copynumber: 1.9 Consensus size: 45
1244262 ATTTCATCTT
*
1244272 TTCAGATATTCACATAGTTCAATATCACATAGCTTATATCACATG
1 TTCAGATATTCACATAGTCCAATATCACATAGCTTATATCACATG
* * **
1244317 TTCATATATTCACGTAGTCCGGTATCACATAGCTTATATCA
1 TTCAGATATTCACATAGTCCAATATCACATAGCTTATATCA
1244358 TTTTCTCAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 36 1.00
ACGTcount: A:0.33, C:0.21, G:0.10, T:0.36
Consensus pattern (45 bp):
TTCAGATATTCACATAGTCCAATATCACATAGCTTATATCACATG
Found at i:1244629 original size:23 final size:23
Alignment explanation
Indices: 1244595--1244669 Score: 105
Period size: 23 Copynumber: 3.3 Consensus size: 23
1244585 GTATAAATTG
*
1244595 CATAGAAATGTCTCGAATGACCA
1 CATAGAAATGTCCCGAATGACCA
* * *
1244618 CATAGTACTGTCCCGAATGACCG
1 CATAGAAATGTCCCGAATGACCA
*
1244641 CATAGAAATGTCCCGAAAGACCA
1 CATAGAAATGTCCCGAATGACCA
1244664 CATAGA
1 CATAGA
1244670 GTTGTCCCAA
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.37, C:0.25, G:0.19, T:0.19
Consensus pattern (23 bp):
CATAGAAATGTCCCGAATGACCA
Found at i:1244693 original size:46 final size:46
Alignment explanation
Indices: 1244594--1244693 Score: 121
Period size: 46 Copynumber: 2.2 Consensus size: 46
1244584 TGTATAAATT
* * * *
1244594 GCATAGAAATGTCTCGAATGACCACATAGTACTGTCCCGAATGACC
1 GCATAGAAATGTCCCGAAAGACCACATAGTACTGTCCCAAAGGACC
* *
1244640 GCATAGAAATGTCCCGAAAGACCACATAG-AGTTGTCCCAAAGGATC
1 GCATAGAAATGTCCCGAAAGACCACATAGTA-CTGTCCCAAAGGACC
*
1244686 GCGTAGAA
1 GCATAGAA
1244694 CCCTCGACTC
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
45 1 0.02
46 45 0.98
ACGTcount: A:0.35, C:0.24, G:0.22, T:0.19
Consensus pattern (46 bp):
GCATAGAAATGTCCCGAAAGACCACATAGTACTGTCCCAAAGGACC
Found at i:1251292 original size:29 final size:29
Alignment explanation
Indices: 1251250--1251309 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
1251240 TCGGTATCTG
1251250 ACCGGAAAGTAGGTTTTCCGACAAGTCGA
1 ACCGGAAAGTAGGTTTTCCGACAAGTCGA
1251279 ACCGGAAAGTAGGTTTTCCGACAAGTCGA
1 ACCGGAAAGTAGGTTTTCCGACAAGTCGA
1251308 AC
1 AC
1251310 GATTCAATGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.32, C:0.22, G:0.27, T:0.20
Consensus pattern (29 bp):
ACCGGAAAGTAGGTTTTCCGACAAGTCGA
Found at i:1255049 original size:21 final size:21
Alignment explanation
Indices: 1255025--1255085 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
1255015 CATTGTAGAC
*
1255025 TGTCACGTCAACACTGTGAAT
1 TGTCACGTCAACACTGTAAAT
* *
1255046 TGTCATGTCAGCA-TAGTAAAT
1 TGTCACGTCAACACT-GTAAAT
*
1255067 TGTCACGTCAATACTGTAA
1 TGTCACGTCAACACTGTAA
1255086 CGGTCAACGA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Consensus pattern (21 bp):
TGTCACGTCAACACTGTAAAT
Found at i:1265413 original size:2 final size:2
Alignment explanation
Indices: 1265406--1265453 Score: 51
Period size: 2 Copynumber: 24.0 Consensus size: 2
1265396 TTTCTATCCA
* * * * *
1265406 AT AT AT AT AT AT AT AT AT AG AT AG AT AT AT AT AT TT AA AA AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1265448 AT AT AT
1 AT AT AT
1265454 TTCTACCCAA
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (2 bp):
AT
Found at i:1271152 original size:30 final size:29
Alignment explanation
Indices: 1271112--1271178 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 29
1271102 TCATTTGCAC
* * *
1271112 AAAAAATTATTT-GATTTTTTGATATTTTAT
1 AAAATATTATTTAGAATTTTT-A-ATTTAAT
1271142 AAAATATTATTTAGAATTTTTAATTTAAT
1 AAAATATTATTTAGAATTTTTAATTTAAT
1271171 AATAATAT
1 AA-AATAT
1271179 ATATCGTAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
29 8 0.25
30 17 0.53
31 7 0.22
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.52
Consensus pattern (29 bp):
AAAATATTATTTAGAATTTTTAATTTAAT
Found at i:1271359 original size:23 final size:23
Alignment explanation
Indices: 1271333--1271395 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
1271323 ATATAACCAC
1271333 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
1271356 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
1271379 TACCTATTACATCATAT
1 TACCTATTACATTATAT
1271396 GTTTACCTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:1273036 original size:200 final size:199
Alignment explanation
Indices: 1272117--1273284 Score: 2096
Period size: 198 Copynumber: 5.9 Consensus size: 199
1272107 TTTAAATTAG
*
1272117 TATCGACACAAACTATA--ACGTGTCGACACATTATTTAGACATATTCTCTCATAAAACAGGTAT
1 TATCGACACAAACTATATTA-GTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAT
*
1272180 ACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGA
65 AATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGA
1272245 TCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAA
130 TCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAA
1272310 AAAAA
195 AAAAA
* *
1272315 TATCGACACAAACTATATTAGTGTCGACACATTATTTATACATATTATCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1272380 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
1272445 CGACAC-TTTT-TATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGG-AAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
1272507 AAAA
196 AAAA
1272511 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1272576 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
1272641 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
1272706 AAAA
196 AAAA
* * *
1272710 -ATCGACACAAACTATATTAGTGTCGACACATTATTTATACATATTATCTCATAAAACCAGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1272774 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
1272839 TGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGG-AAA
1272904 AAAAA
195 AAAAA
*
1272909 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGATATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1272974 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* * *
1273039 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTACATTCATTATGGACAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
1273104 AAAA
196 AAAA
*
1273108 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAGA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
* * *
1273173 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGG-GTTCGATGATTTTGGGA
* **
1273238 TTGACACTTTTTATATATGGATCGACACTTTATGGGCACACCCTGTT
130 TCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTT
1273285 GGCCATATTG
Statistics
Matches: 936, Mismatches: 26, Indels: 14
0.96 0.03 0.01
Matches are distributed among these distances:
196 141 0.15
197 53 0.06
198 256 0.27
199 243 0.26
200 243 0.26
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.37
Consensus pattern (199 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
AAAA
Found at i:1273449 original size:19 final size:19
Alignment explanation
Indices: 1273403--1273451 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
1273393 TTATATTCAC
*
1273403 ATACAAAAATATAAATCGT
1 ATACAAAATTATAAATCGT
*
1273422 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
1273441 ATACAAAATTA
1 ATACAAAATTA
1273452 ACCCTACATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.57, C:0.10, G:0.02, T:0.31
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:1275377 original size:21 final size:21
Alignment explanation
Indices: 1275353--1275400 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
1275343 CTGTATCTTT
* *
1275353 GACTCTCTCGAGTTTCTCTAC
1 GACTCTATCAAGTTTCTCTAC
* *
1275374 GACTCGATCAAGTTTCTCTTC
1 GACTCTATCAAGTTTCTCTAC
1275395 GACTCT
1 GACTCT
1275401 TGATTGTCTT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.17, C:0.31, G:0.15, T:0.38
Consensus pattern (21 bp):
GACTCTATCAAGTTTCTCTAC
Found at i:1277691 original size:20 final size:20
Alignment explanation
Indices: 1277635--1277682 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
1277625 ATTCGGTATC
1277635 ATTT-TACCGGTTTTATCAT
1 ATTTGTACCGGTTTTATCAT
1277654 -TTTGATACCGGTTTTATCAT
1 ATTTG-TACCGGTTTTATCAT
1277674 ATTTGTACC
1 ATTTGTACC
1277683 TGTTATATCG
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
18 3 0.12
20 19 0.73
21 4 0.15
ACGTcount: A:0.21, C:0.17, G:0.12, T:0.50
Consensus pattern (20 bp):
ATTTGTACCGGTTTTATCAT
Found at i:1277833 original size:20 final size:20
Alignment explanation
Indices: 1277803--1277848 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
1277793 CACTTTTAAA
*
1277803 TTTACCGGTTTTATCAT-TT
1 TTTACCAGTTTTATCATATT
1277822 TGTTACCAGTTTTATCATATT
1 T-TTACCAGTTTTATCATATT
1277843 TTTACC
1 TTTACC
1277849 TGGTATATCG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 1 0.04
20 20 0.83
21 3 0.12
ACGTcount: A:0.20, C:0.17, G:0.09, T:0.54
Consensus pattern (20 bp):
TTTACCAGTTTTATCATATT
Found at i:1283117 original size:35 final size:34
Alignment explanation
Indices: 1283076--1283167 Score: 105
Period size: 35 Copynumber: 2.6 Consensus size: 34
1283066 GAACATATAA
* * *
1283076 GCACACATAGTGCTATCACATCATAAT-TGTAATAT
1 GCACACA-AGTGCAATCACATCAGAATCAG-AATAT
*
1283111 GCACACAAAGTACAATCACATCAGAATCAGAATAT
1 GCACAC-AAGTGCAATCACATCAGAATCAGAATAT
1283146 GCACACAAGGTGCAATCACATC
1 GCACACAA-GTGCAATCACATC
1283168 GAAAATATAC
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
34 2 0.04
35 45 0.92
36 2 0.04
ACGTcount: A:0.41, C:0.24, G:0.13, T:0.22
Consensus pattern (34 bp):
GCACACAAGTGCAATCACATCAGAATCAGAATAT
Found at i:1283262 original size:35 final size:35
Alignment explanation
Indices: 1283223--1283326 Score: 127
Period size: 35 Copynumber: 2.9 Consensus size: 35
1283213 TCAGAATTGT
* **
1283223 AATATGCACACATAGTGCAATCACATCGGAATCAA
1 AATATGCACACAAAGTGCAATCACATCAAAATCAA
1283258 AATATGCACACAAAGTGCAATCACATCAAAATCAA
1 AATATGCACACAAAGTGCAATCACATCAAAATCAA
* ***
1283293 AATATACACGTTAAGTGCAATTCACATCGAAAAT
1 AATATGCACACAAAGTGCAA-TCACATC-AAAAT
1283327 ATACTAGTGT
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
35 48 0.80
36 7 0.12
37 5 0.08
ACGTcount: A:0.46, C:0.21, G:0.12, T:0.21
Consensus pattern (35 bp):
AATATGCACACAAAGTGCAATCACATCAAAATCAA
Found at i:1288352 original size:78 final size:78
Alignment explanation
Indices: 1288258--1288408 Score: 248
Period size: 78 Copynumber: 1.9 Consensus size: 78
1288248 ATATATTAAA
* * *
1288258 AATAAATAAAAAATTTACCAAGCTCGTCTTAATTAAAAATATATATTTATAGAAAATAAAAATAT
1 AATAAATAAAAAATTTACCAAGCTCGCCTCAATTAAAAAAATATATTTATAGAAAATAAAAATAT
*
1288323 TTTTACCCGTTAC
66 TTTAACCCGTTAC
* *
1288336 AATAAATGAAAAATTTACCAAGCTCGCCTCATTTAAAAAAATATATTTATAGAAAATAAAAATAT
1 AATAAATAAAAAATTTACCAAGCTCGCCTCAATTAAAAAAATATATTTATAGAAAATAAAAATAT
1288401 TTTAACCC
66 TTTAACCC
1288409 AACTACAATA
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
78 67 1.00
ACGTcount: A:0.50, C:0.13, G:0.05, T:0.32
Consensus pattern (78 bp):
AATAAATAAAAAATTTACCAAGCTCGCCTCAATTAAAAAAATATATTTATAGAAAATAAAAATAT
TTTAACCCGTTAC
Found at i:1292707 original size:6 final size:6
Alignment explanation
Indices: 1292696--1292721 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
1292686 ACAAGAAGCC
1292696 CGACCA CGACCA CGACCA CGACCA CG
1 CGACCA CGACCA CGACCA CGACCA CG
1292722 GTTAGCAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.31, C:0.50, G:0.19, T:0.00
Consensus pattern (6 bp):
CGACCA
Found at i:1293507 original size:37 final size:36
Alignment explanation
Indices: 1293466--1293536 Score: 90
Period size: 37 Copynumber: 1.9 Consensus size: 36
1293456 TTGAATTGAG
*
1293466 TCGGGTCG-GAAGGAGGATATAAAATTTTCGGGTCGGA
1 TCGGGTCGAG-AGGAGGATAT-AAATTTTCAGGTCGGA
* *
1293503 TCGGGTCGAGTGGAGGATATATATTTTCAGGTCG
1 TCGGGTCGAGAGGAGGATATAAATTTTCAGGTCG
1293537 AGTTGGGTTG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
36 12 0.40
37 17 0.57
38 1 0.03
ACGTcount: A:0.24, C:0.11, G:0.37, T:0.28
Consensus pattern (36 bp):
TCGGGTCGAGAGGAGGATATAAATTTTCAGGTCGGA
Found at i:1295995 original size:100 final size:100
Alignment explanation
Indices: 1295822--1296018 Score: 385
Period size: 100 Copynumber: 2.0 Consensus size: 100
1295812 ATCAAAAAAC
*
1295822 AAATGTCGTGAAAATCTTTGTACGAGCACTAACATGATTGCAGAGGTATGCGAAAAATACTATTA
1 AAATGTCGTGAAAATCTTTGTACGAGCACCAACATGATTGCAGAGGTATGCGAAAAATACTATTA
1295887 GATTAAAAAGTTTGGAAGGGACAAGAGCACTTAAT
66 GATTAAAAAGTTTGGAAGGGACAAGAGCACTTAAT
1295922 AAATGTCGTGAAAATCTTTGTACGAGCACCAACATGATTGCAGAGGTATGCGAAAAATACTATTA
1 AAATGTCGTGAAAATCTTTGTACGAGCACCAACATGATTGCAGAGGTATGCGAAAAATACTATTA
1295987 GATTAAAAAGTTTGGAAGGGACAAGAGCACTT
66 GATTAAAAAGTTTGGAAGGGACAAGAGCACTT
1296019 TTTTTTAATA
Statistics
Matches: 96, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
100 96 1.00
ACGTcount: A:0.40, C:0.13, G:0.22, T:0.25
Consensus pattern (100 bp):
AAATGTCGTGAAAATCTTTGTACGAGCACCAACATGATTGCAGAGGTATGCGAAAAATACTATTA
GATTAAAAAGTTTGGAAGGGACAAGAGCACTTAAT
Found at i:1298333 original size:20 final size:20
Alignment explanation
Indices: 1298304--1298424 Score: 190
Period size: 20 Copynumber: 6.0 Consensus size: 20
1298294 CATATAGATT
*
1298304 CGTTGCGATTTTACTATTCA
1 CGTTGTGATTTTACTATTCA
*
1298324 TGTTGTGATTTTACTATTCA
1 CGTTGTGATTTTACTATTCA
1298344 CGTTGTGATTTTACTATTCA
1 CGTTGTGATTTTACTATTCA
*
1298364 TGTTGCT-ATTTTACTATTCA
1 CGTTG-TGATTTTACTATTCA
*
1298384 CGTTGCGATTTTACTATTCA
1 CGTTGTGATTTTACTATTCA
1298404 CGTTGTGATTTTACTATTCA
1 CGTTGTGATTTTACTATTCA
1298424 C
1 C
1298425 ATTGCGAATT
Statistics
Matches: 92, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
20 91 0.99
21 1 0.01
ACGTcount: A:0.20, C:0.17, G:0.14, T:0.50
Consensus pattern (20 bp):
CGTTGTGATTTTACTATTCA
Found at i:1298348 original size:40 final size:40
Alignment explanation
Indices: 1298304--1298441 Score: 215
Period size: 40 Copynumber: 3.4 Consensus size: 40
1298294 CATATAGATT
1298304 CGTTGCGATTTTACTATTCATGTTGTGATTTTACTATTCA
1 CGTTGCGATTTTACTATTCATGTTGTGATTTTACTATTCA
*
1298344 CGTTGTGATTTTACTATTCATGTTGCT-ATTTTACTATTCA
1 CGTTGCGATTTTACTATTCATGTTG-TGATTTTACTATTCA
*
1298384 CGTTGCGATTTTACTATTCACGTTGTGATTTTACTATTCA
1 CGTTGCGATTTTACTATTCATGTTGTGATTTTACTATTCA
* *
1298424 CATTGCGAATTTGACTAT
1 CGTTGCG-ATTTTACTAT
1298442 CGCGTTGCGA
Statistics
Matches: 90, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
39 1 0.01
40 79 0.88
41 10 0.11
ACGTcount: A:0.21, C:0.16, G:0.14, T:0.49
Consensus pattern (40 bp):
CGTTGCGATTTTACTATTCATGTTGTGATTTTACTATTCA
Found at i:1298398 original size:60 final size:60
Alignment explanation
Indices: 1298305--1298451 Score: 215
Period size: 60 Copynumber: 2.5 Consensus size: 60
1298295 ATATAGATTC
* *
1298305 GTTGCGATTTTACTATTCATGTTGTGATTTTACTATTCACGTTGTGATTTTACTATTCAT
1 GTTGCGATTTTACTATTCACGTTGCGATTTTACTATTCACGTTGTGATTTTACTATTCAT
* *
1298365 GTTGCTATTTTACTATTCACGTTGCGATTTTACTATTCACGTTGTGATTTTACTATTCAC
1 GTTGCGATTTTACTATTCACGTTGCGATTTTACTATTCACGTTGTGATTTTACTATTCAT
* * *
1298425 ATTGCGAATTTGACTA-TCGCGTTGCGA
1 GTTGCG-ATTTTACTATTCACGTTGCGA
1298452 ATTTGACTTT
Statistics
Matches: 78, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
60 70 0.90
61 8 0.10
ACGTcount: A:0.20, C:0.16, G:0.16, T:0.47
Consensus pattern (60 bp):
GTTGCGATTTTACTATTCACGTTGCGATTTTACTATTCACGTTGTGATTTTACTATTCAT
Found at i:1298451 original size:20 final size:19
Alignment explanation
Indices: 1298426--1298511 Score: 109
Period size: 20 Copynumber: 4.3 Consensus size: 19
1298416 ACTATTCACA
*
1298426 TTGCGAATTTGACTATCGCG
1 TTGCGAATTTGACT-TCGTG
*
1298446 TTGCGAATTTGACTTTTGTG
1 TTGCGAATTTGAC-TTCGTG
1298466 TTGCGAATTTGACTTCTGTG
1 TTGCGAATTTGACTTC-GTG
*
1298486 TTGTGAATTTGACTTCTGTG
1 TTGCGAATTTGACTTC-GTG
1298506 TTGCGA
1 TTGCGA
1298512 TTTACATATT
Statistics
Matches: 59, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
19 2 0.03
20 56 0.95
21 1 0.02
ACGTcount: A:0.16, C:0.14, G:0.26, T:0.44
Consensus pattern (19 bp):
TTGCGAATTTGACTTCGTG
Found at i:1298470 original size:40 final size:40
Alignment explanation
Indices: 1298426--1298532 Score: 139
Period size: 40 Copynumber: 2.7 Consensus size: 40
1298416 ACTATTCACA
*
1298426 TTGCGAATTTGACTATCGCGTTGCGAATTTGACTTTTGTG
1 TTGCGAATTTGACTATCGCGTTGCGAATTTGACTTCTGTG
* *
1298466 TTGCGAATTTGACT-TCTGTGTTGTGAATTTGACTTCTGTG
1 TTGCGAATTTGACTATC-GCGTTGCGAATTTGACTTCTGTG
1298506 TTGCG-ATTT-ACATATTCGCGTTGCGAA
1 TTGCGAATTTGAC-TA-TCGCGTTGCGAA
1298533 ATTGGAAACT
Statistics
Matches: 58, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
38 2 0.03
39 7 0.12
40 47 0.81
41 2 0.03
ACGTcount: A:0.18, C:0.15, G:0.24, T:0.43
Consensus pattern (40 bp):
TTGCGAATTTGACTATCGCGTTGCGAATTTGACTTCTGTG
Found at i:1298568 original size:20 final size:20
Alignment explanation
Indices: 1298523--1298576 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
1298513 TTACATATTC
1298523 GCGTTGCGAAATTGGAAACT
1 GCGTTGCGAAATTGGAAACT
* ***
1298543 GGGTTGCGAAATTGGAGTTT
1 GCGTTGCGAAATTGGAAACT
1298563 GCGTTGCGAAATTG
1 GCGTTGCGAAATTG
1298577 TTGGTCATTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.24, C:0.11, G:0.35, T:0.30
Consensus pattern (20 bp):
GCGTTGCGAAATTGGAAACT
Found at i:1305764 original size:33 final size:34
Alignment explanation
Indices: 1305709--1305777 Score: 88
Period size: 33 Copynumber: 2.1 Consensus size: 34
1305699 TTGTCATAAA
*
1305709 CCCTAAATTAACAAAATCTCAAAAT-CCT-AAATT
1 CCCTAAATTAACAAAAACTC-AAATCCCTAAAATT
* *
1305742 CCCTAAATTATCAAAAAGTCAAATCCCTAAAATT
1 CCCTAAATTAACAAAAACTCAAATCCCTAAAATT
1305776 CC
1 CC
1305778 AACTATTATC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
32 4 0.13
33 20 0.65
34 7 0.23
ACGTcount: A:0.46, C:0.26, G:0.01, T:0.26
Consensus pattern (34 bp):
CCCTAAATTAACAAAAACTCAAATCCCTAAAATT
Found at i:1308936 original size:29 final size:29
Alignment explanation
Indices: 1308842--1308937 Score: 86
Period size: 29 Copynumber: 3.2 Consensus size: 29
1308832 GAACATAATG
* *
1308842 AATAGTCGGGTGACCATTTTGTAACTTTT
1 AATAGTCGAGTGACCATTTTATAACTTTT
* * ** *
1308871 TATAGTCGAGTGACTCAATAAAGTAACACTTT
1 AATAGTCGAGTGAC-CATTTTA-TAAC-TTTT
*
1308903 -ATAGTCGAATGACCATTTTATAACTTTT
1 AATAGTCGAGTGACCATTTTATAACTTTT
1308931 AATAGTC
1 AATAGTC
1308938 TATAAACTTA
Statistics
Matches: 51, Mismatches: 12, Indels: 8
0.72 0.17 0.11
Matches are distributed among these distances:
28 3 0.06
29 22 0.43
30 7 0.14
31 16 0.31
32 3 0.06
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.38
Consensus pattern (29 bp):
AATAGTCGAGTGACCATTTTATAACTTTT
Found at i:1310658 original size:2 final size:2
Alignment explanation
Indices: 1310651--1310682 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1310641 CATATTTTTC
1310651 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
1310683 GTGTGTGTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1313384 original size:42 final size:42
Alignment explanation
Indices: 1313311--1313420 Score: 161
Period size: 42 Copynumber: 2.6 Consensus size: 42
1313301 CTGAAATACT
* * *
1313311 GTGTTTGCTTCATGTAATT-GTTTTCCGAAAAATGTTTTTCC
1 GTGTTTGTTTCACGTAATTAGTTTTCCGAAAAATGTTTTCCC
1313352 GTGTTTGTTTCACGTAATTAGTTTTCCGAAAAATGTTTTCCC
1 GTGTTTGTTTCACGTAATTAGTTTTCCGAAAAATGTTTTCCC
*
1313394 TTGTTTGTTTCACGTAATTCA-TTTTCC
1 GTGTTTGTTTCACGTAATT-AGTTTTCC
1313421 TAGTAACATA
Statistics
Matches: 63, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
41 17 0.27
42 45 0.71
43 1 0.02
ACGTcount: A:0.19, C:0.16, G:0.15, T:0.49
Consensus pattern (42 bp):
GTGTTTGTTTCACGTAATTAGTTTTCCGAAAAATGTTTTCCC
Found at i:1314933 original size:4 final size:4
Alignment explanation
Indices: 1314926--1314952 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
1314916 TCTGCTTGTT
1314926 TGTA TGTA TGTA TGTA TGTA TGTA TGT
1 TGTA TGTA TGTA TGTA TGTA TGTA TGT
1314953 TTCTTCGATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.26, T:0.52
Consensus pattern (4 bp):
TGTA
Found at i:1316309 original size:15 final size:15
Alignment explanation
Indices: 1316255--1316323 Score: 66
Period size: 15 Copynumber: 4.6 Consensus size: 15
1316245 CTCACAGACC
* *
1316255 TGCTTCTCCAATGGT
1 TGCTTCTCCTAGGGT
* * *
1316270 TCCTTCTCCGAGGAT
1 TGCTTCTCCTAGGGT
*
1316285 TGCCTCTCCTAGGGT
1 TGCTTCTCCTAGGGT
*
1316300 TGCTTCTCCTAGGGC
1 TGCTTCTCCTAGGGT
*
1316315 AGCTTCTCC
1 TGCTTCTCC
1316324 GAGAACTGGT
Statistics
Matches: 43, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 43 1.00
ACGTcount: A:0.10, C:0.33, G:0.22, T:0.35
Consensus pattern (15 bp):
TGCTTCTCCTAGGGT
Found at i:1337994 original size:2 final size:2
Alignment explanation
Indices: 1337987--1338014 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1337977 TTTCCTTCAA
1337987 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
1338015 TCTAAACAAA
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:1347341 original size:60 final size:60
Alignment explanation
Indices: 1347293--1347504 Score: 266
Period size: 60 Copynumber: 3.5 Consensus size: 60
1347283 GTTTTTATTT
* ** *
1347293 TAAATTAGTCATTAAA-TTTTTAAATATTTTAAATTCATCCCCAAACTATGACTGGCATTC
1 TAAATTAGTCTTTAAACTTTTTAAA-ATTCCAAATTCATCCCCAAACTATGATTGGCATTC
*
1347353 TAAATTAGTCTTTAAACTTTTTAAAATTCCACATTCATCCCCAAACTATGATTGGCATTC
1 TAAATTAGTCTTTAAACTTTTTAAAATTCCAAATTCATCCCCAAACTATGATTGGCATTC
* * **
1347413 TAAATTGGTCTTTAAACTTTTTAAAATTCCAAATTCAT-CCCAAAGCTATGACTCTCATTC
1 TAAATTAGTCTTTAAACTTTTTAAAATTCCAAATTCATCCCCAAA-CTATGATTGGCATTC
* * * * *
1347473 TAAATCAGTCCTCAAACTTTTGAACATTCCAA
1 TAAATTAGTCTTTAAACTTTTTAAAATTCCAA
1347505 TAACCTCCCC
Statistics
Matches: 134, Mismatches: 16, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
59 6 0.04
60 120 0.90
61 8 0.06
ACGTcount: A:0.35, C:0.21, G:0.07, T:0.38
Consensus pattern (60 bp):
TAAATTAGTCTTTAAACTTTTTAAAATTCCAAATTCATCCCCAAACTATGATTGGCATTC
Found at i:1350012 original size:2 final size:2
Alignment explanation
Indices: 1350000--1350035 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
1349990 GTGCTGGTGT
*
1350000 TA TA TA T- TA TA TA TA TT 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 TA TA T
1350036 CGTGATCTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (2 bp):
TA
Found at i:1350392 original size:2 final size:2
Alignment explanation
Indices: 1350385--1350413 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1350375 ATTCCTAACA
1350385 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 A
1350414 AATTAGGATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1352395 original size:14 final size:14
Alignment explanation
Indices: 1352361--1352396 Score: 51
Period size: 12 Copynumber: 2.8 Consensus size: 14
1352351 AGATAAAAAA
1352361 TTAATT-TAATATT
1 TTAATTATAATATT
1352374 TT--TTATAATATT
1 TTAATTATAATATT
1352386 TTAATTATAAT
1 TTAATTATAAT
1352397 TTTATAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
11 2 0.10
12 9 0.45
13 2 0.10
14 7 0.35
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (14 bp):
TTAATTATAATATT
Found at i:1358615 original size:2 final size:2
Alignment explanation
Indices: 1358608--1358657 Score: 61
Period size: 2 Copynumber: 26.5 Consensus size: 2
1358598 ATATCTGTCC
*
1358608 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT -T A- AT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
1358647 AT GT AT AT AT A
1 AT AT AT AT AT A
1358658 ATTTTTGTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
1 3 0.07
2 38 0.93
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (2 bp):
AT
Found at i:1358659 original size:15 final size:14
Alignment explanation
Indices: 1358619--1358661 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
1358609 TATATATATA
*
1358619 TATATATATATATAT
1 TATATATA-ATTTAT
1358634 TATATATTAATTTAT
1 TATATA-TAATTTAT
1358649 GTATATATAATTT
1 -TATATATAATTT
1358662 TTGTTTTGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
15 17 0.68
16 8 0.32
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (14 bp):
TATATATAATTTAT
Found at i:1367511 original size:2 final size:2
Alignment explanation
Indices: 1367504--1367528 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1367494 TTAAATTTTG
1367504 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
1367529 TCTCTGCAGT
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:1378639 original size:26 final size:26
Alignment explanation
Indices: 1378571--1378650 Score: 99
Period size: 26 Copynumber: 3.1 Consensus size: 26
1378561 ATTTAGCGCA
* *
1378571 TATGGTGGGCACGACCTTATGTGTAA
1 TATGGTGGGAACGACCTTATGTGTAT
* *
1378597 TATGAT-GGACACAACCTTATGTGTAT
1 TATGGTGGGA-ACGACCTTATGTGTAT
*
1378623 TATGGTGGGAATGACCTTATGTGTAT
1 TATGGTGGGAACGACCTTATGTGTAT
1378649 TA
1 TA
1378651 GCACTTCGAT
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
25 2 0.04
26 40 0.89
27 3 0.07
ACGTcount: A:0.26, C:0.12, G:0.26, T:0.35
Consensus pattern (26 bp):
TATGGTGGGAACGACCTTATGTGTAT
Found at i:1379476 original size:89 final size:89
Alignment explanation
Indices: 1379325--1379505 Score: 362
Period size: 89 Copynumber: 2.0 Consensus size: 89
1379315 CTTAAATCGA
1379325 AATTAGTTTGATTAAAAAAATAAAAATTGATATTACTCGATAAATCAATATATGGTTAATTGTAA
1 AATTAGTTTGATTAAAAAAATAAAAATTGATATTACTCGATAAATCAATATATGGTTAATTGTAA
1379390 TTTTTGAATGAATAACTTCTAGTG
66 TTTTTGAATGAATAACTTCTAGTG
1379414 AATTAGTTTGATTAAAAAAATAAAAATTGATATTACTCGATAAATCAATATATGGTTAATTGTAA
1 AATTAGTTTGATTAAAAAAATAAAAATTGATATTACTCGATAAATCAATATATGGTTAATTGTAA
1379479 TTTTTGAATGAATAACTTCTAGTG
66 TTTTTGAATGAATAACTTCTAGTG
1379503 AAT
1 AAT
1379506 GTTAGTAAAT
Statistics
Matches: 92, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
89 92 1.00
ACGTcount: A:0.43, C:0.06, G:0.12, T:0.39
Consensus pattern (89 bp):
AATTAGTTTGATTAAAAAAATAAAAATTGATATTACTCGATAAATCAATATATGGTTAATTGTAA
TTTTTGAATGAATAACTTCTAGTG
Found at i:1380332 original size:21 final size:22
Alignment explanation
Indices: 1380298--1380339 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
1380288 TTAATATTGA
1380298 AAAAATTGAAAGTTTAGGTACC
1 AAAAATTGAAAGTTTAGGTACC
*
1380320 AAAAA-TGATAGTTTAGGTAC
1 AAAAATTGAAAGTTTAGGTAC
1380340 TAAATGTGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.45, C:0.07, G:0.19, T:0.29
Consensus pattern (22 bp):
AAAAATTGAAAGTTTAGGTACC
Found at i:1393797 original size:29 final size:29
Alignment explanation
Indices: 1393752--1393821 Score: 104
Period size: 29 Copynumber: 2.4 Consensus size: 29
1393742 AGAGGAAGTG
* **
1393752 CATGGCGACCTATAAGGTCGCCCGGATTA
1 CATGGCGACCTACAAGGTCGCCCGGAGGA
*
1393781 CATGGCGACCTACAAGGTCGCCCGGAGGG
1 CATGGCGACCTACAAGGTCGCCCGGAGGA
1393810 CATGGCGACCTA
1 CATGGCGACCTA
1393822 TGCTTGGGGA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.23, C:0.30, G:0.31, T:0.16
Consensus pattern (29 bp):
CATGGCGACCTACAAGGTCGCCCGGAGGA
Found at i:1394710 original size:21 final size:22
Alignment explanation
Indices: 1394686--1394726 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
1394676 ATTAAAATGA
1394686 ACTAAAAGTG-ATAGTTTAGAT
1 ACTAAAAGTGTATAGTTTAGAT
* *
1394707 ACTAAATGTGTGTAGTTTAG
1 ACTAAAAGTGTATAGTTTAG
1394727 CTTAATTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.37, C:0.05, G:0.22, T:0.37
Consensus pattern (22 bp):
ACTAAAAGTGTATAGTTTAGAT
Found at i:1394918 original size:35 final size:33
Alignment explanation
Indices: 1394862--1394927 Score: 89
Period size: 35 Copynumber: 1.9 Consensus size: 33
1394852 TTTATGTTAT
*
1394862 AAACTATAAAAAAATTCTTAAGTGATTAATACG
1 AAACTATAAAAAAATTCTTAAGTGATCAATACG
1394895 AAACGTATATAAAAAATAT-TTAAGTGATCAATA
1 AAAC-TATA-AAAAAAT-TCTTAAGTGATCAATA
1394928 AGAGTATATC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 4 0.14
34 4 0.14
35 20 0.69
36 1 0.03
ACGTcount: A:0.53, C:0.08, G:0.09, T:0.30
Consensus pattern (33 bp):
AAACTATAAAAAAATTCTTAAGTGATCAATACG
Found at i:1400323 original size:48 final size:48
Alignment explanation
Indices: 1400264--1400359 Score: 174
Period size: 48 Copynumber: 2.0 Consensus size: 48
1400254 TTCAACAGAG
* *
1400264 ACTATCGATGTCCTTTCTCCTAAACCCTACTTTACTGTCTTTGCTTTT
1 ACTATCCATGTCCTTTCTCCTAAACCCCACTTTACTGTCTTTGCTTTT
1400312 ACTATCCATGTCCTTTCTCCTAAACCCCACTTTACTGTCTTTGCTTTT
1 ACTATCCATGTCCTTTCTCCTAAACCCCACTTTACTGTCTTTGCTTTT
1400360 GCTACTTCAA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.17, C:0.31, G:0.07, T:0.45
Consensus pattern (48 bp):
ACTATCCATGTCCTTTCTCCTAAACCCCACTTTACTGTCTTTGCTTTT
Found at i:1400581 original size:19 final size:18
Alignment explanation
Indices: 1400553--1400591 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
1400543 TCGAGAGATC
1400553 TAATATATTAACAATTAT
1 TAATATATTAACAATTAT
*
1400571 TAATAATATTAACATTTAT
1 TAAT-ATATTAACAATTAT
1400590 TA
1 TA
1400592 TTTGACATTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (18 bp):
TAATATATTAACAATTAT
Found at i:1401672 original size:98 final size:98
Alignment explanation
Indices: 1401503--1401694 Score: 276
Period size: 98 Copynumber: 2.0 Consensus size: 98
1401493 ATTTTTTATT
* * * * * * * *
1401503 TAAAAATTAGATCTTGGGAAATATTTTTAAGCTCAAATTGGATCAAGTGATGAGTGAAATGATGT
1 TAAAAATTAGACCATGAGAAATATTCTTAAACTCAAATTAGATCAAGTGACGAGTGAAATGATAT
*
1401568 AATACTCAGATCATGTTTGAGTGACCCAAGAAC
66 AATACTCAGATCAGGTTTGAGTGACCCAAGAAC
*
1401601 TAAAAATTAGACCATGAGAAATATTCTTAAACTCAAATTAGATCAAGTGACGGGTGAAATGATAT
1 TAAAAATTAGACCATGAGAAATATTCTTAAACTCAAATTAGATCAAGTGACGAGTGAAATGATAT
* *
1401666 AATACTCATATCAGGTTTGAGTGAGCCAA
66 AATACTCAGATCAGGTTTGAGTGACCCAA
1401695 TAACCTGATC
Statistics
Matches: 82, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
98 82 1.00
ACGTcount: A:0.40, C:0.12, G:0.19, T:0.29
Consensus pattern (98 bp):
TAAAAATTAGACCATGAGAAATATTCTTAAACTCAAATTAGATCAAGTGACGAGTGAAATGATAT
AATACTCAGATCAGGTTTGAGTGACCCAAGAAC
Found at i:1406559 original size:29 final size:29
Alignment explanation
Indices: 1406526--1406618 Score: 73
Period size: 29 Copynumber: 3.1 Consensus size: 29
1406516 ATTGGTCCCT
1406526 AAACTTTTGAATATTTTAATTTCATCCTC
1 AAACTTTTGAATATTTTAATTTCATCCTC
* * * *
1406555 AAAC-TATGATACTCATTCTAAATT-AGTCCTT
1 AAACTTTTGA-A-T-ATTTTAATTTCA-TCCTC
** *
1406586 AAACTTTTGAGCATTTCAATTTCATCCTC
1 AAACTTTTGAATATTTTAATTTCATCCTC
1406615 AAAC
1 AAAC
1406619 AATGACCCGT
Statistics
Matches: 47, Mismatches: 11, Indels: 12
0.67 0.16 0.17
Matches are distributed among these distances:
28 4 0.09
29 20 0.43
30 3 0.06
31 16 0.34
32 4 0.09
ACGTcount: A:0.33, C:0.20, G:0.05, T:0.41
Consensus pattern (29 bp):
AAACTTTTGAATATTTTAATTTCATCCTC
Found at i:1406607 original size:60 final size:59
Alignment explanation
Indices: 1406507--1406623 Score: 162
Period size: 60 Copynumber: 2.0 Consensus size: 59
1406497 AACTATGGCC
* * * * *
1406507 CTCATCTATATTGGTCCCTAAACTTTTGAATATTTTAATTTCATCCTCAAACTATGATA
1 CTCATCTAAATTAGTCCCTAAACTTTTGAACATTTCAATTTCATCCTCAAACAATGATA
* *
1406566 CTCATTCTAAATTAGTCCTTAAACTTTTGAGCATTTCAATTTCATCCTCAAACAATGA
1 CTCA-TCTAAATTAGTCCCTAAACTTTTGAACATTTCAATTTCATCCTCAAACAATGA
1406624 CCCGTATTCT
Statistics
Matches: 50, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
59 4 0.08
60 46 0.92
ACGTcount: A:0.32, C:0.21, G:0.07, T:0.40
Consensus pattern (59 bp):
CTCATCTAAATTAGTCCCTAAACTTTTGAACATTTCAATTTCATCCTCAAACAATGATA
Found at i:1406633 original size:60 final size:60
Alignment explanation
Indices: 1406507--1406677 Score: 161
Period size: 60 Copynumber: 2.9 Consensus size: 60
1406497 AACTATGGCC
* * * * * *
1406507 CTCA-TCTATATTGGTCCCTAAACTTTTGAATATTTTAATTTCATCCTCAAACTATGATA
1 CTCATTCTAAATTAGTCCCTAAACTTTTGAACATTTCAATTTCATCCTCAAACAATGACA
* * *
1406566 CTCATTCTAAATTAGTCCTTAAACTTTTGAGCATTTCAATTTCATCCTCAAACAATGACC
1 CTCATTCTAAATTAGTCCCTAAACTTTTGAACATTTCAATTTCATCCTCAAACAATGACA
* * * * *
1406626 CGT-ATTCTAAATTGGCCCCCAAGCTTTT-AA-ATCTTCCAATTTCATCCCCAAA
1 C-TCATTCTAAATTAGTCCCTAAACTTTTGAACAT-TT-CAATTTCATCCTCAAA
1406678 TTCATCCAAA
Statistics
Matches: 92, Mismatches: 16, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
58 2 0.02
59 7 0.08
60 82 0.89
61 1 0.01
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.37
Consensus pattern (60 bp):
CTCATTCTAAATTAGTCCCTAAACTTTTGAACATTTCAATTTCATCCTCAAACAATGACA
Found at i:1414049 original size:23 final size:24
Alignment explanation
Indices: 1414006--1414053 Score: 89
Period size: 23 Copynumber: 2.0 Consensus size: 24
1413996 AGTATTTTGT
1414006 ATTGTCCTTTTATTTTTTTATATC
1 ATTGTCCTTTTATTTTTTTATATC
1414030 ATTGTCCTTTTA-TTTTTTATATC
1 ATTGTCCTTTTATTTTTTTATATC
1414053 A
1 A
1414054 CATATTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 12 0.50
24 12 0.50
ACGTcount: A:0.19, C:0.12, G:0.04, T:0.65
Consensus pattern (24 bp):
ATTGTCCTTTTATTTTTTTATATC
Found at i:1417215 original size:12 final size:13
Alignment explanation
Indices: 1417198--1417243 Score: 53
Period size: 12 Copynumber: 3.6 Consensus size: 13
1417188 TTTCCCTTTG
1417198 ATTTGTTTA-TTT
1 ATTTGTTTATTTT
1417210 ATTTGTTTATTTT
1 ATTTGTTTATTTT
1417223 ATTTTTGTTT-TTTT
1 A--TTTGTTTATTTT
1417237 A-TTGTTT
1 ATTTGTTT
1417244 TTACTTTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
11 6 0.19
12 9 0.29
13 4 0.13
14 5 0.16
15 7 0.23
ACGTcount: A:0.13, C:0.00, G:0.09, T:0.78
Consensus pattern (13 bp):
ATTTGTTTATTTT
Found at i:1417254 original size:27 final size:27
Alignment explanation
Indices: 1417199--1417254 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
1417189 TTCCCTTTGA
*
1417199 TTTGTTTATTTATTTGTTTATTTTATT
1 TTTGTTTATTTATTTGTTTACTTTATT
* *
1417226 TTTGTTTTTTTATTGTTTTTACTTT-TT
1 TTTGTTTATTTATT-TGTTTACTTTATT
1417253 TT
1 TT
1417255 CCTTTGATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 17 0.68
28 8 0.32
ACGTcount: A:0.11, C:0.02, G:0.07, T:0.80
Consensus pattern (27 bp):
TTTGTTTATTTATTTGTTTACTTTATT
Found at i:1421307 original size:95 final size:95
Alignment explanation
Indices: 1421143--1421321 Score: 270
Period size: 95 Copynumber: 1.9 Consensus size: 95
1421133 ATATTATTTA
* * * * *
1421143 TATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTATGGATAAT
1 TATACAATAAAACTTGAGCTGTCCCTCTAGAGCAATTAGTTAAACGCCCCGACTTTATGGATAAG
*
1421208 ATTCAGCTAGCCTAATAAAGGTGATTATAC
66 ATTCAGCTAACCTAATAAAGGTGATTATAC
*
1421238 TATACAATAAAACTTGAGCTGTCCCTCTA-AGGCAATTAGTTAAATGCCCCGACTTTATGGATAA
1 TATACAATAAAACTTGAGCTGTCCCTCTAGA-GCAATTAGTTAAACGCCCCGACTTTATGGATAA
*
1421302 GATTCAGCTAACCTGATAAA
65 GATTCAGCTAACCTAATAAA
1421322 AGTATTTGCA
Statistics
Matches: 75, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
94 1 0.01
95 74 0.99
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.30
Consensus pattern (95 bp):
TATACAATAAAACTTGAGCTGTCCCTCTAGAGCAATTAGTTAAACGCCCCGACTTTATGGATAAG
ATTCAGCTAACCTAATAAAGGTGATTATAC
Found at i:1422753 original size:36 final size:36
Alignment explanation
Indices: 1422704--1422857 Score: 209
Period size: 36 Copynumber: 4.2 Consensus size: 36
1422694 TAATTTACTC
*
1422704 AAAACAAAGTTTTGTCTCTTTTGAGACAATTTCTCTT
1 AAAACAAA-TTTTGTCTCTCTTGAGACAATTTCTCTT
* *
1422741 AAAACAAATTTTGTCTCTCTTGAGATAATTTCTCGTA
1 AAAACAAATTTTGTCTCTCTTGAGACAATTTCTC-TT
* *
1422778 AAAACAAATTTTGTCTCTCTTGAGATATTTTCTCTT
1 AAAACAAATTTTGTCTCTCTTGAGACAATTTCTCTT
* * *
1422814 AAAACAAATTTTGTCTATCTTGAGACAGTTTCCCTT
1 AAAACAAATTTTGTCTCTCTTGAGACAATTTCTCTT
*
1422850 GAAACAAA
1 AAAACAAA
1422858 ATCTTTGAAT
Statistics
Matches: 106, Mismatches: 10, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
36 64 0.60
37 42 0.40
ACGTcount: A:0.32, C:0.17, G:0.10, T:0.40
Consensus pattern (36 bp):
AAAACAAATTTTGTCTCTCTTGAGACAATTTCTCTT
Found at i:1422920 original size:65 final size:65
Alignment explanation
Indices: 1422797--1423201 Score: 287
Period size: 65 Copynumber: 6.1 Consensus size: 65
1422787 TTTGTCTCTC
* ** *
1422797 TTGAGATA-TTTTCTCTTAAAACAAATTTTGTCTATCTTGAGACAGTTTCCCTTGAAACAAAATC
1 TTGA-ATATTTTTCTCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTAAAACAAAATC
1422861 T
65 T
* **
1422862 TTGAATATGTTTTC-CTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTAAAACAAATAT
1 TTGAATAT-TTTTCTCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTAAAACAAA-A-
1422926 TGTCTCT
63 ----TCT
* * *
1422933 CTTGAGACA-TTTTCTCTT---A-AAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAAT
1 -TTGA-ATATTTTTCTCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTAAAACAAAAT
1422993 CT
64 CT
* * * *
1422995 TTGAATCTGTTTTC-CTTGAAACAAATTTCGTCTCCCTGGAGACAG-TTCCTTTTAAAACAAATT
1 TTGAATAT-TTTTCTCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCC-CTTAAAACAAA--
*
1423058 TTGTCTCT
62 ----ATCT
* * * *
1423066 CTTGAGACA-TTTTCTCTT---AGAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAAT
1 -TTGA-ATATTTTTCTCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTAAAACAAAAT
1423127 CT
64 CT
* * * * * **
1423129 TTGAATCTATTTCCCTTGAAACAAGTTTTGTCTCCCTTGAGACAATTTTTCTTGAAACACAAAAT
1 TTGAATATTTTTCTCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTT-AAA-ACAAAAT
1423194 CT
64 CT
1423196 TTGAAT
1 TTGAAT
1423202 TTATTTCCAT
Statistics
Matches: 265, Mismatches: 41, Indels: 66
0.71 0.11 0.18
Matches are distributed among these distances:
60 1 0.00
61 8 0.03
62 19 0.07
63 3 0.01
64 8 0.03
65 100 0.38
66 8 0.03
67 16 0.06
68 34 0.13
69 31 0.12
70 4 0.02
71 16 0.06
72 14 0.05
73 3 0.01
ACGTcount: A:0.28, C:0.20, G:0.12, T:0.40
Consensus pattern (65 bp):
TTGAATATTTTTCTCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTAAAACAAAATCT
Found at i:1422931 original size:36 final size:34
Alignment explanation
Indices: 1422705--1422990 Score: 205
Period size: 36 Copynumber: 8.2 Consensus size: 34
1422695 AATTTACTCA
* *
1422705 AAACAAAGTTTTGTCTCTTTTGAGACAATTTCTCTT
1 AAACAAA--TTTGTCTCTCTTGAGACAGTTTCTCTT
* * *
1422741 AAAACAAATTTTGTCTCTCTTGAGATAATTTCTCGTAA
1 -AAACAAA-TTTGTCTCTCTTGAGACAGTTTCTC-T-T
* *
1422779 AAACAAATTTTGTCTCTCTTGAGATATTTTCTCTT
1 AAACAAA-TTTGTCTCTCTTGAGACAGTTTCTCTT
* *
1422814 AAAACAAATTTTGTCTATCTTGAGACAGTTTCCCTT
1 -AAACAAA-TTTGTCTCTCTTGAGACAGTTTCTCTT
* *
1422850 GAAACAAA-----ATCT-TTGA-ATATGTTT-TCCTT
1 -AAACAAATTTGTCTCTCTTGAGACA-GTTTCT-CTT
* *
1422879 GAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTT
1 -AAACAAATTT-GTCTCTCTTGAGACAGTTTCTCTT
*
1422915 AAAACAAATATTGTCTCTCTTGAGACATTTTCTCTT
1 -AAACAAAT-TTGTCTCTCTTGAGACAGTTTCTCTT
* *
1422951 -AA-AATTTTGTCTCTCTTGAGACAGTTTCCCTT
1 AAACAAATTTGTCTCTCTTGAGACAGTTTCTCTT
1422983 GAAACAAA
1 -AAACAAA
1422991 ATCTTTGAAT
Statistics
Matches: 205, Mismatches: 26, Indels: 38
0.76 0.10 0.14
Matches are distributed among these distances:
28 2 0.01
29 19 0.09
30 2 0.01
32 24 0.12
33 3 0.01
34 4 0.02
35 4 0.02
36 102 0.50
37 45 0.22
ACGTcount: A:0.30, C:0.18, G:0.11, T:0.41
Consensus pattern (34 bp):
AAACAAATTTGTCTCTCTTGAGACAGTTTCTCTT
Found at i:1422990 original size:133 final size:134
Alignment explanation
Indices: 1422733--1423172 Score: 666
Period size: 133 Copynumber: 3.3 Consensus size: 134
1422723 TTTGAGACAA
* * * * * * *
1422733 TTTCTCTTAAAACAAATTTTGTCTCTCTTGAGATAATTTCTCGTAAAAACAAATTTTGTCTCTCT
1 TTTC-CTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCT-TTTAAAACAAATTTTGTCTCTCT
* *
1422798 TGAGATATTTTCTCTTAAAACAAATTTTGTCTATCTTGAGACAGTTTCCCTTGAAACAAAATCTT
64 TGAGACATTTTCTCTT---ACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTT
*
1422863 TGAATATGT
126 TGAATCTGT
*
1422872 TTTCCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTAAAACAAATATTGTCTCTCTTG
1 TTTCCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTAAAACAAATTTTGTCTCTCTTG
1422937 AGACATTTTCTCTTA-AAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAAT
66 AGACATTTTCTCTTACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAAT
1423001 CTGT
131 CTGT
* *
1423005 TTTCCTTGAAACAAATTTCGTCTCCCTGGAGACAGTTCCTTTTAAAACAAATTTTGTCTCTCTTG
1 TTTCCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTAAAACAAATTTTGTCTCTCTTG
*
1423070 AGACATTTTCTCTTAGAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAAT
66 AGACATTTTCTCTTACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAAT
*
1423135 CTAT
131 CTGT
* * *
1423139 TTCCCTTGAAACAAGTTTTGTCTCCCTTGAGACA
1 TTTCCTTGAAACAAATTTCGTCTCCCTTGAGACA
1423173 ATTTTTCTTG
Statistics
Matches: 281, Mismatches: 19, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
133 128 0.46
134 83 0.30
137 35 0.12
138 31 0.11
139 4 0.01
ACGTcount: A:0.28, C:0.20, G:0.11, T:0.41
Consensus pattern (134 bp):
TTTCCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTAAAACAAATTTTGTCTCTCTTG
AGACATTTTCTCTTACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAAT
CTGT
Found at i:1423095 original size:33 final size:32
Alignment explanation
Indices: 1423053--1423120 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 32
1423043 CTTTTAAAAC
* *
1423053 AAATTTTGTCTCTCTTGAGACATTTTCTCTTAG
1 AAATTTTGTCTCTCTTGAGACAGTTTCCCTT-G
1423086 AAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
1 AAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
1423118 AAA
1 AAA
1423121 CAAAATCTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
32 4 0.12
33 29 0.88
ACGTcount: A:0.24, C:0.19, G:0.13, T:0.44
Consensus pattern (32 bp):
AAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
Found at i:1425007 original size:12 final size:12
Alignment explanation
Indices: 1424990--1425025 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
1424980 TTTTCCTTTG
1424990 ATTTGTTTATTT
1 ATTTGTTTATTT
1425002 ATTTGTTTATTTT
1 ATTTGTTTA-TTT
*
1425015 ATTTTTTTATT
1 ATTTGTTTATT
1425026 GTTTTTACTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.17, C:0.00, G:0.06, T:0.78
Consensus pattern (12 bp):
ATTTGTTTATTT
Found at i:1425032 original size:9 final size:8
Alignment explanation
Indices: 1424990--1425087 Score: 63
Period size: 8 Copynumber: 11.5 Consensus size: 8
1424980 TTTTCCTTTG
*
1424990 ATTTGTTT
1 ATTTTTTT
*
1424998 ATTTATTT
1 ATTTTTTT
*
1425006 GTTTATTTT
1 ATTT-TTTT
1425015 ATTTTTTT
1 ATTTTTTT
1425023 ATTGTTTTT
1 ATT-TTTTT
*
1425032 ACTTTTTTC
1 A-TTTTTTT
*
1425041 CTTTTGATTT
1 ATTTT--TTT
1425051 ATTTTTTT
1 ATTTTTTT
*
1425059 ATTATTTTC
1 ATT-TTTTT
1425068 A-TTTTTT
1 ATTTTTTT
*
1425075 ACGTTTTTT
1 A-TTTTTTT
1425084 ATTT
1 ATTT
1425088 GATTTATTTA
Statistics
Matches: 71, Mismatches: 11, Indels: 16
0.72 0.11 0.16
Matches are distributed among these distances:
7 5 0.07
8 30 0.42
9 28 0.39
10 8 0.11
ACGTcount: A:0.14, C:0.05, G:0.05, T:0.76
Consensus pattern (8 bp):
ATTTTTTT
Found at i:1425073 original size:28 final size:28
Alignment explanation
Indices: 1425020--1425072 Score: 74
Period size: 27 Copynumber: 1.9 Consensus size: 28
1425010 ATTTTATTTT
1425020 TTTATTGTTTTTACTTTTTTCCTTTTGA
1 TTTATTGTTTTTACTTTTTTCCTTTTGA
*
1425048 TTTATT-TTTTTA-TTATTTTCATTTT
1 TTTATTGTTTTTACTT-TTTTCCTTTT
1425073 TTACGTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 2 0.09
27 15 0.65
28 6 0.26
ACGTcount: A:0.13, C:0.08, G:0.04, T:0.75
Consensus pattern (28 bp):
TTTATTGTTTTTACTTTTTTCCTTTTGA
Found at i:1426163 original size:95 final size:95
Alignment explanation
Indices: 1425999--1426177 Score: 270
Period size: 95 Copynumber: 1.9 Consensus size: 95
1425989 ATATTATTTA
* * * * *
1425999 TATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTATGGATAAT
1 TATACAATAAAACTTGAGCTGTCCCTCTAGAGCAATTAGTTAAACGCCCCGACTTTATGGATAAG
*
1426064 ATTCAGCTAGCCTAATAAAGGTGATTATAC
66 ATTCAGCTAACCTAATAAAGGTGATTATAC
*
1426094 TATACAATAAAACTTGAGCTGTCCCTCTA-AGGCAATTAGTTAAATGCCCCGACTTTATGGATAA
1 TATACAATAAAACTTGAGCTGTCCCTCTAGA-GCAATTAGTTAAACGCCCCGACTTTATGGATAA
*
1426158 GATTCAGCTAACCTGATAAA
65 GATTCAGCTAACCTAATAAA
1426178 AGTATTTGCA
Statistics
Matches: 75, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
94 1 0.01
95 74 0.99
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.30
Consensus pattern (95 bp):
TATACAATAAAACTTGAGCTGTCCCTCTAGAGCAATTAGTTAAACGCCCCGACTTTATGGATAAG
ATTCAGCTAACCTAATAAAGGTGATTATAC
Done.