Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001840.1 Hibiscus syriacus cultivar Beakdansim tig00003725_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: 2412736
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 12
Found at i:1271646 original size:136 final size:135
Alignment explanation
Indices: 1271402--1271942 Score: 888
Period size: 136 Copynumber: 4.0 Consensus size: 135
1271392 CTATTTCCCA
* * *
1271402 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTTCAATG
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCAGGTCATCTGTAAGTCCTTCAGTG
* * * *
1271467 CATGATGTTTTCAAAACCTTTGGGTCATCTGTAAGTCCTTCAGTGCACGATATTTTCAAAAACCT
66 CATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTC-AAAACCT
1271532 TCGGGT
130 TCGGGT
1271538 CATCTGTAAGCCCTTCAGTGCATGATG-TTTCAAAAACCTTCAGGTCATCTGTAAGTCCTTCAGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTC-AAAACCTTCAGGTCATCTGTAAGTCCTTCAGT
*
1271602 GCATGATGTTTTCAAAACCTACGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACC
65 GCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTC-AAAACC
1271667 TTCGGGT
129 TTCGGGT
*
1271674 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTG
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCAGGTCATCTGTAAGTCCTTCAGTG
* *
1271739 CATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTC
66 CATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTT
1271804 CGGGT
131 CGGGT
* * *
1271809 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTT-AGGGTCATCTGTAAGCCCTTTAGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCA-GGTCATCTGTAAGTCCTTCAGT
* *
1271873 GCATGATGTTTTCAAAACCTTCGGGCCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAGCCT
65 GCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCT
1271938 TCGGG
130 TCGGG
1271943 CCATTTTTAA
Statistics
Matches: 382, Mismatches: 20, Indels: 7
0.93 0.05 0.02
Matches are distributed among these distances:
135 141 0.37
136 237 0.62
137 4 0.01
ACGTcount: A:0.23, C:0.23, G:0.20, T:0.34
Consensus pattern (135 bp):
CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCAGGTCATCTGTAAGTCCTTCAGTG
CATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTT
CGGGT
Found at i:1271955 original size:45 final size:45
Alignment explanation
Indices: 1271402--1271942 Score: 904
Period size: 45 Copynumber: 12.0 Consensus size: 45
1271392 CTATTTCCCA
1271402 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* *
1271447 CATCTGTAAGTCCTTCAATGCATGATGTTTTCAAAACCTTTGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* *
1271492 CATCTGTAAGTCCTTCAGTGCACGATATTTTCAAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTC-AAAACCTTCGGGT
* *
1271538 CATCTGTAAGCCCTTCAGTGCATGATG-TTTCAAAAACCTTCAGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTC-AAAACCTTCGGGT
*
1271583 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTACGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
*
1271628 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTC-AAAACCTTCGGGT
*
1271674 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1271719 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
*
1271764 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTCCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
*
1271809 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTAGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* * *
1271854 CATCTGTAAGCCCTTTAGTGCATGATGTTTTCAAAACCTTCGGGC
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* *
1271899 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAGCCTTCGGG
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGG
1271943 CCATTTTTAA
Statistics
Matches: 468, Mismatches: 25, Indels: 6
0.94 0.05 0.01
Matches are distributed among these distances:
45 384 0.82
46 84 0.18
ACGTcount: A:0.23, C:0.23, G:0.20, T:0.34
Consensus pattern (45 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
Found at i:1272150 original size:3 final size:3
Alignment explanation
Indices: 1272142--1272226 Score: 80
Period size: 3 Copynumber: 28.0 Consensus size: 3
1272132 TTTCATATAG
* ** *
1272142 TTA TTA TTA TTA TTA TTA TGA TTA TTA AAA TTA TTA TTT TTA TTA TATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
* * * * *
1272191 TTC TTA TTA ATA TTA TTA CTC TTA ATA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1272227 AAAAAATAAT
Statistics
Matches: 63, Mismatches: 18, Indels: 2
0.76 0.22 0.02
Matches are distributed among these distances:
3 60 0.95
4 3 0.05
ACGTcount: A:0.35, C:0.04, G:0.01, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:1285753 original size:23 final size:24
Alignment explanation
Indices: 1285723--1285770 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
1285713 GTCCGTGACA
1285723 CGAGGCTCTCG-CCCCACCCTGTG
1 CGAGGCTCTCGCCCCCACCCTGTG
* *
1285746 CGAGGCTCTTGCCCCCACCTTGTG
1 CGAGGCTCTCGCCCCCACCCTGTG
1285770 C
1 C
1285771 CAGACGCTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 10 0.45
24 12 0.55
ACGTcount: A:0.08, C:0.46, G:0.25, T:0.21
Consensus pattern (24 bp):
CGAGGCTCTCGCCCCCACCCTGTG
Found at i:1294284 original size:25 final size:25
Alignment explanation
Indices: 1294256--1294307 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
1294246 ACACCTACTT
1294256 TAAACACCCTTCCTGAAAATACACA
1 TAAACACCCTTCCTGAAAATACACA
1294281 TAAACACCCTTCCTGAAAATACACA
1 TAAACACCCTTCCTGAAAATACACA
1294306 TA
1 TA
1294308 CTCCCATTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.44, C:0.31, G:0.04, T:0.21
Consensus pattern (25 bp):
TAAACACCCTTCCTGAAAATACACA
Found at i:1303396 original size:33 final size:33
Alignment explanation
Indices: 1303357--1303423 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
1303347 TATAAATTAC
1303357 CGATTTAATAAAAATGCTAAATAGATTTTGAAA
1 CGATTTAATAAAAATGCTAAATAGATTTTGAAA
1303390 CGATTTAATAAAAATGCTAAATAGATTTTGAAA
1 CGATTTAATAAAAATGCTAAATAGATTTTGAAA
1303423 C
1 C
1303424 AAATTTATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.48, C:0.07, G:0.12, T:0.33
Consensus pattern (33 bp):
CGATTTAATAAAAATGCTAAATAGATTTTGAAA
Found at i:1309506 original size:16 final size:16
Alignment explanation
Indices: 1309481--1309525 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
1309471 AAAAAACGGC
*
1309481 GTGACCGGTTAAACAA
1 GTGACTGGTTAAACAA
*
1309497 GTGACTGGTTAAATAA
1 GTGACTGGTTAAACAA
1309513 GTGA-TCGGTTAAA
1 GTGACT-GGTTAAA
1309526 ATTTAGACTG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
15 1 0.04
16 25 0.96
ACGTcount: A:0.36, C:0.11, G:0.27, T:0.27
Consensus pattern (16 bp):
GTGACTGGTTAAACAA
Found at i:1309655 original size:23 final size:23
Alignment explanation
Indices: 1309585--1309649 Score: 121
Period size: 23 Copynumber: 2.8 Consensus size: 23
1309575 AATAACATAT
1309585 TAGGTAGCGCTTATATAATGTAA
1 TAGGTAGCGCTTATATAATGTAA
1309608 TAGGTAGCGCTTATATAATGTAA
1 TAGGTAGCGCTTATATAATGTAA
*
1309631 TAGGTATCGCTTATATAAT
1 TAGGTAGCGCTTATATAAT
1309650 AAAATATACA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.34, C:0.09, G:0.20, T:0.37
Consensus pattern (23 bp):
TAGGTAGCGCTTATATAATGTAA
Found at i:1310161 original size:200 final size:196
Alignment explanation
Indices: 1309733--1310256 Score: 685
Period size: 200 Copynumber: 2.6 Consensus size: 196
1309723 GCACTTATAT
* *
1309733 TGACATATTTTCTAAGT-AAACCGGTATATTTATACCGGTAACATTGCAAATTTACCTATTACAT
1 TGACATATTTTCTAA-TAAAACCGGTATATTTATACAGGT-ACATTGTAAATTTACCTATTACAT
* *
1309797 TATAATTATCGGTTTCGATGTTTTTTGGATCGATACAATTT--TAAATGTATCGACACTTTATGC
64 TATAATTATCGGTTTCGATG-TTTTGGGATCGATAC-TTTTAATAAATGTATCGACACTTTATGC
* * * **
1309860 ATGCACCTCATTGGGCATTCATTCTGGGAAAAAGTATCGACACAAACTTAAAAAGTGTCGATACA
127 ATGCACCCCATTGGACATTCATTATGACAAAAAGTATCGACACAAACTTAAAAAGTGTCGATACA
*
1309925 TTATT
192 TTATC
* * * *
1309930 TAGACATATTTTCTCATAAAACCGGTATATTTCTATCGGGTACATTGTAAATTTACCTATCACAT
1 T-GACATATTTTCTAATAAAACCGGTATATTTATA-CAGGTACATTGTAAATTTACCTATTACAT
* *
1309995 TGTAATTATCGGTTTCGATGTTTGTGGGATCGATACTTTTAATAAATGTATCGACACTTTATGCG
64 TATAATTATCGGTTTCGATGTTT-TGGGATCGATACTTTTAATAAATGTATCGACACTTTATGCA
* * * ** *
1310060 TGCACCCCGTTTGACATTCATTATAGACAAAAAGTATCGACACAAATTTAAATGGTGTCGATACT
128 TGCACCCCATTGGACATTCATTAT-GACAAAAAGTATCGACACAAACTTAAAAAGTGTCGATACA
1310125 TTATGC
192 TTAT-C
* * * *
1310131 TGACCTATTTTCTTATAAAACCGATATATTTATACCAGTTACATTGTAAATTTACCTATTACATT
1 TGACATATTTTCTAATAAAACCGGTATATTTATA-CAGGTACATTGTAAATTTACCTATTACATT
*
1310196 ATAATTATCGGTTTCGATGTTATTGGGATCGATACTTTTAATAAATGTATCGACAGTTTAT
65 ATAATTATCGGTTTCGATGTT-TTGGGATCGATACTTTTAATAAATGTATCGACACTTTAT
1310257 ATTATGGACA
Statistics
Matches: 287, Mismatches: 31, Indels: 15
0.86 0.09 0.05
Matches are distributed among these distances:
197 8 0.03
198 81 0.28
199 45 0.16
200 151 0.53
201 2 0.01
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.38
Consensus pattern (196 bp):
TGACATATTTTCTAATAAAACCGGTATATTTATACAGGTACATTGTAAATTTACCTATTACATTA
TAATTATCGGTTTCGATGTTTTGGGATCGATACTTTTAATAAATGTATCGACACTTTATGCATGC
ACCCCATTGGACATTCATTATGACAAAAAGTATCGACACAAACTTAAAAAGTGTCGATACATTAT
C
Found at i:1310388 original size:177 final size:178
Alignment explanation
Indices: 1310079--1310427 Score: 488
Period size: 177 Copynumber: 2.0 Consensus size: 178
1310069 TTTGACATTC
* ** * *
1310079 ATTATAGACAAAAAGTATCGACACAAATTTAAATGGTGTCGATACTTTATGCTGACCTATTTTCT
1 ATTATAGACAAAAAGTATCGACACAAATTAAAAAAGTGTCGATACATTATGCTGACATATTTTCT
*
1310144 TATAAAACCGATATATTTATACCAGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTT
66 AATAAAACCGATATATTTATACCAGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTT
1310209 TCGATGTTATTGGGATCGATACTTTTA-ATAAATGTATCGACAGTTTAT
131 TCGATGTTATTGGGATCGATACTTTTAGA-AAATGTATCGACAGTTTAT
* * ** * *
1310257 ATTATGGACAATAAGTATCGGTACAAATTAAAAAAGTGTCGATACATTATGTTGACATGTTTTCT
1 ATTATAGACAAAAAGTATCGACACAAATTAAAAAAGTGTCGATACATTATGCTGACATATTTTCT
* * * * *
1310322 AAT-TAACC-AGTATATTTATATCGGTTACATTGTTAATTTACCTATTACATTATAATTATTGGT
66 AATAAAACCGA-TATATTTATACCAGTTACATTGTAAATTTACCTATTACATTATAATTATCGGT
* *
1310385 TTCGATGTTTTTGGGGTCGATACTTTTAGAAAATGTATCGACA
130 TTCGATGTTATTGGGATCGATACTTTTAGAAAATGTATCGACA
1310428 CCTATTTAGC
Statistics
Matches: 150, Mismatches: 19, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
176 1 0.01
177 92 0.61
178 57 0.38
ACGTcount: A:0.34, C:0.12, G:0.14, T:0.40
Consensus pattern (178 bp):
ATTATAGACAAAAAGTATCGACACAAATTAAAAAAGTGTCGATACATTATGCTGACATATTTTCT
AATAAAACCGATATATTTATACCAGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTT
TCGATGTTATTGGGATCGATACTTTTAGAAAATGTATCGACAGTTTAT
Found at i:1312886 original size:19 final size:19
Alignment explanation
Indices: 1312841--1312889 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
1312831 TTACATTCAC
1312841 ATACAAAATTATAAATCGT
1 ATACAAAATTATAAATCGT
** *
1312860 ATGTAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
1312879 ATACAAAATTA
1 ATACAAAATTA
1312890 ACCCTACATT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.53, C:0.08, G:0.04, T:0.35
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:1315185 original size:199 final size:197
Alignment explanation
Indices: 1314487--1315454 Score: 1168
Period size: 199 Copynumber: 4.9 Consensus size: 197
1314477 CGCGTTATTT
* * * * **
1314487 AAAAAGTATCGACACAAATTTAAAAATATCGATACATTATGTTGACCTATTCTCTCATAAAATTG
1 AAAAAGTATCGACACAAATTCAAAAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAACCG
* * *
1314552 GTATATTTATACCGGTTACACTGTAAATTTACCTATTACGTTATAATTATTGGTTTCGATGTTTT
66 GTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTT
** * * * *
1314617 TGGGATCGATACAATTTAAAATGTATCGACACTTTCTGCCTGCACCCCGTTTGGCATTCATTATG
131 TGGGATCGATACTTTTTAAAATGTATCGACACTTTATGCGTGCA-CCAGTTTGGCATTCATTTTG
1314682 GAC
195 GAC
* * * ** *
1314685 AAAATGTATCGACACAAA-TCTAAAACGTGTTGATAAATTATGTTCACCTATTTTCTCATAAAAC
1 AAAAAGTATCGACACAAATTC-AAAA-GTGTCGATACATTATGTAGACCTATTCTCTCATAAAAC
** * * *
1314749 TAGTAAATTTATACTGGTTACATTGTAAATTTACCTATTACATTATAATAATCGGTTTCGATGTT
64 CGGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTT
* **
1314814 TTTGGGATCGATACTTTTTAAAAATATATCGACACTTTATGCGTGCAACCCTTTTGGCATTCATT
129 TTTGGGATCGATACTTTTT-AAAATGTATCGACACTTTATGCGTGC-ACCAGTTTGGCATTCATT
*
1314879 TTAGAC
192 TTGGAC
*
1314885 AAAAAAGTATCGACACAAATTCTATAAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAAC
1 -AAAAAGTATCGACACAAATTC-AAAAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAAC
* * * * * **
1314950 CGGTATAGTTATACTGGTTATATTATAAATTTACCTATTACATTATAATTATGGGTTTTAATGTT
64 CGGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTT
* * * * *
1315015 TCTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTTCACCATTTTGGGATTCATTC
129 TTTGGGATCGATACTTTTTA-AAATGTATCGACACTTTATGCGTGCACCAGTTTGGCATTCATTT
1315080 TGGAC
193 TGGAC
* * *
1315085 AAAAGGTATCGACAAAAAATTCAAAAGTGTCGACACATTATGTAGACCTATTCTCAT-ATAAAAC
1 AAAAAGTATCGAC-ACAAATTCAAAAGTGTCGATACATTATGTAGACCTATTCTC-TCATAAAAC
** * * ** * *
1315149 CATTATATCTATACCGGTTATATTACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTT
64 CGGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTT
* * * *
1315214 TTTGGGATCGATACTTTTTATAAATATATCGATACTGTATGGGTGCACCACGTTTGGCATTCATT
129 TTTGGGATCGATACTTTTTA-AAATGTATCGACACTTTATGCGTGCACCA-GTTTGGCATTCATT
* *
1315279 TTGAAT
192 TTGGAC
* * * *
1315285 AAAAAGTATCGACACAAATTCCATAAGTGTCGATACATTATGTATATCTATTTTCTCA-ATAAAC
1 AAAAAGTATCGACACAAATT-CAAAAGTGTCGATACATTATGTAGACCTATTCTCTCATA-AAAC
* * *
1315349 CGGTATATTTATACCAGTTACATTGTAAATTTACCTATTACATTAAAATTTTCGGTTTCGATGTT
64 CGGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTT
*
1315414 TTTGGGACCGATACTTTTTAAACATGTATCGACACTTTATG
129 TTTGGGATCGATACTTTTTAAA-ATGTATCGACACTTTATG
1315455 GGAAACTTTA
Statistics
Matches: 662, Mismatches: 94, Indels: 26
0.85 0.12 0.03
Matches are distributed among these distances:
197 1 0.00
198 21 0.03
199 266 0.40
200 221 0.33
201 147 0.22
202 6 0.01
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.38
Consensus pattern (197 bp):
AAAAAGTATCGACACAAATTCAAAAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAACCG
GTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTT
TGGGATCGATACTTTTTAAAATGTATCGACACTTTATGCGTGCACCAGTTTGGCATTCATTTTGG
AC
Found at i:1315272 original size:400 final size:399
Alignment explanation
Indices: 1314486--1315454 Score: 1279
Period size: 400 Copynumber: 2.4 Consensus size: 399
1314476 ACGCGTTATT
* * * * *
1314486 TAAAAAGTATCGACACAAATT-TAAAAATATCGATACATTATGTTGACCTATTCTCTCATAAAAT
1 TAAAAAGTATCGACACAAATTCTATAAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAAC
* * * *
1314550 TGGTATATTTATACCGGTTACACTGTAAATTTACCTATTACGTTATAATTATTGGTTTCGATGTT
66 CGGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTT
** * *
1314615 TTTGGGATCGATACAATTTAAAATGTATCGACACTTTCTGCCTGCACCCCGTTTGGCATTCATTA
131 TTTGGGATCGATACTTTTTAAAATGTATCGACACTTTATGCCTGCACCCAGTTTGGCATTCATTA
* * * * * *
1314680 TGGACAAAATGTATCGACACAAATCTAAAACGTGTTGATAAATTATGTTCACCTATTTTCTCATA
196 TGGACAAAAGGTATCGACAAAAATCTAAAACGTGTCGACAAATTATGTACACCTATTCTCTCATA
* * * ** *
1314745 AAACTAGTAAATTTATACTGGTTACATTGTAAATTTACCTATTACATTATAATAATCGGTTTCGA
261 AAACCAGTAAATCTATACCGGTTACATTACAAAATTACCTATTACATTATAATAATCGGTTTCGA
* *
1314810 TGTTTTTGGGATCGATACTTTTTAAAAATATATCGACACTTTATGCGTGCAACCCTTTTGGCATT
326 TGTTTTTGGGATCGATACTTTTTAAAAATATATCGACACTGTATGCGTGCAACCCGTTTGGCATT
1314875 CATTTTAGACA
391 CATTTT-GA-A
1314886 -AAAAAGTATCGACACAAATTCTATAAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAAC
1 TAAAAAGTATCGACACAAATTCTATAAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAAC
* * * * * **
1314950 CGGTATAGTTATACTGGTTATATTATAAATTTACCTATTACATTATAATTATGGGTTTTAATGTT
66 CGGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTT
* * * * *
1315015 TCTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTTCA-CCATTTTGGGATTCATT
131 TTTGGGATCGATACTTTTTA-AAATGTATCGACACTTTATGCCTGCACCCAGTTTGGCATTCATT
* * *
1315079 CTGGACAAAAGGTATCGACAAAAAAT-TCAAAA-GTGTCGACACATTATGTAGACCTATTCTCAT
195 ATGGACAAAAGGTATCGAC-AAAAATCT-AAAACGTGTCGACAAATTATGTACACCTATTCTC-T
* * * * *
1315142 -ATAAAACCATTATATCTATACCGGTTATATTACAAAATTACCTATTACATTATAATTATGGGTT
257 CATAAAACCAGTAAATCTATACCGGTTACATTACAAAATTACCTATTACATTATAATAATCGGTT
* * *
1315206 TCGATGTTTTTGGGATCGATACTTTTTATAAATATATCGATACTGTATGGGTGC-ACCACGTTTG
322 TCGATGTTTTTGGGATCGATACTTTTTAAAAATATATCGACACTGTATGCGTGCAACC-CGTTTG
1315270 GCATTCATTTTGAA
386 GCATTCATTTTGAA
* * * *
1315284 TAAAAAGTATCGACACAAATTCCATAAGTGTCGATACATTATGTATATCTATTTTCTCA-ATAAA
1 TAAAAAGTATCGACACAAATTCTATAAGTGTCGATACATTATGTAGACCTATTCTCTCATA-AAA
* * *
1315348 CCGGTATATTTATACCAGTTACATTGTAAATTTACCTATTACATTAAAATTTTCGGTTTCGATGT
65 CCGGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGT
*
1315413 TTTTGGGACCGATACTTTTTAAACATGTATCGACACTTTATG
130 TTTTGGGATCGATACTTTTTAAA-ATGTATCGACACTTTATG
1315455 GGAAACTTTA
Statistics
Matches: 495, Mismatches: 65, Indels: 19
0.85 0.11 0.03
Matches are distributed among these distances:
398 4 0.01
399 174 0.35
400 284 0.57
401 33 0.07
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.38
Consensus pattern (399 bp):
TAAAAAGTATCGACACAAATTCTATAAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAAC
CGGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTT
TTTGGGATCGATACTTTTTAAAATGTATCGACACTTTATGCCTGCACCCAGTTTGGCATTCATTA
TGGACAAAAGGTATCGACAAAAATCTAAAACGTGTCGACAAATTATGTACACCTATTCTCTCATA
AAACCAGTAAATCTATACCGGTTACATTACAAAATTACCTATTACATTATAATAATCGGTTTCGA
TGTTTTTGGGATCGATACTTTTTAAAAATATATCGACACTGTATGCGTGCAACCCGTTTGGCATT
CATTTTGAA
Found at i:1316543 original size:17 final size:17
Alignment explanation
Indices: 1316500--1316532 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
1316490 TTACCGGATT
1316500 ATAAATCATTTTTTCCG
1 ATAAATCATTTTTTCCG
1316517 ATAAATCATTTTTTCC
1 ATAAATCATTTTTTCC
1316533 AGTGAATCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.30, C:0.18, G:0.03, T:0.48
Consensus pattern (17 bp):
ATAAATCATTTTTTCCG
Found at i:1316835 original size:18 final size:18
Alignment explanation
Indices: 1316812--1316860 Score: 80
Period size: 18 Copynumber: 2.7 Consensus size: 18
1316802 GTAATCAAGT
1316812 TTGAATGTTAACATTTAA
1 TTGAATGTTAACATTTAA
1316830 TTGAATGTTAACATTTAA
1 TTGAATGTTAACATTTAA
* *
1316848 TTGTATATTAACA
1 TTGAATGTTAACA
1316861 ATTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.39, C:0.06, G:0.10, T:0.45
Consensus pattern (18 bp):
TTGAATGTTAACATTTAA
Found at i:1317200 original size:12 final size:12
Alignment explanation
Indices: 1317185--1317227 Score: 77
Period size: 12 Copynumber: 3.6 Consensus size: 12
1317175 ATCATAATCT
1317185 TCTTCATCGTCA
1 TCTTCATCGTCA
1317197 TCTTCATCGTCA
1 TCTTCATCGTCA
*
1317209 TCTTCATCTTCA
1 TCTTCATCGTCA
1317221 TCTTCAT
1 TCTTCAT
1317228 TGACCTCTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.16, C:0.33, G:0.05, T:0.47
Consensus pattern (12 bp):
TCTTCATCGTCA
Found at i:1317209 original size:18 final size:18
Alignment explanation
Indices: 1317188--1317227 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
1317178 ATAATCTTCT
1317188 TCATCGTCATCTTCATCG
1 TCATCGTCATCTTCATCG
* *
1317206 TCATCTTCATCTTCATCT
1 TCATCGTCATCTTCATCG
1317224 TCAT
1 TCAT
1317228 TGACCTCTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.17, C:0.33, G:0.05, T:0.45
Consensus pattern (18 bp):
TCATCGTCATCTTCATCG
Found at i:1319256 original size:200 final size:197
Alignment explanation
Indices: 1318700--1319456 Score: 876
Period size: 201 Copynumber: 3.8 Consensus size: 197
1318690 TTTTAAAATG
* * * * * * * *
1318700 GTATCGACACAAATTTAACAATTGTCGATACTTTATGCT-GGCCTGTTTTCTCATAAAACTGGTA
1 GTATCGACACAAATTTCA-AAGTGTCGATACATTATG-TAGACCTATTCTCACATAAAACCGGTA
* * * *
1318764 TATTTATACCGGTTACATTGGAAATTTACCTATTACATTGTAATTA-GTGGTTTCGATGTTTTTG
64 TATTTATACCGGTTACATTGAAAAATTACCTATTACATTATAATTATG-GGTTTCGATGTTTCTG
* *
1318828 GGATCGACACTTTTTAAAAATGTATTGACACTTTATGCGTTCACCATTTTGGGCATTCATTTTGG
128 GGATCGACACTTTTTAAAAATGTATCGACACTTTATGCG-TCACCATTTTGGG-ATTCATTCTGG
1318893 ACAAAAA
191 ACAAAAA
* * ** * * * *
1318900 GTATTGATACCGATTTCAAATGTGTCGATACAATATGTAGACATATTCTCACATAAAATCAGTAT
1 GTATCGACACAAATTTCAAA-GTGTCGATACATTATGTAGACCTATTCTCACATAAAACCGGTAT
* * *
1318965 ATTTATATCGGTTACATTAGAAAAAATACCTATTACATTATAATTATGGGTTTCGATGTCTCTGG
65 ATTTATACCGGTTACATT-GAAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTCTGG
* * ** * * *
1319030 GATCGACACTTTTAAAAAATGTATCGACATTTTATTTGTGCACCCTTTTGGGAATCCCTTCTGGA
129 GATCGACACTTTTTAAAAATGTATCGACACTTTATGCGT-CACCATTTTGGG-ATTCATTCTGGA
*
1319095 CAAACA
192 CAAAAA
* *
1319101 GTATCGACACAAATTCCATAAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAACCGGTAT
1 GTATCGACACAAATTTCA-AAGTGTCGATACATTATGTAGACCTATTCTCACATAAAACCGGTAT
* ** * *
1319166 AGTTT-TACCGATTATGTTGAAAAATTACCTATTACATTATAATTATGGGTTTCGATATTTCTAG
65 A-TTTATACCGGTTACATTGAAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTCTGG
* *
1319230 GATCGATACTTTTTATAAATGTATCGACACTTTATGCGCTCACCATTTTGGGATTCATTCTGGAC
129 GATCGACACTTTTTAAAAATGTATCGACACTTTATGCG-TCACCATTTTGGGATTCATTCTGGAC
1319295 AAAAA
193 AAAAA
* * * *
1319300 GTATAGACACAAATTTAAAAGTGTTGATACATTATGTAGACCTATTCTCACATAAAATCGGTATA
1 GTATCGACACAAATTTCAAAGTGTCGATACATTATGTAGACCTATTCTCACATAAAACCGGTATA
* * ** *
1319365 TTTATACCTGTTATATT-ACAAAATTACCTATTACATTATAATTATGGGTTTTAAT-TTTTTGGG
66 TTTATACCGGTTACATTGA-AAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTCTGGG
* * *
1319428 ATCGATACTTTTTATAAATGTATCAACAC
130 ATCGACACTTTTTAAAAATGTATCGACAC
1319457 ATCTGCTTAC
Statistics
Matches: 471, Mismatches: 76, Indels: 23
0.83 0.13 0.04
Matches are distributed among these distances:
197 38 0.08
198 88 0.19
199 33 0.07
200 147 0.31
201 159 0.34
202 6 0.01
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.38
Consensus pattern (197 bp):
GTATCGACACAAATTTCAAAGTGTCGATACATTATGTAGACCTATTCTCACATAAAACCGGTATA
TTTATACCGGTTACATTGAAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTCTGGGA
TCGACACTTTTTAAAAATGTATCGACACTTTATGCGTCACCATTTTGGGATTCATTCTGGACAAA
AA
Found at i:1322390 original size:182 final size:182
Alignment explanation
Indices: 1321997--1322661 Score: 860
Period size: 182 Copynumber: 3.7 Consensus size: 182
1321987 CGTACTTAAT
* * * * * * * * *
1321997 AAGTATCGACACTTTAAATATATCCGATAGCGCTTTACCAGTTTTGTCATTTTGAGACCGGTTTT
1 AAGTATCGACACTTTCAATATATCCGGTCGCTCTATACCGGTTTTGTCCTTTAGAGACCGATTTT
* * * * *
1322062 CTCAT-TTTTTACTTGTTATATCGTTGTGGACCGATATATTGTTATAAAGTATTGACACTTTAT-
66 GTCATATTTTTACATGTTATATCGTTGTGGATCGATACATTGTTATAAAGTATCGACACTTTATG
* *
1322125 AGGTGCTAAAACTGCTTCTC-TTTAAATTCACAAATTGTCGATACTTATATTA
131 AGCT-CTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATACTTATATTA
** **
1322177 AAGTATCGACAC-TTCAAATATATATGGTCGCTCTATACCGGTTTTGTCCTTTAGAGATTGATTT
1 AAGTATCGACACTTTC-AATATATCCGGTCGCTCTATACCGGTTTTGTCCTTTAGAGACCGATTT
* *
1322241 TATCATATTTTTACATGTTATATCGTTTTGGATCGATACATTGTTATAAAGTATCGACACTTTAT
65 TGTCATATTTTTACATGTTATATCGTTGTGGATCGATACATTGTTATAAAGTATCGACACTTTAT
*
1322306 GAGCTCTAAAACTGCTTATCTTTTAAATTCACAAAGTGTCGATACTTATATTA
130 GAGCTCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATACTTATATTA
* *
1322359 AAGTATCGACACTTTCAATATATCCGGTCGCTCTATACCGATTTTGTCCTTTAGAGACCGGTTTT
1 AAGTATCGACACTTTCAATATATCCGGTCGCTCTATACCGGTTTTGTCCTTTAGAGACCGATTTT
*
1322424 GTCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTGTTATAAAGTATCGACACTTTATG
66 GTCATATTTTTACATGTTATATCGTTGTGGATCGATACATTGTTATAAAGTATCGACACTTTATG
* * * **
1322489 -GACGCTAAAATTACTTCTCTTTTAAATTCACAAAGTGTTAATACTTATATTA
131 AG-CTCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATACTTATATTA
* * * *
1322541 AAGTATCGACACTTTCAATATATCTGGTACCGCT-T-TACCGGTTTTGTCTTTTTGATACCGATT
1 AAGTATCGACACTTTCAATATATCCGGT--CGCTCTATACCGGTTTTGTCCTTTAGAGACCGATT
* * * * *
1322604 TTGTCATATTTTTACATGTTATATTGATGTGAATAGATACAATT-TTATAAATTATCGA
64 TTGTCATATTTTTACATGTTATATCGTTGTGGATCGATAC-ATTGTTATAAAGTATCGA
1322662 TATAAACCAC
Statistics
Matches: 427, Mismatches: 49, Indels: 16
0.87 0.10 0.03
Matches are distributed among these distances:
179 2 0.00
180 53 0.12
181 68 0.16
182 293 0.69
183 7 0.02
184 4 0.01
ACGTcount: A:0.28, C:0.16, G:0.14, T:0.42
Consensus pattern (182 bp):
AAGTATCGACACTTTCAATATATCCGGTCGCTCTATACCGGTTTTGTCCTTTAGAGACCGATTTT
GTCATATTTTTACATGTTATATCGTTGTGGATCGATACATTGTTATAAAGTATCGACACTTTATG
AGCTCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATACTTATATTA
Found at i:1323753 original size:21 final size:21
Alignment explanation
Indices: 1323723--1323772 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
1323713 TTTAGAATTA
1323723 AAGACATACCAATTCCTAACT
1 AAGACATACCAATTCCTAACT
*
1323744 AAGACGTACCAATTCCTAACT
1 AAGACATACCAATTCCTAACT
*
1323765 AACACATA
1 AAGACATA
1323773 TCAAGACATC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.44, C:0.28, G:0.06, T:0.22
Consensus pattern (21 bp):
AAGACATACCAATTCCTAACT
Found at i:1326922 original size:20 final size:22
Alignment explanation
Indices: 1326877--1326934 Score: 84
Period size: 20 Copynumber: 2.6 Consensus size: 22
1326867 GCATGGGTAG
1326877 TGCATCGATGCACGTGTTAAAGAA
1 TGCATCGATGCAC-TGTT-AAGAA
1326901 TGCATCGATGCACTG-T-AGAA
1 TGCATCGATGCACTGTTAAGAA
1326921 TGCATCGATGCACT
1 TGCATCGATGCACT
1326935 TCAAGGGGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 18 0.53
22 1 0.03
23 2 0.06
24 13 0.38
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (22 bp):
TGCATCGATGCACTGTTAAGAA
Found at i:1327677 original size:2 final size:2
Alignment explanation
Indices: 1327670--1327697 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1327660 GATTAAATTA
1327670 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
1327698 GAATTATGTA
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:1331926 original size:65 final size:64
Alignment explanation
Indices: 1331788--1331950 Score: 172
Period size: 65 Copynumber: 2.5 Consensus size: 64
1331778 AATTGTTCAG
* * * * *
1331788 AGTGTATCGATTCACA-GGAAGTGCATCGATGCA-CCCATTAAAAATGGAAACATCGAATGTAGT
1 AGTGTATCGA-T-ACATGGGAGTGCATCGATGCACCCCATTAAAAATGAAAACATCAAAGGTAAT
1331851 T
64 T
* *
1331852 AGTGCATCGATACATTGGGAGTGCATCGATGCACCCCCCTT-AAAATGAAAACATCAAAGGTAAA
1 AGTGTATCGATACA-TGGGAGTGCATCGATGCA-CCCCATTAAAAATGAAAACATCAAAGGT-AA
1331916 TT
63 TT
*
1331918 -GTGTATCGATGCATGGGTAGTGCATCGATGCAC
1 AGTGTATCGATACATGGG-AGTGCATCGATGCAC
1331951 GTGTTGAAGA
Statistics
Matches: 84, Mismatches: 9, Indels: 12
0.80 0.09 0.11
Matches are distributed among these distances:
62 3 0.04
63 1 0.01
64 30 0.36
65 42 0.50
66 8 0.10
ACGTcount: A:0.33, C:0.19, G:0.23, T:0.25
Consensus pattern (64 bp):
AGTGTATCGATACATGGGAGTGCATCGATGCACCCCATTAAAAATGAAAACATCAAAGGTAATT
Found at i:1331983 original size:20 final size:22
Alignment explanation
Indices: 1331938--1331995 Score: 84
Period size: 20 Copynumber: 2.6 Consensus size: 22
1331928 GCATGGGTAG
1331938 TGCATCGATGCACGTGTTGAAGAA
1 TGCATCGATGCAC-TGTT-AAGAA
1331962 TGCATCGATGCACTG-T-AGAA
1 TGCATCGATGCACTGTTAAGAA
1331982 TGCATCGATGCACT
1 TGCATCGATGCACT
1331996 TCAAGGGGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 18 0.53
22 1 0.03
23 2 0.06
24 13 0.38
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.26
Consensus pattern (22 bp):
TGCATCGATGCACTGTTAAGAA
Found at i:1335438 original size:23 final size:23
Alignment explanation
Indices: 1335373--1335438 Score: 69
Period size: 23 Copynumber: 2.9 Consensus size: 23
1335363 TTTTATATGG
* * *
1335373 CACTTCGGTGCAATCCTACGTGG
1 CACTTCGGTGCAATTCTACGCGA
* * *
1335396 CACTACGTTGCATTTCTACGCGA
1 CACTTCGGTGCAATTCTACGCGA
*
1335419 CACTTCGGTGCAATTATACG
1 CACTTCGGTGCAATTCTACG
1335439 AGCTGTGGTG
Statistics
Matches: 33, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.21, C:0.29, G:0.21, T:0.29
Consensus pattern (23 bp):
CACTTCGGTGCAATTCTACGCGA
Found at i:1338469 original size:63 final size:64
Alignment explanation
Indices: 1338391--1338514 Score: 214
Period size: 63 Copynumber: 2.0 Consensus size: 64
1338381 TCGGATTTGA
*
1338391 GCAAAAATTCCAGAATGAAAAGAGGGTACAGATA-CCCCCAGGGGTATCCATACCCCCTGGAAG
1 GCAAAAATTCCAGAATGAAAAGAGGGTACAGATACCCCCCAGGGGTACCCATACCCCCTGGAAG
* *
1338454 GCAAAAATTCCAGAATGCAAAGAGGGTACCGATACCCCCCAGGGGTACCCATACCCCCTGG
1 GCAAAAATTCCAGAATGAAAAGAGGGTACAGATACCCCCCAGGGGTACCCATACCCCCTGG
1338515 CTGCAACAAC
Statistics
Matches: 57, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
63 32 0.56
64 25 0.44
ACGTcount: A:0.34, C:0.29, G:0.23, T:0.14
Consensus pattern (64 bp):
GCAAAAATTCCAGAATGAAAAGAGGGTACAGATACCCCCCAGGGGTACCCATACCCCCTGGAAG
Found at i:1339106 original size:15 final size:15
Alignment explanation
Indices: 1339086--1339161 Score: 70
Period size: 15 Copynumber: 5.3 Consensus size: 15
1339076 GTGAAGTTCT
1339086 AATTATTTAAATAAA
1 AATTATTTAAATAAA
*
1339101 AATTATTTATATAAA
1 AATTATTTAAATAAA
*
1339116 AATTCA--TCAAT-AA
1 AATT-ATTTAAATAAA
* *
1339129 TA-TAATTAAATAAA
1 AATTATTTAAATAAA
*
1339143 AATTATTTATATAAA
1 AATTATTTAAATAAA
1339158 AATT
1 AATT
1339162 CATCGATAAT
Statistics
Matches: 48, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
11 1 0.02
12 1 0.02
13 7 0.15
14 6 0.12
15 32 0.67
16 1 0.02
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.41
Consensus pattern (15 bp):
AATTATTTAAATAAA
Found at i:1339139 original size:42 final size:42
Alignment explanation
Indices: 1339092--1339174 Score: 157
Period size: 42 Copynumber: 2.0 Consensus size: 42
1339082 TTCTAATTAT
1339092 TTAAATAAAAATTATTTATATAAAAATTCATCAATAATATAA
1 TTAAATAAAAATTATTTATATAAAAATTCATCAATAATATAA
*
1339134 TTAAATAAAAATTATTTATATAAAAATTCATCGATAATATA
1 TTAAATAAAAATTATTTATATAAAAATTCATCAATAATATA
1339175 TTATTTTATT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.55, C:0.05, G:0.01, T:0.39
Consensus pattern (42 bp):
TTAAATAAAAATTATTTATATAAAAATTCATCAATAATATAA
Found at i:1339160 original size:21 final size:21
Alignment explanation
Indices: 1339094--1339160 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
1339084 CTAATTATTT
1339094 AAATAAAAATTATTTATATAA
1 AAATAAAAATTATTTATATAA
** * * *
1339115 AAATTCATCAATAATATA-AT-T
1 AAA-T-AAAAATTATTTATATAA
1339136 AAATAAAAATTATTTATATAA
1 AAATAAAAATTATTTATATAA
1339157 AAAT
1 AAAT
1339161 TCATCGATAA
Statistics
Matches: 32, Mismatches: 10, Indels: 8
0.64 0.20 0.16
Matches are distributed among these distances:
19 8 0.25
20 3 0.09
21 10 0.31
22 3 0.09
23 8 0.25
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (21 bp):
AAATAAAAATTATTTATATAA
Found at i:1343643 original size:20 final size:21
Alignment explanation
Indices: 1343615--1343655 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
1343605 TATATTTTAG
*
1343615 ATATTTTTTTA-TATTTAAAA
1 ATATATTTTTACTATTTAAAA
*
1343635 ATATATTTTTACTCTTTAAAA
1 ATATATTTTTACTATTTAAAA
1343656 TTTTATAAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.56
Consensus pattern (21 bp):
ATATATTTTTACTATTTAAAA
Found at i:1345516 original size:43 final size:42
Alignment explanation
Indices: 1345427--1345690 Score: 289
Period size: 43 Copynumber: 6.2 Consensus size: 42
1345417 AAAATCTTAG
* *
1345427 TTATAAAAGTAAAAAGTGAGATTGAAAAAAATTAGGGACCTAAA
1 TTATAAATGTAAAAAGTGAGATTG-AAAAAATTAGGG-CCTCAA
**
1345471 TTATAAATGTAAAAAGTGAGATTGAAAAAATTAAGGGTTTCAA
1 TTATAAATGTAAAAAGTGAGATTGAAAAAATT-AGGGCCTCAA
* * *
1345514 TTATAAAGGCAAAAAGTGATATTGAAAAAATTAGGAGCCTCAA
1 TTATAAATGTAAAAAGTGAGATTGAAAAAATTAGG-GCCTCAA
* * *
1345557 TTATAAATATTAAAAGTG-GAATTGAAAAAATTAGGGACTCAA
1 TTATAAATGTAAAAAGTGAG-ATTGAAAAAATTAGGGCCTCAA
* * * **
1345599 TTATAAATGTAAAAAGTGGGATTGAAAAAAATGGAGGCCTTTA
1 TTATAAATGTAAAAAGTGAGATTGAAAAAATTAG-GGCCTCAA
* * *
1345642 -TATAAAGGTAAAAAATGAGATTAAAAAAATTAGGGACCTCAA
1 TTATAAATGTAAAAAGTGAGATTGAAAAAATTAGGG-CCTCAA
1345684 TTATAAA
1 TTATAAA
1345691 GAGAAAAAAT
Statistics
Matches: 183, Mismatches: 30, Indels: 15
0.80 0.13 0.07
Matches are distributed among these distances:
41 2 0.01
42 68 0.37
43 86 0.47
44 27 0.15
ACGTcount: A:0.50, C:0.05, G:0.18, T:0.26
Consensus pattern (42 bp):
TTATAAATGTAAAAAGTGAGATTGAAAAAATTAGGGCCTCAA
Found at i:1345623 original size:85 final size:85
Alignment explanation
Indices: 1345427--1345699 Score: 302
Period size: 85 Copynumber: 3.2 Consensus size: 85
1345417 AAAATCTTAG
1345427 TTATAAAAGTAAAAAGTGAGATTGAAAAAAATTAGG-GACCTAAATTATAAATGTAAAAAGTGAG
1 TTATAAAAGTAAAAAGTGAGATTG-AAAAAATTAGGAG-CCTAAATTATAAATGTAAAAAGTGAG
**
1345491 ATTGAAAAAATTAAGGGTTTCAA
64 ATTGAAAAAATT-AGGGACTCAA
* * * * * *
1345514 TTATAAAGGCAAAAAGTGATATTGAAAAAATTAGGAGCCTCAATTATAAATATTAAAAGTG-GAA
1 TTATAAAAGTAAAAAGTGAGATTGAAAAAATTAGGAGCCTAAATTATAAATGTAAAAAGTGAG-A
1345578 TTGAAAAAATTAGGGACTCAA
65 TTGAAAAAATTAGGGACTCAA
* * * ** * *
1345599 TTATAAATGTAAAAAGTGGGATTGAAAAAAAT-GGAGGCCTTTA-TATAAAGGTAAAAAATGAGA
1 TTATAAAAGTAAAAAGTGAGATTGAAAAAATTAGGA-GCCTAAATTATAAATGTAAAAAGTGAGA
*
1345662 TTAAAAAAATTAGGGACCTCAA
65 TTGAAAAAATTAGGGA-CTCAA
*
1345684 TTATAAAGAGAAAAAA
1 TTATAAA-AGTAAAAA
1345700 TAAAATAAAA
Statistics
Matches: 158, Mismatches: 22, Indels: 13
0.82 0.11 0.07
Matches are distributed among these distances:
84 32 0.20
85 54 0.34
86 50 0.32
87 22 0.14
ACGTcount: A:0.51, C:0.05, G:0.18, T:0.25
Consensus pattern (85 bp):
TTATAAAAGTAAAAAGTGAGATTGAAAAAATTAGGAGCCTAAATTATAAATGTAAAAAGTGAGAT
TGAAAAAATTAGGGACTCAA
Found at i:1345691 original size:43 final size:43
Alignment explanation
Indices: 1345427--1345753 Score: 269
Period size: 43 Copynumber: 7.7 Consensus size: 43
1345417 AAAATCTTAG
* *
1345427 TTATAAAAGTAAAAAGTGAGATTGAAAAAAATTAGGGACCTAAA
1 TTATAAAGGTAAAAAGTGAGATT-AAAAAAATTAGGGACCTCAA
* * **
1345471 TTATAAATGTAAAAAGTGAGATTGAAAAAATTAAGGG-TTTCAA
1 TTATAAAGGTAAAAAGTGAGATTAAAAAAATT-AGGGACCTCAA
* * *
1345514 TTATAAAGGCAAAAAGTGATATTGAAAAAATTA-GGAGCCTCAA
1 TTATAAAGGTAAAAAGTGAGATTAAAAAAATTAGGGA-CCTCAA
** * *
1345557 TTATAAATATTAAAAGTG-GAATTGAAAAAATTAGGGA-CTCAA
1 TTATAAAGGTAAAAAGTGAG-ATTAAAAAAATTAGGGACCTCAA
* * * **
1345599 TTATAAATGTAAAAAGTGGGATTGAAAAAAA-T-GGAGGCCTTTA
1 TTATAAAGGTAAAAAGTGAGATT-AAAAAAATTAGG-GACCTCAA
*
1345642 -TATAAAGGTAAAAAATGAGATTAAAAAAATTAGGGACCTCAA
1 TTATAAAGGTAAAAAGTGAGATTAAAAAAATTAGGGACCTCAA
* * * * *
1345684 TTATAAAGAG-AAAAAAT-AAAAT-AAAAAATTAAGGATCTCAA
1 TTATAAAG-GTAAAAAGTGAGATTAAAAAAATTAGGGACCTCAA
** *
1345725 TTATAAAGAAAAAAAAGTAAGATTAAAAA
1 TTATAAAG-GTAAAAAGTGAGATTAAAAA
1345754 TTTTGGGTCT
Statistics
Matches: 232, Mismatches: 35, Indels: 32
0.78 0.12 0.11
Matches are distributed among these distances:
41 37 0.16
42 61 0.26
43 100 0.43
44 34 0.15
ACGTcount: A:0.54, C:0.05, G:0.17, T:0.25
Consensus pattern (43 bp):
TTATAAAGGTAAAAAGTGAGATTAAAAAAATTAGGGACCTCAA
Found at i:1345710 original size:41 final size:42
Alignment explanation
Indices: 1345665--1345755 Score: 130
Period size: 41 Copynumber: 2.2 Consensus size: 42
1345655 AATGAGATTA
* *
1345665 AAAAAATTAGGGACCTCAATTATAAAGAGAAAAAA-TAAAAT
1 AAAAAATTAAGGACCTCAATTATAAAGAAAAAAAAGTAAAAT
* *
1345706 AAAAAATTAAGGATCTCAATTATAAAGAAAAAAAAGTAAGAT
1 AAAAAATTAAGGACCTCAATTATAAAGAAAAAAAAGTAAAAT
*
1345748 TAAAAATT
1 AAAAAATT
1345756 TTGGGTCTTA
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
41 32 0.73
42 12 0.27
ACGTcount: A:0.62, C:0.05, G:0.11, T:0.22
Consensus pattern (42 bp):
AAAAAATTAAGGACCTCAATTATAAAGAAAAAAAAGTAAAAT
Found at i:1358444 original size:30 final size:30
Alignment explanation
Indices: 1358403--1358562 Score: 118
Period size: 29 Copynumber: 5.4 Consensus size: 30
1358393 GTAATTACGG
1358403 TTTTAG-CCTTTAAAGTTTATGTTTTATTA
1 TTTTAGTCCTTTAAAGTTTATGTTTTATTA
** *
1358432 TTTTAGTCCTTTAATTTTTAT-TTCTT-CTA
1 TTTTAGTCCTTTAAAGTTTATGTT-TTATTA
** *
1358461 TTTTAACCCTTT-AAGTTTTTGTTTTATCTA
1 TTTTAGTCCTTTAAAGTTTATGTTTTAT-TA
* * *
1358491 TTTTAGTCC-CT-AAGTTTCTGTTTTAGCTA
1 TTTTAGTCCTTTAAAGTTTATGTTTTA-TTA
* *
1358520 TTTCAGTCCTTTAAA-TTTTTGTTTATATTA
1 TTTTAGTCCTTTAAAGTTTATGTTT-TATTA
*
1358550 TTTTGGGTCCTTT
1 TTTT-AGTCCTTT
1358563 GAGTTTTTAT
Statistics
Matches: 101, Mismatches: 20, Indels: 18
0.73 0.14 0.13
Matches are distributed among these distances:
28 7 0.07
29 46 0.46
30 37 0.37
31 11 0.11
ACGTcount: A:0.19, C:0.12, G:0.09, T:0.59
Consensus pattern (30 bp):
TTTTAGTCCTTTAAAGTTTATGTTTTATTA
Found at i:1358521 original size:59 final size:58
Alignment explanation
Indices: 1358409--1358553 Score: 150
Period size: 59 Copynumber: 2.4 Consensus size: 58
1358399 ACGGTTTTAG
* * * * *
1358409 CCTTTAAAGTTTATGTTTTATTATTTTAGTCCTTTAATTTTTATTTCTTCTATTTTAAC
1 CCTTT-AAGTTTTTGTTTTATTATTTTAGTCCTCTAATTTCTATTTCTGCTATTTCAAC
* **
1358468 CCTTTAAGTTTTTGTTTTATCTATTTTAGTCC-CTAAGTTTCTGTTT-TAGCTATTTCAGT
1 CCTTTAAGTTTTTGTTTTAT-TATTTTAGTCCTCTAA-TTTCTATTTCT-GCTATTTCAAC
*
1358527 CCTTTAAATTTTTGTTTATATTATTTT
1 CCTTTAAGTTTTTGTTT-TATTATTTT
1358554 GGGTCCTTTG
Statistics
Matches: 73, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
58 18 0.25
59 52 0.71
60 3 0.04
ACGTcount: A:0.20, C:0.12, G:0.08, T:0.60
Consensus pattern (58 bp):
CCTTTAAGTTTTTGTTTTATTATTTTAGTCCTCTAATTTCTATTTCTGCTATTTCAAC
Found at i:1360474 original size:31 final size:30
Alignment explanation
Indices: 1360415--1360477 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 30
1360405 TTATCATTTG
*
1360415 TACTAACTCATTTTTCTCTGGTGTTTGTGT
1 TACTAACTCATTTTTCTCTGGTGCTTGTGT
*
1360445 TACTAACTCATTTTTTCTCAT-TTGCTTGTGT
1 TACTAACTCA-TTTTTCTC-TGGTGCTTGTGT
1360476 TA
1 TA
1360478 TTTTTCACAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
30 10 0.34
31 18 0.62
32 1 0.03
ACGTcount: A:0.16, C:0.17, G:0.13, T:0.54
Consensus pattern (30 bp):
TACTAACTCATTTTTCTCTGGTGCTTGTGT
Found at i:1360579 original size:22 final size:22
Alignment explanation
Indices: 1360547--1360604 Score: 100
Period size: 22 Copynumber: 2.7 Consensus size: 22
1360537 GGGATAATCA
1360547 AGAT-AAAATTTTCACAAGAAG
1 AGATAAAAATTTTCACAAGAAG
1360568 AGATAAAAATTTTCACAAGAAG
1 AGATAAAAATTTTCACAAGAAG
*
1360590 AGATAAAAGTTTTCA
1 AGATAAAAATTTTCA
1360605 ATCAAGCAGT
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
21 4 0.11
22 31 0.89
ACGTcount: A:0.52, C:0.09, G:0.14, T:0.26
Consensus pattern (22 bp):
AGATAAAAATTTTCACAAGAAG
Found at i:1364605 original size:24 final size:24
Alignment explanation
Indices: 1364577--1364624 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
1364567 TTGAATTTGA
1364577 TTCACTTGAAACAAAATTAATCTC
1 TTCACTTGAAACAAAATTAATCTC
1364601 TTCACTTGAAACAAAATTAATCTC
1 TTCACTTGAAACAAAATTAATCTC
1364625 ACTTGAGATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.42, C:0.21, G:0.04, T:0.33
Consensus pattern (24 bp):
TTCACTTGAAACAAAATTAATCTC
Found at i:1364628 original size:21 final size:23
Alignment explanation
Indices: 1364577--1364630 Score: 85
Period size: 24 Copynumber: 2.4 Consensus size: 23
1364567 TTGAATTTGA
1364577 TTCACTTGAAACAAAATTAATCTC
1 TTCACTTGAAACAAAATTAA-CTC
1364601 TTCACTTGAAACAAAATTAA-TC
1 TTCACTTGAAACAAAATTAACTC
1364623 -TCACTTGA
1 TTCACTTGA
1364631 GATTTTTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
21 8 0.27
22 2 0.07
24 20 0.67
ACGTcount: A:0.41, C:0.20, G:0.06, T:0.33
Consensus pattern (23 bp):
TTCACTTGAAACAAAATTAACTC
Found at i:1365205 original size:65 final size:68
Alignment explanation
Indices: 1365122--1365295 Score: 196
Period size: 65 Copynumber: 2.6 Consensus size: 68
1365112 AGACGTAATC
* * *
1365122 CATCTTTGAGTCTATTTCTTTGGAAACAAAATTTTGTCTCTATTAAGACAA-TTTCTTTTGAAA-
1 CATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTATTAAGACAATTTTCTCTTAAAAC
1365185 AAA
66 AAA
* * * * *
1365188 -ATCTTTGAGTCTGTTTCTATGAAAACAAAGTTTTGTCTCTTTTGAGACAATTTTCTCTTAAAAC
1 CATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTATTAAGACAATTTTCTCTTAAAAC
1365252 AAA
66 AAA
* *
1365255 CATCTTTGAGATC-GTTTCCATT-GAAACAAATTTTTTGTCTC
1 CATCTTTGAG-TCTGTTT-CTTTGGAAACAAA-ATTTTGTCTC
1365296 CCTTGAGGCA
Statistics
Matches: 90, Mismatches: 12, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
65 44 0.49
66 10 0.11
67 3 0.03
68 20 0.22
69 13 0.14
ACGTcount: A:0.30, C:0.16, G:0.11, T:0.43
Consensus pattern (68 bp):
CATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTATTAAGACAATTTTCTCTTAAAAC
AAA
Found at i:1365214 original size:119 final size:119
Alignment explanation
Indices: 1365003--1365226 Score: 285
Period size: 119 Copynumber: 1.9 Consensus size: 119
1364993 AACAACAAAT
* * * *
1365003 CATCTTTGAGTCATTTCTTTTAAAACAAATTTTGTCTCCCTTGAGACAGTTTCTAATGAAAAACC
1 CATCTTTGAGTCATTTCTTTGAAAACAAATTTTGTCTCCATTAAGACAATTTCTAATGAAAAA-C
*
1365068 AATCTTTGAGATTGTTTCCTTTGAAACAAA-TTTCGTCTCACTTAAGACGTAATC
65 AATCTTTGAGATTGTTTCCTATGAAACAAAGTTTCGTCTCACTTAAGACGTAATC
* * **
1365122 CATCTTTGAGTCTATTTCTTTGGAAACAAAATTTTGTCTCTATTAAGACAATTTCTTTTGAAAAA
1 CATCTTTGAGTC-ATTTCTTTGAAAAC-AAATTTTGTCTCCATTAAGACAATTTCTAATGAAAAA
*
1365187 -AATCTTTGAG-TCTGTTT-CTATGAAAACAAAGTTTTGTCTC
64 CAATCTTTGAGAT-TGTTTCCTATG-AAACAAAGTTTCGTCTC
1365227 TTTTGAGACA
Statistics
Matches: 90, Mismatches: 10, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
118 5 0.06
119 34 0.38
120 20 0.22
121 31 0.34
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.41
Consensus pattern (119 bp):
CATCTTTGAGTCATTTCTTTGAAAACAAATTTTGTCTCCATTAAGACAATTTCTAATGAAAAACA
ATCTTTGAGATTGTTTCCTATGAAACAAAGTTTCGTCTCACTTAAGACGTAATC
Found at i:1365282 original size:68 final size:66
Alignment explanation
Indices: 1365144--1365350 Score: 190
Period size: 69 Copynumber: 3.1 Consensus size: 66
1365134 TATTTCTTTG
* * * *
1365144 GAAACAAAATTTTGTCTCTATTAAGACAA-TTTCTTTTGAAA-AAAATCTTTGAGTCTGTTTCTA
1 GAAACAAAATTTTGTCTCTATTGAGACAATTTTC-TTTAAAACAAAATCTTTGAGTCGGTTTCCA
1365207 -T
65 TT
* *
1365208 GAAAACAAAGTTTTGTCTCTTTTGAGACAATTTTCTCTTAAAACAAACATCTTTGAGATC-GTTT
1 G-AAACAAAATTTTGTCTCTATTGAGACAATTTTCT-TTAAAACAAA-ATCTTTGAG-TCGGTTT
1365272 CCATT
62 CCATT
* ** * *
1365277 GAAACAAATTTTTTGTCTCCCTTGAGGCAGTTTT-TTTAGAAACACAAAATCTTTGAGTCGGTTT
1 GAAACAAA-ATTTTGTCTCTATTGAGACAATTTTCTTT--AAA-ACAAAATCTTTGAGTCGGTTT
*
1365341 CCCTT
62 CCATT
1365346 GAAAC
1 GAAAC
1365351 TATTATCCCT
Statistics
Matches: 120, Mismatches: 11, Indels: 19
0.80 0.07 0.13
Matches are distributed among these distances:
64 1 0.01
65 26 0.22
66 9 0.08
67 5 0.04
68 25 0.21
69 49 0.41
70 5 0.04
ACGTcount: A:0.31, C:0.16, G:0.13, T:0.39
Consensus pattern (66 bp):
GAAACAAAATTTTGTCTCTATTGAGACAATTTTCTTTAAAACAAAATCTTTGAGTCGGTTTCCAT
T
Found at i:1365705 original size:132 final size:133
Alignment explanation
Indices: 1365396--1365710 Score: 379
Period size: 134 Copynumber: 2.4 Consensus size: 133
1365386 GTAGGAACCT
* *
1365396 TGTCATCCCTTGACCAGA-TCTCCTCATCACCTAGGAGTCGTGTCACCCTTAGATAACCAGCTGT
1 TGTCATCCCCTGACCAGACT-TCCTCATCACGTAGGAGTCGTGTCACCC-TAGATAACCAGCTGT
* * * *
1365460 CCTCATCACGTAGGAACCGAGTTATCACCCTCCTTAAGGATGTCCAAAACTCTTCATCATGTATG
64 CCTCATCACGTAGGAACCGAGTTATCACCCTCCTTAAGGACGACCAAAACTCTTCAACACGTATG
*
1365525 AGCTG
129 AGCAG
* * * * * *
1365530 AGTCCTCCACTGACCAGACCTCCTCATCGCGTAGGAGCCGTGTCAACCCTAGATAACCAG-TCGT
1 TGTCATCCCCTGACCAGACTTCCTCATCACGTAGGAGTCGTGTC-ACCCTAGATAACCAGCT-GT
* * * **
1365594 CCTCATCGCGTAGGAACCGAGTTATCGCACTTCC-T-A-GACGACCCGAACTCTTCAACACGTAT
64 CCTCATCACGTAGGAACCGAGTTATCAC-CCTCCTTAAGGACGACCAAAACTCTTCAACACGTAT
1365656 GAGCAG
128 GAGCAG
*
1365662 TGTCATCCCCTGACCAGACTTCCTCATCACGTAGGAGTTGTGTCACCCT
1 TGTCATCCCCTGACCAGACTTCCTCATCACGTAGGAGTCGTGTCACCCT
1365711 TAGACGACCT
Statistics
Matches: 152, Mismatches: 25, Indels: 11
0.81 0.13 0.06
Matches are distributed among these distances:
131 5 0.03
132 62 0.41
133 2 0.01
134 75 0.49
135 8 0.05
ACGTcount: A:0.24, C:0.33, G:0.19, T:0.25
Consensus pattern (133 bp):
TGTCATCCCCTGACCAGACTTCCTCATCACGTAGGAGTCGTGTCACCCTAGATAACCAGCTGTCC
TCATCACGTAGGAACCGAGTTATCACCCTCCTTAAGGACGACCAAAACTCTTCAACACGTATGAG
CAG
Found at i:1365736 original size:83 final size:82
Alignment explanation
Indices: 1365628--1365838 Score: 287
Period size: 83 Copynumber: 2.5 Consensus size: 82
1365618 TCGCACTTCC
* ** *
1365628 TAGACGACCCGAACTCTTCAACACGTATGAGCAGTGTCATCCCCTGACCAGACTTCCTCATCACG
1 TAGACGA-CCGAACTCTTCATCACGTATGAGCAGTGTCATCCCCACACCAGACTTCCTCATCACA
1365693 TAGGAGTTGTGTCACCCT
65 TAGGAGTTGTGTCACCCT
* * * *
1365711 TAGACGACCTGAACTCATCATCACGTATGAACAGTTTCATCCCCACACCAGATTTCCTCATCACA
1 TAGACGACC-GAACTCTTCATCACGTATGAGCAGTGTCATCCCCACACCAGACTTCCTCATCACA
*
1365776 TAGGAGTTTTGTCACCCT
65 TAGGAGTTGTGTCACCCT
* * *
1365794 TAGTCGAACCGAACTCTTCATCAAGTATGAGCAGTGTCGTCCCCA
1 TAGACG-ACCGAACTCTTCATCACGTATGAGCAGTGTCATCCCCA
1365839 ACAACTAACA
Statistics
Matches: 111, Mismatches: 15, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
82 2 0.02
83 106 0.95
84 3 0.03
ACGTcount: A:0.26, C:0.31, G:0.17, T:0.26
Consensus pattern (82 bp):
TAGACGACCGAACTCTTCATCACGTATGAGCAGTGTCATCCCCACACCAGACTTCCTCATCACAT
AGGAGTTGTGTCACCCT
Found at i:1365997 original size:3 final size:3
Alignment explanation
Indices: 1365989--1366035 Score: 60
Period size: 3 Copynumber: 15.0 Consensus size: 3
1365979 GGGTTTTTTA
1365989 TAT TAT TATT TAT T-T TAAT TAT TAT TAT TATT TAT TAT TAT TAT TAT
1 TAT TAT TA-T TAT TAT T-AT TAT TAT TAT TA-T TAT TAT TAT TAT TAT
1366036 ATTTTTGCAG
Statistics
Matches: 40, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
2 2 0.05
3 30 0.75
4 8 0.20
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:1366011 original size:13 final size:12
Alignment explanation
Indices: 1365985--1366040 Score: 55
Period size: 13 Copynumber: 4.7 Consensus size: 12
1365975 GTCCGGGTTT
*
1365985 TTTATATTATTA
1 TTTATTTTATTA
1365997 TTTATTTTA--A
1 TTTATTTTATTA
1366007 -TTATTATTATTA
1 TTTATT-TTATTA
1366019 TTTATTATTATTA
1 TTTATT-TTATTA
1366032 TTATATTTT
1 TT-TATTTT
1366041 TGCAGGCCAG
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
9 5 0.13
10 4 0.11
12 9 0.24
13 16 0.42
14 4 0.11
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (12 bp):
TTTATTTTATTA
Found at i:1366011 original size:16 final size:16
Alignment explanation
Indices: 1365984--1366030 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
1365974 TGTCCGGGTT
1365984 TTTTATATTATTATTTA
1 TTTTA-ATTATTATTTA
1366001 TTTTAATTATTA-TTA
1 TTTTAATTATTATTTA
*
1366016 TTATTTATTATTATT
1 TT-TTAATTATTATT
1366031 ATTATATTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
15 5 0.19
16 16 0.59
17 6 0.22
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
TTTTAATTATTATTTA
Found at i:1366011 original size:19 final size:18
Alignment explanation
Indices: 1365984--1366040 Score: 75
Period size: 19 Copynumber: 3.2 Consensus size: 18
1365974 TGTCCGGGTT
1365984 TTTTA-TATTATTATTTA
1 TTTTATTATTATTATTTA
1366001 TTTTAATTATTATTA-TTA
1 TTTT-ATTATTATTATTTA
1366019 -TTTATTATTATTATTATA
1 TTTTATTATTATTATT-TA
1366037 TTTT
1 TTTT
1366041 TGCAGGCCAG
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
16 10 0.29
17 8 0.23
18 6 0.17
19 11 0.31
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (18 bp):
TTTTATTATTATTATTTA
Found at i:1366017 original size:22 final size:22
Alignment explanation
Indices: 1365989--1366035 Score: 78
Period size: 22 Copynumber: 2.1 Consensus size: 22
1365979 GGGTTTTTTA
1365989 TATTATTATTTATT-TTAATTAT
1 TATTATTATTTATTATT-ATTAT
1366011 TATTATTATTTATTATTATTAT
1 TATTATTATTTATTATTATTAT
1366033 TAT
1 TAT
1366036 ATTTTTGCAG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 22 0.92
23 2 0.08
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (22 bp):
TATTATTATTTATTATTATTAT
Found at i:1366031 original size:16 final size:16
Alignment explanation
Indices: 1365989--1366035 Score: 69
Period size: 16 Copynumber: 2.9 Consensus size: 16
1365979 GGGTTTTTTA
1365989 TATTATTATTTATT-TT
1 TATTATTA-TTATTATT
*
1366005 AATTATTATTATTATT
1 TATTATTATTATTATT
1366021 TATTATTATTATTAT
1 TATTATTATTATTAT
1366036 ATTTTTGCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
15 5 0.18
16 23 0.82
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TATTATTATTATTATT
Found at i:1367352 original size:30 final size:29
Alignment explanation
Indices: 1367311--1367478 Score: 137
Period size: 29 Copynumber: 5.7 Consensus size: 29
1367301 GCAATTACAG
*
1367311 TTTTAG-CCTTTAAAGTTTATGTTTTATTA
1 TTTTAGTCCTTT-AAGTTTTTGTTTTATTA
1367340 TTTTAGTCCTTTAA-TTTTTGTTTCT-TCTA
1 TTTTAGTCCTTTAAGTTTTTGTTT-TAT-TA
** * *
1367369 TTTTAACCCTTTATGTTTTCGTTTTATCTA
1 TTTTAGTCCTTTAAGTTTTTGTTTTAT-TA
* * * *
1367399 TTTTAGTCC-CTAAGTTTCTATTTTAGCTA
1 TTTTAGTCCTTTAAGTTTTTGTTTTA-TTA
*
1367428 TTTTAGTCCTTTAAATTTTTGTTTATATTA
1 TTTTAGTCCTTTAAGTTTTTGTTT-TATTA
* *
1367458 TTTTGGGTCCTTTGAGTTTTT
1 TTTT-AGTCCTTTAAGTTTTT
1367479 ATTCTTGCTA
Statistics
Matches: 109, Mismatches: 21, Indels: 16
0.75 0.14 0.11
Matches are distributed among these distances:
28 9 0.08
29 45 0.41
30 40 0.37
31 15 0.14
ACGTcount: A:0.18, C:0.12, G:0.10, T:0.60
Consensus pattern (29 bp):
TTTTAGTCCTTTAAGTTTTTGTTTTATTA
Found at i:1367460 original size:59 final size:57
Alignment explanation
Indices: 1367311--1367461 Score: 144
Period size: 59 Copynumber: 2.6 Consensus size: 57
1367301 GCAATTACAG
* * * * *
1367311 TTTTAGCCTTTAAAGTTTATGTTTTATTATTTTAGTCCTTTAATTTTTGTTTCTTCTA
1 TTTTAGCCTTTAAA-TTTTTGTTTTATTATTTTAGTCCTCTAATTTCTATTTCTGCTA
* ** *
1367369 TTTTAACCCTTTATGTTTTCGTTTTATCTATTTTAGTCC-CTAAGTTTCTATTT-TAGCTA
1 TTTT-AGCCTTTAAATTTTTGTTTTAT-TATTTTAGTCCTCTAA-TTTCTATTTCT-GCTA
1367428 TTTTAGTCCTTTAAATTTTTGTTTATATTATTTT
1 TTTTAG-CCTTTAAATTTTTGTTT-TATTATTTT
1367462 GGGTCCTTTG
Statistics
Matches: 74, Mismatches: 13, Indels: 11
0.76 0.13 0.11
Matches are distributed among these distances:
58 19 0.26
59 52 0.70
60 3 0.04
ACGTcount: A:0.19, C:0.12, G:0.08, T:0.61
Consensus pattern (57 bp):
TTTTAGCCTTTAAATTTTTGTTTTATTATTTTAGTCCTCTAATTTCTATTTCTGCTA
Found at i:1369382 original size:31 final size:30
Alignment explanation
Indices: 1369323--1369385 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 30
1369313 TTATCATTTG
*
1369323 TACTAACTCATTTTTCTCTGGTGTTTGTGT
1 TACTAACTCATTTTTCTCTGGTGCTTGTGT
*
1369353 TACTAACTCATTTTTTCTCAT-TTGCTTGTGT
1 TACTAACTCA-TTTTTCTC-TGGTGCTTGTGT
1369384 TA
1 TA
1369386 TTTTTCACAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
30 10 0.34
31 18 0.62
32 1 0.03
ACGTcount: A:0.16, C:0.17, G:0.13, T:0.54
Consensus pattern (30 bp):
TACTAACTCATTTTTCTCTGGTGCTTGTGT
Found at i:1373497 original size:24 final size:24
Alignment explanation
Indices: 1373469--1373516 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
1373459 TTGAATTTGA
1373469 TTCACTTGAAACAAAATTAATCTC
1 TTCACTTGAAACAAAATTAATCTC
1373493 TTCACTTGAAACAAAATTAATCTC
1 TTCACTTGAAACAAAATTAATCTC
1373517 ACTTGAGATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.42, C:0.21, G:0.04, T:0.33
Consensus pattern (24 bp):
TTCACTTGAAACAAAATTAATCTC
Found at i:1373520 original size:21 final size:23
Alignment explanation
Indices: 1373469--1373522 Score: 85
Period size: 24 Copynumber: 2.4 Consensus size: 23
1373459 TTGAATTTGA
1373469 TTCACTTGAAACAAAATTAATCTC
1 TTCACTTGAAACAAAATTAA-CTC
1373493 TTCACTTGAAACAAAATTAA-TC
1 TTCACTTGAAACAAAATTAACTC
1373515 -TCACTTGA
1 TTCACTTGA
1373523 GATTGTTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
21 8 0.27
22 2 0.07
24 20 0.67
ACGTcount: A:0.41, C:0.20, G:0.06, T:0.33
Consensus pattern (23 bp):
TTCACTTGAAACAAAATTAACTC
Found at i:1374106 original size:119 final size:119
Alignment explanation
Indices: 1373895--1374118 Score: 267
Period size: 119 Copynumber: 1.9 Consensus size: 119
1373885 AACAACAAAT
* * * * *
1373895 CATCTTTGAGTCGTTTCTTTTAAAACAAATTTTGTCTCTTTTGAGACAGGTTCTAATGAAAAACC
1 CATCTTTGAGTCATTTCTTTGAAAACAAATTTTGTCTCTATTAAGACAAGTTCTAATGAAAAA-C
*
1373960 AACCTTTGAGATTGTTTCCTTTGAAACAAA-TTTCGTCTCACTTAAGACGTAATC
65 AACCTTTGAGATTGTTTCCTATGAAACAAAGTTTCGTCTCACTTAAGACGTAATC
* * **
1374014 CATCTTTGAGTCTATTTCTTTGGAAACAAAATTTTGTCTCTATTAAGACAATTTCTTTTGAAAAA
1 CATCTTTGAGTC-ATTTCTTTGAAAAC-AAATTTTGTCTCTATTAAGACAAGTTCTAATGAAAAA
* *
1374079 -AATCTTTGAG-TATGTTT-CTATGAAAACAAAGTTTTGTCTC
64 CAACCTTTGAGAT-TGTTTCCTATG-AAACAAAGTTTCGTCTC
1374119 TTTTGAGACA
Statistics
Matches: 88, Mismatches: 12, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
118 5 0.06
119 33 0.38
120 19 0.22
121 31 0.35
ACGTcount: A:0.30, C:0.16, G:0.13, T:0.41
Consensus pattern (119 bp):
CATCTTTGAGTCATTTCTTTGAAAACAAATTTTGTCTCTATTAAGACAAGTTCTAATGAAAAACA
ACCTTTGAGATTGTTTCCTATGAAACAAAGTTTCGTCTCACTTAAGACGTAATC
Found at i:1374119 original size:65 final size:67
Alignment explanation
Indices: 1374014--1374187 Score: 185
Period size: 65 Copynumber: 2.6 Consensus size: 67
1374004 AGACGTAATC
* * * * *
1374014 CATCTTTGAGTCTATTTCTTTGGAAACAAAATTTTGTCTCTATTAAGACAA-TTTCTTTTGAAA-
1 CATCTTTGAGTATGTTTCTAT-GAAACAAAATTTTGTCTCTATTAAGACAATTTTCTCTTAAAAT
1374077 AAA
65 AAA
* * *
1374080 -ATCTTTGAGTATGTTTCTATGAAAACAAAGTTTTGTCTCTTTTGAGACAATTTTCTCTTAAAAT
1 CATCTTTGAGTATGTTTCTATG-AAACAAAATTTTGTCTCTATTAAGACAATTTTCTCTTAAAAT
1374144 AAA
65 AAA
* *
1374147 CATCTTTGAG-ATCGTTTCCATTGAAACAAATTTTTTGTCTC
1 CATCTTTGAGTAT-GTTTCTA-TGAAACAAA-ATTTTGTCTC
1374188 CCTTGAGGCA
Statistics
Matches: 91, Mismatches: 10, Indels: 11
0.81 0.09 0.10
Matches are distributed among these distances:
64 1 0.01
65 42 0.46
66 10 0.11
67 5 0.05
68 22 0.24
69 11 0.12
ACGTcount: A:0.31, C:0.14, G:0.11, T:0.43
Consensus pattern (67 bp):
CATCTTTGAGTATGTTTCTATGAAACAAAATTTTGTCTCTATTAAGACAATTTTCTCTTAAAATA
AA
Found at i:1374596 original size:132 final size:133
Alignment explanation
Indices: 1374307--1374602 Score: 341
Period size: 134 Copynumber: 2.2 Consensus size: 133
1374297 TCGGCTAGAT
* * *
1374307 CTCCTCATCACCTAGGAGCCGTGTCACCCTTAGATAACCAGCTGTCCTCATCACGTAGGAACCGA
1 CTCCTCATCGCGTAGGAGCTGTGTCACCC-TAGATAACCAGCTGTCCTCATCACGTAGGAACCGA
* * * * * *
1374372 GTTATCACCCTCTTTAAGGATGGCCAAAACTCTTCATCATGTATGAGCTGAGTCATCCACTGACC
65 GTTATCACCCTCTCTAAGGACGACCAAAACTCTTCAACACGTATGAGCTGAGTCATCCACCGACC
*
1374437 AGAC
130 AAAC
* *
1374441 CTCCTCATCGCGTAGGAGCTGTGTCAACCCTGGATAACCAG-TCGTCCTCATCGCGTAGGAACCG
1 CTCCTCATCGCGTAGGAGCTGTGTC-ACCCTAGATAACCAGCT-GTCCTCATCACGTAGGAACCG
* ** * *
1374505 AGTTATCGCCCT-TCCT-A-GACGACCCGAACTCTTCAACACGTATGAG-TAGTGTCATCCCCCG
64 AGTTATCACCCTCT-CTAAGGACGACCAAAACTCTTCAACACGTATGAGCT-GAGTCATCCACCG
1374566 ACCAAAC
127 ACCAAAC
* *
1374573 TTCCTCATCGCGTAGGAGTTGTGTCACCCT
1 CTCCTCATCGCGTAGGAGCTGTGTCACCCT
1374603 TAGACGACCC
Statistics
Matches: 139, Mismatches: 19, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
131 6 0.04
132 62 0.45
133 3 0.02
134 64 0.46
135 4 0.03
ACGTcount: A:0.24, C:0.32, G:0.20, T:0.24
Consensus pattern (133 bp):
CTCCTCATCGCGTAGGAGCTGTGTCACCCTAGATAACCAGCTGTCCTCATCACGTAGGAACCGAG
TTATCACCCTCTCTAAGGACGACCAAAACTCTTCAACACGTATGAGCTGAGTCATCCACCGACCA
AAC
Found at i:1374624 original size:43 final size:43
Alignment explanation
Indices: 1374520--1374712 Score: 125
Period size: 40 Copynumber: 4.6 Consensus size: 43
1374510 TCGCCCTTCC
* * *
1374520 TAGACGACCCGAACTCTTCAACACGTATGAGTAGTGTCATCCC-
1 TAGACGACCCGAACTCTTCATCACGTAGGAGTTGTGTCA-CCCT
* * * *
1374563 ---CCGA-CCAAACTTCCTCATCGCGTAGGAGTTGTGTCACCCT
1 TAGACGACCCGAAC-TCTTCATCACGTAGGAGTTGTGTCACCCT
** ***
1374603 TAGACGACCCGAACTCTTCATCACGTATAAACAGTGTCATCCC-
1 TAGACGACCCGAACTCTTCATCACGTAGGAGTTGTGTCA-CCCT
* * ** * *
1374646 ---CCGACCAGATTTCCTCATCACATAGGAGTTGTGTCACCCT
1 TAGACGACCCGAACTCTTCATCACGTAGGAGTTGTGTCACCCT
*
1374686 TAGACGAACCGAACTCTTCATCACGTA
1 TAGACGACCCGAACTCTTCATCACGTA
1374713 TGAGCAGTGT
Statistics
Matches: 105, Mismatches: 34, Indels: 22
0.65 0.21 0.14
Matches are distributed among these distances:
39 11 0.10
40 48 0.46
43 38 0.36
44 8 0.08
ACGTcount: A:0.26, C:0.32, G:0.17, T:0.24
Consensus pattern (43 bp):
TAGACGACCCGAACTCTTCATCACGTAGGAGTTGTGTCACCCT
Found at i:1374630 original size:83 final size:83
Alignment explanation
Indices: 1374520--1374729 Score: 330
Period size: 83 Copynumber: 2.5 Consensus size: 83
1374510 TCGCCCTTCC
* * * *
1374520 TAGACGACCCGAACTCTTCAACACGTATGAGTAGTGTCATCCCCCGACCAAACTTCCTCATCGCG
1 TAGACGACCCGAACTCTTCATCACGTATGAGCAGTGTCATCCCCCGACCAAACTTCCTCATCACA
1374585 TAGGAGTTGTGTCACCCT
66 TAGGAGTTGTGTCACCCT
* * * *
1374603 TAGACGACCCGAACTCTTCATCACGTATAAACAGTGTCATCCCCCGACCAGATTTCCTCATCACA
1 TAGACGACCCGAACTCTTCATCACGTATGAGCAGTGTCATCCCCCGACCAAACTTCCTCATCACA
1374668 TAGGAGTTGTGTCACCCT
66 TAGGAGTTGTGTCACCCT
* *
1374686 TAGACGAACCGAACTCTTCATCACGTATGAGCAGTGTCGTCCCC
1 TAGACGACCCGAACTCTTCATCACGTATGAGCAGTGTCATCCCC
1374730 AACAACTAAC
Statistics
Matches: 115, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
83 115 1.00
ACGTcount: A:0.25, C:0.32, G:0.18, T:0.24
Consensus pattern (83 bp):
TAGACGACCCGAACTCTTCATCACGTATGAGCAGTGTCATCCCCCGACCAAACTTCCTCATCACA
TAGGAGTTGTGTCACCCT
Found at i:1374723 original size:43 final size:43
Alignment explanation
Indices: 1374518--1374728 Score: 127
Period size: 43 Copynumber: 5.0 Consensus size: 43
1374508 TATCGCCCTT
* *
1374518 CCTAGACGACCCGAACTCTTCAACACGTATGAGTAGTGTCATC
1 CCTAGACGAACCGAACTCTTCATCACGTATGAGTAGTGTCATC
* * * * * *
1374561 CC---CCG-ACCAAACTTCCTCATCGCGTAGGAGTTGTGTCA-C
1 CCTAGACGAACCGAAC-TCTTCATCACGTATGAGTAGTGTCATC
* * **
1374600 CCTTAGACGACCCGAACTCTTCATCACGTATAAACAGTGTCATC
1 CC-TAGACGAACCGAACTCTTCATCACGTATGAGTAGTGTCATC
* ** * * * *
1374644 CC---CCG-ACCAGATTTCCTCATCACATAGGAGTTGTGTCA-C
1 CCTAGACGAACC-GAACTCTTCATCACGTATGAGTAGTGTCATC
* *
1374683 CCTTAGACGAACCGAACTCTTCATCACGTATGAGCAGTGTCGTC
1 CC-TAGACGAACCGAACTCTTCATCACGTATGAGTAGTGTCATC
1374727 CC
1 CC
1374729 CAACAACTAA
Statistics
Matches: 116, Mismatches: 38, Indels: 27
0.64 0.21 0.15
Matches are distributed among these distances:
39 13 0.11
40 44 0.38
43 45 0.39
44 14 0.12
ACGTcount: A:0.25, C:0.33, G:0.18, T:0.24
Consensus pattern (43 bp):
CCTAGACGAACCGAACTCTTCATCACGTATGAGTAGTGTCATC
Found at i:1374888 original size:3 final size:3
Alignment explanation
Indices: 1374882--1374928 Score: 60
Period size: 3 Copynumber: 15.0 Consensus size: 3
1374872 GGTTTTTTTA
1374882 TAT TAT TATT TAT T-T TAAT TAT TAT TAT TATT TAT TAT TAT TAT TAT
1 TAT TAT TA-T TAT TAT T-AT TAT TAT TAT TA-T TAT TAT TAT TAT TAT
1374929 ATTTTTACAG
Statistics
Matches: 40, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
2 2 0.05
3 30 0.75
4 8 0.20
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:1374904 original size:13 final size:12
Alignment explanation
Indices: 1374878--1374933 Score: 55
Period size: 13 Copynumber: 4.7 Consensus size: 12
1374868 TCCGGGTTTT
*
1374878 TTTATATTATTA
1 TTTATTTTATTA
1374890 TTTATTTTA--A
1 TTTATTTTATTA
1374900 -TTATTATTATTA
1 TTTATT-TTATTA
1374912 TTTATTATTATTA
1 TTTATT-TTATTA
1374925 TTATATTTT
1 TT-TATTTT
1374934 TACAGGCCAG
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
9 5 0.13
10 4 0.11
12 9 0.24
13 16 0.42
14 4 0.11
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (12 bp):
TTTATTTTATTA
Found at i:1374904 original size:16 final size:16
Alignment explanation
Indices: 1374877--1374923 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
1374867 GTCCGGGTTT
1374877 TTTTATATTATTATTTA
1 TTTTA-ATTATTATTTA
1374894 TTTTAATTATTA-TTA
1 TTTTAATTATTATTTA
*
1374909 TTATTTATTATTATT
1 TT-TTAATTATTATT
1374924 ATTATATTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
15 5 0.19
16 16 0.59
17 6 0.22
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
TTTTAATTATTATTTA
Found at i:1374904 original size:19 final size:18
Alignment explanation
Indices: 1374877--1374933 Score: 75
Period size: 19 Copynumber: 3.2 Consensus size: 18
1374867 GTCCGGGTTT
1374877 TTTTA-TATTATTATTTA
1 TTTTATTATTATTATTTA
1374894 TTTTAATTATTATTA-TTA
1 TTTT-ATTATTATTATTTA
1374912 -TTTATTATTATTATTATA
1 TTTTATTATTATTATT-TA
1374930 TTTT
1 TTTT
1374934 TACAGGCCAG
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
16 10 0.29
17 8 0.23
18 6 0.17
19 11 0.31
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (18 bp):
TTTTATTATTATTATTTA
Found at i:1374924 original size:16 final size:16
Alignment explanation
Indices: 1374882--1374928 Score: 69
Period size: 16 Copynumber: 2.9 Consensus size: 16
1374872 GGTTTTTTTA
1374882 TATTATTATTTATT-TT
1 TATTATTA-TTATTATT
*
1374898 AATTATTATTATTATT
1 TATTATTATTATTATT
1374914 TATTATTATTATTAT
1 TATTATTATTATTAT
1374929 ATTTTTACAG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
15 5 0.18
16 23 0.82
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TATTATTATTATTATT
Found at i:1376263 original size:29 final size:30
Alignment explanation
Indices: 1376203--1376371 Score: 161
Period size: 29 Copynumber: 5.7 Consensus size: 30
1376193 TGTAATTACG
*
1376203 ATTTTAG-CCTTTAAAGTTTCTGTTTTAT-T
1 ATTTTAGTCCTTT-AAGTTTTTGTTTTATCT
1376232 ATTTTAGTCCTTTAA-TTTTTGTTTCT-TCT
1 ATTTTAGTCCTTTAAGTTTTTGTTT-TATCT
**
1376261 ATTTTAACCCTTTAAGTTTTTGTTTTATCT
1 ATTTTAGTCCTTTAAGTTTTTGTTTTATCT
* * *
1376291 ATTTTAGTCC-CTAAGTTTCTGTTTTAGCT
1 ATTTTAGTCCTTTAAGTTTTTGTTTTATCT
* * * *
1376320 ATTTCAATCCTTTAAATTTTTATTTATAT-T
1 ATTTTAGTCCTTTAAGTTTTTGTTT-TATCT
*
1376350 ATTTTGGGTCCTTTAAGTTTTT
1 ATTTT-AGTCCTTTAAGTTTTT
1376372 ATTCTTGCTA
Statistics
Matches: 113, Mismatches: 19, Indels: 14
0.77 0.13 0.10
Matches are distributed among these distances:
28 9 0.08
29 49 0.43
30 40 0.35
31 15 0.13
ACGTcount: A:0.20, C:0.12, G:0.09, T:0.59
Consensus pattern (30 bp):
ATTTTAGTCCTTTAAGTTTTTGTTTTATCT
Found at i:1376275 original size:59 final size:60
Alignment explanation
Indices: 1376210--1376385 Score: 184
Period size: 59 Copynumber: 3.0 Consensus size: 60
1376200 ACGATTTTAG
*
1376210 CCTTTAAAGTTTCTGTTTTATTATTTTAGTCCTTTAA-TTTTTGTTTCTTCTATTTTAAC
1 CCTTTAAAGTTTTTGTTTTATTATTTTAGTCCTTTAAGTTTTTGTTTCTTCTATTTTAAC
* * * * *
1376269 CCTTT-AAGTTTTTGTTTTATCTATTTTAGTCC-CTAAGTTTCTGTTT-TAGCTATTTCAAT
1 CCTTTAAAGTTTTTGTTTTAT-TATTTTAGTCCTTTAAGTTTTTGTTTCT-TCTATTTTAAC
* * *
1376328 CCTTTAAA-TTTTTATTTATATTATTTTGGGTCCTTTAAGTTTTT-ATTCTTGCTATTTT
1 CCTTTAAAGTTTTTGTTT-TATTATTTT-AGTCCTTTAAGTTTTTGTTTCTT-CTATTTT
1376386 GGTCCTTGTA
Statistics
Matches: 95, Mismatches: 13, Indels: 16
0.77 0.10 0.13
Matches are distributed among these distances:
58 18 0.19
59 51 0.54
60 11 0.12
61 15 0.16
ACGTcount: A:0.19, C:0.13, G:0.09, T:0.60
Consensus pattern (60 bp):
CCTTTAAAGTTTTTGTTTTATTATTTTAGTCCTTTAAGTTTTTGTTTCTTCTATTTTAAC
Found at i:1376384 original size:31 final size:30
Alignment explanation
Indices: 1376327--1376392 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 30
1376317 GCTATTTCAA
*
1376327 TCCTTTAAATTTTTATTTATATTATTTTGGG
1 TCCTTTAAATTTTTATTTATACTATTTT-GG
* *
1376358 TCCTTTAAGTTTTTATTCT-TGCTATTTTGG
1 TCCTTTAAATTTTTATT-TATACTATTTTGG
1376388 TCCTT
1 TCCTT
1376393 GTATTTAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
30 7 0.23
31 23 0.74
32 1 0.03
ACGTcount: A:0.17, C:0.12, G:0.11, T:0.61
Consensus pattern (30 bp):
TCCTTTAAATTTTTATTTATACTATTTTGG
Found at i:1376392 original size:30 final size:29
Alignment explanation
Indices: 1376203--1376392 Score: 116
Period size: 29 Copynumber: 6.4 Consensus size: 29
1376193 TGTAATTACG
* * **
1376203 ATTTTAG-CCTTTAAAGTTTCTGTTTTATT
1 ATTTTAGTCCTTT-AAGTTTTTATTTTGCT
* *
1376232 ATTTTAGTCCTTTAA-TTTTTGTTTCTTCT
1 ATTTTAGTCCTTTAAGTTTTTATTT-TGCT
** * *
1376261 ATTTTAACCCTTTAAGTTTTTGTTTTATCT
1 ATTTTAGTCCTTTAAGTTTTTATTTT-GCT
* * *
1376291 ATTTTAGTCC-CTAAGTTTCTGTTTTAGCT
1 ATTTTAGTCCTTTAAGTTTTTATTTT-GCT
* * * **
1376320 ATTTCAATCCTTTAAATTTTTATTTATATT
1 ATTTTAGTCCTTTAAGTTTTTATTT-TGCT
*
1376350 ATTTTGGGTCCTTTAAGTTTTTATTCTTGCT
1 ATTTT-AGTCCTTTAAGTTTTTATT-TTGCT
*
1376381 ATTTTGGTCCTT
1 ATTTTAGTCCTT
1376393 GTATTTAAAT
Statistics
Matches: 129, Mismatches: 24, Indels: 15
0.77 0.14 0.09
Matches are distributed among these distances:
28 8 0.06
29 49 0.38
30 47 0.36
31 24 0.19
32 1 0.01
ACGTcount: A:0.18, C:0.13, G:0.09, T:0.59
Consensus pattern (29 bp):
ATTTTAGTCCTTTAAGTTTTTATTTTGCT
Found at i:1378626 original size:12 final size:12
Alignment explanation
Indices: 1378591--1378627 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
1378581 AGAAAATCTG
*
1378591 TTTATTAATTAA
1 TTTATTAATTAT
*
1378603 TTAATTAATTAT
1 TTTATTAATTAT
1378615 TTTATTAATTAT
1 TTTATTAATTAT
1378627 T
1 T
1378628 CCCACCTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
TTTATTAATTAT
Found at i:1379706 original size:19 final size:19
Alignment explanation
Indices: 1379682--1379729 Score: 96
Period size: 19 Copynumber: 2.5 Consensus size: 19
1379672 TCGTTAAAAA
1379682 GTTGAAAACAATATGAGTT
1 GTTGAAAACAATATGAGTT
1379701 GTTGAAAACAATATGAGTT
1 GTTGAAAACAATATGAGTT
1379720 GTTGAAAACA
1 GTTGAAAACA
1379730 TGAGCTAGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.44, C:0.06, G:0.21, T:0.29
Consensus pattern (19 bp):
GTTGAAAACAATATGAGTT
Found at i:1381231 original size:60 final size:59
Alignment explanation
Indices: 1381167--1381349 Score: 174
Period size: 60 Copynumber: 3.1 Consensus size: 59
1381157 TATATGTCTT
* * *
1381167 CAAACTATAATTCTCATTTTAAATTAATAATTAAA-TATTTAAATATTTTAATTTCATCTC
1 CAAACTATGACTCTCATTTTAAATTAAT-CTTAAACT-TTTAAATATTTTAATTTCATCTC
* * * * * * *
1381227 CAAACTATGGCTCTCATTCTAAATTAGTCCTTAAAGTTTTGAACATTCTAATTTCATC-C
1 CAAACTATGACTCTCATTTTAAATTAAT-CTTAAACTTTTAAATATTTTAATTTCATCTC
* * *
1381286 CTAAACTATGACCCTC-TTTCTAAATTGATCTTCAAACTTTTAAATATTTGAATTTCATCTC
1 C-AAACTATGACTCTCATTT-TAAATTAATCTT-AAACTTTTAAATATTTTAATTTCATCTC
1381347 CAA
1 CAA
1381350 TTTCATCCAA
Statistics
Matches: 98, Mismatches: 20, Indels: 10
0.77 0.16 0.08
Matches are distributed among these distances:
59 7 0.07
60 88 0.90
61 3 0.03
ACGTcount: A:0.35, C:0.19, G:0.04, T:0.42
Consensus pattern (59 bp):
CAAACTATGACTCTCATTTTAAATTAATCTTAAACTTTTAAATATTTTAATTTCATCTC
Found at i:1384238 original size:21 final size:21
Alignment explanation
Indices: 1384214--1384253 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1384204 TTTAGTAAAA
*
1384214 TATTACATAAAATGTTAATTT
1 TATTACATAAAATATTAATTT
**
1384235 TATTATTTAAAATATTAAT
1 TATTACATAAAATATTAAT
1384254 GTTTTTAACG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.50
Consensus pattern (21 bp):
TATTACATAAAATATTAATTT
Found at i:1385011 original size:9 final size:9
Alignment explanation
Indices: 1384999--1385038 Score: 55
Period size: 9 Copynumber: 4.6 Consensus size: 9
1384989 TAATATTTTG
1384999 TATTTAATT
1 TATTTAATT
*
1385008 TATTTAA-G
1 TATTTAATT
1385016 TATTTAATT
1 TATTTAATT
1385025 TATTTAATT
1 TATTTAATT
*
1385034 AATTT
1 TATTT
1385039 TTTTGCAGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
8 7 0.26
9 20 0.74
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (9 bp):
TATTTAATT
Found at i:1385020 original size:17 final size:17
Alignment explanation
Indices: 1384998--1385031 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1384988 TTAATATTTT
1384998 GTATTTAATTTATTTAA
1 GTATTTAATTTATTTAA
1385015 GTATTTAATTTATTTAA
1 GTATTTAATTTATTTAA
1385032 TTAATTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (17 bp):
GTATTTAATTTATTTAA
Found at i:1387289 original size:13 final size:13
Alignment explanation
Indices: 1387249--1387291 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
1387239 TATTTAGTAC
*
1387249 TTTTTATTGT-AG
1 TTTTTATTGTAAT
* *
1387261 TTTTTATTGGACT
1 TTTTTATTGTAAT
1387274 TTTTTATTGTAAT
1 TTTTTATTGTAAT
1387287 TTTTT
1 TTTTT
1387292 TATTATTTAT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
12 9 0.36
13 16 0.64
ACGTcount: A:0.16, C:0.02, G:0.12, T:0.70
Consensus pattern (13 bp):
TTTTTATTGTAAT
Found at i:1392632 original size:15 final size:14
Alignment explanation
Indices: 1392611--1392653 Score: 70
Period size: 15 Copynumber: 3.1 Consensus size: 14
1392601 GGAAGAGAAG
1392611 AGTAAATTATTTTT
1 AGTAAATTATTTTT
1392625 ATGTAAATTATTTTT
1 A-GTAAATTATTTTT
1392640 A-TAAATTATTTTT
1 AGTAAATTATTTTT
1392653 A
1 A
1392654 AAATAATATC
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
13 13 0.46
14 1 0.04
15 14 0.50
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (14 bp):
AGTAAATTATTTTT
Found at i:1392646 original size:13 final size:13
Alignment explanation
Indices: 1392613--1392657 Score: 65
Period size: 13 Copynumber: 3.4 Consensus size: 13
1392603 AAGAGAAGAG
1392613 TAAATTATTTTTA
1 TAAATTATTTTTA
1392626 TGTAAATTATTTTTA
1 --TAAATTATTTTTA
1392641 TAAATTATTTTTA
1 TAAATTATTTTTA
1392654 -AAAT
1 TAAAT
1392658 AATATCAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
12 4 0.13
13 13 0.43
15 13 0.43
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (13 bp):
TAAATTATTTTTA
Found at i:1392686 original size:15 final size:14
Alignment explanation
Indices: 1392613--1392686 Score: 55
Period size: 13 Copynumber: 5.1 Consensus size: 14
1392603 AAGAGAAGAG
*
1392613 TAAATTATTTTTATG
1 TAAATTA-TTTTATA
1392628 TAAATTATTTT-TA
1 TAAATTATTTTATA
1392641 TAAATTATTTT-TA
1 TAAATTATTTTATA
*
1392654 -AAATAATATCAATTATA
1 TAAAT--TAT--TTTATA
1392671 TAAATTACTTTTATA
1 TAAATTA-TTTTATA
1392686 T
1 T
1392687 TTTTATAAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 14
0.74 0.05 0.21
Matches are distributed among these distances:
12 4 0.08
13 14 0.29
14 7 0.14
15 13 0.27
16 4 0.08
17 3 0.06
18 4 0.08
ACGTcount: A:0.42, C:0.03, G:0.01, T:0.54
Consensus pattern (14 bp):
TAAATTATTTTATA
Found at i:1395292 original size:16 final size:16
Alignment explanation
Indices: 1395273--1395310 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
1395263 TTTTTTAAGT
1395273 TATATAAATCTTA-AAA
1 TATATAAAT-TTATAAA
*
1395289 TATATAAATTTATATA
1 TATATAAATTTATAAA
1395305 TATATA
1 TATATA
1395311 TTTAAGTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 3 0.15
16 17 0.85
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (16 bp):
TATATAAATTTATAAA
Found at i:1395305 original size:14 final size:14
Alignment explanation
Indices: 1395273--1395315 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
1395263 TTTTTTAAGT
1395273 TATATAAATCTTAAAA
1 TATATAAAT-TT-AAA
*
1395289 TATATAAATTTATA
1 TATATAAATTTAAA
*
1395303 TATATATATTTAA
1 TATATAAATTTAA
1395316 GTTATTTATG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 13 0.54
15 2 0.08
16 9 0.38
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (14 bp):
TATATAAATTTAAA
Found at i:1395565 original size:15 final size:15
Alignment explanation
Indices: 1395547--1395591 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
1395537 TCTCATTTAC
1395547 AATTTTATATAATTT
1 AATTTTATATAATTT
1395562 AATTTTCATAT-ATTT
1 AATTTT-ATATAATTT
1395577 -ATTATTA-ATAATTT
1 AATT-TTATATAATTT
1395591 A
1 A
1395592 TTTCAATCGT
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
13 2 0.08
14 8 0.31
15 12 0.46
16 4 0.15
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (15 bp):
AATTTTATATAATTT
Found at i:1395574 original size:85 final size:85
Alignment explanation
Indices: 1395457--1395615 Score: 212
Period size: 85 Copynumber: 1.9 Consensus size: 85
1395447 TCATGAAATT
* * * * *
1395457 TTTAAAATTTTATATAACTTAAATTTTTTATATTTTTTATTGATAACATGTTTCGACCGTCTTAA
1 TTTAAAATTTTATATAACTTAAATTTTATATATTTATTATTAATAACATATTTCAACCGTCTTAA
1395522 AATTTTATAAAATTGTCTCA
66 AATTTTATAAAATTGTCTCA
* * ** *
1395542 TTTACAATTTTATATAA-TTTAATTTTCATATATTTATTATTAATAATTTATTTCAATCGTCTTA
1 TTTAAAATTTTATATAACTTAAATTTT-ATATATTTATTATTAATAACATATTTCAACCGTCTTA
1395606 AAATTTTATA
65 AAATTTTATA
1395616 CATTCGCCTC
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
84 8 0.13
85 55 0.87
ACGTcount: A:0.35, C:0.08, G:0.04, T:0.53
Consensus pattern (85 bp):
TTTAAAATTTTATATAACTTAAATTTTATATATTTATTATTAATAACATATTTCAACCGTCTTAA
AATTTTATAAAATTGTCTCA
Found at i:1395636 original size:85 final size:84
Alignment explanation
Indices: 1395462--1395644 Score: 199
Period size: 85 Copynumber: 2.2 Consensus size: 84
1395452 AAATTTTTAA
* * * * *
1395462 AATTTTATATAACTTAAATTTTTTATATTTTTTATTGATAACATGTTTCGACCGTCTTAAAATTT
1 AATTTTATATAA-TTAAATTTTATATATTTATTATTAATAACATATTTCAACCGTCTTAAAATTT
* **
1395527 TATAAAATTGTCTCATTTAC
65 TATAAAATTGCCTCACCTAC
* ** *
1395547 AATTTTATATAATTTAATTTTCATATATTTATTATTAATAATTTATTTCAATCGTCTTAAAATTT
1 AATTTTATATAATTAAATTTT-ATATATTTATTATTAATAACATATTTCAACCGTCTTAAAATTT
* *
1395612 TAT-ACATTCGCCTCACCTAT
65 TATAAAATT-GCCTCACCTAC
1395632 AATTTTATA-AATT
1 AATTTTATATAATT
1395645 CACACTCTAT
Statistics
Matches: 82, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
84 16 0.20
85 66 0.80
ACGTcount: A:0.34, C:0.11, G:0.04, T:0.51
Consensus pattern (84 bp):
AATTTTATATAATTAAATTTTATATATTTATTATTAATAACATATTTCAACCGTCTTAAAATTTT
ATAAAATTGCCTCACCTAC
Found at i:1398823 original size:15 final size:16
Alignment explanation
Indices: 1398805--1398837 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
1398795 GTGGCAGATC
1398805 AAAATCCAG-ACGGGA
1 AAAATCCAGAACGGGA
*
1398820 AAAATCTAGAACGGGA
1 AAAATCCAGAACGGGA
1398836 AA
1 AA
1398838 GAAAGATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.52, C:0.15, G:0.24, T:0.09
Consensus pattern (16 bp):
AAAATCCAGAACGGGA
Found at i:1403081 original size:51 final size:51
Alignment explanation
Indices: 1403024--1403132 Score: 157
Period size: 51 Copynumber: 2.1 Consensus size: 51
1403014 TAAATCTCTC
*
1403024 GATTATTAAAAGTTAAAAAATAATCATTCGATTATA-GATTGTTAATTTATT
1 GATTATTAAAAGTTAAAAAATAATCATTCGATTATATG-TCGTTAATTTATT
* * *
1403075 GATTATTAAAAGTTACAAAATGATCATTCGATTATATGTCGTTACTTTATT
1 GATTATTAAAAGTTAAAAAATAATCATTCGATTATATGTCGTTAATTTATT
*
1403126 GAATATT
1 GATTATT
1403133 CTATTTATTA
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
51 51 0.98
52 1 0.02
ACGTcount: A:0.39, C:0.06, G:0.11, T:0.43
Consensus pattern (51 bp):
GATTATTAAAAGTTAAAAAATAATCATTCGATTATATGTCGTTAATTTATT
Found at i:1420537 original size:18 final size:18
Alignment explanation
Indices: 1420516--1420564 Score: 57
Period size: 17 Copynumber: 2.8 Consensus size: 18
1420506 AAAACAAAAC
1420516 AAAACAAAACA-AAAGAGA
1 AAAACAAAA-AGAAAGAGA
*
1420534 AAAATAAAAAGAAAGAG-
1 AAAACAAAAAGAAAGAGA
*
1420551 AAAAGAAAAAGAAA
1 AAAACAAAAAGAAA
1420565 ATGGAAATGG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 14 0.50
18 14 0.50
ACGTcount: A:0.80, C:0.04, G:0.14, T:0.02
Consensus pattern (18 bp):
AAAACAAAAAGAAAGAGA
Found at i:1420557 original size:5 final size:5
Alignment explanation
Indices: 1420478--1420654 Score: 55
Period size: 5 Copynumber: 34.4 Consensus size: 5
1420468 ATTACAACTG
* * * * * * *
1420478 AAGAA AAGGA AAG-A GAGAA AAGGAA AAAAA AACAA AACAA AACAA AACAA
1 AAGAA AAGAA AAGAA AAGAA AA-GAA AAGAA AAGAA AAGAA AAGAA AAGAA
* *
1420528 AAGAGA AA-AA TA-AA AAGAA AGAGAA AAGAAA AAGAA AATGGAA ATGGAA
1 AAGA-A AAGAA AAGAA AAGAA A-AGAA AAG-AA AAGAA AA--GAA A-AGAA
* * * *
1420577 ATGGAA AAAAA AAGAA AAGAA AAG-T AAGTAA AATGAA AA-AGA ATGAA
1 A-AGAA AAGAA AAGAA AAGAA AAGAA AAG-AA AA-GAA AAGA-A AAGAA
*
1420624 AA-AA TAAGAA AA-AT AAGAA AA-AA AGAGAA AA
1 AAGAA -AAGAA AAGAA AAGAA AAGAA A-AGAA AA
1420655 AATTGAAAAG
Statistics
Matches: 135, Mismatches: 18, Indels: 38
0.71 0.09 0.20
Matches are distributed among these distances:
4 20 0.15
5 70 0.52
6 40 0.30
7 5 0.04
ACGTcount: A:0.74, C:0.02, G:0.18, T:0.06
Consensus pattern (5 bp):
AAGAA
Found at i:1420560 original size:17 final size:18
Alignment explanation
Indices: 1420478--1420564 Score: 61
Period size: 20 Copynumber: 4.7 Consensus size: 18
1420468 ATTACAACTG
*
1420478 AAGAAAAGGAAAGAGAGAA
1 AAGAAAAAGAAAGAGA-AA
* *
1420497 AAGGAAAAAAAAACA-AAA
1 AA-GAAAAAGAAAGAGAAA
* *
1420515 CAAAACAAAACAAAAGAGAAA
1 -AAGA-AAAA-GAAAGAGAAA
*
1420536 AATAAAAAGAAAGAG-AA
1 AAGAAAAAGAAAGAGAAA
1420553 AAGAAAAAGAAA
1 AAGAAAAAGAAA
1420565 ATGGAAATGG
Statistics
Matches: 55, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
17 13 0.24
18 9 0.16
19 13 0.24
20 17 0.31
21 3 0.05
ACGTcount: A:0.77, C:0.05, G:0.17, T:0.01
Consensus pattern (18 bp):
AAGAAAAAGAAAGAGAAA
Found at i:1420643 original size:19 final size:20
Alignment explanation
Indices: 1420611--1420655 Score: 58
Period size: 19 Copynumber: 2.3 Consensus size: 20
1420601 TAAGTAAAAT
1420611 GAAAAAGAATGAAAAAATA-A
1 GAAAAAGAATGAAAAAA-AGA
*
1420631 GAAAAATAA-GAAAAAAAGA
1 GAAAAAGAATGAAAAAAAGA
1420650 GAAAAA
1 GAAAAA
1420656 ATTGAAAAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 1 0.04
19 14 0.61
20 8 0.35
ACGTcount: A:0.78, C:0.00, G:0.16, T:0.07
Consensus pattern (20 bp):
GAAAAAGAATGAAAAAAAGA
Found at i:1420654 original size:27 final size:27
Alignment explanation
Indices: 1420585--1420654 Score: 72
Period size: 27 Copynumber: 2.6 Consensus size: 27
1420575 AAATGGAAAA
* *
1420585 AAAAAGAAAAGAAAAGTAAGTAAAATG
1 AAAAAGAAGAGAAAAGTAAGAAAAATG
*
1420612 AAAAAGAATGA-AAAAATAAGAAAAATAAG
1 AAAAAGAA-GAGAAAAGTAAGAAAAAT--G
1420641 AAAAA-AAGAGAAAA
1 AAAAAGAAGAGAAAA
1420655 AATTGAAAAG
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
27 23 0.64
28 7 0.19
29 6 0.17
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.09
Consensus pattern (27 bp):
AAAAAGAAGAGAAAAGTAAGAAAAATG
Found at i:1422876 original size:102 final size:102
Alignment explanation
Indices: 1422780--1423173 Score: 562
Period size: 102 Copynumber: 3.9 Consensus size: 102
1422770 ACACAAACCT
*
1422780 TGAAATTGTTTCACTCGAAACAAAATTAATATTACTTGAGATTGTTTTTC-CTAAAACCAATTTC
1 TGAAATTGTTTCACTCGAAACAAAATTGATATTACTTGAGATTGTTTTTCTC-AAAACCAATTTC
* *
1422844 ATCTCACTTGGGACAGTTTTCCCTTGAAACACAAATTC
65 ATCTCGCTTGAGACAGTTTTCCCTTGAAACACAAATTC
*
1422882 TGAAATTGTTTCACTTGAAACAAAATTGATCA-TACTTGAGATTGTTTTTCTCAAAACCAATTTC
1 TGAAATTGTTTCACTCGAAACAAAATTGAT-ATTACTTGAGATTGTTTTTCTCAAAACCAATTTC
* * * ** *
1422946 ATCTCGCTTAAAACAG-TTCCCCTTGGGACAAAAACTT-
65 ATCTCGCTTGAGACAGTTTTCCCTTGAAACACAAA-TTC
* *
1422983 TGAAATTGTTTCACTTGAAACAAAATTGATCTTACTTGAGATTGTTTTTCTCAAAACCAATTTCA
1 TGAAATTGTTTCACTCGAAACAAAATTGATATTACTTGAGATTGTTTTTCTCAAAACCAATTTCA
*
1423048 TCTCGCTTGAGACAGTTTTCCCTTGAAACACAAATTG
66 TCTCGCTTGAGACAGTTTTCCCTTGAAACACAAATTC
* * *
1423085 TGAAGTTGTTTCACTCGAAAAAAAATTGATCTTACTTGAGATTGTTTTTCTCAAAACCAATTTCA
1 TGAAATTGTTTCACTCGAAACAAAATTGATATTACTTGAGATTGTTTTTCTCAAAACCAATTTCA
* * *
1423150 TCTCGCTTAAGACAATTTTTCCTT
66 TCTCGCTTGAGACAGTTTTCCCTT
1423174 CACTCGAAAC
Statistics
Matches: 263, Mismatches: 23, Indels: 12
0.88 0.08 0.04
Matches are distributed among these distances:
101 92 0.35
102 169 0.64
103 2 0.01
ACGTcount: A:0.32, C:0.19, G:0.12, T:0.37
Consensus pattern (102 bp):
TGAAATTGTTTCACTCGAAACAAAATTGATATTACTTGAGATTGTTTTTCTCAAAACCAATTTCA
TCTCGCTTGAGACAGTTTTCCCTTGAAACACAAATTC
Found at i:1423096 original size:203 final size:203
Alignment explanation
Indices: 1422744--1423159 Score: 690
Period size: 203 Copynumber: 2.0 Consensus size: 203
1422734 AAAAAATTTG
* * *
1422744 TCTCGCTTAAAATAGTTCCCTTTGGGACACAAACCTTGAAATTGTTTCACTCGAAACAAAATTAA
1 TCTCGCTTAAAACAGTTCCCCTTGGGACAAAAACCTTGAAATTGTTTCACTCGAAACAAAATTAA
*
1422809 TATTACTTGAGATTGTTTTTCCTAAAACCAATTTCATCTCACTTGGGACAGTTTTCCCTTGAAAC
66 TATTACTTGAGATTGTTTTTCCTAAAACCAATTTCATCTCACTTGAGACAGTTTTCCCTTGAAAC
* *
1422874 ACAAATTCTGAAATTGTTTCACTTGAAACAAAATTGATCATACTTGAGATTGTTTTTCTCAAAAC
131 ACAAATTCTGAAATTGTTTCACTCGAAAAAAAATTGATCATACTTGAGATTGTTTTTCTCAAAAC
1422939 CAATTTCA
196 CAATTTCA
* * *
1422947 TCTCGCTTAAAACAGTTCCCCTTGGGACAAAAACTTTGAAATTGTTTCACTTGAAACAAAATTGA
1 TCTCGCTTAAAACAGTTCCCCTTGGGACAAAAACCTTGAAATTGTTTCACTCGAAACAAAATTAA
* *
1423012 TCTTACTTGAGATTGTTTTT-CTCAAAACCAATTTCATCTCGCTTGAGACAGTTTTCCCTTGAAA
66 TATTACTTGAGATTGTTTTTCCT-AAAACCAATTTCATCTCACTTGAGACAGTTTTCCCTTGAAA
* * *
1423076 CACAAATTGTGAAGTTGTTTCACTCGAAAAAAAATTGATCTTACTTGAGATTGTTTTTCTCAAAA
130 CACAAATTCTGAAATTGTTTCACTCGAAAAAAAATTGATCATACTTGAGATTGTTTTTCTCAAAA
1423141 CCAATTTCA
195 CCAATTTCA
1423150 TCTCGCTTAA
1 TCTCGCTTAA
1423160 GACAATTTTT
Statistics
Matches: 198, Mismatches: 14, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
202 2 0.01
203 196 0.99
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (203 bp):
TCTCGCTTAAAACAGTTCCCCTTGGGACAAAAACCTTGAAATTGTTTCACTCGAAACAAAATTAA
TATTACTTGAGATTGTTTTTCCTAAAACCAATTTCATCTCACTTGAGACAGTTTTCCCTTGAAAC
ACAAATTCTGAAATTGTTTCACTCGAAAAAAAATTGATCATACTTGAGATTGTTTTTCTCAAAAC
CAATTTCA
Found at i:1423525 original size:32 final size:32
Alignment explanation
Indices: 1423488--1423569 Score: 137
Period size: 32 Copynumber: 2.6 Consensus size: 32
1423478 GCCAGAAGAA
* *
1423488 TTCATAATGAGAAGAATTCGTCCCAAGAAAAG
1 TTCATAATGAGAAGAACTCATCCCAAGAAAAG
*
1423520 TTCATAATGAGAATAACTCATCCCAAGAAAAG
1 TTCATAATGAGAAGAACTCATCCCAAGAAAAG
1423552 TTCATAATGAGAAGAACT
1 TTCATAATGAGAAGAACT
1423570 TGTTCACCCT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 46 1.00
ACGTcount: A:0.45, C:0.16, G:0.16, T:0.23
Consensus pattern (32 bp):
TTCATAATGAGAAGAACTCATCCCAAGAAAAG
Found at i:1423739 original size:29 final size:29
Alignment explanation
Indices: 1423697--1423759 Score: 126
Period size: 29 Copynumber: 2.2 Consensus size: 29
1423687 TTTTTTTTCT
1423697 TACAACATTATTATTATAAAGGTAAATTA
1 TACAACATTATTATTATAAAGGTAAATTA
1423726 TACAACATTATTATTATAAAGGTAAATTA
1 TACAACATTATTATTATAAAGGTAAATTA
1423755 TACAA
1 TACAA
1423760 GTCACTTAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.49, C:0.08, G:0.06, T:0.37
Consensus pattern (29 bp):
TACAACATTATTATTATAAAGGTAAATTA
Found at i:1430165 original size:13 final size:13
Alignment explanation
Indices: 1430147--1430201 Score: 74
Period size: 13 Copynumber: 4.2 Consensus size: 13
1430137 TGTGTCATAA
**
1430147 ATTTATGATGCGC
1 ATTTATGACACGC
1430160 ATTTATGACACGC
1 ATTTATGACACGC
*
1430173 ATTTATGACACAC
1 ATTTATGACACGC
*
1430186 ATTTATGACGCGC
1 ATTTATGACACGC
1430199 ATT
1 ATT
1430202 GAGCGTCATT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 37 1.00
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.35
Consensus pattern (13 bp):
ATTTATGACACGC
Found at i:1430335 original size:85 final size:84
Alignment explanation
Indices: 1430173--1430336 Score: 222
Period size: 85 Copynumber: 2.0 Consensus size: 84
1430163 TATGACACGC
* *
1430173 ATTTATGACACACATTTATGACGCGCATTGAGCGTCATTGAAGCCCCCGTCATAAATAAAGATGA
1 ATTTATGACACACATGTATGACGCACATTGAGCGTCATTGAAGCCCCCGTCATAAATAAAGATGA
1430238 CACACATTTGTGTGTCATAA
66 -ACACATTTGTGTGTCATAA
* ** * * * *
1430258 ATTTATGACACGCATGTATGACTTACATTGCGTGTCATTGAGGCCCCCGTCATAAATGAAGATG-
1 ATTTATGACACACATGTATGACGCACATTGAGCGTCATTGAAGCCCCCGTCATAAATAAAGATGA
*
1430322 ACACATTCGTGTGTC
66 ACACATTTGTGTGTC
1430337 GTGATTGTAT
Statistics
Matches: 69, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
83 14 0.20
85 55 0.80
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.29
Consensus pattern (84 bp):
ATTTATGACACACATGTATGACGCACATTGAGCGTCATTGAAGCCCCCGTCATAAATAAAGATGA
ACACATTTGTGTGTCATAA
Found at i:1430362 original size:2 final size:2
Alignment explanation
Indices: 1430355--1430380 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1430345 ATTTCGTAAA
1430355 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
1430381 TGTAGATTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1434102 original size:59 final size:57
Alignment explanation
Indices: 1434039--1434535 Score: 330
Period size: 59 Copynumber: 8.4 Consensus size: 57
1434029 TGACACTATA
*
1434039 TGTGCTAAAATGATAAGGAAATCATATTGAATGTATGAATTTCCATATGGAGCACTGAG
1 TGTGCTAAAATGATAAGGAAATCATATT-AATGTATGGATTTCCATATGG-GCACTGAG
* *
1434098 TGTGCTAAAATGATAA-GAAATTCATACTGAGTGTATGGATTTCCATATGGAGCACTGAG
1 TGTGCTAAAATGATAAGGAAA-TCATA-TTAATGTATGGATTTCCATATGG-GCACTGAG
* * * *
1434157 TGTGCTAAAATGATAAGGAAATCATATTGAATATATGGATTTCCAGATAGGGCA-TTATA
1 TGTGCTAAAATGATAAGGAAATCATATT-AATGTATGGATTTCCATAT-GGGCACTGA-G
* * * * *** *
1434216 TGTGCTAAAATGGTAAGGGAATCATATTGAGTGTATGGATTTCCAGAAAAAAGCACTAAG
1 TGTGCTAAAATGATAAGGAAATCATATT-AATGTATGGATTTCC--ATATGGGCACTGAG
* * * * * *
1434276 GGTGCTACAAGGATAAGGAAATCATACTAATAGTATGGATTTTCATATAGGGCACTTCA-
1 TGTGCTAAAATGATAAGGAAATCATATTAAT-GTATGGATTTCCATAT-GGGCAC-TGAG
* * * * *
1434335 TGTGCTAAAAATGGTAAAGG-GATCATACTAATGGTATGGATTCTCGAATAT-GGCACTTTA-
1 TGTGCT-AAAATGAT-AAGGAAATCATATTAAT-GTATGGATT-TC-CATATGGGCAC-TGAG
* * **
1434395 TGTGCTAAAAATGGTAAAGG-AATCATCA-TAATGGTATGGATTCTCGA-ATAGGGCACTTCG
1 TGTGCT-AAAATGAT-AAGGAAATCAT-ATTAAT-GTATGGATT-TCCATAT-GGGCACTGAG
* * * *
1434455 TGTGCTAAAATGAGAAGGAAATCATATTAA-GTATATGATATTCCAGATAGAGCACTGAG
1 TGTGCTAAAATGATAAGGAAATCATATTAATGTAT-GGAT-TTCCATAT-GGGCACTGAG
* * *
1434514 AGTGCTAATATTATAAGGAAAT
1 TGTGCTAAAATGATAAGGAAAT
1434536 TATACGAATT
Statistics
Matches: 358, Mismatches: 55, Indels: 50
0.77 0.12 0.11
Matches are distributed among these distances:
57 4 0.01
58 22 0.06
59 187 0.52
60 131 0.37
61 10 0.03
62 4 0.01
ACGTcount: A:0.37, C:0.11, G:0.23, T:0.30
Consensus pattern (57 bp):
TGTGCTAAAATGATAAGGAAATCATATTAATGTATGGATTTCCATATGGGCACTGAG
Found at i:1434220 original size:118 final size:119
Alignment explanation
Indices: 1434039--1434535 Score: 378
Period size: 119 Copynumber: 4.2 Consensus size: 119
1434029 TGACACTATA
* * * *
1434039 TGTGCTAAAATGATAAGGAAATCATATTGAATGTATGAATTTCCATAT-GGAGCACTGAGTGTGC
1 TGTGCTAAAATGATAAGGAAATCATATTGAATATATGGATTTCCATATAGG-GCACTTAATGTGC
* *** *
1434103 TAAAATGATAA-GAAATTCATACTGAGTGTATGGATTTCCA-TATGGAGCACTGAG
65 TAAAATGATAAGGAAA-TCATACTGAGTGTATGGATTTCCAGAAAAAAGCACTAAG
*
1434157 TGTGCTAAAATGATAAGGAAATCATATTGAATATATGGATTTCCAGATAGGGCA-TTATATGTGC
1 TGTGCTAAAATGATAAGGAAATCATATTGAATATATGGATTTCCATATAGGGCACTTA-ATGTGC
* * *
1434221 TAAAATGGTAAGGGAATCATATTGAGTGTATGGATTTCCAGAAAAAAGCACTAAG
65 TAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCAGAAAAAAGCACTAAG
* * * * * *
1434276 GGTGCTACAAGGATAAGGAAATCATACT-AATAGTATGGATTTTCATATAGGGCACTTCATGTGC
1 TGTGCTAAAATGATAAGGAAATCATATTGAATA-TATGGATTTCCATATAGGGCACTTAATGTGC
* * * * ** *
1434340 TAAAAATGGTAAAGG-GATCATACT-AATGGTATGGA-TTCTC-GAATATGGCACTTTA-
65 T-AAAATGAT-AAGGAAATCATACTGAGT-GTATGGATTTC-CAGAAAAAAGCAC-TAAG
* * * **
1434395 TGTGCTAAAAATGGTAAAGG-AATCATCA-T-AATGGTATGGATTCTCGA-ATAGGGCACTTCGT
1 TGTGCT-AAAATGAT-AAGGAAATCAT-ATTGAAT-ATATGGATT-TCCATATAGGGCACTTAAT
* * * * * * *
1434456 GTGCTAAAATGAGAAGGAAATCATATTAAGTATAT-GATATTCCAG-ATAGAGCACTGAG
61 GTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGAT-TTCCAGAAAAAAGCACTAAG
* * *
1434514 AGTGCTAATATTATAAGGAAAT
1 TGTGCTAAAATGATAAGGAAAT
1434536 TATACGAATT
Statistics
Matches: 308, Mismatches: 48, Indels: 46
0.77 0.12 0.11
Matches are distributed among these distances:
117 6 0.02
118 106 0.34
119 111 0.36
120 74 0.24
121 11 0.04
ACGTcount: A:0.37, C:0.11, G:0.23, T:0.30
Consensus pattern (119 bp):
TGTGCTAAAATGATAAGGAAATCATATTGAATATATGGATTTCCATATAGGGCACTTAATGTGCT
AAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCAGAAAAAAGCACTAAG
Found at i:1434326 original size:119 final size:119
Alignment explanation
Indices: 1434040--1434376 Score: 384
Period size: 118 Copynumber: 2.8 Consensus size: 119
1434030 GACACTATAT
* * *
1434040 GTGCTAAAATGATAAGGAAATCATATTGAAT-GTATGAATTTCCATAT-GGAGCACTGAGTGTGC
1 GTGCTAAAATGATAAGGAAATCATATTGAATAGTATGGATTTCCATATAGG-GCACTTAATGTGC
* * * *** * *
1434103 TAAAATGATAA-GAAATTCATACTGAGTGTATGGATTTCCATATGGAGCACTGAGT
65 TAAAATGGTAAGGGAA-TCATACTGAGTGTATGGATTTCCAAAAAAAGCACTAAGG
*
1434158 GTGCTAAAATGATAAGGAAATCATATTGAATA-TATGGATTTCCAGATAGGGCA-TTATATGTGC
1 GTGCTAAAATGATAAGGAAATCATATTGAATAGTATGGATTTCCATATAGGGCACTTA-ATGTGC
*
1434221 TAAAATGGTAAGGGAATCATATTGAGTGTATGGATTTCCAGAAAAAAGCACTAAGG
65 TAAAATGGTAAGGGAATCATACTGAGTGTATGGATTTCCA-AAAAAAGCACTAAGG
* * * * *
1434277 GTGCTACAAGGATAAGGAAATCATACT-AATAGTATGGATTTTCATATAGGGCACTTCATGTGCT
1 GTGCTAAAATGATAAGGAAATCATATTGAATAGTATGGATTTCCATATAGGGCACTTAATGTGCT
*
1434341 AAAAATGGTAAAGGG-ATCATACT-AATGGTATGGATT
66 -AAAATGGT-AAGGGAATCATACTGAGT-GTATGGATT
1434377 CTCGAATATG
Statistics
Matches: 188, Mismatches: 21, Indels: 18
0.83 0.09 0.08
Matches are distributed among these distances:
117 2 0.01
118 89 0.47
119 66 0.35
120 26 0.14
121 5 0.03
ACGTcount: A:0.37, C:0.10, G:0.23, T:0.30
Consensus pattern (119 bp):
GTGCTAAAATGATAAGGAAATCATATTGAATAGTATGGATTTCCATATAGGGCACTTAATGTGCT
AAAATGGTAAGGGAATCATACTGAGTGTATGGATTTCCAAAAAAAGCACTAAGG
Found at i:1434360 original size:60 final size:60
Alignment explanation
Indices: 1434290--1434464 Score: 255
Period size: 60 Copynumber: 2.9 Consensus size: 60
1434280 CTACAAGGAT
* *
1434290 AAGGAAATCATACTAATAGTATGGATTTTC-ATATAGGGCACTTCATGTGCTAAAAATGGTA
1 AAGG-AATCATACTAATGGTATGGATTCTCGA-ATAGGGCACTTCATGTGCTAAAAATGGTA
* * *
1434351 AAGGGATCATACTAATGGTATGGATTCTCGAATATGGCACTTTATGTGCTAAAAATGGTA
1 AAGGAATCATACTAATGGTATGGATTCTCGAATAGGGCACTTCATGTGCTAAAAATGGTA
*
1434411 AAGGAATCAT-CATAATGGTATGGATTCTCGAATAGGGCACTTCGTGTGCTAAAA
1 AAGGAATCATAC-TAATGGTATGGATTCTCGAATAGGGCACTTCATGTGCTAAAA
1434465 TGAGAAGGAA
Statistics
Matches: 103, Mismatches: 9, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
59 1 0.01
60 97 0.94
61 5 0.05
ACGTcount: A:0.35, C:0.13, G:0.22, T:0.30
Consensus pattern (60 bp):
AAGGAATCATACTAATGGTATGGATTCTCGAATAGGGCACTTCATGTGCTAAAAATGGTA
Found at i:1434680 original size:44 final size:44
Alignment explanation
Indices: 1434618--1435186 Score: 1002
Period size: 44 Copynumber: 13.0 Consensus size: 44
1434608 CAGTGATGCA
*
1434618 AATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGA
1 AATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGG
*
1434662 AATTATAGTAAGTATATTGTTAAAATAAGCTTACGAGCTTATGG
1 AATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGG
* *
1434706 AATTATAGTAATTATAATGGTAAAATAAGCTTACGAGCTTATGG
1 AATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGG
1434750 AATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGG
1 AATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGG
1434794 AATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGG
1 AATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGG
1434838 AATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGG
1 AATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGG
1434882 AATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGG
1 AATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGG
*
1434926 AATTATAGTAAGTATATTGGTAAAATAAGCTCACGAGCTTATGG
1 AATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGG
*
1434970 AATTATAGTAAGTATATTGGTAAAATAAGCTCACGAGCTTATGG
1 AATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGG
1435014 AATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGG
1 AATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGG
1435058 AATTATAGTAAGTATATTGGTAAAATAAG----CGAGCTTATGG
1 AATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGG
* *
1435098 AATAATAGTAAGTATATTGATAAAATAAGCTTACGAGCTTATGG
1 AATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGG
* * * *
1435142 AATAATGGTAAGTATATTGGTAAAATAAGTTTATGAGCTTATGG
1 AATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGG
1435186 A
1 A
1435187 TTAAATGGTA
Statistics
Matches: 506, Mismatches: 15, Indels: 8
0.96 0.03 0.02
Matches are distributed among these distances:
40 38 0.08
44 468 0.92
ACGTcount: A:0.40, C:0.07, G:0.20, T:0.34
Consensus pattern (44 bp):
AATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGG
Found at i:1435214 original size:22 final size:23
Alignment explanation
Indices: 1435189--1435232 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
1435179 CTTATGGATT
1435189 AAATGGTAT-GTATATTGATAAG
1 AAATGGTATAGTATATTGATAAG
** *
1435211 AAATTTTATAGTATTTTGATAA
1 AAATGGTATAGTATATTGATAA
1435233 TGGTAAAATA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.41, C:0.00, G:0.16, T:0.43
Consensus pattern (23 bp):
AAATGGTATAGTATATTGATAAG
Found at i:1435620 original size:21 final size:21
Alignment explanation
Indices: 1435596--1435635 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1435586 TTTGGAAGTT
*
1435596 ACTGTAGTAGTGCATCGATGA
1 ACTGTAGCAGTGCATCGATGA
1435617 ACTGTAGCAGTGCATCGAT
1 ACTGTAGCAGTGCATCGAT
1435636 ACACATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.28
Consensus pattern (21 bp):
ACTGTAGCAGTGCATCGATGA
Found at i:1443841 original size:23 final size:23
Alignment explanation
Indices: 1443815--1443863 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
1443805 GAGAAGATCG
* *
1443815 AAAACATGTCAAAAAGTCATAGA
1 AAAACATGTCAAAAAGACAGAGA
*
1443838 AAAACATGTCACAAAGACAGAGA
1 AAAACATGTCAAAAAGACAGAGA
1443861 AAA
1 AAA
1443864 TCGCGCCATG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.59, C:0.14, G:0.14, T:0.12
Consensus pattern (23 bp):
AAAACATGTCAAAAAGACAGAGA
Found at i:1447055 original size:3 final size:3
Alignment explanation
Indices: 1447036--1447101 Score: 55
Period size: 3 Copynumber: 21.7 Consensus size: 3
1447026 TTTTATTGTT
* * * *
1447036 TTA TT- TTA TTT TTA TTA TTA TAA TTA TTAA ATA TTA GATA TTAA TT-
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA -TTA TT-A TTA
1447082 TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TT
1447102 TTTAGGTCAT
Statistics
Matches: 50, Mismatches: 8, Indels: 10
0.74 0.12 0.15
Matches are distributed among these distances:
2 4 0.08
3 39 0.78
4 7 0.14
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:1448522 original size:2 final size:2
Alignment explanation
Indices: 1448515--1448576 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
1448505 TTACAAATTA
1448515 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1448557 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
1448577 GTTGGGTATA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1449454 original size:43 final size:43
Alignment explanation
Indices: 1449406--1449497 Score: 184
Period size: 43 Copynumber: 2.1 Consensus size: 43
1449396 TTTTAAATTA
1449406 AAAATCAATTGAAAGAGGATAATTAAGAATTAATGTGGTTTTT
1 AAAATCAATTGAAAGAGGATAATTAAGAATTAATGTGGTTTTT
1449449 AAAATCAATTGAAAGAGGATAATTAAGAATTAATGTGGTTTTT
1 AAAATCAATTGAAAGAGGATAATTAAGAATTAATGTGGTTTTT
1449492 AAAATC
1 AAAATC
1449498 TCACATTTAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 49 1.00
ACGTcount: A:0.46, C:0.03, G:0.17, T:0.34
Consensus pattern (43 bp):
AAAATCAATTGAAAGAGGATAATTAAGAATTAATGTGGTTTTT
Found at i:1451009 original size:6 final size:6
Alignment explanation
Indices: 1450998--1451033 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
1450988 TAACACCTTG
* *
1450998 TGCATT TGCATT TGCATT CGCATT CGCATT TGCATT
1 TGCATT TGCATT TGCATT TGCATT TGCATT TGCATT
1451034 CTTATTAGCT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.17, C:0.22, G:0.17, T:0.44
Consensus pattern (6 bp):
TGCATT
Found at i:1451026 original size:18 final size:18
Alignment explanation
Indices: 1450999--1451034 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1450989 AACACCTTGT
*
1450999 GCATTTGCATTTGCATTC
1 GCATTCGCATTTGCATTC
1451017 GCATTCGCATTTGCATTC
1 GCATTCGCATTTGCATTC
1451035 TTATTAGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.25, G:0.17, T:0.42
Consensus pattern (18 bp):
GCATTCGCATTTGCATTC
Found at i:1454989 original size:59 final size:57
Alignment explanation
Indices: 1454926--1455422 Score: 330
Period size: 59 Copynumber: 8.4 Consensus size: 57
1454916 TGACACTATA
*
1454926 TGTGCTAAAATGATAAGGAAATCATATTGAATGTATGAATTTCCATATGGAGCACTGAG
1 TGTGCTAAAATGATAAGGAAATCATATT-AATGTATGGATTTCCATATGG-GCACTGAG
* *
1454985 TGTGCTAAAATGATAA-GAAATTCATACTGAGTGTATGGATTTCCATATGGAGCACTGAG
1 TGTGCTAAAATGATAAGGAAA-TCATA-TTAATGTATGGATTTCCATATGG-GCACTGAG
* * * *
1455044 TGTGCTAAAATGATAAGGAAATCATATTGAATATATGGATTTCCAGATAGGGCA-TTATA
1 TGTGCTAAAATGATAAGGAAATCATATT-AATGTATGGATTTCCATAT-GGGCACTGA-G
* * * * *** *
1455103 TGTGCTAAAATGGTAAGGGAATCATATTGAGTGTATGGATTTCCAGAAAAAAGCACTAAG
1 TGTGCTAAAATGATAAGGAAATCATATT-AATGTATGGATTTCC--ATATGGGCACTGAG
* * * * * *
1455163 GGTGCTACAAGGATAAGGAAATCATACTAATAGTATGGATTTTCATATAGGGCACTTCA-
1 TGTGCTAAAATGATAAGGAAATCATATTAAT-GTATGGATTTCCATAT-GGGCAC-TGAG
* * * * *
1455222 TGTGCTAAAAATGGTAAAGG-GATCATACTAATGGTATGGATTCTCGAATAT-GGCACTTTA-
1 TGTGCT-AAAATGAT-AAGGAAATCATATTAAT-GTATGGATT-TC-CATATGGGCAC-TGAG
* * **
1455282 TGTGCTAAAAATGGTAAAGG-AATCATCA-TAATGGTATGGATTCTCGA-ATAGGGCACTTCG
1 TGTGCT-AAAATGAT-AAGGAAATCAT-ATTAAT-GTATGGATT-TCCATAT-GGGCACTGAG
* * * *
1455342 TGTGCTAAAATGAGAAGGAAATCATATTAA-GTATATGATATTCCAGATAGAGCACTGAG
1 TGTGCTAAAATGATAAGGAAATCATATTAATGTAT-GGAT-TTCCATAT-GGGCACTGAG
* * *
1455401 AGTGCTAATATTATAAGGAAAT
1 TGTGCTAAAATGATAAGGAAAT
1455423 TATACGAATT
Statistics
Matches: 358, Mismatches: 55, Indels: 50
0.77 0.12 0.11
Matches are distributed among these distances:
57 4 0.01
58 22 0.06
59 187 0.52
60 131 0.37
61 10 0.03
62 4 0.01
ACGTcount: A:0.37, C:0.11, G:0.23, T:0.30
Consensus pattern (57 bp):
TGTGCTAAAATGATAAGGAAATCATATTAATGTATGGATTTCCATATGGGCACTGAG
Found at i:1455107 original size:118 final size:119
Alignment explanation
Indices: 1454926--1455422 Score: 378
Period size: 119 Copynumber: 4.2 Consensus size: 119
1454916 TGACACTATA
* * * *
1454926 TGTGCTAAAATGATAAGGAAATCATATTGAATGTATGAATTTCCATAT-GGAGCACTGAGTGTGC
1 TGTGCTAAAATGATAAGGAAATCATATTGAATATATGGATTTCCATATAGG-GCACTTAATGTGC
* *** *
1454990 TAAAATGATAA-GAAATTCATACTGAGTGTATGGATTTCCA-TATGGAGCACTGAG
65 TAAAATGATAAGGAAA-TCATACTGAGTGTATGGATTTCCAGAAAAAAGCACTAAG
*
1455044 TGTGCTAAAATGATAAGGAAATCATATTGAATATATGGATTTCCAGATAGGGCA-TTATATGTGC
1 TGTGCTAAAATGATAAGGAAATCATATTGAATATATGGATTTCCATATAGGGCACTTA-ATGTGC
* * *
1455108 TAAAATGGTAAGGGAATCATATTGAGTGTATGGATTTCCAGAAAAAAGCACTAAG
65 TAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCAGAAAAAAGCACTAAG
* * * * * *
1455163 GGTGCTACAAGGATAAGGAAATCATACT-AATAGTATGGATTTTCATATAGGGCACTTCATGTGC
1 TGTGCTAAAATGATAAGGAAATCATATTGAATA-TATGGATTTCCATATAGGGCACTTAATGTGC
* * * * ** *
1455227 TAAAAATGGTAAAGG-GATCATACT-AATGGTATGGA-TTCTC-GAATATGGCACTTTA-
65 T-AAAATGAT-AAGGAAATCATACTGAGT-GTATGGATTTC-CAGAAAAAAGCAC-TAAG
* * * **
1455282 TGTGCTAAAAATGGTAAAGG-AATCATCA-T-AATGGTATGGATTCTCGA-ATAGGGCACTTCGT
1 TGTGCT-AAAATGAT-AAGGAAATCAT-ATTGAAT-ATATGGATT-TCCATATAGGGCACTTAAT
* * * * * * *
1455343 GTGCTAAAATGAGAAGGAAATCATATTAAGTATAT-GATATTCCAG-ATAGAGCACTGAG
61 GTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGAT-TTCCAGAAAAAAGCACTAAG
* * *
1455401 AGTGCTAATATTATAAGGAAAT
1 TGTGCTAAAATGATAAGGAAAT
1455423 TATACGAATT
Statistics
Matches: 308, Mismatches: 48, Indels: 46
0.77 0.12 0.11
Matches are distributed among these distances:
117 6 0.02
118 106 0.34
119 111 0.36
120 74 0.24
121 11 0.04
ACGTcount: A:0.37, C:0.11, G:0.23, T:0.30
Consensus pattern (119 bp):
TGTGCTAAAATGATAAGGAAATCATATTGAATATATGGATTTCCATATAGGGCACTTAATGTGCT
AAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCAGAAAAAAGCACTAAG
Found at i:1455213 original size:119 final size:119
Alignment explanation
Indices: 1454927--1455263 Score: 384
Period size: 118 Copynumber: 2.8 Consensus size: 119
1454917 GACACTATAT
* * *
1454927 GTGCTAAAATGATAAGGAAATCATATTGAAT-GTATGAATTTCCATAT-GGAGCACTGAGTGTGC
1 GTGCTAAAATGATAAGGAAATCATATTGAATAGTATGGATTTCCATATAGG-GCACTTAATGTGC
* * * *** * *
1454990 TAAAATGATAA-GAAATTCATACTGAGTGTATGGATTTCCATATGGAGCACTGAGT
65 TAAAATGGTAAGGGAA-TCATACTGAGTGTATGGATTTCCAAAAAAAGCACTAAGG
*
1455045 GTGCTAAAATGATAAGGAAATCATATTGAATA-TATGGATTTCCAGATAGGGCA-TTATATGTGC
1 GTGCTAAAATGATAAGGAAATCATATTGAATAGTATGGATTTCCATATAGGGCACTTA-ATGTGC
*
1455108 TAAAATGGTAAGGGAATCATATTGAGTGTATGGATTTCCAGAAAAAAGCACTAAGG
65 TAAAATGGTAAGGGAATCATACTGAGTGTATGGATTTCCA-AAAAAAGCACTAAGG
* * * * *
1455164 GTGCTACAAGGATAAGGAAATCATACT-AATAGTATGGATTTTCATATAGGGCACTTCATGTGCT
1 GTGCTAAAATGATAAGGAAATCATATTGAATAGTATGGATTTCCATATAGGGCACTTAATGTGCT
*
1455228 AAAAATGGTAAAGGG-ATCATACT-AATGGTATGGATT
66 -AAAATGGT-AAGGGAATCATACTGAGT-GTATGGATT
1455264 CTCGAATATG
Statistics
Matches: 188, Mismatches: 21, Indels: 18
0.83 0.09 0.08
Matches are distributed among these distances:
117 2 0.01
118 89 0.47
119 66 0.35
120 26 0.14
121 5 0.03
ACGTcount: A:0.37, C:0.10, G:0.23, T:0.30
Consensus pattern (119 bp):
GTGCTAAAATGATAAGGAAATCATATTGAATAGTATGGATTTCCATATAGGGCACTTAATGTGCT
AAAATGGTAAGGGAATCATACTGAGTGTATGGATTTCCAAAAAAAGCACTAAGG
Found at i:1455247 original size:60 final size:60
Alignment explanation
Indices: 1455177--1455351 Score: 255
Period size: 60 Copynumber: 2.9 Consensus size: 60
1455167 CTACAAGGAT
* *
1455177 AAGGAAATCATACTAATAGTATGGATTTTC-ATATAGGGCACTTCATGTGCTAAAAATGGTA
1 AAGG-AATCATACTAATGGTATGGATTCTCGA-ATAGGGCACTTCATGTGCTAAAAATGGTA
* * *
1455238 AAGGGATCATACTAATGGTATGGATTCTCGAATATGGCACTTTATGTGCTAAAAATGGTA
1 AAGGAATCATACTAATGGTATGGATTCTCGAATAGGGCACTTCATGTGCTAAAAATGGTA
*
1455298 AAGGAATCAT-CATAATGGTATGGATTCTCGAATAGGGCACTTCGTGTGCTAAAA
1 AAGGAATCATAC-TAATGGTATGGATTCTCGAATAGGGCACTTCATGTGCTAAAA
1455352 TGAGAAGGAA
Statistics
Matches: 103, Mismatches: 9, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
59 1 0.01
60 97 0.94
61 5 0.05
ACGTcount: A:0.35, C:0.13, G:0.22, T:0.30
Consensus pattern (60 bp):
AAGGAATCATACTAATGGTATGGATTCTCGAATAGGGCACTTCATGTGCTAAAAATGGTA
Found at i:1455567 original size:44 final size:44
Alignment explanation
Indices: 1455505--1456073 Score: 1002
Period size: 44 Copynumber: 13.0 Consensus size: 44
1455495 CAGTGATGCA
*
1455505 AATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGA
1 AATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGG
*
1455549 AATTATAGTAAGTATATTGTTAAAATAAGCTTACGAGCTTATGG
1 AATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGG
* *
1455593 AATTATAGTAATTATAATGGTAAAATAAGCTTACGAGCTTATGG
1 AATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGG
1455637 AATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGG
1 AATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGG
1455681 AATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGG
1 AATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGG
1455725 AATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGG
1 AATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGG
1455769 AATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGG
1 AATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGG
*
1455813 AATTATAGTAAGTATATTGGTAAAATAAGCTCACGAGCTTATGG
1 AATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGG
*
1455857 AATTATAGTAAGTATATTGGTAAAATAAGCTCACGAGCTTATGG
1 AATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGG
1455901 AATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGG
1 AATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGG
1455945 AATTATAGTAAGTATATTGGTAAAATAAG----CGAGCTTATGG
1 AATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGG
* *
1455985 AATAATAGTAAGTATATTGATAAAATAAGCTTACGAGCTTATGG
1 AATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGG
* * * *
1456029 AATAATGGTAAGTATATTGGTAAAATAAGTTTATGAGCTTATGG
1 AATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGG
1456073 A
1 A
1456074 TTAAATGGTA
Statistics
Matches: 506, Mismatches: 15, Indels: 8
0.96 0.03 0.02
Matches are distributed among these distances:
40 38 0.08
44 468 0.92
ACGTcount: A:0.40, C:0.07, G:0.20, T:0.34
Consensus pattern (44 bp):
AATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGG
Found at i:1456101 original size:22 final size:23
Alignment explanation
Indices: 1456076--1456119 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
1456066 CTTATGGATT
1456076 AAATGGTAT-GTATATTGATAAG
1 AAATGGTATAGTATATTGATAAG
** *
1456098 AAATTTTATAGTATTTTGATAA
1 AAATGGTATAGTATATTGATAA
1456120 TGGTAAAATA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.41, C:0.00, G:0.16, T:0.43
Consensus pattern (23 bp):
AAATGGTATAGTATATTGATAAG
Found at i:1456506 original size:21 final size:21
Alignment explanation
Indices: 1456482--1456521 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1456472 TTTGGAAGTT
*
1456482 ACTGTAGTAGTGCATCGATGA
1 ACTGTAGCAGTGCATCGATGA
1456503 ACTGTAGCAGTGCATCGAT
1 ACTGTAGCAGTGCATCGAT
1456522 ACACATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.28
Consensus pattern (21 bp):
ACTGTAGCAGTGCATCGATGA
Done.