Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001991.1 Hibiscus syriacus cultivar Beakdansim tig00004072_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: 2373627
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 13
Found at i:1682592 original size:40 final size:44
Alignment explanation
Indices: 1682509--1682601 Score: 113
Period size: 43 Copynumber: 2.2 Consensus size: 44
1682499 ATTTTTTATT
* *
1682509 AATAATATTAGTAATAAATAATAATATTAGTAATTATAATTATAAG
1 AATAATATTA-TAATAAATAATAATAATAATAATTAT-ATTATAAG
*
1682555 AATAATATT-TAAT-AATAATAATAATAATAATT-T-TTATAAT
1 AATAATATTATAATAAATAATAATAATAATAATTATATTATAAG
1682595 AATAATA
1 AATAATA
1682602 AATAAATTAA
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
40 13 0.30
42 1 0.02
43 17 0.39
44 4 0.09
46 9 0.20
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (44 bp):
AATAATATTATAATAAATAATAATAATAATAATTATATTATAAG
Found at i:1682606 original size:37 final size:39
Alignment explanation
Indices: 1682520--1682606 Score: 97
Period size: 37 Copynumber: 2.3 Consensus size: 39
1682510 ATAATATTAG
*
1682520 TAATAAATAATAATATTAGTAATTATAATTATAAGAATAA
1 TAATAAATAATAATA-TAGTAATAATAATTATAAGAATAA
* * * * *
1682560 TATTTAATAATAATA-A-TAATAATAATTTTTATAATAA
1 TAATAAATAATAATATAGTAATAATAATTATAAGAATAA
1682597 TAATAAATAA
1 TAATAAATAA
1682607 ATTAATATGG
Statistics
Matches: 39, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
37 25 0.64
38 1 0.03
40 13 0.33
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (39 bp):
TAATAAATAATAATATAGTAATAATAATTATAAGAATAA
Found at i:1688191 original size:21 final size:21
Alignment explanation
Indices: 1688165--1688204 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1688155 CATATGGCTT
*
1688165 CTTTTCATGTAATTCATATCA
1 CTTTTCATATAATTCATATCA
1688186 CTTTTCATATAATTCATAT
1 CTTTTCATATAATTCATAT
1688205 GTTCACATAT
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:0.30, C:0.17, G:0.03, T:0.50
Consensus pattern (21 bp):
CTTTTCATATAATTCATATCA
Found at i:1690176 original size:21 final size:21
Alignment explanation
Indices: 1690150--1690189 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1690140 CATATGGCTT
*
1690150 CTTTTCATGTAATTCATATCA
1 CTTTTCATATAATTCATATCA
1690171 CTTTTCATATAATTCATAT
1 CTTTTCATATAATTCATAT
1690190 GTTCACATAT
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:0.30, C:0.17, G:0.03, T:0.50
Consensus pattern (21 bp):
CTTTTCATATAATTCATATCA
Found at i:1690811 original size:20 final size:20
Alignment explanation
Indices: 1690786--1690823 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1690776 TTCCCCTTGA
1690786 AGTGCATCGATACATTCTAC
1 AGTGCATCGATACATTCTAC
*
1690806 AGTGCATCGATGCATTCT
1 AGTGCATCGATACATTCT
1690824 TTAACATGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (20 bp):
AGTGCATCGATACATTCTAC
Found at i:1699299 original size:21 final size:22
Alignment explanation
Indices: 1699275--1699318 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
1699265 GCCATGGAAG
*
1699275 GATGACTTGTGG-TCGAAGAAA
1 GATGACTTGGGGCTCGAAGAAA
**
1699296 GATGGTTTGGGGCTCGAAGAAA
1 GATGACTTGGGGCTCGAAGAAA
1699318 G
1 G
1699319 TGAGGTGAGA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.30, C:0.09, G:0.39, T:0.23
Consensus pattern (22 bp):
GATGACTTGGGGCTCGAAGAAA
Found at i:1700677 original size:14 final size:14
Alignment explanation
Indices: 1700658--1700713 Score: 66
Period size: 14 Copynumber: 4.3 Consensus size: 14
1700648 CGTTCGTGAA
1700658 CGTTCGATTATGTT
1 CGTTCGATTATGTT
*
1700672 CGTTCGGTTATG-T
1 CGTTCGATTATGTT
*
1700685 --TT-GTTTATGTT
1 CGTTCGATTATGTT
1700696 CGTTCGATTATGTT
1 CGTTCGATTATGTT
1700710 CGTT
1 CGTT
1700714 TATGTTCATT
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
10 6 0.17
11 3 0.09
13 3 0.09
14 23 0.66
ACGTcount: A:0.11, C:0.12, G:0.23, T:0.54
Consensus pattern (14 bp):
CGTTCGATTATGTT
Found at i:1700692 original size:24 final size:24
Alignment explanation
Indices: 1700665--1700734 Score: 97
Period size: 24 Copynumber: 2.9 Consensus size: 24
1700655 GAACGTTCGA
*
1700665 TTATGTTCGTTCGGTTATGTTTGT
1 TTATGTTCGTTCGATTATGTTTGT
*
1700689 TTATGTTCGTTCGATTATGTTCGT
1 TTATGTTCGTTCGATTATGTTTGT
*
1700713 TTATGTTCATTC-ATTTATGTTT
1 TTATGTTCGTTCGA-TTATGTTT
1700735 AACTCAATCT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
23 1 0.02
24 40 0.98
ACGTcount: A:0.13, C:0.10, G:0.19, T:0.59
Consensus pattern (24 bp):
TTATGTTCGTTCGATTATGTTTGT
Found at i:1701474 original size:10 final size:10
Alignment explanation
Indices: 1701459--1701533 Score: 61
Period size: 10 Copynumber: 7.7 Consensus size: 10
1701449 GGGTCTCCAA
1701459 CGTTTATGTT
1 CGTTTATGTT
1701469 CGTTTATGTT
1 CGTTTATGTT
1701479 CGTGTTCAT-TT
1 CGT-TT-ATGTT
* **
1701490 ATGTTCGTGTT
1 -CGTTTATGTT
1701501 CGTTTATGTT
1 CGTTTATGTT
1701511 CG----TGTT
1 CGTTTATGTT
1701517 CGTTTATGTT
1 CGTTTATGTT
1701527 CGTTTAT
1 CGTTTAT
1701534 TTATTAAATG
Statistics
Matches: 51, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
6 6 0.12
10 34 0.67
11 7 0.14
12 4 0.08
ACGTcount: A:0.09, C:0.12, G:0.21, T:0.57
Consensus pattern (10 bp):
CGTTTATGTT
Found at i:1701490 original size:16 final size:16
Alignment explanation
Indices: 1701465--1701529 Score: 121
Period size: 16 Copynumber: 4.1 Consensus size: 16
1701455 CCAACGTTTA
1701465 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
*
1701481 TGTTCATTTATGTTCG
1 TGTTCGTTTATGTTCG
1701497 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
1701513 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
1701529 T
1 T
1701530 TTATTTATTA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.08, C:0.12, G:0.23, T:0.57
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:1710254 original size:14 final size:14
Alignment explanation
Indices: 1710235--1710274 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
1710225 AGAAAATGGT
1710235 GGAGACTGGAGACC
1 GGAGACTGGAGACC
1710249 GGAGACTGGAGACC
1 GGAGACTGGAGACC
* *
1710263 GAAGAGTGGAGA
1 GGAGACTGGAGA
1710275 GTCAAGAATG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.33, C:0.15, G:0.45, T:0.07
Consensus pattern (14 bp):
GGAGACTGGAGACC
Found at i:1711278 original size:31 final size:31
Alignment explanation
Indices: 1711243--1711309 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 31
1711233 TTGAATATAA
*
1711243 ACCTTAATTGTACTGTGCACTATCTGAATGC
1 ACCTTAACTGTACTGTGCACTATCTGAATGC
* * * *
1711274 ACCTTGACTGTATTGTGCATTATTTGAATGC
1 ACCTTAACTGTACTGTGCACTATCTGAATGC
1711305 ACCTT
1 ACCTT
1711310 GACTAGTATT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.24, C:0.21, G:0.16, T:0.39
Consensus pattern (31 bp):
ACCTTAACTGTACTGTGCACTATCTGAATGC
Found at i:1711310 original size:31 final size:31
Alignment explanation
Indices: 1711251--1711319 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
1711241 AAACCTTAAT
*
1711251 TGTACTGTGCACTATCTGAATGCACCTTGAC
1 TGTATTGTGCACTATCTGAATGCACCTTGAC
* *
1711282 TGTATTGTGCATTATTTGAATGCACCTTGAC
1 TGTATTGTGCACTATCTGAATGCACCTTGAC
1711313 TAGTATT
1 T-GTATT
1711320 TAGTCTCACA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
31 29 0.85
32 5 0.15
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.39
Consensus pattern (31 bp):
TGTATTGTGCACTATCTGAATGCACCTTGAC
Found at i:1712365 original size:20 final size:21
Alignment explanation
Indices: 1712341--1712417 Score: 88
Period size: 20 Copynumber: 3.8 Consensus size: 21
1712331 TGATACCAAG
*
1712341 CCTTCGATATGAATACTCAAT
1 CCTTCGATATGAAGACTCAAT
* * *
1712362 -CTTCGGTATGGAGA-TCAGT
1 CCTTCGATATGAAGACTCAAT
1712381 CCTTCGATATGAAGAC-CAAT
1 CCTTCGATATGAAGACTCAAT
*
1712401 CCTTCTATATGAAGACT
1 CCTTCGATATGAAGACT
1712418 AGTTCTTTAG
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
19 4 0.09
20 41 0.91
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.31
Consensus pattern (21 bp):
CCTTCGATATGAAGACTCAAT
Found at i:1712504 original size:20 final size:20
Alignment explanation
Indices: 1712481--1712530 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
1712471 CTAAACCCTT
* *
1712481 AGTATCGATATCAAAGGGTC
1 AGTATCGATATCAAAGGATA
1712501 AGTATCGATATCAAAGGATA
1 AGTATCGATATCAAAGGATA
1712521 AGTATCGATA
1 AGTATCGATA
1712531 CTATTTCCCT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.40, C:0.12, G:0.22, T:0.26
Consensus pattern (20 bp):
AGTATCGATATCAAAGGATA
Found at i:1718436 original size:68 final size:68
Alignment explanation
Indices: 1718354--1718495 Score: 239
Period size: 68 Copynumber: 2.1 Consensus size: 68
1718344 GTCTTATAAG
* * *
1718354 AAAAAAAATAAAAACATTAGAACATCATACATTTAGATGAATTTTATGTATTTTGAATGAGTTCT
1 AAAAAAAATAAAAACATTAGAACATCAAACATTTAGATGAATTTTATCTATTTTGAATGAGTTCC
1718419 AGA
66 AGA
* *
1718422 AAAAAAAATTAAAACATTAGAACATGAAACATTTAGATGAATTTTATCTATTTTGAATGAGTTCC
1 AAAAAAAATAAAAACATTAGAACATCAAACATTTAGATGAATTTTATCTATTTTGAATGAGTTCC
1718487 AGA
66 AGA
1718490 AAAAAA
1 AAAAAA
1718496 TTATTCCTAA
Statistics
Matches: 69, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
68 69 1.00
ACGTcount: A:0.49, C:0.08, G:0.11, T:0.32
Consensus pattern (68 bp):
AAAAAAAATAAAAACATTAGAACATCAAACATTTAGATGAATTTTATCTATTTTGAATGAGTTCC
AGA
Found at i:1720663 original size:228 final size:229
Alignment explanation
Indices: 1719982--1720665 Score: 775
Period size: 228 Copynumber: 3.0 Consensus size: 229
1719972 AGCCAAACAA
* * * * *
1719982 GATGCAGATCTTCGTCAAGACCCTGACCGGAAAGACAATCACCCTTGAAGTCGAGAGTTCCGATA
1 GATGCAGATCTTCGTCAAGACTCTGACCGGAAAAACCATAACCCTAGAAGTCGAGAGTTCCGATA
* *
1720047 CCATCGACAACGTCAAGGCCAAGATCCAAGACAAGGAAGGGA-TCCCACCGGATCAGCAG-CGTC
66 CGATCGACAACGTCAAGGCCAAGATCCAAGACAAGGAAGGGATTCCC-CCGGATCAGCAGAGGT-
*
1720110 TCATCTTCGCCGGAAAACAGCTCGAAGACGGCCGGACT-TTGGCCGATTACAACATCCAGAAGGA
129 TCATCTTCGCTGGAAAACAGCTCGAAGACGGCCGGACTCTTGGCCGATTACAACATCCAGAAGGA
* * * * *
1720174 GTCAACCCTCCACCTCGTCCTCCGTCTTCGTGGAGG
194 ATCAACCCTTCACCTCGTCTTGCGTCTTCGTGGTGG
* * * ** * * * *
1720210 CATGCAGATCTTCGTCAAAACTCTCACCGGAAAAACCATAACTTTGGAAGTTGAGAGCTCCGACA
1 GATGCAGATCTTCGTCAAGACTCTGACCGGAAAAACCATAACCCTAGAAGTCGAGAGTTCCGATA
* * *
1720275 CGATCGACAACGTCAAGGCCAAGATCCAAGACAAGGAAGGGATTCCACCGGACCAGCAGAGGCTC
66 CGATCGACAACGTCAAGGCCAAGATCCAAGACAAGGAAGGGATTCCCCCGGATCAGCAGAGGTTC
* *
1720340 ATCTTCGCTGGAAAACAGCTCGAAGACGGCCGGAC-CTTGGCCGATTATAACATTCAGAAGGAAT
131 ATCTTCGCTGGAAAACAGCTCGAAGACGGCCGGACTCTTGGCCGATTACAACATCCAGAAGGAAT
* * * * * *
1720404 CGACCCTTCATCTGGTTTTGAGGCTTCGTGGTGG
196 CAACCCTTCACCTCGTCTTGCGTCTTCGTGGTGG
* * * * *
1720438 GATGCAGATCTTCGTCAAGACTTTGACTGGAAAAACCATAACCCTAGAGGTGGAGAGTTCTGATA
1 GATGCAGATCTTCGTCAAGACTCTGACCGGAAAAACCATAACCCTAGAAGTCGAGAGTTCCGATA
* * * * * * * * *
1720503 CGATCGATAATGTTAAGGCGAAGATTCAGGACAAAGAAGGGATTCCCCCAGATCAGCAGAGGTTG
66 CGATCGACAACGTCAAGGCCAAGATCCAAGACAAGGAAGGGATTCCCCCGGATCAGCAGAGGTTC
* * ** * * ** * *
1720568 ATTTTCGCTGGGAAACAATTGGAAGATGGAAGGACTCTT-GCTGATTACAATATCCAGAAGGAAT
131 ATCTTCGCTGGAAAACAGCTCGAAGACGGCCGGACTCTTGGCCGATTACAACATCCAGAAGGAAT
* * *
1720632 CCACTCTTCACCTTGTCTTGCGTCTTCGTGGTGG
196 CAACCCTTCACCTCGTCTTGCGTCTTCGTGGTGG
1720666 TTTCTAAGCT
Statistics
Matches: 376, Mismatches: 76, Indels: 8
0.82 0.17 0.02
Matches are distributed among these distances:
228 369 0.98
229 7 0.02
ACGTcount: A:0.29, C:0.25, G:0.25, T:0.21
Consensus pattern (229 bp):
GATGCAGATCTTCGTCAAGACTCTGACCGGAAAAACCATAACCCTAGAAGTCGAGAGTTCCGATA
CGATCGACAACGTCAAGGCCAAGATCCAAGACAAGGAAGGGATTCCCCCGGATCAGCAGAGGTTC
ATCTTCGCTGGAAAACAGCTCGAAGACGGCCGGACTCTTGGCCGATTACAACATCCAGAAGGAAT
CAACCCTTCACCTCGTCTTGCGTCTTCGTGGTGG
Found at i:1730391 original size:21 final size:22
Alignment explanation
Indices: 1730358--1730399 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 22
1730348 ATGCACAAAG
1730358 TCGGATAAAAAACCGATCCGGA
1 TCGGATAAAAAACCGATCCGGA
1730380 TCGGAT-AAAAACCGATCCGG
1 TCGGATAAAAAACCGATCCGG
1730400 TTTTTTCATC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.38, C:0.24, G:0.24, T:0.14
Consensus pattern (22 bp):
TCGGATAAAAAACCGATCCGGA
Found at i:1731607 original size:12 final size:12
Alignment explanation
Indices: 1731567--1731608 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
1731557 CGGATAAAAA
1731567 CCGGTTTTT-AT
1 CCGGTTTTTAAT
*
1731578 CCGGTTTTTTCAAA
1 CCGG-TTTTT-AAT
1731592 CCGGTTTTTAAT
1 CCGGTTTTTAAT
1731604 CCGGT
1 CCGGT
1731609 AAAAAAACTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
11 4 0.15
12 12 0.46
13 5 0.19
14 5 0.19
ACGTcount: A:0.14, C:0.21, G:0.19, T:0.45
Consensus pattern (12 bp):
CCGGTTTTTAAT
Found at i:1736694 original size:21 final size:21
Alignment explanation
Indices: 1736650--1736694 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1736640 ACCAAGGAAA
* *
1736650 CATCTACACAATCGGGTTCGT
1 CATCTACACAATCAGGTTCAT
* *
1736671 CATCTACTCAATCAGTTTCAT
1 CATCTACACAATCAGGTTCAT
1736692 CAT
1 CAT
1736695 TGGACTTCAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.27, C:0.29, G:0.11, T:0.33
Consensus pattern (21 bp):
CATCTACACAATCAGGTTCAT
Found at i:1736747 original size:311 final size:306
Alignment explanation
Indices: 1736153--1736900 Score: 789
Period size: 311 Copynumber: 2.4 Consensus size: 306
1736143 CACAATAAAA
* * * *
1736153 TTCATTATTATTTTGTTACAGGTATTGATCAATCAGTGGGATATGAACCGAAAATAGAGAAGATG
1 TTCATTAATATTTTGTTACAGGTATTGATCAATCAATGGGATCTGAACAG-AAATAGAGAAGATG
* ** * * * *
1736218 AAAATCCAGTCATGCACTGATCTTTTAGATGTTAGGGAGAAACCAAAAAGGAGAAAGAAGAACAC
65 AAAA-CCAGTCTTGCACTGATCTTCCAAATGTTACGGAGAAACGAAAAAGGAGAAAGAAGAAAAC
* * * * * * * * *
1736283 TTCCATTGCTGGCTCCTGTTCCTTGAAATCTCAACGATTGTCCAAGACGAATGGAACGTCTACTC
129 TTCCATTGCCGGCTCATCTTCCTCGAAATCACAAAGATTGTCCAAGACCAATGGAACATCTACAC
* * * * * *
1736348 AATTGGGTTCGCCATCTACTCAATTGTGTTTATCACTCAAATTCAGATCATCATGCATGACTATT
194 AATCGGGTTCGCCATCTACTCAATAGTGTTTATCACTCAAATTCACATCAACACGCATGACTATA
* * * * * *
1736413 TCTTACTAAAATATTAGAGATTCCCATGAACATAATAAAGTTGAAATCGAT
259 TCTTACT---ATACTAGAGATTCCCATAAACACAACAAAGTTGAAACCAAT
* * *
1736464 TTCATTACTATTTTG-CAGCAGGTATTGATCAATCAATGGGATCTGAACTAGAAGTAGAGAAGAT
1 TTCATTAATATTTTGTTA-CAGGTATTGATCAATCAATGGGATCTGAAC-AGAAATAGAGAAGAT
*
1736528 GAGAAACCAGTCTTGCACTGATCTTCCAAATGTTATGGAGAAACGAAAAAGGAGAAAGAAGAAAA
64 GA-AAACCAGTCTTGCACTGATCTTCCAAATGTTACGGAGAAACGAAAAAGGAGAAAGAAGAAAA
1736593 CTTCCACTT-CCGAG-TCATCTTCCTCGAAATCACAAAGATTGTCCAAGACCAA-GGAAACATCT
128 CTTCCA-TTGCCG-GCTCATCTTCCTCGAAATCACAAAGATTGTCCAAGACCAATGG-AACATCT
* *
1736655 ACACAATCGGGTTCGTCATCTACTCAATCAGT-TTCATCATTGGACTTCAAAATATACACATCAA
190 ACACAATCGGGTTCGCCATCTACTCAAT-AGTGTT--T-A-T-CAC-TC-AAAT-T-CACATCAA
* * *
1736719 CACGCGTGA-T-TAT-TTA-T-TACTA-AGATTCCCATAAACACGACAAAGTTGAAGCCAAT
245 CACGCATGACTATATCTTACTATACTAGAGATTCCCATAAACACAACAAAGTTGAAACCAAT
* *
1736775 TTCATTAATATTTTGTTACAGGAATTGATCAATCAATGGGATCTGAACCAGAAACAGAGAAGATG
1 TTCATTAATATTTTGTTACAGGTATTGATCAATCAATGGGATCTGAA-CAGAAATAGAGAAGATG
* * * *
1736840 ATAAACCAATCTTGCACTGATCTTCCAAATGTTACAGAGAAACGAAAAAGAAGAAGGAAGA
65 A-AAACCAGTCTTGCACTGATCTTCCAAATGTTACGGAGAAACGAAAAAGGAGAAAGAAGA
1736901 GCTCCACTGC
Statistics
Matches: 369, Mismatches: 50, Indels: 36
0.81 0.11 0.08
Matches are distributed among these distances:
310 3 0.01
311 319 0.86
312 15 0.04
313 1 0.00
314 1 0.00
315 1 0.00
316 3 0.01
317 5 0.01
318 6 0.02
319 2 0.01
320 13 0.04
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.27
Consensus pattern (306 bp):
TTCATTAATATTTTGTTACAGGTATTGATCAATCAATGGGATCTGAACAGAAATAGAGAAGATGA
AAACCAGTCTTGCACTGATCTTCCAAATGTTACGGAGAAACGAAAAAGGAGAAAGAAGAAAACTT
CCATTGCCGGCTCATCTTCCTCGAAATCACAAAGATTGTCCAAGACCAATGGAACATCTACACAA
TCGGGTTCGCCATCTACTCAATAGTGTTTATCACTCAAATTCACATCAACACGCATGACTATATC
TTACTATACTAGAGATTCCCATAAACACAACAAAGTTGAAACCAAT
Found at i:1737301 original size:615 final size:618
Alignment explanation
Indices: 1736392--1737759 Score: 1714
Period size: 615 Copynumber: 2.2 Consensus size: 618
1736382 ACTCAAATTC
* * * * * * *
1736392 AGATCATCATGCATGACTATTTCTTACTAAAATATTAGAGATTCCCATGAACATAATAAAGTTGA
1 AGATCATCATGCATGATTATTTCTTACTAATATATT-GAGATTCTCATAAACACAACAAAGTCGA
* * * * * * * *
1736457 AATCGATTTCATTACTA-TTTTG-CAGCAGGTATTGATCAATCAATGGGATCTGAACTAGAAGTA
65 AATCAATTTCATTATTATTTTTGTTA-CAGATATTGATCAATTAATGGGATCTGAACCAGCAGCA
* * *
1736520 GAGAAGATGAGAAACCAGTCTTGCACTGATCTTCCAAATGTTATGGAGAAACGAAAAAGGAGAAA
129 GAGAAGATGAAAAACCAGTCTTGCACTGATCTCCCAAATGTTATGGAGAAACCAAAAAGGAGAAA
* * * *
1736585 GAAGAAAACTTCCACTTCCGAGTCATCTTCCTCGAAATCACAAAGATTGTCCAAGACCAAGGAAA
194 GAAGAAAACTTCCACTTCCGAGTCATCCTCCTCGAAATCACAAAGATTATCCAAAACCAAAGAAA
* *** *
1736650 CATCTACACAATCGGGTTCGTCATCTACTCAATCAGTTTCATCATTGGACTTCAAAATATACACA
259 CATCTACACAATCGGGTTCATCATCTACTCAATCAGTTTCATCATCCAACTTCAAAATATAAACA
* * ** *
1736715 TCAACACGC-G-TGA-TTATT-T-AT-TA-CTAAGATTCCCATAAACACGACAAAGTTGAAGCCA
324 TCAACACGCAGCTGATTTATTATAATATATCTAAGATTCCCATAAACACAACAAACTCCAAGCAA
* *
1736773 ATTTCATTAATATTTTGTTACAGGAATTGATCAATCAATGG-GATCTGAACCAGAAACAGAGAAG
389 ATTTCATTAATATTTTGTTACAGGAATTGATCAATCAATGGAG-GCTGAACCAGAAACAGAGAAA
*
1736837 ATGATAAACCAATCTTGCACTGATCTTCCAAATGTTACAGAGAAACGAAAAAGAAGAAGGAAGAG
453 ATGAGAAACCAATCTTGCACTGATCTTCCAAATGTTACAGAGAAACGAAAAA-AAGAAGGAAGAG
* *
1736902 -C-TCCACTGCCGAGTCTTCTTCTTCTCTTTCAAAATATAAACGATTATCCAAGATGAAGAAAAT
517 CCTTCCACTGCCGAGGCTTCTTC-T-TC-TTCAAAATATAAACGATTAACCAAGATGAAGAAAAT
* * * * *
1736965 ATCTTCTCAATTGGGTTCGTTAGTAGACTTCAAAATATGA
579 ATCTACACAATTAGGTTCGTCACTAGACTTCAAAATATGA
* * *
1737005 AGATCATCATGCATGATTATTTCTTACTAATATATTTGAGATTCTTATCAACACAAGAAAGTCGA
1 AGATCATCATGCATGATTATTTCTTACTAATATA-TTGAGATTCTCATAAACACAACAAAGTCGA
* *
1737070 AATCAATTTCATTATTACTTTTTGTTACAGATATTGATCAATTTATTGGATCTGAACCAGCAGCA
65 AATCAATTTCATTATTA-TTTTTGTTACAGATATTGATCAATTAATGGGATCTGAACCAGCAGCA
1737135 GAGAAGATGAAAAACCAGTCTTGCACTGATCTCCCAAATGTTATGGAGAAACCAAAAAGGAGAAA
129 GAGAAGATGAAAAACCAGTCTTGCACTGATCTCCCAAATGTTATGGAGAAACCAAAAAGGAGAAA
* * * * *
1737200 GAAGAGAAGTTCCACTTCCGAGTCATCCTCCTCGAAATCTCAACGATTATCCAAAACTAAAGAAA
194 GAAGAAAACTTCCACTTCCGAGTCATCCTCCTCGAAATCACAAAGATTATCCAAAACCAAAGAAA
* * * * * *
1737265 CATCTACTCAATTGGGTTCATTATGTACTTAATCAGTTTCATCATCCAACTTCAAAATATAAAGA
259 CATCTACACAATCGGGTTCATCATCTACTCAATCAGTTTCATCATCCAACTTCAAAATATAAACA
* ** * * * * *
1737330 TCACCGTGCAAGCTTATTTCTTACTAATATATTTAAGATTCTCATAAACACAACAAACTCCAAGT
324 TCAACACGC-AGCTGATTTATTA-TAATATATCTAAGATTCCCATAAACACAACAAACTCCAAGC
* * * *
1737395 AAATTTTATTAATATTTTGTTACAGGTATTGATCAATCAATGGAGGCTGAAGCAGAAGCAGAGAA
387 AAATTTCATTAATATTTTGTTACAGGAATTGATCAATCAATGGAGGCTGAACCAGAAACAGAGAA
* * *
1737460 AATGAGAAACCAGTCTTGCATTGATCTTTCAAATGTTACAGAGAAACGAAAAAAAGAAGGAAGAG
452 AATGAGAAACCAATCTTGCACTGATCTTCCAAATGTTACAGAGAAACGAAAAAAAGAAGGAAGAG
* *
1737525 CTCTTCCACTGCTGAGGCTTCTTCTTCTTCGAAATATAAACGATTAACCAAGATGAAGAAAATAT
517 C-CTTCCACTGCCGAGGCTTCTTCTTCTTCAAAATATAAACGATTAACCAAGATGAAGAAAATAT
1737590 CTACACAATTAGGTTCGTCACTAGACTTCAAAATATGA
581 CTACACAATTAGGTTCGTCACTAGACTTCAAAATATGA
*
1737628 AGATCATCATGCATGATTATTTC-T--T-AT-TA---AGATTCTCATAAACACAACAAAGTGGAA
1 AGATCATCATGCATGATTATTTCTTACTAATATATTGAGATTCTCATAAACACAACAAAGTCGAA
* * * *
1737685 GTCAATTTTATTACTAATATTTTTTTATTACATATATTGATCAATTAATGGGATCTGAACCAGCA
66 ATCAATTTCATTA-T--TA--TTTTTGTTACAGATATTGATCAATTAATGGGATCTGAACCAGCA
*
1737750 ACAGAGAAGA
126 GCAGAGAAGA
1737760 GCACCGATTT
Statistics
Matches: 649, Mismatches: 85, Indels: 37
0.84 0.11 0.05
Matches are distributed among these distances:
613 69 0.11
614 37 0.06
615 215 0.33
616 1 0.00
617 3 0.00
618 53 0.08
619 6 0.01
620 1 0.00
621 1 0.00
622 3 0.00
623 106 0.16
624 133 0.20
625 3 0.00
626 18 0.03
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.29
Consensus pattern (618 bp):
AGATCATCATGCATGATTATTTCTTACTAATATATTGAGATTCTCATAAACACAACAAAGTCGAA
ATCAATTTCATTATTATTTTTGTTACAGATATTGATCAATTAATGGGATCTGAACCAGCAGCAGA
GAAGATGAAAAACCAGTCTTGCACTGATCTCCCAAATGTTATGGAGAAACCAAAAAGGAGAAAGA
AGAAAACTTCCACTTCCGAGTCATCCTCCTCGAAATCACAAAGATTATCCAAAACCAAAGAAACA
TCTACACAATCGGGTTCATCATCTACTCAATCAGTTTCATCATCCAACTTCAAAATATAAACATC
AACACGCAGCTGATTTATTATAATATATCTAAGATTCCCATAAACACAACAAACTCCAAGCAAAT
TTCATTAATATTTTGTTACAGGAATTGATCAATCAATGGAGGCTGAACCAGAAACAGAGAAAATG
AGAAACCAATCTTGCACTGATCTTCCAAATGTTACAGAGAAACGAAAAAAAGAAGGAAGAGCCTT
CCACTGCCGAGGCTTCTTCTTCTTCAAAATATAAACGATTAACCAAGATGAAGAAAATATCTACA
CAATTAGGTTCGTCACTAGACTTCAAAATATGA
Found at i:1738441 original size:24 final size:24
Alignment explanation
Indices: 1738413--1738460 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1738403 AGATGAAAAA
*
1738413 TAGAATTGAAAGTATTCTGCAAAT
1 TAGAATTAAAAGTATTCTGCAAAT
* *
1738437 TAGAATTAAAAGTGTTGTGCAAAT
1 TAGAATTAAAAGTATTCTGCAAAT
1738461 AATGACTTGG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.42, C:0.06, G:0.19, T:0.33
Consensus pattern (24 bp):
TAGAATTAAAAGTATTCTGCAAAT
Found at i:1741325 original size:13 final size:15
Alignment explanation
Indices: 1741309--1741340 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
1741299 GCTCTCTCAA
1741309 TTCTCTC-TAT-TTT
1 TTCTCTCGTATATTT
1741322 TTCTCTCGTATATTT
1 TTCTCTCGTATATTT
1741337 TTCT
1 TTCT
1741341 TTTGCTCACT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 7 0.41
14 3 0.18
15 7 0.41
ACGTcount: A:0.09, C:0.22, G:0.03, T:0.66
Consensus pattern (15 bp):
TTCTCTCGTATATTT
Found at i:1742349 original size:30 final size:30
Alignment explanation
Indices: 1742230--1742359 Score: 179
Period size: 30 Copynumber: 4.3 Consensus size: 30
1742220 TCCGAATGAC
*
1742230 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCATAGGTCATAAAGATCCTCGGTAA
*
1742260 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCATAGGTCATAAAGATCCTCGGTAA
*
1742290 CTATCCATAGGTTATAAAGATCCTCGGTAA
1 CTATCCATAGGTCATAAAGATCCTCGGTAA
*** * *
1742320 CTATCCATAGGTCCCGAAGAACCTAGGTAAA
1 CTATCCATAGGTCATAAAGATCCTCGGT-AA
1742351 CTATCCATA
1 CTATCCATA
1742360 TATTCCTTAG
Statistics
Matches: 91, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
30 80 0.88
31 11 0.12
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.25
Consensus pattern (30 bp):
CTATCCATAGGTCATAAAGATCCTCGGTAA
Found at i:1742406 original size:31 final size:30
Alignment explanation
Indices: 1742315--1742410 Score: 88
Period size: 31 Copynumber: 3.1 Consensus size: 30
1742305 AAAGATCCTC
* * *
1742315 GGTAACTATCCATAGGTCCCGAAGAACCTA
1 GGTAACTATCCATATGTCTCGAAGAACATA
* **
1742345 GGTAAACTATCCATATAT-TCCTTAGAACATA
1 GGT-AACTATCCATATGTCT-CGAAGAACATA
1742376 GGTATACTATCCATATGTCTCGAA-AGACATA
1 GGTA-ACTATCCATATGTCTCGAAGA-ACATA
1742407 GGTA
1 GGTA
1742411 GTTCTTTGAC
Statistics
Matches: 52, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
30 5 0.10
31 46 0.88
32 1 0.02
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (30 bp):
GGTAACTATCCATATGTCTCGAAGAACATA
Found at i:1742834 original size:22 final size:22
Alignment explanation
Indices: 1742809--1742863 Score: 110
Period size: 22 Copynumber: 2.5 Consensus size: 22
1742799 CCCTCATATG
1742809 ATTTCATATTCATATGCTACAT
1 ATTTCATATTCATATGCTACAT
1742831 ATTTCATATTCATATGCTACAT
1 ATTTCATATTCATATGCTACAT
1742853 ATTTCATATTC
1 ATTTCATATTC
1742864 TTTCTATGTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.31, C:0.18, G:0.04, T:0.47
Consensus pattern (22 bp):
ATTTCATATTCATATGCTACAT
Found at i:1748052 original size:30 final size:30
Alignment explanation
Indices: 1748016--1748118 Score: 188
Period size: 30 Copynumber: 3.4 Consensus size: 30
1748006 TCCGAATGAC
1748016 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1748046 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1748076 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
1748106 TTATCCATAGGTC
1 CTATCCAGAGGTC
1748119 CCGAAGAACC
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 71 1.00
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.25
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:1748135 original size:60 final size:61
Alignment explanation
Indices: 1748016--1748143 Score: 186
Period size: 60 Copynumber: 2.1 Consensus size: 61
1748006 TCCGAATGAC
* * *
1748016 CTATCCAGAGGTCATAAAGATCCTCGGTAACTATCCAGAGGTCATAAAGATCCTCGGT-AA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAACTATCCAGAGGTCACAAAGAACCTAGGTAAA
* * * *
1748076 CTATCCAGAGGTCATAAAGATCCTCGGTAATTATCCATAGGTCCCGAAGAACCTAGGTAAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAACTATCCAGAGGTCACAAAGAACCTAGGTAAA
1748137 CTATCCA
1 CTATCCA
1748144 TATGTTCCTT
Statistics
Matches: 60, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
60 51 0.85
61 9 0.15
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.23
Consensus pattern (61 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAACTATCCAGAGGTCACAAAGAACCTAGGTAAA
Found at i:1753632 original size:13 final size:15
Alignment explanation
Indices: 1753616--1753647 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
1753606 GCTCTCTCAA
1753616 TTCTCTC-TAT-TTT
1 TTCTCTCGTATATTT
1753629 TTCTCTCGTATATTT
1 TTCTCTCGTATATTT
1753644 TTCT
1 TTCT
1753648 TTTGCTCACT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 7 0.41
14 3 0.18
15 7 0.41
ACGTcount: A:0.09, C:0.22, G:0.03, T:0.66
Consensus pattern (15 bp):
TTCTCTCGTATATTT
Found at i:1756377 original size:30 final size:30
Alignment explanation
Indices: 1756315--1756391 Score: 93
Period size: 31 Copynumber: 2.6 Consensus size: 30
1756305 GGAAAAAATG
* * *
1756315 AATACTTTATGTACTTATTTTGACCAAAAA
1 AATAATTTAAGTACTTATTTTAACCAAAAA
*
1756345 AATAAATTTAAGTATTTATTTTAACC-AAAA
1 AAT-AATTTAAGTACTTATTTTAACCAAAAA
*
1756375 AATATTTTAAGTACTTA
1 AATAATTTAAGTACTTA
1756392 AATGAAAAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
29 12 0.30
30 10 0.25
31 18 0.45
ACGTcount: A:0.44, C:0.09, G:0.05, T:0.42
Consensus pattern (30 bp):
AATAATTTAAGTACTTATTTTAACCAAAAA
Found at i:1762129 original size:22 final size:22
Alignment explanation
Indices: 1762104--1762160 Score: 78
Period size: 24 Copynumber: 2.5 Consensus size: 22
1762094 CAATATATTG
1762104 TTGGAAGTCAAAATTGGAGGCT
1 TTGGAAGTCAAAATTGGAGGCT
*
1762126 TTGGGGAAGTCAAAATTGGGGGCT
1 TT--GGAAGTCAAAATTGGAGGCT
*
1762150 TTGGAATTCAA
1 TTGGAAGTCAA
1762161 CAAAGAGGGC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
22 10 0.32
24 21 0.68
ACGTcount: A:0.30, C:0.09, G:0.33, T:0.28
Consensus pattern (22 bp):
TTGGAAGTCAAAATTGGAGGCT
Found at i:1762133 original size:24 final size:24
Alignment explanation
Indices: 1762106--1762153 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
1762096 ATATATTGTT
1762106 GGAAGTCAAAATTGGAGGCTTTGG
1 GGAAGTCAAAATTGGAGGCTTTGG
*
1762130 GGAAGTCAAAATTGGGGGCTTTGG
1 GGAAGTCAAAATTGGAGGCTTTGG
1762154 AATTCAACAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.27, C:0.08, G:0.40, T:0.25
Consensus pattern (24 bp):
GGAAGTCAAAATTGGAGGCTTTGG
Found at i:1766695 original size:22 final size:22
Alignment explanation
Indices: 1766670--1766750 Score: 90
Period size: 24 Copynumber: 3.5 Consensus size: 22
1766660 TGGGAGATTG
*
1766670 TTGGAAGTCAAAATTATAGGCT
1 TTGGAAGTCAAAATTAGAGGCT
1766692 TTGGGGAAGTCAAAATTAGAGGCT
1 TT--GGAAGTCAAAATTAGAGGCT
* *
1766716 TCGGGGAAGTCAAAATTAGGGGCT
1 T--TGGAAGTCAAAATTAGAGGCT
*
1766740 TTGGAATTCAA
1 TTGGAAGTCAA
1766751 CAAAGAGGAC
Statistics
Matches: 50, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
22 10 0.20
24 40 0.80
ACGTcount: A:0.33, C:0.10, G:0.30, T:0.27
Consensus pattern (22 bp):
TTGGAAGTCAAAATTAGAGGCT
Found at i:1766702 original size:24 final size:24
Alignment explanation
Indices: 1766672--1766743 Score: 117
Period size: 24 Copynumber: 3.0 Consensus size: 24
1766662 GGAGATTGTT
*
1766672 GGAAGTCAAAATTATAGGCTTTGG
1 GGAAGTCAAAATTAGAGGCTTTGG
*
1766696 GGAAGTCAAAATTAGAGGCTTCGG
1 GGAAGTCAAAATTAGAGGCTTTGG
*
1766720 GGAAGTCAAAATTAGGGGCTTTGG
1 GGAAGTCAAAATTAGAGGCTTTGG
1766744 AATTCAACAA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 44 1.00
ACGTcount: A:0.32, C:0.10, G:0.33, T:0.25
Consensus pattern (24 bp):
GGAAGTCAAAATTAGAGGCTTTGG
Found at i:1771088 original size:24 final size:20
Alignment explanation
Indices: 1771052--1771205 Score: 123
Period size: 20 Copynumber: 7.4 Consensus size: 20
1771042 TACCAACAAA
*
1771052 ATCGCAATGCGATCTCTAAATCGT
1 ATCGCAACGCGAT-TCT-AA-C-T
*
1771076 ATCGCAACACGATTCTAACT
1 ATCGCAACGCGATTCTAACT
**
1771096 ATCGCAACGCGATAAT-ACAT
1 ATCGCAACGCGATTCTAAC-T
*
1771116 AATCGCAACGCGATTCTGACT
1 -ATCGCAACGCGATTCTAACT
**
1771137 ATCGCAACGCGATAAT-ACAT
1 ATCGCAACGCGATTCTAAC-T
*
1771157 AATCGCAACGCGATTCTGACT
1 -ATCGCAACGCGATTCTAACT
* *
1771178 ATCGCAACGTGATTCTTACT
1 ATCGCAACGCGATTCTAACT
*
1771198 GTCGCAAC
1 ATCGCAAC
1771206 ACTGAATTTC
Statistics
Matches: 110, Mismatches: 14, Indels: 16
0.79 0.10 0.11
Matches are distributed among these distances:
19 4 0.04
20 55 0.50
21 31 0.28
22 6 0.05
23 3 0.03
24 11 0.10
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATTCTAACT
Found at i:1771100 original size:20 final size:19
Alignment explanation
Indices: 1771075--1771205 Score: 127
Period size: 20 Copynumber: 6.5 Consensus size: 19
1771065 CTCTAAATCG
*
1771075 TATCGCAACACGATTCTAAC
1 TATCGCAACGCGATTCT-AC
**
1771095 TATCGCAACGCGATAATAC
1 TATCGCAACGCGATTCTAC
1771114 ATAATCGCAACGCGATTCTGAC
1 -T-ATCGCAACGCGATTCT-AC
**
1771136 TATCGCAACGCGATAATAC
1 TATCGCAACGCGATTCTAC
1771155 ATAATCGCAACGCGATTCTGAC
1 -T-ATCGCAACGCGATTCT-AC
*
1771177 TATCGCAACGTGATTCTTAC
1 TATCGCAACGCGATTC-TAC
*
1771197 TGTCGCAAC
1 TATCGCAAC
1771206 ACTGAATTTC
Statistics
Matches: 93, Mismatches: 11, Indels: 14
0.79 0.09 0.12
Matches are distributed among these distances:
19 4 0.04
20 54 0.58
21 31 0.33
22 4 0.04
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.24
Consensus pattern (19 bp):
TATCGCAACGCGATTCTAC
Found at i:1771122 original size:21 final size:21
Alignment explanation
Indices: 1771096--1771170 Score: 109
Period size: 21 Copynumber: 3.6 Consensus size: 21
1771086 GATTCTAACT
1771096 ATCGCAACGCGATAATACATA
1 ATCGCAACGCGATAATACATA
**
1771117 ATCGCAACGCGATTCTGAC-T-
1 ATCGCAACGCGATAAT-ACATA
1771137 ATCGCAACGCGATAATACATA
1 ATCGCAACGCGATAATACATA
1771158 ATCGCAACGCGAT
1 ATCGCAACGCGAT
1771171 TCTGACTATC
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
19 2 0.04
20 15 0.32
21 28 0.60
22 2 0.04
ACGTcount: A:0.36, C:0.27, G:0.17, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGATAATACATA
Found at i:1771130 original size:41 final size:41
Alignment explanation
Indices: 1771076--1771186 Score: 204
Period size: 41 Copynumber: 2.7 Consensus size: 41
1771066 TCTAAATCGT
* *
1771076 ATCGCAACACGATTCTAACTATCGCAACGCGATAATACATA
1 ATCGCAACGCGATTCTGACTATCGCAACGCGATAATACATA
1771117 ATCGCAACGCGATTCTGACTATCGCAACGCGATAATACATA
1 ATCGCAACGCGATTCTGACTATCGCAACGCGATAATACATA
1771158 ATCGCAACGCGATTCTGACTATCGCAACG
1 ATCGCAACGCGATTCTGACTATCGCAACG
1771187 TGATTCTTAC
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 68 1.00
ACGTcount: A:0.34, C:0.28, G:0.16, T:0.22
Consensus pattern (41 bp):
ATCGCAACGCGATTCTGACTATCGCAACGCGATAATACATA
Found at i:1774362 original size:18 final size:18
Alignment explanation
Indices: 1774339--1774373 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1774329 AAAAAAAGGC
*
1774339 AATCAAAATCGCAATCAA
1 AATCAAAATCCCAATCAA
1774357 AATCAAAATCCCAATCA
1 AATCAAAATCCCAATCA
1774374 CAACTGGCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.26, G:0.03, T:0.17
Consensus pattern (18 bp):
AATCAAAATCCCAATCAA
Found at i:1774683 original size:140 final size:140
Alignment explanation
Indices: 1774431--1774713 Score: 539
Period size: 140 Copynumber: 2.0 Consensus size: 140
1774421 GCAAACGTTG
1774431 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
1 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
* *
1774496 TTGAACATTGCTATGATTTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATTGCAACG
66 TTGAACATTGCTATGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
*
1774561 CGAATTTGAC
131 CAAATTTGAC
1774571 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
1 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
1774636 TTGAACATTGCTATGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
66 TTGAACATTGCTATGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
1774701 CAAATTTGAC
131 CAAATTTGAC
1774711 TAT
1 TAT
1774714 CGCAACGCGA
Statistics
Matches: 140, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
140 140 1.00
ACGTcount: A:0.29, C:0.12, G:0.15, T:0.44
Consensus pattern (140 bp):
TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
TTGAACATTGCTATGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
CAAATTTGAC
Found at i:1774771 original size:20 final size:20
Alignment explanation
Indices: 1774684--1774842 Score: 126
Period size: 20 Copynumber: 8.6 Consensus size: 20
1774674 TTACACATTC
* *
1774684 ATTTGAATATCGCAACGCAA
1 ATTTGACTATCGCAACGCGA
1774704 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* *
1774724 ATTTGATTATCGCAACTC-A
1 ATTTGACTATCGCAACGCGA
*
1774743 A----A-AATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
**
1774758 ATTTGACTATCGCAACATGA
1 ATTTGACTATCGCAACGCGA
* *
1774778 ATATGACTATCGCAATGC-A
1 ATTTGACTATCGCAACGCGA
*
1774797 A----A-AATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* *
1774812 ATTTGACTATCGCAACGGGT
1 ATTTGACTATCGCAACGCGA
1774832 ATTTGACTATC
1 ATTTGACTATC
1774843 ACAATGAGAA
Statistics
Matches: 109, Mismatches: 18, Indels: 24
0.72 0.12 0.16
Matches are distributed among these distances:
14 18 0.17
15 6 0.06
19 6 0.06
20 79 0.72
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.26
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:1774789 original size:54 final size:53
Alignment explanation
Indices: 1774692--1774897 Score: 261
Period size: 54 Copynumber: 3.8 Consensus size: 53
1774682 TCATTTGAAT
* *
1774692 ATCGCAACGCAAATTTGACTATCGCAACGCGAATTTGATTATCGCAACTCAAAA
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAA-TCAAAA
** *
1774746 ATCGCAACGCGAATTTGACTATCGCAACATGAATATGACTATCGCAATGCAAAA
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAAT-CAAAA
* * * *
1774800 ATCGCAACGCGAATTTGACTATCGCAACGGGTATTTGACTATCACAATGAGAAA
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAATCA-AAA
* * * *
1774854 ATCGCAAAGCGTATTAGACTATCGCAACGCGAA-TTGACTTTCGC
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGC
1774898 GTTGCGATTT
Statistics
Matches: 132, Mismatches: 18, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
53 11 0.08
54 121 0.92
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (53 bp):
ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAATCAAAA
Found at i:1774897 original size:19 final size:20
Alignment explanation
Indices: 1774854--1774897 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
1774844 CAATGAGAAA
*
1774854 ATCGCAAAGCGTATTAGACT
1 ATCGCAAAGCGAATTAGACT
*
1774874 ATCGCAACGCGAATT-GACT
1 ATCGCAAAGCGAATTAGACT
*
1774893 TTCGC
1 ATCGC
1774898 GTTGCGATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (20 bp):
ATCGCAAAGCGAATTAGACT
Found at i:1775085 original size:14 final size:14
Alignment explanation
Indices: 1775066--1775097 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
1775056 TCAATATTAA
1775066 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1775080 ACAAATCAATTTTT
1 ACAAATCAACTTTT
1775094 ACAA
1 ACAA
1775098 GCAAAAAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.47, C:0.19, G:0.00, T:0.34
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1776531 original size:21 final size:21
Alignment explanation
Indices: 1776507--1776585 Score: 61
Period size: 21 Copynumber: 3.8 Consensus size: 21
1776497 CAACGAAGAC
1776507 AGGGGCCTCTTGAACGGTGGG
1 AGGGGCCTCTTGAACGGTGGG
* * **
1776528 AGGGGACTCTTG-AGGGATGAT
1 AGGGGCCTCTTGAACGG-TGGG
* *
1776549 AGGGTCCTCTTGAACGGTAGG
1 AGGGGCCTCTTGAACGGTGGG
***
1776570 ACATGCCTCTTGAACG
1 AGGGGCCTCTTGAACG
1776586 ATGACAGGTG
Statistics
Matches: 42, Mismatches: 14, Indels: 4
0.70 0.23 0.07
Matches are distributed among these distances:
20 3 0.07
21 36 0.86
22 3 0.07
ACGTcount: A:0.20, C:0.19, G:0.38, T:0.23
Consensus pattern (21 bp):
AGGGGCCTCTTGAACGGTGGG
Found at i:1776589 original size:42 final size:42
Alignment explanation
Indices: 1776498--1776593 Score: 102
Period size: 42 Copynumber: 2.3 Consensus size: 42
1776488 GGACCTTTTC
* * **
1776498 AACGAAGACAGGGGCCTCTTGAACGGTGGGAGGGGACTCTTG
1 AACGATGACAGGGGCCTCTTGAACGGTAGGACAGGACTCTTG
** * * * *
1776540 AGGGATGATAGGGTCCTCTTGAACGGTAGGACATGCCTCTTG
1 AACGATGACAGGGGCCTCTTGAACGGTAGGACAGGACTCTTG
1776582 AACGATGACAGG
1 AACGATGACAGG
1776594 TGAGTCGGGC
Statistics
Matches: 41, Mismatches: 13, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.25, C:0.19, G:0.36, T:0.20
Consensus pattern (42 bp):
AACGATGACAGGGGCCTCTTGAACGGTAGGACAGGACTCTTG
Found at i:1777123 original size:20 final size:20
Alignment explanation
Indices: 1777098--1777146 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
1777088 CGAACCTTAA
1777098 ATCGCAACGCGGAA-ATGACT
1 ATCGCAACGC-GAATATGACT
*
1777118 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAATATGACT
1777138 ATCGCAACG
1 ATCGCAACG
1777147 GGATAATCGC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 3 0.11
20 24 0.89
ACGTcount: A:0.33, C:0.27, G:0.22, T:0.18
Consensus pattern (20 bp):
ATCGCAACGCGAATATGACT
Found at i:1777175 original size:19 final size:20
Alignment explanation
Indices: 1777151--1777189 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
1777141 GCAACGGGAT
*
1777151 AATCGCAATGCGAAA-TAAA
1 AATCGCAACGCGAAACTAAA
1777170 AATCGCAACGCGAAACTAAA
1 AATCGCAACGCGAAACTAAA
1777190 TTCGCGTTGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.51, C:0.21, G:0.15, T:0.13
Consensus pattern (20 bp):
AATCGCAACGCGAAACTAAA
Found at i:1777286 original size:20 final size:19
Alignment explanation
Indices: 1777261--1777389 Score: 172
Period size: 20 Copynumber: 6.5 Consensus size: 19
1777251 GCGATTATCC
1777261 CGTTGCGATAGTCAACTTT-G
1 CGTTGCGATAGTC-A-TTTCG
1777281 CGTTGCGATAGTCAACTTT-G
1 CGTTGCGATAGTC-A-TTTCG
1777301 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTT-CG
1777321 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTT-CG
1777341 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTT-CG
1777361 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCA-TTTCG
1777381 CGTTGCGAT
1 CGTTGCGAT
1777390 TTAAGTTTCG
Statistics
Matches: 106, Mismatches: 0, Indels: 6
0.95 0.00 0.05
Matches are distributed among these distances:
18 3 0.03
19 1 0.01
20 99 0.93
21 3 0.03
ACGTcount: A:0.16, C:0.22, G:0.26, T:0.36
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:1779331 original size:19 final size:19
Alignment explanation
Indices: 1779295--1779357 Score: 63
Period size: 19 Copynumber: 3.2 Consensus size: 19
1779285 GAAACTTAAA
*
1779295 ATCGCAACACGAAAATGACT
1 ATCGCAACGCG-AAATGACT
**
1779315 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
* *
1779334 ATCACAACGCGAATTTGACT
1 ATCGCAACGCGAA-ATGACT
1779354 ATCG
1 ATCG
1779358 TTGCGATTTT
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
19 18 0.53
20 16 0.47
ACGTcount: A:0.41, C:0.24, G:0.17, T:0.17
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:1779763 original size:22 final size:22
Alignment explanation
Indices: 1779736--1779799 Score: 92
Period size: 22 Copynumber: 2.9 Consensus size: 22
1779726 GAGATAGACA
*
1779736 GATTTCGCCGGAGATGGGAACG
1 GATTTCGTCGGAGATGGGAACG
* *
1779758 GATTTCGTCAGAGATGGGGACG
1 GATTTCGTCGGAGATGGGAACG
1779780 GATTTCGTCGGAGATAGGGA
1 GATTTCGTCGGAGAT-GGGA
1779800 CATATATCGC
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
22 33 0.92
23 3 0.08
ACGTcount: A:0.23, C:0.14, G:0.41, T:0.22
Consensus pattern (22 bp):
GATTTCGTCGGAGATGGGAACG
Found at i:1780014 original size:21 final size:20
Alignment explanation
Indices: 1779975--1780015 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
1779965 CAGAATCATG
* *
1779975 TTGCGATTTACATATTCGCA
1 TTGCGATTTACAAAATCGCA
1779995 TTGCGATTTTACAAAATCGCA
1 TTGCGA-TTTACAAAATCGCA
1780016 ACGCGAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.37
Consensus pattern (20 bp):
TTGCGATTTACAAAATCGCA
Found at i:1780021 original size:21 final size:21
Alignment explanation
Indices: 1779997--1780046 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
1779987 TATTCGCATT
*
1779997 GCGATTTTACAAAATCGCAAC
1 GCGAATTTACAAAATCGCAAC
**
1780018 GCGAATTTGGAAAATCGCAAC
1 GCGAATTTACAAAATCGCAAC
1780039 GCGAATTT
1 GCGAATTT
1780047 GGAAACTGAT
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:0.36, C:0.20, G:0.20, T:0.24
Consensus pattern (21 bp):
GCGAATTTACAAAATCGCAAC
Found at i:1780047 original size:21 final size:21
Alignment explanation
Indices: 1780007--1780051 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
1779997 GCGATTTTAC
1780007 AAAATCGCAACGCGAATTTGG
1 AAAATCGCAACGCGAATTTGG
1780028 AAAATCGCAACGCGAATTTGG
1 AAAATCGCAACGCGAATTTGG
1780049 AAA
1 AAA
1780052 CTGATTTACG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.42, C:0.18, G:0.22, T:0.18
Consensus pattern (21 bp):
AAAATCGCAACGCGAATTTGG
Found at i:1780092 original size:19 final size:19
Alignment explanation
Indices: 1780068--1780104 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1780058 TACGATACTG
* *
1780068 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTACGATTTA
1780087 GAGATCGCATTACGATTT
1 GAGATCGCATTACGATTT
1780105 TGTTGGTCAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTACGATTTA
Found at i:1781675 original size:200 final size:200
Alignment explanation
Indices: 1781327--1781720 Score: 506
Period size: 199 Copynumber: 2.0 Consensus size: 200
1781317 AAAAAAATTT
* * * *
1781327 AAATTACAATATTATATAGAGTAAAGCACACAAATGGTTCCTCGATTATAGGGTACTGCTTTGCT
1 AAATTACAATATTATACAGAGGAAAGCACACAAATGGTTCCTCGATTATAGGATACTACTTTGCT
* * * * * * * *
1781392 AAGTCTCTTAACTATTGAAAGTTTCATAATAATCCCCGACTATAGGGTGTTGTTTTGTTGAGTCA
66 AAGTCCCTCAACTATTAAAAATTACATAATAATCCCCAAATATAGGGTGTTGCTTTGTTGAGTCA
* *
1781457 TTCAAATATTAAAAATTACAGAAT-GACATTTGATTATTCATGTGTTCAAGT-CTTATCATTTTT
131 TTCAAATATTAAAAATTACAAAATGGACATTTGATTATTCATATGTTCAA-TACTTATCATTTTT
1781520 ATTTAA
195 ATTTAA
* * * * * **
1781526 AAATTTCAATATTATACAGAGGAAAGTACATAAATGG-TCTCTCGATTATAGGATATTATTTTTT
1 AAATTACAATATTATACAGAGGAAAGCACACAAATGGTTC-CTCGATTATAGGATACTACTTTGC
* *
1781590 TGAGTCCCTCAACTATTAAAAAATTACATAATAGTCCCCAAATATAGGGTGTTGCTTTGTTGAGT
65 TAAGTCCCTCAACTATT-AAAAATTACATAATAATCCCCAAATATAGGGTGTTGCTTTGTTGAGT
* * *
1781655 CATTCGAATATTAGAAATTACAAAATGGTCATTTGATTATTCATATGTTCAATACTTATCATTTT
129 CATTCAAATATTAAAAATTACAAAATGGACATTTGATTATTCATATGTTCAATACTTATCATTTT
1781720 T
194 T
1781721 CGTTGAAAAA
Statistics
Matches: 165, Mismatches: 26, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
198 2 0.01
199 64 0.39
200 64 0.39
201 35 0.21
ACGTcount: A:0.34, C:0.13, G:0.14, T:0.39
Consensus pattern (200 bp):
AAATTACAATATTATACAGAGGAAAGCACACAAATGGTTCCTCGATTATAGGATACTACTTTGCT
AAGTCCCTCAACTATTAAAAATTACATAATAATCCCCAAATATAGGGTGTTGCTTTGTTGAGTCA
TTCAAATATTAAAAATTACAAAATGGACATTTGATTATTCATATGTTCAATACTTATCATTTTTA
TTTAA
Found at i:1785426 original size:18 final size:19
Alignment explanation
Indices: 1785381--1785425 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
1785371 AAGTTCTTTC
1785381 TTTTC-TTTTCTTTTTAAG
1 TTTTCATTTTCTTTTTAAG
*
1785399 TTTTCATTTTC-TTTTAGG
1 TTTTCATTTTCTTTTTAAG
1785417 TTTT-ATTTT
1 TTTTCATTTT
1785426 TAAAATGATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 5 0.20
18 15 0.60
19 5 0.20
ACGTcount: A:0.11, C:0.09, G:0.07, T:0.73
Consensus pattern (19 bp):
TTTTCATTTTCTTTTTAAG
Found at i:1786629 original size:23 final size:24
Alignment explanation
Indices: 1786544--1786664 Score: 156
Period size: 24 Copynumber: 5.1 Consensus size: 24
1786534 GAAGTGCCAT
* *
1786544 GTAGAATTTGTCCCGAAGGACCGC
1 GTAGAATTTGTCCTGAAGGACCAC
* * *
1786568 ATAGAATTTGTCCTAAAGGACCGC
1 GTAGAATTTGTCCTGAAGGACCAC
*
1786592 GTAGAATTTGTCCTGAAGGACCAT
1 GTAGAATTTGTCCTGAAGGACCAC
*
1786616 GTAGAA-TTGTCCTGAAGTACCAC
1 GTAGAATTTGTCCTGAAGGACCAC
*
1786639 GTAGAA-TTGTCCTGAAGGACCGC
1 GTAGAATTTGTCCTGAAGGACCAC
1786662 GTA
1 GTA
1786665 AAACCCTCGA
Statistics
Matches: 86, Mismatches: 11, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
23 39 0.45
24 47 0.55
ACGTcount: A:0.29, C:0.21, G:0.26, T:0.25
Consensus pattern (24 bp):
GTAGAATTTGTCCTGAAGGACCAC
Found at i:1795104 original size:20 final size:20
Alignment explanation
Indices: 1795081--1795130 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
1795071 AAAGCCCTCA
1795081 GTATCGATACTAG-TCTATGG
1 GTATCGATACTAGCT-TATGG
1795101 GTATCGATACTAGCTTATGG
1 GTATCGATACTAGCTTATGG
1795121 GTATCGATAC
1 GTATCGATAC
1795131 CACTGAGTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 28 0.97
21 1 0.03
ACGTcount: A:0.26, C:0.16, G:0.24, T:0.34
Consensus pattern (20 bp):
GTATCGATACTAGCTTATGG
Found at i:1812520 original size:28 final size:28
Alignment explanation
Indices: 1812480--1812536 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
1812470 CCACCGTTGC
* **
1812480 TTTCGAGCACTGACTCAACAGTATAATG
1 TTTCAAGCACTGACTCAACAACATAATG
1812508 TTTCAAGCACTGACTCAACAACATAATG
1 TTTCAAGCACTGACTCAACAACATAATG
1812536 T
1 T
1812537 AAATGAAGAG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.35, C:0.23, G:0.14, T:0.28
Consensus pattern (28 bp):
TTTCAAGCACTGACTCAACAACATAATG
Found at i:1812867 original size:26 final size:26
Alignment explanation
Indices: 1812836--1812887 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
1812826 ACCCAAATTA
1812836 CTAAAATCTCTTTTACACATATATAT
1 CTAAAATCTCTTTTACACATATATAT
*
1812862 CTAAAATCTCTTTTACATATATATAT
1 CTAAAATCTCTTTTACACATATATAT
1812888 TATATATATA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.38, C:0.17, G:0.00, T:0.44
Consensus pattern (26 bp):
CTAAAATCTCTTTTACACATATATAT
Found at i:1812885 original size:2 final size:2
Alignment explanation
Indices: 1812878--1812968 Score: 152
Period size: 2 Copynumber: 47.0 Consensus size: 2
1812868 TCTCTTTTAC
*
1812878 AT AT AT AT AT -T AT AT AT AT AT -T AT AT AT AT AT AT AT AT CT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1812918 AT A- 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
1812959 AT AT AT AT AT
1 AT AT AT AT AT
1812969 TATTTTCTTT
Statistics
Matches: 84, Mismatches: 2, Indels: 6
0.91 0.02 0.07
Matches are distributed among these distances:
1 3 0.04
2 81 0.96
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1813184 original size:29 final size:29
Alignment explanation
Indices: 1813142--1813207 Score: 105
Period size: 29 Copynumber: 2.3 Consensus size: 29
1813132 TGTACACTTT
* **
1813142 TGGTCACTAATTTCAAAATTTATAGGATA
1 TGGTCACTAATTTCAAAATTCATACCATA
1813171 TGGTCACTAATTTCAAAATTCATACCATA
1 TGGTCACTAATTTCAAAATTCATACCATA
1813200 TGGTCACT
1 TGGTCACT
1813208 TACGTTTTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.36
Consensus pattern (29 bp):
TGGTCACTAATTTCAAAATTCATACCATA
Found at i:1817823 original size:58 final size:58
Alignment explanation
Indices: 1817725--1817836 Score: 147
Period size: 58 Copynumber: 1.9 Consensus size: 58
1817715 AGTGTTCCTT
* *
1817725 GAATCATACCTTAAGCCCTAAATCAAGAAATATCCTCACCACCACCACACAAAATGAAG
1 GAATCATACCTTAAACCCTAAATCAAGAAATATCCTCACCACCA-CACAAAAAATGAAG
* * *
1817784 GAAT-ATACCTTAAACCCTAAATCAAGTACTAT-CTCCACCATCACACAAAAAAT
1 GAATCATACCTTAAACCCTAAATCAAGAAATATCCT-CACCACCACACAAAAAAT
1817837 ACCACATAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
57 11 0.23
58 32 0.68
59 4 0.09
ACGTcount: A:0.45, C:0.29, G:0.06, T:0.20
Consensus pattern (58 bp):
GAATCATACCTTAAACCCTAAATCAAGAAATATCCTCACCACCACACAAAAAATGAAG
Found at i:1818188 original size:10 final size:10
Alignment explanation
Indices: 1818173--1818199 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
1818163 CCATCTTCTT
1818173 TTTCTTCGTC
1 TTTCTTCGTC
1818183 TTTCTTCGTC
1 TTTCTTCGTC
1818193 TTTCTTC
1 TTTCTTC
1818200 ATCGCTGTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.00, C:0.30, G:0.07, T:0.63
Consensus pattern (10 bp):
TTTCTTCGTC
Found at i:1822582 original size:15 final size:15
Alignment explanation
Indices: 1822564--1822593 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1822554 TAGTGTATGA
*
1822564 TGTATGGATGTATCT
1 TGTATGCATGTATCT
1822579 TGTATGCATGTATCT
1 TGTATGCATGTATCT
1822594 AATACAAGTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.10, G:0.23, T:0.47
Consensus pattern (15 bp):
TGTATGCATGTATCT
Found at i:1826459 original size:11 final size:11
Alignment explanation
Indices: 1826445--1826471 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
1826435 AAAATATGTG
1826445 AAAATTTAAAA
1 AAAATTTAAAA
1826456 AAAATTTAAAA
1 AAAATTTAAAA
1826467 AAAAT
1 AAAAT
1826472 CATTACTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (11 bp):
AAAATTTAAAA
Found at i:1827616 original size:24 final size:25
Alignment explanation
Indices: 1827589--1827640 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
1827579 ATCTTACATT
1827589 AAATTCAATTA-TTTAAAATTATAA
1 AAATTCAATTAGTTTAAAATTATAA
* * *
1827613 AAATTTATTTAGTTTAAATTTATAA
1 AAATTCAATTAGTTTAAAATTATAA
1827638 AAA
1 AAA
1827641 ATATTTTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 9 0.38
25 15 0.62
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (25 bp):
AAATTCAATTAGTTTAAAATTATAA
Found at i:1827645 original size:24 final size:25
Alignment explanation
Indices: 1827600--1827646 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
1827590 AATTCAATTA
*
1827600 TTTAAAATTATAAAAATTTATTTAG
1 TTTAAAATTATAAAAATATATTTAG
*
1827625 TTTAAATTTATAAAAA-ATATTT
1 TTTAAAATTATAAAAATATATTT
1827647 TTATTTTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 5 0.25
25 15 0.75
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (25 bp):
TTTAAAATTATAAAAATATATTTAG
Found at i:1831635 original size:17 final size:17
Alignment explanation
Indices: 1831613--1831678 Score: 62
Period size: 17 Copynumber: 3.7 Consensus size: 17
1831603 AATTATTATC
1831613 TTATTAATTTATTAAAA
1 TTATTAATTTATTAAAA
1831630 TTATTAATTTATGATAAAAA
1 TTATTAATTTAT--T-AAAA
* * *
1831650 TCATTATTTTA-AAAATA
1 TTATTAATTTATTAAA-A
1831667 TTATTAATTTAT
1 TTATTAATTTAT
1831679 CGAGTATTAA
Statistics
Matches: 39, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
16 3 0.08
17 22 0.56
19 1 0.03
20 13 0.33
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (17 bp):
TTATTAATTTATTAAAA
Found at i:1832247 original size:54 final size:56
Alignment explanation
Indices: 1832119--1832248 Score: 167
Period size: 59 Copynumber: 2.3 Consensus size: 56
1832109 TGACATCTTT
* *
1832119 TAAATAGTTTAGTGATCTGATTGACAAAATTGAAAAATCGATGATAAAAGTGACAGGGC
1 TAAATAGTTTAGTGGTCTGATTGACAAAATTAAAAAATCGATGAT-AAA--GACAGGGC
* *
1832178 TAAATAGTTTGGTGGTTTGATTGACAAAATTAAAAAAATCGATGAT-AA-A-AGGGC
1 TAAATAGTTTAGTGGTCTGATTGACAAAATT-AAAAAATCGATGATAAAGACAGGGC
1832232 TAAATAGTTTAGTGGTC
1 TAAATAGTTTAGTGGTC
1832249 AATGATATAG
Statistics
Matches: 64, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
54 20 0.31
55 1 0.02
58 2 0.03
59 28 0.44
60 13 0.20
ACGTcount: A:0.41, C:0.07, G:0.22, T:0.30
Consensus pattern (56 bp):
TAAATAGTTTAGTGGTCTGATTGACAAAATTAAAAAATCGATGATAAAGACAGGGC
Found at i:1832974 original size:4 final size:4
Alignment explanation
Indices: 1832967--1832999 Score: 66
Period size: 4 Copynumber: 8.2 Consensus size: 4
1832957 TATAAAGCTA
1832967 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT A
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT A
1833000 GAAAGGGGGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.27, C:0.00, G:0.24, T:0.48
Consensus pattern (4 bp):
ATGT
Found at i:1835803 original size:16 final size:16
Alignment explanation
Indices: 1835782--1835813 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1835772 ATAAGTTGCT
*
1835782 TCATTGAGATACAATC
1 TCATTGAAATACAATC
1835798 TCATTGAAATACAATC
1 TCATTGAAATACAATC
1835814 CCACAGAAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.19, G:0.09, T:0.31
Consensus pattern (16 bp):
TCATTGAAATACAATC
Found at i:1842272 original size:12 final size:11
Alignment explanation
Indices: 1842240--1842278 Score: 51
Period size: 12 Copynumber: 3.4 Consensus size: 11
1842230 AACATGTTTA
*
1842240 AAAATAAAACTT
1 AAAATAAAA-TG
1842252 AAAATAAAATG
1 AAAATAAAATG
1842263 AAAATGAAAATG
1 AAAAT-AAAATG
1842275 AAAA
1 AAAA
1842279 CTTGCAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 6 0.24
12 19 0.76
ACGTcount: A:0.72, C:0.03, G:0.08, T:0.18
Consensus pattern (11 bp):
AAAATAAAATG
Found at i:1842553 original size:27 final size:26
Alignment explanation
Indices: 1842512--1842563 Score: 77
Period size: 27 Copynumber: 2.0 Consensus size: 26
1842502 TTCAGAAGAC
*
1842512 GCTGACTAGATCTTCTATAAAACTGTT
1 GCTGACTAGACCTTCTA-AAAACTGTT
*
1842539 GCTGACTGGACCTTCTAAAAACTGT
1 GCTGACTAGACCTTCTAAAAACTGT
1842564 CACGTCAGAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 8 0.35
27 15 0.65
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Consensus pattern (26 bp):
GCTGACTAGACCTTCTAAAAACTGTT
Found at i:1843949 original size:41 final size:41
Alignment explanation
Indices: 1843892--1844073 Score: 185
Period size: 41 Copynumber: 4.5 Consensus size: 41
1843882 TTATAGAAGC
*
1843892 CCATTTCGCGTTGCGATAGTTGGAGATCGCGTTGCGATTTT
1 CCATTTCGCGTTGCGATAGTTGGAAATCGCGTTGCGATTTT
* *** *
1843933 CCATTTCGTGTTGCGATAGTT-GAAATCGCAACGCGA-TCT
1 CCATTTCGCGTTGCGATAGTTGGAAATCGCGTTGCGATTTT
* * * * **
1843972 CCATCATCGCAAATT-CG--CGTTGCATTTCGCGTTGCGATTTT
1 CCAT-TTCGC--GTTGCGATAGTTGGAAATCGCGTTGCGATTTT
*
1844013 CCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTT
1 CCATTTCGCGTTGCGATAGTTGGAAATCGCGTTGCGATTTT
1844054 CCATTTCGCGTTGCGATAGT
1 CCATTTCGCGTTGCGATAGT
1844074 CTACAGTTGT
Statistics
Matches: 110, Mismatches: 23, Indels: 16
0.74 0.15 0.11
Matches are distributed among these distances:
38 2 0.02
39 11 0.10
40 27 0.25
41 68 0.62
42 2 0.02
ACGTcount: A:0.18, C:0.23, G:0.24, T:0.35
Consensus pattern (41 bp):
CCATTTCGCGTTGCGATAGTTGGAAATCGCGTTGCGATTTT
Found at i:1844017 original size:20 final size:20
Alignment explanation
Indices: 1843994--1844070 Score: 100
Period size: 20 Copynumber: 3.8 Consensus size: 20
1843984 ATTCGCGTTG
1843994 CATTTCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATTTTC
* *
1844014 CATTTCGCGTTGCGATAGTTG
1 CATTTCGCGTTGCGAT-TTTC
* **
1844035 AAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATTTTC
1844055 CATTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
1844071 AGTCTACAGT
Statistics
Matches: 46, Mismatches: 10, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
20 31 0.67
21 15 0.33
ACGTcount: A:0.16, C:0.22, G:0.23, T:0.39
Consensus pattern (20 bp):
CATTTCGCGTTGCGATTTTC
Found at i:1844740 original size:6 final size:6
Alignment explanation
Indices: 1844704--1844791 Score: 141
Period size: 6 Copynumber: 15.5 Consensus size: 6
1844694 TCTCGTCTCG
1844704 GGTCG- GGTCG- GGTCG- GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1844747 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1844792 AATGGTAATG
Statistics
Matches: 82, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
5 25 0.30
6 57 0.70
ACGTcount: A:0.00, C:0.17, G:0.53, T:0.30
Consensus pattern (6 bp):
GGTCGT
Found at i:1844797 original size:6 final size:6
Alignment explanation
Indices: 1844788--1844824 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
1844778 GTCGTGGTCG
1844788 TGGTAA TGGTAA TGGTAA TGGTAA TGGTAA TGGTAA T
1 TGGTAA TGGTAA TGGTAA TGGTAA TGGTAA TGGTAA T
1844825 ACGTGTCTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.35
Consensus pattern (6 bp):
TGGTAA
Found at i:1844899 original size:21 final size:21
Alignment explanation
Indices: 1844873--1844926 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
1844863 AAAATGGAAA
1844873 ATCGCAACGCGACTGT-AGACT
1 ATCGCAACGCGACTGTCA-ACT
* *
1844894 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGACTGTCAACT
1844915 ATCGCAACGCGA
1 ATCGCAACGCGA
1844927 ATTTGCGATA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 29 0.97
22 1 0.03
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGACTGTCAACT
Found at i:1847499 original size:29 final size:28
Alignment explanation
Indices: 1847464--1847519 Score: 103
Period size: 29 Copynumber: 2.0 Consensus size: 28
1847454 GAGAATTGCA
1847464 TATGCCGAAAATATGAGCATTCAATTGTG
1 TATGCCGAAAATATGAGCATTC-ATTGTG
1847493 TATGCCGAAAATATGAGCATTCATTGT
1 TATGCCGAAAATATGAGCATTCATTGT
1847520 CAAAGAATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
28 5 0.19
29 22 0.81
ACGTcount: A:0.34, C:0.14, G:0.20, T:0.32
Consensus pattern (28 bp):
TATGCCGAAAATATGAGCATTCATTGTG
Found at i:1850071 original size:20 final size:20
Alignment explanation
Indices: 1850046--1850159 Score: 65
Period size: 20 Copynumber: 5.5 Consensus size: 20
1850036 TTCGTATTTA
1850046 GTTTTTATGTTTAATGTTAT
1 GTTTTTATGTTTAATGTTAT
* * *
1850066 GTTTTT-TAATTGAATATTAT
1 GTTTTTAT-GTTTAATGTTAT
*
1850086 GTTTTAATG-TT-ATGTT-T
1 GTTTTTATGTTTAATGTTAT
*
1850103 TTATATTTATGTTTAATGTTATGT
1 GT-T-TTTATGTTTAATGTTA--T
* *
1850127 AGTTTTTATGGTTTTATATTAT
1 -GTTTTTAT-GTTTAATGTTAT
*
1850149 GTTTTAATGTT
1 GTTTTTATGTT
1850160 ATGTTCTTAT
Statistics
Matches: 70, Mismatches: 13, Indels: 22
0.67 0.12 0.21
Matches are distributed among these distances:
17 2 0.03
18 5 0.07
19 7 0.10
20 25 0.36
21 13 0.19
22 1 0.01
23 5 0.07
24 11 0.16
25 1 0.01
ACGTcount: A:0.23, C:0.00, G:0.14, T:0.63
Consensus pattern (20 bp):
GTTTTTATGTTTAATGTTAT
Found at i:1850100 original size:13 final size:13
Alignment explanation
Indices: 1850082--1850164 Score: 70
Period size: 12 Copynumber: 6.5 Consensus size: 13
1850072 TAATTGAATA
1850082 TTATGTTTTAATG
1 TTATGTTTTAATG
1850095 TTATGTTTTTATAT-
1 TTATG-TTTTA-ATG
1850109 TTATG-TTTAATG
1 TTATGTTTTAATG
*
1850121 TTATGTAGTT--T-
1 TTATGT-TTTAATG
*
1850132 TTATGGTTTT-ATA
1 TTAT-GTTTTAATG
1850145 TTATGTTTTAATG
1 TTATGTTTTAATG
1850158 TTATGTT
1 TTATGTT
1850165 CTTATCTTAT
Statistics
Matches: 58, Mismatches: 3, Indels: 18
0.73 0.04 0.23
Matches are distributed among these distances:
11 8 0.14
12 18 0.31
13 18 0.31
14 12 0.21
15 2 0.03
ACGTcount: A:0.22, C:0.00, G:0.14, T:0.64
Consensus pattern (13 bp):
TTATGTTTTAATG
Found at i:1850160 original size:63 final size:59
Alignment explanation
Indices: 1850049--1850169 Score: 170
Period size: 63 Copynumber: 2.0 Consensus size: 59
1850039 GTATTTAGTT
*
1850049 TTTATGTTTAATGTTATGTTTTTTAATTGAATATTATGTTTTAATGTTATGTTTTTATA
1 TTTATGTTTAATGTTATGTTTTTTAATTGAATATTATGTTTTAATGTTATGTTCTTATA
* **
1850108 TTTATGTTTAATGTTATGTAGTTTTTATGGTTTTATATTATGTTTTAATGTTATGTTCTTAT
1 TTTATGTTTAATGTTATGT--TTTTTA--ATTGAATATTATGTTTTAATGTTATGTTCTTAT
1850170 CTTATCTTAT
Statistics
Matches: 54, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
59 19 0.35
61 6 0.11
63 29 0.54
ACGTcount: A:0.23, C:0.01, G:0.13, T:0.63
Consensus pattern (59 bp):
TTTATGTTTAATGTTATGTTTTTTAATTGAATATTATGTTTTAATGTTATGTTCTTATA
Found at i:1850174 original size:13 final size:12
Alignment explanation
Indices: 1850079--1850174 Score: 61
Period size: 13 Copynumber: 7.6 Consensus size: 12
1850069 TTTTAATTGA
1850079 ATATTATGTTTT
1 ATATTATGTTTT
*
1850091 AATGTTATGTTTTT
1 -ATATTATG-TTTT
*
1850105 ATATTTATGTTTA
1 ATA-TTATGTTTT
* *
1850118 ATGTTATGTAGTT
1 ATATTATGT-TTT
1850131 -T-TTATGGTTTT
1 ATATTAT-GTTTT
1850142 ATATTATGTTTT
1 ATATTATGTTTT
*
1850154 AATGTTATGTTCTT
1 -ATATTATGTT-TT
*
1850168 ATCTTAT
1 ATATTAT
1850175 CTTATCTTTA
Statistics
Matches: 66, Mismatches: 9, Indels: 16
0.73 0.10 0.18
Matches are distributed among these distances:
11 6 0.09
12 15 0.23
13 34 0.52
14 11 0.17
ACGTcount: A:0.23, C:0.02, G:0.12, T:0.62
Consensus pattern (12 bp):
ATATTATGTTTT
Found at i:1852859 original size:23 final size:23
Alignment explanation
Indices: 1852829--1852886 Score: 107
Period size: 23 Copynumber: 2.5 Consensus size: 23
1852819 CAGGGATAAA
1852829 AGTGAGTGACTTATGCAACGTAG
1 AGTGAGTGACTTATGCAACGTAG
1852852 AGTGAGTGACTTATGCAACGTAG
1 AGTGAGTGACTTATGCAACGTAG
*
1852875 AGTGAGAGACTT
1 AGTGAGTGACTT
1852887 TAGACCGAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.31, C:0.12, G:0.31, T:0.26
Consensus pattern (23 bp):
AGTGAGTGACTTATGCAACGTAG
Found at i:1855843 original size:60 final size:58
Alignment explanation
Indices: 1855728--1855862 Score: 157
Period size: 60 Copynumber: 2.3 Consensus size: 58
1855718 GAGCATGAGG
* * * * * *
1855728 AATGAATGTCATAATTTAGGGATAATTAGAATGTTCAAAAGTTTAATGACTAATTTAT
1 AATGAAGGTCATAGTTTAGGAATAATTAGAATATTCAAAAGTTTAAGGACTAATTTAA
1855786 AAT-AAGAGTCATAGTTTAGGAATTAAATTAGAATATTCAAAAGTTTAAGGA-TCAATTTAA
1 AATGAAG-GTCATAGTTTAGGAA-T-AATTAGAATATTCAAAAGTTTAAGGACT-AATTTAA
*
1855846 AATGAAGGTTATAGTTT
1 AATGAAGGTCATAGTTT
1855863 GGGGACATAT
Statistics
Matches: 65, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
57 2 0.03
58 16 0.25
59 2 0.03
60 42 0.65
61 3 0.05
ACGTcount: A:0.43, C:0.04, G:0.16, T:0.36
Consensus pattern (58 bp):
AATGAAGGTCATAGTTTAGGAATAATTAGAATATTCAAAAGTTTAAGGACTAATTTAA
Found at i:1856045 original size:29 final size:30
Alignment explanation
Indices: 1856008--1856097 Score: 85
Period size: 29 Copynumber: 3.1 Consensus size: 30
1855998 TTTAAATTAG
1856008 TCCTTAAACTTTTAAATATTCTAATTTAAT
1 TCCTTAAACTTTTAAATATTCTAATTTAAT
* * ** * * * *
1856038 TCC-TAAACTATGACTTGTGCTAAATTGA-
1 TCCTTAAACTTTTAAATATTCTAATTTAAT
*
1856066 TCCTTAAACTTTTAAATATTCTAATTTCAT
1 TCCTTAAACTTTTAAATATTCTAATTTAAT
1856096 TC
1 TC
1856098 TCAAATTATG
Statistics
Matches: 42, Mismatches: 16, Indels: 4
0.68 0.26 0.06
Matches are distributed among these distances:
28 3 0.07
29 34 0.81
30 5 0.12
ACGTcount: A:0.33, C:0.17, G:0.04, T:0.46
Consensus pattern (30 bp):
TCCTTAAACTTTTAAATATTCTAATTTAAT
Found at i:1856154 original size:60 final size:60
Alignment explanation
Indices: 1856000--1856183 Score: 191
Period size: 60 Copynumber: 3.1 Consensus size: 60
1855990 ACCTTCATTT
* * * * *
1856000 TAAATTAGTCCTT-AAACTTTTAAATATTCTAATTTAATTCCTAAACTATGACT-T-GTGC
1 TAAATTAGT-CTTAAAACTTTTAAATATTCTAATTTCATCCCCAAACTATGACTCTAATTC
* * *
1856058 TAAATT-GATCCTT-AAACTTTTAAATATTCTAATTTCATTCTCAAATTATGACTCTAATTC
1 TAAATTAG-T-CTTAAAACTTTTAAATATTCTAATTTCATCCCCAAACTATGACTCTAATTC
* * *
1856118 TAAATTAGTCTTAAAACTTTTAAAT-TTTTCAGTTTCATCCCCAAACTATGACTCTCATTC
1 TAAATTAGTCTTAAAACTTTTAAATATTCT-AATTTCATCCCCAAACTATGACTCTAATTC
1856178 TAAATT
1 TAAATT
1856184 GATCCCAAAG
Statistics
Matches: 108, Mismatches: 12, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
57 1 0.01
58 47 0.44
59 7 0.06
60 52 0.48
61 1 0.01
ACGTcount: A:0.34, C:0.17, G:0.05, T:0.43
Consensus pattern (60 bp):
TAAATTAGTCTTAAAACTTTTAAATATTCTAATTTCATCCCCAAACTATGACTCTAATTC
Found at i:1856480 original size:2 final size:2
Alignment explanation
Indices: 1856473--1856502 Score: 51
Period size: 2 Copynumber: 14.5 Consensus size: 2
1856463 AATAATTTGA
1856473 AT AT AT AT AT AT AT AT AT AT AT AT ACT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT A
1856503 ACAAAAAAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 25 0.93
3 2 0.07
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1857920 original size:4 final size:4
Alignment explanation
Indices: 1857911--1857936 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
1857901 TGAAGGCTCC
1857911 CGGT CGGT CGGT CGGT CGGT CGGT CG
1 CGGT CGGT CGGT CGGT CGGT CGGT CG
1857937 TGACATACTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.00, C:0.27, G:0.50, T:0.23
Consensus pattern (4 bp):
CGGT
Found at i:1865453 original size:21 final size:21
Alignment explanation
Indices: 1865429--1865478 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
1865419 CATTTTTACC
*
1865429 CTAAATCTCAAAA-TCTCAAAT
1 CTAAATCTCAAAACCCT-AAAT
1865450 CTAAAT-TCAAAACCCTAAAT
1 CTAAATCTCAAAACCCTAAAT
1865470 CTTAAATCT
1 C-TAAATCT
1865479 TAACCTTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 11 0.44
21 13 0.52
22 1 0.04
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (21 bp):
CTAAATCTCAAAACCCTAAAT
Found at i:1865529 original size:24 final size:24
Alignment explanation
Indices: 1865499--1865552 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
1865489 AGGAAAAAAT
*
1865499 ATTATTTTACTCTGAGTTAAAGAA
1 ATTATTTTACTCAGAGTTAAAGAA
* *
1865523 ATTATTTTACTGAGAGTTAAATAA
1 ATTATTTTACTCAGAGTTAAAGAA
1865547 A-TATTT
1 ATTATTT
1865553 ATTTATGGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 5 0.19
24 22 0.81
ACGTcount: A:0.39, C:0.06, G:0.11, T:0.44
Consensus pattern (24 bp):
ATTATTTTACTCAGAGTTAAAGAA
Found at i:1865680 original size:2 final size:2
Alignment explanation
Indices: 1865669--1865722 Score: 85
Period size: 2 Copynumber: 27.5 Consensus size: 2
1865659 AACCTAATCC
1865669 TA TA -A TA TA TA T- TCA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA
1865710 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
1865723 CATAATTGAG
Statistics
Matches: 49, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.04
2 46 0.94
3 1 0.02
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1866817 original size:3 final size:3
Alignment explanation
Indices: 1866749--1866802 Score: 108
Period size: 3 Copynumber: 18.0 Consensus size: 3
1866739 TATATCAGTC
1866749 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1866797 TAT TAT
1 TAT TAT
1866803 GTTTATGTTT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1869367 original size:53 final size:53
Alignment explanation
Indices: 1869304--1869413 Score: 211
Period size: 53 Copynumber: 2.1 Consensus size: 53
1869294 GATATAAAGG
*
1869304 TTCTTGAATACCTTCCTGATACACCTGAATCGTGAATGGTCATGAAACATCAA
1 TTCTTGAATACCTTCCTGATACACCTGAATCATGAATGGTCATGAAACATCAA
1869357 TTCTTGAATACCTTCCTGATACACCTGAATCATGAATGGTCATGAAACATCAA
1 TTCTTGAATACCTTCCTGATACACCTGAATCATGAATGGTCATGAAACATCAA
1869410 TTCT
1 TTCT
1869414 AAATGCCTAA
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 56 1.00
ACGTcount: A:0.32, C:0.23, G:0.14, T:0.32
Consensus pattern (53 bp):
TTCTTGAATACCTTCCTGATACACCTGAATCATGAATGGTCATGAAACATCAA
Found at i:1871559 original size:21 final size:21
Alignment explanation
Indices: 1871533--1871609 Score: 118
Period size: 21 Copynumber: 3.7 Consensus size: 21
1871523 TTCTGGGCAA
* *
1871533 TGTGCATCGATGCATATTCAT
1 TGTGCACCGATGCACATTCAT
*
1871554 TGTGCACCGATGTACATTCAT
1 TGTGCACCGATGCACATTCAT
1871575 TGTGCACCGATGCACATTCAT
1 TGTGCACCGATGCACATTCAT
*
1871596 TGTACACCGATGCA
1 TGTGCACCGATGCA
1871610 TCGATGATAA
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 51 1.00
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.31
Consensus pattern (21 bp):
TGTGCACCGATGCACATTCAT
Found at i:1871752 original size:64 final size:65
Alignment explanation
Indices: 1871684--1871811 Score: 190
Period size: 64 Copynumber: 2.0 Consensus size: 65
1871674 TTTAAAAAGA
1871684 AAACATCGAATAGGATTTATGCATCGATGAATAAGG-AGTGCATCGATGCAT-CC-CCATTAAAT
1 AAACATCGAATAGGATTTATGCATCGATGAAT--GGTAGTGCATCGATGCATACCTCCATTAAAT
1871746 AC
64 AC
*
1871748 AAACATCGAATAGGATTTATGCATCGATGCATGGTATAGTGCATCGATGCATACCTCCATTAAA
1 AAACATCGAATAGGATTTATGCATCGATGAATGG--TAGTGCATCGATGCATACCTCCATTAAA
1871812 AGATGAAAAT
Statistics
Matches: 58, Mismatches: 1, Indels: 7
0.88 0.02 0.11
Matches are distributed among these distances:
62 2 0.03
64 31 0.53
65 15 0.26
66 2 0.03
67 8 0.14
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.27
Consensus pattern (65 bp):
AAACATCGAATAGGATTTATGCATCGATGAATGGTAGTGCATCGATGCATACCTCCATTAAATAC
Found at i:1872552 original size:23 final size:23
Alignment explanation
Indices: 1872495--1872557 Score: 65
Period size: 23 Copynumber: 2.7 Consensus size: 23
1872485 ATTATTATAT
1872495 GGCACT-ACGGTGCAATTCAACGC
1 GGCACTCA-GGTGCAATTCAACGC
* * *
1872518 GGCACTCCGGTGCAATTCTACGT
1 GGCACTCAGGTGCAATTCAACGC
* *
1872541 GGCGCTTAGGTGCAATT
1 GGCACTCAGGTGCAATT
1872558 ATATGAGCTG
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.21, C:0.27, G:0.29, T:0.24
Consensus pattern (23 bp):
GGCACTCAGGTGCAATTCAACGC
Found at i:1878620 original size:21 final size:21
Alignment explanation
Indices: 1878594--1878670 Score: 127
Period size: 21 Copynumber: 3.7 Consensus size: 21
1878584 TTCTGGGCAA
*
1878594 TGTGCATCGATGCACATTCAT
1 TGTGCACCGATGCACATTCAT
*
1878615 TGTGCACCGATACACATTCAT
1 TGTGCACCGATGCACATTCAT
*
1878636 TATGCACCGATGCACATTCAT
1 TGTGCACCGATGCACATTCAT
1878657 TGTGCACCGATGCA
1 TGTGCACCGATGCA
1878671 TCGATGATAA
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 51 1.00
ACGTcount: A:0.26, C:0.27, G:0.18, T:0.29
Consensus pattern (21 bp):
TGTGCACCGATGCACATTCAT
Found at i:1878774 original size:64 final size:63
Alignment explanation
Indices: 1878701--1878861 Score: 180
Period size: 64 Copynumber: 2.5 Consensus size: 63
1878691 TTGTTTAAGG
* *
1878701 TGCATCGATGCACATGCAGTGCATCGATGTAT-TAATTTAAAAAGAAAACATCGAATAGGATTTA
1 TGCATCGATGCACATGCAGTGCATCGATGCATCCAA-TTAAAAA-AAAACATCGAATAGGATTTA
* * * * * *
1878765 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATACAAACATCGAATAGGATTTA
1 TGCATCGATGCACATGCAGTGCATCGATGCAT-CCAATTAAAAAAAAACATCGAATAGGATTTA
** *
1878829 TGCATCGATGCATGGTGTAGTGCATCGATGCAT
1 TGCATCGATGCA-CATGCAGTGCATCGATGCAT
1878862 ACCTCCATTA
Statistics
Matches: 82, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
64 59 0.72
65 22 0.27
66 1 0.01
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.27
Consensus pattern (63 bp):
TGCATCGATGCACATGCAGTGCATCGATGCATCCAATTAAAAAAAAACATCGAATAGGATTTA
Found at i:1879501 original size:103 final size:103
Alignment explanation
Indices: 1879322--1879549 Score: 420
Period size: 103 Copynumber: 2.2 Consensus size: 103
1879312 GTAGAGGGTC
*
1879322 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTTGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
1879387 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
*
1879425 TATGTGGTCTTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
1879490 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
**
1879528 TATGTGGTCCTTATGGACATAT
1 TATGTGGTCCTTCGGGACATAT
1879550 TATATGGCAC
Statistics
Matches: 120, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 120 1.00
ACGTcount: A:0.25, C:0.13, G:0.25, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:1879593 original size:23 final size:23
Alignment explanation
Indices: 1879555--1879616 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 23
1879545 CATATTATAT
1879555 GGCACTACGG-GCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
1879577 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
*
1879600 GGCGCTTA-GGTGCAATT
1 GGCAC-TACGGTGCAATT
1879617 AATGAGCTGT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
22 9 0.26
23 24 0.71
24 1 0.03
ACGTcount: A:0.19, C:0.27, G:0.29, T:0.24
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:1881924 original size:21 final size:20
Alignment explanation
Indices: 1881891--1881934 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
1881881 ATATTTATTT
1881891 AAAAAAATAAAAA-TGCAATA
1 AAAAAAATAAAAAGTG-AATA
*
1881911 AAAAAGAATTAAAAGTGAATA
1 AAAAA-AATAAAAAGTGAATA
1881932 AAA
1 AAA
1881935 TTTAGTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 5 0.24
21 14 0.67
22 2 0.10
ACGTcount: A:0.73, C:0.02, G:0.09, T:0.16
Consensus pattern (20 bp):
AAAAAAATAAAAAGTGAATA
Found at i:1903212 original size:77 final size:77
Alignment explanation
Indices: 1903085--1903316 Score: 419
Period size: 77 Copynumber: 3.0 Consensus size: 77
1903075 CGATTCAAAA
* *
1903085 ATGAAAGTGATTCCATTATAGGGACGGATATATGTATGACTTTATGTGAGGCATGAATAAAAATA
1 ATGAAAGTGATTCCATTAAAGGGACGGATATATGTATGACTTTATGTGAGGCATGAATAAACATA
1903150 TGATTTTATGTT
66 TGATTTTATGTT
1903162 ATGAAAGTGATTCCATTAAAGGGACGGATATATGTATGACTTTATGTGAGGCATGAATAAACATA
1 ATGAAAGTGATTCCATTAAAGGGACGGATATATGTATGACTTTATGTGAGGCATGAATAAACATA
1903227 TGATTTTATGTT
66 TGATTTTATGTT
* * *
1903239 AAGAAAGTGCTTCCATTAAAGGGATGGATATATGTATGACTTTATGTGAGGCATGAATAAACATA
1 ATGAAAGTGATTCCATTAAAGGGACGGATATATGTATGACTTTATGTGAGGCATGAATAAACATA
1903304 TGATTTTATGTT
66 TGATTTTATGTT
1903316 A
1 A
1903317 GGTAGTACGA
Statistics
Matches: 150, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
77 150 1.00
ACGTcount: A:0.35, C:0.07, G:0.22, T:0.35
Consensus pattern (77 bp):
ATGAAAGTGATTCCATTAAAGGGACGGATATATGTATGACTTTATGTGAGGCATGAATAAACATA
TGATTTTATGTT
Found at i:1909722 original size:17 final size:17
Alignment explanation
Indices: 1909700--1909736 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
1909690 CTTCATTTAC
1909700 TTACTCTGACATTATAT
1 TTACTCTGACATTATAT
*
1909717 TTACTCTTACATTATAT
1 TTACTCTGACATTATAT
1909734 TTA
1 TTA
1909737 ATTCATGCAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.30, C:0.16, G:0.03, T:0.51
Consensus pattern (17 bp):
TTACTCTGACATTATAT
Found at i:1911384 original size:174 final size:173
Alignment explanation
Indices: 1910836--1911398 Score: 769
Period size: 171 Copynumber: 3.3 Consensus size: 173
1910826 GAGGAGGAGG
* * * * * * * **
1910836 TTTATGAAGCAGAAGCAAGCAATAACAAAAATTCAAAGTAATTTCAGGCGACTGAGATGTTGGAG
1 TTTATGAAGAAGAAGCAAGCAATAATAAAAATCCAAAGTAATTTCCGACGACTGAAATGCTACAG
* *
1910901 GGCCTTTCAGATTGCTAGGAAGGAATTTGTCTGTAAATCTCTTCAAAATCAGACATTAGCTGCTA
66 GGCCTTTCAGATTGCTAGGAAGGAATTTGCCTGTAGATCTCTTCAAAATCAGACATTAGCTGCTA
* * *
1910966 CCAAAATTCAGAGTCATTTCTGTGCTTGGCTGTT-A-AGAAGT
131 CCAAAATTCAGAGTCAGTTCCGTGCTTGGCAGTTGAGAGAAGT
* ** * * *
1911007 TATAAAAAGAAGAAACAAGCAATAATAAAAATTCAAAGTAATATT-CGAAGACTGAAATGCTACA
1 TTTATGAAGAAGAAGCAAGCAATAATAAAAATCCAAAGTAAT-TTCCGACGACTGAAATGCTACA
* *
1911071 GGGCCTTTCAGATTGCAAGGAAGGAATTTGCCTGTAGATCTCTTCAAAATCA-A-A-CAGCTGCT
65 GGGCCTTTCAGATTGCTAGGAAGGAATTTGCCTGTAGATCTCTTCAAAATCAGACATTAGCTGCT
*
1911133 ACCAAAATTCAGAATCAGTTCCGTGCTTGGCAGTTGAGAAGAAGT
130 ACCAAAATTCAGAGTCAGTTCCGTGCTTGGCAGTTGAG-AGAAGT
* *
1911178 TTTATGAAGAAGAAGCAAGCAATAATAAAAATCCAAAGCAATTTCCGACGACTGAAATGCTATAG
1 TTTATGAAGAAGAAGCAAGCAATAATAAAAATCCAAAGTAATTTCCGACGACTGAAATGCTACAG
* * *
1911243 GACCTTTCAGATTGCTAGGAAGGAGTTTGCCTGTAGATCTCTTCAAAATCAGACATTAGCTGCAA
66 GGCCTTTCAGATTGCTAGGAAGGAATTTGCCTGTAGATCTCTTCAAAATCAGACATTAGCTGCTA
* ** *
1911308 CCGAAATTCAGAGTTGGTTCCGTGCTTGGCAGTTGAGGATAAGT
131 CCAAAATTCAGAGTCAGTTCCGTGCTTGGCAGTTGA-GAGAAGT
1911352 TTTATGAAGAAGAAGCAAGCAATAATAAAAATCCAAAGTAATTTCCG
1 TTTATGAAGAAGAAGCAAGCAATAATAAAAATCCAAAGTAATTTCCG
1911399 GCGGCGAAAA
Statistics
Matches: 343, Mismatches: 40, Indels: 15
0.86 0.10 0.04
Matches are distributed among these distances:
168 38 0.11
169 2 0.01
170 3 0.01
171 205 0.60
172 3 0.01
173 1 0.00
174 90 0.26
175 1 0.00
ACGTcount: A:0.37, C:0.16, G:0.21, T:0.26
Consensus pattern (173 bp):
TTTATGAAGAAGAAGCAAGCAATAATAAAAATCCAAAGTAATTTCCGACGACTGAAATGCTACAG
GGCCTTTCAGATTGCTAGGAAGGAATTTGCCTGTAGATCTCTTCAAAATCAGACATTAGCTGCTA
CCAAAATTCAGAGTCAGTTCCGTGCTTGGCAGTTGAGAGAAGT
Found at i:1917329 original size:2 final size:2
Alignment explanation
Indices: 1917322--1917351 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1917312 CTACTCGATA
1917322 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1917352 GCGCCAAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1919072 original size:2 final size:2
Alignment explanation
Indices: 1919060--1919094 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
1919050 TTCTTTAACC
1919060 AT AT A- 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
1919095 TTCACACTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1919923 original size:19 final size:20
Alignment explanation
Indices: 1919872--1919923 Score: 54
Period size: 19 Copynumber: 2.6 Consensus size: 20
1919862 TAAAGAAAAT
*
1919872 ATAATATTATGAA-TATATTTT
1 ATAATATTA--AATTATATTTG
*
1919893 ATAATTTTAAATTATATTTG
1 ATAATATTAAATTATATTTG
1919913 AT-ATATTAAAT
1 ATAATATTAAAT
1919924 AAAATTATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 10 0.37
20 9 0.33
21 8 0.30
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (20 bp):
ATAATATTAAATTATATTTG
Found at i:1923179 original size:2 final size:2
Alignment explanation
Indices: 1923172--1923200 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1923162 CAGTTGTCAT
1923172 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1923201 TCATATTAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1924999 original size:42 final size:42
Alignment explanation
Indices: 1924942--1925141 Score: 200
Period size: 42 Copynumber: 5.2 Consensus size: 42
1924932 TGATTTTGAT
* *
1924942 TTTA-TTTAAACTTATTGAGACTTATTAGTGTTATGGTGTTA
1 TTTATTTTAGACTTATTGAGACTTAATAGTGTTATGGTGTTA
*
1924983 TTTATTTTAGACTTATTGAGACTTAATAGTGTTATGGTGTTG
1 TTTATTTTAGACTTATTGAGACTTAATAGTGTTATGGTGTTA
1925025 TTTATTTTAGACTTATTGAGAC-T--TA-----ATGGTGTTA
1 TTTATTTTAGACTTATTGAGACTTAATAGTGTTATGGTGTTA
* * * *
1925059 TTTATTTTAGATTTTTTTAGACTTAATGGTGTTA--------
1 TTTATTTTAGACTTATTGAGACTTAATAGTGTTATGGTGTTA
* *
1925093 TTTATTTTAGACTTATTGAGACTTAATATTGTTATGATGTTA
1 TTTATTTTAGACTTATTGAGACTTAATAGTGTTATGGTGTTA
1925135 TTTATTT
1 TTTATTT
1925142 ACTTGTTTAT
Statistics
Matches: 129, Mismatches: 13, Indels: 33
0.74 0.07 0.19
Matches are distributed among these distances:
34 56 0.43
35 1 0.01
37 1 0.01
39 2 0.02
41 5 0.04
42 64 0.50
ACGTcount: A:0.26, C:0.04, G:0.17, T:0.54
Consensus pattern (42 bp):
TTTATTTTAGACTTATTGAGACTTAATAGTGTTATGGTGTTA
Found at i:1925127 original size:34 final size:34
Alignment explanation
Indices: 1925016--1925119 Score: 172
Period size: 34 Copynumber: 3.1 Consensus size: 34
1925006 TAATAGTGTT
*
1925016 ATGGTGTTGTTTATTTTAGACTTATTGAGACTTA
1 ATGGTGTTATTTATTTTAGACTTATTGAGACTTA
* * *
1925050 ATGGTGTTATTTATTTTAGATTTTTTTAGACTTA
1 ATGGTGTTATTTATTTTAGACTTATTGAGACTTA
1925084 ATGGTGTTATTTATTTTAGACTTATTGAGACTTA
1 ATGGTGTTATTTATTTTAGACTTATTGAGACTTA
1925118 AT
1 AT
1925120 ATTGTTATGA
Statistics
Matches: 63, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 63 1.00
ACGTcount: A:0.25, C:0.05, G:0.17, T:0.53
Consensus pattern (34 bp):
ATGGTGTTATTTATTTTAGACTTATTGAGACTTA
Found at i:1933474 original size:47 final size:47
Alignment explanation
Indices: 1933402--1933495 Score: 152
Period size: 47 Copynumber: 2.0 Consensus size: 47
1933392 ACCTTGCAGC
* *
1933402 CTTGGCAATGAATGCACATACATTATATAGATACTGCTACTCGAACT
1 CTTGGCAATGAATGCACATACATTATATAGATACCGCTACTCAAACT
* *
1933449 CTTGGCAATGAATGCACGTATATTATATAGATACCGCTACTCAAACT
1 CTTGGCAATGAATGCACATACATTATATAGATACCGCTACTCAAACT
1933496 TAAAATCTCT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 43 1.00
ACGTcount: A:0.34, C:0.21, G:0.15, T:0.30
Consensus pattern (47 bp):
CTTGGCAATGAATGCACATACATTATATAGATACCGCTACTCAAACT
Found at i:1945265 original size:14 final size:14
Alignment explanation
Indices: 1945246--1945275 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1945236 CATTTTTGAA
1945246 AGGAGATCTAGATG
1 AGGAGATCTAGATG
*
1945260 AGGAGATCTATATG
1 AGGAGATCTAGATG
1945274 AG
1 AG
1945276 AACAATGGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.37, C:0.07, G:0.33, T:0.23
Consensus pattern (14 bp):
AGGAGATCTAGATG
Found at i:1946875 original size:96 final size:96
Alignment explanation
Indices: 1946761--1946960 Score: 373
Period size: 96 Copynumber: 2.1 Consensus size: 96
1946751 CCCAGAGTTT
1946761 GGGTGGTTCATTTATAATGAACTTGAAGAAAGTCACCATACTCTTTATGAGGTTGAGCTTTTATA
1 GGGTGGTTCATTTATAATGAACTTGAAGAAAGTCACCATACTCTTTATGAGGTTGAGCTTTTATA
*
1946826 AAAGCTCTTAATTATTGCATATCTCTGTTAA
66 AAAGCTCTTAATTATTGCATATCCCTGTTAA
* *
1946857 GGGTGGTTCATTTATAATGAACTTGAAGAAAGTCATCATACTCTTTGTGAGGTTGAGCTTTTATA
1 GGGTGGTTCATTTATAATGAACTTGAAGAAAGTCACCATACTCTTTATGAGGTTGAGCTTTTATA
1946922 AAAGCTCTTAATTATTGCATATCCCTGTTAA
66 AAAGCTCTTAATTATTGCATATCCCTGTTAA
1946953 GGGTGGTT
1 GGGTGGTT
1946961 TATATCGAGA
Statistics
Matches: 101, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
96 101 1.00
ACGTcount: A:0.28, C:0.13, G:0.20, T:0.39
Consensus pattern (96 bp):
GGGTGGTTCATTTATAATGAACTTGAAGAAAGTCACCATACTCTTTATGAGGTTGAGCTTTTATA
AAAGCTCTTAATTATTGCATATCCCTGTTAA
Found at i:1954588 original size:2 final size:2
Alignment explanation
Indices: 1954576--1954624 Score: 89
Period size: 2 Copynumber: 24.0 Consensus size: 2
1954566 TGTTATAATC
1954576 AT AT AT GAT 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
1954619 AT AT AT
1 AT AT AT
1954625 TCGTATTTTT
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 44 0.96
3 2 0.04
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1958354 original size:26 final size:26
Alignment explanation
Indices: 1958325--1958385 Score: 83
Period size: 26 Copynumber: 2.4 Consensus size: 26
1958315 TATTAATAAT
1958325 TTATTTCTTAAAATTTTATAAATTTA
1 TTATTTCTTAAAATTTTATAAATTTA
*
1958351 TTATCTTC-TAAAGTTTTATAAATTTA
1 TTAT-TTCTTAAAATTTTATAAATTTA
1958377 -TA-TTCTTAA
1 TTATTTCTTAA
1958386 CATAAAATCA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
23 3 0.09
24 3 0.09
25 2 0.06
26 21 0.66
27 3 0.09
ACGTcount: A:0.36, C:0.07, G:0.02, T:0.56
Consensus pattern (26 bp):
TTATTTCTTAAAATTTTATAAATTTA
Found at i:1962966 original size:24 final size:20
Alignment explanation
Indices: 1962913--1962970 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 20
1962903 TTCCCCTTGA
*
1962913 AGTGCATCGATACATTCTAC
1 AGTGCATCGATGCATTCTAC
1962933 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC--T-AC
1962956 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
1962971 CTACCCATGC
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 16 0.48
22 1 0.03
23 3 0.09
24 13 0.39
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Done.