Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008526.1 Hibiscus syriacus cultivar Beakdansim tig00111398_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: 3043201
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 12
Found at i:1563178 original size:20 final size:20
Alignment explanation
Indices: 1563153--1563259 Score: 142
Period size: 20 Copynumber: 5.3 Consensus size: 20
1563143 GATTCTCTCG
**
1563153 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
**
1563173 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
1563193 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
* * *
1563213 TTACGATAGTCATTTTCACG
1 TTGCGATAGTCATTTTCGCA
*
1563233 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
1563253 TTGCGAT
1 TTGCGAT
1563260 TTTAAGTTTC
Statistics
Matches: 80, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 80 1.00
ACGTcount: A:0.23, C:0.20, G:0.21, T:0.36
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:1563270 original size:40 final size:40
Alignment explanation
Indices: 1563151--1563270 Score: 116
Period size: 40 Copynumber: 3.0 Consensus size: 40
1563141 GCGATTCTCT
** * * *
1563151 CGTTGCGATAGTCAAATTCGCATTGCGATAGTCAA-ATTCG
1 CGTTGCGATAGTCATTTTCGCATTACGATAGT-AAGTTTCA
* * *
1563191 CATTGCGATAGTCATTTTCGCATTACGATAGTCATTTTCA
1 CGTTGCGATAGTCATTTTCGCATTACGATAGTAAGTTTCA
* * **
1563231 CGTTGCGATAGTCATTTTCGCGTTGCGATTTTAAGTTTCA
1 CGTTGCGATAGTCATTTTCGCATTACGATAGTAAGTTTCA
1563271 GATTCTATTC
Statistics
Matches: 65, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
39 1 0.02
40 64 0.98
ACGTcount: A:0.23, C:0.19, G:0.20, T:0.38
Consensus pattern (40 bp):
CGTTGCGATAGTCATTTTCGCATTACGATAGTAAGTTTCA
Found at i:1563834 original size:21 final size:21
Alignment explanation
Indices: 1563743--1563841 Score: 92
Period size: 21 Copynumber: 4.7 Consensus size: 21
1563733 GACTCACCTG
*
1563743 TCATCGTTCAAGAGGCCTCCCC
1 TCATCGTTCAAGAGGCC-CCTC
*
1563765 T-ATCGTTCAAGAGGCCCCTA
1 TCATCGTTCAAGAGGCCCCTC
** *
1563785 TCATCCCTCAAGAGTCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
* * * *
1563806 CCACCGTTCAAGAGGCCACTG
1 TCATCGTTCAAGAGGCCCCTC
*
1563827 TCATCGTTAAAGAGG
1 TCATCGTTCAAGAGG
1563842 TCTCTCCCAA
Statistics
Matches: 60, Mismatches: 16, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
20 3 0.05
21 56 0.93
22 1 0.02
ACGTcount: A:0.23, C:0.35, G:0.19, T:0.22
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:1563840 original size:42 final size:42
Alignment explanation
Indices: 1563740--1563850 Score: 116
Period size: 42 Copynumber: 2.6 Consensus size: 42
1563730 CCCGACTCAC
* * *
1563740 CTGTCATCGTTCAAGAGGCCTCCCCTATCGTTCAAGAGGCCC
1 CTGTCATCGTTCAAGAGGCCTCCCCCACCGTTCAAGAGGCCA
* ** *
1563782 CTATCATCCCTCAAGAGTCC-CCTCCCACCGTTCAAGAGGCCA
1 CTGTCATCGTTCAAGAGGCCTCC-CCCACCGTTCAAGAGGCCA
* * *
1563824 CTGTCATCGTTAAAGAGGTCTCTCCCA
1 CTGTCATCGTTCAAGAGGCCTCCCCCA
1563851 ACATTCTAGA
Statistics
Matches: 53, Mismatches: 14, Indels: 4
0.75 0.20 0.06
Matches are distributed among these distances:
41 2 0.04
42 50 0.94
43 1 0.02
ACGTcount: A:0.22, C:0.37, G:0.18, T:0.23
Consensus pattern (42 bp):
CTGTCATCGTTCAAGAGGCCTCCCCCACCGTTCAAGAGGCCA
Found at i:1565251 original size:14 final size:14
Alignment explanation
Indices: 1565232--1565267 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1565222 ATTGTTTAAT
1565232 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
1565246 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
1565260 TGATTTGT
1 TGATTTGT
1565268 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1565392 original size:14 final size:14
Alignment explanation
Indices: 1565373--1565426 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
1565363 AAAACAGACT
1565373 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
1565387 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAGA
1565406 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
1565420 ATCGCAA
1 ATCGCAA
1565427 TGCGAAAATG
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 17 0.52
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.30
ACGTcount: A:0.44, C:0.20, G:0.24, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:1565410 original size:33 final size:34
Alignment explanation
Indices: 1565373--1565445 Score: 139
Period size: 33 Copynumber: 2.2 Consensus size: 34
1565363 AAAACAGACT
1565373 ATCGCAACGAGAGAATCGCAATGCG-AAATGAAA
1 ATCGCAACGAGAGAATCGCAATGCGAAAATGAAA
1565406 ATCGCAACGAGAGAATCGCAATGCGAAAATGAAA
1 ATCGCAACGAGAGAATCGCAATGCGAAAATGAAA
1565440 ATCGCA
1 ATCGCA
1565446 GCGCGAAACT
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
33 25 0.64
34 14 0.36
ACGTcount: A:0.45, C:0.19, G:0.23, T:0.12
Consensus pattern (34 bp):
ATCGCAACGAGAGAATCGCAATGCGAAAATGAAA
Found at i:1565520 original size:33 final size:34
Alignment explanation
Indices: 1565463--1565538 Score: 127
Period size: 33 Copynumber: 2.3 Consensus size: 34
1565453 ACTAAATTCG
1565463 CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
*
1565497 CGTTGCGATTTTCA-TTTCGCATTGTGATTCTCT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
*
1565530 CGATGCGAT
1 CGTTGCGAT
1565539 AGTCAATTCC
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 26 0.65
34 14 0.35
ACGTcount: A:0.13, C:0.22, G:0.20, T:0.45
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
Found at i:1565558 original size:20 final size:20
Alignment explanation
Indices: 1565533--1565598 Score: 98
Period size: 20 Copynumber: 3.3 Consensus size: 20
1565523 ATTCTCTCGA
1565533 TGCGATAGTCAATTCCGCGT
1 TGCGATAGTCAATTCCGCGT
* *
1565553 TGCGATAGTCATTTCCGTGT
1 TGCGATAGTCAATTCCGCGT
1565573 TGCGATAGTCATATT-CGCGT
1 TGCGATAGTCA-ATTCCGCGT
1565593 TGCGAT
1 TGCGAT
1565599 TTCCGCGTTG
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
20 39 0.95
21 2 0.05
ACGTcount: A:0.18, C:0.21, G:0.26, T:0.35
Consensus pattern (20 bp):
TGCGATAGTCAATTCCGCGT
Found at i:1568064 original size:24 final size:24
Alignment explanation
Indices: 1568031--1568083 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
1568021 TGAAAAATCG
1568031 TCAAAATCCGAGTATTGACCAAGA
1 TCAAAATCCGAGTATTGACCAAGA
* *
1568055 TCAAAGTCCGGGTATTGACCAAGA
1 TCAAAATCCGAGTATTGACCAAGA
1568079 TCAAA
1 TCAAA
1568084 TTTGGAATAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.21
Consensus pattern (24 bp):
TCAAAATCCGAGTATTGACCAAGA
Found at i:1568954 original size:20 final size:20
Alignment explanation
Indices: 1568926--1568992 Score: 100
Period size: 20 Copynumber: 3.4 Consensus size: 20
1568916 AAATTCAGTA
*
1568926 TTGCAATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCTCG
1568946 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCTCG
*
1568966 TTGCGATAGTCAG-ATTTCCG
1 TTGCGATAGTCAGAATCT-CG
1568986 TTGCGAT
1 TTGCGAT
1568993 TTACGTATTC
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
19 3 0.07
20 41 0.93
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCTCG
Found at i:1569032 original size:21 final size:21
Alignment explanation
Indices: 1569008--1569053 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
1568998 TATTCGCATT
1569008 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* *
1569029 GCGAATTTGGAAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
1569050 GCGA
1 GCGA
1569054 TAGTCAGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.39, C:0.17, G:0.26, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:1570726 original size:21 final size:21
Alignment explanation
Indices: 1570702--1570741 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1570692 ATGTCTCTTG
*
1570702 TTTTTC-TTTTATTTTAAATT
1 TTTTTCATTTGATTTTAAATT
1570722 TTTTTCATTTGATTTTAAAT
1 TTTTTCATTTGATTTTAAAT
1570742 AAATAAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.23, C:0.05, G:0.03, T:0.70
Consensus pattern (21 bp):
TTTTTCATTTGATTTTAAATT
Found at i:1576547 original size:16 final size:16
Alignment explanation
Indices: 1576526--1576558 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1576516 ATTATGGATT
1576526 TGAAATAAATGGATAA
1 TGAAATAAATGGATAA
1576542 TGAAATAAATGGATAA
1 TGAAATAAATGGATAA
1576558 T
1 T
1576559 ACTATGTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.55, C:0.00, G:0.18, T:0.27
Consensus pattern (16 bp):
TGAAATAAATGGATAA
Found at i:1577456 original size:2 final size:2
Alignment explanation
Indices: 1577438--1577488 Score: 54
Period size: 2 Copynumber: 26.5 Consensus size: 2
1577428 ATTAATAAAT
* *
1577438 TA TA TA T- TCA TA AA TA TA T- TA AA TA TA -A TA TA TA TA TA TA
1 TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1577478 TA TA TA TA TA T
1 TA TA TA TA TA T
1577489 CAAGAAAAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
1 3 0.07
2 37 0.90
3 1 0.02
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1577588 original size:25 final size:25
Alignment explanation
Indices: 1577560--1577609 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
1577550 TTTGAGAAGG
*
1577560 ATTTCTAGAAACAGGGAAATGATAT
1 ATTTATAGAAACAGGGAAATGATAT
* *
1577585 ATTTATTGAAACATGGAAATGATAT
1 ATTTATAGAAACAGGGAAATGATAT
1577610 TGAATTTAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.44, C:0.06, G:0.18, T:0.32
Consensus pattern (25 bp):
ATTTATAGAAACAGGGAAATGATAT
Found at i:1579698 original size:19 final size:19
Alignment explanation
Indices: 1579674--1579713 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
1579664 TTAAATATCT
1579674 TTCGTGCAAGTATATGC-AG
1 TTCGTG-AAGTATATGCTAG
*
1579693 TTCGTGATGTATATGCTAG
1 TTCGTGAAGTATATGCTAG
1579712 TT
1 TT
1579714 TAACAACACA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.23, C:0.12, G:0.25, T:0.40
Consensus pattern (19 bp):
TTCGTGAAGTATATGCTAG
Found at i:1585039 original size:52 final size:52
Alignment explanation
Indices: 1584961--1585065 Score: 183
Period size: 52 Copynumber: 2.0 Consensus size: 52
1584951 CCAACTCTTG
* *
1584961 TCTGCTATTTTTATATTGATTTTTATTATAATCAAGGCGCATGCACTTGCTT
1 TCTGCTATTTTTATATTCATTTTTATTACAATCAAGGCGCATGCACTTGCTT
*
1585013 TCTGCTATTTTTATATTCATTTTTATTACAATCACGGCGCATGCACTTGCTT
1 TCTGCTATTTTTATATTCATTTTTATTACAATCAAGGCGCATGCACTTGCTT
1585065 T
1 T
1585066 TTTTTTATTT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.22, C:0.18, G:0.12, T:0.48
Consensus pattern (52 bp):
TCTGCTATTTTTATATTCATTTTTATTACAATCAAGGCGCATGCACTTGCTT
Found at i:1593159 original size:17 final size:18
Alignment explanation
Indices: 1593120--1593167 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
1593110 GCTTTCTGAG
1593120 GGAATTGGAATCTGTGAA
1 GGAATTGGAATCTGTGAA
* *
1593138 GGAATTGAAATCTGT-CA
1 GGAATTGGAATCTGTGAA
1593155 GGAATTGGAATCT
1 GGAATTGGAATCT
1593168 AATTCCACAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 13 0.48
18 14 0.52
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.29
Consensus pattern (18 bp):
GGAATTGGAATCTGTGAA
Found at i:1598321 original size:13 final size:13
Alignment explanation
Indices: 1598303--1598327 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1598293 TTCGATAGAA
1598303 TATTATAAAAATG
1 TATTATAAAAATG
1598316 TATTATAAAAAT
1 TATTATAAAAAT
1598328 AAATTCATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (13 bp):
TATTATAAAAATG
Found at i:1605399 original size:21 final size:20
Alignment explanation
Indices: 1605375--1605414 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
1605365 AAAAATAGCA
1605375 GTTCGAAAAAGAAAAAAAACT
1 GTTCGAAAAA-AAAAAAAACT
*
1605396 GTTCGAAAGAAAAAAAAAC
1 GTTCGAAAAAAAAAAAAAC
1605415 ATGAAAGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.62, C:0.10, G:0.15, T:0.12
Consensus pattern (20 bp):
GTTCGAAAAAAAAAAAAACT
Found at i:1610355 original size:23 final size:23
Alignment explanation
Indices: 1610327--1610384 Score: 102
Period size: 23 Copynumber: 2.6 Consensus size: 23
1610317 AAATTAATAA
1610327 TATATTATGTAAAATGTTTCGAT
1 TATATTATGTAAAATGTTTCGAT
1610350 TATATTATGTAAAATGTTTCGAT
1 TATATTATGTAAAATGTTTCGAT
1610373 TATA--ATGTAAAA
1 TATATTATGTAAAA
1610385 ATTATAACTA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
21 8 0.23
23 27 0.77
ACGTcount: A:0.40, C:0.03, G:0.12, T:0.45
Consensus pattern (23 bp):
TATATTATGTAAAATGTTTCGAT
Found at i:1610427 original size:13 final size:13
Alignment explanation
Indices: 1610398--1610432 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
1610388 ATAACTAATA
*
1610398 ATATTAAAT-ATT
1 ATATTAAATAAAT
1610410 ATATTAAATAAAT
1 ATATTAAATAAAT
1610423 ATATTAAATA
1 ATATTAAATA
1610433 TATTTATGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 9 0.43
13 12 0.57
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
ATATTAAATAAAT
Found at i:1613439 original size:8 final size:8
Alignment explanation
Indices: 1613426--1613466 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
1613416 CTCATTTTCA
1613426 GAGAATTT
1 GAGAATTT
1613434 GAGAATTT
1 GAGAATTT
*
1613442 -AGAGTTT
1 GAGAATTT
*
1613449 GGGAATTT
1 GAGAATTT
1613457 GAGAATTT
1 GAGAATTT
1613465 GA
1 GA
1613467 AAGATTGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:1613759 original size:126 final size:126
Alignment explanation
Indices: 1613534--1614263 Score: 1417
Period size: 126 Copynumber: 5.8 Consensus size: 126
1613524 CTATAATCGG
1613534 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
* *
1613599 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAATACCTATTAT
66 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTACTAT
1613660 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1613725 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTACTAT
66 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTACTAT
1613786 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1613851 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTACTAT
66 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTACTAT
1613912 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1613977 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTACTAT
66 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTACTAT
1614038 TTCACTATTCACGTGAAGGCGCGTTCCC-GGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
*
1614102 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACATACTAT
66 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTACTAT
1614163 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
*
1614228 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGA
66 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGA
1614264 ATAACTTAAA
Statistics
Matches: 599, Mismatches: 4, Indels: 2
0.99 0.01 0.00
Matches are distributed among these distances:
125 124 0.21
126 475 0.79
ACGTcount: A:0.22, C:0.26, G:0.20, T:0.32
Consensus pattern (126 bp):
TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTACTAT
Found at i:1614712 original size:33 final size:34
Alignment explanation
Indices: 1614651--1614750 Score: 139
Period size: 33 Copynumber: 3.0 Consensus size: 34
1614641 AAATTTAATG
*
1614651 TTAAATTTCGAATACTATAATTTATATTTTAAAT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
* * * *
1614685 TTAAATTT-GAATAATATTATTTTTATTTTTATT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
*
1614718 TTAAATTTCGAATAATATAATTTGTATTTTAAA
1 TTAAATTTCGAATAATATAATTTATATTTTAAA
1614751 AACATTTATC
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
33 28 0.50
34 28 0.50
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.54
Consensus pattern (34 bp):
TTAAATTTCGAATAATATAATTTATATTTTAAAT
Found at i:1615384 original size:21 final size:21
Alignment explanation
Indices: 1615276--1615381 Score: 160
Period size: 21 Copynumber: 5.0 Consensus size: 21
1615266 ATAAAACCCT
*
1615276 GCGGGCTAGGCATGTAACCTG
1 GCGGGCTAGGAATGTAACCTG
*
1615297 GCGGGCTAGGCATGTAACCTG
1 GCGGGCTAGGAATGTAACCTG
1615318 GCGGGCTAGGAATGTAACCTG
1 GCGGGCTAGGAATGTAACCTG
1615339 GCGGGCTAGGAATGTAACCCT-
1 GCGGGCTAGGAATGTAA-CCTG
*
1615360 GCGGGCTCGGAATGTAATCCTG
1 GCGGGCTAGGAATGTAA-CCTG
1615382 CGGAGATGGC
Statistics
Matches: 80, Mismatches: 3, Indels: 3
0.93 0.03 0.03
Matches are distributed among these distances:
21 77 0.96
22 3 0.04
ACGTcount: A:0.21, C:0.23, G:0.37, T:0.20
Consensus pattern (21 bp):
GCGGGCTAGGAATGTAACCTG
Found at i:1615408 original size:63 final size:63
Alignment explanation
Indices: 1615276--1615408 Score: 146
Period size: 63 Copynumber: 2.1 Consensus size: 63
1615266 ATAAAACCCT
* * * * *
1615276 GCGGGCTAGGCATGTAACCTGGCGGGCTAGGCATGTAACCTGGCGGGCTAGGAATGTAACCTG
1 GCGGGCTAGGAATGTAACCTGGCGGGCTAGGAATGTAACCTGGCGGGATAGGAATATAAACTG
* *
1615339 GCGGGCTAGGAATGTAACCCT-GCGGGCTCGGAATGTAATCCT-GCGGAGAT-GGCATATAAACT
1 GCGGGCTAGGAATGTAA-CCTGGCGGGCTAGGAATGTAA-CCTGGCGG-GATAGGAATATAAACT
1615401 G
63 G
*
1615402 GTGGGCT
1 GCGGGCT
1615409 TGGCATATGA
Statistics
Matches: 59, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
63 51 0.86
64 8 0.14
ACGTcount: A:0.22, C:0.21, G:0.37, T:0.20
Consensus pattern (63 bp):
GCGGGCTAGGAATGTAACCTGGCGGGCTAGGAATGTAACCTGGCGGGATAGGAATATAAACTG
Found at i:1615414 original size:21 final size:21
Alignment explanation
Indices: 1615388--1615435 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
1615378 CCTGCGGAGA
*
1615388 TGGCATATAAACTGGTGGGCT
1 TGGCATATAAACTGGAGGGCT
* *
1615409 TGGCATATGAAGTGGAGGGCT
1 TGGCATATAAACTGGAGGGCT
*
1615430 GGGCAT
1 TGGCAT
1615436 GTACCCCTGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.12, G:0.40, T:0.25
Consensus pattern (21 bp):
TGGCATATAAACTGGAGGGCT
Found at i:1617196 original size:34 final size:32
Alignment explanation
Indices: 1617151--1617239 Score: 90
Period size: 34 Copynumber: 2.7 Consensus size: 32
1617141 TTAATAATTC
1617151 TAAATAAATAATAATTATATAAATATTATTTTAATA
1 TAAA-AAATAATAATTATATAAATA-TA--TTAATA
* * *
1617187 -ATAAAATAATATTTACATAAATATATTAATA
1 TAAAAAATAATAATTATATAAATATATTAATA
* *
1617218 TAAAAAATAATAACTATTTAAA
1 TAAAAAATAATAATTATATAAA
1617240 AAATACTAAC
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
31 6 0.14
32 16 0.36
33 2 0.05
34 18 0.41
35 2 0.05
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.39
Consensus pattern (32 bp):
TAAAAAATAATAATTATATAAATATATTAATA
Found at i:1617220 original size:14 final size:15
Alignment explanation
Indices: 1617154--1617226 Score: 51
Period size: 15 Copynumber: 4.7 Consensus size: 15
1617144 ATAATTCTAA
1617154 ATAAATAATAATT-AT
1 ATAAATAAT-ATTAAT
*
1617169 ATAAATATTATTTTAAT
1 ATAAATA--ATATTAAT
* *
1617186 AATAAAATAATATTTAC
1 -AT-AAATAATATTAAT
1617203 ATAAAT-ATATTAAT
1 ATAAATAATATTAAT
*
1617217 ATAAAAAATA
1 ATAAATAATA
1617227 ATAACTATTT
Statistics
Matches: 45, Mismatches: 7, Indels: 12
0.70 0.11 0.19
Matches are distributed among these distances:
14 11 0.24
15 14 0.31
16 4 0.09
17 9 0.20
18 2 0.04
19 5 0.11
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (15 bp):
ATAAATAATATTAAT
Found at i:1618152 original size:2 final size:2
Alignment explanation
Indices: 1618147--1618184 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1618137 AGGCAGAAAG
1618147 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
1618185 TATTTTAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1637545 original size:15 final size:17
Alignment explanation
Indices: 1637527--1637559 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
1637517 TTTGATTTTT
1637527 TTAAATT-CAAG-TAGA
1 TTAAATTGCAAGATAGA
1637542 TTAAATTGCAAGATAGA
1 TTAAATTGCAAGATAGA
1637559 T
1 T
1637560 AAAAAAACAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 4 0.25
17 5 0.31
ACGTcount: A:0.45, C:0.06, G:0.15, T:0.33
Consensus pattern (17 bp):
TTAAATTGCAAGATAGA
Found at i:1637597 original size:21 final size:21
Alignment explanation
Indices: 1637555--1637597 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1637545 AATTGCAAGA
**
1637555 TAGATAAAAAAACATTGAAAT
1 TAGATAAAAAAACATACAAAT
* *
1637576 TAGATAAATAAACATACTAAT
1 TAGATAAAAAAACATACAAAT
1637597 T
1 T
1637598 TTTTTATTTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.58, C:0.07, G:0.07, T:0.28
Consensus pattern (21 bp):
TAGATAAAAAAACATACAAAT
Found at i:1644578 original size:28 final size:28
Alignment explanation
Indices: 1644507--1644578 Score: 76
Period size: 29 Copynumber: 2.6 Consensus size: 28
1644497 ACTCCCTAAA
1644507 TGTTTTTGGG-ATTTTTAGGAATTTAGG
1 TGTTTTTGGGAATTTTTAGGAATTTAGG
* ** *
1644534 AGTTTTT-TTAGATTTTTTGGAATTTAAGG
1 TGTTTTTGGGA-ATTTTTAGGAATTT-AGG
1644563 TGTTTTTGGGAATTTT
1 TGTTTTTGGGAATTTT
1644579 AATAATTTCA
Statistics
Matches: 34, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
27 6 0.18
28 13 0.38
29 14 0.41
30 1 0.03
ACGTcount: A:0.19, C:0.00, G:0.25, T:0.56
Consensus pattern (28 bp):
TGTTTTTGGGAATTTTTAGGAATTTAGG
Found at i:1645437 original size:21 final size:21
Alignment explanation
Indices: 1645412--1645455 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
1645402 ATTATTATAT
* *
1645412 TTTTATAGTTGAGATTTTTAA
1 TTTTATAATTAAGATTTTTAA
1645433 TTTTATAATTAAGATTTTTAA
1 TTTTATAATTAAGATTTTTAA
1645454 TT
1 TT
1645456 CTACTTTTAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.32, C:0.00, G:0.09, T:0.59
Consensus pattern (21 bp):
TTTTATAATTAAGATTTTTAA
Found at i:1647797 original size:29 final size:29
Alignment explanation
Indices: 1647765--1647862 Score: 72
Period size: 29 Copynumber: 3.1 Consensus size: 29
1647755 AAAATGTCAT
1647765 AATTGAAATGTATCATTTTACATATTTTA
1 AATTGAAATGTATCATTTTACATATTTTA
* * * *
1647794 AATTAATAAATTGTCTTCATTATT-CTAATTTTTTTG
1 AATT--GAAA-TGT-ATCATT-TTAC--A-TATTTTA
*
1647830 AATTGAAATGTATCATTTTACATGTTTTA
1 AATTGAAATGTATCATTTTACATATTTTA
1647859 AATT
1 AATT
1647863 AATAAATTGT
Statistics
Matches: 52, Mismatches: 8, Indels: 18
0.67 0.10 0.23
Matches are distributed among these distances:
29 13 0.25
30 1 0.02
31 5 0.10
32 9 0.17
33 9 0.17
34 5 0.10
35 1 0.02
36 9 0.17
ACGTcount: A:0.35, C:0.07, G:0.07, T:0.51
Consensus pattern (29 bp):
AATTGAAATGTATCATTTTACATATTTTA
Found at i:1647814 original size:33 final size:33
Alignment explanation
Indices: 1647777--1647879 Score: 92
Period size: 33 Copynumber: 3.2 Consensus size: 33
1647767 TTGAAATGTA
1647777 TCATTTTACATATTTTAAATTAATAAATTGTCT
1 TCATTTTACATATTTTAAATTAATAAATTGTCT
* *
1647810 TCATTATT-C-TAATTTT--TTTGAATTGAAA-TGT-A
1 TCATT-TTACAT-ATTTTAAATT-AA-T-AAATTGTCT
*
1647842 TCATTTTACATGTTTTAAATTAATAAATTGTCT
1 TCATTTTACATATTTTAAATTAATAAATTGTCT
1647875 TCATT
1 TCATT
1647880 ATTCTAATTT
Statistics
Matches: 54, Mismatches: 5, Indels: 22
0.67 0.06 0.27
Matches are distributed among these distances:
31 7 0.13
32 17 0.31
33 23 0.43
34 7 0.13
ACGTcount: A:0.33, C:0.09, G:0.06, T:0.52
Consensus pattern (33 bp):
TCATTTTACATATTTTAAATTAATAAATTGTCT
Found at i:1647841 original size:65 final size:65
Alignment explanation
Indices: 1647765--1647910 Score: 265
Period size: 65 Copynumber: 2.2 Consensus size: 65
1647755 AAAATGTCAT
*
1647765 AATTGAAATGTATCATTTTACATATTTTAAATTAATAAATTGTCTTCATTATTCTAATTTTTTTG
1 AATTGAAATGTATCATTTTACATATTTTAAATTAATAAATTGTCTTCATTATTCTAATTTTATTG
*
1647830 AATTGAAATGTATCATTTTACATGTTTTAAATTAATAAATTGTCTTCATTATTCTAATTTTATTG
1 AATTGAAATGTATCATTTTACATATTTTAAATTAATAAATTGTCTTCATTATTCTAATTTTATTG
*
1647895 AATTGAAATATATCAT
1 AATTGAAATGTATCAT
1647911 ATCTTATATT
Statistics
Matches: 78, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
65 78 1.00
ACGTcount: A:0.36, C:0.08, G:0.07, T:0.50
Consensus pattern (65 bp):
AATTGAAATGTATCATTTTACATATTTTAAATTAATAAATTGTCTTCATTATTCTAATTTTATTG
Found at i:1647891 original size:33 final size:33
Alignment explanation
Indices: 1647788--1647891 Score: 94
Period size: 33 Copynumber: 3.2 Consensus size: 33
1647778 CATTTTACAT
1647788 ATTTTAAATTAATAAATTGTCTTCATTATTCTA
1 ATTTTAAATTAATAAATTGTCTTCATTATTCTA
* *
1647821 ATTTT--TTTGAATTGAAA-TGT-ATCATT-TTAC-A
1 ATTTTAAATT-AA-T-AAATTGTCTTCATTATT-CTA
*
1647852 TGTTTTAAATTAATAAATTGTCTTCATTATTCTA
1 -ATTTTAAATTAATAAATTGTCTTCATTATTCTA
1647886 ATTTTA
1 ATTTTA
1647892 TTGAATTGAA
Statistics
Matches: 54, Mismatches: 6, Indels: 22
0.66 0.07 0.27
Matches are distributed among these distances:
31 8 0.15
32 16 0.30
33 22 0.41
34 8 0.15
ACGTcount: A:0.34, C:0.08, G:0.06, T:0.53
Consensus pattern (33 bp):
ATTTTAAATTAATAAATTGTCTTCATTATTCTA
Found at i:1648354 original size:2 final size:2
Alignment explanation
Indices: 1648349--1648377 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1648339 TGCCATTAAC
1648349 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
1648378 TATGTCATGA
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:1673337 original size:18 final size:18
Alignment explanation
Indices: 1673316--1673350 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1673306 ATTAAAATAT
1673316 AAAATATTTATAAAAAAC
1 AAAATATTTATAAAAAAC
* *
1673334 AAAATGTTTGTAAAAAA
1 AAAATATTTATAAAAAA
1673351 TATCATTAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.63, C:0.03, G:0.06, T:0.29
Consensus pattern (18 bp):
AAAATATTTATAAAAAAC
Found at i:1673740 original size:2 final size:2
Alignment explanation
Indices: 1673733--1673763 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1673723 GTGCGATCGC
1673733 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1673764 GAAAGAGTGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1686058 original size:23 final size:26
Alignment explanation
Indices: 1686031--1686077 Score: 73
Period size: 23 Copynumber: 1.9 Consensus size: 26
1686021 ATTTATTGAT
1686031 TTAAATAAAA-A-ATAAG-AATAAAA
1 TTAAATAAAATACATAAGTAATAAAA
1686054 TTAAATAAAATACATAAGTAATAA
1 TTAAATAAAATACATAAGTAATAA
1686078 GAATAAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 10 0.48
24 1 0.05
25 5 0.24
26 5 0.24
ACGTcount: A:0.68, C:0.02, G:0.04, T:0.26
Consensus pattern (26 bp):
TTAAATAAAATACATAAGTAATAAAA
Found at i:1687437 original size:5 final size:5
Alignment explanation
Indices: 1687427--1687452 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
1687417 TGACTTAGAA
1687427 ACCCG ACCCG ACCCG ACCCG ACCCG A
1 ACCCG ACCCG ACCCG ACCCG ACCCG A
1687453 AATAATAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.58, G:0.19, T:0.00
Consensus pattern (5 bp):
ACCCG
Found at i:1689502 original size:22 final size:20
Alignment explanation
Indices: 1689477--1689516 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 20
1689467 CCCTTGGGGT
1689477 TAATGAAATTACAATATTACTA
1 TAATGAAATTA-AA-ATTACTA
*
1689499 TAATGATATTAAAATTAC
1 TAATGAAATTAAAATTAC
1689517 GAGATTATCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 2 0.12
22 10 0.59
ACGTcount: A:0.50, C:0.07, G:0.05, T:0.38
Consensus pattern (20 bp):
TAATGAAATTAAAATTACTA
Found at i:1689759 original size:2 final size:2
Alignment explanation
Indices: 1689754--1689790 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1689744 ATACATTGTA
1689754 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1689791 ACTTATTTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1690783 original size:17 final size:17
Alignment explanation
Indices: 1690743--1690808 Score: 61
Period size: 15 Copynumber: 4.1 Consensus size: 17
1690733 GTTTTTTAGG
*
1690743 AAAAAATATAAA-TA-T
1 AAAAAATAAAAATTATT
*
1690758 AAAATATAAAAATGT-TT
1 AAAAAATAAAAAT-TATT
1690775 AAAAAAT--AAATTATT
1 AAAAAATAAAAATTATT
1690790 AAAAAATAAAAATATATT
1 AAAAAATAAAAAT-TATT
1690808 A
1 A
1690809 TTATTTTTAC
Statistics
Matches: 41, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
14 1 0.02
15 23 0.56
17 12 0.29
18 5 0.12
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (17 bp):
AAAAAATAAAAATTATT
Found at i:1692127 original size:31 final size:31
Alignment explanation
Indices: 1692089--1692154 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
1692079 CATGGCTGAG
* *
1692089 GGATTAAAATGGAACGGATCGATAACGTTAA
1 GGATTAAAATCGAACGGATCGATAACATTAA
* * *
1692120 GGATTAAAATCGAATGTATCGATAACATTAG
1 GGATTAAAATCGAACGGATCGATAACATTAA
1692151 GGAT
1 GGAT
1692155 CATATACCCT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.41, C:0.09, G:0.24, T:0.26
Consensus pattern (31 bp):
GGATTAAAATCGAACGGATCGATAACATTAA
Found at i:1693487 original size:57 final size:61
Alignment explanation
Indices: 1693397--1693536 Score: 152
Period size: 57 Copynumber: 2.4 Consensus size: 61
1693387 GTCCCCAAAA
* *
1693397 TATTGAAAGTTATAAAAT-AGT-ATCCGATCATA-GG-TTTGTTCTTTGTTGAG-TC-CC-GAC
1 TATTAAAAGTTATAAAATGA-TCATCCGATCATAGGGCGTTGTT-TTT-TTGAGCTCTCCTGAC
* *
1693454 TATT-AAATTTATAAAATGATCATCCGATTATAGGGCGTTGTTTTTTTGAGCTCTCCTGAC
1 TATTAAAAGTTATAAAATGATCATCCGATCATAGGGCGTTGTTTTTTTGAGCTCTCCTGAC
*
1693514 TATTAAAAGTTACAAAATGATCA
1 TATTAAAAGTTATAAAATGATCA
1693537 CTTGACTATT
Statistics
Matches: 70, Mismatches: 5, Indels: 12
0.80 0.06 0.14
Matches are distributed among these distances:
56 13 0.19
57 20 0.29
58 7 0.10
59 7 0.10
60 7 0.10
61 16 0.23
ACGTcount: A:0.31, C:0.14, G:0.16, T:0.39
Consensus pattern (61 bp):
TATTAAAAGTTATAAAATGATCATCCGATCATAGGGCGTTGTTTTTTTGAGCTCTCCTGAC
Found at i:1693851 original size:60 final size:60
Alignment explanation
Indices: 1693781--1693940 Score: 162
Period size: 60 Copynumber: 2.7 Consensus size: 60
1693771 TCGAGTGATA
* * * ** *
1693781 ATTTTTTAACTTTTAATAGTCGATAAACTCAACAAAGTAACGCCCTATAGTT-AAGGAATT
1 ATTTTATAACTTTTAATAGCCAATAAACTCAACAAAACAACACCCTATAGTTGAAGG-ATT
** * *
1693841 ATTTTATAACTTTTAATAGCCAATGGACTCAACAAAACGACACCCTATAGTTGATGGATT
1 ATTTTATAACTTTTAATAGCCAATAAACTCAACAAAACAACACCCTATAGTTGAAGGATT
* ** *
1693901 ATTTTGTAACTTTTAATAATCAAGTGAA-TCAACAAAACAA
1 ATTTTATAACTTTTAATAGCCAA-TAAACTCAACAAAACAA
1693941 GATCTTATGG
Statistics
Matches: 83, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
60 77 0.93
61 6 0.07
ACGTcount: A:0.40, C:0.16, G:0.11, T:0.33
Consensus pattern (60 bp):
ATTTTATAACTTTTAATAGCCAATAAACTCAACAAAACAACACCCTATAGTTGAAGGATT
Found at i:1694384 original size:19 final size:19
Alignment explanation
Indices: 1694348--1694385 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
1694338 CAAACGATAT
1694348 TATCAATAATAATAATAAA
1 TATCAATAATAATAATAAA
*
1694367 TATCATATAA-AATTATAAA
1 TATCA-ATAATAATAATAAA
1694386 ATTTGGAGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (19 bp):
TATCAATAATAATAATAAA
Found at i:1695710 original size:24 final size:24
Alignment explanation
Indices: 1695683--1695782 Score: 76
Period size: 24 Copynumber: 4.2 Consensus size: 24
1695673 GATATCAAAA
*
1695683 ATCAAAACATAATTCAGATCAGAT
1 ATCAAAACAAAATTCAGATCAGAT
* * * *
1695707 ATCATAACAAAATCCAGGTTAAGA-
1 ATCAAAACAAAATTCA-GATCAGAT
* * * *
1695731 ATTAGAACAGATTTCAGATCAGAT
1 ATCAAAACAAAATTCAGATCAGAT
* * *
1695755 GTCAAAACAAAATTCAAATCAGAA
1 ATCAAAACAAAATTCAGATCAGAT
1695779 ATCA
1 ATCA
1695783 GATAAAATAT
Statistics
Matches: 54, Mismatches: 20, Indels: 4
0.69 0.26 0.05
Matches are distributed among these distances:
23 5 0.09
24 44 0.81
25 5 0.09
ACGTcount: A:0.50, C:0.16, G:0.11, T:0.23
Consensus pattern (24 bp):
ATCAAAACAAAATTCAGATCAGAT
Found at i:1698306 original size:13 final size:13
Alignment explanation
Indices: 1698288--1698330 Score: 77
Period size: 13 Copynumber: 3.3 Consensus size: 13
1698278 ACGGTCAATA
1698288 GGTCAACGGGTCG
1 GGTCAACGGGTCG
*
1698301 GGTCAATGGGTCG
1 GGTCAACGGGTCG
1698314 GGTCAACGGGTCG
1 GGTCAACGGGTCG
1698327 GGTC
1 GGTC
1698331 GAGTTATGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.14, C:0.21, G:0.47, T:0.19
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:1700422 original size:24 final size:24
Alignment explanation
Indices: 1700395--1700494 Score: 87
Period size: 24 Copynumber: 4.2 Consensus size: 24
1700385 GATATCAAAA
*
1700395 ATCAAAACATAATTCAGATCAGAT
1 ATCAAAACAGAATTCAGATCAGAT
* * *
1700419 ATCATAACAGAA-TCTAGGTTAGGA-
1 ATCAAAACAGAATTC-AGATCA-GAT
* *
1700443 ATCAGAACAGATTTCAGATCAGAT
1 ATCAAAACAGAATTCAGATCAGAT
* * *
1700467 GTCAAAACAGAATTCAAATCAGAA
1 ATCAAAACAGAATTCAGATCAGAT
1700491 ATCA
1 ATCA
1700495 GATAAAATAT
Statistics
Matches: 58, Mismatches: 14, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
23 4 0.07
24 50 0.86
25 4 0.07
ACGTcount: A:0.47, C:0.16, G:0.14, T:0.23
Consensus pattern (24 bp):
ATCAAAACAGAATTCAGATCAGAT
Found at i:1700494 original size:48 final size:48
Alignment explanation
Indices: 1700388--1700496 Score: 112
Period size: 48 Copynumber: 2.3 Consensus size: 48
1700378 AAACGGAGAT
* * * * *
1700388 ATCAAAAATCAAAACATAATTCAGATCAGATATCATAACAGAATCTAG
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCTAA
* * * * *
1700436 GTTAGGAATCAGAACAGATTTCAGATCAGATGTCAAAACAGAAT-TCAA
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCT-AA
1700484 ATCAGAAATCAGA
1 ATCAGAAATCAGA
1700497 TAAAATATTC
Statistics
Matches: 47, Mismatches: 13, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
47 1 0.02
48 46 0.98
ACGTcount: A:0.49, C:0.16, G:0.14, T:0.22
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCTAA
Found at i:1703040 original size:18 final size:18
Alignment explanation
Indices: 1703017--1703062 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
1703007 GGGTGTCAAT
1703017 GGGTCGGGTCAACGGATC
1 GGGTCGGGTCAACGGATC
* *
1703035 GGGTCGGGTAAACGGGTC
1 GGGTCGGGTCAACGGATC
1703053 GGGTCGGGTC
1 GGGTCGGGTC
1703063 GGTTTGGGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.13, C:0.20, G:0.50, T:0.17
Consensus pattern (18 bp):
GGGTCGGGTCAACGGATC
Found at i:1705192 original size:21 final size:21
Alignment explanation
Indices: 1705166--1705207 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
1705156 TTATAATTTT
1705166 TCTTGACCATTAAAAATGTAA
1 TCTTGACCATTAAAAATGTAA
1705187 TCTTGACCATTAAAAATGTAA
1 TCTTGACCATTAAAAATGTAA
1705208 ACAAGTCCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.14, G:0.10, T:0.33
Consensus pattern (21 bp):
TCTTGACCATTAAAAATGTAA
Found at i:1716169 original size:16 final size:15
Alignment explanation
Indices: 1716147--1716199 Score: 56
Period size: 16 Copynumber: 3.5 Consensus size: 15
1716137 ACAGGTTGAC
1716147 AACTATACAGAATAA
1 AACTATACAGAATAA
* *
1716162 ATCTTATA-A-AAAAA
1 AAC-TATACAGAATAA
1716176 AACTATACAGAATAA
1 AACTATACAGAATAA
1716191 AGACTATAC
1 A-ACTATAC
1716200 CCAAAATTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
13 4 0.13
14 7 0.23
15 8 0.27
16 11 0.37
ACGTcount: A:0.58, C:0.13, G:0.06, T:0.23
Consensus pattern (15 bp):
AACTATACAGAATAA
Found at i:1727083 original size:50 final size:50
Alignment explanation
Indices: 1727008--1727108 Score: 202
Period size: 50 Copynumber: 2.0 Consensus size: 50
1726998 CTCACTTTAC
1727008 GTATTTGTTTCTATGGTCTCAATCAATGGTGTTAAAGTTCCGTTCTTATT
1 GTATTTGTTTCTATGGTCTCAATCAATGGTGTTAAAGTTCCGTTCTTATT
1727058 GTATTTGTTTCTATGGTCTCAATCAATGGTGTTAAAGTTCCGTTCTTATT
1 GTATTTGTTTCTATGGTCTCAATCAATGGTGTTAAAGTTCCGTTCTTATT
1727108 G
1 G
1727109 CCTGGACTGA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.20, C:0.14, G:0.19, T:0.48
Consensus pattern (50 bp):
GTATTTGTTTCTATGGTCTCAATCAATGGTGTTAAAGTTCCGTTCTTATT
Found at i:1735586 original size:24 final size:25
Alignment explanation
Indices: 1735540--1735589 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
1735530 TATTTGCCGT
** *
1735540 AAAAATATAATCTATCTATTTAATA
1 AAAAATATAATCTATAAAATTAATA
1735565 AAAAATATAAT-TATAAAATTAATA
1 AAAAATATAATCTATAAAATTAATA
1735589 A
1 A
1735590 CATATTGCGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 11 0.50
25 11 0.50
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (25 bp):
AAAAATATAATCTATAAAATTAATA
Found at i:1735812 original size:4 final size:4
Alignment explanation
Indices: 1735803--1735833 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
1735793 TTTAAACAAA
1735803 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1735834 TATATATATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.52, C:0.23, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:1737930 original size:17 final size:17
Alignment explanation
Indices: 1737904--1737937 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1737894 GAGGTGTGAC
*
1737904 ACATAGATTAAATTTTA
1 ACATAAATTAAATTTTA
1737921 ACATAAATTAAATTTTA
1 ACATAAATTAAATTTTA
1737938 TTTATCATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.41
Consensus pattern (17 bp):
ACATAAATTAAATTTTA
Found at i:1738683 original size:22 final size:24
Alignment explanation
Indices: 1738656--1738714 Score: 68
Period size: 22 Copynumber: 2.5 Consensus size: 24
1738646 AATGTTTAAG
*
1738656 ATTAAAATATTTA-AAAATATAA-
1 ATTAAAATATTTATAAAATAAAAT
* *
1738678 ATTAAAATAATTATATAATAAAAT
1 ATTAAAATATTTATAAAATAAAAT
1738702 ATTAAAAATATTT
1 ATT-AAAATATTT
1738715 TTTAATATTA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
22 12 0.40
23 7 0.23
24 3 0.10
25 8 0.27
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (24 bp):
ATTAAAATATTTATAAAATAAAAT
Found at i:1738685 original size:37 final size:37
Alignment explanation
Indices: 1738639--1738712 Score: 96
Period size: 37 Copynumber: 2.0 Consensus size: 37
1738629 GTATTTGATA
** *
1738639 AAATTAAAATGTTTA-AGATTAAAATATTTAAAAATAT
1 AAATTAAAATAATTATAGAATAAAATA-TTAAAAATAT
*
1738676 AAATTAAAATAATTATATAATAAAATATTAAAAATAT
1 AAATTAAAATAATTATAGAATAAAATATTAAAAATAT
1738713 TTTTTAATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
37 23 0.72
38 9 0.28
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (37 bp):
AAATTAAAATAATTATAGAATAAAATATTAAAAATAT
Found at i:1740747 original size:19 final size:19
Alignment explanation
Indices: 1740723--1740784 Score: 78
Period size: 19 Copynumber: 3.4 Consensus size: 19
1740713 TTATTAAAAG
1740723 AATAAAAAAGTAATATAAA
1 AATAAAAAAGTAATATAAA
*
1740742 AAT-AAAAA-T-CTA-AAA
1 AATAAAAAAGTAATATAAA
1740757 GAATAAAAAAGTAATATAAA
1 -AATAAAAAAGTAATATAAA
1740777 AATAAAAA
1 AATAAAAA
1740785 TCTACCAGTG
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
15 3 0.08
16 5 0.14
17 6 0.17
18 6 0.17
19 13 0.36
20 3 0.08
ACGTcount: A:0.74, C:0.02, G:0.05, T:0.19
Consensus pattern (19 bp):
AATAAAAAAGTAATATAAA
Found at i:1740763 original size:35 final size:35
Alignment explanation
Indices: 1740717--1740788 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
1740707 GGTAATTTAT
1740717 TAAAAGAATAAAAAAGTAATATAAAAATAAAAATC
1 TAAAAGAATAAAAAAGTAATATAAAAATAAAAATC
1740752 TAAAAGAATAAAAAAGTAATATAAAAATAAAAATC
1 TAAAAGAATAAAAAAGTAATATAAAAATAAAAATC
1740787 TA
1 TA
1740789 CCAGTGACTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.71, C:0.03, G:0.06, T:0.21
Consensus pattern (35 bp):
TAAAAGAATAAAAAAGTAATATAAAAATAAAAATC
Found at i:1745862 original size:120 final size:120
Alignment explanation
Indices: 1745647--1745878 Score: 367
Period size: 120 Copynumber: 1.9 Consensus size: 120
1745637 TCTTGCTAGC
* * *
1745647 TAAACTTAATAATATTCAGAGTCGATTTATCTTATTTACACTCGTAAAACTGACAAGCCTAATTG
1 TAAACTTAATAATATTCAGACTCGATTTATCTTATTTACACTCATAAAACTGACAAACCTAATTG
*
1745712 TTCACAAGCAGTTTTAATCGTTACTGTTATTAGCATAAAACTAATACGAATAGTT
66 GTCACAAGCAGTTTTAATCGTTACTGTTATTAGCATAAAACTAATACGAATAGTT
* * * *
1745767 TAAACTTAATAATATTCCGACTC-AGTTTATCTTATTTATACTCATAAAACTGACAAACTTGATT
1 TAAACTTAATAATATTCAGACTCGA-TTTATCTTATTTACACTCATAAAACTGACAAACCTAATT
*
1745831 GGTCACAAGCAGTTTTAATCGTTACTTTTATTAGCATAAAACTAATAC
65 GGTCACAAGCAGTTTTAATCGTTACTGTTATTAGCATAAAACTAATAC
1745879 TTTTTATAAT
Statistics
Matches: 102, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
119 1 0.01
120 101 0.99
ACGTcount: A:0.37, C:0.16, G:0.10, T:0.37
Consensus pattern (120 bp):
TAAACTTAATAATATTCAGACTCGATTTATCTTATTTACACTCATAAAACTGACAAACCTAATTG
GTCACAAGCAGTTTTAATCGTTACTGTTATTAGCATAAAACTAATACGAATAGTT
Found at i:1746415 original size:7 final size:7
Alignment explanation
Indices: 1746364--1746417 Score: 54
Period size: 7 Copynumber: 7.6 Consensus size: 7
1746354 CTCTTAAACC
1746364 TAAATTT
1 TAAATTT
* *
1746371 TATATTC
1 TAAATTT
1746378 TAAATTT
1 TAAATTT
*
1746385 TAAATCT
1 TAAATTT
1746392 TAAATTT
1 TAAATTT
* *
1746399 CATAAGTT
1 TA-AATTT
1746407 TAAATTT
1 TAAATTT
1746414 TAAA
1 TAAA
1746418 ATAGATAAAT
Statistics
Matches: 36, Mismatches: 10, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
7 31 0.86
8 5 0.14
ACGTcount: A:0.43, C:0.06, G:0.02, T:0.50
Consensus pattern (7 bp):
TAAATTT
Found at i:1747013 original size:76 final size:77
Alignment explanation
Indices: 1746921--1747063 Score: 218
Period size: 78 Copynumber: 1.9 Consensus size: 77
1746911 AAAAAACAAC
*
1746921 TAAAGAAAAATTTATTC-GCCCCTCAATTAAAAAA-ATATATTTATGAAAAATAAAAAATACTTT
1 TAAAGAAAAATTTATTCTCCCCCTCAATTAAAAAATATATATTTATG-AAAATAAAAAATACTTT
1746984 AACCCCACCTTAA
65 AACCCCACCTTAA
* * *
1746997 TAAAGAAAAATTTATTCTCCCCCTCATTTAAAAAATTTTATATTTATGAAAATAAAAAATATTTT
1 TAAAGAAAAATTTATTCTCCCCCTCAATTAAAAAA-TATATATTTATGAAAATAAAAAATACTTT
1747062 AA
65 AA
1747064 TCTCCGTCTT
Statistics
Matches: 60, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
76 17 0.28
77 15 0.25
78 18 0.30
79 10 0.17
ACGTcount: A:0.49, C:0.14, G:0.03, T:0.34
Consensus pattern (77 bp):
TAAAGAAAAATTTATTCTCCCCCTCAATTAAAAAATATATATTTATGAAAATAAAAAATACTTTA
ACCCCACCTTAA
Found at i:1762087 original size:23 final size:23
Alignment explanation
Indices: 1762046--1762123 Score: 95
Period size: 23 Copynumber: 3.4 Consensus size: 23
1762036 ACAATCAAAA
*
1762046 GGTACCC-AAACGATACTAAACT
1 GGTACCCAAAACGATACTAAACC
*
1762068 GGTACCCAAAATGATACTAAACC
1 GGTACCCAAAACGATACTAAACC
* *
1762091 GGTACCCAAAACGAAACGAAACC
1 GGTACCCAAAACGATACTAAACC
* *
1762114 CGTATCCAAA
1 GGTACCCAAA
1762124 CAAAGGCAGC
Statistics
Matches: 48, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
22 7 0.15
23 41 0.85
ACGTcount: A:0.44, C:0.28, G:0.14, T:0.14
Consensus pattern (23 bp):
GGTACCCAAAACGATACTAAACC
Found at i:1772538 original size:42 final size:43
Alignment explanation
Indices: 1772481--1772566 Score: 165
Period size: 42 Copynumber: 2.0 Consensus size: 43
1772471 TTTTCTTATC
1772481 ACCATATGTTAAAAAAATAAAATATAAAGTTAAGTATGATTTT
1 ACCATATGTTAAAAAAATAAAATATAAAGTTAAGTATGATTTT
1772524 ACCATATGTT-AAAAAATAAAATATAAAGTTAAGTATGATTTT
1 ACCATATGTTAAAAAAATAAAATATAAAGTTAAGTATGATTTT
1772566 A
1 A
1772567 AAAAAAATAA
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
42 33 0.77
43 10 0.23
ACGTcount: A:0.51, C:0.05, G:0.09, T:0.35
Consensus pattern (43 bp):
ACCATATGTTAAAAAAATAAAATATAAAGTTAAGTATGATTTT
Found at i:1782938 original size:22 final size:22
Alignment explanation
Indices: 1782910--1782953 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
1782900 CCACATAGTA
1782910 TTAACTTTAATAAGAAACAAGG
1 TTAACTTTAATAAGAAACAAGG
1782932 TTAACTTTAATAAGAAACAAGG
1 TTAACTTTAATAAGAAACAAGG
1782954 ACGAAATAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.50, C:0.09, G:0.14, T:0.27
Consensus pattern (22 bp):
TTAACTTTAATAAGAAACAAGG
Found at i:1783259 original size:14 final size:14
Alignment explanation
Indices: 1783240--1783274 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
1783230 CGTTCGATTA
1783240 TATGTTCGCTCATT
1 TATGTTCGCTCATT
*
1783254 TATGTTCGTTCATT
1 TATGTTCGCTCATT
1783268 TATGTTC
1 TATGTTC
1783275 ATTTATGTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.54
Consensus pattern (14 bp):
TATGTTCGCTCATT
Found at i:1783555 original size:23 final size:23
Alignment explanation
Indices: 1783525--1783591 Score: 80
Period size: 23 Copynumber: 2.9 Consensus size: 23
1783515 TTTTTTGTGT
* *
1783525 TGTTCGTTTATGTTTGTTTATTG
1 TGTTCGTTTATGTTAGTTTATTA
*
1783548 TGTTCGTTTATGTTAATTTATTA
1 TGTTCGTTTATGTTAGTTTATTA
** *
1783571 TGTTATTTTATGTTCGTTTAT
1 TGTTCGTTTATGTTAGTTTAT
1783592 CATTTAAATG
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.15, C:0.04, G:0.16, T:0.64
Consensus pattern (23 bp):
TGTTCGTTTATGTTAGTTTATTA
Found at i:1783633 original size:31 final size:31
Alignment explanation
Indices: 1783598--1783678 Score: 126
Period size: 31 Copynumber: 2.6 Consensus size: 31
1783588 TTATCATTTA
* * *
1783598 AATGAACAAATATGAACAAACTATATTCTTT
1 AATGAACGAACATGAACAAACTATATTCCTT
*
1783629 AATGAACGAACATGAACAAGCTATATTCCTT
1 AATGAACGAACATGAACAAACTATATTCCTT
1783660 AATGAACGAACATGAACAA
1 AATGAACGAACATGAACAA
1783679 CAACAAAAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 46 1.00
ACGTcount: A:0.48, C:0.16, G:0.11, T:0.25
Consensus pattern (31 bp):
AATGAACGAACATGAACAAACTATATTCCTT
Found at i:1784735 original size:35 final size:35
Alignment explanation
Indices: 1784689--1784758 Score: 113
Period size: 35 Copynumber: 2.0 Consensus size: 35
1784679 AGAAAAATGG
* *
1784689 TTGCTCGTTTCAGCTGAGTCCAAGAACCAACGGCT
1 TTGCTCGTTTCAACTGAGTCCAAAAACCAACGGCT
*
1784724 TTGCTTGTTTCAACTGAGTCCAAAAACCAACGGCT
1 TTGCTCGTTTCAACTGAGTCCAAAAACCAACGGCT
1784759 GGTTTTGATT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.26, C:0.27, G:0.20, T:0.27
Consensus pattern (35 bp):
TTGCTCGTTTCAACTGAGTCCAAAAACCAACGGCT
Found at i:1787800 original size:21 final size:20
Alignment explanation
Indices: 1787776--1787823 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
1787766 TTTATTAAAA
*
1787776 ATATTTTAAAATTTATATTTT
1 ATATTTTAAAATTAATA-TTT
*
1787797 ATATTATTAATATTAATATTT
1 ATATT-TTAAAATTAATATTT
1787818 ATATTT
1 ATATTT
1787824 ATATATTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 1 0.04
21 13 0.54
22 10 0.42
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
ATATTTTAAAATTAATATTT
Found at i:1787812 original size:28 final size:26
Alignment explanation
Indices: 1787781--1787839 Score: 82
Period size: 26 Copynumber: 2.2 Consensus size: 26
1787771 TAAAAATATT
*
1787781 TTAAAATTTATATTTTATATTATTAATA
1 TTAAAATTTATA-TTTATA-TATTAAAA
*
1787809 TTAATATTTATATTTATATATTAAAA
1 TTAAAATTTATATTTATATATTAAAA
1787835 TTAAA
1 TTAAA
1787840 TAAAAATATT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 11 0.39
27 6 0.21
28 11 0.39
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (26 bp):
TTAAAATTTATATTTATATATTAAAA
Found at i:1796269 original size:20 final size:20
Alignment explanation
Indices: 1796244--1796284 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
1796234 AATAAAAAAT
1796244 AAGAATTATAATAATTTATC
1 AAGAATTATAATAATTTATC
1796264 AAGAATTATAATAATTTATC
1 AAGAATTATAATAATTTATC
1796284 A
1 A
1796285 TAATGTTATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.51, C:0.05, G:0.05, T:0.39
Consensus pattern (20 bp):
AAGAATTATAATAATTTATC
Found at i:1806547 original size:16 final size:17
Alignment explanation
Indices: 1806526--1806577 Score: 67
Period size: 15 Copynumber: 3.2 Consensus size: 17
1806516 TTTTTAATTT
1806526 AATTACT-TAACTTTCA
1 AATTACTCTAACTTTCA
1806542 AATTACTCCTAA-TTT--
1 AATTACT-CTAACTTTCA
1806557 AATTACTCTAACTTTCA
1 AATTACTCTAACTTTCA
1806574 AATT
1 AATT
1806578 TATTTTTTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
14 4 0.13
15 10 0.32
16 7 0.23
17 7 0.23
18 3 0.10
ACGTcount: A:0.37, C:0.19, G:0.00, T:0.44
Consensus pattern (17 bp):
AATTACTCTAACTTTCA
Found at i:1806562 original size:15 final size:14
Alignment explanation
Indices: 1806520--1806567 Score: 53
Period size: 14 Copynumber: 3.2 Consensus size: 14
1806510 TTAATTTTTT
1806520 TAATTTAATTACT-
1 TAATTTAATTACTC
1806533 TAACTTTCAAATTACTCC
1 TAA-TTT--AATTACT-C
1806551 TAATTTAATTACTC
1 TAATTTAATTACTC
1806565 TAA
1 TAA
1806568 CTTTCAAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
13 3 0.10
14 7 0.23
15 7 0.23
16 7 0.23
17 3 0.10
18 3 0.10
ACGTcount: A:0.38, C:0.17, G:0.00, T:0.46
Consensus pattern (14 bp):
TAATTTAATTACTC
Found at i:1834497 original size:12 final size:12
Alignment explanation
Indices: 1834480--1834504 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1834470 CAATTGTTGG
1834480 AATCGTCGCTTC
1 AATCGTCGCTTC
1834492 AATCGTCGCTTC
1 AATCGTCGCTTC
1834504 A
1 A
1834505 CCTAACCGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.20, C:0.32, G:0.16, T:0.32
Consensus pattern (12 bp):
AATCGTCGCTTC
Found at i:1838596 original size:16 final size:15
Alignment explanation
Indices: 1838563--1838601 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
1838553 ATTTCTTCAT
*
1838563 TTTTTCTCTCTTTTC
1 TTTTTCTTTCTTTTC
*
1838578 TTTTTCTTTTTTTTCC
1 TTTTTCTTTCTTTT-C
1838594 TTTTTCTT
1 TTTTTCTT
1838602 GTTAATGTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 12 0.57
16 9 0.43
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTTTCTTTCTTTTC
Found at i:1852400 original size:26 final size:27
Alignment explanation
Indices: 1852365--1852437 Score: 87
Period size: 31 Copynumber: 2.6 Consensus size: 27
1852355 TTTATAGTTA
*
1852365 ATTTT-TAAAATTTTAAGAA-ATGACG
1 ATTTTATAAAATTTTAAAAATATGACG
1852390 ATTTTATAAAATTTTAATAAAAAATATGACG
1 ATTTTATAAAA-TTT--T-AAAAATATGACG
1852421 ATTTTATAAAATTTTAA
1 ATTTTATAAAATTTTAA
1852438 TAAAAAAATT
Statistics
Matches: 41, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
25 5 0.12
26 5 0.12
27 5 0.12
28 1 0.02
29 1 0.02
30 7 0.17
31 17 0.41
ACGTcount: A:0.48, C:0.03, G:0.07, T:0.42
Consensus pattern (27 bp):
ATTTTATAAAATTTTAAAAATATGACG
Found at i:1852420 original size:31 final size:31
Alignment explanation
Indices: 1852384--1852444 Score: 122
Period size: 31 Copynumber: 2.0 Consensus size: 31
1852374 ATTTTAAGAA
1852384 ATGACGATTTTATAAAATTTTAATAAAAAAT
1 ATGACGATTTTATAAAATTTTAATAAAAAAT
1852415 ATGACGATTTTATAAAATTTTAATAAAAAA
1 ATGACGATTTTATAAAATTTTAATAAAAAA
1852445 ATTAAAATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.52, C:0.03, G:0.07, T:0.38
Consensus pattern (31 bp):
ATGACGATTTTATAAAATTTTAATAAAAAAT
Found at i:1853999 original size:45 final size:45
Alignment explanation
Indices: 1853948--1854041 Score: 125
Period size: 45 Copynumber: 2.1 Consensus size: 45
1853938 TTAATAAGTT
* * * * * *
1853948 AACGAGAGTTAATGGTTGAGGGAGTAACTTTTTCATTAAGGAGTC
1 AACGAGAGTTAACGGTTAAGAGACTAACATTTTCATTAAAGAGTC
*
1853993 AACGAGAGTTAACGGTTAAGAGACTAACATTTTCATTAAAGAGTT
1 AACGAGAGTTAACGGTTAAGAGACTAACATTTTCATTAAAGAGTC
1854038 AACG
1 AACG
1854042 GTTAATAGAT
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.36, C:0.11, G:0.24, T:0.29
Consensus pattern (45 bp):
AACGAGAGTTAACGGTTAAGAGACTAACATTTTCATTAAAGAGTC
Found at i:1854687 original size:28 final size:27
Alignment explanation
Indices: 1854656--1854725 Score: 63
Period size: 28 Copynumber: 2.6 Consensus size: 27
1854646 CTTTTTATGG
1854656 ATAATATAT-TTTTATCCTCTAAAATTTT
1 ATAATATATATTTTAT--TCTAAAATTTT
* * *
1854684 ATAA-ATTTATTTTATTTTAAACTTTT
1 ATAATATATATTTTATTCTAAAATTTT
*
1854710 ATAAGTATATCTTTTA
1 ATAA-TATATATTTTA
1854726 ACATAAGTAT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
26 13 0.38
27 3 0.09
28 18 0.53
ACGTcount: A:0.36, C:0.07, G:0.01, T:0.56
Consensus pattern (27 bp):
ATAATATATATTTTATTCTAAAATTTT
Found at i:1856260 original size:22 final size:21
Alignment explanation
Indices: 1856231--1856286 Score: 69
Period size: 22 Copynumber: 2.7 Consensus size: 21
1856221 CTATATCGGT
1856231 AATTGAGTTGCGAAATTGACG
1 AATTGAGTTGCGAAATTGACG
* *
1856252 AATTCGAGTTGCGAATTTGA-A
1 AATT-GAGTTGCGAAATTGACG
*
1856273 AACTGAGTTGCGAA
1 AATTGAGTTGCGAA
1856287 TAGTTGTGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
20 10 0.32
21 7 0.23
22 14 0.45
ACGTcount: A:0.34, C:0.11, G:0.27, T:0.29
Consensus pattern (21 bp):
AATTGAGTTGCGAAATTGACG
Found at i:1863639 original size:2 final size:2
Alignment explanation
Indices: 1863632--1863666 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
1863622 TTATTCTCTG
1863632 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1863667 GTATTCATGC
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:1871289 original size:21 final size:21
Alignment explanation
Indices: 1871265--1871333 Score: 86
Period size: 21 Copynumber: 3.3 Consensus size: 21
1871255 TTTGGAATAA
*
1871265 ATCGCAATGCGATA-GTCGACT
1 ATCGCAATGCGA-ACTTCGACT
* *
1871286 ATCGCAATACGAACTTGGACT
1 ATCGCAATGCGAACTTCGACT
*
1871307 ATCACAATGCGAACTTCGACT
1 ATCGCAATGCGAACTTCGACT
1871328 ATCGCA
1 ATCGCA
1871334 TTGTGATTTA
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 1 0.03
21 39 0.98
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.23
Consensus pattern (21 bp):
ATCGCAATGCGAACTTCGACT
Found at i:1871374 original size:21 final size:21
Alignment explanation
Indices: 1871348--1871415 Score: 118
Period size: 21 Copynumber: 3.2 Consensus size: 21
1871338 GATTTACATA
1871348 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
1871369 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
* *
1871390 TTCGCATTGCGATAATCGAAG
1 TTCGCATTGCGATAGTCCAAG
1871411 TTCGC
1 TTCGC
1871416 GTTACGAATC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 45 1.00
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.29
Consensus pattern (21 bp):
TTCGCATTGCGATAGTCCAAG
Found at i:1874596 original size:9 final size:9
Alignment explanation
Indices: 1874582--1874616 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
1874572 GATTTCTTCT
1874582 TCTTCCTCC
1 TCTTCCTCC
*
1874591 TCTTCCTCT
1 TCTTCCTCC
*
1874600 TCCTCCTCC
1 TCTTCCTCC
1874609 TCTTCCTC
1 TCTTCCTC
1874617 TTCATCATCT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.00, C:0.54, G:0.00, T:0.46
Consensus pattern (9 bp):
TCTTCCTCC
Found at i:1874600 original size:15 final size:15
Alignment explanation
Indices: 1874576--1874607 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1874566 TTGCACGATT
*
1874576 TCTTCTTCTTCCTCC
1 TCTTCCTCTTCCTCC
1874591 TCTTCCTCTTCCTCC
1 TCTTCCTCTTCCTCC
1874606 TC
1 TC
1874608 CTCTTCCTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (15 bp):
TCTTCCTCTTCCTCC
Found at i:1874603 original size:12 final size:12
Alignment explanation
Indices: 1874588--1874619 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
1874578 TTCTTCTTCC
1874588 TCCTCTTCCTCT
1 TCCTCTTCCTCT
*
1874600 TCCTCCTCCTCT
1 TCCTCTTCCTCT
1874612 TCCTCTTC
1 TCCTCTTC
1874620 ATCATCTTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (12 bp):
TCCTCTTCCTCT
Found at i:1874606 original size:18 final size:18
Alignment explanation
Indices: 1874579--1874619 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
1874569 CACGATTTCT
*
1874579 TCTTCTTCCTCCTCTTCC
1 TCTTCCTCCTCCTCTTCC
1874597 TCTTCCTCCTCCTCTTCC
1 TCTTCCTCCTCCTCTTCC
1874615 TCTTC
1 TCTTC
1874620 ATCATCTTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (18 bp):
TCTTCCTCCTCCTCTTCC
Found at i:1875305 original size:36 final size:36
Alignment explanation
Indices: 1875175--1875354 Score: 157
Period size: 36 Copynumber: 5.0 Consensus size: 36
1875165 AAATTGTACG
1875175 GTTCTGAGCCGGCGGTGGCT-CAGATTGTTTAGCTTT
1 GTTCTGAGCCGGCGGTGG-TGCAGATTGTTTAGCTTT
* * * * * *
1875211 TTTCTGAGTCAGCTGTGGTGCATATTGTTTATCTTT
1 GTTCTGAGCCGGCGGTGGTGCAGATTGTTTAGCTTT
* *** * *
1875247 CCTT-TTTTCCGACGGTGCTGCAGATTGTTTAGCTTT
1 -GTTCTGAGCCGGCGGTGGTGCAGATTGTTTAGCTTT
* *
1875283 GTTCTGAGCCGGTGGTGGTGCAGATTGTTTAGCATT
1 GTTCTGAGCCGGCGGTGGTGCAGATTGTTTAGCTTT
* ** * *
1875319 GTTCTGAGCGGGCACTGGAGCAGCTTGTTTAGCTTT
1 GTTCTGAGCCGGCGGTGGTGCAGATTGTTTAGCTTT
1875355 TCCCAAAACG
Statistics
Matches: 109, Mismatches: 32, Indels: 6
0.74 0.22 0.04
Matches are distributed among these distances:
35 3 0.03
36 104 0.95
37 2 0.02
ACGTcount: A:0.13, C:0.18, G:0.29, T:0.40
Consensus pattern (36 bp):
GTTCTGAGCCGGCGGTGGTGCAGATTGTTTAGCTTT
Found at i:1879672 original size:38 final size:38
Alignment explanation
Indices: 1879621--1879696 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
1879611 TTATACTTTA
1879621 TCCTAAATTATAAATAATGATATAGATAAACAATGATT
1 TCCTAAATTATAAATAATGATATAGATAAACAATGATT
1879659 TCCTAAATTATAAATAATGATATAGATAAACAATGATT
1 TCCTAAATTATAAATAATGATATAGATAAACAATGATT
1879697 GAATAATTTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.50, C:0.08, G:0.08, T:0.34
Consensus pattern (38 bp):
TCCTAAATTATAAATAATGATATAGATAAACAATGATT
Found at i:1884136 original size:14 final size:16
Alignment explanation
Indices: 1884119--1884156 Score: 53
Period size: 14 Copynumber: 2.5 Consensus size: 16
1884109 GTATATTAGT
1884119 AATTAATTCA-AAA-A
1 AATTAATTCATAAATA
*
1884133 AATTAACTCATAAATA
1 AATTAATTCATAAATA
1884149 AATTAATT
1 AATTAATT
1884157 TTTAATTTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 9 0.45
15 3 0.15
16 8 0.40
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.34
Consensus pattern (16 bp):
AATTAATTCATAAATA
Found at i:1885950 original size:187 final size:185
Alignment explanation
Indices: 1885476--1886001 Score: 520
Period size: 188 Copynumber: 2.8 Consensus size: 185
1885466 CGAATTTGTT
* * * *
1885476 TAATATTTTCGGCTTTCAACATATTTTTGTTACCTT-GATTAATTCCTTTGACTCGTTTGCTCAA
1 TAATATTTTC-GCTTTCAACTTA-TTTTGTTACCTTGGA-TATTTCATTTGACTCGTTTGCTAAA
* * * * * *
1885540 CTCCAGTAACAATTTCGGTCAAAACCAGATTTGTTCAAGCAACTTATAACAATATCGATCTCAAC
63 CTCCAGTAACAATTTAGGTCAAAATCA-ATTTGTTAAAGCAACTTATAACATTCTAGATCTCAAC
* * * * * * * * * * *
1885605 CTACTTTCTTTGTGACTGTTAATATTCTTGAGCGCAATCGGATTTGTTAACATGATTGA
127 CTAATATCTTAGCGACCGCTCACATTCTTGAGCGCAATCAGATTTGTTAACACGACTGA
* * ** * * *
1885664 TAACATTTTTCGACTTTCAACTTATTTTGTTA-CTGTGGGTATTTTGTTTAACCCGTTCGCTAAA
1 TAATA-TTTTCG-CTTTCAACTTATTTTGTTACCT-TGGATATTTCATTTGACTCGTTTGCTAAA
* * * * * * *
1885728 CTACGGTAATAATTTTGGTTAAAATCGAATTTGTTAAAGCAACTTATAACATTCTAAATCTTAAC
63 CTCCAGTAACAATTTAGGTCAAAATC-AATTTGTTAAAGCAACTTATAACATTCTAGATCTCAAC
* * * *
1885793 CGAATATCTTGGCGACCACTCACATTCTTG-GACGCAA-CTAGATTTGTTAACGCGACTGA
127 CTAATATCTTAGCGACCGCTCACATTCTTGAG-CGCAATC-AGATTTGTTAACACGACTGA
* *
1885852 TAATATTTTCAGCTTTCAACTTACTTTGTTACCTTGGATATTTCATTTGACTCATTTGCTAAACT
1 TAATATTTTC-GCTTTCAACTTATTTTGTTACCTTGGATATTTCATTTGACTCGTTTGCTAAACT
* * *
1885917 CCAGTAACAATTTAGGTCGAAATTATATTTGTTAAAGCAACTTATAACATTCTTGATCTCAACCT
65 CCAGTAACAATTTAGGTCAAAATCA-ATTTGTTAAAGCAACTTATAACATTCTAGATCTCAACCT
1885982 AATATCTTAGCGACCGCTCA
129 AATATCTTAGCGACCGCTCA
1886002 TGTTCTTTGA
Statistics
Matches: 270, Mismatches: 58, Indels: 21
0.77 0.17 0.06
Matches are distributed among these distances:
186 1 0.00
187 121 0.45
188 131 0.49
189 17 0.06
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.39
Consensus pattern (185 bp):
TAATATTTTCGCTTTCAACTTATTTTGTTACCTTGGATATTTCATTTGACTCGTTTGCTAAACTC
CAGTAACAATTTAGGTCAAAATCAATTTGTTAAAGCAACTTATAACATTCTAGATCTCAACCTAA
TATCTTAGCGACCGCTCACATTCTTGAGCGCAATCAGATTTGTTAACACGACTGA
Found at i:1886026 original size:187 final size:185
Alignment explanation
Indices: 1885476--1886069 Score: 546
Period size: 187 Copynumber: 3.2 Consensus size: 185
1885466 CGAATTTGTT
* * * *
1885476 TAATATTTTCGGCTTTCAACATATTTTTGTTACCTT-GATTAATTCCTTTGACTCGTTTGCTCAA
1 TAATATTTTC-GCTTTCAACTTA-TTTTGTTACCTTGGA-TATTTCATTTGACTCGTTTGCTAAA
* * * * * *
1885540 CTCCAGTAACAATTTCGGTCAAAACCAGATTTGTTCAAGCAACTTATAACAATATCGATCTCAAC
63 CTCCAGTAACAATTTAGGTCAAAATCA-ATTTGTTAAAGCAACTTATAACATTCTAGATCTCAAC
* * * * * * * * ** *
1885605 CTACTTTCTTTGTGACTGTTAATATTC-TTGAGCGCAATCGGATTTGTTAACATGATTGA
127 CTAATATCTTAGCGACCGCTCATATTCTTTGA-CGCAACCGGATTTGTTAACGCGACTGA
* * ** * * *
1885664 TAACATTTTTCGACTTTCAACTTATTTTGTTA-CTGTGGGTATTTTGTTTAACCCGTTCGCTAAA
1 TAATA-TTTTCG-CTTTCAACTTATTTTGTTACCT-TGGATATTTCATTTGACTCGTTTGCTAAA
* * * * * * *
1885728 CTACGGTAATAATTTTGGTTAAAATCGAATTTGTTAAAGCAACTTATAACATTCTAAATCTTAAC
63 CTCCAGTAACAATTTAGGTCAAAATC-AATTTGTTAAAGCAACTTATAACATTCTAGATCTCAAC
* * * * * **
1885793 CGAATATCTTGGCGACCACTCACATTCTTGGACGCAACTAGATTTGTTAACGCGACTGA
127 CTAATATCTTAGCGACCGCTCATATTCTTTGACGCAACCGGATTTGTTAACGCGACTGA
* *
1885852 TAATATTTTCAGCTTTCAACTTACTTTGTTACCTTGGATATTTCATTTGACTCATTTGCTAAACT
1 TAATATTTTC-GCTTTCAACTTATTTTGTTACCTTGGATATTTCATTTGACTCGTTTGCTAAACT
* * *
1885917 CCAGTAACAATTTAGGTCGAAATTATATTTGTTAAAGCAACTTATAACATTCTTGATCTCAACCT
65 CCAGTAACAATTTAGGTCAAAATCA-ATTTGTTAAAGCAACTTATAACATTCTAGATCTCAACCT
* * * * *
1885982 AATATCTTAGCGACCGCTCATGTTCTTTGATGCAGCCGGATTTGTTAACGCCATTGA
129 AATATCTTAGCGACCGCTCATATTCTTTGACGCAACCGGATTTGTTAACGCGACTGA
*** * * *
1886039 TGGCATTCTAGCTTTCAACTTATTTTATTAC
1 TAATATTTTCGCTTTCAACTTATTTTGTTAC
1886070 TGTCCTTATT
Statistics
Matches: 320, Mismatches: 77, Indels: 20
0.77 0.18 0.05
Matches are distributed among these distances:
186 20 0.06
187 152 0.47
188 128 0.40
189 20 0.06
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39
Consensus pattern (185 bp):
TAATATTTTCGCTTTCAACTTATTTTGTTACCTTGGATATTTCATTTGACTCGTTTGCTAAACTC
CAGTAACAATTTAGGTCAAAATCAATTTGTTAAAGCAACTTATAACATTCTAGATCTCAACCTAA
TATCTTAGCGACCGCTCATATTCTTTGACGCAACCGGATTTGTTAACGCGACTGA
Found at i:1888678 original size:31 final size:31
Alignment explanation
Indices: 1888640--1888712 Score: 128
Period size: 31 Copynumber: 2.4 Consensus size: 31
1888630 AAACAAAATG
1888640 AAAAAACCAACGCAAAAGATCATATCATAAC
1 AAAAAACCAACGCAAAAGATCATATCATAAC
*
1888671 AAAAAACCAACGCAAAAGATCATGTCATAAC
1 AAAAAACCAACGCAAAAGATCATATCATAAC
*
1888702 ATAAAACCAAC
1 AAAAAACCAAC
1888713 ACTGTCAACA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.58, C:0.23, G:0.07, T:0.12
Consensus pattern (31 bp):
AAAAAACCAACGCAAAAGATCATATCATAAC
Found at i:1890801 original size:21 final size:20
Alignment explanation
Indices: 1890762--1890810 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 20
1890752 TCTTCCCTTA
1890762 TTTTCTCTTTTTTCTTCTTC
1 TTTTCTCTTTTTTCTTCTTC
1890782 TTTTCATCTTCTTTTC-TCTTC
1 TTTTC-TCTT-TTTTCTTCTTC
*
1890803 ATTTCTCT
1 TTTTCTCT
1890811 ACTCAATCGG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 8 0.31
21 13 0.50
22 5 0.19
ACGTcount: A:0.04, C:0.27, G:0.00, T:0.69
Consensus pattern (20 bp):
TTTTCTCTTTTTTCTTCTTC
Found at i:1890807 original size:10 final size:10
Alignment explanation
Indices: 1890762--1890810 Score: 64
Period size: 10 Copynumber: 4.8 Consensus size: 10
1890752 TCTTCCCTTA
1890762 TTTTCTCTT-
1 TTTTCTCTTC
1890771 TTTTCTTCTTC
1 TTTTC-TCTTC
1890782 TTTTCATCTTC
1 TTTTC-TCTTC
1890793 TTTTCTCTTC
1 TTTTCTCTTC
*
1890803 ATTTCTCT
1 TTTTCTCT
1890811 ACTCAATCGG
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
9 5 0.14
10 16 0.44
11 15 0.42
ACGTcount: A:0.04, C:0.27, G:0.00, T:0.69
Consensus pattern (10 bp):
TTTTCTCTTC
Found at i:1890957 original size:24 final size:25
Alignment explanation
Indices: 1890912--1890958 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
1890902 AATAAAAAAG
* * *
1890912 AAATAAAAATAGTTTAGTAAAATAA
1 AAATAAAAATACTATAGAAAAATAA
1890937 AAATAAAAA-ACTATAGAAAAAT
1 AAATAAAAATACTATAGAAAAAT
1890959 GACACTTAAG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 10 0.53
25 9 0.47
ACGTcount: A:0.68, C:0.02, G:0.06, T:0.23
Consensus pattern (25 bp):
AAATAAAAATACTATAGAAAAATAA
Found at i:1897083 original size:28 final size:28
Alignment explanation
Indices: 1897041--1897099 Score: 93
Period size: 28 Copynumber: 2.1 Consensus size: 28
1897031 CCTAAACCCG
1897041 AACCCGACCCAAATAGCACACTTAAAAA
1 AACCCGACCCAAATAGCACACTTAAAAA
*
1897069 AACCCGA-CCAGAATATCACACTTAAAAA
1 AACCCGACCCA-AATAGCACACTTAAAAA
1897097 AAC
1 AAC
1897100 GGACTTGACA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
27 3 0.10
28 26 0.90
ACGTcount: A:0.51, C:0.31, G:0.07, T:0.12
Consensus pattern (28 bp):
AACCCGACCCAAATAGCACACTTAAAAA
Found at i:1898000 original size:15 final size:14
Alignment explanation
Indices: 1897967--1897993 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1897957 TAATGAGAAA
1897967 ATTAATTTTAAAAT
1 ATTAATTTTAAAAT
1897981 ATTAATTTTAAAA
1 ATTAATTTTAAAA
1897994 ACGTTAAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
ATTAATTTTAAAAT
Found at i:1903445 original size:27 final size:27
Alignment explanation
Indices: 1903409--1903462 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
1903399 AACTGTCAGT
1903409 AAAGAAAGAAACAATCAACACAATATA
1 AAAGAAAGAAACAATCAACACAATATA
* *
1903436 AAAGAAAGAAGCAATCAACATAATATA
1 AAAGAAAGAAACAATCAACACAATATA
1903463 GCTGCATACG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.65, C:0.13, G:0.09, T:0.13
Consensus pattern (27 bp):
AAAGAAAGAAACAATCAACACAATATA
Found at i:1912406 original size:24 final size:25
Alignment explanation
Indices: 1912379--1912426 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
1912369 AAAATTGATT
1912379 TTATT-AAAAAAAATTAATTTTAAG
1 TTATTCAAAAAAAATTAATTTTAAG
**
1912403 TTATTCAAATCAAATTAATTTTAA
1 TTATTCAAAAAAAATTAATTTTAA
1912427 ATTCAATTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 5 0.24
25 16 0.76
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (25 bp):
TTATTCAAAAAAAATTAATTTTAAG
Found at i:1922874 original size:19 final size:21
Alignment explanation
Indices: 1922835--1922874 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1922825 ATGAATAATG
*
1922835 GGTGTCAATTTATTATTTAAA
1 GGTGTCAATTAATTATTTAAA
1922856 GGTGTCAA-TAATT-TTTAAA
1 GGTGTCAATTAATTATTTAAA
1922875 ATATGTATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 6 0.33
20 4 0.22
21 8 0.44
ACGTcount: A:0.35, C:0.05, G:0.15, T:0.45
Consensus pattern (21 bp):
GGTGTCAATTAATTATTTAAA
Found at i:1924889 original size:137 final size:139
Alignment explanation
Indices: 1924706--1924980 Score: 396
Period size: 137 Copynumber: 2.0 Consensus size: 139
1924696 AGTAAGAGAT
* ** *
1924706 TATAAGATTTTGAAGAGATAAAATTGTAGTTAAATTTAAAAATTAAATATG-ATTCTAATTAATT
1 TATAAGATTTTGAAGAGATAAAAGTACAGTTAAATTTAAAAATTAAATAAGAATT-TAATTAATT
*
1924770 TAATTTTGATTAAATAAAATTATAAATAAAATTAAATTTAATAAGGTTATAAAATTATA-TT-TT
65 TAATTTTGATTAAATAAAATTATAAATAAAATTAAATTTAATAAAGTTATAAAATTATATTTATT
1924833 TTTCTCTTAC
130 TTTCTCTTAC
*
1924843 TATAAGATTCTTGAAGAGATAAAAGTACAGTTAAA-TTCAAAATTAAATAAGAATTTAATTAATT
1 TATAAGATT-TTGAAGAGATAAAAGTACAGTTAAATTTAAAAATTAAATAAGAATTTAATTAATT
* * * * * *
1924907 TAATTTTTATTAAATAAAATTGTAATTAAATTTAAATTTAATAAATTTATATAATTATATTTATT
65 TAATTTTGATTAAATAAAATTATAAATAAAATTAAATTTAATAAAGTTATAAAATTATATTTATT
1924972 TTTCTCTTA
130 TTTCTCTTA
1924981 GCATGGCCTC
Statistics
Matches: 122, Mismatches: 12, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
137 84 0.69
138 27 0.22
139 11 0.09
ACGTcount: A:0.46, C:0.03, G:0.07, T:0.44
Consensus pattern (139 bp):
TATAAGATTTTGAAGAGATAAAAGTACAGTTAAATTTAAAAATTAAATAAGAATTTAATTAATTT
AATTTTGATTAAATAAAATTATAAATAAAATTAAATTTAATAAAGTTATAAAATTATATTTATTT
TTCTCTTAC
Found at i:1924904 original size:16 final size:15
Alignment explanation
Indices: 1924883--1924952 Score: 61
Period size: 15 Copynumber: 4.5 Consensus size: 15
1924873 TTAAATTCAA
1924883 AATTAAATAAGAATTT
1 AATTAAATAA-AATTT
* * *
1924899 AATTAATTTAATTTT
1 AATTAAATAAAATTT
*
1924914 TATTAAATAAAATTGT
1 AATTAAATAAAATT-T
*
1924930 AATTAAATTTAAATTT
1 AATTAAA-TAAAATTT
1924946 AA-TAAAT
1 AATTAAAT
1924953 TTATATAATT
Statistics
Matches: 43, Mismatches: 9, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
14 1 0.02
15 18 0.42
16 18 0.42
17 6 0.14
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (15 bp):
AATTAAATAAAATTT
Found at i:1924952 original size:31 final size:31
Alignment explanation
Indices: 1924886--1924952 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
1924876 AATTCAAAAT
* *
1924886 TAAATAAGAATTTAATTAATTTAATTTTTAT
1 TAAATAAGAATTTAATTAATTTAATATTTAA
1924917 TAAATAA-AATTGTAATTAAATTTAA-ATTTAA
1 TAAATAAGAATT-TAATT-AATTTAATATTTAA
1924948 TAAAT
1 TAAAT
1924953 TTATATAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
30 4 0.12
31 21 0.66
32 7 0.22
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (31 bp):
TAAATAAGAATTTAATTAATTTAATATTTAA
Found at i:1925863 original size:22 final size:22
Alignment explanation
Indices: 1925837--1925880 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
1925827 TAAAAAATTA
* *
1925837 TAAATTAA-ATTATTTAACTATT
1 TAAA-TAATATTAATTAAATATT
1925859 TAAATAATATTAATTAAATATT
1 TAAATAATATTAATTAAATATT
1925881 ATCTTAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 3 0.16
22 16 0.84
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (22 bp):
TAAATAATATTAATTAAATATT
Found at i:1934398 original size:11 final size:11
Alignment explanation
Indices: 1934368--1934406 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
1934358 CAACTTTAAA
*
1934368 AAATGTTTTGT
1 AAATGTTTGGT
1934379 AAA-GTTTGGT
1 AAATGTTTGGT
1934389 AAATGTTTGGT
1 AAATGTTTGGT
*
1934400 AGATGTT
1 AAATGTT
1934407 CACTTTAATC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 9 0.36
11 16 0.64
ACGTcount: A:0.28, C:0.00, G:0.26, T:0.46
Consensus pattern (11 bp):
AAATGTTTGGT
Found at i:1940549 original size:80 final size:80
Alignment explanation
Indices: 1940448--1940730 Score: 449
Period size: 80 Copynumber: 3.5 Consensus size: 80
1940438 CTTATGGATG
* * * *
1940448 ACCCGAAGGATTTCATCATCATGCTCAAAAGACTTACTGACGGATTTGCTTCACTGCTCTTCCGT
1 ACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGATTTGCTTCACTACTCTTCCGT
1940513 GAAGGCTTAAAAATT
66 GAAGGCTTAAAAATT
* * *
1940528 ACCCGAAGGATTTAATTATCATGCTCGAAAGACTTACTGATGGGTTTGCTTCACTACTCTTCGGT
1 ACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGATTTGCTTCACTACTCTTCCGT
1940593 GAAGGCTTAAAAATT
66 GAAGGCTTAAAAATT
* * *
1940608 ACCCAAAGGATTTAATTATCATGCTCGAAAGACTTACTGATGAATTTGCTTCACTACTCTTCCGT
1 ACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGATTTGCTTCACTACTCTTCCGT
** *
1940673 GAAGGCTTACCAGTT
66 GAAGGCTTAAAAATT
1940688 ACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGG
1 ACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGG
1940731 CCCGAAGGAC
Statistics
Matches: 186, Mismatches: 17, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
80 186 1.00
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (80 bp):
ACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGATTTGCTTCACTACTCTTCCGT
GAAGGCTTAAAAATT
Found at i:1941144 original size:38 final size:38
Alignment explanation
Indices: 1941102--1941218 Score: 170
Period size: 38 Copynumber: 3.2 Consensus size: 38
1941092 TCTTGCTCTA
1941102 AAGGCTTACAGATGGATTTGCTTCACTACTCTTCCGTG
1 AAGGCTTACAGATGGATTTGCTTCACTACTCTTCCGTG
*
1941140 AAGGCTTA-AGATGG---TGCTTCACTACTCTTCGGTG
1 AAGGCTTACAGATGGATTTGCTTCACTACTCTTCCGTG
** *
1941174 AAGTTTTACAAATGGATTTGCTTCACTACTCTTCCGTG
1 AAGGCTTACAGATGGATTTGCTTCACTACTCTTCCGTG
1941212 AAGGCTT
1 AAGGCTT
1941219 GACTTTGCCC
Statistics
Matches: 68, Mismatches: 7, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
34 25 0.37
35 5 0.07
37 6 0.09
38 32 0.47
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.35
Consensus pattern (38 bp):
AAGGCTTACAGATGGATTTGCTTCACTACTCTTCCGTG
Found at i:1952579 original size:2 final size:2
Alignment explanation
Indices: 1952572--1952614 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1952562 CGCGTAGTAT
1952572 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1952614 T
1 T
1952615 GGAGTAGTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1963035 original size:38 final size:39
Alignment explanation
Indices: 1962993--1963080 Score: 115
Period size: 40 Copynumber: 2.3 Consensus size: 39
1962983 ATTTTTTTAC
* * *
1962993 TAATATTTTCAGTTG-AACCTAAAATGTTACGAATAATA
1 TAATATTTTCAGTTGCAACCAAAAATATTACGAAAAATA
* *
1963031 TAATATTTTCAGTTGTCAGCCAAAAATATTATGAAAAATA
1 TAATATTTTCAGTTG-CAACCAAAAATATTACGAAAAATA
1963071 TAATATTTTC
1 TAATATTTTC
1963081 GGTTAAATAT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
38 15 0.35
40 28 0.65
ACGTcount: A:0.42, C:0.10, G:0.09, T:0.39
Consensus pattern (39 bp):
TAATATTTTCAGTTGCAACCAAAAATATTACGAAAAATA
Found at i:1973401 original size:15 final size:15
Alignment explanation
Indices: 1973383--1973417 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
1973373 GTTACATCAG
1973383 ATTGACATACAATTA
1 ATTGACATACAATTA
1973398 ATTGACATACAATTA
1 ATTGACATACAATTA
1973413 ATTGA
1 ATTGA
1973418 AATCAAAGCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.46, C:0.11, G:0.09, T:0.34
Consensus pattern (15 bp):
ATTGACATACAATTA
Done.