Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008397.1 Hibiscus syriacus cultivar Beakdansim tig00111166_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: 2560905
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 13
Found at i:1786934 original size:19 final size:19
Alignment explanation
Indices: 1786912--1786993 Score: 95
Period size: 18 Copynumber: 4.6 Consensus size: 19
1786902 GAAACACAAA
1786912 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
1786931 TCGCGTTGCGA-TTTCATT
1 TCGCATTGCGATTTTCATT
*
1786949 TCGCATTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
*
1786965 TCG--TTGCGATTTTCATA
1 TCGCATTGCGATTTTCATT
1786982 TCGCATTGCGAT
1 TCGCATTGCGAT
1786994 AGCCATTTCC
Statistics
Matches: 54, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
14 6 0.11
15 3 0.06
16 4 0.07
17 4 0.07
18 20 0.37
19 17 0.31
ACGTcount: A:0.15, C:0.21, G:0.21, T:0.44
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:1787012 original size:20 final size:20
Alignment explanation
Indices: 1786987--1787032 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
1786977 TCATATCGCA
1786987 TTGCGATAGCCATTTCCGCG
1 TTGCGATAGCCATTTCCGCG
* * *
1787007 TTGCGATAGTCATTTTCGTG
1 TTGCGATAGCCATTTCCGCG
1787027 TTGCGA
1 TTGCGA
1787033 AAGTAAACTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.15, C:0.22, G:0.26, T:0.37
Consensus pattern (20 bp):
TTGCGATAGCCATTTCCGCG
Found at i:1787541 original size:18 final size:18
Alignment explanation
Indices: 1787520--1787557 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
1787510 AGATGATGGG
*
1787520 TCTGGGTGAGGTGATAGC
1 TCTGGGCGAGGTGATAGC
*
1787538 TCTGGGCGAGGTGATGGC
1 TCTGGGCGAGGTGATAGC
1787556 TC
1 TC
1787558 CCGAAGTGGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.13, C:0.16, G:0.45, T:0.26
Consensus pattern (18 bp):
TCTGGGCGAGGTGATAGC
Found at i:1789203 original size:22 final size:22
Alignment explanation
Indices: 1789178--1789221 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1789168 GATTTAGATA
1789178 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
1789200 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
1789222 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:1789438 original size:20 final size:20
Alignment explanation
Indices: 1789413--1789502 Score: 72
Period size: 20 Copynumber: 4.5 Consensus size: 20
1789403 ATGTATTATT
1789413 GCGTTGCGAAAGTCAGTATC
1 GCGTTGCGAAAGTCAGTATC
* *
1789433 GCGTTGCAAAAGTAAGTATC
1 GCGTTGCGAAAGTCAGTATC
* *** * *
1789453 TCGTTGCGATTTTTTATTATC
1 GCGTTGCGA-AAGTCAGTATC
* *
1789474 GCATTGCGATAGTCAGTATC
1 GCGTTGCGAAAGTCAGTATC
*
1789494 GCATTGCGA
1 GCGTTGCGA
1789503 TTTTCCCAAT
Statistics
Matches: 54, Mismatches: 15, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
20 41 0.76
21 13 0.24
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.33
Consensus pattern (20 bp):
GCGTTGCGAAAGTCAGTATC
Found at i:1789474 original size:41 final size:41
Alignment explanation
Indices: 1789429--1789506 Score: 102
Period size: 41 Copynumber: 1.9 Consensus size: 41
1789419 CGAAAGTCAG
* * *
1789429 TATCGCGTTGCAAAAGTAAGTATCTCGTTGCGATTTTTTAT
1 TATCGCATTGCAAAAGTAAGTATCGCATTGCGATTTTTTAT
* * *
1789470 TATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 TATCGCATTGCAAAAGTAAGTATCGCATTGCGATTTT
1789507 CCCAATTCGC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 31 1.00
ACGTcount: A:0.23, C:0.17, G:0.21, T:0.40
Consensus pattern (41 bp):
TATCGCATTGCAAAAGTAAGTATCGCATTGCGATTTTTTAT
Found at i:1789480 original size:21 final size:21
Alignment explanation
Indices: 1789447--1789547 Score: 59
Period size: 20 Copynumber: 4.9 Consensus size: 21
1789437 TGCAAAAGTA
* * *
1789447 AGTATCTCGTTGCGATTTTTT
1 AGTATCGCATTGCGATTTTTC
* **
1789468 ATTATCGCATTGCGA-TAGTC
1 AGTATCGCATTGCGATTTTTC
*
1789488 AGTATCGCATTGCGATTTTCCC
1 AGTATCGCATTGCGATTTT-TC
* *
1789510 AAT-TCGCGTTGCGATTTACTT-
1 AGTATCGCATTGCGATTT--TTC
1789531 A-T-TCGCATTGCGATTTT
1 AGTATCGCATTGCGATTTT
1789548 CCCAATTCGC
Statistics
Matches: 62, Mismatches: 14, Indels: 11
0.71 0.16 0.13
Matches are distributed among these distances:
18 1 0.02
20 30 0.48
21 27 0.44
22 3 0.05
23 1 0.02
ACGTcount: A:0.19, C:0.20, G:0.19, T:0.43
Consensus pattern (21 bp):
AGTATCGCATTGCGATTTTTC
Found at i:1789503 original size:20 final size:20
Alignment explanation
Indices: 1789389--1789503 Score: 70
Period size: 20 Copynumber: 5.7 Consensus size: 20
1789379 CGCTTTGAAA
*
1789389 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* * *
1789410 ATTGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * * *
1789430 ATCGCGTTGCAAAAGTAAGT
1 ATCGCATTGCGATAGTCAGT
* * ** * *
1789450 ATCTCGTTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTCAGT
1789471 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
1789491 ATCGCATTGCGAT
1 ATCGCATTGCGAT
1789504 TTTCCCAATT
Statistics
Matches: 72, Mismatches: 20, Indels: 5
0.74 0.21 0.05
Matches are distributed among these distances:
19 2 0.03
20 47 0.65
21 23 0.32
ACGTcount: A:0.24, C:0.17, G:0.23, T:0.37
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:1789557 original size:21 final size:21
Alignment explanation
Indices: 1789492--1789605 Score: 124
Period size: 21 Copynumber: 5.5 Consensus size: 21
1789482 ATAGTCAGTA
1789492 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
1789513 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
1789533 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* *
1789554 TCGCGTTGTGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
1789575 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
1789595 TCGCATTGCGA
1 TCGCATTGCGA
1789606 ATTGGGAAAA
Statistics
Matches: 77, Mismatches: 15, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
20 32 0.42
21 45 0.58
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:1792409 original size:20 final size:19
Alignment explanation
Indices: 1792380--1792450 Score: 70
Period size: 20 Copynumber: 3.5 Consensus size: 19
1792370 CGCGATCTCG
*
1792380 AATTCACAACACAGTTTCCA
1 AATTCGCAACACAGTTT-CA
**
1792400 AATTCGCAACACAGAAGTCA
1 AATTCGCAACACAG-TTTCA
*
1792420 AATTCGCAACACTGAATTTCA
1 AATTCGCAACAC--AGTTTCA
1792441 AATTCGCAAC
1 AATTCGCAAC
1792451 TCGATTTCTG
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
20 27 0.64
21 14 0.33
22 1 0.02
ACGTcount: A:0.41, C:0.27, G:0.10, T:0.23
Consensus pattern (19 bp):
AATTCGCAACACAGTTTCA
Found at i:1792466 original size:20 final size:20
Alignment explanation
Indices: 1792420--1792486 Score: 82
Period size: 20 Copynumber: 3.3 Consensus size: 20
1792410 ACAGAAGTCA
* * *
1792420 AATTCGCAACACTGAATTTCA
1 AATTCGCAACTC-GATTTTCG
1792441 AATTCGCAACTCGA-TTTCTG
1 AATTCGCAACTCGATTTTC-G
1792461 AATTCGCAACTCGATTTTCG
1 AATTCGCAACTCGATTTTCG
1792481 AATTCG
1 AATTCG
1792487 TAACACAAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
19 4 0.10
20 23 0.55
21 15 0.36
ACGTcount: A:0.30, C:0.24, G:0.13, T:0.33
Consensus pattern (20 bp):
AATTCGCAACTCGATTTTCG
Found at i:1793396 original size:24 final size:24
Alignment explanation
Indices: 1793331--1793398 Score: 73
Period size: 24 Copynumber: 2.8 Consensus size: 24
1793321 GTGAGTACTA
* *
1793331 GTCAATATTCGAAATTTGATCTTG
1 GTCAATACTCGGAATTTGATCTTG
* * * *
1793355 GTTAATACCCAGACTTTGATCTTG
1 GTCAATACTCGGAATTTGATCTTG
*
1793379 GTCAATACTCGGATTTTGAT
1 GTCAATACTCGGAATTTGAT
1793399 GATGTTTCAG
Statistics
Matches: 34, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.26, C:0.16, G:0.18, T:0.40
Consensus pattern (24 bp):
GTCAATACTCGGAATTTGATCTTG
Found at i:1795655 original size:12 final size:12
Alignment explanation
Indices: 1795638--1795666 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
1795628 AGCAAAAGGA
1795638 AATCAAAATCGC
1 AATCAAAATCGC
1795650 AATCAAAATCGC
1 AATCAAAATCGC
1795662 AATCA
1 AATCA
1795667 CAACCGGCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.52, C:0.24, G:0.07, T:0.17
Consensus pattern (12 bp):
AATCAAAATCGC
Found at i:1797409 original size:21 final size:21
Alignment explanation
Indices: 1797385--1797457 Score: 101
Period size: 21 Copynumber: 3.5 Consensus size: 21
1797375 GTGAATCGGG
* *
1797385 CTCTTGAACGGTGAGAGAGAC
1 CTCTTGAACGGTGAGAGGGGC
* *
1797406 CTCTTGAACGATGACAGGGGC
1 CTCTTGAACGGTGAGAGGGGC
*
1797427 CTCTTGAACGGTGGGAGGGGC
1 CTCTTGAACGGTGAGAGGGGC
1797448 CTCTTGAACG
1 CTCTTGAACG
1797458 ATGACAGGTG
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 45 1.00
ACGTcount: A:0.22, C:0.22, G:0.36, T:0.21
Consensus pattern (21 bp):
CTCTTGAACGGTGAGAGGGGC
Found at i:1797451 original size:42 final size:42
Alignment explanation
Indices: 1797385--1797465 Score: 135
Period size: 42 Copynumber: 1.9 Consensus size: 42
1797375 GTGAATCGGG
1797385 CTCTTGAACGGTGAGAGAGACCTCTTGAACGATGACAGGGGC
1 CTCTTGAACGGTGAGAGAGACCTCTTGAACGATGACAGGGGC
* * *
1797427 CTCTTGAACGGTGGGAGGGGCCTCTTGAACGATGACAGG
1 CTCTTGAACGGTGAGAGAGACCTCTTGAACGATGACAGG
1797466 TGAATCGGGC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.23, C:0.21, G:0.36, T:0.20
Consensus pattern (42 bp):
CTCTTGAACGGTGAGAGAGACCTCTTGAACGATGACAGGGGC
Found at i:1797886 original size:21 final size:21
Alignment explanation
Indices: 1797862--1797914 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
1797852 TGCACCATTT
1797862 TCATCACGTAAAGT-ACCGACC
1 TCATCACGTAAA-TCACCGACC
* *
1797883 TCATCACGCAAATCACTGACC
1 TCATCACGTAAATCACCGACC
*
1797904 TCTTCACGTAA
1 TCATCACGTAA
1797915 CTCCCCTAAC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 1 0.04
21 26 0.96
ACGTcount: A:0.32, C:0.34, G:0.11, T:0.23
Consensus pattern (21 bp):
TCATCACGTAAATCACCGACC
Found at i:1799493 original size:20 final size:20
Alignment explanation
Indices: 1799468--1799506 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
1799458 TCACATTGTG
1799468 ATTTTCGTGTTGCGAATTTT
1 ATTTTCGTGTTGCGAATTTT
1799488 ATTTTCGTGTTGCGAATTT
1 ATTTTCGTGTTGCGAATTT
1799507 AAGTTTCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.15, C:0.10, G:0.21, T:0.54
Consensus pattern (20 bp):
ATTTTCGTGTTGCGAATTTT
Found at i:1799513 original size:20 final size:20
Alignment explanation
Indices: 1799470--1799513 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
1799460 ACATTGTGAT
* *
1799470 TTTCGTGTTGCGAATTTTAT
1 TTTCGTGTTGCGAATTTAAG
1799490 TTTCGTGTTGCGAATTTAAG
1 TTTCGTGTTGCGAATTTAAG
1799510 TTTC
1 TTTC
1799514 AAAATTCTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.16, C:0.11, G:0.20, T:0.52
Consensus pattern (20 bp):
TTTCGTGTTGCGAATTTAAG
Found at i:1799867 original size:22 final size:22
Alignment explanation
Indices: 1799833--1799890 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
1799823 TCTGAGAGAT
*
1799833 GGAGAT-A-GACGGATTTCGTC
1 GGAGATGAGGACGGATTTCGCC
1799853 GGAGATGAGGACGGATTTCGCC
1 GGAGATGAGGACGGATTTCGCC
* *
1799875 AGAGATGGGGACGGAT
1 GGAGATGAGGACGGAT
1799891 GTCATCGTAG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
20 6 0.18
21 1 0.03
22 26 0.79
ACGTcount: A:0.26, C:0.14, G:0.41, T:0.19
Consensus pattern (22 bp):
GGAGATGAGGACGGATTTCGCC
Found at i:1800074 original size:20 final size:19
Alignment explanation
Indices: 1800049--1800115 Score: 55
Period size: 20 Copynumber: 3.4 Consensus size: 19
1800039 CGCGTTTTGT
1800049 GAATTTGACTTCTGTGTTGC
1 GAATTTGA-TTCTGTGTTGC
**
1800069 GAATTTGGAAACTGTGTTGC
1 GAATTT-GATTCTGTGTTGC
* *
1800089 GAAATTGGAGTTC-GCGTTGC
1 G-AATTTGA-TTCTGTGTTGC
1800109 GAATTTG
1 GAATTTG
1800116 TTGGTCATTT
Statistics
Matches: 37, Mismatches: 7, Indels: 7
0.73 0.14 0.14
Matches are distributed among these distances:
19 5 0.14
20 25 0.68
21 7 0.19
ACGTcount: A:0.21, C:0.12, G:0.30, T:0.37
Consensus pattern (19 bp):
GAATTTGATTCTGTGTTGC
Found at i:1806568 original size:8 final size:8
Alignment explanation
Indices: 1806548--1806580 Score: 57
Period size: 8 Copynumber: 4.0 Consensus size: 8
1806538 ATTTTATTTC
1806548 TTTTAACAA
1 TTTTAA-AA
1806557 TTTTAAAA
1 TTTTAAAA
1806565 TTTTAAAA
1 TTTTAAAA
1806573 TTTTAAAA
1 TTTTAAAA
1806581 GTTTCATTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 18 0.75
9 6 0.25
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (8 bp):
TTTTAAAA
Found at i:1807004 original size:2 final size:2
Alignment explanation
Indices: 1806997--1807025 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1806987 CTTACAGCAT
1806997 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
1807026 GCAACATCCT
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:1810457 original size:123 final size:123
Alignment explanation
Indices: 1810233--1810471 Score: 469
Period size: 123 Copynumber: 1.9 Consensus size: 123
1810223 GAAAATGAAA
1810233 TGTTCTTGTTGTTATTAGAATATTCCTTCTAATCTGTTTTTCTACCCTTTCTTTAAGAATGTGAT
1 TGTTCTTGTTGTTATTAGAATATTCCTTCTAATCTGTTTTTCTACCCTTTCTTTAAGAATGTGAT
1810298 TACCTGAGCTTGTTTGAGCTTAAACTAACGTGCTTAACTTAGATTAGGACCATGTTCT
66 TACCTGAGCTTGTTTGAGCTTAAACTAACGTGCTTAACTTAGATTAGGACCATGTTCT
*
1810356 TGTTGTTGTTGTTATTAGAATATTCCTTCTAATCTGTTTTTCTACCCTTTCTTTAAGAATGTGAT
1 TGTTCTTGTTGTTATTAGAATATTCCTTCTAATCTGTTTTTCTACCCTTTCTTTAAGAATGTGAT
1810421 TACCTGAGCTTGTTTGAGCTTAAACTAACGTGCTTAACTTAGATTAGGACC
66 TACCTGAGCTTGTTTGAGCTTAAACTAACGTGCTTAACTTAGATTAGGACC
1810472 CTCAATCGTG
Statistics
Matches: 115, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
123 115 1.00
ACGTcount: A:0.23, C:0.17, G:0.16, T:0.44
Consensus pattern (123 bp):
TGTTCTTGTTGTTATTAGAATATTCCTTCTAATCTGTTTTTCTACCCTTTCTTTAAGAATGTGAT
TACCTGAGCTTGTTTGAGCTTAAACTAACGTGCTTAACTTAGATTAGGACCATGTTCT
Found at i:1819568 original size:5 final size:5
Alignment explanation
Indices: 1819547--1819610 Score: 71
Period size: 5 Copynumber: 13.0 Consensus size: 5
1819537 GATAAAATGG
*
1819547 TAAAA T-AAA T-AAA -AAAA CAAAA TAAAA TAAAA TAAAA TAAAA TGAATAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA T-AA-AA
*
1819596 AAAAA TAAAA TAAAA
1 TAAAA TAAAA TAAAA
1819611 ATAAGACATA
Statistics
Matches: 52, Mismatches: 3, Indels: 8
0.83 0.05 0.13
Matches are distributed among these distances:
4 10 0.19
5 36 0.69
6 4 0.08
7 2 0.04
ACGTcount: A:0.80, C:0.02, G:0.02, T:0.17
Consensus pattern (5 bp):
TAAAA
Found at i:1819573 original size:10 final size:10
Alignment explanation
Indices: 1819560--1819632 Score: 56
Period size: 10 Copynumber: 6.8 Consensus size: 10
1819550 AATAAATAAA
1819560 AAAACAAAAT
1 AAAACAAAAT
*
1819570 AAAATAAAAT
1 AAAACAAAAT
*
1819580 AAAATAAAAT
1 AAAACAAAAT
*
1819590 GAATAAAAAAAT
1 -AA-AACAAAAT
*
1819602 AAAATAAAAAT
1 AAAA-CAAAAT
*
1819613 AAGACATAAAT
1 AAAACA-AAAT
1819624 AACAACAAA
1 AA-AACAAA
1819633 GGAAAAAAAT
Statistics
Matches: 53, Mismatches: 5, Indels: 9
0.79 0.07 0.13
Matches are distributed among these distances:
10 22 0.42
11 21 0.40
12 10 0.19
ACGTcount: A:0.77, C:0.05, G:0.03, T:0.15
Consensus pattern (10 bp):
AAAACAAAAT
Found at i:1819577 original size:27 final size:26
Alignment explanation
Indices: 1819550--1819609 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 26
1819540 AAAATGGTAA
1819550 AATAAATAAAA-AAACAAAATAAAATAA
1 AATAAATAAAATAAA-AAAA-AAAATAA
* *
1819577 AATAAAATAAAATGAATAAAAAAATAA
1 AAT-AAATAAAATAAAAAAAAAAATAA
1819604 AATAAA
1 AATAAA
1819610 AATAAGACAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
26 3 0.10
27 13 0.45
28 11 0.38
29 2 0.07
ACGTcount: A:0.80, C:0.02, G:0.02, T:0.17
Consensus pattern (26 bp):
AATAAATAAAATAAAAAAAAAAATAA
Found at i:1819845 original size:13 final size:14
Alignment explanation
Indices: 1819784--1819856 Score: 55
Period size: 13 Copynumber: 5.4 Consensus size: 14
1819774 AGCGAGAGTC
*
1819784 AAAAATACAATATGT
1 AAAAATA-AATATAT
*
1819799 -AAAATATATATAT
1 AAAAATAAATATAT
*
1819812 -AATA-AAATAGTAT
1 AAAAATAAATA-TAT
**
1819825 CTAAATAAATATA-
1 AAAAATAAATATAT
1819838 AAAAATAAATATAT
1 AAAAATAAATATAT
1819852 AAAAA
1 AAAAA
1819857 ATAATAATAG
Statistics
Matches: 46, Mismatches: 8, Indels: 9
0.73 0.13 0.14
Matches are distributed among these distances:
12 4 0.09
13 22 0.48
14 15 0.33
15 5 0.11
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.29
Consensus pattern (14 bp):
AAAAATAAATATAT
Found at i:1819854 original size:25 final size:25
Alignment explanation
Indices: 1819784--1819859 Score: 66
Period size: 25 Copynumber: 2.9 Consensus size: 25
1819774 AGCGAGAGTC
*
1819784 AAAAATACAATATGTAAAATATATATATA
1 AAAAATA-AATATAT-AAATA-A-ATATA
* *
1819813 ATAAAAT-AGTATCTAAATAAATATA
1 A-AAAATAAATATATAAATAAATATA
1819838 AAAAATAAATATATAAA-AAATA
1 AAAAATAAATATATAAATAAATA
1819860 ATAATAGTAA
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
24 10 0.24
25 14 0.34
26 1 0.02
27 5 0.12
28 5 0.12
29 1 0.02
30 5 0.12
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.29
Consensus pattern (25 bp):
AAAAATAAATATATAAATAAATATA
Found at i:1819865 original size:17 final size:17
Alignment explanation
Indices: 1819828--1819865 Score: 55
Period size: 15 Copynumber: 2.4 Consensus size: 17
1819818 ATAGTATCTA
1819828 AATAA-ATATAAAAAAT
1 AATAATATATAAAAAAT
1819844 -A-AATATATAAAAAAT
1 AATAATATATAAAAAAT
1819859 AATAATA
1 AATAATA
1819866 GTAAAAGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 5
0.79 0.00 0.21
Matches are distributed among these distances:
14 2 0.11
15 12 0.63
16 1 0.05
17 4 0.21
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (17 bp):
AATAATATATAAAAAAT
Found at i:1819879 original size:17 final size:15
Alignment explanation
Indices: 1819827--1819879 Score: 54
Period size: 15 Copynumber: 3.3 Consensus size: 15
1819817 AATAGTATCT
1819827 AAATAAATATAAAAAA
1 AAAT-AATATAAAAAA
1819843 TAAAT-ATATAAAAAA
1 -AAATAATATAAAAAA
*
1819858 TAATAATAGTAAAAGAA
1 AAATAATA-TAAAA-AA
1819875 AAATA
1 AAATA
1819880 CATAATGATA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
14 3 0.10
15 13 0.42
16 5 0.16
17 10 0.32
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.23
Consensus pattern (15 bp):
AAATAATATAAAAAA
Found at i:1819991 original size:2 final size:2
Alignment explanation
Indices: 1819979--1820028 Score: 57
Period size: 2 Copynumber: 25.5 Consensus size: 2
1819969 CTAAAGAATG
* * *
1819979 AT AT A- AT AT AT AT AT AT AT AT AT AT AC AT AT AC AT AT AC AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
1820020 AT AC AT AT A
1 AT AT AT AT A
1820029 AGATAATATA
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (2 bp):
AT
Found at i:1819995 original size:6 final size:6
Alignment explanation
Indices: 1819988--1820028 Score: 64
Period size: 6 Copynumber: 6.8 Consensus size: 6
1819978 GATATAATAT
* *
1819988 ATATAT ATATAT ATATAC ATATAC ATATAC ATATAC ATATA
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATA
1820029 AGATAATATA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.51, C:0.10, G:0.00, T:0.39
Consensus pattern (6 bp):
ATATAC
Found at i:1821232 original size:26 final size:25
Alignment explanation
Indices: 1821144--1821235 Score: 113
Period size: 24 Copynumber: 3.8 Consensus size: 25
1821134 ATAAAAATAA
1821144 TATATATATATATA-TATATATATA
1 TATATATATATATATTATATATATA
*
1821168 TA-ATATAT-TCTA-TATATATATA
1 TATATATATATATATTATATATATA
1821190 TATATATATATAT-TTATATATATA
1 TATATATATATATATTATATATATA
* *
1821214 TATATATAGTTTGTATTATATA
1 TATATATA-TATATATTATATA
1821236 AAATAATATC
Statistics
Matches: 59, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
22 15 0.25
23 12 0.20
24 22 0.37
25 3 0.05
26 7 0.12
ACGTcount: A:0.45, C:0.01, G:0.02, T:0.52
Consensus pattern (25 bp):
TATATATATATATATTATATATATA
Found at i:1821235 original size:2 final size:2
Alignment explanation
Indices: 1821143--1821221 Score: 126
Period size: 2 Copynumber: 40.5 Consensus size: 2
1821133 AATAAAAATA
*
1821143 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT -T CT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
1821183 AT AT AT AT AT AT AT AT AT AT TT 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 AT A
1821222 GTTTGTATTA
Statistics
Matches: 72, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
1 2 0.03
2 70 0.97
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1822033 original size:124 final size:124
Alignment explanation
Indices: 1821810--1822114 Score: 448
Period size: 124 Copynumber: 2.5 Consensus size: 124
1821800 GGAAAGCCCC
* * * * *
1821810 TTCGTTGTGAAGTTGAGCTTTGAATTGGATATCCTTTGTTGTGAAGTTGAAATCTAATCTAGAGA
1 TTCGTTGTGAAGTTGAGCATTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGA
* * * *
1821875 TGGATGCTGCTGGTGGGCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGACCCT
66 TGAATGCTGCTGGTGGGCACAATATCCTTCGTCGTGAAGTTAAAATCGTGGATGACCCA
* * * *
1821934 TTTGTTGTAAAGTTGAGCCTTGAATTGGATATCCTTCATCGTGAAGTTGAAATCCAATCTAAAGA
1 TTCGTTGTGAAGTTGAGCATTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGA
* * * *
1821999 TGAATGTTGCTGGTGGGCACAATATCCTTCGTCGTGAAGTTAAAATTGTGGATGGCTCA
66 TGAATGCTGCTGGTGGGCACAATATCCTTCGTCGTGAAGTTAAAATCGTGGATGACCCA
*
1822058 TTCGTTGTGAAGTTGAGCATTGAATTGGATATCATTCGTCGTGAAGTTGAAATCCAA
1 TTCGTTGTGAAGTTGAGCATTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAA
1822115 AGATTATTGG
Statistics
Matches: 160, Mismatches: 21, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
124 160 1.00
ACGTcount: A:0.26, C:0.14, G:0.26, T:0.34
Consensus pattern (124 bp):
TTCGTTGTGAAGTTGAGCATTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGA
TGAATGCTGCTGGTGGGCACAATATCCTTCGTCGTGAAGTTAAAATCGTGGATGACCCA
Found at i:1822096 original size:34 final size:34
Alignment explanation
Indices: 1822055--1822178 Score: 97
Period size: 34 Copynumber: 3.5 Consensus size: 34
1822045 TGTGGATGGC
*
1822055 TCATTCGTTGTGAAGTTGAGCATTGAATTGGATA
1 TCATTCGTTGTGAAGTTGACCATTGAATTGGATA
* ** *
1822089 TCATTCGTCGTGAAGTTGAAATCCAAAGATTATTGGCACGA
1 TCATTCGTTGTGAAGTTG--A-CCATTGA--ATTGG-A-TA
* *
1822130 -CATTCGTTGTGAAGTTGATCTTTGAATTGGATA
1 TCATTCGTTGTGAAGTTGACCATTGAATTGGATA
* *
1822163 TCCTTTGTTGTGAAGT
1 TCATTCGTTGTGAAGT
1822179 CAAAATCCAA
Statistics
Matches: 69, Mismatches: 13, Indels: 16
0.70 0.13 0.16
Matches are distributed among these distances:
33 1 0.01
34 31 0.45
35 5 0.07
36 1 0.01
37 7 0.10
38 1 0.01
39 5 0.07
40 17 0.25
41 1 0.01
ACGTcount: A:0.26, C:0.12, G:0.24, T:0.38
Consensus pattern (34 bp):
TCATTCGTTGTGAAGTTGACCATTGAATTGGATA
Found at i:1822177 original size:74 final size:74
Alignment explanation
Indices: 1822056--1822203 Score: 215
Period size: 74 Copynumber: 2.0 Consensus size: 74
1822046 GTGGATGGCT
**
1822056 CATTCGTTGTGAAGTTGAGCATTGAATTGGATATCATTCGTCGTGAAGTTGAAATCCAAAGATTA
1 CATTCGTTGTGAAGTTGAGCATTGAATTGGATATCATTCGTCGTGAAGTCAAAATCCAAAGATTA
1822121 TTGGCACGA
66 TTGGCACGA
* * * * * * *
1822130 CATTCGTTGTGAAGTTGATCTTTGAATTGGATATCCTTTGTTGTGAAGTCAAAATCCAAGGATTG
1 CATTCGTTGTGAAGTTGAGCATTGAATTGGATATCATTCGTCGTGAAGTCAAAATCCAAAGATTA
1822195 TTGGCACGA
66 TTGGCACGA
1822204 TATCCTTCGC
Statistics
Matches: 65, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
74 65 1.00
ACGTcount: A:0.28, C:0.14, G:0.24, T:0.34
Consensus pattern (74 bp):
CATTCGTTGTGAAGTTGAGCATTGAATTGGATATCATTCGTCGTGAAGTCAAAATCCAAAGATTA
TTGGCACGA
Found at i:1822264 original size:109 final size:109
Alignment explanation
Indices: 1822130--1822512 Score: 559
Period size: 109 Copynumber: 3.5 Consensus size: 109
1822120 ATTGGCACGA
* * * *
1822130 CATTCGTTGTGAAGTTGATCTTTGAATTGGATATCCTTTGTTGTGAAGTCAAAATCCAAGGATTG
1 CATTCGTTGTGAAGTTGAGCTTTGAATTGGATATCATTCGTTGTGAAGTCGAAATCCAAGGATTG
* *
1822195 TTGGCACGATATCCTTCGCCGTGAAGTTTAAATCGTAGATGGCT
66 TTGGCACGATATCCTTCGTCGTGAAGTTGAAATCGTAGATGGCT
* * *
1822239 CATTCGTTGTGAAGTTAAGCTTTGAATTGGATATCATTCGTTGTGAAGTTGAAATCCAAGTATTG
1 CATTCGTTGTGAAGTTGAGCTTTGAATTGGATATCATTCGTTGTGAAGTCGAAATCCAAGGATTG
* * * * * *
1822304 TTGGCACGATATCCTTCATTGTAAAGTTGAAATCATAGATGACC
66 TTGGCACGATATCCTTCGTCGTGAAGTTGAAATCGTAGATGGCT
* * *
1822348 CCTTCTTTGTGAAGTTGAGCTTTGAATTAGATATCATTCGTTGTGAAGTCGAAATCCAAGGATTG
1 CATTCGTTGTGAAGTTGAGCTTTGAATTGGATATCATTCGTTGTGAAGTCGAAATCCAAGGATTG
* *
1822413 TTGGCATGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCT
66 TTGGCACGATATCCTTCGTCGTGAAGTTGAAATCGTAGATGGCT
* * *
1822457 CATTCATTGGGAAGTTGAGCTTTGAATTGGATATCATTCGTTGTGAAGTTGAAATC
1 CATTCGTTGTGAAGTTGAGCTTTGAATTGGATATCATTCGTTGTGAAGTCGAAATC
1822513 ATTGATGGCC
Statistics
Matches: 240, Mismatches: 34, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
109 240 1.00
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.36
Consensus pattern (109 bp):
CATTCGTTGTGAAGTTGAGCTTTGAATTGGATATCATTCGTTGTGAAGTCGAAATCCAAGGATTG
TTGGCACGATATCCTTCGTCGTGAAGTTGAAATCGTAGATGGCT
Found at i:1822504 original size:66 final size:66
Alignment explanation
Indices: 1822420--1822578 Score: 246
Period size: 66 Copynumber: 2.4 Consensus size: 66
1822410 TTGTTGGCAT
* * * * * *
1822420 GATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCTCATTCATTGGGAAGTTGAGCTTTGAATT
1 GATATCATTCGTTGTGAAGTTGAAATCATGGATGGCCCATTCATTGGAAAGTTAAGCTTTGAATT
1822485 G
66 G
* *
1822486 GATATCATTCGTTGTGAAGTTGAAATCATTGATGGCCCATTCATTGTAAAGTTAAGCTTTGAATT
1 GATATCATTCGTTGTGAAGTTGAAATCATGGATGGCCCATTCATTGGAAAGTTAAGCTTTGAATT
1822551 G
66 G
1822552 GATATCATTCGTTGTGAAGTTGAAATC
1 GATATCATTCGTTGTGAAGTTGAAATC
1822579 CAAGAATTGT
Statistics
Matches: 85, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
66 85 1.00
ACGTcount: A:0.26, C:0.13, G:0.25, T:0.36
Consensus pattern (66 bp):
GATATCATTCGTTGTGAAGTTGAAATCATGGATGGCCCATTCATTGGAAAGTTAAGCTTTGAATT
G
Found at i:1822505 original size:34 final size:34
Alignment explanation
Indices: 1822456--1822574 Score: 111
Period size: 34 Copynumber: 3.6 Consensus size: 34
1822446 CGTGGATGGC
*
1822456 TCATTCATTGGGAAGTTGAGCTTTGAATTGGATA
1 TCATTCATTGTGAAGTTGAGCTTTGAATTGGATA
* * * *
1822490 TCATTCGTTGTGAAGTTGAAATCATTG-A-TGG--C
1 TCATTCATTGTGAAGTTG--AGCTTTGAATTGGATA
* * *
1822522 CCATTCATTGTAAAGTTAAGCTTTGAATTGGATA
1 TCATTCATTGTGAAGTTGAGCTTTGAATTGGATA
*
1822556 TCATTCGTTGTGAAGTTGA
1 TCATTCATTGTGAAGTTGA
1822575 AATCCAAGAA
Statistics
Matches: 63, Mismatches: 16, Indels: 12
0.69 0.18 0.13
Matches are distributed among these distances:
30 5 0.08
31 1 0.02
32 17 0.27
34 34 0.54
35 1 0.02
36 5 0.08
ACGTcount: A:0.27, C:0.11, G:0.24, T:0.39
Consensus pattern (34 bp):
TCATTCATTGTGAAGTTGAGCTTTGAATTGGATA
Found at i:1823492 original size:7 final size:7
Alignment explanation
Indices: 1823474--1823561 Score: 69
Period size: 7 Copynumber: 12.9 Consensus size: 7
1823464 CACCTTATTT
1823474 TCTTTT-
1 TCTTTTC
1823480 TCTTTTC
1 TCTTTTC
*
1823487 TCTTTTT
1 TCTTTTC
*
1823494 TCTTTTT
1 TCTTTTC
*
1823501 TCTTTTT
1 TCTTTTC
1823508 TCTTTTC
1 TCTTTTC
1823515 T-TTGTTC
1 TCTT-TTC
1823522 T-TTGTTC
1 TCTT-TTC
*
1823529 TCTTTTT
1 TCTTTTC
1823536 TCTTTTC
1 TCTTTTC
*
1823543 T-TTGTTA
1 TCTT-TTC
1823550 T-TTTTC
1 TCTTTTC
1823556 TCTTTT
1 TCTTTT
1823562 TTTTTTCAAT
Statistics
Matches: 71, Mismatches: 6, Indels: 9
0.83 0.07 0.10
Matches are distributed among these distances:
6 13 0.18
7 56 0.79
8 2 0.03
ACGTcount: A:0.01, C:0.17, G:0.03, T:0.78
Consensus pattern (7 bp):
TCTTTTC
Found at i:1823503 original size:16 final size:14
Alignment explanation
Indices: 1823471--1823567 Score: 89
Period size: 14 Copynumber: 7.1 Consensus size: 14
1823461 ACCCACCTTA
1823471 TTTTC-TTTTTCTT
1 TTTTCTTTTTTCTT
*
1823484 TTCTCTTTTTTCTT
1 TTTTCTTTTTTCTT
1823498 TTTTCTTTTTTC--
1 TTTTCTTTTTTCTT
*
1823510 TTTTCTTTGTTCTT
1 TTTTCTTTTTTCTT
1823524 TGTTCTCTTTTTTC--
1 T-TT-TCTTTTTTCTT
* *
1823538 TTTTCTTTGTTATT
1 TTTTCTTTTTTCTT
1823552 TTTCTCTTTTTT-TT
1 TTT-TCTTTTTTCTT
1823566 TT
1 TT
1823568 CAATTTAGGG
Statistics
Matches: 69, Mismatches: 7, Indels: 15
0.76 0.08 0.16
Matches are distributed among these distances:
12 18 0.26
13 6 0.09
14 28 0.41
15 9 0.13
16 8 0.12
ACGTcount: A:0.01, C:0.15, G:0.03, T:0.80
Consensus pattern (14 bp):
TTTTCTTTTTTCTT
Found at i:1823507 original size:28 final size:28
Alignment explanation
Indices: 1823471--1823568 Score: 100
Period size: 27 Copynumber: 3.6 Consensus size: 28
1823461 ACCCACCTTA
1823471 TTTTC-TTTTTCTTTTCTCTTTTTTCTT
1 TTTTCTTTTTTCTTTTCTCTTTTTTCTT
*
1823498 TTTTCTTTTTTC-TTT-TCTTTGTTCTT
1 TTTTCTTTTTTCTTTTCTCTTTTTTCTT
*
1823524 TGTTCTCTTTTTTCTTTTCT-TTGTTAT-TT
1 T-TT-TCTTTTTTCTTTTCTCTT-TTTTCTT
*
1823553 TTCTCTTTTTT-TTTTC
1 TTTTCTTTTTTCTTTTC
1823569 AATTTAGGGC
Statistics
Matches: 61, Mismatches: 4, Indels: 13
0.78 0.05 0.17
Matches are distributed among these distances:
26 16 0.26
27 18 0.30
28 16 0.26
29 8 0.13
30 3 0.05
ACGTcount: A:0.01, C:0.16, G:0.03, T:0.80
Consensus pattern (28 bp):
TTTTCTTTTTTCTTTTCTCTTTTTTCTT
Found at i:1823816 original size:58 final size:58
Alignment explanation
Indices: 1823726--1823841 Score: 232
Period size: 58 Copynumber: 2.0 Consensus size: 58
1823716 ATTTCAGCCA
1823726 GGACAAGGGCTCCTCCGGAAAAGGCCTTTTTCACGACATAAGGTTTTTCCATATTTGG
1 GGACAAGGGCTCCTCCGGAAAAGGCCTTTTTCACGACATAAGGTTTTTCCATATTTGG
1823784 GGACAAGGGCTCCTCCGGAAAAGGCCTTTTTCACGACATAAGGTTTTTCCATATTTGG
1 GGACAAGGGCTCCTCCGGAAAAGGCCTTTTTCACGACATAAGGTTTTTCCATATTTGG
1823842 CATCCATTTT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 58 1.00
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.29
Consensus pattern (58 bp):
GGACAAGGGCTCCTCCGGAAAAGGCCTTTTTCACGACATAAGGTTTTTCCATATTTGG
Found at i:1826839 original size:174 final size:175
Alignment explanation
Indices: 1826549--1826897 Score: 691
Period size: 174 Copynumber: 2.0 Consensus size: 175
1826539 TGTGTCAATG
1826549 TGAGGTAGAGGAAAGTTGTCTTTGGGACTCGCCTTGTTAAGGTCCCGGTAATCGACACACATGTG
1 TGAGGTAGAGGAAAGTTGTCTTTGGGACTCGCCTTGTTAAGGTCCCGGTAATCGACACACATGTG
1826614 CACTTTCTCATCTTTCTTCGGAAACGATACAATGTTAGCCACCCACTCTGGAAATAAGACTATCA
66 CACTTTCTCATCTTTCTTCGGAAACGATACAATGTTAGCCACCCACTCTGGAAATAAGACTATCA
1826679 GGTTTTGTCTTACTTCAGTCGAAAGAGTTGTGTCGA-TTTAACCT
131 GGTTTTGTCTTACTTCAGTCGAAAGAGTTGTGTCGATTTTAACCT
1826723 TGAGGTAGAGGAAAGTTGTCTTTGGGACTCGCCTTGTTAAGGTCCCGGTAATCGACACACATGTG
1 TGAGGTAGAGGAAAGTTGTCTTTGGGACTCGCCTTGTTAAGGTCCCGGTAATCGACACACATGTG
1826788 CACTTTCTCATCTTTCTTCGGAAACGATACAATGTTAGCCACCCACTCTGGAAATAAGACTATCA
66 CACTTTCTCATCTTTCTTCGGAAACGATACAATGTTAGCCACCCACTCTGGAAATAAGACTATCA
1826853 GGTTTTGTCTTACTTCAGTCGAAAGAGTTGTGTCGATTTTAACCT
131 GGTTTTGTCTTACTTCAGTCGAAAGAGTTGTGTCGATTTTAACCT
1826898 CATTTCTATC
Statistics
Matches: 174, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
174 166 0.95
175 8 0.05
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.32
Consensus pattern (175 bp):
TGAGGTAGAGGAAAGTTGTCTTTGGGACTCGCCTTGTTAAGGTCCCGGTAATCGACACACATGTG
CACTTTCTCATCTTTCTTCGGAAACGATACAATGTTAGCCACCCACTCTGGAAATAAGACTATCA
GGTTTTGTCTTACTTCAGTCGAAAGAGTTGTGTCGATTTTAACCT
Found at i:1832619 original size:13 final size:12
Alignment explanation
Indices: 1832601--1832631 Score: 53
Period size: 13 Copynumber: 2.5 Consensus size: 12
1832591 TGTCATAGCA
1832601 TTTTTATTTTTC
1 TTTTTATTTTTC
1832613 TTGTTTATTTTTC
1 TT-TTTATTTTTC
1832626 TTTTTA
1 TTTTTA
1832632 AGATAGTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 6 0.33
13 12 0.67
ACGTcount: A:0.10, C:0.06, G:0.03, T:0.81
Consensus pattern (12 bp):
TTTTTATTTTTC
Found at i:1843527 original size:18 final size:18
Alignment explanation
Indices: 1843504--1843548 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
1843494 AGGGATTATC
1843504 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
*
1843522 AGTGGTCTTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
*
1843540 AGTGATCCT
1 AGTGGTCCT
1843549 ATTGGACAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.18, C:0.20, G:0.31, T:0.31
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:1844805 original size:21 final size:20
Alignment explanation
Indices: 1844767--1844813 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 20
1844757 TGCAAGCCAT
*
1844767 ATTTTTAGACATTGTTAAGG
1 ATTTTTAGAAATTGTTAAGG
* *
1844787 ATTTTCTAGAAATTTTTAATG
1 ATTTT-TAGAAATTGTTAAGG
1844808 ATTTTT
1 ATTTTT
1844814 CTGTTTCTAG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 6 0.26
21 17 0.74
ACGTcount: A:0.30, C:0.04, G:0.13, T:0.53
Consensus pattern (20 bp):
ATTTTTAGAAATTGTTAAGG
Found at i:1852863 original size:15 final size:13
Alignment explanation
Indices: 1852788--1852858 Score: 72
Period size: 13 Copynumber: 5.3 Consensus size: 13
1852778 GCGATAGTCA
*
1852788 AAAATACAATATGT
1 AAAATA-AATATAT
*
1852802 AAAATATATATAT
1 AAAATAAATATAT
*
1852815 AATA-AAATAGTAT
1 AAAATAAATA-TAT
*
1852828 CTAAATAAATATAT
1 -AAAATAAATATAT
1852842 AAAATAAATATAT
1 AAAATAAATATAT
1852855 AAAA
1 AAAA
1852859 AATAATAATA
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
12 4 0.09
13 27 0.57
14 11 0.23
15 5 0.11
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (13 bp):
AAAATAAATATAT
Found at i:1853014 original size:21 final size:21
Alignment explanation
Indices: 1852990--1853029 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1852980 CTAAAGAATG
1852990 ATATAAAAT-ATATACATATAC
1 ATATAAAATAATATA-ATATAC
*
1853011 ATATAAGATAATATAATAT
1 ATATAAAATAATATAATAT
1853030 TAAATAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.57, C:0.05, G:0.03, T:0.35
Consensus pattern (21 bp):
ATATAAAATAATATAATATAC
Found at i:1853927 original size:18 final size:19
Alignment explanation
Indices: 1853892--1853928 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
1853882 CACGGAATGT
1853892 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
1853912 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
1853929 TGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:1855463 original size:20 final size:20
Alignment explanation
Indices: 1855415--1855476 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 20
1855405 AACTTAAATC
*
1855415 AAAATAATTAAAATAA-ATAT
1 AAAATAATT-TAATAATATAT
1855435 AAAAT--TTTAATAATATAT
1 AAAATAATTTAATAATATAT
1855453 AAAATAATTT-AT-ATGATAT
1 AAAATAATTTAATAAT-ATAT
1855472 AAAAT
1 AAAAT
1855477 TAAATATCTA
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
17 5 0.14
18 13 0.35
19 11 0.30
20 8 0.22
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (20 bp):
AAAATAATTTAATAATATAT
Found at i:1855547 original size:64 final size:64
Alignment explanation
Indices: 1855471--1855627 Score: 266
Period size: 64 Copynumber: 2.5 Consensus size: 64
1855461 TTATATGATA
1855471 TAAAATTAAATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAAAAAATTAATAT
1 TAAAATT-AATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAAAAAATTAATAT
*
1855536 TAAAATTAATATCTATAATATAATATTAAAATATTAATATTTAATTTATTTAAAAAATTAATAT
1 TAAAATTAATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAAAAAATTAATAT
*
1855600 TAAAATTAAAAT-TA-AATATAATA-TAAAA
1 TAAAATTAATATCTATAATATAATATTAAAA
1855628 TTAAATAAAA
Statistics
Matches: 90, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
61 5 0.06
62 9 0.10
63 2 0.02
64 67 0.74
65 7 0.08
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (64 bp):
TAAAATTAATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAAAAAATTAATAT
Found at i:1855580 original size:26 final size:25
Alignment explanation
Indices: 1855527--1855631 Score: 94
Period size: 25 Copynumber: 4.2 Consensus size: 25
1855517 TTATTTAAAA
1855527 AATTAATATT-AAAATTAATATCTAT
1 AATTAATATTAAAAATTAATAT-TAT
1855552 AATATAATATTAAAATATTAATATT-T
1 AAT-TAATATTAAAA-ATTAATATTAT
* *
1855578 AATTTAT-TTAAAAAATTAATATTAA
1 AATTAATATT-AAAAATTAATATTAT
* * *
1855603 AATTAAAATTAAATA-TAATA-TAA
1 AATTAATATTAAAAATTAATATTAT
1855626 AATTAA
1 AATTAA
1855632 ATAAAACCTC
Statistics
Matches: 69, Mismatches: 5, Indels: 14
0.78 0.06 0.16
Matches are distributed among these distances:
23 9 0.13
24 16 0.23
25 19 0.28
26 13 0.19
27 4 0.06
28 8 0.12
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (25 bp):
AATTAATATTAAAAATTAATATTAT
Found at i:1855595 original size:24 final size:27
Alignment explanation
Indices: 1855530--1855615 Score: 85
Period size: 26 Copynumber: 3.4 Consensus size: 27
1855520 TTTAAAAAAT
1855530 TAATATT--AAAATTAATATCTATAATA
1 TAATATTAAAAAATTAATAT-TATAATA
*
1855556 TAATATTAAAATATTAATATT-TAAT-
1 TAATATTAAAAAATTAATATTATAATA
* *
1855581 TTAT-TTAAAAAATTAATATTAAAAT-
1 TAATATTAAAAAATTAATATTATAATA
*
1855606 TAAAATTAAA
1 TAATATTAAA
1855616 TATAATATAA
Statistics
Matches: 50, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
24 15 0.30
25 8 0.16
26 16 0.32
27 1 0.02
28 10 0.20
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (27 bp):
TAATATTAAAAAATTAATATTATAATA
Found at i:1858541 original size:39 final size:39
Alignment explanation
Indices: 1858482--1858561 Score: 142
Period size: 39 Copynumber: 2.1 Consensus size: 39
1858472 GGGTGTTTCA
* *
1858482 AATTATCAAAGGGAGTCCATGAAGAGCATAACTGGATTT
1 AATTATCAAAGAGAGGCCATGAAGAGCATAACTGGATTT
1858521 AATTATCAAAGAGAGGCCATGAAGAGCATAACTGGATTT
1 AATTATCAAAGAGAGGCCATGAAGAGCATAACTGGATTT
1858560 AA
1 AA
1858562 ACTTAGTTGT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.41, C:0.12, G:0.23, T:0.24
Consensus pattern (39 bp):
AATTATCAAAGAGAGGCCATGAAGAGCATAACTGGATTT
Found at i:1860440 original size:27 final size:28
Alignment explanation
Indices: 1860390--1860447 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 28
1860380 AGGGGTGCAC
*
1860390 AAAAAATCCGAATATCCGATTTTGCGAA
1 AAAAAATCCGAATATCCGATTTTGAGAA
*
1860418 AAAAATATCCGAA-ATCGGA-TTTGAGAA
1 AAAAA-ATCCGAATATCCGATTTTGAGAA
1860445 AAA
1 AAA
1860448 CCGGTTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
27 10 0.37
28 10 0.37
29 7 0.26
ACGTcount: A:0.48, C:0.14, G:0.16, T:0.22
Consensus pattern (28 bp):
AAAAAATCCGAATATCCGATTTTGAGAA
Found at i:1862853 original size:21 final size:21
Alignment explanation
Indices: 1862829--1862868 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1862819 TTTATTTTAT
1862829 AACTTTATTTCAATTATCGTA
1 AACTTTATTTCAATTATCGTA
*
1862850 AACTTTGTTTCAATTATCG
1 AACTTTATTTCAATTATCG
1862869 AACTTGAAGT
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:0.15, G:0.07, T:0.47
Consensus pattern (21 bp):
AACTTTATTTCAATTATCGTA
Found at i:1862956 original size:33 final size:33
Alignment explanation
Indices: 1862863--1862962 Score: 148
Period size: 34 Copynumber: 3.0 Consensus size: 33
1862853 TTTGTTTCAA
*
1862863 TTATCGAACTT-GAAGTTTTTAAGCATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1862895 TTATCGAACTTGGAAGTTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAG-TTTTTAAGTATTTGAAT
* * *
1862929 TTATCAAACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1862962 T
1 T
1862963 ATGTTGAGTT
Statistics
Matches: 62, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
32 11 0.18
33 20 0.32
34 31 0.50
ACGTcount: A:0.32, C:0.08, G:0.15, T:0.45
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:1863224 original size:21 final size:21
Alignment explanation
Indices: 1863198--1863254 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
1863188 TGGAGTGTGG
*
1863198 GGGAATCGGTACCCTCTCATA
1 GGGAATCGGTTCCCTCTCATA
*
1863219 GGGAATCGGTTTCCTCTCATA
1 GGGAATCGGTTCCCTCTCATA
1863240 GGGAATCGGTTCCCT
1 GGGAATCGGTTCCCT
1863255 AAGTGTAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.19, C:0.26, G:0.26, T:0.28
Consensus pattern (21 bp):
GGGAATCGGTTCCCTCTCATA
Found at i:1863459 original size:17 final size:18
Alignment explanation
Indices: 1863439--1863472 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1863429 GTTTTTTTAT
1863439 AACC-GATTTTTTAAAAA
1 AACCGGATTTTTTAAAAA
*
1863456 AACCGGTTTTTTTAAAA
1 AACCGGATTTTTTAAAA
1863473 CCGAAACCGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.41, C:0.12, G:0.09, T:0.38
Consensus pattern (18 bp):
AACCGGATTTTTTAAAAA
Found at i:1863472 original size:15 final size:15
Alignment explanation
Indices: 1863420--1863475 Score: 58
Period size: 15 Copynumber: 3.6 Consensus size: 15
1863410 ATCTGGAATA
*
1863420 TTAAAATCGGTTTTT
1 TTAAAACCGGTTTTT
* *
1863435 TTATAACCGATTTTT
1 TTAAAACCGGTTTTT
*
1863450 TAAAAAAACCGGTTTTT
1 T--TAAAACCGGTTTTT
1863467 TTAAAACCG
1 TTAAAACCG
1863476 AAACCGGTTA
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
15 20 0.62
17 12 0.38
ACGTcount: A:0.34, C:0.12, G:0.11, T:0.43
Consensus pattern (15 bp):
TTAAAACCGGTTTTT
Found at i:1863592 original size:15 final size:17
Alignment explanation
Indices: 1863566--1863597 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1863556 TTCTATGGGA
1863566 AAAAACCGGAT-CGGAT
1 AAAAACCGGATCCGGAT
1863582 AAAAACC-GATCCGGAT
1 AAAAACCGGATCCGGAT
1863598 CGGATTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.20
16 12 0.80
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (17 bp):
AAAAACCGGATCCGGAT
Found at i:1869535 original size:21 final size:23
Alignment explanation
Indices: 1869509--1869553 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
1869499 AAAAAATACT
1869509 TAATTA-AAAAT-GTTACATATC
1 TAATTACAAAATAGTTACATATC
*
1869530 TAATTACAAAATAGTTAGATATC
1 TAATTACAAAATAGTTACATATC
1869553 T
1 T
1869554 TGAATTGGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 6 0.29
22 5 0.24
23 10 0.48
ACGTcount: A:0.47, C:0.09, G:0.07, T:0.38
Consensus pattern (23 bp):
TAATTACAAAATAGTTACATATC
Found at i:1876940 original size:22 final size:23
Alignment explanation
Indices: 1876902--1876948 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
1876892 AACCCTAAAC
1876902 AAGCCCAAAAATCGTATCTGCTA
1 AAGCCCAAAAATCGTATCTGCTA
* *
1876925 AAGCCC-AAAATTGTATCTTCTA
1 AAGCCCAAAAATCGTATCTGCTA
1876947 AA
1 AA
1876949 CTCGCGATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 16 0.73
23 6 0.27
ACGTcount: A:0.40, C:0.23, G:0.11, T:0.26
Consensus pattern (23 bp):
AAGCCCAAAAATCGTATCTGCTA
Found at i:1880771 original size:3 final size:3
Alignment explanation
Indices: 1880763--1880821 Score: 118
Period size: 3 Copynumber: 19.7 Consensus size: 3
1880753 AGCAGTCGTC
1880763 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1880811 TTA TTA TTA TT
1 TTA TTA TTA TT
1880822 TCATCGATGA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1885980 original size:29 final size:29
Alignment explanation
Indices: 1885939--1886103 Score: 140
Period size: 29 Copynumber: 5.7 Consensus size: 29
1885929 AGTTTTGAAT
* * *
1885939 TTTATTATGATTTATAAAAAGGTTTGTCC
1 TTTATTGTAATTTATAAAAAGGTTTATCC
* * * *
1885968 TTTGTTGTAATTTGTAAAAA-ATTTGGTCC
1 TTTATTGTAATTTATAAAAAGGTTT-ATCC
* * *
1885997 TTTATTTTAATTTACAATAAGGTTTAT--
1 TTTATTGTAATTTATAAAAAGGTTTATCC
* *
1886024 TTTATTGTAATTTACAAAAAAAAGTTTATCC
1 TTTATTGTAATTT--ATAAAAAGGTTTATCC
* *
1886055 TTTATTATAATTTACAAAAAGGTTTATCC
1 TTTATTGTAATTTATAAAAAGGTTTATCC
1886084 TTTAATT-TAATTTATAAAAA
1 TTT-ATTGTAATTTATAAAAA
1886104 TAGTGACGAT
Statistics
Matches: 109, Mismatches: 20, Indels: 14
0.76 0.14 0.10
Matches are distributed among these distances:
27 12 0.11
28 3 0.03
29 76 0.70
30 6 0.06
31 12 0.11
ACGTcount: A:0.36, C:0.07, G:0.09, T:0.48
Consensus pattern (29 bp):
TTTATTGTAATTTATAAAAAGGTTTATCC
Found at i:1886010 original size:58 final size:58
Alignment explanation
Indices: 1885939--1886103 Score: 185
Period size: 58 Copynumber: 2.8 Consensus size: 58
1885929 AGTTTTGAAT
* * * * * *
1885939 TTTATTATGATTTATAAAAAGGTTTGTCCTTTGTTGTAATTTGTAAAAAA-TTTGGTCC
1 TTTATTATAATTTACAAAAAGGTTTATCCTTTATTGTAATTTATAAAAAAGTTT-ATCC
* * *
1885997 TTTATTTTAATTTACAATAAGGTTTAT--TTTATTGTAATTTACAAAAAAAAGTTTATCC
1 TTTATTATAATTTACAAAAAGGTTTATCCTTTATTGTAATTT--ATAAAAAAGTTTATCC
1886055 TTTATTATAATTTACAAAAAGGTTTATCCTTTAATT-TAATTTATAAAAA
1 TTTATTATAATTTACAAAAAGGTTTATCCTTT-ATTGTAATTTATAAAAA
1886104 TAGTGACGAT
Statistics
Matches: 89, Mismatches: 12, Indels: 12
0.79 0.11 0.11
Matches are distributed among these distances:
56 12 0.13
58 62 0.70
59 3 0.03
60 9 0.10
61 3 0.03
ACGTcount: A:0.36, C:0.07, G:0.09, T:0.48
Consensus pattern (58 bp):
TTTATTATAATTTACAAAAAGGTTTATCCTTTATTGTAATTTATAAAAAAGTTTATCC
Found at i:1887315 original size:30 final size:30
Alignment explanation
Indices: 1887276--1887333 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
1887266 AGTGACCATT
*
1887276 ATAGATCTCCAAGAACACATGACGATCTCC
1 ATAGATCTCCAAGAACACACGACGATCTCC
* * *
1887306 ATAGGTCTCCAGGAGCACACGACGATCT
1 ATAGATCTCCAAGAACACACGACGATCT
1887334 ATAGAGTACT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.33, C:0.29, G:0.19, T:0.19
Consensus pattern (30 bp):
ATAGATCTCCAAGAACACACGACGATCTCC
Found at i:1892280 original size:21 final size:22
Alignment explanation
Indices: 1892254--1892312 Score: 66
Period size: 24 Copynumber: 2.6 Consensus size: 22
1892244 AATAATGTAG
1892254 GTATCGATGCACTCT-ACAAGT
1 GTATCGATGCACTCTAACAAGT
* *
1892275 GTATCGATGCATCCTTTAACGAGT
1 GTATCGATGCA--CTCTAACAAGT
*
1892299 GCATCGATGCACTC
1 GTATCGATGCACTC
1892313 CTTATGTATC
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
21 11 0.35
22 2 0.06
23 3 0.10
24 15 0.48
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.29
Consensus pattern (22 bp):
GTATCGATGCACTCTAACAAGT
Found at i:1898672 original size:18 final size:18
Alignment explanation
Indices: 1898649--1898683 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1898639 ATTAGTCATG
*
1898649 CACGAGTGTACCAGCATT
1 CACGAGCGTACCAGCATT
1898667 CACGAGCGTACCAGCAT
1 CACGAGCGTACCAGCAT
1898684 GCATGTATGC
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:0.29, C:0.31, G:0.23, T:0.17
Consensus pattern (18 bp):
CACGAGCGTACCAGCATT
Found at i:1903288 original size:24 final size:25
Alignment explanation
Indices: 1903256--1903302 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
1903246 GCGTATCAGC
*
1903256 ATGCATCCTC-GCGTACCAACATGT
1 ATGCATCCTCAACGTACCAACATGT
1903280 ATGCATCCTCAACGTACCAACAT
1 ATGCATCCTCAACGTACCAACAT
1903303 ACATCTTCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 10 0.48
25 11 0.52
ACGTcount: A:0.30, C:0.34, G:0.13, T:0.23
Consensus pattern (25 bp):
ATGCATCCTCAACGTACCAACATGT
Found at i:1909201 original size:15 final size:15
Alignment explanation
Indices: 1909181--1909230 Score: 91
Period size: 15 Copynumber: 3.3 Consensus size: 15
1909171 TGTTTTGCTA
1909181 AATCAGTCAACACTG
1 AATCAGTCAACACTG
1909196 AATCAGTCAACACTG
1 AATCAGTCAACACTG
*
1909211 AATCAATCAACACTG
1 AATCAGTCAACACTG
1909226 AATCA
1 AATCA
1909231 TGGCCCTGAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 34 1.00
ACGTcount: A:0.44, C:0.26, G:0.10, T:0.20
Consensus pattern (15 bp):
AATCAGTCAACACTG
Found at i:1911767 original size:125 final size:125
Alignment explanation
Indices: 1911608--1911867 Score: 364
Period size: 125 Copynumber: 2.1 Consensus size: 125
1911598 TTGGTAGCAA
* * * *
1911608 TTTTGTTATTGTTGTGCATAATTAAATCGATAAAAATTACT-GAAAACATCATTATTTCTACTGA
1 TTTTGTTATTGTTGTGCATAATCAAAACGATAAAAATTA-TAAAAAAAATCATTATTTCTACTGA
* * *
1911672 TTTTGTTATTATTTTAGTATTCTACCGGATTTCTTAACAAAA-CTGGTAAAAGTGCTACCGG
65 TTTTATTATTATTTTAGCATTCTACCGGATTTCTTAACAAAATC-GGTAAAAGCGCTACCGG
* *
1911733 TTTTGTTATTGTTGTGCATAA-CAAAACGGGTAAAAATTATAAAAAAAATCATTATTTCTACTGG
1 TTTTGTTATTGTTGTGCATAATCAAAAC-GATAAAAATTATAAAAAAAATCATTATTTCTACTGA
* * *
1911797 TTTTATTATTATTTTGGCATTTTACCGGGTTTCTTAACAAAATCGGTAAAAGCGCTACCGG
65 TTTTATTATTATTTTAGCATTCTACCGGATTTCTTAACAAAATCGGTAAAAGCGCTACCGG
1911858 TTTTGTTATT
1 TTTTGTTATT
1911868 TTTTTACCGA
Statistics
Matches: 120, Mismatches: 12, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
124 5 0.04
125 114 0.95
126 1 0.01
ACGTcount: A:0.32, C:0.12, G:0.15, T:0.42
Consensus pattern (125 bp):
TTTTGTTATTGTTGTGCATAATCAAAACGATAAAAATTATAAAAAAAATCATTATTTCTACTGAT
TTTATTATTATTTTAGCATTCTACCGGATTTCTTAACAAAATCGGTAAAAGCGCTACCGG
Found at i:1912553 original size:200 final size:199
Alignment explanation
Indices: 1912199--1912691 Score: 603
Period size: 200 Copynumber: 2.5 Consensus size: 199
1912189 GTAAACATAT
* * *
1912199 GTGTCGATACATTT-TCTAAAAGTATCGA-CCCAAAAACACCAAAACCGATAATTATAATGTAAT
1 GTGTCGATACATTTAT-TAAAAGTATTGATCCCAAAAACATCGAAACCGATAATTATAATGTAAT
*
1912262 AGGTAAATTTACAATGTAACTGGTATAAATATACCGATTTTATGATAGAATAGGTCAACATAATG
65 AGGTAAATTTACAATGTAACTGATATAAATATACCGATTTTATGATAGAATAGGTCAACATAATG
* * *
1912327 TATCGACACAAATTTAAAAAGTGTCGATACATTTTGTCCATAATGAATGCCAAACGAGGTGCACG
130 TATCGACACAAATTTAAAAAGTGTCGATAC-TTTTGTCCAGAATGAATGCCAAACGAAGTGCACA
1912392 CATAAA
194 CATAAA
* *
1912398 GTGTCGATACATTTATTAAAAGTATTGATCCCAAAAACATCGAAACGGATAATTACAATGTAATA
1 GTGTCGATACATTTATTAAAAGTATTGATCCCAAAAACATCGAAACCGATAATTATAATGTAATA
* * *
1912463 GGTAAATTTACAATGT-ACT-ATATAGAAATATATCGGTTTTATGAATA-AATAGGTCTACATAA
66 GGTAAATTTACAATGTAACTGATAT--AAATATACCGATTTTATG-ATAGAATAGGTCAACATAA
** *** * * *
1912525 TGTATCGACAC-GTTTTAAGTTTGTGTCGATTCTTTTTTCCAGAATGAATGCCCAACGAAGTGCA
128 TGTATCGACACAAATTTAA-AAAGTGTCGATACTTTTGTCCAGAATGAATGCCAAACGAAGTGCA
1912589 CACATAAA
192 CACATAAA
* *
1912597 GTGTCGATACATTTA--AAATTGTATCT-ATTCCAAAAACATCGAAACCGATAATTATAATAG-A
1 GTGTCGATACATTTATTAAA-AGTAT-TGATCCCAAAAACATCGAAACCGATAATTATAAT-GTA
** *
1912658 ATAGGT-AATTTGTAATGTCACTGATATAAATATA
63 ATAGGTAAATTTACAATGTAACTGATATAAATATA
1912692 ATGGTTTAGT
Statistics
Matches: 257, Mismatches: 26, Indels: 24
0.84 0.08 0.08
Matches are distributed among these distances:
197 20 0.08
198 46 0.18
199 89 0.35
200 99 0.39
201 3 0.01
ACGTcount: A:0.40, C:0.14, G:0.15, T:0.31
Consensus pattern (199 bp):
GTGTCGATACATTTATTAAAAGTATTGATCCCAAAAACATCGAAACCGATAATTATAATGTAATA
GGTAAATTTACAATGTAACTGATATAAATATACCGATTTTATGATAGAATAGGTCAACATAATGT
ATCGACACAAATTTAAAAAGTGTCGATACTTTTGTCCAGAATGAATGCCAAACGAAGTGCACACA
TAAA
Found at i:1912804 original size:64 final size:64
Alignment explanation
Indices: 1912726--1912875 Score: 212
Period size: 64 Copynumber: 2.3 Consensus size: 64
1912716 ATATAAACGC
** * * *
1912726 TACCTATTACATTATATAAGCGTTACCTAATATGTTATTGTACTTGATAATATTTCA-GGTTAAA
1 TACCTATTTTATTATATAAGCGATACCTAATATGTTATTATACTTGATAATATTT-ATGATTAAA
*
1912790 TACCTATTTTATTATATAAGCGATACCTAATATGTTATTATATTTGATAATATTTATGATTAAA
1 TACCTATTTTATTATATAAGCGATACCTAATATGTTATTATACTTGATAATATTTATGATTAAA
* *
1912854 TGCTTATTTTATTATATAAGCG
1 TACCTATTTTATTATATAAGCG
1912876 CTACTTATTA
Statistics
Matches: 77, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
63 1 0.01
64 76 0.99
ACGTcount: A:0.35, C:0.10, G:0.10, T:0.45
Consensus pattern (64 bp):
TACCTATTTTATTATATAAGCGATACCTAATATGTTATTATACTTGATAATATTTATGATTAAA
Found at i:1912916 original size:26 final size:24
Alignment explanation
Indices: 1912862--1912918 Score: 71
Period size: 23 Copynumber: 2.3 Consensus size: 24
1912852 AATGCTTATT
*
1912862 TTATTATATAAGCGCTACTTATTA
1 TTATTATATAAGCGCTACTAATTA
*
1912886 -CATTATATAAGCGCTAACTAATATA
1 TTATTATATAAGCGCT-ACTAAT-TA
1912911 TTATTATA
1 TTATTATA
1912919 CTTGATAATG
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
23 14 0.52
24 5 0.19
25 2 0.07
26 6 0.22
ACGTcount: A:0.39, C:0.12, G:0.07, T:0.42
Consensus pattern (24 bp):
TTATTATATAAGCGCTACTAATTA
Found at i:1920856 original size:10 final size:10
Alignment explanation
Indices: 1920841--1920866 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
1920831 AAAAAGTTAC
1920841 ATAATTAATA
1 ATAATTAATA
1920851 ATAATTAATA
1 ATAATTAATA
1920861 ATAATT
1 ATAATT
1920867 TTTTAAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (10 bp):
ATAATTAATA
Found at i:1921124 original size:48 final size:47
Alignment explanation
Indices: 1921053--1921147 Score: 181
Period size: 48 Copynumber: 2.0 Consensus size: 47
1921043 TTTTACGCAT
1921053 GTAAACCCCACCCACCCAAAGCATAAACACAGGGAACAGTCATTGGAG
1 GTAAACCCCACCCACCCAAAGCATAAACACAGGGAACAGTCA-TGGAG
1921101 GTAAACCCCACCCACCCAAAGCATAAACACAGGGAACAGTCATGGAG
1 GTAAACCCCACCCACCCAAAGCATAAACACAGGGAACAGTCATGGAG
1921148 AGCAACACAG
Statistics
Matches: 47, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
47 5 0.11
48 42 0.89
ACGTcount: A:0.40, C:0.32, G:0.19, T:0.09
Consensus pattern (47 bp):
GTAAACCCCACCCACCCAAAGCATAAACACAGGGAACAGTCATGGAG
Found at i:1929099 original size:77 final size:78
Alignment explanation
Indices: 1928963--1929117 Score: 267
Period size: 77 Copynumber: 2.0 Consensus size: 78
1928953 GATAATCTAT
* *
1928963 CGACTCTTCGAGATATTTCCCATGAGACTATAACTATTGATGAGTAAATTTTGTGAAAATTCAAG
1 CGACTCATCGAGATATTTCCCATGAGAC-ATAACTATTGATGAGTAAATTTTGTAAAAATTCAAG
1929028 ATTGCAGAAACTCC
65 ATTGCAGAAACTCC
1929042 CGACTCATCGAGATATTTCCCATGAGAC-TAACTATTGATGAGTAAATTTTGTAAAAATTCAAGA
1 CGACTCATCGAGATATTTCCCATGAGACATAACTATTGATGAGTAAATTTTGTAAAAATTCAAGA
*
1929106 TTGCAGAGACTC
66 TTGCAGAAACTC
1929118 AACAGGAGAT
Statistics
Matches: 73, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
77 46 0.63
79 27 0.37
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Consensus pattern (78 bp):
CGACTCATCGAGATATTTCCCATGAGACATAACTATTGATGAGTAAATTTTGTAAAAATTCAAGA
TTGCAGAAACTCC
Found at i:1932398 original size:20 final size:20
Alignment explanation
Indices: 1932369--1932406 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1932359 TCATTCAATC
*
1932369 GTAATTAAAAGAATTAAGGT
1 GTAATCAAAAGAATTAAGGT
1932389 GTAATCAAAAGAATTAAG
1 GTAATCAAAAGAATTAAG
1932407 TTTTGTTACA
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:0.53, C:0.03, G:0.18, T:0.26
Consensus pattern (20 bp):
GTAATCAAAAGAATTAAGGT
Found at i:1936905 original size:20 final size:19
Alignment explanation
Indices: 1936820--1936911 Score: 139
Period size: 19 Copynumber: 4.7 Consensus size: 19
1936810 AACGCAGAAG
1936820 TCAAATTCGCAATACTGAATT
1 TCAAATTCGC-A-ACTGAATT
1936841 TCAAATTCGCAACTGAATT
1 TCAAATTCGCAACTGAATT
1936860 TCAAATTCGCAACTGAATT
1 TCAAATTCGCAACTGAATT
*
1936879 TCAAATTCGCAACTCGATTT
1 TCAAATTCGCAACT-GAATT
*
1936899 TCGAATTCGCAAC
1 TCAAATTCGCAAC
1936912 AGGTTTTAGT
Statistics
Matches: 68, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
19 41 0.60
20 17 0.25
21 10 0.15
ACGTcount: A:0.35, C:0.23, G:0.11, T:0.32
Consensus pattern (19 bp):
TCAAATTCGCAACTGAATT
Found at i:1937895 original size:24 final size:24
Alignment explanation
Indices: 1937828--1937897 Score: 77
Period size: 24 Copynumber: 2.9 Consensus size: 24
1937818 TTGTGAGTAC
* *
1937828 TAGTCAGTACTCAAAATTTGATCT
1 TAGTCAATACTCGAAATTTGATCT
* * *
1937852 TAGTCAATACCCGGACTTTGATCT
1 TAGTCAATACTCGAAATTTGATCT
* *
1937876 TGGTCAATACTCGAATTTTGAT
1 TAGTCAATACTCGAAATTTGAT
1937898 GATGTTTCAG
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.37
Consensus pattern (24 bp):
TAGTCAATACTCGAAATTTGATCT
Found at i:1940332 original size:20 final size:20
Alignment explanation
Indices: 1940299--1940358 Score: 84
Period size: 20 Copynumber: 3.0 Consensus size: 20
1940289 TTGTGATTGT
*
1940299 TGCGAAAGTTAAATTCGCAA
1 TGCGAAAGTCAAATTCGCAA
*
1940319 TGCGATAGTCAAATTCGCAA
1 TGCGAAAGTCAAATTCGCAA
* *
1940339 TGCGAAAATCAAAATCGCAA
1 TGCGAAAGTCAAATTCGCAA
1940359 ACTGAAAATC
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.42, C:0.18, G:0.18, T:0.22
Consensus pattern (20 bp):
TGCGAAAGTCAAATTCGCAA
Found at i:1940397 original size:20 final size:20
Alignment explanation
Indices: 1940374--1940532 Score: 114
Period size: 20 Copynumber: 8.2 Consensus size: 20
1940364 AAATCGCAAC
*
1940374 GCGAATTTGACTTTCGCGTT
1 GCGAATTTGACTTTCGCATT
* ** *
1940394 GCGAATTTAACTTTAACGTT
1 GCGAATTTGACTTTCGCATT
* **
1940414 GCGAATTTGACTATCGCAAC
1 GCGAATTTGACTTTCGCATT
* *
1940434 GCGAA----A--ATCGCAAT
1 GCGAATTTGACTTTCGCATT
*
1940448 GCGAATTTGACTTTCACATT
1 GCGAATTTGACTTTCGCATT
* **
1940468 GCGAATTTGACTATCGCAAC
1 GCGAATTTGACTTTCGCATT
* *
1940488 ACGAATTTGACTTTCGCGTT
1 GCGAATTTGACTTTCGCATT
* *
1940508 GCGAATTTGATTTTCGCGTT
1 GCGAATTTGACTTTCGCATT
1940528 GCGAA
1 GCGAA
1940533 AGTGTACCTT
Statistics
Matches: 108, Mismatches: 25, Indels: 12
0.74 0.17 0.08
Matches are distributed among these distances:
14 12 0.11
16 1 0.01
18 1 0.01
20 94 0.87
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.33
Consensus pattern (20 bp):
GCGAATTTGACTTTCGCATT
Found at i:1940512 original size:74 final size:74
Alignment explanation
Indices: 1940362--1940504 Score: 178
Period size: 74 Copynumber: 1.9 Consensus size: 74
1940352 ATCGCAAACT
* * * ****
1940362 GAAAATCGCAACGCGAATTTGACTTTCGCGTTGCGAATTTAACTTTAACGTTGCGAATTTGACTA
1 GAAAATCGCAACGCGAATTTGACTTTCACATTGCGAATTTAACTATAACAACACGAATTTGACTA
1940427 TCGCAACGC
66 TCGCAACGC
* * ** *
1940436 GAAAATCGCAATGCGAATTTGACTTTCACATTGCGAATTTGACTATCGCAACACGAATTTGACTT
1 GAAAATCGCAACGCGAATTTGACTTTCACATTGCGAATTTAACTATAACAACACGAATTTGACTA
1940501 TCGC
66 TCGC
1940505 GTTGCGAATT
Statistics
Matches: 57, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
74 57 1.00
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30
Consensus pattern (74 bp):
GAAAATCGCAACGCGAATTTGACTTTCACATTGCGAATTTAACTATAACAACACGAATTTGACTA
TCGCAACGC
Found at i:1941480 original size:154 final size:154
Alignment explanation
Indices: 1941200--1941503 Score: 563
Period size: 154 Copynumber: 2.0 Consensus size: 154
1941190 TTGAACTTTT
* *
1941200 TTGGCTTCTTATTTCCAGAATTAGTCCAATAATTAATCGCGTCCAAGTATTTCGCCAAATGAGCG
1 TTGGCTTCTTATTTCCAGAATTAGTACAATAATCAATCGCGTCCAAGTATTTCGCCAAATGAGCG
*
1941265 CTCCATCCCTTACAAATAATATCTCTCAAATCAGACAATGGTATGTAATTCAACATGCTGTCATA
66 CTCCATCCCTTACAAATAATATCTCTCAAATCAGACAATGGTATATAATTCAACATGCTGTCATA
1941330 TACCATTGTCTTCAAGGATGGGAG
131 TACCATTGTCTTCAAGGATGGGAG
1941354 TTGGCTTCTTATTTCCAGAATTAGTACAATAATCAATCGCGTCCAAGTATTTCGCCAAATGAGCG
1 TTGGCTTCTTATTTCCAGAATTAGTACAATAATCAATCGCGTCCAAGTATTTCGCCAAATGAGCG
1941419 CTCCATCCCTTACAAATAATATCTCTCAAATCAGACAATGGTATATAATTCAACATGCTGTCATA
66 CTCCATCCCTTACAAATAATATCTCTCAAATCAGACAATGGTATATAATTCAACATGCTGTCATA
* *
1941484 TACTATTGTCTTCAGGGATG
131 TACCATTGTCTTCAAGGATG
1941504 AGAGATGAAG
Statistics
Matches: 145, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
154 145 1.00
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.32
Consensus pattern (154 bp):
TTGGCTTCTTATTTCCAGAATTAGTACAATAATCAATCGCGTCCAAGTATTTCGCCAAATGAGCG
CTCCATCCCTTACAAATAATATCTCTCAAATCAGACAATGGTATATAATTCAACATGCTGTCATA
TACCATTGTCTTCAAGGATGGGAG
Found at i:1942198 original size:21 final size:21
Alignment explanation
Indices: 1942170--1942268 Score: 98
Period size: 21 Copynumber: 4.7 Consensus size: 21
1942160 GCAGGCGGGA
*
1942170 CCTCTTGAACGATGACAGGGG
1 CCTCTTGAACGATGAGAGGGG
*
1942191 CCTTTTGAAC-AGTG-GAAGGGG
1 CCTCTTGAACGA-TGAG-AGGGG
*
1942212 CCTCTTCG-ATGATGAGAGGGG
1 CCTCTT-GAACGATGAGAGGGG
*
1942233 CCTCTTGAACGAT-AGGAGGCG
1 CCTCTTGAACGATGA-GAGGGG
1942254 CCTCTTGAACGATGA
1 CCTCTTGAACGATGA
1942269 TAGGTGCATC
Statistics
Matches: 64, Mismatches: 6, Indels: 15
0.75 0.07 0.18
Matches are distributed among these distances:
20 3 0.05
21 57 0.89
22 4 0.06
ACGTcount: A:0.23, C:0.21, G:0.33, T:0.22
Consensus pattern (21 bp):
CCTCTTGAACGATGAGAGGGG
Found at i:1942216 original size:42 final size:42
Alignment explanation
Indices: 1942170--1942268 Score: 114
Period size: 42 Copynumber: 2.4 Consensus size: 42
1942160 GCAGGCGGGA
* *
1942170 CCTCTTGAACGATGACAGGGGCCTTTTGAAC-AGT-GGAAGGGG
1 CCTCTTGAACGATGACAGGGGCCTCTTGAACGA-TAGG-AGGCG
* *
1942212 CCTCTTCG-ATGATGAGAGGGGCCTCTTGAACGATAGGAGGCG
1 CCTCTT-GAACGATGACAGGGGCCTCTTGAACGATAGGAGGCG
1942254 CCTCTTGAACGATGA
1 CCTCTTGAACGATGA
1942269 TAGGTGCATC
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
41 1 0.02
42 43 0.90
43 4 0.08
ACGTcount: A:0.23, C:0.21, G:0.33, T:0.22
Consensus pattern (42 bp):
CCTCTTGAACGATGACAGGGGCCTCTTGAACGATAGGAGGCG
Found at i:1942444 original size:4 final size:4
Alignment explanation
Indices: 1942412--1942465 Score: 72
Period size: 4 Copynumber: 13.5 Consensus size: 4
1942402 GGACCGTTGA
* * * *
1942412 AAAT AAAT TAAT ACAT AAAT CAGT AAAT AAAT AAAT AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
1942460 AAAT AA
1 AAAT AA
1942466 TGCTGAAAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
4 42 1.00
ACGTcount: A:0.69, C:0.04, G:0.02, T:0.26
Consensus pattern (4 bp):
AAAT
Found at i:1942867 original size:39 final size:39
Alignment explanation
Indices: 1942813--1942887 Score: 114
Period size: 39 Copynumber: 1.9 Consensus size: 39
1942803 GCCTATCATG
* * * *
1942813 AGGTGATGGTGGAGAAGAGGCTCGATGATGTGATGGAAT
1 AGGTGATGATAGAGAAGAGGCTCGATCAGGTGATGGAAT
1942852 AGGTGATGATAGAGAAGAGGCTCGATCAGGTGATGG
1 AGGTGATGATAGAGAAGAGGCTCGATCAGGTGATGG
1942888 CTTCGGGTGT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 32 1.00
ACGTcount: A:0.29, C:0.07, G:0.43, T:0.21
Consensus pattern (39 bp):
AGGTGATGATAGAGAAGAGGCTCGATCAGGTGATGGAAT
Found at i:1944444 original size:20 final size:20
Alignment explanation
Indices: 1944415--1944462 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
1944405 TTTCTTAAAC
*
1944415 TTAAATTCGCAACGCGAAAA
1 TTAAAATCGCAACGCGAAAA
*
1944435 TTAAAATCGCAACGCGAATA
1 TTAAAATCGCAACGCGAAAA
*
1944455 TGAAAATC
1 TTAAAATC
1944463 ATAGATTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.46, C:0.19, G:0.15, T:0.21
Consensus pattern (20 bp):
TTAAAATCGCAACGCGAAAA
Found at i:1944491 original size:20 final size:20
Alignment explanation
Indices: 1944466--1944527 Score: 97
Period size: 20 Copynumber: 3.1 Consensus size: 20
1944456 GAAAATCATA
* *
1944466 GATTTTTATTTTCGCGTTGC
1 GATTTTCATATTCGCGTTGC
*
1944486 GATTTTCATGTTCGCGTTGC
1 GATTTTCATATTCGCGTTGC
1944506 GATTTTCATATTCGCGTTGC
1 GATTTTCATATTCGCGTTGC
1944526 GA
1 GA
1944528 ATTTAAGTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.13, C:0.18, G:0.23, T:0.47
Consensus pattern (20 bp):
GATTTTCATATTCGCGTTGC
Found at i:1944876 original size:22 final size:22
Alignment explanation
Indices: 1944846--1944893 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
1944836 GATGGAGATA
*
1944846 GACGGATTTCGTCGGAGATGGG
1 GACGAATTTCGTCGGAGATGGG
*
1944868 GACGAATTTCGTTGGAGATGGG
1 GACGAATTTCGTCGGAGATGGG
1944890 GACG
1 GACG
1944894 GATGTCGCCG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.21, C:0.12, G:0.44, T:0.23
Consensus pattern (22 bp):
GACGAATTTCGTCGGAGATGGG
Found at i:1945076 original size:20 final size:20
Alignment explanation
Indices: 1945051--1945136 Score: 127
Period size: 20 Copynumber: 4.3 Consensus size: 20
1945041 TAAACGTGCT
1945051 TTGCGAATTTGACTTCTGTG
1 TTGCGAATTTGACTTCTGTG
*
1945071 TTGCGAATTTGACTTATGTG
1 TTGCGAATTTGACTTCTGTG
* * *
1945091 TTACGAATTTTACTTTTGTG
1 TTGCGAATTTGACTTCTGTG
*
1945111 TTGTGAATTTGACTTCTGTG
1 TTGCGAATTTGACTTCTGTG
1945131 TTGCGA
1 TTGCGA
1945137 TTTACAAATT
Statistics
Matches: 57, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 57 1.00
ACGTcount: A:0.17, C:0.12, G:0.23, T:0.48
Consensus pattern (20 bp):
TTGCGAATTTGACTTCTGTG
Found at i:1945546 original size:250 final size:250
Alignment explanation
Indices: 1945105--1945609 Score: 1010
Period size: 250 Copynumber: 2.0 Consensus size: 250
1945095 GAATTTTACT
1945105 TTTGTGTTGTGAATTTGACTTCTGTGTTGCGATTTACAAATTCACGTTGCGAATTTGGAAACTGG
1 TTTGTGTTGTGAATTTGACTTCTGTGTTGCGATTTACAAATTCACGTTGCGAATTTGGAAACTGG
1945170 GTTGCGAAATAGGAATTCGAATTGCGAATTTGTTGGTCATTTTCGCAAATCTAAAAAAAATTGGT
66 GTTGCGAAATAGGAATTCGAATTGCGAATTTGTTGGTCATTTTCGCAAATCTAAAAAAAATTGGT
1945235 TAAAATCGTATATTATAAGGCATTTTCTGTCACTGAGGTTATTTTCTCTTATAACAATCATGTCA
131 TAAAATCGTATATTATAAGGCATTTTCTGTCACTGAGGTTATTTTCTCTTATAACAATCATGTCA
1945300 TTTAATTTATAGATTGTTATAATCAAAAGACCCAATTATAATAAAGAAGCTAACA
196 TTTAATTTATAGATTGTTATAATCAAAAGACCCAATTATAATAAAGAAGCTAACA
1945355 TTTGTGTTGTGAATTTGACTTCTGTGTTGCGATTTACAAATTCACGTTGCGAATTTGGAAACTGG
1 TTTGTGTTGTGAATTTGACTTCTGTGTTGCGATTTACAAATTCACGTTGCGAATTTGGAAACTGG
1945420 GTTGCGAAATAGGAATTCGAATTGCGAATTTGTTGGTCATTTTCGCAAATCTAAAAAAAATTGGT
66 GTTGCGAAATAGGAATTCGAATTGCGAATTTGTTGGTCATTTTCGCAAATCTAAAAAAAATTGGT
1945485 TAAAATCGTATATTATAAGGCATTTTCTGTCACTGAGGTTATTTTCTCTTATAACAATCATGTCA
131 TAAAATCGTATATTATAAGGCATTTTCTGTCACTGAGGTTATTTTCTCTTATAACAATCATGTCA
1945550 TTTAATTTATAGATTGTTATAATCAAAAGACCCAATTATAATAAAGAAGCTAACA
196 TTTAATTTATAGATTGTTATAATCAAAAGACCCAATTATAATAAAGAAGCTAACA
1945605 TTTGT
1 TTTGT
1945610 TAAACACTTA
Statistics
Matches: 255, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
250 255 1.00
ACGTcount: A:0.32, C:0.12, G:0.17, T:0.38
Consensus pattern (250 bp):
TTTGTGTTGTGAATTTGACTTCTGTGTTGCGATTTACAAATTCACGTTGCGAATTTGGAAACTGG
GTTGCGAAATAGGAATTCGAATTGCGAATTTGTTGGTCATTTTCGCAAATCTAAAAAAAATTGGT
TAAAATCGTATATTATAAGGCATTTTCTGTCACTGAGGTTATTTTCTCTTATAACAATCATGTCA
TTTAATTTATAGATTGTTATAATCAAAAGACCCAATTATAATAAAGAAGCTAACA
Found at i:1948918 original size:141 final size:141
Alignment explanation
Indices: 1948664--1948945 Score: 555
Period size: 141 Copynumber: 2.0 Consensus size: 141
1948654 TAATGCTCAA
1948664 TAAGGTAACTCTTCTATCCTTTTGATTATGAATTTTAAACTAATGACTTGGAATTGTCAGGGTTG
1 TAAGGTAACTCTTCTATCCTTTTGATTATGAATTTTAAACTAATGACTTGGAATTGTCAGGGTTG
*
1948729 TGGCGGACACAGGTTTCCTTGGATTCTTAAGGAGTATACCCAGGAGCATAAACCAGATTTAATGG
66 TGGCGGACACAGGTTTCCTCGGATTCTTAAGGAGTATACCCAGGAGCATAAACCAGATTTAATGG
1948794 CGTTACTGGAG
131 CGTTACTGGAG
1948805 TAAGGTAACTCTTCTATCCTTTTGATTATGAATTTTAAACTAATGACTTGGAATTGTCAGGGTTG
1 TAAGGTAACTCTTCTATCCTTTTGATTATGAATTTTAAACTAATGACTTGGAATTGTCAGGGTTG
1948870 TGGCGGACACAGGTTTCCTCGGATTCTTAAGGAGTATACCCAGGAGCATAAACCAGATTTAATGG
66 TGGCGGACACAGGTTTCCTCGGATTCTTAAGGAGTATACCCAGGAGCATAAACCAGATTTAATGG
1948935 CGTTACTGGAG
131 CGTTACTGGAG
1948946 ACTTGTATTA
Statistics
Matches: 140, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
141 140 1.00
ACGTcount: A:0.28, C:0.16, G:0.23, T:0.33
Consensus pattern (141 bp):
TAAGGTAACTCTTCTATCCTTTTGATTATGAATTTTAAACTAATGACTTGGAATTGTCAGGGTTG
TGGCGGACACAGGTTTCCTCGGATTCTTAAGGAGTATACCCAGGAGCATAAACCAGATTTAATGG
CGTTACTGGAG
Found at i:1953198 original size:23 final size:24
Alignment explanation
Indices: 1953172--1953227 Score: 105
Period size: 23 Copynumber: 2.4 Consensus size: 24
1953162 GAACTGTTGT
1953172 TTTTTTTTCTTCGCATTCAA-CCC
1 TTTTTTTTCTTCGCATTCAACCCC
1953195 TTTTTTTTCTTCGCATTCAACCCC
1 TTTTTTTTCTTCGCATTCAACCCC
1953219 TTTTTTTTC
1 TTTTTTTTC
1953228 GATGGAGCAT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
23 20 0.62
24 12 0.38
ACGTcount: A:0.11, C:0.29, G:0.04, T:0.57
Consensus pattern (24 bp):
TTTTTTTTCTTCGCATTCAACCCC
Found at i:1958642 original size:178 final size:181
Alignment explanation
Indices: 1958303--1958659 Score: 661
Period size: 178 Copynumber: 2.0 Consensus size: 181
1958293 GGAAGAAACC
1958303 TGAAAATCCATCAAGACAACAATAATGAGACTTACCAGCTAATCGTTCTATCATTTGATCCATAA
1 TGAAAATCCATCAAGACAACAATAATGAGACTTACCAGCTAATCGTTCTATCATTTGATCCATAA
1958368 ATGGAAGAGGAAAATGGTCTTTCCGAGTTAAAGAATTCAACTTCCTGTAATCGATGCAGACTCTC
66 ATGGAAGAGGAAAATGGTCTTTCCGAGTTAAAGAATTCAACTTCCTGTAATCGATGCAGACTCTC
1958433 CATCCATTGAACTCGTGTTGGTACAAGTTCTCCTTCAGAATTTTCAACCCA
131 CATCCATTGAACTCGTGTTGGTACAAGTTCTCCTTCAGAATTTTCAACCCA
1958484 TGAAAATCCATCAAGACAACAATAATGAGACTTACCAG-TAATCGTTCT-TCATTTGATCCATAA
1 TGAAAATCCATCAAGACAACAATAATGAGACTTACCAGCTAATCGTTCTATCATTTGATCCATAA
1958547 ATGGAAGAGGAAAA-GGTCTTTCCGAGTTAAAGAATTCAACTTCCTGTAATCGATG-AGACTCTC
66 ATGGAAGAGGAAAATGGTCTTTCCGAGTTAAAGAATTCAACTTCCTGTAATCGATGCAGACTCTC
1958610 CATCCCATTTGAACTCGTGTTGGTAC-AGTTCTCCTTCAGAATTTTCAACC
131 CAT-CCA-TTGAACTCGTGTTGGTACAAGTTCTCCTTCAGAATTTTCAACC
1958660 ACAGTAACTC
Statistics
Matches: 174, Mismatches: 0, Indels: 7
0.96 0.00 0.04
Matches are distributed among these distances:
177 11 0.06
178 68 0.39
179 47 0.27
180 10 0.06
181 38 0.22
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.30
Consensus pattern (181 bp):
TGAAAATCCATCAAGACAACAATAATGAGACTTACCAGCTAATCGTTCTATCATTTGATCCATAA
ATGGAAGAGGAAAATGGTCTTTCCGAGTTAAAGAATTCAACTTCCTGTAATCGATGCAGACTCTC
CATCCATTGAACTCGTGTTGGTACAAGTTCTCCTTCAGAATTTTCAACCCA
Found at i:1963018 original size:96 final size:96
Alignment explanation
Indices: 1962854--1963045 Score: 384
Period size: 96 Copynumber: 2.0 Consensus size: 96
1962844 AATTGGTCCC
1962854 GAAACGTGAATGTATATCATAACAACTATCCCTATATAAAAAAATTAAGAACAATTCTTCAACAA
1 GAAACGTGAATGTATATCATAACAACTATCCCTATATAAAAAAATTAAGAACAATTCTTCAACAA
1962919 CTGAATACAACTATTATAAGTAATGTTCAAT
66 CTGAATACAACTATTATAAGTAATGTTCAAT
1962950 GAAACGTGAATGTATATCATAACAACTATCCCTATATAAAAAAATTAAGAACAATTCTTCAACAA
1 GAAACGTGAATGTATATCATAACAACTATCCCTATATAAAAAAATTAAGAACAATTCTTCAACAA
1963015 CTGAATACAACTATTATAAGTAATGTTCAAT
66 CTGAATACAACTATTATAAGTAATGTTCAAT
1963046 CATGCACTCC
Statistics
Matches: 96, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
96 96 1.00
ACGTcount: A:0.47, C:0.16, G:0.08, T:0.29
Consensus pattern (96 bp):
GAAACGTGAATGTATATCATAACAACTATCCCTATATAAAAAAATTAAGAACAATTCTTCAACAA
CTGAATACAACTATTATAAGTAATGTTCAAT
Found at i:1964099 original size:194 final size:192
Alignment explanation
Indices: 1963653--1964348 Score: 863
Period size: 194 Copynumber: 3.6 Consensus size: 192
1963643 CGTGTTATTT
* * * * **
1963653 AAAAAGTATCAACACAAATTTAAAAGTCTCGATACATTATGTGGACCTATTCTCTCATAAAACCG
1 AAAATGTATCGACACAAATCTAAAAGTGTCGATACATTATGTTCACCTATTCTCTCATAAAACCG
* * *
1963718 GTATATTTATATCGGTTACATTGTAAATTTACCTATTACGTTATAATTATCAGTTTCGATGTTTT
66 GTAAATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCAGTTTCGA----TT
* **
1963783 TGGGATCGATACAATTTCAAATGTATCGATACTTTTTGCTGCACCCCGTTTGGCATTCATTCTGG
127 TGGGATCGATACAATTTCAAATGTATCGACACTTTTTGCTG-ACAACGTTTGGCATTCATTCTGG
1963848 AC
191 AC
* * *
1963850 AAAATGTATTGACACAAATATAAAACGTGTCGATACATTATGTTCACCTATTTTCTCATAAAACC
1 AAAATGTATCGACACAAATCTAAAA-GTGTCGATACATTATGTTCACCTATTCTCTCATAAAACC
* *
1963915 GGTAAATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGA-ATGG
65 GGTAAATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCAGTTTCGATTTGG
1963979 GATCGATACAATTTCAAATGTATCGACACTTTTTGCCTGAACAACGTTTGGCATTCATTCTGGAC
130 GATCGATACAATTTCAAATGTATCGACACTTTTTG-CTG-ACAACGTTTGGCATTCATTCTGGAC
* *
1964044 AAAATGTATCGACACAAATCTAAAACGTGTCGATACATTATGTTCACCTATTTTCTTATAAAACC
1 AAAATGTATCGACACAAATCTAAAA-GTGTCGATACATTATGTTCACCTATTCTCTCATAAAACC
*
1964109 GGTAAATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCAGTTTTGATGTTT
65 GGTAAATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCAGTTTCGA----T
* * * * * * *
1964174 TTGGGATCAATAC--TTTAAAATGTATCAACACTTTATGCTG-CAACCCTTTGGCATTCATTTTA
126 TTGGGATCGATACAATTTCAAATGTATCGACACTTTTTGCTGACAA-CGTTTGGCATTCATTCTG
1964236 GAC
190 GAC
* * * ** *
1964239 AAAA-GTATCGACACAAATTCCACAA-TGTCAATACATTATGTAGACATATTCTCTCAT-AAA-C
1 AAAATGTATCGACACAAA-TCTAAAAGTGTCGATACATTATGTTCACCTATTCTCTCATAAAACC
* * *
1964300 -ATATAGTTATACC-GTTACATTGTAAATTTACCTATTACATTATAATTAT
65 GGTAAATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTAT
1964349 GGGTATAAAA
Statistics
Matches: 449, Mismatches: 41, Indels: 26
0.87 0.08 0.05
Matches are distributed among these distances:
189 36 0.08
190 10 0.02
191 1 0.00
192 3 0.01
193 63 0.14
194 162 0.36
195 27 0.06
196 3 0.01
197 42 0.09
198 91 0.20
199 11 0.02
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.37
Consensus pattern (192 bp):
AAAATGTATCGACACAAATCTAAAAGTGTCGATACATTATGTTCACCTATTCTCTCATAAAACCG
GTAAATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCAGTTTCGATTTGGG
ATCGATACAATTTCAAATGTATCGACACTTTTTGCTGACAACGTTTGGCATTCATTCTGGAC
Found at i:1966963 original size:26 final size:27
Alignment explanation
Indices: 1966927--1966984 Score: 109
Period size: 27 Copynumber: 2.2 Consensus size: 27
1966917 GTAAGCATTT
1966927 GTGAAACACTCTCGA-TCTACATCTAG
1 GTGAAACACTCTCGACTCTACATCTAG
1966953 GTGAAACACTCTCGACTCTACATCTAG
1 GTGAAACACTCTCGACTCTACATCTAG
1966980 GTGAA
1 GTGAA
1966985 TTGGATTATT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 15 0.48
27 16 0.52
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.26
Consensus pattern (27 bp):
GTGAAACACTCTCGACTCTACATCTAG
Found at i:1968111 original size:199 final size:199
Alignment explanation
Indices: 1967750--1969090 Score: 1386
Period size: 199 Copynumber: 6.8 Consensus size: 199
1967740 TGCGATTTTT
* * * * *
1967750 AAAATAGTATC-AACACAAATTT-AACAATTATCGATACTTTATGCT-GACCTATTTTCTCATAA
1 AAAA-AGTATCGAA-ACAAATTTCAA-AAGTGTCGATACATTATG-TAGACCTATTCTCACATAA
* *
1967812 AACCGGTATATTTATACCGGTTACATTGGAAATTTACCTATTACATTATAATTACT-GGTTTCGA
62 AACCGGTATATTTATACCGGTTACATTGAAAAATTACCTATTACATTATAATTA-TGGGTTTCGA
* * * * * * * *
1967876 TATTTTTGGGATCGACACTTTTTAAAAATATATCGACACTTAATGGGTGCACCCTTTTGGCATTT
126 TGTTTCTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCATTTTGGCA-TT
*
1967941 C-TTCTAGAC
190 CATTCTGGAC
* * * ** * *
1967950 AAAAAGTATCGAAACAAATTCCAAAAGTGTCGATACATTTTCTAGACCTATTCTCGTAGAAAACT
1 AAAAAGTATCGAAACAAATTTCAAAAGTGTCGATACATTATGTAGACCTATTCTCACATAAAACC
* * *
1968015 GGTATATTTATATCGGTTACATTGAAAAATTACCTATTACATTATAATCATGGGTTTTGATGTTT
66 GGTATATTTATACCGGTTACATTGAAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTT
** * *
1968080 CTGTAATCGATATTTTTTATAAATGTATCGACACTTTATGCGTGCACCATTTTTTGGGCATTTAT
131 CTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCA--TTTT-GGCATTCAT
1968145 TCTGGAC
193 TCTGGAC
* ** *
1968152 AAAATGTATCGATGCATAA-TTAAAAAGTGTCGATACATTATGTAGACCTATTCTCACATAAAAC
1 AAAAAGTATCGAAACA-AATTTCAAAAGTGTCGATACATTATGTAGACCTATTCTCACATAAAAC
* * *
1968216 CGATATATTTATACCGGTTACATT-ACAAAATTACCTATTACATTATAATTATGAG-TTCGATAT
65 CGGTATATTTATACCGGTTACATTGA-AAAATTACCTATTACATTATAATTATGGGTTTCGATGT
* * * *
1968279 CTCTGGGATCGATACTTTTTAAAAATGTATCAACACTTTATGCGTTCACCATTTTGGGCATTCAT
129 TTCTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCATTTT-GGCATTCAT
* *
1968344 TATGGATA
193 TCTGGA-C
* * *
1968352 AAAAAGTATC-AACACCAATTTCAAATA-TGTCGATACTTTATGTAGACATATTCTCACATAAAA
1 AAAAAGTATCGAA-ACAAATTTCAAA-AGTGTCGATACATTATGTAGACCTATTCTCACATAAAA
*
1968415 CCGGTATATTTATACCAGTTACATT-ACAAAATTACCTATTACA-T-TAATTATGGGTTTCGATG
64 CCGGTATATTTATACCGGTTACATTGA-AAAATTACCTATTACATTATAATTATGGGTTTCGATG
* * *
1968477 TCTCTGGGATCGACAC--TTTAT---T-TAT-GCACCCTTT-TG-G-G---CA--TT--C---C-
128 TTTCTGGGATCGATACTTTTTATAAATGTATCG-ACACTTTATGCGTGCACCATTTTGGCATTCA
*
1968521 TTCTAGAC
192 TTCTGGAC
* * * * * * * *
1968529 AAATAGTATCAACACAAATTCCATAAGTGTCAATACATTATGTAGACCTATTCTCTCATAAAACA
1 AAAAAGTATCGAAACAAATTTCAAAAGTGTCGATACATTATGTAGACCTATTCTCACATAAAACC
* ** * * *
1968594 AGTATAGTTT-TACCGGTTATGTTGAAAAAAATACATATTACATTATAATTATGAGTTTCGATGT
66 GGTATA-TTTATACCGGTTACATTG-AAAAATTACCTATTACATTATAATTATGGGTTTCGATGT
* * * * *
1968658 TTTTGAGATCGATACTTTTTATAAATGTATCAACACTTTATGCGTTCACCATTTTGGGATTCATT
129 TTCTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCATTTTGGCATTCATT
* *
1968723 TTGGAA
194 CTGGAC
* * ** *
1968729 AAAAAGTATCGACACCAATTTCAAAAGTGTTAATACATTATATAGACCTATTCTCACATAAAACC
1 AAAAAGTATCGAAACAAATTTCAAAAGTGTCGATACATTATGTAGACCTATTCTCACATAAAACC
* * **
1968794 GATATATTTATACCGGTTATATTTTAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTT
66 GGTATATTTATACCGGTTACATTGAAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTT
* * * *
1968859 CTGGGATCGATATTTTTTATAAATATATCGACACTTTATGCGTTCACCATTTTGGGATTCATTCT
131 CTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCATTTTGGCATTCATTCT
1968924 GGAC
196 GGAC
* * * * * **
1968928 AAAAAATATCGACACCAATTTCTAAAGTGTAGATACATTATGTAGACCTATTCTCACATAAAATT
1 AAAAAGTATCGAAACAAATTTCAAAAGTGTCGATACATTATGTAGACCTATTCTCACATAAAACC
* * * *
1968993 GGTATATTTATACCGGTTATATTAAAAAATTACATATTACATTATAATTATGGGTTTCAATGTTT
66 GGTATATTTATACCGGTTACATTGAAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTT
*
1969058 TTGGGATCGATAC-TTTTATAAATGTATCGACAC
131 CTGGGATCGATACTTTTTATAAATGTATCGACAC
1969091 ATCTGCTTAC
Statistics
Matches: 954, Mismatches: 142, Indels: 92
0.80 0.12 0.08
Matches are distributed among these distances:
176 1 0.00
177 66 0.07
178 23 0.02
179 3 0.00
180 29 0.03
182 6 0.01
185 3 0.00
186 9 0.01
187 4 0.00
188 1 0.00
191 1 0.00
192 4 0.00
193 9 0.01
194 3 0.00
197 4 0.00
198 30 0.03
199 413 0.43
200 175 0.18
201 58 0.06
202 110 0.12
203 2 0.00
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.38
Consensus pattern (199 bp):
AAAAAGTATCGAAACAAATTTCAAAAGTGTCGATACATTATGTAGACCTATTCTCACATAAAACC
GGTATATTTATACCGGTTACATTGAAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTT
CTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCATTTTGGCATTCATTCT
GGAC
Found at i:1968802 original size:377 final size:387
Alignment explanation
Indices: 1967795--1969090 Score: 1206
Period size: 377 Copynumber: 3.3 Consensus size: 387
1967785 ACTTTATGCT
* * * * ** * *
1967795 GACCTATTTTCTCATAAAACCGGTATATTTATACCGGTTACATTGGAAATTTACCTATTACATTA
1 GACCTATTCTCACATAAAA-CAGTATATTTATACCGGTTATATTAAAAAATTACATATTACATTA
* * * * * * *
1967860 TAATTACTG-GTTTCGATATTTTTGGGATCGACACTTTTTAAAAATATATCGACACTTAATGGGT
65 TAATTA-TGAGTTTCGATGTTTTTGGGATCGATACTTTTTATAAATGTATCAACACTTTATGCGT
* * * * * * * *
1967924 GCACCCTTTT-GGCATTTC-TTCTAGA-CAAAAAGTATCGAA-ACAAATTCCAAA-AGTGTCGAT
129 TCACCATTTTGGGCA-TTCATTATGGATAAAAAAGTATC-AACACCAATTTCAAATA-TGTCAAT
* * * ** * * * * *
1967984 ACATTTTCTAGACCTATTCTCGTAGAAAACTGGTATATTTATATCGGTTACATTGA-AAAATTAC
191 ACATTATATAGACATATTCTCACATAAAACCGATATATTTATACCAGTTACATT-ACAAAATTAC
* * * ** * * *
1968048 CTATTACATTATAATCATGGGTTTTGATGTTTCTGTAATCGATATTTTTTATAAATGTATCGACA
255 CTATTACATTATAATTATGGGTTTCGATGTCTCTGGGATCGACA-TCTTTAT--ATATATCG--A
* * ** * ** **
1968113 CTTTATGCGTGCACCATTTTTTGGGCATTTATTCTGGACAAAATGTATCGATGCATAATT-AAAA
315 C--TA----T-CACCA--TTTTGGG-ATTCATTCTAGACAAAAAATATCAACACA-AATTCCTAA
*
1968177 AGTGTCGATACATTATGTA
369 AGTGTCAATACATTATGTA
* * * *
1968196 GACCTATTCTCACATAAAACCGATATATTTATACCGGTTACATTACAAAATTACCTATTACATTA
1 GACCTATTCTCACATAAAACAG-TATATTTATACCGGTTATATTAAAAAATTACATATTACATTA
* * * *
1968261 TAATTATGAG-TTCGATATCTCTGGGATCGATACTTTTTAAAAATGTATCAACACTTTATGCGTT
65 TAATTATGAGTTTCGATGTTTTTGGGATCGATACTTTTTATAAATGTATCAACACTTTATGCGTT
* *
1968325 CACCATTTTGGGCATTCATTATGGATAAAAAAGTATCAACACCAATTTCAAATATGTCGATACTT
130 CACCATTTTGGGCATTCATTATGGATAAAAAAGTATCAACACCAATTTCAAATATGTCAATACAT
* *
1968390 TATGTAGACATATTCTCACATAAAACCGGTATATTTATACCAGTTACATTACAAAATTACCTATT
195 TATATAGACATATTCTCACATAAAACCGATATATTTATACCAGTTACATTACAAAATTACCTATT
1968455 ACA-T-TAATTATGGGTTTCGATGTCTCTGGGATCGACA-CTTTAT-T-TAT-G-C-A-C-CC-T
260 ACATTATAATTATGGGTTTCGATGTCTCTGGGATCGACATCTTTATATATATCGACTATCACCAT
* * *
1968509 TTTGGGCATTCCTTCTAGACAAATAGTATCAACACAAATTCC-ATAAGTGTCAATACATTATGTA
325 TTTGGG-ATTCATTCTAGACAAAAAATATCAACACAAATTCCTA-AAGTGTCAATACATTATGTA
* * *
1968573 GACCTATTCTCTCATAAAACAAGTATAGTTT-TACCGGTTATGTTGAAAAAAATACATATTACAT
1 GACCTATTCTCACATAAAAC-AGTATA-TTTATACCGGTTATATT-AAAAAATTACATATTACAT
*
1968637 TATAATTATGAGTTTCGATGTTTTTGAGATCGATACTTTTTATAAATGTATCAACACTTTATGCG
63 TATAATTATGAGTTTCGATGTTTTTGGGATCGATACTTTTTATAAATGTATCAACACTTTATGCG
* * *
1968702 TTCACCATTTTGGG-ATTCATTTTGGA-AAAAAAGTATCGACACCAATTTCAAA-AGTGTTAATA
128 TTCACCATTTTGGGCATTCATTATGGATAAAAAAGTATCAACACCAATTTCAAATA-TGTCAATA
* * * **
1968764 CATTATATAGACCTATTCTCACATAAAACCGATATATTTATACCGGTTATATTTTAAAATTACCT
192 CATTATATAGACATATTCTCACATAAAACCGATATATTTATACCAGTTACATTACAAAATTACCT
* * *
1968829 ATTACATTATAATTATGGGTTTCGATGTTTCTGGGATCGATATTTTTTATAAATATATCGACACT
257 ATTACATTATAATTATGGGTTTCGATGTCTCTGGGATCGACA-TCTTTAT--ATATATCG--AC-
* * * *
1968894 TTATGCGTTCACCATTTTGGGATTCATTCTGGACAAAAAATATCGACACCAATTTCTAAAGTGT-
316 -TA-----TCACCATTTTGGGATTCATTCTAGACAAAAAATATCAACACAAATTCCTAAAGTGTC
1968958 AGATACATTATGTA
375 A-ATACATTATGTA
**
1968972 GACCTATTCTCACATAAAATTGGTATATTTATACCGGTTATATTAAAAAATTACATATTACATTA
1 GACCTATTCTCACATAAAA-CAGTATATTTATACCGGTTATATTAAAAAATTACATATTACATTA
* * *
1969037 TAATTATGGGTTTCAATGTTTTTGGGATCGATAC-TTTTATAAATGTATCGACAC
65 TAATTATGAGTTTCGATGTTTTTGGGATCGATACTTTTTATAAATGTATCAACAC
1969091 ATCTGCTTAC
Statistics
Matches: 763, Mismatches: 90, Indels: 88
0.81 0.10 0.09
Matches are distributed among these distances:
376 6 0.01
377 176 0.23
378 44 0.06
379 92 0.12
380 2 0.00
381 6 0.01
384 1 0.00
385 3 0.00
386 1 0.00
387 1 0.00
389 1 0.00
390 1 0.00
392 1 0.00
393 1 0.00
394 3 0.00
395 1 0.00
397 19 0.02
398 61 0.08
399 83 0.11
400 96 0.13
401 76 0.10
402 87 0.11
403 1 0.00
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.38
Consensus pattern (387 bp):
GACCTATTCTCACATAAAACAGTATATTTATACCGGTTATATTAAAAAATTACATATTACATTAT
AATTATGAGTTTCGATGTTTTTGGGATCGATACTTTTTATAAATGTATCAACACTTTATGCGTTC
ACCATTTTGGGCATTCATTATGGATAAAAAAGTATCAACACCAATTTCAAATATGTCAATACATT
ATATAGACATATTCTCACATAAAACCGATATATTTATACCAGTTACATTACAAAATTACCTATTA
CATTATAATTATGGGTTTCGATGTCTCTGGGATCGACATCTTTATATATATCGACTATCACCATT
TTGGGATTCATTCTAGACAAAAAATATCAACACAAATTCCTAAAGTGTCAATACATTATGTA
Found at i:1971187 original size:25 final size:25
Alignment explanation
Indices: 1971159--1971215 Score: 80
Period size: 25 Copynumber: 2.3 Consensus size: 25
1971149 CCTCTCAACA
*
1971159 CCTCAACTT-CTTTCACCACTTCACC
1 CCTCAACTTCCTTT-ACCAATTCACC
*
1971184 CCTCAACTTCCTTTACGAATTCACC
1 CCTCAACTTCCTTTACCAATTCACC
1971209 CCTCAAC
1 CCTCAAC
1971216 ACCTTAACTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 25 0.86
26 4 0.14
ACGTcount: A:0.23, C:0.46, G:0.02, T:0.30
Consensus pattern (25 bp):
CCTCAACTTCCTTTACCAATTCACC
Found at i:1971325 original size:23 final size:21
Alignment explanation
Indices: 1971270--1971334 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
1971260 CCCCTTATGC
*
1971270 CTCTCAAGTGTCTCTTCGACT
1 CTCTCAAGTCTCTCTTCGACT
1971291 CTCTCAAGTCTCTCTTCGACT
1 CTCTCAAGTCTCTCTTCGACT
* *
1971312 CTCTCAAGTATCTCTTCAACT
1 CTCTCAAGTCTCTCTTCGACT
1971333 CT
1 CT
1971335 TGATTGTCTT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.17, C:0.35, G:0.09, T:0.38
Consensus pattern (21 bp):
CTCTCAAGTCTCTCTTCGACT
Found at i:1971437 original size:15 final size:15
Alignment explanation
Indices: 1971417--1971447 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1971407 ACTCTGTTTT
1971417 CTCTCACCATCATCC
1 CTCTCACCATCATCC
1971432 CTCTCACCATCATCC
1 CTCTCACCATCATCC
1971447 C
1 C
1971448 CCAATACAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.55, G:0.00, T:0.26
Consensus pattern (15 bp):
CTCTCACCATCATCC
Found at i:1974054 original size:182 final size:182
Alignment explanation
Indices: 1973746--1974601 Score: 1153
Period size: 182 Copynumber: 4.7 Consensus size: 182
1973736 TACGCGTACT
* * * * *
1973746 TATTAAAGTATCGAAACTTTCAATATATCCGGTAG-TGCTTTACCGGTTTTTTCATTTCAAGACC
1 TATTAAAGTATCGACACTTTCAATATATCCGGTCGCT-CTATACCGGTTTTGTCATTTAAAGACC
* ** *
1973810 GGTTTTGTCATATTTTTACCTGTTATATCGTTGTGGGCCGATACATTGCTATAAAGTATCGACAC
65 GATTTTGTCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTGTTATAAAGTATCGACAC
* *
1973875 TTTATAGGCGCTAACACTACTTCTCTTTTAAATTCACAAAGTGTCGATACTTA
130 TTTATAGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATACTTA
*
1973928 TATTAAAGTATCGACACTTTAAATATATCCGGTCGCTCTATACCGGTTTTGTCATTTAAAGACCG
1 TATTAAAGTATCGACACTTTCAATATATCCGGTCGCTCTATACCGGTTTTGTCATTTAAAGACCG
* * * *
1973993 ATTTTGTCATAATTTTACCTGTTATATTGTTTTGGATCGATACATTGTTATAAAATATCGACACT
66 ATTTTGTCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTGTTATAAAGTATCGACACT
* *
1974058 TTATGGGCGCTAAAACTGTTTCTCTTTTAAATTCACAAAGTGTCGATACTTA
131 TTATAGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATACTTA
* * * * * *
1974110 TATGAAAGTATCGACACTTTAAATATATTCGGTCGCTCTATACCGATTTTGTCCTTTAGAGACCG
1 TATTAAAGTATCGACACTTTCAATATATCCGGTCGCTCTATACCGGTTTTGTCATTTAAAGACCG
* * * * * * *
1974175 GTTTTGTCATATTTTTACATGTTATATCATTTTAGATTGATACATTGTTACAAAGTATCGACACT
66 ATTTTGTCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTGTTATAAAGTATCGACACT
* *
1974240 TTATGGGCGCTAAAACTGTTTCTCTTTTAAATTCACAAAGTGTCGATACTTA
131 TTATAGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATACTTA
* * *
1974292 TATTAAAGTATCGACACTTTCAATATATCCGGTCTCTCTATACCGGTTTTGTCCTTTAGAGACCG
1 TATTAAAGTATCGACACTTTCAATATATCCGGTCGCTCTATACCGGTTTTGTCATTTAAAGACCG
*
1974357 ATTTTGTCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTGTTATAAACTATCGACACT
66 ATTTTGTCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTGTTATAAAGTATCGACACT
* ** * * * *
1974422 TTATAGGCTCTGGAACTGCTTCTCTTTTAAATTCATAAATTATCAATACTTA
131 TTATAGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATACTTA
* * * * * * *
1974474 TATTAAAGTATCGAAACTTTCAATATATCCGGTACAACT-T-TATCGGTTTTGTCTTTTCAGGAT
1 TATTAAAGTATCGACACTTTCAATATATCCGGT-C-GCTCTATACCGGTTTTGTCATTTAAAGAC
* * * *
1974537 TGATTTTGTCATATTTTTACTTGTTATATTGATGTGGATCGATACAGTT-TTATAAAGTATCGAC
64 CGATTTTGTCATATTTTTACCTGTTATATCGTTGTGGATCGATACA-TTGTTATAAAGTATCGAC
1974601 A
128 A
1974602 TAAATCGCCA
Statistics
Matches: 603, Mismatches: 67, Indels: 8
0.89 0.10 0.01
Matches are distributed among these distances:
182 596 0.99
183 5 0.01
184 2 0.00
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.41
Consensus pattern (182 bp):
TATTAAAGTATCGACACTTTCAATATATCCGGTCGCTCTATACCGGTTTTGTCATTTAAAGACCG
ATTTTGTCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTGTTATAAAGTATCGACACT
TTATAGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATACTTA
Found at i:1979303 original size:463 final size:469
Alignment explanation
Indices: 1978424--1979363 Score: 1694
Period size: 463 Copynumber: 2.0 Consensus size: 469
1978414 ACTTTTAGGG
1978424 GAACCCAGCTTTTAGAGTCTAAACCATTTCCAGATTACCATTCGTCGGATTCTACTCGCTCGCAA
1 GAACCCAGCTTTTAGAGTCTAAACCATTTCCAGATTACCATTCGTCGGATTCTACTCGCTCGCAA
*
1978489 AGCGGAGTCCGGTTGTTTTCGACTTATCGCCGAATTGTAAGTTCTGTGTTTCTGTTAATTCTATT
66 AGCGGAGTCCGG-TG-TTTCGA-TTATCGCCGAATTGTAAGTTCCGTGTTTCTGTTAATTCTATT
* *
1978554 ATGTTTATGGGTACGTGCAGTTATGTGGATCCATGTTTTGATTGTTTGACAGCTTGATTTTGAGC
128 ATGTTTATGGGTACGTGCAGTTATGTGGATCCATATTTCGATTGTTTGACAGCTTGATTTTGAGC
*
1978619 TACTAGTATTCCATTTTTATCTGCTTTTTTAGCTACAGTTTGCAGTTTCAAGGCAATATTTTCAA
193 TACTAGTATTCCATTTTTATCTGCTTTTTTAGCTACAGTTTGCAGTTTCAAAGCAATATTTTCAA
1978684 CATATGCAACAAAAAATGACACTGAAAGTGATATACATTCTAGGATGATGGAAAAACAAAATAGG
258 CATATGCAACAAAAAATGACACTGAAAGTGATATACATTCTAGGATGATGGAAAAACAAAATAGG
1978749 GGAAGGGAAAAAAGAGATGAGCATCATAAAAATGAACCAAATAAGTATCTGATGTTAATGTTGTT
323 GGAAGGGAAAAAAGAGATGAGCATCATAAAAATGAACCAAATAAGTATCTGATGTTAATGTTGTT
*
1978814 ATCTATACGAAATAAGAACTTGATCTAGCAGTAAAAGGAAAAGCAGTAGGTTCAAGTTCCACAAT
388 ATCTATACGAAATAAGAACTTGATCTAGCAGTAAAAGGAAAAGCAGTAGGTTCAAGTCCCACAAT
1978879 GCACTCATGTGCAGGTC
453 GCACTCATGTGCAGGTC
* *
1978896 GAACTCAGCTTTTAGAGTCTAAACCATTTCCAGATTACCATTCGTTGGATTCTACTCGCTCGCAA
1 GAACCCAGCTTTTAGAGTCTAAACCATTTCCAGATTACCATTCGTCGGATTCTACTCGCTCGCAA
* *
1978961 AGCGGAGTCC-G-G-TT-G-TTATCGTCGACTTGTAAGTTCCGTGTTTCTGTTAATTCTATTATG
66 AGCGGAGTCCGGTGTTTCGATTATCGCCGAATTGTAAGTTCCGTGTTTCTGTTAATTCTATTATG
* *
1979021 TTTATGGGTACGTTCAGTTATGTGGATCTATATTTCGATTGTTTGACAGCTTGATTTTGAGCTAC
131 TTTATGGGTACGTGCAGTTATGTGGATCCATATTTCGATTGTTTGACAGCTTGATTTTGAGCTAC
1979086 TAGTATTCCATTTTTATCTGC-TTTTTAGCTACAGTTTGCAGTTTCAAAGCAATATTTTCAACAT
196 TAGTATTCCATTTTTATCTGCTTTTTTAGCTACAGTTTGCAGTTTCAAAGCAATATTTTCAACAT
1979150 ATGCAACAAAAAATGACACTGAAAGTGATATACATTCTAGGATGATGGAAAAACAAAATAGGGGA
261 ATGCAACAAAAAATGACACTGAAAGTGATATACATTCTAGGATGATGGAAAAACAAAATAGGGGA
1979215 AGGGAAAAAAGAGATGAGCATCATAAAAATGAACCAAATAAGTATCTGATGTTAATGTTGTTATC
326 AGGGAAAAAAGAGATGAGCATCATAAAAATGAACCAAATAAGTATCTGATGTTAATGTTGTTATC
*
1979280 TATACGAAATAAGAACTTGATCTAGCAGTAAAAGGAAAAGCAGTAGGTTCAAGTCCCACACTGCA
391 TATACGAAATAAGAACTTGATCTAGCAGTAAAAGGAAAAGCAGTAGGTTCAAGTCCCACAATGCA
*
1979345 CTCATGTGCAGGTT
456 CTCATGTGCAGGTC
1979359 GAACC
1 GAACC
1979364 GTAGTCGCTT
Statistics
Matches: 454, Mismatches: 14, Indels: 9
0.95 0.03 0.02
Matches are distributed among these distances:
463 252 0.56
464 124 0.27
466 1 0.00
467 2 0.00
469 1 0.00
471 1 0.00
472 73 0.16
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (469 bp):
GAACCCAGCTTTTAGAGTCTAAACCATTTCCAGATTACCATTCGTCGGATTCTACTCGCTCGCAA
AGCGGAGTCCGGTGTTTCGATTATCGCCGAATTGTAAGTTCCGTGTTTCTGTTAATTCTATTATG
TTTATGGGTACGTGCAGTTATGTGGATCCATATTTCGATTGTTTGACAGCTTGATTTTGAGCTAC
TAGTATTCCATTTTTATCTGCTTTTTTAGCTACAGTTTGCAGTTTCAAAGCAATATTTTCAACAT
ATGCAACAAAAAATGACACTGAAAGTGATATACATTCTAGGATGATGGAAAAACAAAATAGGGGA
AGGGAAAAAAGAGATGAGCATCATAAAAATGAACCAAATAAGTATCTGATGTTAATGTTGTTATC
TATACGAAATAAGAACTTGATCTAGCAGTAAAAGGAAAAGCAGTAGGTTCAAGTCCCACAATGCA
CTCATGTGCAGGTC
Found at i:1982314 original size:24 final size:24
Alignment explanation
Indices: 1982287--1982338 Score: 104
Period size: 24 Copynumber: 2.2 Consensus size: 24
1982277 GTATGATAAA
1982287 CTATATCATGTTACATTGCATATT
1 CTATATCATGTTACATTGCATATT
1982311 CTATATCATGTTACATTGCATATT
1 CTATATCATGTTACATTGCATATT
1982335 CTAT
1 CTAT
1982339 CTTACCTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.29, C:0.17, G:0.08, T:0.46
Consensus pattern (24 bp):
CTATATCATGTTACATTGCATATT
Found at i:1984424 original size:68 final size:68
Alignment explanation
Indices: 1984327--1984718 Score: 577
Period size: 68 Copynumber: 5.8 Consensus size: 68
1984317 TATTTAACCG
* * * *
1984327 TTCATATAACTGGCATAATTGACATCTTTCTGTCAAATGCACAGTTAGGCTTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
1984392 CCT
66 CCT
** * *
1984395 TTCATCTATTTGGCATAAATGACACCTTTCTATCAAATGCACAGTTAGGCTTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
1984460 CCT
66 CCT
* *
1984463 TTCATCTAACTGGCATAAATGACACCTTTATGTCGAATGCACAGTTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
1984528 CCT
66 CCT
* * * * * *
1984531 TTCATCAAACTGGCATAAATGACACATTTCTGTCAAATGCACAATTAGGCCACAAAGACTCTTAG
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
1984596 CCT
66 CCT
* * * *
1984599 TTCATCTAACTGGCATAAATGACACCTTTCTGTAAAATGCATATTTAGACCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
1984664 CCT
66 CCT
* * *
1984667 TTCATCTAACTGACATAAATGACACATTTCTGTCAAATGCACAATTAGGCCT
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATGCACAGTTAGGCCT
1984719 ATTAATATTT
Statistics
Matches: 289, Mismatches: 35, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
68 289 1.00
ACGTcount: A:0.32, C:0.24, G:0.15, T:0.30
Consensus pattern (68 bp):
TTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
CCT
Found at i:1985185 original size:59 final size:58
Alignment explanation
Indices: 1985058--1985274 Score: 294
Period size: 58 Copynumber: 3.7 Consensus size: 58
1985048 TTTCCCATAT
** *
1985058 GGAAATTCATACACTTAGTATGAATCTCTTAACGGTTTGCACACAAAGTGCCCAATAC
1 GGAAATTCATACACTTAGTATGAATCTCTTAACTTTTTGCACACGAAGTGCCCAATAC
* * ** *
1985116 AGAGATTCATACACTTAGTATGAATCTCTTAACATTTTTGCACACGAAGTGCTTAATAT
1 GGAAATTCATACACTTAGTATGAATCTCTTAAC-TTTTTGCACACGAAGTGCCCAATAC
* *
1985175 GGAAATTCATACACTTAGTATGAAGT-TCTTGACTTTTTACACACGAAGTGCCCAATAC
1 GGAAATTCATACACTTAGTATGAA-TCTCTTAACTTTTTGCACACGAAGTGCCCAATAC
* *
1985233 GGAAATTCATACACTTAGTATGGATTTCTTAAC-TTTTGCACA
1 GGAAATTCATACACTTAGTATGAATCTCTTAACTTTTTGCACA
1985275 GTTAGTGCCA
Statistics
Matches: 138, Mismatches: 18, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
57 9 0.07
58 81 0.59
59 47 0.34
60 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.33
Consensus pattern (58 bp):
GGAAATTCATACACTTAGTATGAATCTCTTAACTTTTTGCACACGAAGTGCCCAATAC
Found at i:1985188 original size:117 final size:115
Alignment explanation
Indices: 1985054--1985274 Score: 327
Period size: 117 Copynumber: 1.9 Consensus size: 115
1985044 CACATTTCCC
*
1985054 ATATGGAAATTCATACACTTAGTATGAA-TCTCTTAACGGTTTGCACACAAAGTGCCCAATACAG
1 ATATGGAAATTCATACACTTAGTATGAAGT-TCTTAACGGTTTACACACAAAGTGCCCAATACAG
*
1985118 AGATTCATACACTTAGTATGAATCTCTTAACATTTTTGCACACGAAGTGCTTA
65 AAATTCATACACTTAGTATGAATCTCTTAAC--TTTTGCACACGAAGTGCTTA
* ** * *
1985171 ATATGGAAATTCATACACTTAGTATGAAGTTCTTGACTTTTTACACACGAAGTGCCCAATACGGA
1 ATATGGAAATTCATACACTTAGTATGAAGTTCTTAACGGTTTACACACAAAGTGCCCAATACAGA
* *
1985236 AATTCATACACTTAGTATGGATTTCTTAACTTTTGCACA
66 AATTCATACACTTAGTATGAATCTCTTAACTTTTGCACA
1985275 GTTAGTGCCA
Statistics
Matches: 94, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
115 9 0.10
117 84 0.89
118 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.33
Consensus pattern (115 bp):
ATATGGAAATTCATACACTTAGTATGAAGTTCTTAACGGTTTACACACAAAGTGCCCAATACAGA
AATTCATACACTTAGTATGAATCTCTTAACTTTTGCACACGAAGTGCTTA
Found at i:1989990 original size:68 final size:68
Alignment explanation
Indices: 1989881--1990192 Score: 351
Period size: 68 Copynumber: 4.6 Consensus size: 68
1989871 TATTTAATCG
* * *
1989881 TTCATCTAACTGGCATAATTGACACCTTTCTATCAAATGCACAATTAGTCTTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATGCACAATTAGTCCTCAAAGGCACTTAG
*
1989946 CCA
66 CCT
* * * * *
1989949 TTCATCTATCTGGCATAAATGACACTTTTCTATCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATGCACAATTAGTCCTCAAAGGCACTTAG
1990014 CCT
66 CCT
* * * * * * *
1990017 TTCATCTAACTGGCATAAATGATACCTTTATGTCGAACGCACAGTTAGACCTCAAAGACACTTAG
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATGCACAATTAGTCCTCAAAGGCACTTAG
1990082 CCT
66 CCT
* * *** * *
1990085 TTTATCTTACTAATAAAAATGACACCTTTCTGTCAAATGCA-AAGTTA-TGCCTC-AAGGAACTT
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATGCACAA-TTAGT-CCTCAAAGGCACTT
*
1990147 AACCT
64 AGCCT
* *
1990152 TTCATCAAACTGGCATAAATGACACATTTCTGTCAAATGCA
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATGCA
1990193 TAGTTAGACC
Statistics
Matches: 203, Mismatches: 39, Indels: 5
0.82 0.16 0.02
Matches are distributed among these distances:
67 45 0.22
68 158 0.78
ACGTcount: A:0.33, C:0.24, G:0.13, T:0.30
Consensus pattern (68 bp):
TTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATGCACAATTAGTCCTCAAAGGCACTTAG
CCT
Found at i:1990125 original size:136 final size:135
Alignment explanation
Indices: 1989881--1990205 Score: 400
Period size: 136 Copynumber: 2.4 Consensus size: 135
1989871 TATTTAATCG
* * * * * *
1989881 TTCATCTAACTGGCATAATTGACACCTTTCTATCAAATGCACAATTAGTCTTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATGCACAGTTAGACCTCAAAGACACTTAG
** * * * *
1989946 CCATTCATCTATCTGGCATAAATGACACTTTTCTATCAAATGCACAGTTAGGCCTCAAAGGCACT
66 CCATTCATCTATCTAACAAAAATGACACCTTTCTATCAAATGCAAAGTTAGGCCTC-AAGGAACT
*
1990011 TAGCCT
130 TAACCT
* * * *
1990017 TTCATCTAACTGGCATAAATGATACCTTTATGTCGAACGCACAGTTAGACCTCAAAGACACTTAG
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATGCACAGTTAGACCTCAAAGACACTTAG
* * * * *
1990082 CCTTTTATCT-TACTAATAAAAATGACACCTTTCTGTCAAATGCAAAGTTATGCCTCAAGGAACT
66 CCATTCATCTAT-CTAACAAAAATGACACCTTTCTATCAAATGCAAAGTTAGGCCTCAAGGAACT
1990146 TAACCT
130 TAACCT
* * *
1990152 TTCATCAAACTGGCATAAATGACACATTTCTGTCAAATGCATAGTTAGACCTCA
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATGCACAGTTAGACCTCA
1990206 TGATACATGC
Statistics
Matches: 159, Mismatches: 29, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
135 60 0.38
136 99 0.62
ACGTcount: A:0.33, C:0.24, G:0.13, T:0.30
Consensus pattern (135 bp):
TTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATGCACAGTTAGACCTCAAAGACACTTAG
CCATTCATCTATCTAACAAAAATGACACCTTTCTATCAAATGCAAAGTTAGGCCTCAAGGAACTT
AACCT
Found at i:1995248 original size:23 final size:22
Alignment explanation
Indices: 1995210--1995252 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
1995200 CAATTCATTT
1995210 ATCTTTTCTTTATCTTGTTTTA
1 ATCTTTTCTTTATCTTGTTTTA
*
1995232 ATCTTATTTTTTATCTTGTTT
1 ATCTT-TTCTTTATCTTGTTT
1995253 CCAGCACCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.14, C:0.12, G:0.05, T:0.70
Consensus pattern (22 bp):
ATCTTTTCTTTATCTTGTTTTA
Found at i:1995512 original size:68 final size:68
Alignment explanation
Indices: 1995403--1995541 Score: 251
Period size: 68 Copynumber: 2.0 Consensus size: 68
1995393 TTCCCTATCA
* * *
1995403 CCTCAAAGGCACTTAGCCTTTCATCTAAGTGGCATAAATGACACATTTCTGTCAAATGCACAGTT
1 CCTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAAATGACACATTTCTATCAAAGGCACAGTT
1995468 AGG
66 AGG
1995471 CCTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAAATGACACATTTCTATCAAAGGCACAGTT
1 CCTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAAATGACACATTTCTATCAAAGGCACAGTT
1995536 AGG
66 AGG
1995539 CCT
1 CCT
1995542 ATTAATATTT
Statistics
Matches: 68, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
68 68 1.00
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.27
Consensus pattern (68 bp):
CCTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAAATGACACATTTCTATCAAAGGCACAGTT
AGG
Found at i:1995953 original size:58 final size:58
Alignment explanation
Indices: 1995864--1996123 Score: 342
Period size: 58 Copynumber: 4.5 Consensus size: 58
1995854 TTTTGTTTAT
* * * **
1995864 ACATAAATTTCCC-ATATGGAAATTCATACACTTAGTATGAATCTCTTAACGGTTTGC
1 ACATAAAGTGCCCAATACGGAAATTCATACACTTAGTATGAATCTCTTAACTTTTTGC
* *
1995921 ACATAAAGTGCCCAATACGGAAATTCATACACTAAGTATGAATTTCTTAACTTTTTGC
1 ACATAAAGTGCCCAATACGGAAATTCATACACTTAGTATGAATCTCTTAACTTTTTGC
* * *
1995979 ACATGAAGTGCCCAATACGAAAATTCCTACACTTAGTATGAATCTCTTAACATTTTTGC
1 ACATAAAGTGCCCAATACGGAAATTCATACACTTAGTATGAATCTCTTAAC-TTTTTGC
** * * * *
1996038 ACACGAAGTGCCCAATACGTAAATTCATACACTTAGTATGAATTTCTTGACTTTTTAC
1 ACATAAAGTGCCCAATACGGAAATTCATACACTTAGTATGAATCTCTTAACTTTTTGC
* *
1996096 ACACAAAGTGCCCAATACAGAAATTCAT
1 ACATAAAGTGCCCAATACGGAAATTCAT
1996124 GCACATATTT
Statistics
Matches: 180, Mismatches: 21, Indels: 3
0.88 0.10 0.01
Matches are distributed among these distances:
57 11 0.06
58 116 0.64
59 53 0.29
ACGTcount: A:0.35, C:0.21, G:0.12, T:0.32
Consensus pattern (58 bp):
ACATAAAGTGCCCAATACGGAAATTCATACACTTAGTATGAATCTCTTAACTTTTTGC
Found at i:1996091 original size:117 final size:117
Alignment explanation
Indices: 1995883--1996123 Score: 360
Period size: 117 Copynumber: 2.1 Consensus size: 117
1995873 TCCCATATGG
*
1995883 AAATTCATACACTTAGTATGAATCTCTTAACGGTTTGCACATAAAGTGCCCAATACGGAAATTCA
1 AAATTCATACACTTAGTATGAATCTCTTAACGGTTTGCACACAAAGTGCCCAATACGGAAATTCA
* **
1995948 TACACTAAGTATGAATTTCTTAACTTTTTGCACATGAAGTGCCCAATAC-GA
66 TACACTAAGTATGAATTTCTTAACTTTTTACACACAAAGTGCCCAATACAGA
* ** * *
1995999 AAATTCCTACACTTAGTATGAATCTCTTAACATTTTTGCACACGAAGTGCCCAATACGTAAATTC
1 AAATTCATACACTTAGTATGAATCTCTTAAC-GGTTTGCACACAAAGTGCCCAATACGGAAATTC
* *
1996064 ATACACTTAGTATGAATTTCTTGACTTTTTACACACAAAGTGCCCAATACAG-
65 ATACACTAAGTATGAATTTCTTAACTTTTTACACACAAAGTGCCCAATACAGA
1996116 AAATTCAT
1 AAATTCAT
1996124 GCACATATTT
Statistics
Matches: 111, Mismatches: 12, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
116 30 0.27
117 80 0.72
118 1 0.01
ACGTcount: A:0.35, C:0.21, G:0.12, T:0.32
Consensus pattern (117 bp):
AAATTCATACACTTAGTATGAATCTCTTAACGGTTTGCACACAAAGTGCCCAATACGGAAATTCA
TACACTAAGTATGAATTTCTTAACTTTTTACACACAAAGTGCCCAATACAGA
Found at i:1998480 original size:19 final size:19
Alignment explanation
Indices: 1998456--1998499 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
1998446 GTAAACTCTA
*
1998456 GTCAAAGTCAATATGTCAG
1 GTCAAAGTCAATAGGTCAG
*
1998475 GTCAAAGTCAATGGGTCAG
1 GTCAAAGTCAATAGGTCAG
1998494 GTCAAA
1 GTCAAA
1998500 CAGACCCGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.36, C:0.16, G:0.25, T:0.23
Consensus pattern (19 bp):
GTCAAAGTCAATAGGTCAG
Done.