Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold28
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: 2815568
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.30
Warning! 166732 characters in sequence are not A, C, G, or T
File 11 of 16
Found at i:1692508 original size:32 final size:32
Alignment explanation
Indices: 1692467--1692527 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
1692457 GCTAATTATG
*
1692467 TATCGATACAATACTTATGTATCGATACATTA
1 TATCGATACAAAACTTATGTATCGATACATTA
1692499 TATCGATACAAAACTTATGTATCGATACA
1 TATCGATACAAAACTTATGTATCGATACA
1692528 AATTGTTGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.39, C:0.16, G:0.10, T:0.34
Consensus pattern (32 bp):
TATCGATACAAAACTTATGTATCGATACATTA
Found at i:1692591 original size:21 final size:21
Alignment explanation
Indices: 1692565--1692641 Score: 93
Period size: 21 Copynumber: 3.7 Consensus size: 21
1692555 GTTGGGACCC
* *
1692565 TGTATCGATACATTTGTA-GAA
1 TGTATCGATACA-TTCTACAAA
* *
1692586 TGTATCAATACATTCCACAAA
1 TGTATCGATACATTCTACAAA
*
1692607 CGTATCGATACATTCTACAAA
1 TGTATCGATACATTCTACAAA
1692628 TGTATCGATACATT
1 TGTATCGATACATT
1692642 TGAATTTTTT
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 3 0.06
21 44 0.94
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.34
Consensus pattern (21 bp):
TGTATCGATACATTCTACAAA
Found at i:1693413 original size:20 final size:20
Alignment explanation
Indices: 1693388--1693465 Score: 77
Period size: 20 Copynumber: 3.9 Consensus size: 20
1693378 TTACAAGCCA
*
1693388 ATGTATCGATACATTTGGTC
1 ATGTATCGATACATTTGATC
* *
1693408 ATGTATCGATAC-TGTGCATT
1 ATGTATCGATACATTTG-ATC
* **
1693428 ATGTATCGATACATCTGAAG
1 ATGTATCGATACATTTGATC
*
1693448 GTGTATCGATACATTTGA
1 ATGTATCGATACATTTGA
1693466 GGGTTTTGAC
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
19 3 0.06
20 42 0.88
21 3 0.06
ACGTcount: A:0.28, C:0.14, G:0.21, T:0.37
Consensus pattern (20 bp):
ATGTATCGATACATTTGATC
Found at i:1695995 original size:51 final size:51
Alignment explanation
Indices: 1695928--1696034 Score: 196
Period size: 51 Copynumber: 2.1 Consensus size: 51
1695918 TACATCTGGG
1695928 TTTTCCAGATGTATCGATACATTGAATCAATGTATCAATACATTCTGGAAA
1 TTTTCCAGATGTATCGATACATTGAATCAATGTATCAATACATTCTGGAAA
* *
1695979 TTTTGCAGATGTATCGATACATTGAATCAATGTATCGATACATTCTGGAAA
1 TTTTCCAGATGTATCGATACATTGAATCAATGTATCAATACATTCTGGAAA
1696030 TTTTC
1 TTTTC
1696035 TAGAATTAAG
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
51 53 1.00
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (51 bp):
TTTTCCAGATGTATCGATACATTGAATCAATGTATCAATACATTCTGGAAA
Found at i:1701809 original size:241 final size:238
Alignment explanation
Indices: 1701364--1701824 Score: 592
Period size: 241 Copynumber: 1.9 Consensus size: 238
1701354 TCAAGGAATA
* * **** * *
1701364 AACCAAGAGGGGGGTGAATTGGTTCTTTTCGAATTTTTAGTGTTTTGAAGGTTTTTGAACACAGC
1 AACCAAGAGGGGGGTGAATTGCTTCTTTTCGAATTTTTAGGGTTTTGAACAAATTTGAACAAAAC
*
1701429 AATTCGAAATATGAAAGAAATTAAGGGAGAAAAGCTAGACACAAGGTTTATAGAGGTTCGGTCCA
66 AATTCGAAATA-GAAAGAAATTAAGGGAGAAAAGCTAGACACAAGATTTATAGAGGTTCGGTCCA
* * * * * *
1701494 ACTTCGTACCTACATCCTCTCTCCTTGATACTTCCTCATCGAGTGGTTATCCAATTCACTACTAG
130 ACTACGCACCTACATCCTCTCTCCTCGACACTTCCTCATCGAGTGATTACCCAATTCACTACTAG
1701559 AATTGATTACCTTTAAGGCAAAGGTGAAAGCTTATCAAGTAACG
195 AATTGATTACCTTTAAGGCAAAGGTGAAAGCTTATCAAGTAACG
*
1701603 AACCAAGAGGGGGGTGAATTGCTTCTTTTCGAA-TTTTCGGGTTTTGAACAAATTTGAAACAAAA
1 AACCAAGAGGGGGGTGAATTGCTTCTTTTCGAATTTTTAGGGTTTTGAACAAATTTG-AACAAAA
* *
1701667 CAATTCGAAAT-GAAAAGAGATT-AGGGAAGGAAAA-CTTGACACAAGATATTTATAGAGGTTCG
65 CAATTCGAAATAG-AAAGAAATTAAGGG-A-GAAAAGCTAGACACAAG--ATTTATAGAGGTTCG
* **
1701729 GTCCATAC-ACGGCACCTACGTCCTCTCTCCTCGACACTTCCTTGTCGAGTGATTACCCAATTCA
125 GTCCA-ACTAC-GCACCTACATCCTCTCTCCTCGACACTTCCTCATCGAGTGATTACCCAATTCA
*
1701793 CTAAC-CGAATTGATTACCTTTAAGGCAAAGGT
188 CT-ACTAGAATTGATTACCTTTAAGGCAAAGGT
1701825 ATAACCTTAC
Statistics
Matches: 191, Mismatches: 22, Indels: 16
0.83 0.10 0.07
Matches are distributed among these distances:
237 5 0.03
238 36 0.19
239 53 0.28
240 20 0.10
241 75 0.39
242 2 0.01
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (238 bp):
AACCAAGAGGGGGGTGAATTGCTTCTTTTCGAATTTTTAGGGTTTTGAACAAATTTGAACAAAAC
AATTCGAAATAGAAAGAAATTAAGGGAGAAAAGCTAGACACAAGATTTATAGAGGTTCGGTCCAA
CTACGCACCTACATCCTCTCTCCTCGACACTTCCTCATCGAGTGATTACCCAATTCACTACTAGA
ATTGATTACCTTTAAGGCAAAGGTGAAAGCTTATCAAGTAACG
Found at i:1702375 original size:13 final size:13
Alignment explanation
Indices: 1702357--1702382 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1702347 ATTTTTTTTG
1702357 TGTATCGATACAT
1 TGTATCGATACAT
1702370 TGTATCGATACAT
1 TGTATCGATACAT
1702383 ACTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1703320 original size:13 final size:13
Alignment explanation
Indices: 1703302--1703326 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1703292 ACATATGGTC
1703302 ATGTATCGATACA
1 ATGTATCGATACA
1703315 ATGTATCGATAC
1 ATGTATCGATAC
1703327 TGTGCATTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1703339 original size:33 final size:33
Alignment explanation
Indices: 1703280--1703347 Score: 93
Period size: 33 Copynumber: 2.1 Consensus size: 33
1703270 TGTTACAAGC
*
1703280 CAATGTATCGATACATATGGTCATGTATCGATA
1 CAATGTATCGATACATATGATCATGTATCGATA
* *
1703313 CAATGTATCGATAC-TGTGCATTATGTATCGATA
1 CAATGTATCGATACATATG-ATCATGTATCGATA
1703346 CA
1 CA
1703348 TCTGAAGGTG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
32 3 0.10
33 28 0.90
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (33 bp):
CAATGTATCGATACATATGATCATGTATCGATA
Found at i:1706219 original size:13 final size:13
Alignment explanation
Indices: 1706201--1706228 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1706191 CATTATTCAA
1706201 TGTATCGATACAT
1 TGTATCGATACAT
1706214 TGTATCGATACAT
1 TGTATCGATACAT
1706227 TG
1 TG
1706229 ATCTCTGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1706223 original size:33 final size:33
Alignment explanation
Indices: 1706181--1706247 Score: 102
Period size: 33 Copynumber: 2.0 Consensus size: 33
1706171 GCTAAGGAAA
1706181 TGTATCGATACATT-AT-TCAATGTATCGATACAT
1 TGTATCGATACATTGATCTC--TGTATCGATACAT
1706214 TGTATCGATACATTGATCTCTGTATCGATACAT
1 TGTATCGATACATTGATCTCTGTATCGATACAT
1706247 T
1 T
1706248 TGGGGAATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
33 28 0.88
34 2 0.06
35 2 0.06
ACGTcount: A:0.30, C:0.16, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATTGATCTCTGTATCGATACAT
Found at i:1713523 original size:20 final size:20
Alignment explanation
Indices: 1713475--1713533 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
1713465 TATAATGAGA
1713475 AATGTATCGATACAATTGTAAG
1 AATGTATCGATAC-ATT-TAAG
* **
1713497 CATGTATCGATACATTTACT
1 AATGTATCGATACATTTAAG
*
1713517 AATGTATCAATACATTT
1 AATGTATCGATACATTT
1713534 CCTTGGTAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
20 17 0.53
21 3 0.09
22 12 0.38
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.37
Consensus pattern (20 bp):
AATGTATCGATACATTTAAG
Found at i:1713816 original size:20 final size:21
Alignment explanation
Indices: 1713791--1713836 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
1713781 GTGGTCCTCT
* *
1713791 ATACATTCATTTA-TGTATCG
1 ATACATTCACTAATTGTATCG
1713811 ATACATTCACTAATTGTATCG
1 ATACATTCACTAATTGTATCG
1713832 ATACA
1 ATACA
1713837 AATTGTAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 11 0.48
21 12 0.52
ACGTcount: A:0.35, C:0.17, G:0.09, T:0.39
Consensus pattern (21 bp):
ATACATTCACTAATTGTATCG
Found at i:1719655 original size:2 final size:2
Alignment explanation
Indices: 1719613--1719637 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1719603 TAGTTGTCAC
1719613 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1719638 CACCGATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1721574 original size:14 final size:15
Alignment explanation
Indices: 1721549--1721590 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 15
1721539 AGGATAATTG
1721549 TTAAAAATAATTTTT
1 TTAAAAATAATTTTT
1721564 TTAAAAA-AA---TT
1 TTAAAAATAATTTTT
1721575 TTAAAAATAATTTTT
1 TTAAAAATAATTTTT
1721590 T
1 T
1721591 ATTTTTAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 8
0.74 0.00 0.26
Matches are distributed among these distances:
11 9 0.39
12 2 0.09
14 2 0.09
15 10 0.43
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TTAAAAATAATTTTT
Found at i:1721589 original size:13 final size:13
Alignment explanation
Indices: 1721542--1721589 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 13
1721532 ATTTTAGAGG
*
1721542 ATAATTGTTAAAA
1 ATAATTTTTAAAA
1721555 ATAATTTTTTTAAAA
1 ATAA--TTTTTAAAA
1721570 A-AA-TTTTAAAA
1 ATAATTTTTAAAA
1721581 ATAATTTTT
1 ATAATTTTT
1721590 TATTTTTAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
11 9 0.30
12 2 0.07
13 8 0.27
14 2 0.07
15 9 0.30
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (13 bp):
ATAATTTTTAAAA
Found at i:1721591 original size:14 final size:14
Alignment explanation
Indices: 1721549--1721591 Score: 56
Period size: 11 Copynumber: 3.2 Consensus size: 14
1721539 AGGATAATTG
1721549 TTAAAAATAATTTTT
1 TTAAAAATAA-TTTT
1721564 TTAAAAA-AA--TT
1 TTAAAAATAATTTT
1721575 TTAAAAATAATTTT
1 TTAAAAATAATTTT
1721589 TTA
1 TTA
1721592 TTTTTAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
11 9 0.36
12 2 0.08
14 7 0.28
15 7 0.28
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
TTAAAAATAATTTT
Found at i:1723477 original size:28 final size:28
Alignment explanation
Indices: 1723433--1723487 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
1723423 CAAATAAACA
1723433 ACATTGTCTCTACGATTACTTGATACTG
1 ACATTGTCTCTACGATTACTTGATACTG
* *
1723461 ACATTGTTTCTATGATTACTTGATACT
1 ACATTGTCTCTACGATTACTTGATACT
1723488 TTTCTTTCGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.25, C:0.18, G:0.13, T:0.44
Consensus pattern (28 bp):
ACATTGTCTCTACGATTACTTGATACTG
Found at i:1723724 original size:17 final size:17
Alignment explanation
Indices: 1723694--1723727 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
1723684 TAATTTTATT
1723694 TAAATTTAATTATAATA
1 TAAATTTAATTATAATA
1723711 TAAATATTAA-TATAATA
1 TAAAT-TTAATTATAATA
1723728 ATTATTAGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TAAATTTAATTATAATA
Found at i:1724777 original size:2 final size:2
Alignment explanation
Indices: 1724770--1724794 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1724760 CTCAGTAATC
1724770 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1724795 TTACATTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1726595 original size:18 final size:18
Alignment explanation
Indices: 1726572--1726620 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
1726562 ATCAATTTGT
1726572 TAAAATATTAATTAAATA
1 TAAAATATTAATTAAATA
1726590 TAAAAT-TATAA--AAATA
1 TAAAATAT-TAATTAAATA
1726606 TATAAA-ATTAATTAA
1 TA-AAATATTAATTAA
1726621 TTTTATATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 10
0.72 0.00 0.28
Matches are distributed among these distances:
16 10 0.38
17 5 0.19
18 11 0.42
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
TAAAATATTAATTAAATA
Found at i:1727112 original size:20 final size:20
Alignment explanation
Indices: 1727068--1727105 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1727058 ATTAAAATAT
*
1727068 AATATAATGTAAAAAATTTA
1 AATATAATATAAAAAATTTA
*
1727088 AATATAATATAAATAATT
1 AATATAATATAAAAAATT
1727106 AATATATTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (20 bp):
AATATAATATAAAAAATTTA
Found at i:1727134 original size:32 final size:32
Alignment explanation
Indices: 1727080--1727158 Score: 122
Period size: 32 Copynumber: 2.4 Consensus size: 32
1727070 TATAATGTAA
*
1727080 AAAATTTAAATATAATATAAATAATTAATATATT
1 AAAATTT--ATATAATACAAATAATTAATATATT
*
1727114 AAAATTTATATAATACAAATAATTAATTTATT
1 AAAATTTATATAATACAAATAATTAATATATT
1727146 AAAATTTATATAA
1 AAAATTTATATAA
1727159 ATATATAATA
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
32 36 0.84
34 7 0.16
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (32 bp):
AAAATTTATATAATACAAATAATTAATATATT
Found at i:1731098 original size:18 final size:18
Alignment explanation
Indices: 1731072--1731112 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
1731062 ACTGTTTTTA
*
1731072 TTGATCCTTTTTTACTAT
1 TTGACCCTTTTTTACTAT
1731090 TTGACCCTTTTTTACTAT
1 TTGACCCTTTTTTACTAT
1731108 TTGAC
1 TTGAC
1731113 TTTCGATCCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.17, C:0.20, G:0.07, T:0.56
Consensus pattern (18 bp):
TTGACCCTTTTTTACTAT
Found at i:1733266 original size:3 final size:3
Alignment explanation
Indices: 1733258--1733291 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
1733248 TCCTTTTTAT
* *
1733258 TAA TAA TAA TAA TAA TAA TAA CAA TGA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1733292 TATTAGAAGG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:1743557 original size:23 final size:22
Alignment explanation
Indices: 1743525--1743585 Score: 81
Period size: 20 Copynumber: 2.8 Consensus size: 22
1743515 TTTTAAAAGA
*
1743525 TAATTGTTAAAAATAATTTTTT
1 TAATTTTTAAAAATAATTTTTT
*
1743547 TAAATTTTTAAAGATAA-TTTTT
1 T-AATTTTTAAAAATAATTTTTT
1743569 T-ATTTTTAAAAATAATT
1 TAATTTTTAAAAATAATT
1743586 ATTGATCGTA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
20 13 0.38
21 1 0.03
22 7 0.21
23 13 0.38
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (22 bp):
TAATTTTTAAAAATAATTTTTT
Found at i:1745454 original size:28 final size:28
Alignment explanation
Indices: 1745410--1745464 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
1745400 CAAATAAACA
1745410 ACATTGTTTCTACGATTACTTGATACTG
1 ACATTGTTTCTACGATTACTTGATACTG
*
1745438 ACATTGTTTCTATGATTACTTGATACT
1 ACATTGTTTCTACGATTACTTGATACT
1745465 TTTCTTTCGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.25, C:0.16, G:0.13, T:0.45
Consensus pattern (28 bp):
ACATTGTTTCTACGATTACTTGATACTG
Found at i:1746755 original size:2 final size:2
Alignment explanation
Indices: 1746748--1746772 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1746738 CTCAGTAATC
1746748 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1746773 TTACATTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1748577 original size:18 final size:18
Alignment explanation
Indices: 1748554--1748602 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
1748544 ATCAATTTGT
1748554 TAAAATATTAATTAAATA
1 TAAAATATTAATTAAATA
1748572 TAAAAT-TATAA--AAATA
1 TAAAATAT-TAATTAAATA
1748588 TATAAA-ATTAATTAA
1 TA-AAATATTAATTAA
1748603 TTTTATATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 10
0.72 0.00 0.28
Matches are distributed among these distances:
16 10 0.38
17 5 0.19
18 11 0.42
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
TAAAATATTAATTAAATA
Found at i:1749057 original size:5 final size:5
Alignment explanation
Indices: 1749047--1749179 Score: 54
Period size: 5 Copynumber: 28.4 Consensus size: 5
1749037 TTATTATTAA
* * *
1749047 AATAT AATAT AATGT AA-AA AATTT AAATAT AATAT AA-AT AAT-T AATAT
1 AATAT AATAT AATAT AATAT AATAT -AATAT AATAT AATAT AATAT AATAT
* * * * * * *
1749095 ATTAA AAT-T TATAT AATAT AA-AT AAT-T AATTT ATTAA AAT-T TATAT
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
* * *
1749141 AA-AT -ATAT AATAT --TTT AATTT AATTAT ATTAT AATAT AA
1 AATAT AATAT AATAT AATAT AATAT AA-TAT AATAT AATAT AA
1749180 AAATATATAA
Statistics
Matches: 92, Mismatches: 23, Indels: 26
0.65 0.16 0.18
Matches are distributed among these distances:
3 3 0.03
4 26 0.28
5 56 0.61
6 7 0.08
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (5 bp):
AATAT
Found at i:1749114 original size:32 final size:32
Alignment explanation
Indices: 1749064--1749152 Score: 133
Period size: 32 Copynumber: 2.7 Consensus size: 32
1749054 TATAATGTAA
1749064 AAAATTTAAATATAATATAAATAATTAATATATT
1 AAAATTT--ATATAATATAAATAATTAATATATT
*
1749098 AAAATTTATATAATATAAATAATTAATTTATT
1 AAAATTTATATAATATAAATAATTAATATATT
1749130 AAAATTTATATAAATATATAATA
1 AAAATTTATAT-AATATA-AATA
1749153 TTTTAATTTA
Statistics
Matches: 52, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
32 35 0.67
33 6 0.12
34 11 0.21
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (32 bp):
AAAATTTATATAATATAAATAATTAATATATT
Found at i:1749118 original size:25 final size:26
Alignment explanation
Indices: 1749041--1749123 Score: 82
Period size: 25 Copynumber: 3.2 Consensus size: 26
1749031 ATTTTTTTAT
*
1749041 TATTAAAATATAATATAATGTAAA-A
1 TATTAAAATATAATATAATATAAATA
* * *
1749066 AATTTAAATATAATATAAATAATTAATA
1 TATTAAAATATAATAT-AAT-ATAAATA
*
1749094 TATTAAAAT-TTATATAATATAAATA
1 TATTAAAATATAATATAATATAAATA
1749119 -ATTAA
1 TATTAA
1749124 TTTATTAAAA
Statistics
Matches: 47, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
24 5 0.11
25 20 0.43
26 6 0.13
27 8 0.17
28 8 0.17
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (26 bp):
TATTAAAATATAATATAATATAAATA
Found at i:1750490 original size:20 final size:20
Alignment explanation
Indices: 1750465--1750518 Score: 83
Period size: 20 Copynumber: 2.7 Consensus size: 20
1750455 GTTATAAGCA
*
1750465 ATGTATCGATACAAT-TCATC
1 ATGTATCGATACAATAT-ACC
1750485 ATGTATCGATACAATATACC
1 ATGTATCGATACAATATACC
1750505 ATGTATCGATACAA
1 ATGTATCGATACAA
1750519 ACAGTGGTAG
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 31 0.97
21 1 0.03
ACGTcount: A:0.39, C:0.19, G:0.11, T:0.31
Consensus pattern (20 bp):
ATGTATCGATACAATATACC
Found at i:1750573 original size:20 final size:20
Alignment explanation
Indices: 1750548--1750601 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 20
1750538 TGCCAGTTTT
**
1750548 ATGTATCGATACAATTGTAC
1 ATGTATCGATACAATTAAAC
1750568 ATGTATCGATACAA-TAAAC
1 ATGTATCGATACAATTAAAC
*
1750587 ATGTATCAATACAAT
1 ATGTATCGATACAAT
1750602 GTATCGATAC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
19 16 0.53
20 14 0.47
ACGTcount: A:0.43, C:0.15, G:0.11, T:0.31
Consensus pattern (20 bp):
ATGTATCGATACAATTAAAC
Found at i:1751230 original size:22 final size:22
Alignment explanation
Indices: 1751205--1751246 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
1751195 AGATAAACAT
1751205 ATTTCTCCCCCTTTATCAAAGC
1 ATTTCTCCCCCTTTATCAAAGC
*
1751227 ATTTCTCCCTCTTTATCAAA
1 ATTTCTCCCCCTTTATCAAA
1751247 AAAAAATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.24, C:0.33, G:0.02, T:0.40
Consensus pattern (22 bp):
ATTTCTCCCCCTTTATCAAAGC
Found at i:1753254 original size:22 final size:20
Alignment explanation
Indices: 1753214--1753254 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
1753204 CTATAGACCC
*
1753214 TAATTCATATCAAACAAATA
1 TAATTCATAACAAACAAATA
1753234 TAATTCATTAACACAACAAAT
1 TAATTCA-TAACA-AACAAAT
1753255 TTAAACACCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
21 4 0.22
22 7 0.39
ACGTcount: A:0.54, C:0.17, G:0.00, T:0.29
Consensus pattern (20 bp):
TAATTCATAACAAACAAATA
Found at i:1759236 original size:19 final size:20
Alignment explanation
Indices: 1759199--1759236 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1759189 TCCCTAGGCC
1759199 ATGTATCGATACAATTGATA
1 ATGTATCGATACAATTGATA
1759219 ATGTATCGATAC-ATTGAT
1 ATGTATCGATACAATTGAT
1759237 TTGAAATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.37
Consensus pattern (20 bp):
ATGTATCGATACAATTGATA
Found at i:1759296 original size:20 final size:20
Alignment explanation
Indices: 1759271--1759324 Score: 83
Period size: 20 Copynumber: 2.7 Consensus size: 20
1759261 GTTATAAGCA
*
1759271 ATGTATCGATACAAT-TCATC
1 ATGTATCGATACAATGT-ACC
1759291 ATGTATCGATACAATGTACC
1 ATGTATCGATACAATGTACC
1759311 ATGTATCGATACAA
1 ATGTATCGATACAA
1759325 ACAGTGGTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 31 0.97
21 1 0.03
ACGTcount: A:0.37, C:0.19, G:0.13, T:0.31
Consensus pattern (20 bp):
ATGTATCGATACAATGTACC
Found at i:1760536 original size:32 final size:33
Alignment explanation
Indices: 1760500--1760563 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
1760490 AATTTTAAGG
* *
1760500 TGTATCGATACTATG-AACATGTATTGATACAA
1 TGTATCGATACTAAGTAACATGTATCGATACAA
*
1760532 TGTATCGATACTAAGTAATATGTATCGATACA
1 TGTATCGATACTAAGTAACATGTATCGATACA
1760564 TCTGGGTATG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 14 0.50
33 14 0.50
ACGTcount: A:0.38, C:0.12, G:0.16, T:0.34
Consensus pattern (33 bp):
TGTATCGATACTAAGTAACATGTATCGATACAA
Found at i:1761602 original size:12 final size:12
Alignment explanation
Indices: 1761585--1761619 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
1761575 AGTTCTAGTA
*
1761585 TATGACTACTCC
1 TATGACTAATCC
1761597 TATGACTAATCC
1 TATGACTAATCC
*
1761609 TATGACAAATC
1 TATGACTAATC
1761620 GTCACTCAGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.34, C:0.26, G:0.09, T:0.31
Consensus pattern (12 bp):
TATGACTAATCC
Found at i:1765506 original size:13 final size:13
Alignment explanation
Indices: 1765488--1765514 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1765478 ACATTATGCT
1765488 TTGTATCGATACA
1 TTGTATCGATACA
1765501 TTGTATCGATACA
1 TTGTATCGATACA
1765514 T
1 T
1765515 GGATAATTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1767240 original size:18 final size:18
Alignment explanation
Indices: 1767217--1767251 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1767207 AGTCAACCAT
1767217 TAATGATGATGAAGATGA
1 TAATGATGATGAAGATGA
*
1767235 TAATGATGATGATGATG
1 TAATGATGATGAAGATG
1767252 GTGACTCGGA
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:0.40, C:0.00, G:0.29, T:0.31
Consensus pattern (18 bp):
TAATGATGATGAAGATGA
Found at i:1768094 original size:13 final size:13
Alignment explanation
Indices: 1768076--1768101 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1768066 CATTTTTTGG
1768076 TGTATCGATACAT
1 TGTATCGATACAT
1768089 TGTATCGATACAT
1 TGTATCGATACAT
1768102 ACTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1768116 original size:32 final size:33
Alignment explanation
Indices: 1768056--1768119 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
1768046 TACAAGCTAA
**
1768056 TGTATCGATACATTTTTTGGTGTATCGATACAT
1 TGTATCGATACATACTTTGGTGTATCGATACAT
1768089 TGTATCGATACATACTTT-GTGTATCGATACA
1 TGTATCGATACATACTTTGGTGTATCGATACA
1768120 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 13 0.45
33 16 0.55
ACGTcount: A:0.27, C:0.14, G:0.17, T:0.42
Consensus pattern (33 bp):
TGTATCGATACATACTTTGGTGTATCGATACAT
Found at i:1772662 original size:20 final size:19
Alignment explanation
Indices: 1772634--1772708 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 19
1772624 TTTTACCCAG
1772634 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTT-A
* * *
1772654 ATATATCGATACATGTATGA
1 ATGTATCGATACAT-TTTTA
*
1772674 ATGTATCGATATATTCTTTA
1 ATGTATCGATACATT-TTTA
1772694 ATGTATCGATACATT
1 ATGTATCGATACATT
1772709 ATATCTTTTT
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
19 1 0.02
20 42 0.93
21 2 0.04
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.43
Consensus pattern (19 bp):
ATGTATCGATACATTTTTA
Found at i:1774079 original size:32 final size:33
Alignment explanation
Indices: 1774038--1774105 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
1774028 CCTTAACTGT
1774038 TTGTATCGATACAT-A-CAAGATGTATCAATACA
1 TTGTATCGATACATGACCAA-ATGTATCAATACA
*
1774070 TTGTATCGATACATGACCAAATGTATCGATACA
1 TTGTATCGATACATGACCAAATGTATCAATACA
1774103 TTG
1 TTG
1774106 GCTTGTAACG
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
32 14 0.42
33 16 0.48
34 3 0.09
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.32
Consensus pattern (33 bp):
TTGTATCGATACATGACCAAATGTATCAATACA
Found at i:1780264 original size:13 final size:13
Alignment explanation
Indices: 1780246--1780270 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1780236 CAACATTCTT
1780246 TGTATCGATACAG
1 TGTATCGATACAG
1780259 TGTATCGATACA
1 TGTATCGATACA
1780271 AAGGGTTTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:1782135 original size:24 final size:24
Alignment explanation
Indices: 1782103--1782151 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
1782093 TGAGGAAACA
*
1782103 TGTGATTAAAGGAAATTGTTTTAT
1 TGTGATTAAAGGAAATTATTTTAT
1782127 TGTGATTAAAGGAAATTATTTTAT
1 TGTGATTAAAGGAAATTATTTTAT
1782151 T
1 T
1782152 AAGGGGGAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.35, C:0.00, G:0.18, T:0.47
Consensus pattern (24 bp):
TGTGATTAAAGGAAATTATTTTAT
Found at i:1782832 original size:13 final size:13
Alignment explanation
Indices: 1782814--1782839 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1782804 ACATACAAGA
1782814 TGTATCGATACAT
1 TGTATCGATACAT
1782827 TGTATCGATACAT
1 TGTATCGATACAT
1782840 GACCAAATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1782855 original size:33 final size:32
Alignment explanation
Indices: 1782794--1782861 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 32
1782784 CCTTAACTGT
1782794 TTGTATCGATACATACAAGATGTATCGATACA
1 TTGTATCGATACATACAAGATGTATCGATACA
1782826 TTGTATCGATACATGACCAA-ATGTATCGATACA
1 TTGTATCGATACAT-A-CAAGATGTATCGATACA
1782859 TTG
1 TTG
1782862 GCTTGCAATG
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
32 14 0.41
33 17 0.50
34 3 0.09
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.32
Consensus pattern (32 bp):
TTGTATCGATACATACAAGATGTATCGATACA
Found at i:1797883 original size:28 final size:28
Alignment explanation
Indices: 1797843--1799056 Score: 1109
Period size: 28 Copynumber: 42.4 Consensus size: 28
1797833 TGTTCATCCA
*
1797843 TTTCAAAGCCCACAAGTTAGTGGCACTC
1 TTTCAAAGCCCACAAGTCAGTGGCACTC
*
1797871 TTTCAAAGCCCACAAGTCAATGGCACTC
1 TTTCAAAGCCCACAAGTCAGTGGCACTC
* *
1797899 TTTCAAAGCCCATAAGTCAGTTGCACTC
1 TTTCAAAGCCCACAAGTCAGTGGCACTC
* * * * * *
1797927 TTTTCAAAACCAATAAGTTAGTGGCATTT
1 -TTTCAAAGCCCACAAGTCAGTGGCACTC
1797956 TTTCAAAGCCCACAAGTCAGTGGCACTCC
1 TTTCAAAGCCCACAAGTCAGTGGCACT-C
*
1797985 TTTCAAAGCCCACACAAGTCGGTGGCAACTC
1 TTTCAAAG-CC-CACAAGTCAGTGGC-ACTC
1798016 ATTTCAAAGCCCACAAGTCAGTGGCA-TCC
1 -TTTCAAAGCCCACAAGTCAGTGGCACT-C
* *
1798045 TTTCGAAGCCCACGCAAGTCAGTGGCACCC
1 TTTCAAAGCCCA--CAAGTCAGTGGCACTC
1798075 TTT-AAAGCCCACACAAGTCAGTGGCAC-C
1 TTTCAAAG-CC-CACAAGTCAGTGGCACTC
* *
1798103 TTTTC-AAGCCCACGAGTTAGTGGCACTC
1 -TTTCAAAGCCCACAAGTCAGTGGCACTC
1798131 TTTCAAAGCCCACAAGTCAAGTGGCA-TCC
1 TTTCAAAGCCCACAAGTC-AGTGGCACT-C
*
1798160 TTTCAAAGCCCACGCATGTCAGTGGCAC-C
1 TTTCAAAGCCCA--CAAGTCAGTGGCACTC
* *
1798189 TTTTTAAAGCCCACGCAAGTCAGTGGCACCC
1 -TTTCAAAGCCCA--CAAGTCAGTGGCACTC
*
1798220 TTTTAAAGCCCACACAAGTCAGTGGCAC-C
1 TTTCAAAG-CC-CACAAGTCAGTGGCACTC
* *
1798249 GTTTTAAAGCCCATGCAAGTCAGTGGCACCC
1 -TTTCAAAGCCCA--CAAGTCAGTGGCACTC
*
1798280 TTTTAAAGCCCACGCAAGTCAGTGGCACTCC
1 TTTCAAAGCCCA--CAAGTCAGTGGCACT-C
* ** * *
1798311 TTTCAAAGTCCATGAGTGAGTGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCACTC
* **
1798339 TTTTAAAGCCCATGAGTCAAGTGGCA-TC
1 TTTCAAAGCCCACAAGTC-AGTGGCACTC
** *
1798367 TTTTTAAGCCCACGAA-TCAGT-GCACTT
1 TTTCAAAGCCCAC-AAGTCAGTGGCACTC
* * *
1798394 TTTC-AAGCCCACGAGTTAGTGGCACTT
1 TTTCAAAGCCCACAAGTCAGTGGCACTC
*
1798421 TTTCAAAGCCCACAAGTCAGTGGCACTT
1 TTTCAAAGCCCACAAGTCAGTGGCACTC
1798449 TTTCAAAGCCCACAAGTCAGTGGCA-TCC
1 TTTCAAAGCCCACAAGTCAGTGGCACT-C
1798477 TTTCAAAGCCCACAAGTCAGTGGCAC-C
1 TTTCAAAGCCCACAAGTCAGTGGCACTC
* * *
1798504 TTTTTAAAGTCCACAAGTTAGTGGCACTC
1 -TTTCAAAGCCCACAAGTCAGTGGCACTC
* * * *
1798533 TTTTCAAAGACCATAAGCCAGTGGTAACTC
1 -TTTCAAAGCCCACAAGTCAGTGG-CACTC
* *
1798563 TTTTC-AAGCCCACGAGTTAGTGGCACTC
1 -TTTCAAAGCCCACAAGTCAGTGGCACTC
*
1798591 TTTCAAAGCCCACAAGGCAGTGGCA-TCC
1 TTTCAAAGCCCACAAGTCAGTGGCACT-C
*
1798619 TTTCAAAGCCCACGCAAGTCAGTGGCACCC
1 TTTCAAAGCCCA--CAAGTCAGTGGCACTC
1798649 TTT-AAAGCCCACACAAGTCAGTGGCACAT-
1 TTTCAAAG-CC-CACAAGTCAGTGGCAC-TC
*
1798678 TTTC-AAGCCCA-AGAGTCAATGGCACTC
1 TTTCAAAGCCCACA-AGTCAGTGGCACTC
* *
1798705 TTTCAAAGCCCATAAGTCGGT-GCA-TCC
1 TTTCAAAGCCCACAAGTCAGTGGCACT-C
* *
1798732 TTTCAAA-CACGCAAGTCAGTGGCAAC-C
1 TTTCAAAGCCCACAAGTCAGTGGC-ACTC
*
1798759 TTTTAAAGCCCACGCAAGTCAGTGGCAC-C
1 TTTCAAAGCCCA--CAAGTCAGTGGCACTC
*
1798788 TTTTTAAAGCCCACGCAAGTCAGTGGCACTCC
1 -TTTCAAAGCCCA--CAAGTCAGTGGCACT-C
** *
1798820 TTTCAAAGCCCATGAGTCAGTGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCACTC
** *
1798848 TTTCAAAGCCCATGAGACAGTGGCA-TC
1 TTTCAAAGCCCACAAGTCAGTGGCACTC
** * *
1798875 TTTTTAAGCCCACGAGTCAGTGGCACTT
1 TTTCAAAGCCCACAAGTCAGTGGCACTC
* *
1798903 TTTC-AAGCCCACGAGTCAGTGGCACTT
1 TTTCAAAGCCCACAAGTCAGTGGCACTC
1798930 TTTCAAAGCCCACAAGTCAGTGGCA-TCC
1 TTTCAAAGCCCACAAGTCAGTGGCACT-C
1798958 TTTCAAAGCCCACAAGTCAGTGGCAC-C
1 TTTCAAAGCCCACAAGTCAGTGGCACTC
*
1798985 TTTTCAAAGCCCACAAGTTAGTGGCACTC
1 -TTTCAAAGCCCACAAGTCAGTGGCACTC
*
1799014 TTTTCAAAGCCCACAAGCCAGTGGTAACACT-
1 -TTTCAAAGCCCACAAGTCAGTGG---CACTC
1799045 TTTCAAAGCCCA
1 TTTCAAAGCCCA
1799057 TACGTGTCGG
Statistics
Matches: 1014, Mismatches: 99, Indels: 144
0.81 0.08 0.11
Matches are distributed among these distances:
25 1 0.00
26 27 0.03
27 130 0.13
28 376 0.37
29 194 0.19
30 217 0.21
31 51 0.05
32 18 0.02
ACGTcount: A:0.28, C:0.29, G:0.19, T:0.24
Consensus pattern (28 bp):
TTTCAAAGCCCACAAGTCAGTGGCACTC
Found at i:1798846 original size:509 final size:510
Alignment explanation
Indices: 1797912--1799056 Score: 1423
Period size: 509 Copynumber: 2.2 Consensus size: 510
1797902 CAAAGCCCAT
* * * * * **
1797912 AAGTCAGTTGCACTCTTTTCAAAACCAATAAGTTAGTGGCATTTTTTCAAAGCCCACAAGTCAGT
1 AAGTCAGTGGCA-TCTTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCAGT
* * * * *
1797977 GGCACTCCTTTCAAAGCCCACACAAGTCGGTGGCAACTCATTTCAAAGCCCACAAGTCAGTGG-C
65 GGCACTCTTTTCAAAG-CC-CACAAGTCAGTGG-AACTCTTTTCAAAGCCCACAAGCCAGTGGTA
* * *
1798041 ATCC-TTTCGAAGCCCACGCAAGTCAGTGGCACCCTTTAAAGCCCACACAAGTCAGTGGCACCTT
127 ATCCTTTTC-AAGCCCAC-CAAGTCAGTGGCACTCTTTAAAG-CC-CACAAGGCAGTGGCACCCT
* * * *
1798105 TTC-AAGCCCACGAGTTAGTGGCACTCTTTCAAAGCCCACA-AGTCAAGTGGC-ATCCTTTCAAA
188 TTCAAAGCCCACAAGTCAGTGGCACCCTTTAAAAGCCCACACAGTCAAGTGGCAAT-CTTTC-AA
* * * *
1798167 GCCCAC-GCATGTCAGTGGCAC-CTTTTTAAAGCCCACGCAAGTCAGTGGCACCCTTTTAAAGCC
251 GCCCACAG-A-GTCAATGGCACTCTTTTCAAA--CCACACAAGTCAGT-GCACCCTTTCAAA---
*
1798230 CACACAAGTCAGTGGC-ACCGTTTTAAAGCCCATGCAAGTCAGTGGCACCCTTTTAAAGCCCACG
308 CACACAAGTCAGTGGCAACC-TTTTAAAGCCCACGCAAGTCAGTGGCACCCTTTTAAAGCCCACG
* * *
1798294 CAAGTCAGTGGCACTCCTTTCAAAGTCCATGAGTGAGTGGCACCCTTTTAAAGCCCATGAGTCAA
372 -AAGTCAGTGGCACTCCTTTCAAAGCCCATGAGT-AGTGGCACCCTTTCAAAGCCCATGAGACAA
* *
1798359 GTGGCATCTTTTTAAGCCCACGAATCAGT-GCACTTTTTCAAGCCCACGAGTTAGTGGCACTTTT
435 GTGGCATCTTTTTAAGCCCACGAGTCAGTGGCACTTTTTCAAGCCCACGAGTCAGTGGCACTTTT
1798423 TCAAAGCCCAC
500 TCAAAGCCCAC
1798434 AAGTCAGTGGCA-CTTTTTCAAAGCCCACAAGTCAGTGGCATCC-TTTCAAAGCCCACAAGTCAG
1 AAGTCAGTGGCATC-TTTTCAAAGCCCACAAGTCAGTGGCA-CCTTTTCAAAGCCCACAAGTCAG
* * * * * *
1798497 TGGCAC-CTTTTTAAAGTCCACAAGTTAGTGGCACTCTTTTCAAAGACCATAAGCCAGTGGTAA-
64 TGGCACTCTTTTCAAAGCCCACAAGTCAGTGGAACTCTTTTCAAAGCCCACAAGCCAGTGGTAAT
* * *
1798560 CTCTTTTCAAGCCCA-CGAGTTAGTGGCACTCTTTCAAAGCCCACAAGGCAGTGGCATCCTTTCA
129 C-CTTTTCAAGCCCACCAAGTCAGTGGCACTCTTT-AAAGCCCACAAGGCAGTGGCACCCTTTCA
1798624 AAGCCCACGCAAGTCAGTGGCACCCTTT-AAAGCCCACACAAGTC-AGTGGCACAT-TTTCAAGC
192 AAGCCCA--CAAGTCAGTGGCACCCTTTAAAAGCCCACAC-AGTCAAGTGGCA-ATCTTTCAAGC
* * * *
1798686 CCA-AGAGTCAATGGCACTC-TTTCAAAGCC-CATAAGTCGGTGCATCCTTTCAAACACGCAAGT
253 CCACAGAGTCAATGGCACTCTTTTCAAA-CCACACAAGTCAGTGCACCCTTTCAAACACACAAGT
*
1798748 CAGTGGCAACCTTTTAAAGCCCACGCAAGTCAGTGGCACCTTTTTAAAGCCCACGCAAGTCAGTG
317 CAGTGGCAACCTTTTAAAGCCCACGCAAGTCAGTGGCACCCTTTTAAAGCCCACG-AAGTCAGTG
1798813 GCACTCCTTTCAAAGCCCATGAGTCAGTGGCACCCTTTCAAAGCCCATGAGAC-AGTGGCATCTT
381 GCACTCCTTTCAAAGCCCATGAGT-AGTGGCACCCTTTCAAAGCCCATGAGACAAGTGGCATCTT
1798877 TTTAAGCCCACGAGTCAGTGGCACTTTTTCAAGCCCACGAGTCAGTGGCACTTTTTCAAAGCCCA
445 TTTAAGCCCACGAGTCAGTGGCACTTTTTCAAGCCCACGAGTCAGTGGCACTTTTTCAAAGCCCA
1798942 C
510 C
* *
1798943 AAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTTAGTG
1 AAGTCAGTGGCATCTTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCAGTG
* *
1799008 GCACTCTTTTCAAAGCCCACAAGCCAGTGGTAACACTTTTCAAAGCCCA
66 GCACTCTTTTCAAAGCCCACAAGTCAGTGG-AACTCTTTTCAAAGCCCA
1799057 TACGTGTCGG
Statistics
Matches: 549, Mismatches: 53, Indels: 53
0.84 0.08 0.08
Matches are distributed among these distances:
508 31 0.06
509 223 0.41
510 25 0.05
511 15 0.03
512 11 0.02
513 8 0.01
514 2 0.00
515 35 0.06
516 27 0.05
517 47 0.09
518 46 0.08
519 9 0.02
520 11 0.02
521 48 0.09
522 11 0.02
ACGTcount: A:0.28, C:0.29, G:0.19, T:0.24
Consensus pattern (510 bp):
AAGTCAGTGGCATCTTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCAGTG
GCACTCTTTTCAAAGCCCACAAGTCAGTGGAACTCTTTTCAAAGCCCACAAGCCAGTGGTAATCC
TTTTCAAGCCCACCAAGTCAGTGGCACTCTTTAAAGCCCACAAGGCAGTGGCACCCTTTCAAAGC
CCACAAGTCAGTGGCACCCTTTAAAAGCCCACACAGTCAAGTGGCAATCTTTCAAGCCCACAGAG
TCAATGGCACTCTTTTCAAACCACACAAGTCAGTGCACCCTTTCAAACACACAAGTCAGTGGCAA
CCTTTTAAAGCCCACGCAAGTCAGTGGCACCCTTTTAAAGCCCACGAAGTCAGTGGCACTCCTTT
CAAAGCCCATGAGTAGTGGCACCCTTTCAAAGCCCATGAGACAAGTGGCATCTTTTTAAGCCCAC
GAGTCAGTGGCACTTTTTCAAGCCCACGAGTCAGTGGCACTTTTTCAAAGCCCAC
Found at i:1799717 original size:20 final size:19
Alignment explanation
Indices: 1799667--1799744 Score: 66
Period size: 20 Copynumber: 3.9 Consensus size: 19
1799657 TTTTACCCAG
* *
1799667 ATGTATTGATACATTTTTCA
1 ATGTATTGATACA-TTATGA
* *
1799687 ATATATCGATACATGTATGA
1 ATGTATTGATACAT-TATGA
* * *
1799707 ATGTATTGATATATTCTTTA
1 ATGTATTGATACATT-ATGA
1799727 ATGTATTGATACATTATG
1 ATGTATTGATACATTATG
1799745 TCTTTTTACC
Statistics
Matches: 44, Mismatches: 12, Indels: 5
0.72 0.20 0.08
Matches are distributed among these distances:
19 3 0.07
20 41 0.93
ACGTcount: A:0.33, C:0.08, G:0.13, T:0.46
Consensus pattern (19 bp):
ATGTATTGATACATTATGA
Found at i:1799738 original size:40 final size:39
Alignment explanation
Indices: 1799667--1799744 Score: 104
Period size: 40 Copynumber: 2.0 Consensus size: 39
1799657 TTTTACCCAG
1799667 ATGTATTGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATTGATACATTTTTCAATATATCGATACAT-TATGA
* * *
1799707 ATGTATTGATATATTCTTT-AATGTATTGATACATTATG
1 ATGTATTGATACATT-TTTCAATATATCGATACATTATG
1799745 TCTTTTTACC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
39 4 0.12
40 27 0.79
41 3 0.09
ACGTcount: A:0.33, C:0.08, G:0.13, T:0.46
Consensus pattern (39 bp):
ATGTATTGATACATTTTTCAATATATCGATACATTATGA
Found at i:1806651 original size:32 final size:32
Alignment explanation
Indices: 1806615--1806677 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
1806605 TTCAACGATT
* *
1806615 TGTATCGATATATAAGTGTTGTATCGATACAA
1 TGTATCAATACATAAGTGTTGTATCGATACAA
1806647 TGTATCAATACATAAGTGTTGTATCGATACA
1 TGTATCAATACATAAGTGTTGTATCGATACA
1806678 TAATTAGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.35, C:0.11, G:0.17, T:0.37
Consensus pattern (32 bp):
TGTATCAATACATAAGTGTTGTATCGATACAA
Found at i:1809895 original size:20 final size:20
Alignment explanation
Indices: 1809870--1809947 Score: 79
Period size: 20 Copynumber: 3.9 Consensus size: 20
1809860 GGGTAAAGAC
1809870 AGAATGTA-CTGATACATTGA
1 AGAATGTATC-GATACATTGA
*
1809890 AGAATGTATCGATACATTCA
1 AGAATGTATCGATACATTGA
* * *
1809910 TA-CATGTATAGATACTTTGA
1 -AGAATGTATCGATACATTGA
*
1809930 AAAATGTATCGATACATT
1 AGAATGTATCGATACATT
1809948 TGGGTCTTTT
Statistics
Matches: 47, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
19 1 0.02
20 44 0.94
21 2 0.04
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.33
Consensus pattern (20 bp):
AGAATGTATCGATACATTGA
Found at i:1810545 original size:32 final size:32
Alignment explanation
Indices: 1810509--1810570 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
1810499 TCGAAAAAGG
* *
1810509 TGCCATTAACTTATGTGGGCTTTGAAAAGATT
1 TGCCATCAACTCATGTGGGCTTTGAAAAGATT
*
1810541 TGCCATCGACTCATGTGGGCTTTGAAAAGA
1 TGCCATCAACTCATGTGGGCTTTGAAAAGA
1810571 GTTACCACCA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.32
Consensus pattern (32 bp):
TGCCATCAACTCATGTGGGCTTTGAAAAGATT
Found at i:1810614 original size:28 final size:28
Alignment explanation
Indices: 1810522--1811135 Score: 661
Period size: 28 Copynumber: 21.5 Consensus size: 28
1810512 CATTAACTTA
*
1810522 TGTGGGCTTTGAAAAGATTTGCCA-TCGACT
1 TGTGGGCTTTG-AAAGA-GTGCCACT-GACT
* *
1810552 CATGTGGGCTTTGAAAAGAGTTACCAC-CAGCT
1 --TGTGGGCTTTG-AAAGAG-TGCCACTGA-CT
*
1810584 TGTGAGCTTTGAAAGAGTGCCACTGACT
1 TGTGGGCTTTGAAAGAGTGCCACTGACT
*
1810612 TGTGGACTTTGAAA-AGGTGCCACTGACT
1 TGTGGGCTTTGAAAGA-GTGCCACTGACT
* *
1810640 TGTGGGCTTTGAAAGAGTGTCACTAACT
1 TGTGGGCTTTGAAAGAGTGCCACTGACT
*
1810668 TGTGGGCTTTGAAAAAGTGCCACTGACT
1 TGTGGGCTTTGAAAGAGTGCCACTGACT
** *
1810696 TGTATGTTTTGAAAG-GCTGCCACTGACT
1 TGTGGGCTTTGAAAGAG-TGCCACTGACT
* *
1810724 TGTGGGATTTGAAAG-GATGCCATTGACT
1 TGTGGGCTTTGAAAGAG-TGCCACTGACT
*
1810752 TCTGGGCTTTGAAAAGAGTTGCCA-TCGACT
1 TGTGGGCTTTG-AAAGAG-TGCCACT-GACT
*
1810782 CGTGGGCTTTGAAAG-GATGCCACTGACT
1 TGTGGGCTTTGAAAGAG-TGCCACTGACT
* *
1810810 TGTGGGCTTTCAAAAAAGTGCCACTGACT
1 TGTGGGCTTT-GAAAGAGTGCCACTGACT
*
1810839 TGTGGGCTTTGAAAAAAGTGCCACTGACT
1 TGTGGGCTTTG-AAAGAGTGCCACTGACT
* *
1810868 TGTGGGCTTTGAAAGGGTGCCACTAACT
1 TGTGGGCTTTGAAAGAGTGCCACTGACT
* *
1810896 TGTGGGCTTTGAAA-AGGTGCCACCGACA
1 TGTGGGCTTTGAAAGA-GTGCCACTGACT
* *
1810924 TGTGGGTTTTAAAAGGAGTTGCCACTGACT
1 TGTGGGCTTTGAAA-GAG-TGCCACTGACT
*
1810954 CGTGGGCTTTGAAAG-GATGCCACTGACT
1 TGTGGGCTTTGAAAGAG-TGCCACTGACT
*
1810982 TGTGGCCTTTGAAAAGAGTGCCACTGACT
1 TGTGGGCTTTG-AAAGAGTGCCACTGACT
* * * *
1811011 TATGGGCTTTGAAGGGGTGCCACTAACT
1 TGTGGGCTTTGAAAGAGTGCCACTGACT
* *
1811039 TGTGGGCTTTGAAAGTGTGACACTGACT
1 TGTGGGCTTTGAAAGAGTGCCACTGACT
*
1811067 TGTGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGAGTGCCACTGACT
*
1811095 TGTGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGAGTGCCACTGACT
1811123 TGTGGGCTTTGAA
1 TGTGGGCTTTGAA
1811136 GAGATGAACG
Statistics
Matches: 500, Mismatches: 62, Indels: 44
0.83 0.10 0.07
Matches are distributed among these distances:
27 2 0.00
28 326 0.65
29 96 0.19
30 52 0.10
31 1 0.00
32 23 0.05
ACGTcount: A:0.23, C:0.18, G:0.30, T:0.29
Consensus pattern (28 bp):
TGTGGGCTTTGAAAGAGTGCCACTGACT
Found at i:1810891 original size:172 final size:168
Alignment explanation
Indices: 1810582--1811135 Score: 729
Period size: 172 Copynumber: 3.3 Consensus size: 168
1810572 TTACCACCAG
* * *
1810582 CTTGTGAGCTTTGAAAGAG-TGCCACTGACTTGTGGACTTTGAAAAGG-TGCCACTGACTTGTGG
1 CTTGTGGGCTTTGAAAGAGTTGCCACTGACTCGTGGGCTTTG-AAAGGATGCCACTGACTTGTGG
* * * ** *
1810645 GCTTTGAAAGAGTGTCACTAACTTGTGGGCTTTGAAAAAGTGCCACTGACTTGTATGTTTTGAAA
65 GCTTTAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAAGTGCCACTGACTTGTGGGCTTTGAAA
* * *
1810710 GGCTGCCACTGACTTGTGGGATTTGAAAGGATGCCATTGA
130 GGGTGCCACTGACTTGTGGGCTTTGAAAGG-TGCCACTGA
*
1810750 CTTCTGGGCTTTGAAAAGAGTTGCCA-TCGACTCGTGGGCTTTGAAAGGATGCCACTGACTTGTG
1 CTTGTGGGCTTTG-AAAGAGTTGCCACT-GACTCGTGGGCTTTGAAAGGATGCCACTGACTTGTG
*
1810814 GGCTTTCAAAAAAGTGCCACTGACTTGTGGGCTTTGAAAAAAGTGCCACTGACTTGTGGGCTTTG
64 GGCTTT-AAAAGAGTGCCACTGACTTGTGGGCTTTG-AAAAAGTGCCACTGACTTGTGGGCTTTG
* *
1810879 AAAGGGTGCCACTAACTTGTGGGCTTTGAAAAGGTGCCACCGA
127 AAAGGGTGCCACTGACTTGTGGGCTTTG-AAAGGTGCCACTGA
* * *
1810922 CATGTGGGTTTTAAAAGGAGTTGCCACTGACTCGTGGGCTTTGAAAGGATGCCACTGACTTGTGG
1 CTTGTGGGCTTTGAAA-GAGTTGCCACTGACTCGTGGGCTTTGAAAGGATGCCACTGACTTGTGG
* * *** *
1810987 CCTTTGAAAAGAGTGCCACTGACTTATGGGCTTTGAAGGGGTGCCACTAACTTGTGGGCTTTGAA
65 GCTTT-AAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAAGTGCCACTGACTTGTGGGCTTTGAA
* *
1811052 AGTGTGACACTGACTTGTGGGCTTTGAAAGGGTGCCACTGA
129 AGGGTGCCACTGACTTGTGGGCTTTGAAA-GGTGCCACTGA
* *
1811093 CTTGTGGGCTTTGAAAG-GGTGCCACTGACTTGTGGGCTTTGAA
1 CTTGTGGGCTTTGAAAGAGTTGCCACTGACTCGTGGGCTTTGAA
1811136 GAGATGAACG
Statistics
Matches: 339, Mismatches: 37, Indels: 19
0.86 0.09 0.05
Matches are distributed among these distances:
168 11 0.03
169 36 0.11
170 43 0.13
171 100 0.29
172 143 0.42
173 6 0.02
ACGTcount: A:0.23, C:0.18, G:0.30, T:0.29
Consensus pattern (168 bp):
CTTGTGGGCTTTGAAAGAGTTGCCACTGACTCGTGGGCTTTGAAAGGATGCCACTGACTTGTGGG
CTTTAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAAGTGCCACTGACTTGTGGGCTTTGAAAG
GGTGCCACTGACTTGTGGGCTTTGAAAGGTGCCACTGA
Found at i:1812377 original size:24 final size:24
Alignment explanation
Indices: 1812350--1812419 Score: 74
Period size: 23 Copynumber: 3.0 Consensus size: 24
1812340 TCTGGACCCT
1812350 TTTTCGTTTTTTTGTTATTTTTTC
1 TTTTCGTTTTTTTGTTATTTTTTC
* *
1812374 TTTTAG-TTTTTTGTTATTTTTGGTT
1 TTTTCGTTTTTTTGTTATTTTT--TC
*
1812399 TTTTC-TATTTTT-TTATTTTTT
1 TTTTCGTTTTTTTGTTATTTTTT
1812420 TGTTTTTTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
22 1 0.03
23 15 0.38
24 13 0.33
25 10 0.26
ACGTcount: A:0.07, C:0.04, G:0.09, T:0.80
Consensus pattern (24 bp):
TTTTCGTTTTTTTGTTATTTTTTC
Found at i:1812419 original size:8 final size:8
Alignment explanation
Indices: 1812349--1812428 Score: 65
Period size: 8 Copynumber: 9.8 Consensus size: 8
1812339 ATCTGGACCC
*
1812349 TTTTTCGT
1 TTTTTTGT
1812357 TTTTTTGT
1 TTTTTTGT
1812365 TATTTTT-T
1 T-TTTTTGT
* *
1812373 CTTTTAG-
1 TTTTTTGT
1812380 TTTTTTGT
1 TTTTTTGT
1812388 TATTTTTGGT
1 T-TTTTT-GT
*
1812398 TTTTTCTAT
1 TTTTT-TGT
*
1812407 TTTTTTAT
1 TTTTTTGT
1812415 TTTTTTGT
1 TTTTTTGT
1812423 TTTTTT
1 TTTTTT
1812429 TGGTATGAAG
Statistics
Matches: 59, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
7 9 0.15
8 26 0.44
9 20 0.34
10 4 0.07
ACGTcount: A:0.06, C:0.04, G:0.09, T:0.81
Consensus pattern (8 bp):
TTTTTTGT
Found at i:1812429 original size:17 final size:17
Alignment explanation
Indices: 1812356--1812429 Score: 71
Period size: 17 Copynumber: 4.4 Consensus size: 17
1812346 CCCTTTTTCG
*
1812356 TTTTTTT-GTTATTT-T
1 TTTTTTTAGTTTTTTGT
*
1812371 TTCTTTTAGTTTTTTGT
1 TTTTTTTAGTTTTTTGT
* * *
1812388 TATTTTTGGTTTTTTCT
1 TTTTTTTAGTTTTTTGT
*
1812405 ATTTTTTTATTTTTTTGT
1 -TTTTTTTAGTTTTTTGT
1812423 TTTTTTT
1 TTTTTTT
1812430 GGTATGAAGG
Statistics
Matches: 46, Mismatches: 10, Indels: 4
0.77 0.17 0.07
Matches are distributed among these distances:
15 6 0.13
16 6 0.13
17 21 0.46
18 13 0.28
ACGTcount: A:0.07, C:0.03, G:0.08, T:0.82
Consensus pattern (17 bp):
TTTTTTTAGTTTTTTGT
Found at i:1821760 original size:23 final size:23
Alignment explanation
Indices: 1821733--1821776 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
1821723 AAAATAATGG
*
1821733 GAATGAATAGCAAGAAAAAAAAA
1 GAATGAACAGCAAGAAAAAAAAA
* *
1821756 GAATGAACATCAATAAAAAAA
1 GAATGAACAGCAAGAAAAAAA
1821777 TAGTGGCCCC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.68, C:0.07, G:0.14, T:0.11
Consensus pattern (23 bp):
GAATGAACAGCAAGAAAAAAAAA
Found at i:1825967 original size:20 final size:19
Alignment explanation
Indices: 1825940--1826014 Score: 96
Period size: 20 Copynumber: 3.8 Consensus size: 19
1825930 AAAAAAATAG
1825940 AATGTATCGATACATTGAA
1 AATGTATCGATACATTGAA
* *
1825959 GATTGTATCGATACATTCATA
1 -AATGTATCGATACATTGA-A
*
1825980 CATGTATCGATACATTGAAA
1 AATGTATCGATACATTG-AA
1826000 AATGTATCGATACAT
1 AATGTATCGATACAT
1826015 CTAGGTACTT
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
20 45 0.96
21 2 0.04
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.33
Consensus pattern (19 bp):
AATGTATCGATACATTGAA
Found at i:1828045 original size:51 final size:51
Alignment explanation
Indices: 1827988--1828104 Score: 189
Period size: 51 Copynumber: 2.3 Consensus size: 51
1827978 AACATTATTC
* * *
1827988 AATGTATCGATACATCTGGGTAAAAAGATAGAATGTATCGATACATTGAAA
1 AATGTATCGATACATCTAGGTAAAAAGACAGAATGTATCGACACATTGAAA
* *
1828039 AATGTATTGATACATCTAGGTAAAAAGACAGAATGTATCGACACATTGAAG
1 AATGTATCGATACATCTAGGTAAAAAGACAGAATGTATCGACACATTGAAA
1828090 AATGTATCGATACAT
1 AATGTATCGATACAT
1828105 TCATACATGT
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
51 60 1.00
ACGTcount: A:0.43, C:0.11, G:0.19, T:0.27
Consensus pattern (51 bp):
AATGTATCGATACATCTAGGTAAAAAGACAGAATGTATCGACACATTGAAA
Found at i:1828093 original size:20 final size:20
Alignment explanation
Indices: 1828068--1828144 Score: 102
Period size: 20 Copynumber: 3.9 Consensus size: 20
1828058 GTAAAAAGAC
1828068 AGAATGTATCGACACATTGA
1 AGAATGTATCGACACATTGA
* *
1828088 AGAATGTATCGATACATTCA
1 AGAATGTATCGACACATTGA
*
1828108 TA-CATGTATCGACACATTGA
1 -AGAATGTATCGACACATTGA
*
1828128 AGAATGTATCGATACAT
1 AGAATGTATCGACACAT
1828145 CTGGGTAAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
19 1 0.02
20 46 0.96
21 1 0.02
ACGTcount: A:0.39, C:0.16, G:0.17, T:0.29
Consensus pattern (20 bp):
AGAATGTATCGACACATTGA
Found at i:1829096 original size:32 final size:32
Alignment explanation
Indices: 1829052--1829118 Score: 107
Period size: 32 Copynumber: 2.1 Consensus size: 32
1829042 TTTTTTTAAA
*
1829052 AAAAAAGGTGCCACTAACTTGTGTGGGCTTTG
1 AAAAAAGGTGCCACCAACTTGTGTGGGCTTTG
* *
1829084 AAAAAAGTTGCCACCGACTTGTGTGGGCTTTG
1 AAAAAAGGTGCCACCAACTTGTGTGGGCTTTG
1829116 AAA
1 AAA
1829119 GGGTGCCACT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.30, C:0.16, G:0.27, T:0.27
Consensus pattern (32 bp):
AAAAAAGGTGCCACCAACTTGTGTGGGCTTTG
Found at i:1829145 original size:28 final size:28
Alignment explanation
Indices: 1829058--1829426 Score: 332
Period size: 28 Copynumber: 12.9 Consensus size: 28
1829048 TAAAAAAAAA
* *
1829058 GGTGCCACTAACTTGTGTGGGCTTTGAAAAAA
1 GGTGCCACTGAC-T-TGTGGGCTTTG--AAAG
* *
1829090 GTTGCCACCGACTTGTGTGGGCTTTGAAAG
1 GGTGCCACTGAC-T-TGTGGGCTTTGAAAG
*
1829120 GGTGCCACTGACTTGTGGGCTTTGAAGG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* *
1829148 GGTACCACTGACCTGTGGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
1829176 GGTGCCACTGACTTGTGGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* *
1829204 GGTGCCACTAACTTGTGCGG-TTTGGAAG
1 GGTGCCACTGACTTGTG-GGCTTTGAAAG
* * * *
1829232 GCTGCCACTAATTTGTGAGGGCTTTTAAAG
1 GGTGCCACTGACTTGT--GGGCTTTGAAAG
* *
1829262 GGTGCCACTAACTTGTGGGCTTTGGAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
*
1829290 GGTGCCACTGA-TT-TAGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* * * *
1829316 GATGCCACTGACATATGGTCTTTTG-AAG
1 GGTGCCACTGACTTGTGGGC-TTTGAAAG
* * * *
1829344 AGATGCCATTAACTTGTGGGCTTTGAAAT
1 -GGTGCCACTGACTTGTGGGCTTTGAAAG
* * *
1829373 GATGCCATTAACTTGTGGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* * * *
1829401 GATGCCATTGACCTATGGGCTTTGAA
1 GGTGCCACTGACTTGTGGGCTTTGAA
1829427 GAGATGAACA
Statistics
Matches: 289, Mismatches: 39, Indels: 22
0.83 0.11 0.06
Matches are distributed among these distances:
26 21 0.07
27 3 0.01
28 182 0.63
29 26 0.09
30 34 0.12
32 23 0.08
ACGTcount: A:0.22, C:0.17, G:0.31, T:0.30
Consensus pattern (28 bp):
GGTGCCACTGACTTGTGGGCTTTGAAAG
Found at i:1830712 original size:17 final size:17
Alignment explanation
Indices: 1830675--1830713 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
1830665 ATCTGGACCT
**
1830675 TTTTTTTGTTTGTTTGT
1 TTTTTTTGTTTGTTTAC
*
1830692 TTTTTTTGTTTTTTTAC
1 TTTTTTTGTTTGTTTAC
1830709 TTTTT
1 TTTTT
1830714 ACTTTTTGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.03, C:0.03, G:0.10, T:0.85
Consensus pattern (17 bp):
TTTTTTTGTTTGTTTAC
Found at i:1830734 original size:39 final size:38
Alignment explanation
Indices: 1830677--1830773 Score: 117
Period size: 39 Copynumber: 2.5 Consensus size: 38
1830667 CTGGACCTTT
*
1830677 TTTTTGTTTGTTTG-TTTTTTTTGTTTTTTTACTTTTTAC
1 TTTTTGTTT-TTTGTTTTTTTTTGGTTTTTTA-TTTTTAC
*
1830716 TTTTTGTTTTTTGTTTTTTTTTGGTTTTTTATTTTTTC
1 TTTTTGTTTTTTGTTTTTTTTTGGTTTTTTATTTTTAC
*
1830754 TTGGTTT-ATTTTTGTTTTTT
1 TT--TTTGTTTTTTGTTTTTT
1830774 CGATTTTTTA
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
38 12 0.23
39 37 0.71
40 3 0.06
ACGTcount: A:0.04, C:0.03, G:0.11, T:0.81
Consensus pattern (38 bp):
TTTTTGTTTTTTGTTTTTTTTTGGTTTTTTATTTTTAC
Found at i:1830742 original size:11 final size:10
Alignment explanation
Indices: 1830674--1830773 Score: 59
Period size: 10 Copynumber: 10.5 Consensus size: 10
1830664 CATCTGGACC
1830674 TTTTTTTTG-
1 TTTTTTTTGT
*
1830683 -TTTGTTTG-
1 TTTTTTTTGT
1830691 TTTTTTTTGT
1 TTTTTTTTGT
*
1830701 TTTTTTACT-T
1 TTTTTT-TTGT
**
1830711 TTTACTTT-T
1 TTTTTTTTGT
*
1830720 TGTTTTTTGT
1 TTTTTTTTGT
*
1830730 TTTTTTTTGG
1 TTTTTTTTGT
*
1830740 TTTTTTAT-T
1 TTTTTTTTGT
* *
1830749 TTTTCTTGGT
1 TTTTTTTTGT
*
1830759 TTATTTTTGT
1 TTTTTTTTGT
1830769 TTTTT
1 TTTTT
1830774 CGATTTTTTA
Statistics
Matches: 66, Mismatches: 20, Indels: 9
0.69 0.21 0.09
Matches are distributed among these distances:
8 7 0.11
9 19 0.29
10 39 0.59
11 1 0.02
ACGTcount: A:0.04, C:0.03, G:0.11, T:0.82
Consensus pattern (10 bp):
TTTTTTTTGT
Found at i:1830744 original size:46 final size:43
Alignment explanation
Indices: 1830676--1830791 Score: 119
Period size: 46 Copynumber: 2.5 Consensus size: 43
1830666 TCTGGACCTT
1830676 TTTTTTGTTTGTTTGTTTTTTTTGT-TTTTTTACTT-TTTACTTTTTG
1 TTTTTTGTTT-TTT-TTTTTTTT-TATTTTTT-CTTGTTTA-TTTTTG
1830722 TTTTTTGTTTTTTTTTGGTTTTTTATTTTTTCTTGGTTTATTTTTG
1 TTTTTTGTTTTTTTTT--TTTTTTATTTTTTCTT-GTTTATTTTTG
*
1830768 TTTTTTCGATTTTTTATTTTTTTT
1 TTTTTT-G-TTTTTTTTTTTTTTT
1830792 GGTACGAAGG
Statistics
Matches: 62, Mismatches: 1, Indels: 14
0.81 0.01 0.18
Matches are distributed among these distances:
44 3 0.05
45 7 0.11
46 39 0.63
47 5 0.08
48 8 0.13
ACGTcount: A:0.05, C:0.03, G:0.10, T:0.81
Consensus pattern (43 bp):
TTTTTTGTTTTTTTTTTTTTTTATTTTTTCTTGTTTATTTTTG
Found at i:1835518 original size:21 final size:18
Alignment explanation
Indices: 1835472--1835525 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 18
1835462 TAGCGATACA
1835472 TTGTATCGATACAACACT
1 TTGTATCGATACAACACT
*
1835490 TATGTATCGATACATTTACAGT
1 T-TGTATCGATACA---ACACT
1835512 TTGTATCGATACAA
1 TTGTATCGATACAA
1835526 ATTATTAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
18 2 0.06
19 12 0.39
21 12 0.39
22 5 0.16
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.37
Consensus pattern (18 bp):
TTGTATCGATACAACACT
Found at i:1836399 original size:49 final size:49
Alignment explanation
Indices: 1836243--1836640 Score: 246
Period size: 49 Copynumber: 8.2 Consensus size: 49
1836233 ATGACAATGC
* * ** * * *
1836243 GCTGATTCATGTCCAGCGACATTAGACTTGAAGAAG-A-ATGCCAATGT
1 GCTGATTCAAGGCCAGCGACATCGGACTTAAAGATGAAGATGCCAATAT
** * * * *
1836290 GCTGAGACAAGGCCAGCGACATGGGGCTTAGGAATGTTAAAGATGCCAATAT
1 GCTGATTCAAGGCCAGCGACATCGGACTTA--AA-GATGAAGATGCCAATAT
* * * * *
1836342 GCTGATTCAAGGCCAACGATATCGAACTTAAAGATGAAGATACCAATGT
1 GCTGATTCAAGGCCAGCGACATCGGACTTAAAGATGAAGATGCCAATAT
* *** * * *
1836391 GCTAATTCAAGGTTGGCGACATTGGACTTAAAGGTGAAGATGCCAATGT
1 GCTGATTCAAGGCCAGCGACATCGGACTTAAAGATGAAGATGCCAATAT
* * * * *
1836440 GCTGATTCAAGGCCGGCGACATTGGACTTCAATGATAGTTAAGGTGCCAATCT
1 GCTGATTCAAGGCCAGCGACATCGGACTT-AAAGAT-G--AAGATGCCAATAT
** * * *
1836493 GCTGATTCAAGGCCAATGACATCGGTCTCAAAGATGAAGGTGCCAATAT
1 GCTGATTCAAGGCCAGCGACATCGGACTTAAAGATGAAGATGCCAATAT
* * * *
1836542 GCTGATTCAAGGCCAGCGATATTGGGC-T-----T---G-TGCCAATGT
1 GCTGATTCAAGGCCAGCGACATCGGACTTAAAGATGAAGATGCCAATAT
* * * **
1836581 GCTGATTCAAGGCCAGCGACATTGGCCTTAAAGA-CAAGGCGCCAATAT
1 GCTGATTCAAGGCCAGCGACATCGGACTTAAAGATGAAGATGCCAATAT
1836629 GCTGATTCAAGG
1 GCTGATTCAAGG
1836641 TTAGCAATAT
Statistics
Matches: 273, Mismatches: 59, Indels: 37
0.74 0.16 0.10
Matches are distributed among these distances:
39 33 0.12
40 2 0.01
43 1 0.00
47 23 0.08
48 19 0.07
49 114 0.42
50 7 0.03
51 3 0.01
52 37 0.14
53 34 0.12
ACGTcount: A:0.31, C:0.19, G:0.26, T:0.24
Consensus pattern (49 bp):
GCTGATTCAAGGCCAGCGACATCGGACTTAAAGATGAAGATGCCAATAT
Found at i:1836430 original size:151 final size:150
Alignment explanation
Indices: 1836275--1836553 Score: 355
Period size: 151 Copynumber: 1.8 Consensus size: 150
1836265 TAGACTTGAA
*
1836275 GAAGAATGCCAATGTGCTGAGACAAGGCCAGCGACATGGGGCTT-AGGA-ATGTTAAAGATGCCA
1 GAAG-ATGCCAATGTGCTGAGACAAGGCCAGCGACATGGGACTTAAGGATA-GTT-AAGATGCCA
* * *
1836338 ATATGCTGATTCAAGGCCAACGATATCGAACTTAAAGATGAAGATACCAATGTGCTAATTCAAGG
63 ATATGCTGATTCAAGGCCAACGACATCGAACTCAAAGATGAAGATACCAATATGCTAATTCAAGG
1836403 TTGGCGACATTGGACTTAAAGGT
128 TTGGCGACATTGGACTTAAAGGT
** * * * *
1836426 GAAGATGCCAATGTGCTGATTCAAGGCCGGCGACATTGGACTTCAATGATAGTTAAGGTGCCAAT
1 GAAGATGCCAATGTGCTGAGACAAGGCCAGCGACATGGGACTT-AAGGATAGTTAAGATGCCAAT
* * ** * * *
1836491 CTGCTGATTCAAGGCCAATGACATCGGTCTCAAAGATGAAGGTGCCAATATGCTGATTCAAGG
65 ATGCTGATTCAAGGCCAACGACATCGAACTCAAAGATGAAGATACCAATATGCTAATTCAAGG
1836554 CCAGCGATAT
Statistics
Matches: 108, Mismatches: 17, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
150 34 0.31
151 67 0.62
152 6 0.06
153 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.27, T:0.23
Consensus pattern (150 bp):
GAAGATGCCAATGTGCTGAGACAAGGCCAGCGACATGGGACTTAAGGATAGTTAAGATGCCAATA
TGCTGATTCAAGGCCAACGACATCGAACTCAAAGATGAAGATACCAATATGCTAATTCAAGGTTG
GCGACATTGGACTTAAAGGT
Found at i:1836566 original size:151 final size:151
Alignment explanation
Indices: 1836255--1836566 Score: 348
Period size: 151 Copynumber: 2.1 Consensus size: 151
1836245 TGATTCATGT
* * *
1836255 CCAGCGACATTAGACTTGAA---GAAGAATGCCAATGTGCTGAGACAAGGCCAGCGACATGGGGC
1 CCAGCGACATTGGACTTAAAGGTGAAGAATGCCAATGTGCTGAGACAAGGCCAGCGACATGGGAC
* *
1836317 TTAGGAATGTTAAAGATGCCAATATGCTGATTCAAGGCCAACGATATCGAACTTAAAGATGAAGA
66 TTAGGAATGTTAAAGATGCCAATATGCTGATTCAAGGCCAACGACATCGAACTCAAAGATGAAGA
*
1836382 TACCAATGTGCTAATTCAAGG
131 TACCAATATGCTAATTCAAGG
*** ** * *
1836403 TTGGCGACATTGGACTTAAAGGTGAAG-ATGCCAATGTGCTGATTCAAGGCCGGCGACATTGGAC
1 CCAGCGACATTGGACTTAAAGGTGAAGAATGCCAATGTGCTGAGACAAGGCCAGCGACATGGGAC
* * * * **
1836467 TTCAATG-ATAGTT-AAGGTGCCAATCTGCTGATTCAAGGCCAATGACATCGGTCTCAAAGATGA
66 TT--AGGAAT-GTTAAAGATGCCAATATGCTGATTCAAGGCCAACGACATCGAACTCAAAGATGA
* * *
1836530 AGGTGCCAATATGCTGATTCAAGG
128 AGATACCAATATGCTAATTCAAGG
*
1836554 CCAGCGATATTGG
1 CCAGCGACATTGG
1836567 GCTTGTGCCA
Statistics
Matches: 132, Mismatches: 26, Indels: 9
0.79 0.16 0.05
Matches are distributed among these distances:
148 15 0.11
150 34 0.26
151 78 0.59
152 5 0.04
ACGTcount: A:0.32, C:0.19, G:0.26, T:0.23
Consensus pattern (151 bp):
CCAGCGACATTGGACTTAAAGGTGAAGAATGCCAATGTGCTGAGACAAGGCCAGCGACATGGGAC
TTAGGAATGTTAAAGATGCCAATATGCTGATTCAAGGCCAACGACATCGAACTCAAAGATGAAGA
TACCAATATGCTAATTCAAGG
Found at i:1836653 original size:48 final size:43
Alignment explanation
Indices: 1836529--1836684 Score: 131
Period size: 39 Copynumber: 3.6 Consensus size: 43
1836519 CTCAAAGATG
* * * *
1836529 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTT-
1 AAGGCGCCAATATGCTGATTCAAGGCCAGCAACATTGGCCTTA
* * *
1836571 ---GTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGCCTTAAAGA
1 AAGGCGCCAATATGCTGATTCAAGGCCAGCAACATTGGCCTT----A
** * *
1836615 CAAGGCGCCAATATGCTGATTCAAGGTTAGCAATATTGGGCTTA
1 -AAGGCGCCAATATGCTGATTCAAGGCCAGCAACATTGGCCTTA
*
1836659 AAGGTGCCAATATGCTGATTCAAGGC
1 AAGGCGCCAATATGCTGATTCAAGGC
1836685 AGTGATATTG
Statistics
Matches: 93, Mismatches: 12, Indels: 17
0.76 0.10 0.14
Matches are distributed among these distances:
39 36 0.39
43 24 0.26
44 1 0.01
48 32 0.34
ACGTcount: A:0.28, C:0.20, G:0.27, T:0.25
Consensus pattern (43 bp):
AAGGCGCCAATATGCTGATTCAAGGCCAGCAACATTGGCCTTA
Found at i:1836683 original size:21 final size:21
Alignment explanation
Indices: 1836615--1836683 Score: 61
Period size: 21 Copynumber: 3.2 Consensus size: 21
1836605 GCCTTAAAGA
*
1836615 CAAGGCGCCAATATGCTGATT
1 CAAGGTGCCAATATGCTGATT
* *
1836636 CAAGGTTAG-CAATATTG-GGCTT
1 CAAGG-T-GCCAATA-TGCTGATT
*
1836658 AAAGGTGCCAATATGCTGATT
1 CAAGGTGCCAATATGCTGATT
1836679 CAAGG
1 CAAGG
1836684 CAGTGATATT
Statistics
Matches: 36, Mismatches: 7, Indels: 10
0.68 0.13 0.19
Matches are distributed among these distances:
20 3 0.08
21 18 0.50
22 12 0.33
23 3 0.08
ACGTcount: A:0.30, C:0.17, G:0.26, T:0.26
Consensus pattern (21 bp):
CAAGGTGCCAATATGCTGATT
Found at i:1836809 original size:57 final size:56
Alignment explanation
Indices: 1836722--1836994 Score: 311
Period size: 57 Copynumber: 4.8 Consensus size: 56
1836712 CACCAACTTG
* * * * * *
1836722 TGTGGGCTTTTGAAAGGGTTG-CAGC-AACTTGTGTGCTTTTGAAGGTCGCCACTGCCT
1 TGTGGGCTTTTGAAAAGG-TGCCA-CTGACTTGTGGGCTTTTAAAGAT-GCCACTGACT
* *
1836779 TGTGTGCTTTTGAAAAGGTGCCACTGACTTGTGGGCCTTTAAAAGATGCCACTGACT
1 TGTGGGCTTTTGAAAAGGTGCCACTGACTTGTGGG-CTTTTAAAGATGCCACTGACT
*
1836836 TGTGGGCTTTTGAAAATGTGCCACTGACTTGTGGGCTTTTAAAAAGATGCCACTGACT
1 TGTGGGCTTTTGAAAAGGTGCCACTGACTTGTGGGCTTTT--AAAGATGCCACTGACT
* * * *
1836894 TGTGGGCTTTTG--AAGGTTGCCACAGACTTATGGGCTTTTAAAGGTTGCCACTAACT
1 TGTGGGCTTTTGAAAAGG-TGCCACTGACTTGTGGGCTTTTAAA-GATGCCACTGACT
*
1836950 TGTGGGCTTTTGAAAAGATGCCACTGACTTGTGGGCTTTTGAAAG
1 TGTGGGCTTTTGAAAAGGTGCCACTGACTTGTGGGCTTTT-AAAG
1836995 GGTGAGGAAC
Statistics
Matches: 187, Mismatches: 19, Indels: 20
0.83 0.08 0.09
Matches are distributed among these distances:
55 3 0.02
56 33 0.18
57 109 0.58
58 42 0.22
ACGTcount: A:0.21, C:0.18, G:0.28, T:0.33
Consensus pattern (56 bp):
TGTGGGCTTTTGAAAAGGTGCCACTGACTTGTGGGCTTTTAAAGATGCCACTGACT
Found at i:1836811 original size:29 final size:29
Alignment explanation
Indices: 1836722--1836998 Score: 311
Period size: 29 Copynumber: 9.7 Consensus size: 29
1836712 CACCAACTTG
* *
1836722 TGTGGGCTTTTGAAAGGGTTG-CAGC-AACT
1 TGTGGGCTTTTGAAAAGG-TGCCA-CTGACT
* *
1836751 TGTGTGCTTTTG--AAGGTCGCCACTGCCT
1 TGTGGGCTTTTGAAAAGGT-GCCACTGACT
*
1836779 TGTGTGCTTTTGAAAAGGTGCCACTGACT
1 TGTGGGCTTTTGAAAAGGTGCCACTGACT
* *
1836808 TGTGGGCCTTT-AAAAGATGCCACTGACT
1 TGTGGGCTTTTGAAAAGGTGCCACTGACT
*
1836836 TGTGGGCTTTTGAAAATGTGCCACTGACT
1 TGTGGGCTTTTGAAAAGGTGCCACTGACT
* *
1836865 TGTGGGCTTTTAAAAAGATGCCACTGACT
1 TGTGGGCTTTTGAAAAGGTGCCACTGACT
*
1836894 TGTGGGCTTTTG--AAGGTTGCCACAGACT
1 TGTGGGCTTTTGAAAAGG-TGCCACTGACT
* *
1836922 TATGGGCTTTT--AAAGGTTGCCACTAACT
1 TGTGGGCTTTTGAAAAGG-TGCCACTGACT
*
1836950 TGTGGGCTTTTGAAAAGATGCCACTGACT
1 TGTGGGCTTTTGAAAAGGTGCCACTGACT
*
1836979 TGTGGGCTTTTGAAAGGGTG
1 TGTGGGCTTTTGAAAAGGTG
1836999 AGGAACGTCT
Statistics
Matches: 213, Mismatches: 25, Indels: 20
0.83 0.10 0.08
Matches are distributed among these distances:
26 1 0.00
27 8 0.04
28 86 0.40
29 109 0.51
30 9 0.04
ACGTcount: A:0.21, C:0.17, G:0.29, T:0.33
Consensus pattern (29 bp):
TGTGGGCTTTTGAAAAGGTGCCACTGACT
Found at i:1838428 original size:12 final size:12
Alignment explanation
Indices: 1838411--1838471 Score: 74
Period size: 11 Copynumber: 5.2 Consensus size: 12
1838401 CATCCGGACC
1838411 TTTTTGTTGTTT
1 TTTTTGTTGTTT
1838423 TTTTTGTT-TGTT
1 TTTTTGTTGT-TT
*
1838435 TATTTGTTTGTTT
1 TTTTTG-TTGTTT
1838448 TTTTT-TTGTTT
1 TTTTTGTTGTTT
1838459 TTTTTGTT-TTT
1 TTTTTGTTGTTT
1838470 TT
1 TT
1838472 GTTTTTTCTG
Statistics
Matches: 43, Mismatches: 2, Indels: 9
0.80 0.04 0.17
Matches are distributed among these distances:
11 17 0.40
12 17 0.40
13 8 0.19
14 1 0.02
ACGTcount: A:0.02, C:0.00, G:0.13, T:0.85
Consensus pattern (12 bp):
TTTTTGTTGTTT
Found at i:1838429 original size:9 final size:9
Alignment explanation
Indices: 1838411--1838488 Score: 72
Period size: 9 Copynumber: 8.7 Consensus size: 9
1838401 CATCCGGACC
*
1838411 TTTTTGTTG
1 TTTTTTTTG
1838420 TTTTTTTTG
1 TTTTTTTTG
1838429 TTTGTTTATT-
1 TTT-TTT-TTG
* *
1838439 TGTTTGTT-
1 TTTTTTTTG
1838447 TTTTTTTTG
1 TTTTTTTTG
1838456 TTTTTTTTG
1 TTTTTTTTG
1838465 -TTTTTTTG
1 TTTTTTTTG
*
1838473 TTTTTTCTGG
1 TTTTTT-TTG
1838483 TTTTTT
1 TTTTTT
1838489 GTGCGAATGA
Statistics
Matches: 58, Mismatches: 6, Indels: 9
0.79 0.08 0.12
Matches are distributed among these distances:
8 16 0.28
9 27 0.47
10 13 0.22
11 2 0.03
ACGTcount: A:0.01, C:0.01, G:0.14, T:0.83
Consensus pattern (9 bp):
TTTTTTTTG
Found at i:1838432 original size:4 final size:4
Alignment explanation
Indices: 1838425--1838475 Score: 50
Period size: 4 Copynumber: 12.8 Consensus size: 4
1838415 TGTTGTTTTT
* * * *
1838425 TTTG TTTG TTTA TTTG TTTG TTT- TTTT TTTG TTTTT TTTG TTTT TTTG
1 TTTG TTTG TTTG TTTG TTTG TTTG TTTG TTTG -TTTG TTTG TTTG TTTG
1838473 TTT
1 TTT
1838476 TTTCTGGTTT
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
3 3 0.08
4 32 0.84
5 3 0.08
ACGTcount: A:0.02, C:0.00, G:0.14, T:0.84
Consensus pattern (4 bp):
TTTG
Found at i:1838440 original size:8 final size:8
Alignment explanation
Indices: 1838411--1838490 Score: 83
Period size: 8 Copynumber: 9.9 Consensus size: 8
1838401 CATCCGGACC
1838411 TTTTTGTT
1 TTTTTGTT
1838419 GTTTTT-TT
1 -TTTTTGTT
*
1838427 TGTTTGTT
1 TTTTTGTT
*
1838435 TATTTGTT
1 TTTTTGTT
*
1838443 TGTTT-TT
1 TTTTTGTT
1838450 TTTTTGTTT
1 TTTTTG-TT
1838459 TTTTTGTT
1 TTTTTGTT
1838467 TTTTTGTT
1 TTTTTGTT
*
1838475 TTTTCTGGT
1 TTTT-TGTT
1838484 TTTTTGT
1 TTTTTGT
1838491 GCGAATGATG
Statistics
Matches: 61, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
7 10 0.16
8 31 0.51
9 20 0.33
ACGTcount: A:0.01, C:0.01, G:0.15, T:0.82
Consensus pattern (8 bp):
TTTTTGTT
Found at i:1838444 original size:28 final size:26
Alignment explanation
Indices: 1838412--1838488 Score: 86
Period size: 26 Copynumber: 2.9 Consensus size: 26
1838402 ATCCGGACCT
1838412 TTTTGTTGTTTTTTTTGTTTGTTTATT-
1 TTTTGTTGTTTTTTTTGTTT-TTT-TTG
1838439 TGTTTGTT-TTTTTTTTGTTTTTTTTG
1 T-TTTGTTGTTTTTTTTGTTTTTTTTG
* * *
1838465 TTTTTTTGTTTTTTCTGGTTTTTT
1 TTTTGTTGTTTTTTTTGTTTTTTT
1838489 GTGCGAATGA
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
25 7 0.16
26 18 0.41
27 13 0.30
28 6 0.14
ACGTcount: A:0.01, C:0.01, G:0.14, T:0.83
Consensus pattern (26 bp):
TTTTGTTGTTTTTTTTGTTTTTTTTG
Found at i:1845934 original size:21 final size:20
Alignment explanation
Indices: 1845890--1845942 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
1845880 TAGATTGCAT
**
1845890 TGTATCGATACATGACCAAA
1 TGTATCGATACATGAAAAAA
*
1845910 TGTATCGATACTTGAAAAGAA
1 TGTATCGATACATGAAAA-AA
*
1845931 TGTATCAATACA
1 TGTATCGATACA
1845943 AGTCATTGGC
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 15 0.56
21 12 0.44
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.28
Consensus pattern (20 bp):
TGTATCGATACATGAAAAAA
Found at i:1846012 original size:13 final size:13
Alignment explanation
Indices: 1845994--1846018 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1845984 ACACACAGTA
1845994 TGTATCGATACAT
1 TGTATCGATACAT
1846007 TGTATCGATACA
1 TGTATCGATACA
1846019 CCATAAAATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1846038 original size:33 final size:32
Alignment explanation
Indices: 1845974--1846041 Score: 91
Period size: 33 Copynumber: 2.1 Consensus size: 32
1845964 GTAGCCAAAC
** *
1845974 TTGTATCGATACACACAGTATGTATCGATACA
1 TTGTATCGATACACACAAAATGTATCAATACA
*
1846006 TTGTATCGATACACCATAAAATGTATCAATACA
1 TTGTATCGATACA-CACAAAATGTATCAATACA
1846039 TTG
1 TTG
1846042 GCTTGTAACG
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
32 13 0.42
33 18 0.58
ACGTcount: A:0.37, C:0.18, G:0.13, T:0.32
Consensus pattern (32 bp):
TTGTATCGATACACACAAAATGTATCAATACA
Found at i:1847639 original size:9 final size:9
Alignment explanation
Indices: 1847625--1847658 Score: 59
Period size: 9 Copynumber: 3.8 Consensus size: 9
1847615 AACCATCAAG
1847625 GATGATGAA
1 GATGATGAA
1847634 GATGATGAA
1 GATGATGAA
*
1847643 GATGATGAT
1 GATGATGAA
1847652 GATGATG
1 GATGATG
1847659 GTGACTCAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.38, C:0.00, G:0.35, T:0.26
Consensus pattern (9 bp):
GATGATGAA
Found at i:1847640 original size:3 final size:3
Alignment explanation
Indices: 1847625--1847658 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
1847615 AACCATCAAG
* *
1847625 GAT GAT GAA GAT GAT GAA GAT GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT G
1847659 GTGACTCAGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.38, C:0.00, G:0.35, T:0.26
Consensus pattern (3 bp):
GAT
Found at i:1854726 original size:20 final size:21
Alignment explanation
Indices: 1854697--1854749 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 21
1854687 ATCGATACAT
* **
1854697 TGTATTGATACATGACCAA-A
1 TGTATCGATACATGAAAAAGA
*
1854717 TGTATCGATACTTGAAAAAGA
1 TGTATCGATACATGAAAAAGA
1854738 TGTATCGATACA
1 TGTATCGATACA
1854750 GGTCATTGGC
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 15 0.56
21 12 0.44
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (21 bp):
TGTATCGATACATGAAAAAGA
Found at i:1854819 original size:13 final size:13
Alignment explanation
Indices: 1854801--1854825 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1854791 ACACACAGTA
1854801 TGTATCGATACAT
1 TGTATCGATACAT
1854814 TGTATCGATACA
1 TGTATCGATACA
1854826 CCATAAAATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1854842 original size:33 final size:32
Alignment explanation
Indices: 1854782--1854848 Score: 98
Period size: 33 Copynumber: 2.1 Consensus size: 32
1854772 TACCCAAACA
**
1854782 TGTATCGATACACACAGTATGTATCGATACAT
1 TGTATCGATACACACAAAATGTATCGATACAT
*
1854814 TGTATCGATACACCATAAAATGTATCGATACAT
1 TGTATCGATACA-CACAAAATGTATCGATACAT
1854847 TG
1 TG
1854849 GCTTGTAACG
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
32 12 0.39
33 19 0.61
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Consensus pattern (32 bp):
TGTATCGATACACACAAAATGTATCGATACAT
Found at i:1858172 original size:19 final size:19
Alignment explanation
Indices: 1858148--1858189 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
1858138 ACTATTTTTA
1858148 GATACACAAAGTATGTATC
1 GATACACAAAGTATGTATC
1858167 GATACACAAAGTATGTATC
1 GATACACAAAGTATGTATC
1858186 GATA
1 GATA
1858190 TAATGTATCG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.43, C:0.14, G:0.17, T:0.26
Consensus pattern (19 bp):
GATACACAAAGTATGTATC
Found at i:1858201 original size:32 final size:33
Alignment explanation
Indices: 1858160--1858222 Score: 94
Period size: 32 Copynumber: 1.9 Consensus size: 33
1858150 TACACAAAGT
*
1858160 ATGTATCGATACA-C-AAAGTATGTATCGATATA
1 ATGTATCGATACACCAAAAAT-TGTATCGATATA
1858192 ATGTATCGATACACCAAAAATTGTATCGATA
1 ATGTATCGATACACCAAAAATTGTATCGATA
1858223 CATTGGCTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 13 0.46
33 11 0.39
34 4 0.14
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.30
Consensus pattern (33 bp):
ATGTATCGATACACCAAAAATTGTATCGATATA
Found at i:1863514 original size:19 final size:19
Alignment explanation
Indices: 1863490--1863559 Score: 104
Period size: 19 Copynumber: 3.7 Consensus size: 19
1863480 TTTCAACAAT
*
1863490 TTGTATCGATACATTAGTG
1 TTGTATCGATACATAAGTG
*
1863509 TTGTATCCATACATAAGTG
1 TTGTATCGATACATAAGTG
*
1863528 TTGTATCGATACATAAGTT
1 TTGTATCGATACATAAGTG
*
1863547 TTGTATGGATACA
1 TTGTATCGATACA
1863560 ATGTACTGCT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 46 1.00
ACGTcount: A:0.30, C:0.11, G:0.19, T:0.40
Consensus pattern (19 bp):
TTGTATCGATACATAAGTG
Found at i:1863630 original size:13 final size:13
Alignment explanation
Indices: 1863612--1863636 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1863602 ATTACTCAAA
1863612 TGTATCGATACAT
1 TGTATCGATACAT
1863625 TGTATCGATACA
1 TGTATCGATACA
1863637 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1871507 original size:213 final size:213
Alignment explanation
Indices: 1871140--1871568 Score: 750
Period size: 213 Copynumber: 2.0 Consensus size: 213
1871130 TGAGAAGAAA
* *
1871140 TCTACAGAGAGTTTCAGGAAATATGCCCAAAGGTGGAGAGAAGAGGCAGCCCTAGTCCAGCCTTC
1 TCTACAGAGAGTTTCAGGAAATATGCCCAAAGGTGGAGACAAGAGGCAGCCCTAGTCCAGCCTCC
* *
1871205 TCTTACAGAAAAAGAGATGACGGTCACTTTCATCAATACCCTGCGTGCTCCTTATTATGATAATC
66 TCTTACAGAAAAAGAGATGACGGTCACTTTCATCAATACCCTGCGTGCTCCTTATTATGAGAAAC
* * **
1871270 TCGTAGGGAATGCAACCAAGAGATTTGCGGACTTAGTCCTCTCTGGAGAAATGATTGATGCAGCC
131 TCGTAGGGAATGCAACCAAGAGATTTACGGACTTAGTACTCTCCCGAGAAATGATTGATGCAGCC
1871335 ATTAAGAGTGGTAGGATG
196 ATTAAGAGTGGTAGGATG
* * *
1871353 TCTACAGAGAGTTTCAGGCAATATGCCCAAAGGTGGAGACAAGAGGTAGCCCTAGTCTAGCCTCC
1 TCTACAGAGAGTTTCAGGAAATATGCCCAAAGGTGGAGACAAGAGGCAGCCCTAGTCCAGCCTCC
*
1871418 TCTTATAGAAAAAGAGATGACGGTCACTTTCATCAATACCCTGCGTGCTCCTTATTATGAGAAAC
66 TCTTACAGAAAAAGAGATGACGGTCACTTTCATCAATACCCTGCGTGCTCCTTATTATGAGAAAC
1871483 TCGTAGGGAATGCAACCAAGAGATTTACGGACTTAGTACTCTCCCGAGAAATGATTGATGCAGCC
131 TCGTAGGGAATGCAACCAAGAGATTTACGGACTTAGTACTCTCCCGAGAAATGATTGATGCAGCC
1871548 ATTAAGAGTGGTAGGATG
196 ATTAAGAGTGGTAGGATG
1871566 TCT
1 TCT
1871569 GTCGAAGAAG
Statistics
Matches: 204, Mismatches: 12, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
213 204 1.00
ACGTcount: A:0.30, C:0.21, G:0.24, T:0.25
Consensus pattern (213 bp):
TCTACAGAGAGTTTCAGGAAATATGCCCAAAGGTGGAGACAAGAGGCAGCCCTAGTCCAGCCTCC
TCTTACAGAAAAAGAGATGACGGTCACTTTCATCAATACCCTGCGTGCTCCTTATTATGAGAAAC
TCGTAGGGAATGCAACCAAGAGATTTACGGACTTAGTACTCTCCCGAGAAATGATTGATGCAGCC
ATTAAGAGTGGTAGGATG
Found at i:1875172 original size:34 final size:35
Alignment explanation
Indices: 1875134--1875200 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
1875124 CCTTACAACA
1875134 CTATC-TTTC-AAGGCTAAGATAGAAACCTCTCTCT
1 CTATCTTTTCAAAGGCTAAGATAG-AACCTCTCTCT
1875168 CTATCTTTTTCAAAGGCTAAGATAGAACCTCTC
1 CTATC-TTTTCAAAGGCTAAGATAGAACCTCTC
1875201 AATCACTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 5 0.17
36 12 0.40
37 13 0.43
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (35 bp):
CTATCTTTTCAAAGGCTAAGATAGAACCTCTCTCT
Found at i:1875794 original size:22 final size:22
Alignment explanation
Indices: 1875739--1875794 Score: 96
Period size: 21 Copynumber: 2.6 Consensus size: 22
1875729 CGTGAACAGT
*
1875739 ATGAACAGTGATATATCGATAC
1 ATGAACAGTGATGTATCGATAC
1875761 ATGAA-AGTGATGTATCGATAC
1 ATGAACAGTGATGTATCGATAC
1875782 ATGAACAGTGATG
1 ATGAACAGTGATG
1875795 AATGGTGATG
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
21 20 0.62
22 12 0.38
ACGTcount: A:0.39, C:0.11, G:0.23, T:0.27
Consensus pattern (22 bp):
ATGAACAGTGATGTATCGATAC
Found at i:1875898 original size:34 final size:34
Alignment explanation
Indices: 1875855--1875940 Score: 145
Period size: 34 Copynumber: 2.5 Consensus size: 34
1875845 ACATATTTTG
*
1875855 TGTATCGATACAAATTTGGCTACTGCCAGTGACC
1 TGTATCGATACAAATTTGGCTACTGCCAATGACC
*
1875889 TGTATCGATACAAATTTGGCTACTGCCAATGTCC
1 TGTATCGATACAAATTTGGCTACTGCCAATGACC
*
1875923 TGTATCGATACATATTTG
1 TGTATCGATACAAATTTG
1875941 TGTGTATCGA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 49 1.00
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.34
Consensus pattern (34 bp):
TGTATCGATACAAATTTGGCTACTGCCAATGACC
Found at i:1875986 original size:20 final size:20
Alignment explanation
Indices: 1875923--1875993 Score: 74
Period size: 20 Copynumber: 3.5 Consensus size: 20
1875913 GCCAATGTCC
**
1875923 TGTATCGATACATATTTGTG
1 TGTATCGATACATATTAATG
* *
1875943 TGTATCGATAC-TATGCAATC
1 TGTATCGATACATAT-TAATG
1875963 TGTATCGATACAT-TTAAATG
1 TGTATCGATACATATT-AATG
1875983 TGTATCGATAC
1 TGTATCGATAC
1875994 TTTTCAGGGT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
19 3 0.07
20 38 0.90
21 1 0.02
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.39
Consensus pattern (20 bp):
TGTATCGATACATATTAATG
Found at i:1876059 original size:21 final size:21
Alignment explanation
Indices: 1876033--1876073 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1876023 GTCAACCTTG
1876033 TGTATTAATACCAATA-GTATA
1 TGTATTAATA-CAATACGTATA
*
1876054 TGTATTGATACAATACGTAT
1 TGTATTAATACAATACGTAT
1876074 TTTTACTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (21 bp):
TGTATTAATACAATACGTATA
Found at i:1879153 original size:13 final size:13
Alignment explanation
Indices: 1879135--1879228 Score: 72
Period size: 13 Copynumber: 7.3 Consensus size: 13
1879125 AGAAAAGAAG
1879135 AAAAAAACAAACA
1 AAAAAAACAAACA
*
1879148 AAAAAAAGAGAA-A
1 AAAAAAACA-AACA
*
1879161 AAAACAACAAACA
1 AAAAAAACAAACA
1879174 CAAAAAAA-AAAC-
1 -AAAAAAACAAACA
*
1879186 AAACAAACAAA-A
1 AAAAAAACAAACA
* *
1879198 CAAAAAAAGAAAGA
1 -AAAAAAACAAACA
1879212 AAAAAAAGC-AACA
1 AAAAAAA-CAAACA
1879225 AAAA
1 AAAA
1879229 GGGTCCGGAT
Statistics
Matches: 64, Mismatches: 9, Indels: 16
0.72 0.10 0.18
Matches are distributed among these distances:
11 6 0.09
12 5 0.08
13 44 0.69
14 9 0.14
ACGTcount: A:0.82, C:0.13, G:0.05, T:0.00
Consensus pattern (13 bp):
AAAAAAACAAACA
Found at i:1879159 original size:26 final size:26
Alignment explanation
Indices: 1879127--1879217 Score: 111
Period size: 25 Copynumber: 3.6 Consensus size: 26
1879117 ACGAAAGAAG
1879127 AAAAG-AAGAAAAAAACAAACA-AAA
1 AAAAGAAAGAAAAAAACAAACACAAA
1879151 AAAAGAGAA-AAAAACAACAAACACAAA
1 AAAAGA-AAGAAAAA-AACAAACACAAA
* *
1879178 AAAA-AAACAAACAAACAAA-ACAAA
1 AAAAGAAAGAAAAAAACAAACACAAA
1879202 AAAAGAAAGAAAAAAA
1 AAAAGAAAGAAAAAAA
1879218 AGCAACAAAA
Statistics
Matches: 58, Mismatches: 3, Indels: 11
0.81 0.04 0.15
Matches are distributed among these distances:
24 14 0.24
25 22 0.38
26 15 0.26
27 7 0.12
ACGTcount: A:0.82, C:0.11, G:0.07, T:0.00
Consensus pattern (26 bp):
AAAAGAAAGAAAAAAACAAACACAAA
Found at i:1879214 original size:9 final size:9
Alignment explanation
Indices: 1879108--1879229 Score: 52
Period size: 10 Copynumber: 13.0 Consensus size: 9
1879098 CATCCTCCGC
1879108 AAAAAAAAG
1 AAAAAAAAG
* *
1879117 ACGAAAGAAG
1 A-AAAAAAAG
1879127 AAAAGAAGAA-
1 AAAA-AA-AAG
*
1879137 AAAAACAAAC
1 AAAAA-AAAG
1879147 AAAAAAAAG
1 AAAAAAAAG
*
1879156 AGAAAAAAAC
1 A-AAAAAAAG
* * *
1879166 AACAAACAC
1 AAAAAAAAG
1879175 AAAAAAAA-
1 AAAAAAAAG
*
1879183 AACAAACAAAC
1 AA-AAA-AAAG
*
1879194 AAAACAAA-
1 AAAAAAAAG
*
1879202 AAAAGAAAG
1 AAAAAAAAG
1879211 AAAAAAAAG
1 AAAAAAAAG
*
1879220 CAACAAAAAG
1 -AAAAAAAAG
1879230 GGTCCGGATA
Statistics
Matches: 88, Mismatches: 14, Indels: 21
0.72 0.11 0.17
Matches are distributed among these distances:
8 9 0.10
9 36 0.41
10 39 0.44
11 4 0.05
ACGTcount: A:0.80, C:0.11, G:0.10, T:0.00
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:1879214 original size:17 final size:16
Alignment explanation
Indices: 1879135--1879228 Score: 68
Period size: 17 Copynumber: 5.8 Consensus size: 16
1879125 AGAAAAGAAG
*
1879135 AAAAAAACAAACAAA-
1 AAAAAAACAAAAAAAC
* *
1879150 AAAAAGAGAAAAAAAC
1 AAAAAAACAAAAAAAC
*
1879166 AACAAACACAAAAAAA-
1 AA-AAAAACAAAAAAAC
*
1879182 AAACAAACAAACAAAAC
1 AAAAAAACAAA-AAAAC
*
1879199 AAAAAAAGAAAGAAAA-
1 AAAAAAACAAA-AAAAC
*
1879215 AAAAGCAACAAAAA
1 AAAA-AAACAAAAA
1879229 GGGTCCGGAT
Statistics
Matches: 62, Mismatches: 12, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
15 19 0.31
16 14 0.23
17 29 0.47
ACGTcount: A:0.82, C:0.13, G:0.05, T:0.00
Consensus pattern (16 bp):
AAAAAAACAAAAAAAC
Found at i:1879228 original size:26 final size:26
Alignment explanation
Indices: 1879128--1879228 Score: 86
Period size: 26 Copynumber: 3.8 Consensus size: 26
1879118 CGAAAGAAGA
1879128 AAAGAAGAAAAAAACAAACAAAAAAAAG
1 AAAGAA-AAAAAAAC-AACAAAAAAAAG
1879156 --AGAAAAAAACAACAAACACAAAAAAA-
1 AAAGAAAAAAA-AAC-AACA-AAAAAAAG
* *
1879182 AAACAAACAAACAA-AAC-AAAAAAAG
1 AAAGAAA-AAAAAACAACAAAAAAAAG
*
1879207 AAAGAAAAAAAAGCAACAAAAA
1 AAAGAAAAAAAAACAACAAAAA
1879229 GGGTCCGGAT
Statistics
Matches: 60, Mismatches: 5, Indels: 18
0.72 0.06 0.22
Matches are distributed among these distances:
24 11 0.18
25 14 0.23
26 19 0.32
27 7 0.12
28 6 0.10
29 3 0.05
ACGTcount: A:0.81, C:0.12, G:0.07, T:0.00
Consensus pattern (26 bp):
AAAGAAAAAAAAACAACAAAAAAAAG
Found at i:1880688 original size:102 final size:102
Alignment explanation
Indices: 1880524--1881763 Score: 1400
Period size: 102 Copynumber: 12.3 Consensus size: 102
1880514 TTTCATTAAC
* * * *
1880524 TTTAAGACCAATGTCACTGGCCTTGAATCAACACATTAGCA-----A-CTTTAAGTCCAATATCG
1 TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCG
1880583 CTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATC-
66 CTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCT
**
1880619 TTTAAGTCCAATGTCGCTGGCCATTGAAAT-AGCACATCAGCACCTTCATCTTTAAGTCCAATAT
1 TTTAAGTCCAATGTCGCTGGCC-TTG-AATCAGCACATTGGCACCTTCATCTTTAAGTCCAATAT
*
1880683 CGCTGGCCTTGAATCAGCATATTGGCGCC-CT-TCATC-
64 CGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCT
* * *
1880719 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTTAAGTCCAAT
1 TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACC--T-TCATC-TTTAAGTCCAAT
* * * *
1880784 GTCGCTGGCCTTGAATCAGCACATTTGCACC-TT-T-ATC-
62 ATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCT
* * * * * * * *
1880821 TTTATGTCCAATATCGTTGGCCTTGAATAAGCATATTGACGCCTTTGTCCTCTTTTAAGTCCAAT
1 TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACC--T-TCATC-TTTAAGTCCAAT
* * *
1880886 GTCGCTGGCCTTGAATCAGCACATTGGCACC--T-TCATC-
62 ATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCT
* * * * *
1880923 TTTAAGTCAAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTTAAGTCCATT
1 TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACC--T-TCATC-TTTAAGTCCAAT
* * *
1880988 GTCGCTGGCCTTGAA-CTAGCACATTGGCACC--T-TCATCT
62 ATCGCTGGCCTTGAATC-AGCATATTGGCGCCTTTGTCATCT
* *
1881026 TTTAAGTCCAATGTCCCTGGCCTTGAA-CTAGCACATTGGCACCTTCATCTTTAAGGCCAATATC
1 TTTAAGTCCAATGTCGCTGGCCTTGAATC-AGCACATTGGCACCTTCATCTTTAAGTCCAATATC
* *
1881090 GTTGGCCTTGAATCAGCATATTGGCGCCTTTGTCTTCT
65 GCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCT
* * *
1881128 TTTATGTCCAATGTCGCTGGCCTTGAATCAGTACATTGGCACCTTCATCTTTAAGTCCAATATCA
1 TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCG
* *
1881193 ATGGCCTTGAATTAGCATATTGGCGCCTTTGTCATCT
66 CTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCT
* *
1881230 TTTAAGTTCAATGTCGCTGGCATTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCG
1 TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCG
1881295 CTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCT
66 CTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCT
* *
1881332 TTTAAGTCCAATGTCGTTGGCCTTGAA-CTAGCACATTGGCACCTTCATCTTTAAGTCAAATATC
1 TTTAAGTCCAATGTCGCTGGCCTTGAATC-AGCACATTGGCACCTTCATCTTTAAGTCCAATATC
* * * *
1881396 AGTTAGCC-T---T--G-A-A--GGCACCTTTGTCATCA
65 -GCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCT
* *
1881425 TTTAAGTCTAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCGTTAAGTCCAATATCG
1 TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCG
*
1881490 TTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATC-
66 CTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCT
* * * *
1881526 TTTAAGTCCACTGTCGCTAGCCTTGAATTAGCACATTGGCACCTTCATCTTTAAGTCTAATATCG
1 TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCG
* * *
1881591 CTGGCCTCGAATCAACATATTAGCGCCTTTGTCATCT
66 CTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCT
* * * * *
1881628 TTTAAGTCCAATGTTGCTGGCCTTGAATCAACATATTGGCACCTTCATCTTTATGTCCAATATAG
1 TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCG
* * *
1881693 TTGGCCTTGAATCAGCATATTGGTGCCTTCGTCATCT
66 CTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCT
* ** * *
1881730 TTAAAACCCAATGTCAGTTGACCTTGAATCAGCA
1 TTTAAGTCCAATGTC-GCTGGCCTTGAATCAGCA
1881764 TATTAGCATT
Statistics
Matches: 1007, Mismatches: 101, Indels: 66
0.86 0.09 0.06
Matches are distributed among these distances:
92 6 0.01
93 73 0.07
94 1 0.00
95 21 0.02
96 15 0.01
97 4 0.00
98 4 0.00
99 50 0.05
100 33 0.03
101 100 0.10
102 602 0.60
103 98 0.10
ACGTcount: A:0.23, C:0.25, G:0.18, T:0.34
Consensus pattern (102 bp):
TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCG
CTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCT
Found at i:1880940 original size:254 final size:251
Alignment explanation
Indices: 1880523--1881821 Score: 1426
Period size: 254 Copynumber: 5.2 Consensus size: 251
1880513 CTTTCATTAA
* * * *
1880523 CTTTAAGACCAATGTCACTGGCCTTGAATCAACACATTAGCA-----A-CTTTAAGTCCAATATC
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATC
* *
1880582 GCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATC-TTTAAGTCCAATGTCGCTGGCCATTGA
66 GTTGGCCTTGAATAAGCATATTGGCGCCTTTGTCATCTTTTAAGTCCAATGTCGCTGGCC-TTG-
**
1880646 AAT-AGCACATCAGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCG
129 AATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCG
* *
1880710 CC-CTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCAT
194 CCTCTTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCACC--T-TCAT
* * *
1880770 CTTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTTGCACCTTTATCTTTATGTCCAATAT
1 C-TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATAT
* *
1880835 CGTTGGCCTTGAATAAGCATATTGACGCCTTTGTCCTCTTTTAAGTCCAATGTCGCTGGCCTTGA
65 CGTTGGCCTTGAATAAGCATATTGGCGCCTTTGTCATCTTTTAAGTCCAATGTCGCTGGCCTTGA
*
1880900 ATCAGCACATTGGCACCTTCATCTTTAAGTCAAATATCGCTGGCCTTGAATCAGCATATTGGCGC
130 ATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGC
* * *
1880965 CTTTGTCATCTTTTAAGTCCATTGTCGCTGGCCTTGAA-CTAGCACATTGGCACCTTCAT
195 CTCT-TCATC-TTTAAGTCCAATGTCGCTGGCCTTGAATC-AGCATATTGGCACCTTCAT
* *
1881024 CTTTTAAGTCCAATGTCCCTGGCCTTGAA-CTAGCACATTGGCACCTTCATCTTTAAGGCCAATA
1 C-TTTAAGTCCAATGTCGCTGGCCTTGAATC-AGCACATTGGCACCTTCATCTTTAAGTCCAATA
* * *
1881088 TCGTTGGCCTTGAATCAGCATATTGGCGCCTTTGTCTTCTTTTATGTCCAATGTCGCTGGCCTTG
64 TCGTTGGCCTTGAATAAGCATATTGGCGCCTTTGTCATCTTTTAAGTCCAATGTCGCTGGCCTTG
* ** *
1881153 AATCAGTACATTGGCACCTTCATCTTTAAGTCCAATATCAATGGCCTTGAATTAGCATATTGGCG
129 AATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCG
* * * *
1881218 CCTTTGTCATCTTTTAAGTTCAATGTCGCTGGCATTGAATCAGCACATTGGCACCTTCAT
194 CCTCT-TCATC-TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCACCTTCAT
* * *
1881278 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTTAAGTCCAA
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACC--T-TCATC-TTTAAGTCCAA
* * * * * * *
1881343 TGTCGTTGGCCTTGAACT-AGCACATTGGCACC--T-TCATC-TTTAAGTCAAATATCAGTTAGC
62 TATCGTTGGCCTTGAA-TAAGCATATTGGCGCCTTTGTCATCTTTTAAGTCCAATGTC-GCTGGC
* * * * * *
1881403 CTTGAA--GGCACCTTTG-----TCATCATTTAAGTCTAATGTCGCTGGCCTTGAATCAGCACAT
125 CTTGAATCAGCACATTGGCACCTTCATC-TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATAT
* * * * *
1881461 TGGC-AC-CTTCATCGTTAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGCGCCTTTGTCA
189 TGGCGCCTCTTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCACC--T-TCA
1881524 T
251 T
* * * *
1881525 CTTTAAGTCCACTGTCGCTAGCCTTGAATTAGCACATTGGCACCTTCATCTTTAAGTCTAATATC
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATC
* * * *
1881590 GCTGGCCTCGAATCAA-CATATTAGCGCCTTTGTCATCTTTTAAGTCCAATGTTGCTGGCCTTGA
66 GTTGGCCTTGAAT-AAGCATATTGGCGCCTTTGTCATCTTTTAAGTCCAATGTCGCTGGCCTTGA
* * * * * *
1881654 ATCAACATATTGGCACCTTCATCTTTATGTCCAATATAGTTGGCCTTGAATCAGCATATTGGTGC
130 ATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGC
* ** * * * *
1881719 CTTCGTCATCTTTAAAACCCAATGTCAGTTGACCTTGAATCAGCATATTAGCATTCTTCTCAT
195 C-TCTTCATCTTT-AAGTCCAATGTC-GCTGGCCTTGAATCAGCATATTGGCA--CCT-TCAT
* * ** *
1881782 CTTCAAGTCTAAATGTCGCTAACCGTGAATCAGCACATTG
1 CTTTAAGTC-CAATGTCGCTGGCCTTGAATCAGCACATTG
1881822 AGATCCTTTT
Statistics
Matches: 891, Mismatches: 114, Indels: 83
0.82 0.10 0.08
Matches are distributed among these distances:
242 1 0.00
243 32 0.04
244 42 0.05
245 7 0.01
246 17 0.02
247 61 0.07
248 76 0.09
252 39 0.04
253 60 0.07
254 364 0.41
255 35 0.04
256 20 0.02
257 110 0.12
258 26 0.03
259 1 0.00
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.34
Consensus pattern (251 bp):
CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATC
GTTGGCCTTGAATAAGCATATTGGCGCCTTTGTCATCTTTTAAGTCCAATGTCGCTGGCCTTGAA
TCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCC
TCTTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCACCTTCAT
Found at i:1881222 original size:356 final size:353
Alignment explanation
Indices: 1880524--1881672 Score: 1474
Period size: 356 Copynumber: 3.3 Consensus size: 353
1880514 TTTCATTAAC
* *
1880524 TTTAAGACCAATGTCACTGGCCTTGAATCAACACATTAGCA-----A-CTTTAAGTCCAATATCG
1 TTTAAGTCCAATGTCGCTGGCCTTGAATCAACACATTAGCACCTTCATCTTTAAGTCCAATATCG
1880583 CTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATC-TTTAAGTCCAATGTCGCTGGCCATTGAA
66 CTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTTAAGTCCAATGTCGCTGGCC-TTGAA
* ** *
1880647 ATAGCACATCAGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCC
130 CTAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAAT-AGCACATT-G-GCC
1880712 CTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTTAA
192 CTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTTAA
* * * *
1880777 GTCCAATGTCGCTGGCCTTGAATCAGCACATTTGCACCTTTATCTTTATGTCCAATATCGTTGGC
257 GTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGATGGC
* * *
1880842 CTTGAATAAGCATATTGACGCCTTTGTCCTCT
322 CTTGAATTAGCATATTGGCGCCTTTGTCATCT
* * *
1880874 TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCAAATATCG
1 TTTAAGTCCAATGTCGCTGGCCTTGAATCAACACATTAGCACCTTCATCTTTAAGTCCAATATCG
*
1880939 CTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTTAAGTCCATTGTCGCTGGCCTTGAAC
66 CTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTTAAGTCCAATGTCGCTGGCCTTGAAC
* *
1881004 TAGCACATTGGCACCTTCATCTTTTAAGTCCAATGTCCCTGGCCTTGAACTAGCACATTGGCACC
131 TAGCACATTGGCACCTTCATC-TTTAAGTCCAATATCGCTGGCCTTGAA-TAGCACATTGGC-CC
* * * *
1881069 TTCATCTTTAAGGCCAATATCGTTGGCCTTGAATCAGCATATTGGCGCCTTTGTCTTCTTTTATG
193 TTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTTAAG
* *
1881134 TCCAATGTCGCTGGCCTTGAATCAGTACATTGGCACCTTCATCTTTAAGTCCAATATCAATGGCC
258 TCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGATGGCC
1881199 TTGAATTAGCATATTGGCGCCTTTGTCATCT
323 TTGAATTAGCATATTGGCGCCTTTGTCATCT
* * * *
1881230 TTTAAGTTCAATGTCGCTGGCATTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCG
1 TTTAAGTCCAATGTCGCTGGCCTTGAATCAACACATTAGCACCTTCATCTTTAAGTCCAATATCG
*
1881295 CTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTTAAGTCCAATGTCGTTGGCCTTGAAC
66 CTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTTAAGTCCAATGTCGCTGGCCTTGAAC
* * * * * *
1881360 TAGCACATTGGCACCTTCATCTTTAAGTCAAATATCAGTTAGCCTTGAA-GGCACCTTTG----T
131 TAGCACATTGGCACCTTCATCTTTAAGTCCAATATC-GCTGGCCTTGAATAGCACATTGGCCCTT
* * * * *
1881420 CATCATTTAAGTCTAATGTCGCTGGCCTTGAATCAGCACATTGGCACC--T-TCATC-GTTAAGT
195 CATC-TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTTAAGT
* * * * * * * *
1881481 CCAATATCGTTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTAAGTCCACTGTCGCTAG
259 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACC--T-TCATCTTTAAGTCCAATATCGATGG
* *
1881546 CCTTGAATTAGCACATTGGCACC--T-TCATC-
321 CCTTGAATTAGCATATTGGCGCCTTTGTCATCT
* * * * *
1881575 TTTAAGTCTAATATCGCTGGCCTCGAATCAACATATTAGCGCCTTTGTCATCTTTTAAGTCCAAT
1 TTTAAGTCCAATGTCGCTGGCCTTGAATCAACACATTAGCACC--T-TCATC-TTTAAGTCCAAT
* * * *
1881640 GTTGCTGGCCTTGAATCAACATATTGGCACCTT
62 ATCGCTGGCCTTGAATCAGCATATTGGCGCCTT
1881673 CATCTTTATG
Statistics
Matches: 708, Mismatches: 72, Indels: 39
0.86 0.09 0.05
Matches are distributed among these distances:
345 34 0.05
346 41 0.06
347 6 0.01
348 7 0.01
349 87 0.12
350 74 0.10
354 7 0.01
355 16 0.02
356 382 0.54
357 53 0.07
358 1 0.00
ACGTcount: A:0.23, C:0.25, G:0.18, T:0.34
Consensus pattern (353 bp):
TTTAAGTCCAATGTCGCTGGCCTTGAATCAACACATTAGCACCTTCATCTTTAAGTCCAATATCG
CTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTTAAGTCCAATGTCGCTGGCCTTGAAC
TAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATAGCACATTGGCCCTTC
ATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTTAAGTCC
AATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGATGGCCTTG
AATTAGCATATTGGCGCCTTTGTCATCT
Found at i:1881715 original size:49 final size:49
Alignment explanation
Indices: 1880566--1881715 Score: 1161
Period size: 49 Copynumber: 22.8 Consensus size: 49
1880556 ACATTAGCAA
*
1880566 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC--T-TCAT
* * **
1880618 CTTTAAGTCCAATGTCGCTGGCCATTGAAAT-AGCACATCAGCACCTTCAT
1 CTTTAAGTCCAATATCGCTGGCC-TTG-AATCAGCATATTGGCACCTTCAT
*
1880668 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCCTTCAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGC-ACCTTCAT
*
1880718 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC--T-TCAT
* * * *
1880770 CTTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTTGCACCTTTAT
1 C-TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCAT
* * * * * *
1880820 CTTTATGTCCAATATCGTTGGCCTTGAATAAGCATATTGACGCCTTTGTCCT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC--T-TCAT
* *
1880872 CTTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
1 C-TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCAT
* *
1880922 CTTTAAGTCAAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC--T-TCAT
* * *
1880974 CTTTTAAGTCCATTGTCGCTGGCCTTGAA-CTAGCACATTGGCACCTTCAT
1 C-TTTAAGTCCAATATCGCTGGCCTTGAATC-AGCATATTGGCACCTTCAT
* * *
1881024 CTTTTAAGTCCAATGTCCCTGGCCTTGAA-CTAGCACATTGGCACCTTCAT
1 C-TTTAAGTCCAATATCGCTGGCCTTGAATC-AGCATATTGGCACCTTCAT
* * * *
1881074 CTTTAAGGCCAATATCGTTGGCCTTGAATCAGCATATTGGCGCCTTTGTCTT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC--T-TCAT
* * * *
1881126 CTTTTATGTCCAATGTCGCTGGCCTTGAATCAGTACATTGGCACCTTCAT
1 C-TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCAT
** * *
1881176 CTTTAAGTCCAATATCAATGGCCTTGAATTAGCATATTGGCGCCTTTGTCAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC--T-TCAT
* * * *
1881228 CTTTTAAGTTCAATGTCGCTGGCATTGAATCAGCACATTGGCACCTTCAT
1 C-TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCAT
*
1881278 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC--T-TCAT
* * *
1881330 CTTTTAAGTCCAATGTCGTTGGCCTTGAA-CTAGCACATTGGCACCTTCAT
1 C-TTTAAGTCCAATATCGCTGGCCTTGAATC-AGCATATTGGCACCTTCAT
* * * * * *
1881380 CTTTAAGTCAAATATCAGTTAGCCTTGAAGGCA-CCT-TTGTCA---TCA-
1 CTTTAAGTCCAATATC-GCTGGCCTTGAA-TCAGCATATTGGCACCTTCAT
* * *
1881425 -TTTAAGTCTAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCAT
* * *
1881473 CGTTAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGCGCCTTTGTCAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC--T-TCAT
* * * * *
1881525 CTTTAAGTCCACTGTCGCTAGCCTTGAATTAGCACATTGGCACCTTCAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCAT
* * * * *
1881574 CTTTAAGTCTAATATCGCTGGCCTCGAATCAACATATTAGCGCCTTTGTCAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC--T-TCAT
* * *
1881626 CTTTTAAGTCCAATGTTGCTGGCCTTGAATCAACATATTGGCACCTTCAT
1 C-TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCAT
* * *
1881676 CTTTATGTCCAATATAGTTGGCCTTGAATCAGCATATTGG
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGG
1881716 TGCCTTCGTC
Statistics
Matches: 916, Mismatches: 134, Indels: 99
0.80 0.12 0.09
Matches are distributed among these distances:
42 2 0.00
43 11 0.01
44 18 0.02
46 3 0.00
47 3 0.00
48 3 0.00
49 322 0.35
50 168 0.18
51 17 0.02
52 97 0.11
53 269 0.29
54 3 0.00
ACGTcount: A:0.23, C:0.25, G:0.18, T:0.34
Consensus pattern (49 bp):
CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCAT
Found at i:1882545 original size:19 final size:19
Alignment explanation
Indices: 1882521--1882603 Score: 97
Period size: 19 Copynumber: 4.7 Consensus size: 19
1882511 TTTCAACGAT
*
1882521 TTGTATCGATACATTAGTG
1 TTGTATCGATACATAAGTG
1882540 TTGTATCGATAC--AA---
1 TTGTATCGATACATAAGTG
1882554 -TGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
*
1882572 TTGTATCGATACATAAGTT
1 TTGTATCGATACATAAGTG
*
1882591 TTGTATGGATACA
1 TTGTATCGATACA
1882604 ATGTACTACT
Statistics
Matches: 55, Mismatches: 3, Indels: 12
0.79 0.04 0.17
Matches are distributed among these distances:
13 11 0.20
15 2 0.04
17 1 0.02
19 41 0.75
ACGTcount: A:0.31, C:0.11, G:0.19, T:0.39
Consensus pattern (19 bp):
TTGTATCGATACATAAGTG
Found at i:1882558 original size:32 final size:32
Alignment explanation
Indices: 1882522--1882584 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
1882512 TTCAACGATT
*
1882522 TGTATCGATACATTAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
1882554 TGTATCGATACATAAGTGTTGTATCGATACA
1 TGTATCGATACATAAGTGTTGTATCGATACA
1882585 TAAGTTTTGT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:1882559 original size:13 final size:13
Alignment explanation
Indices: 1882541--1882565 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1882531 ACATTAGTGT
1882541 TGTATCGATACAA
1 TGTATCGATACAA
1882554 TGTATCGATACA
1 TGTATCGATACA
1882566 TAAGTGTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1882733 original size:52 final size:52
Alignment explanation
Indices: 1882688--1882817 Score: 188
Period size: 52 Copynumber: 2.5 Consensus size: 52
1882678 CACTGATCTT
* *
1882688 TGTATCAATACATGCAGGCAAATTTGCCTAGATATATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATATATCGATACACTATGAAA
* * * * *
1882740 AGTATCGATACATACAGGCAAATTTTCCCAGATGTACCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATATATCGATACACTATGAAA
1882792 TGTATCGATACATGCAGGACAAATTT
1 TGTATCGATACATGCAGG-CAAATTT
1882818 TCATATTTCG
Statistics
Matches: 68, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
52 61 0.90
53 7 0.10
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATATATCGATACACTATGAAA
Found at i:1883702 original size:20 final size:20
Alignment explanation
Indices: 1883657--1883702 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
1883647 GATAACAGCC
*
1883657 CATGATTCATGCATTTTAAG
1 CATGTTTCATGCATTTTAAG
1883677 CTATGTTTCATGCA-TTTACAG
1 C-ATGTTTCATGCATTTTA-AG
1883698 CATGT
1 CATGT
1883703 CCAGCACCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 9 0.39
21 14 0.61
ACGTcount: A:0.26, C:0.17, G:0.15, T:0.41
Consensus pattern (20 bp):
CATGTTTCATGCATTTTAAG
Found at i:1897666 original size:19 final size:18
Alignment explanation
Indices: 1897644--1897706 Score: 69
Period size: 19 Copynumber: 3.4 Consensus size: 18
1897634 GTTCTCCGCA
1897644 AAAAAAAAAGATGAAAAAG
1 AAAAAAAAAGA-GAAAAAG
1897663 AAAAAAAAAGAAGAAAAA-
1 AAAAAAAAAG-AGAAAAAG
1897681 AATAAACAAAA-A-AAAAAG
1 AA-AAA-AAAAGAGAAAAAG
1897699 AAAAAAAA
1 AAAAAAAA
1897707 CAACAAACAC
Statistics
Matches: 40, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
16 3 0.08
17 8 0.20
18 5 0.12
19 19 0.47
20 5 0.12
ACGTcount: A:0.86, C:0.02, G:0.10, T:0.03
Consensus pattern (18 bp):
AAAAAAAAAGAGAAAAAG
Found at i:1897668 original size:22 final size:21
Alignment explanation
Indices: 1897643--1897703 Score: 70
Period size: 22 Copynumber: 2.9 Consensus size: 21
1897633 CGTTCTCCGC
1897643 AAAAAAAAAAGATGAAAAAGAA
1 AAAAAAAAAAGA-GAAAAAGAA
* * *
1897665 AAAAAAAGAAGAAAAAAATAA
1 AAAAAAAAAAGAGAAAAAGAA
1897686 ACAAAAAAAAA-AGAAAAA
1 A-AAAAAAAAAGAGAAAAA
1897704 AAACAACAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
21 14 0.42
22 19 0.58
ACGTcount: A:0.85, C:0.02, G:0.10, T:0.03
Consensus pattern (21 bp):
AAAAAAAAAAGAGAAAAAGAA
Found at i:1897691 original size:23 final size:23
Alignment explanation
Indices: 1897642--1897770 Score: 100
Period size: 23 Copynumber: 5.3 Consensus size: 23
1897632 GCGTTCTCCG
** *
1897642 CAAAAAAAAAAGATGAAAAAGAA
1 CAAAAAAAAAAGAAAAAAAACAA
*
1897665 -AAAAAAAGAAGAAAAAAATA-AA
1 CAAAAAAAAAAGAAAAAAA-ACAA
1897687 CAAAAAAAAAAGAAAAAAAACAA
1 CAAAAAAAAAAGAAAAAAAACAA
*
1897710 CAAACACAACAAAAAAAACAAACAAACAAAA
1 C-AA-A-AA-AAAAAGAA-AAA-AAAC--AA
*
1897741 CAAAAAAAGAAAGAAAAAAAGCAA
1 CAAAAAAA-AAAGAAAAAAAACAA
1897765 CAAAAA
1 CAAAAA
1897771 GGGTCCGGAT
Statistics
Matches: 87, Mismatches: 7, Indels: 23
0.74 0.06 0.20
Matches are distributed among these distances:
22 18 0.21
23 21 0.24
24 10 0.11
25 1 0.01
26 5 0.06
27 12 0.14
28 10 0.11
29 5 0.06
30 2 0.02
31 3 0.03
ACGTcount: A:0.81, C:0.10, G:0.07, T:0.02
Consensus pattern (23 bp):
CAAAAAAAAAAGAAAAAAAACAA
Found at i:1897704 original size:22 final size:21
Alignment explanation
Indices: 1897642--1897770 Score: 77
Period size: 21 Copynumber: 6.0 Consensus size: 21
1897632 GCGTTCTCCG
*
1897642 CAAAAAAAAAAGATGAAAAAGAA
1 CAAAAAAAAAAGA--AAAAAAAA
*
1897665 -AAAAAAAGAAGAAAAAAATAAA
1 CAAAAAAAAAAG-AAAAAA-AAA
1897687 CAAAAAAAAAAG-AAAAAAAA
1 CAAAAAAAAAAGAAAAAAAAA
* * *
1897707 CAACAAACACAA-CAAAAAAAA
1 CAA-AAAAAAAAGAAAAAAAAA
* *
1897728 CAAACAAACAAAACAAAAAAAGA
1 CAAA-AAA-AAAAGAAAAAAAAA
* * *
1897751 -AAGAAAAAAAGCAACAAAAA
1 CAAAAAAAAAAGAAAAAAAAA
1897771 GGGTCCGGAT
Statistics
Matches: 84, Mismatches: 14, Indels: 19
0.72 0.12 0.16
Matches are distributed among these distances:
20 17 0.20
21 32 0.38
22 17 0.20
23 18 0.21
ACGTcount: A:0.81, C:0.10, G:0.07, T:0.02
Consensus pattern (21 bp):
CAAAAAAAAAAGAAAAAAAAA
Done.