Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032249.1 Gossypioides kirkii chromosome KI_07
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: 37252039
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 2100 characters in sequence are not A, C, G, or T
File 6 of 120
Found at i:1532867 original size:16 final size:15
Alignment explanation
Indices: 1532837--1532886 Score: 61
Period size: 14 Copynumber: 3.5 Consensus size: 15
1532827 TAAGTAAAAA
1532837 ATAATATATAA-TTT
1 ATAATATATAATTTT
1532851 ATAATATATAATTTTT
1 ATAATATATAA-TTTT
*
1532867 ATAA-AT-TAGTTTT
1 ATAATATATAATTTT
1532880 ATAATAT
1 ATAATAT
1532887 CATTTTAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
13 8 0.25
14 15 0.47
15 2 0.06
16 7 0.22
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (15 bp):
ATAATATATAATTTT
Found at i:1533578 original size:18 final size:18
Alignment explanation
Indices: 1533557--1533591 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1533547 AAGATTAAAA
*
1533557 AATATTGTATAATATTTT
1 AATATTATATAATATTTT
*
1533575 AATATTATATAGTATTT
1 AATATTATATAATATTT
1533592 CAACATGTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (18 bp):
AATATTATATAATATTTT
Found at i:1536074 original size:20 final size:19
Alignment explanation
Indices: 1536041--1536078 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
1536031 AATGTAAATT
1536041 TTTTTAAAAAAATTTAATA
1 TTTTTAAAAAAATTTAATA
*
1536060 TTTTTAATAATAATTTAAT
1 TTTTTAA-AAAAATTTAAT
1536079 TTAAAAAGTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
TTTTTAAAAAAATTTAATA
Found at i:1536095 original size:35 final size:35
Alignment explanation
Indices: 1536056--1536122 Score: 89
Period size: 35 Copynumber: 1.9 Consensus size: 35
1536046 AAAAAAATTT
* * *
1536056 AATATTTTTAATAATAATTTAATTTAAAAAGTCTG
1 AATATTTTGAATAACAAATTAATTTAAAAAGTCTG
* *
1536091 AATATTTTGAATAACAAATTAGTTTTAAAAGT
1 AATATTTTGAATAACAAATTAATTTAAAAAGT
1536123 TAAAATCAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 27 1.00
ACGTcount: A:0.46, C:0.03, G:0.07, T:0.43
Consensus pattern (35 bp):
AATATTTTGAATAACAAATTAATTTAAAAAGTCTG
Found at i:1540079 original size:18 final size:19
Alignment explanation
Indices: 1540053--1540090 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
1540043 TTAATAAGTA
* *
1540053 ATTTGAAAATTATAAAAAT
1 ATTTGAAAAATAAAAAAAT
1540072 ATTT-AAAAATAAAAAAAT
1 ATTTGAAAAATAAAAAAAT
1540090 A
1 A
1540091 AATTAGAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.32
Consensus pattern (19 bp):
ATTTGAAAAATAAAAAAAT
Found at i:1549394 original size:22 final size:20
Alignment explanation
Indices: 1549351--1549394 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
1549341 TTAGTACTTC
* *
1549351 AAATATTTATTTAATTGGAT
1 AAATAATTATTTAATTGAAT
1549371 AAATAATTACTTTAGATTGAAT
1 AAATAATTA-TTTA-ATTGAAT
1549393 AA
1 AA
1549395 TGAATTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 8 0.40
21 4 0.20
22 8 0.40
ACGTcount: A:0.45, C:0.02, G:0.09, T:0.43
Consensus pattern (20 bp):
AAATAATTATTTAATTGAAT
Found at i:1554545 original size:22 final size:22
Alignment explanation
Indices: 1554498--1554542 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
1554488 GAACAATGTT
*
1554498 AATAAATAATAAACAAACAGAC
1 AATAAATAATAAACAAACACAC
* *
1554520 AATAAATAA-ATACATACACAC
1 AATAAATAATAAACAAACACAC
1554541 AA
1 AA
1554543 ATATTATTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.67, C:0.16, G:0.02, T:0.16
Consensus pattern (22 bp):
AATAAATAATAAACAAACACAC
Found at i:1555588 original size:18 final size:18
Alignment explanation
Indices: 1555565--1555599 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1555555 CTATAAAACT
*
1555565 CGAACTCGAACCCGAACC
1 CGAACTCAAACCCGAACC
1555583 CGAACTCAAACCCGAAC
1 CGAACTCAAACCCGAAC
1555600 AGTTGTTAGC
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:0.37, C:0.43, G:0.14, T:0.06
Consensus pattern (18 bp):
CGAACTCAAACCCGAACC
Found at i:1559341 original size:20 final size:20
Alignment explanation
Indices: 1559312--1559357 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
1559302 TATGTTTGAA
*
1559312 ATGTTACGTTTTAGTCACTT
1 ATGTTTCGTTTTAGTCACTT
1559332 ATGTTTCGTTTTAGTCACTT
1 ATGTTTCGTTTTAGTCACTT
1559352 ATGTTT
1 ATGTTT
1559358 GAAATGTTAC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.17, C:0.13, G:0.15, T:0.54
Consensus pattern (20 bp):
ATGTTTCGTTTTAGTCACTT
Found at i:1559363 original size:49 final size:49
Alignment explanation
Indices: 1559291--1559385 Score: 181
Period size: 49 Copynumber: 1.9 Consensus size: 49
1559281 TTAGGTTACA
1559291 TTTTAGCCACTTATGTTTGAAATGTTACGTTTTAGTCACTTATGTTTCG
1 TTTTAGCCACTTATGTTTGAAATGTTACGTTTTAGTCACTTATGTTTCG
*
1559340 TTTTAGTCACTTATGTTTGAAATGTTACGTTTTAGTCACTTATGTT
1 TTTTAGCCACTTATGTTTGAAATGTTACGTTTTAGTCACTTATGTT
1559386 AACGTGTTGT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 45 1.00
ACGTcount: A:0.21, C:0.13, G:0.16, T:0.51
Consensus pattern (49 bp):
TTTTAGCCACTTATGTTTGAAATGTTACGTTTTAGTCACTTATGTTTCG
Found at i:1561163 original size:20 final size:20
Alignment explanation
Indices: 1561140--1561187 Score: 71
Period size: 20 Copynumber: 2.4 Consensus size: 20
1561130 GAAACTAGGT
1561140 GAGGAAAAAAGAA-AAATAGA
1 GAGGAAAAAAGAAGAAA-AGA
1561160 GAGGAAAAAAGAAGAAAAGA
1 GAGGAAAAAAGAAGAAAAGA
1561180 GAGAGAAA
1 GAG-GAAA
1561188 TTGTATAGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
20 19 0.73
21 7 0.27
ACGTcount: A:0.69, C:0.00, G:0.29, T:0.02
Consensus pattern (20 bp):
GAGGAAAAAAGAAGAAAAGA
Found at i:1562949 original size:4 final size:4
Alignment explanation
Indices: 1562942--1562990 Score: 98
Period size: 4 Copynumber: 12.2 Consensus size: 4
1562932 TATATATATA
1562942 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1562990 T
1 T
1562991 GACATACCAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 45 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:1564629 original size:4 final size:4
Alignment explanation
Indices: 1564620--1564652 Score: 66
Period size: 4 Copynumber: 8.2 Consensus size: 4
1564610 ACGGTATGTG
1564620 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
1564653 TATATATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:1564669 original size:18 final size:18
Alignment explanation
Indices: 1564642--1564676 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1564632 ACATACATAC
*
1564642 ATACATACATATATATAT
1 ATACACACATATATATAT
*
1564660 ATACACACATGTATATA
1 ATACACACATATATATA
1564677 CTATGAAGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.49, C:0.14, G:0.03, T:0.34
Consensus pattern (18 bp):
ATACACACATATATATAT
Found at i:1571948 original size:21 final size:21
Alignment explanation
Indices: 1571910--1571949 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1571900 AGTCCATATT
*
1571910 ATATTTAAAATATTTTTAAAA
1 ATATTTAAAATATCTTTAAAA
* *
1571931 ATATTTATATTATCTTTAA
1 ATATTTAAAATATCTTTAA
1571950 TTTATATTTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (21 bp):
ATATTTAAAATATCTTTAAAA
Found at i:1578325 original size:10 final size:9
Alignment explanation
Indices: 1578298--1578379 Score: 50
Period size: 9 Copynumber: 9.1 Consensus size: 9
1578288 AACTTTTTAT
*
1578298 ATTTTTATA
1 ATTTTTAAA
1578307 ATTTTTAAA
1 ATTTTTAAA
1578316 ATTTTCTAAA
1 ATTTT-TAAA
1578326 ATGATTTT---
1 AT--TTTTAAA
1578334 ATTTTT-AA
1 ATTTTTAAA
1578342 A--TTTAAA
1 ATTTTTAAA
1578349 GAGTTTTTAAA
1 -A-TTTTTAAA
*
1578360 ATTTTTCATA
1 ATTTTT-AAA
1578370 ATTTTTAAA
1 ATTTTTAAA
1578379 A
1 A
1578380 AAATTAATTA
Statistics
Matches: 59, Mismatches: 3, Indels: 22
0.70 0.04 0.26
Matches are distributed among these distances:
6 7 0.12
7 2 0.03
8 4 0.07
9 21 0.36
10 15 0.25
11 7 0.12
12 3 0.05
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (9 bp):
ATTTTTAAA
Found at i:1579712 original size:27 final size:29
Alignment explanation
Indices: 1579681--1579747 Score: 75
Period size: 31 Copynumber: 2.3 Consensus size: 29
1579671 TAGAGTTTCA
*
1579681 CATGTATAA-TTG-CACCAAATTAAAGTT
1 CATGTATAAGTTGACACCAAATCAAAGTT
**
1579708 CATGTATACAGTTGTACATTAAATCAAAGTT
1 CATGTATA-AGTTG-ACACCAAATCAAAGTT
1579739 CATGTATAA
1 CATGTATAA
1579748 CTTTGAGATT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
27 8 0.24
28 1 0.03
29 3 0.09
30 1 0.03
31 20 0.61
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (29 bp):
CATGTATAAGTTGACACCAAATCAAAGTT
Found at i:1582066 original size:14 final size:14
Alignment explanation
Indices: 1582049--1582078 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1582039 TAAATATATT
*
1582049 AAATAAAATTAAAA
1 AAATAAAAATAAAA
1582063 AAATAAAAATAAAA
1 AAATAAAAATAAAA
1582077 AA
1 AA
1582079 TTAATAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (14 bp):
AAATAAAAATAAAA
Found at i:1598494 original size:15 final size:15
Alignment explanation
Indices: 1598474--1598506 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
1598464 TTGCAATTTT
1598474 AAAAAATCA-AAATTA
1 AAAAAATCATAAA-TA
1598489 AAAAAATCATAAATA
1 AAAAAATCATAAATA
1598504 AAA
1 AAA
1598507 GGTTATATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 14 0.82
16 3 0.18
ACGTcount: A:0.76, C:0.06, G:0.00, T:0.18
Consensus pattern (15 bp):
AAAAAATCATAAATA
Found at i:1599063 original size:16 final size:16
Alignment explanation
Indices: 1599042--1599072 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1599032 TATGTTGGAG
1599042 CATATAAATTTGAAAT
1 CATATAAATTTGAAAT
*
1599058 CATATATATTTGAAA
1 CATATAAATTTGAAA
1599073 ACTTTTTCAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.06, G:0.06, T:0.39
Consensus pattern (16 bp):
CATATAAATTTGAAAT
Found at i:1612375 original size:26 final size:26
Alignment explanation
Indices: 1612346--1612396 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
1612336 ATACTTGGAG
1612346 ACTGAAAAACTCACCTCCAAATCCTT
1 ACTGAAAAACTCACCTCCAAATCCTT
* *
1612372 ACTGAAACACTCACCTCTAAATCCT
1 ACTGAAAAACTCACCTCCAAATCCT
1612397 CCATTAAGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.37, C:0.35, G:0.04, T:0.24
Consensus pattern (26 bp):
ACTGAAAAACTCACCTCCAAATCCTT
Found at i:1634907 original size:60 final size:60
Alignment explanation
Indices: 1634843--1635018 Score: 219
Period size: 60 Copynumber: 2.9 Consensus size: 60
1634833 TTAATATAAT
*
1634843 ATTTGGTACTTGAACTTGACATTTTTTCCTAATTTGGTACCTAAATTTTTTTTGGGTCCA
1 ATTTGGTACCTGAACTTGACATTTTTTCCTAATTTGGTACCTAAATTTTTTTTGGGTCCA
* ** * * * * * *
1634903 ATTTGATACCCAAACTTGACACTTTTTCTTAAGTTGATACTTAAACTTTTTTTGGGTCCA
1 ATTTGGTACCTGAACTTGACATTTTTTCCTAATTTGGTACCTAAATTTTTTTTGGGTCCA
*
1634963 ATTTGGTACCTGAACTTGACTCTTTTTTTCCTAATTTGGTACCT-AATCTTTTTTTG
1 ATTTGGTACCTGAACTTGA--CATTTTTTCCTAATTTGGTACCTAAAT-TTTTTTTG
1635019 TTCGATTTGG
Statistics
Matches: 93, Mismatches: 20, Indels: 4
0.79 0.17 0.03
Matches are distributed among these distances:
60 66 0.71
61 2 0.02
62 25 0.27
ACGTcount: A:0.22, C:0.17, G:0.13, T:0.48
Consensus pattern (60 bp):
ATTTGGTACCTGAACTTGACATTTTTTCCTAATTTGGTACCTAAATTTTTTTTGGGTCCA
Found at i:1639394 original size:29 final size:29
Alignment explanation
Indices: 1639334--1639393 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
1639324 CAGGTTCATT
* *
1639334 AAATTTAAATTTTTAAATCTAAAAGATAA
1 AAATCTAAATTTTTAAATATAAAAGATAA
1639363 AAATCTAAATTTTTTAAA-ATAAAA-ATAA
1 AAATCTAAA-TTTTTAAATATAAAAGATAA
1639391 AAA
1 AAA
1639394 AATTCAAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 7 0.25
29 13 0.46
30 8 0.29
ACGTcount: A:0.60, C:0.03, G:0.02, T:0.35
Consensus pattern (29 bp):
AAATCTAAATTTTTAAATATAAAAGATAA
Found at i:1639581 original size:12 final size:12
Alignment explanation
Indices: 1639564--1639588 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1639554 AATAAATAAT
1639564 TTCCATTATTGC
1 TTCCATTATTGC
1639576 TTCCATTATTGC
1 TTCCATTATTGC
1639588 T
1 T
1639589 AGATTTCAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.24, G:0.08, T:0.52
Consensus pattern (12 bp):
TTCCATTATTGC
Found at i:1649953 original size:21 final size:21
Alignment explanation
Indices: 1649892--1649959 Score: 66
Period size: 21 Copynumber: 3.1 Consensus size: 21
1649882 ACAAAAAAGA
1649892 TTTGTCTAAGTCACTTCGTTTCTT
1 TTTGTCTAAGTCACTTC---TCTT
* **
1649916 TTTGTCCAAGTTGCTTCTCTT
1 TTTGTCTAAGTCACTTCTCTT
*
1649937 TTTGTCTAACTCACTTC-CTT
1 TTTGTCTAAGTCACTTCTCTT
1649957 TTT
1 TTT
1649960 TCTTTGTGAG
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
20 6 0.16
21 17 0.46
24 14 0.38
ACGTcount: A:0.12, C:0.24, G:0.10, T:0.54
Consensus pattern (21 bp):
TTTGTCTAAGTCACTTCTCTT
Found at i:1650424 original size:28 final size:28
Alignment explanation
Indices: 1650371--1650426 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
1650361 TTCTTGAATA
* *
1650371 AGTGGTCAAAATGTAATTTTTATAATTG
1 AGTGATCAAAATGTAATTTATATAATTG
*
1650399 AGTGATCAAAATTTGAATTTAT-TAATTG
1 AGTGATCAAAATGT-AATTTATATAATTG
1650427 TTGAGTAACA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 18 0.75
29 6 0.25
ACGTcount: A:0.38, C:0.04, G:0.16, T:0.43
Consensus pattern (28 bp):
AGTGATCAAAATGTAATTTATATAATTG
Found at i:1652429 original size:6 final size:6
Alignment explanation
Indices: 1652420--1652448 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
1652410 ATTCATCATC
1652420 ATTTGA ATTTGA ATTTGA ATTTGA ATTTG
1 ATTTGA ATTTGA ATTTGA ATTTGA ATTTG
1652449 CATAATTAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.17, T:0.52
Consensus pattern (6 bp):
ATTTGA
Found at i:1652941 original size:17 final size:17
Alignment explanation
Indices: 1652919--1652952 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1652909 GAAAAATATA
*
1652919 TTTTTATGTTATATCTT
1 TTTTTAAGTTATATCTT
1652936 TTTTTAAGTTATATCTT
1 TTTTTAAGTTATATCTT
1652953 AAATACACAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.21, C:0.06, G:0.06, T:0.68
Consensus pattern (17 bp):
TTTTTAAGTTATATCTT
Found at i:1659359 original size:18 final size:19
Alignment explanation
Indices: 1659319--1659365 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
1659309 TTTCCCGATA
*
1659319 ATTTCAATATCCTTCTAGC
1 ATTTCAATATCCTTCAAGC
*
1659338 ATTTCAA-ATCCTTCAAGG
1 ATTTCAATATCCTTCAAGC
*
1659356 ATTTTAATAT
1 ATTTCAATAT
1659366 AAACTTTACT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 15 0.62
19 9 0.38
ACGTcount: A:0.32, C:0.19, G:0.06, T:0.43
Consensus pattern (19 bp):
ATTTCAATATCCTTCAAGC
Found at i:1664038 original size:21 final size:25
Alignment explanation
Indices: 1663991--1664048 Score: 79
Period size: 24 Copynumber: 2.4 Consensus size: 25
1663981 AACCTCAATT
1663991 TTTTTAATTTTATTACTAGTATATA
1 TTTTTAATTTTATTACTAGTATATA
1664016 TTTTT-ATTTTATTA-TA-T-TATA
1 TTTTTAATTTTATTACTAGTATATA
1664037 TTTTATAATTTT
1 TTTT-TAATTTT
1664049 TTTAAAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
21 8 0.26
22 2 0.06
23 7 0.23
24 9 0.29
25 5 0.16
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (25 bp):
TTTTTAATTTTATTACTAGTATATA
Found at i:1666267 original size:17 final size:17
Alignment explanation
Indices: 1666247--1666283 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
1666237 TTAATCTATC
*
1666247 AATTTTTTTTTAAAAAA
1 AATTGTTTTTTAAAAAA
*
1666264 AATTGTTTTTTAACAAA
1 AATTGTTTTTTAAAAAA
1666281 AAT
1 AAT
1666284 ATTGGGAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (17 bp):
AATTGTTTTTTAAAAAA
Found at i:1666410 original size:28 final size:29
Alignment explanation
Indices: 1666352--1666412 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 29
1666342 ACGCTATTTT
**
1666352 TTTTAAAAATTTTATGAATTTTTTTAGTA
1 TTTTAAAAATTTTATGAATTTTTAAAGTA
* * *
1666381 TTTTAATATTTTTAT-AATTTTTAAATTA
1 TTTTAAAAATTTTATGAATTTTTAAAGTA
1666409 TTTT
1 TTTT
1666413 TTACATAACA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
28 14 0.52
29 13 0.48
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (29 bp):
TTTTAAAAATTTTATGAATTTTTAAAGTA
Found at i:1667989 original size:18 final size:19
Alignment explanation
Indices: 1667947--1667990 Score: 58
Period size: 16 Copynumber: 2.5 Consensus size: 19
1667937 GAAATTTTTA
1667947 TCTAAATTTTATATAATTT
1 TCTAAATTTTATATAATTT
*
1667966 T-T-AATTTT-TTTAATTT
1 TCTAAATTTTATATAATTT
1667982 TCTAAATTT
1 TCTAAATTT
1667991 AACAAAAATC
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
16 8 0.36
17 7 0.32
18 6 0.27
19 1 0.05
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.64
Consensus pattern (19 bp):
TCTAAATTTTATATAATTT
Found at i:1668367 original size:3 final size:3
Alignment explanation
Indices: 1668359--1668411 Score: 79
Period size: 3 Copynumber: 17.3 Consensus size: 3
1668349 ATTAAATAAG
* *
1668359 TAT TAT TAT TTT TGAA TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1668405 TAT TAT T
1 TAT TAT T
1668412 TTAATAATTA
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
3 44 0.98
4 1 0.02
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:1671848 original size:6 final size:6
Alignment explanation
Indices: 1671837--1671887 Score: 59
Period size: 6 Copynumber: 8.3 Consensus size: 6
1671827 TTTTGAATTT
* *
1671837 ATTTAA ATTTAA ATTCAA CTATTTAA ATTT-A TTTTAA ATTTAA ATTTAA
1 ATTTAA ATTTAA ATTTAA --ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
1671886 AT
1 AT
1671888 CAAATTATGA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
5 4 0.11
6 29 0.76
8 5 0.13
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (6 bp):
ATTTAA
Found at i:1672615 original size:20 final size:22
Alignment explanation
Indices: 1672566--1672619 Score: 78
Period size: 21 Copynumber: 2.6 Consensus size: 22
1672556 CTGCTCATTG
1672566 AATATTTTAAAT-GCATTAATT
1 AATATTTTAAATAGCATTAATT
*
1672587 AATATTTTAAATAGTATTAATT
1 AATATTTTAAATAGCATTAATT
1672609 -A-ATTTTAAATA
1 AATATTTTAAATA
1672620 AAAGCATTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
20 10 0.32
21 13 0.42
22 8 0.26
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (22 bp):
AATATTTTAAATAGCATTAATT
Found at i:1673892 original size:29 final size:29
Alignment explanation
Indices: 1673854--1673967 Score: 94
Period size: 29 Copynumber: 3.9 Consensus size: 29
1673844 ACCTCGAAAC
*
1673854 TTCCAAAAATTACCAGTTTACCCCCGAACT
1 TTCCAAAAATTACCATTTTACCCCCGAA-T
*
1673884 TTCC-AAAATT-CCATTTTTAACCCCG-AT
1 TTCCAAAAATTACCA-TTTTACCCCCGAAT
* *
1673911 TTCACCGAAATTTACCATTTTACCTCCC-AAT
1 TT--CCAAAAATTACCATTTTACC-CCCGAAT
*
1673942 AGTCC-AAAATTACCATTTTACCCCCG
1 -TTCCAAAAATTACCATTTTACCCCCG
1673968 GGTATCCAAA
Statistics
Matches: 69, Mismatches: 6, Indels: 19
0.73 0.06 0.20
Matches are distributed among these distances:
27 3 0.04
28 7 0.10
29 33 0.48
30 17 0.25
31 8 0.12
32 1 0.01
ACGTcount: A:0.31, C:0.32, G:0.05, T:0.32
Consensus pattern (29 bp):
TTCCAAAAATTACCATTTTACCCCCGAAT
Found at i:1681378 original size:6 final size:6
Alignment explanation
Indices: 1681367--1681426 Score: 111
Period size: 6 Copynumber: 10.0 Consensus size: 6
1681357 GTCCACTGTC
1681367 CCGCCA CCGCCA CCGCCA CCGCCA CCGCCA CCGCCA CCGCCA CCGCCA
1 CCGCCA CCGCCA CCGCCA CCGCCA CCGCCA CCGCCA CCGCCA CCGCCA
*
1681415 CCGCCT CCGCCA
1 CCGCCA CCGCCA
1681427 TCCCCGTCCC
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 52 1.00
ACGTcount: A:0.15, C:0.67, G:0.17, T:0.02
Consensus pattern (6 bp):
CCGCCA
Found at i:1683639 original size:18 final size:18
Alignment explanation
Indices: 1683616--1683655 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
1683606 AGAAAAAGTT
1683616 GAAATATAATTCGAAAAA
1 GAAATATAATTCGAAAAA
1683634 GAAATATAATTCGAAAAA
1 GAAATATAATTCGAAAAA
1683652 GAAA
1 GAAA
1683656 CCGAACCTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.62, C:0.05, G:0.12, T:0.20
Consensus pattern (18 bp):
GAAATATAATTCGAAAAA
Found at i:1690068 original size:24 final size:24
Alignment explanation
Indices: 1690033--1690170 Score: 179
Period size: 24 Copynumber: 5.8 Consensus size: 24
1690023 TTAGACAAAA
*
1690033 TTAGCTCATACGAGCCCAG-ATAGG
1 TTAGCTCTTACGAGCCCAGAAT-GG
*
1690057 TTAGCTCTTACGTGCCCAGAATGG
1 TTAGCTCTTACGAGCCCAGAATGG
*
1690081 TTAGCTCTTACGAGCCCAAAATGG
1 TTAGCTCTTACGAGCCCAGAATGG
*
1690105 TTAGCTCTTACGAGCCTAGAATGG
1 TTAGCTCTTACGAGCCCAGAATGG
* * *
1690129 TTAGCTCTTTCGAGCCTAGTATGG
1 TTAGCTCTTACGAGCCCAGAATGG
* *
1690153 TTAACTCTTACGGGCCCA
1 TTAGCTCTTACGAGCCCA
1690171 AAATCAAAAT
Statistics
Matches: 101, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
24 99 0.98
25 2 0.02
ACGTcount: A:0.24, C:0.25, G:0.23, T:0.28
Consensus pattern (24 bp):
TTAGCTCTTACGAGCCCAGAATGG
Found at i:1690199 original size:27 final size:27
Alignment explanation
Indices: 1690168--1690277 Score: 130
Period size: 27 Copynumber: 4.1 Consensus size: 27
1690158 TCTTACGGGC
* *
1690168 CCAAAATCAAAATAATGCTCTTTCGAG
1 CCAAAATCAGAATAACGCTCTTTCGAG
* *
1690195 CCAAAATCAGAATAACACTCTTTCAAG
1 CCAAAATCAGAATAACGCTCTTTCGAG
* * *
1690222 CCAGAATCAGATTAACGCTTTTTCGAG
1 CCAAAATCAGAATAACGCTCTTTCGAG
* **
1690249 CCAAAATCAGATTAATTCTCTTTCGAG
1 CCAAAATCAGAATAACGCTCTTTCGAG
1690276 CC
1 CC
1690278 TTTAGTCTCG
Statistics
Matches: 70, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 70 1.00
ACGTcount: A:0.36, C:0.25, G:0.12, T:0.27
Consensus pattern (27 bp):
CCAAAATCAGAATAACGCTCTTTCGAG
Found at i:1698507 original size:19 final size:20
Alignment explanation
Indices: 1698483--1698530 Score: 62
Period size: 23 Copynumber: 2.3 Consensus size: 20
1698473 GATCAGTTGG
1698483 ACCTTT-GATTAATTAACAT
1 ACCTTTGGATTAATTAACAT
1698502 ACCTTTTTTGGATTAATTAACAT
1 ACC---TTTGGATTAATTAACAT
1698525 ACCTTT
1 ACCTTT
1698531 TTTTGACTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
19 3 0.12
20 3 0.12
22 3 0.12
23 16 0.64
ACGTcount: A:0.31, C:0.17, G:0.06, T:0.46
Consensus pattern (20 bp):
ACCTTTGGATTAATTAACAT
Found at i:1698515 original size:23 final size:23
Alignment explanation
Indices: 1698489--1698533 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
1698479 TTGGACCTTT
1698489 GATTAATTAACATACCTTTTTTG
1 GATTAATTAACATACCTTTTTTG
1698512 GATTAATTAACATACCTTTTTT
1 GATTAATTAACATACCTTTTTT
1698534 TGACTGACCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.31, C:0.13, G:0.07, T:0.49
Consensus pattern (23 bp):
GATTAATTAACATACCTTTTTTG
Found at i:1698597 original size:14 final size:14
Alignment explanation
Indices: 1698547--1698607 Score: 60
Period size: 14 Copynumber: 4.6 Consensus size: 14
1698537 CTGACCCCTT
1698547 TAATTTATAATTTAA
1 TAATTTA-AATTTAA
*
1698562 -ATTTTTAAATTT--
1 TA-ATTTAAATTTAA
1698574 TAATTT--ATTTAA
1 TAATTTAAATTTAA
1698586 TAATTTAAATTTAA
1 TAATTTAAATTTAA
1698600 TAATTTAA
1 TAATTTAA
1698608 TCCAAGGAGG
Statistics
Matches: 38, Mismatches: 2, Indels: 13
0.72 0.04 0.25
Matches are distributed among these distances:
10 4 0.11
12 9 0.24
13 1 0.03
14 20 0.53
15 4 0.11
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
TAATTTAAATTTAA
Found at i:1699878 original size:13 final size:13
Alignment explanation
Indices: 1699860--1699884 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1699850 TACTATAAAT
1699860 CTATATTGATTTA
1 CTATATTGATTTA
1699873 CTATATTGATTT
1 CTATATTGATTT
1699885 CAACGAAATC
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:0.28, C:0.08, G:0.08, T:0.56
Consensus pattern (13 bp):
CTATATTGATTTA
Found at i:1700360 original size:23 final size:22
Alignment explanation
Indices: 1700332--1700433 Score: 88
Period size: 21 Copynumber: 4.7 Consensus size: 22
1700322 CATATTTTCT
1700332 TTATATATTTATTTATATATTA
1 TTATATATTTATTTATATATTA
1700354 TTA-ATA-TTATTTATATATTA
1 TTATATATTTATTTATATATTA
* *
1700374 TTCTATA-TTATTAATATATT-
1 TTATATATTTATTTATATATTA
* *
1700394 TTAATTTATATAATTTATATA-TA
1 TT-ATATAT-TTATTTATATATTA
*
1700417 TTAAATATATATATTTA
1 TT--ATATATTTATTTA
1700434 AATGATAAAT
Statistics
Matches: 65, Mismatches: 9, Indels: 11
0.76 0.11 0.13
Matches are distributed among these distances:
20 18 0.28
21 21 0.32
22 4 0.06
23 16 0.25
24 6 0.09
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (22 bp):
TTATATATTTATTTATATATTA
Found at i:1700362 original size:9 final size:9
Alignment explanation
Indices: 1700348--1700411 Score: 51
Period size: 9 Copynumber: 6.8 Consensus size: 9
1700338 ATTTATTTAT
1700348 ATATTATTA
1 ATATTATTA
1700357 ATATTATTTA
1 ATATTA-TTA
*
1700367 TATATTATTCT
1 -ATATTATT-A
1700378 ATATTATTA
1 ATATTATTA
*
1700387 ATATATTTTA
1 ATAT-TATTA
1700397 AT-TTATATA
1 ATATTAT-TA
1700406 AT-TTAT
1 ATATTAT
1700412 ATATATTAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
8 2 0.04
9 19 0.41
10 19 0.41
11 6 0.13
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (9 bp):
ATATTATTA
Found at i:1700365 original size:20 final size:20
Alignment explanation
Indices: 1700340--1700402 Score: 85
Period size: 20 Copynumber: 3.2 Consensus size: 20
1700330 CTTTATATAT
1700340 TTATTTATATATTATTAATA
1 TTATTTATATATTATTAATA
*
1700360 TTATTTATATATTATTCTATA
1 TTATTTATATATTATT-AATA
*
1700381 TTATTAATATATT-TTAAT-
1 TTATTTATATATTATTAATA
1700399 TTAT
1 TTAT
1700403 ATAATTTATA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
18 4 0.10
19 2 0.05
20 18 0.46
21 15 0.38
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (20 bp):
TTATTTATATATTATTAATA
Found at i:1700381 original size:21 final size:20
Alignment explanation
Indices: 1700335--1700415 Score: 90
Period size: 21 Copynumber: 3.8 Consensus size: 20
1700325 ATTTTCTTTA
1700335 TATATTTATTTATATATTATT
1 TATA-TTATTTATATATTATT
*
1700356 AATATTATTTATATATTATT
1 TATATTATTTATATATTATT
*
1700376 CTATATTATTAATATATTTTAATT
1 -TATATTATT--TATATATT-ATT
*
1700400 TATATAATTTATATAT
1 TATATTATTTATATAT
1700416 ATTAAATATA
Statistics
Matches: 51, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
20 16 0.31
21 17 0.33
23 15 0.29
24 3 0.06
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.60
Consensus pattern (20 bp):
TATATTATTTATATATTATT
Found at i:1700381 original size:30 final size:31
Alignment explanation
Indices: 1700331--1700433 Score: 101
Period size: 30 Copynumber: 3.4 Consensus size: 31
1700321 GCATATTTTC
1700331 TTTATATATTTATTTATATATTATTAATATTA
1 TTTATATATTTATTTATATATTATTAATA-TA
*
1700363 TTTATATA-TTA-TTCTATATTATTAATATA
1 TTTATATATTTATTTATATATTATTAATATA
* *
1700392 TTTTAATTTATATAATTTATATA-TATTAA-ATA
1 -TTT-ATATAT-TTATTTATATATTATTAATATA
1700424 --TATATATTTA
1 TTTATATATTTA
1700434 AATGATAAAT
Statistics
Matches: 60, Mismatches: 6, Indels: 15
0.74 0.07 0.19
Matches are distributed among these distances:
27 2 0.03
28 5 0.08
29 3 0.05
30 18 0.30
31 7 0.12
32 11 0.18
33 8 0.13
34 6 0.10
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (31 bp):
TTTATATATTTATTTATATATTATTAATATA
Found at i:1700462 original size:15 final size:15
Alignment explanation
Indices: 1700438--1700475 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
1700428 TATTTAAATG
*
1700438 ATAAATAATAATAAA
1 ATAAACAATAATAAA
1700453 ATAAACAATAATAAA
1 ATAAACAATAATAAA
1700468 ATAAACAA
1 ATAAACAA
1700476 ACCAAATCTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.74, C:0.05, G:0.00, T:0.21
Consensus pattern (15 bp):
ATAAACAATAATAAA
Found at i:1700628 original size:21 final size:21
Alignment explanation
Indices: 1700588--1700626 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1700578 AAATCATGGA
1700588 TAAATCCAAGCGACTCTTTCT
1 TAAATCCAAGCGACTCTTTCT
1700609 TAAATCCAAGCGA-TCTTT
1 TAAATCCAAGCGACTCTTT
1700627 TCGTAGGCGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.31, C:0.26, G:0.10, T:0.33
Consensus pattern (21 bp):
TAAATCCAAGCGACTCTTTCT
Found at i:1704601 original size:13 final size:13
Alignment explanation
Indices: 1704570--1704620 Score: 66
Period size: 13 Copynumber: 3.8 Consensus size: 13
1704560 GTTGACCAAC
*
1704570 CCGTTGACCGTTGA
1 CCGTTGA-CTTTGA
*
1704584 CCGTTGGCTTTGA
1 CCGTTGACTTTGA
*
1704597 TCGTTGACTTTGA
1 CCGTTGACTTTGA
1704610 CCGTTGACTTT
1 CCGTTGACTTT
1704621 TTTCGAGAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
13 26 0.81
14 6 0.19
ACGTcount: A:0.12, C:0.24, G:0.25, T:0.39
Consensus pattern (13 bp):
CCGTTGACTTTGA
Found at i:1705600 original size:66 final size:66
Alignment explanation
Indices: 1705494--1705629 Score: 272
Period size: 66 Copynumber: 2.1 Consensus size: 66
1705484 TTTGTGGTTA
1705494 CTTTTTGCGTTATAAATTGTTGTAATATTATATACTAGGTTGTATGTGCTTTAGAGACGCACTGA
1 CTTTTTGCGTTATAAATTGTTGTAATATTATATACTAGGTTGTATGTGCTTTAGAGACGCACTGA
1705559 G
66 G
1705560 CTTTTTGCGTTATAAATTGTTGTAATATTATATACTAGGTTGTATGTGCTTTAGAGACGCACTGA
1 CTTTTTGCGTTATAAATTGTTGTAATATTATATACTAGGTTGTATGTGCTTTAGAGACGCACTGA
1705625 G
66 G
1705626 CTTT
1 CTTT
1705630 ATAGCTCATT
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 70 1.00
ACGTcount: A:0.25, C:0.11, G:0.21, T:0.43
Consensus pattern (66 bp):
CTTTTTGCGTTATAAATTGTTGTAATATTATATACTAGGTTGTATGTGCTTTAGAGACGCACTGA
G
Found at i:1706457 original size:31 final size:31
Alignment explanation
Indices: 1706403--1706463 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
1706393 TAATCTAGTG
1706403 ACTTAAATAAATATGTTCTAATAGTTTAATA
1 ACTTAAATAAATATGTTCTAATAGTTTAATA
* *
1706434 ACTTAAATAAAT-TTTTTTGAATAGTTTAAT
1 ACTTAAATAAATATGTTCT-AATAGTTTAAT
1706464 GACCTTTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 4 0.15
31 23 0.85
ACGTcount: A:0.43, C:0.05, G:0.07, T:0.46
Consensus pattern (31 bp):
ACTTAAATAAATATGTTCTAATAGTTTAATA
Found at i:1707803 original size:27 final size:26
Alignment explanation
Indices: 1707760--1707810 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
1707750 GTGATATATT
1707760 TTTTTAAACATTAATTTTATTATAAG
1 TTTTTAAACATTAATTTTATTATAAG
* * *
1707786 TTTTTATAATATTTATTTTTTTATA
1 TTTTTA-AACATTAATTTTATTATA
1707811 TAATGTACAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 6 0.29
27 15 0.71
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (26 bp):
TTTTTAAACATTAATTTTATTATAAG
Found at i:1732140 original size:49 final size:48
Alignment explanation
Indices: 1731715--1732141 Score: 228
Period size: 49 Copynumber: 8.7 Consensus size: 48
1731705 AGGTTTCATT
* *
1731715 AGCATGAAGGGAAAGATTTAAGTCGCAACGGTGAATCC-AGTACC--ACGA
1 AGCATGAAGGGAAAGATTTAAGCCGCAACGGCGAA-CCTA-TACCTGA-GA
* * * * * * * * *
1731763 AG-ATGCAAAGGGAACGGTTCAAGTCGCAATGGCAAACCTTGTAACTCAGA
1 AGCATG--AAGGGAAAGATTTAAGCCGCAACGGCGAACC-TATACCTGAGA
* * *
1731813 AGCATGAAGGGAAAGATTTAAGCCGCAACGACAAATCTAGTACC--ACGA
1 AGCATGAAGGGAAAGATTTAAGCCGCAACGGCGAACCTA-TACCTGA-GA
** * * * * *
1731861 AGACACAAAGGGAACGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGA
1 AG-CATGAAGGGAAAGATTTAAGCCGCAACGGCGAACC-TATACCTGAGA
* * *
1731911 AGCATGAAGGGAAAGATTTAAGCCGCAATGGCTAATCCAATA-C-GACGA
1 AGCATGAAGGGAAAGATTTAAGCCGCAACGGCGAA-CCTATACCTGA-GA
** * * * * ** * *
1731959 AGACACAAAGGGAATGGTTTAAGTCGCAATGAAGAACCTTGTACCTTAGA
1 AG-CATGAAGGGAAAGATTTAAGCCGCAACGGCGAACC-TATACCTGAGA
* * * *
1732009 AGCATGAAGGGAAATATTTAAGCCGCGACGACGAATCTAGTACCATGAAGA
1 AGCATGAAGGGAAAGATTTAAGCCGCAACGGCGAACCTA-TACC-TG-AGA
* * *
1732060 TA-CA--AAGGGAAAGGTTTAAGTCGCAATGGCGAACCTTATACCTGAGA
1 -AGCATGAAGGGAAAGATTTAAGCCGCAACGGCGAACC-TATACCTGAGA
*
1732107 AGCATGAAGGGAAAGATTTAAGCCACAACGGCGAA
1 AGCATGAAGGGAAAGATTTAAGCCGCAACGGCGAA
1732142 TATAGAACCA
Statistics
Matches: 282, Mismatches: 70, Indels: 53
0.70 0.17 0.13
Matches are distributed among these distances:
46 1 0.00
47 10 0.04
48 19 0.07
49 221 0.78
50 19 0.07
51 11 0.04
52 1 0.00
ACGTcount: A:0.38, C:0.19, G:0.26, T:0.17
Consensus pattern (48 bp):
AGCATGAAGGGAAAGATTTAAGCCGCAACGGCGAACCTATACCTGAGA
Found at i:1732152 original size:98 final size:98
Alignment explanation
Indices: 1731715--1732151 Score: 595
Period size: 98 Copynumber: 4.5 Consensus size: 98
1731705 AGGTTTCATT
* * * **
1731715 AGCATGAAGGGAAAGATTTAAGTCGCAACGGTGAATCCAGTACCACGAAGATGCAAAGGGAACGG
1 AGCATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCACGAAGACACAAAGGGAACGG
* * *
1731780 TTCAAGTCGCAATGGCAAACCTTGTAACTCAGA
66 TTTAAGTCGCAATGGCGAACCTTGTACCTCAGA
* *
1731813 AGCATGAAGGGAAAGATTTAAGCCGCAACGACAAATCTAGTACCACGAAGACACAAAGGGAACGG
1 AGCATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCACGAAGACACAAAGGGAACGG
*
1731878 TTTAAGTCGCAACGGCGAACCTTGTACCTCAGA
66 TTTAAGTCGCAATGGCGAACCTTGTACCTCAGA
* * * * * *
1731911 AGCATGAAGGGAAAGATTTAAGCCGCAATGGCTAATCCAATACGACGAAGACACAAAGGGAATGG
1 AGCATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCACGAAGACACAAAGGGAACGG
** *
1731976 TTTAAGTCGCAATGAAGAACCTTGTACCTTAGA
66 TTTAAGTCGCAATGGCGAACCTTGTACCTCAGA
* * * * * *
1732009 AGCATGAAGGGAAATATTTAAGCCGCGACGACGAATCTAGTACCATGAAGATACAAAGGGAAAGG
1 AGCATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCACGAAGACACAAAGGGAACGG
* *
1732074 TTTAAGTCGCAATGGCGAACCTTATACCTGAGA
66 TTTAAGTCGCAATGGCGAACCTTGTACCTCAGA
* * *
1732107 AGCATGAAGGGAAAGATTTAAGCCACAACGGCGAATATAGAACCA
1 AGCATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCA
1732152 TAATGACATT
Statistics
Matches: 296, Mismatches: 43, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
98 296 1.00
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (98 bp):
AGCATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCACGAAGACACAAAGGGAACGG
TTTAAGTCGCAATGGCGAACCTTGTACCTCAGA
Found at i:1732650 original size:12 final size:13
Alignment explanation
Indices: 1732626--1732654 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
1732616 TAAAACCCCA
1732626 AAAAATAATAAAT
1 AAAAATAATAAAT
1732639 AAAAATAA-AAAT
1 AAAAATAATAAAT
1732651 AAAA
1 AAAA
1732655 TTCTCAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.50
13 8 0.50
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (13 bp):
AAAAATAATAAAT
Found at i:1733041 original size:24 final size:23
Alignment explanation
Indices: 1732999--1733044 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
1732989 ATACCTGTAA
1732999 ACAGAAGCAAAGAACAACAGAGG
1 ACAGAAGCAAAGAACAACAGAGG
1733022 ACAGCAAGACAAAG-ACAACAGAG
1 ACAG-AAG-CAAAGAACAACAGAG
1733045 AATAACATAC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 4 0.19
24 12 0.57
25 5 0.24
ACGTcount: A:0.57, C:0.20, G:0.24, T:0.00
Consensus pattern (23 bp):
ACAGAAGCAAAGAACAACAGAGG
Found at i:1745247 original size:18 final size:18
Alignment explanation
Indices: 1745208--1745257 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
1745198 TTTTAGATTT
* *
1745208 ATTTCTAAATTTAAATTC
1 ATTTTTAAATTTAAATTA
1745226 ATTTTTAAATTTGAAA-TA
1 ATTTTTAAATTT-AAATTA
*
1745244 A-TTTTAAACTTAAA
1 ATTTTTAAATTTAAA
1745258 CTTTAAAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
16 3 0.11
17 9 0.32
18 13 0.46
19 3 0.11
ACGTcount: A:0.44, C:0.06, G:0.02, T:0.48
Consensus pattern (18 bp):
ATTTTTAAATTTAAATTA
Found at i:1746850 original size:31 final size:30
Alignment explanation
Indices: 1746765--1746882 Score: 127
Period size: 30 Copynumber: 4.0 Consensus size: 30
1746755 TGGAGGTCCT
* * *
1746765 TAAACTGTCCAAAAATTATA-TTTTGACCC
1 TAAACTTTCTAAAAATTATATTTTTAACCC
*
1746794 TCAAACTTCTCT-AAAATTACATTTTTAACCC
1 T-AAACTT-TCTAAAAATTATATTTTTAACCC
*
1746825 TAAACTTTCTAAAAATTATATTTTTTACCCC
1 TAAACTTTCTAAAAATTATA-TTTTTAACCC
*
1746856 TAAACTTTC-AAAAATTCTA-TTTTAACC
1 TAAACTTTCTAAAAATTATATTTTTAACC
1746883 TGGATTTTTC
Statistics
Matches: 76, Mismatches: 8, Indels: 11
0.80 0.08 0.12
Matches are distributed among these distances:
28 7 0.09
29 4 0.05
30 36 0.47
31 29 0.38
ACGTcount: A:0.37, C:0.21, G:0.02, T:0.40
Consensus pattern (30 bp):
TAAACTTTCTAAAAATTATATTTTTAACCC
Found at i:1746922 original size:29 final size:29
Alignment explanation
Indices: 1746766--1747090 Score: 126
Period size: 30 Copynumber: 11.0 Consensus size: 29
1746756 GGAGGTCCTT
* *
1746766 AAACTGTCCAAAAATTA-TATTTTGACCCTC
1 AAACT-TCCAAAAATTACCATTTT-ACCCCC
* * *
1746796 AAACTTCTCTAAAATTA-CATTTTTAACCCT
1 AAACTTC-CAAAAATTACCA-TTTTACCCCC
* * *
1746826 AAACTTTCTAAAAATTA-TATTTTTTACCCCT
1 AAAC-TTCCAAAAATTACCA--TTTTACCCCC
* * ***
1746857 AAACTTTCAAAAATT-CTATTTTAACCTGG
1 AAACTTCCAAAAATTACCATTTT-ACCCCC
*** *
1746886 ATTTTTCCCAAAATTACCATTTTACCCCC
1 AAACTTCCAAAAATTACCATTTTACCCCC
* *
1746915 AAACTTCCAAAAATT-CCATTTTTGATCCCG
1 AAACTTCCAAAAATTACCA-TTTT-ACCCCC
*** * **
1746945 ATTTTTCCTAAAATTACCATTTTACCCTT
1 AAACTTCCAAAAATTACCATTTTACCCCC
* **
1746974 AAACTTCTAAAAATT-CCATTTTTTACCCTG
1 AAACTTCCAAAAATTACCA--TTTTACCCCC
* * *
1747004 AAACTTTCAAAAATTACTATGTTACCCCC
1 AAACTTCCAAAAATTACCATTTTACCCCC
* * **
1747033 AGA-TGTCCAAAAATT-CCATTTTAACCTT
1 AAACT-TCCAAAAATTACCATTTTACCCCC
* * *
1747061 AAATTTTCCTAAAATTATCATTTTACCCCC
1 AAA-CTTCCAAAAATTACCATTTTACCCCC
1747091 GGGCATCCAA
Statistics
Matches: 217, Mismatches: 61, Indels: 34
0.70 0.20 0.11
Matches are distributed among these distances:
28 21 0.10
29 73 0.34
30 97 0.45
31 26 0.12
ACGTcount: A:0.34, C:0.24, G:0.03, T:0.38
Consensus pattern (29 bp):
AAACTTCCAAAAATTACCATTTTACCCCC
Found at i:1747103 original size:58 final size:59
Alignment explanation
Indices: 1746776--1747090 Score: 252
Period size: 59 Copynumber: 5.3 Consensus size: 59
1746766 AAACTGTCCA
* * * * *
1746776 AAAATTA-TATTTTGACCCTCAAACTTCTCTAAAATTACATTTTTAACCCT-AAACTTT-CT
1 AAAATTACCATTTT-ACCCCCAAACTTC-CAAAAATTCCATTTTTAA-CCTGAAATTTTCCT
* * * * * * *
1746835 AAAAATTA-TATTTTTTACCCCTAAACTTTCAAAAATTCTA-TTTTAACCTGGATTTTTCCC
1 -AAAATTACCA--TTTTACCCCCAAACTTCCAAAAATTCCATTTTTAACCTGAAATTTTCCT
* * *
1746895 AAAATTACCATTTTACCCCCAAACTTCCAAAAATTCCATTTTTGATCCCG-ATTTTTCCT
1 AAAATTACCATTTTACCCCCAAACTTCCAAAAATTCCATTTTT-AACCTGAAATTTTCCT
** * * * *
1746954 AAAATTACCATTTTACCCTTAAACTTCTAAAAATTCCATTTTTTACCCTGAAACTTT-CA
1 AAAATTACCATTTTACCCCCAAACTTCCAAAAATTCCA-TTTTTAACCTGAAATTTTCCT
* * * *
1747013 AAAATTACTATGTTACCCCCAGA-TGTCCAAAAATTCCA-TTTTAACCTTAAATTTTCCT
1 AAAATTACCATTTTACCCCCAAACT-TCCAAAAATTCCATTTTTAACCTGAAATTTTCCT
*
1747071 AAAATTATCATTTTACCCCC
1 AAAATTACCATTTTACCCCC
1747091 GGGCATCCAA
Statistics
Matches: 206, Mismatches: 38, Indels: 24
0.77 0.14 0.09
Matches are distributed among these distances:
57 14 0.07
58 47 0.23
59 99 0.48
60 32 0.16
61 10 0.05
62 4 0.02
ACGTcount: A:0.34, C:0.24, G:0.03, T:0.39
Consensus pattern (59 bp):
AAAATTACCATTTTACCCCCAAACTTCCAAAAATTCCATTTTTAACCTGAAATTTTCCT
Found at i:1757941 original size:5 final size:5
Alignment explanation
Indices: 1757931--1757960 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
1757921 GACATCACTA
1757931 GTTGG GTTGG GTTGG GTTGG GTTGG GTTGG
1 GTTGG GTTGG GTTGG GTTGG GTTGG GTTGG
1757961 TGAGTGACAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.60, T:0.40
Consensus pattern (5 bp):
GTTGG
Found at i:1762736 original size:72 final size:69
Alignment explanation
Indices: 1762607--1762743 Score: 188
Period size: 72 Copynumber: 1.9 Consensus size: 69
1762597 TATCCCAATA
*
1762607 GCCTCAAAGAAAGAAAAATATCTTGAAAACTATACATGATATTAAGTTTGGTAAATAACATTAAA
1 GCCTCAAAGAAAGAAAAATATCTTGAAAACTATACATGATATGAAGTTTGGTAAATAACATTAAA
1762672 AGTT
66 AGTT
* *
1762676 GCCT-AAAGATAAGGAAAATATCTTGAAAAGCCTCTTCACAT-ATATGAAGTTTGGTAAATAACA
1 GCCTCAAAGA-AAGAAAAATATCTTGAAAA--CT-AT-ACATGATATGAAGTTTGGTAAATAACA
1762739 TTAAA
61 TTAAA
1762744 GACACATGAA
Statistics
Matches: 60, Mismatches: 3, Indels: 7
0.86 0.04 0.10
Matches are distributed among these distances:
68 5 0.08
69 22 0.37
71 2 0.03
72 27 0.45
73 4 0.07
ACGTcount: A:0.46, C:0.12, G:0.14, T:0.28
Consensus pattern (69 bp):
GCCTCAAAGAAAGAAAAATATCTTGAAAACTATACATGATATGAAGTTTGGTAAATAACATTAAA
AGTT
Found at i:1767706 original size:11 final size:11
Alignment explanation
Indices: 1767672--1767741 Score: 77
Period size: 11 Copynumber: 6.1 Consensus size: 11
1767662 ATAACATCTA
*
1767672 AACAACAAAAAT
1 AACAAC-AAAAC
1767684 AACAACCAAAAC
1 AACAA-CAAAAC
*
1767696 AACAGCAAAAC
1 AACAACAAAAC
*
1767707 AACAACAAAAT
1 AACAACAAAAC
1767718 AACAACAAAAAC
1 AACAAC-AAAAC
*
1767730 AACACCAAAAC
1 AACAACAAAAC
1767741 A
1 A
1767742 GTAAAAACAA
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
11 27 0.54
12 22 0.44
13 1 0.02
ACGTcount: A:0.70, C:0.26, G:0.01, T:0.03
Consensus pattern (11 bp):
AACAACAAAAC
Found at i:1767722 original size:34 final size:35
Alignment explanation
Indices: 1767672--1767741 Score: 115
Period size: 34 Copynumber: 2.0 Consensus size: 35
1767662 ATAACATCTA
* *
1767672 AACAACAAAAATAACAACCAAAACAACAGCAAAAC
1 AACAACAAAAATAACAACAAAAACAACACCAAAAC
1767707 AACAAC-AAAATAACAACAAAAACAACACCAAAAC
1 AACAACAAAAATAACAACAAAAACAACACCAAAAC
1767741 A
1 A
1767742 GTAAAAACAA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
34 27 0.82
35 6 0.18
ACGTcount: A:0.70, C:0.26, G:0.01, T:0.03
Consensus pattern (35 bp):
AACAACAAAAATAACAACAAAAACAACACCAAAAC
Found at i:1768513 original size:22 final size:23
Alignment explanation
Indices: 1768488--1768536 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 23
1768478 ATTTAATAGA
*
1768488 AAAATGACAGCAAAACAACAAC-
1 AAAATGACAACAAAACAACAACT
*
1768510 AAAATGGCAACAAAACAACAACT
1 AAAATGACAACAAAACAACAACT
1768533 AAAA
1 AAAA
1768537 AAGTTCAGAC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 20 0.83
23 4 0.17
ACGTcount: A:0.65, C:0.20, G:0.08, T:0.06
Consensus pattern (23 bp):
AAAATGACAACAAAACAACAACT
Found at i:1769006 original size:43 final size:42
Alignment explanation
Indices: 1768974--1769193 Score: 318
Period size: 43 Copynumber: 5.1 Consensus size: 42
1768964 GAACATGGCT
1768974 TTTAGCGGCGCTTTTCCCACAAGCGCCGCTAAAGGCCATGTTC
1 TTTAGCGGCGCTTTTCCCACAAGCGCCGCTAAA-GCCATGTTC
* *
1769017 TTTAACGGCGCTTTTCCCACAAACGCCGCTAAATGCCATGTTC
1 TTTAGCGGCGCTTTTCCCACAAGCGCCGCTAAA-GCCATGTTC
*
1769060 TTTAGCGGCGCTTTAT-CCACAAGCGCCGCTAAAGGCATGTTC
1 TTTAGCGGCGCTTT-TCCCACAAGCGCCGCTAAAGCCATGTTC
* *
1769102 TTTAGCGGCGCTTTAT-CCACAAGCGCCGCTAAAGGCATGTTT
1 TTTAGCGGCGCTTT-TCCCACAAGCGCCGCTAAAGCCATGTTC
*
1769144 TTTAGCGGCGCTTTTCTCCACAAGCGCCGCTAAAGCCCTTGTTC
1 TTTAGCGGCGCTTTTC-CCACAAGCGCCGCTAAAG-CCATGTTC
1769188 TTTAGC
1 TTTAGC
1769194 TAATATAACA
Statistics
Matches: 163, Mismatches: 10, Indels: 7
0.91 0.06 0.04
Matches are distributed among these distances:
41 1 0.01
42 63 0.39
43 87 0.53
44 12 0.07
ACGTcount: A:0.20, C:0.30, G:0.21, T:0.28
Consensus pattern (42 bp):
TTTAGCGGCGCTTTTCCCACAAGCGCCGCTAAAGCCATGTTC
Found at i:1769504 original size:21 final size:21
Alignment explanation
Indices: 1769479--1769552 Score: 112
Period size: 21 Copynumber: 3.5 Consensus size: 21
1769469 CTTGTAGCCT
* *
1769479 CTGCTTCCTTCGCTTGCCTCG
1 CTGCTGCCTCCGCTTGCCTCG
1769500 CTGCTGCCTCCGCTTGCCTCG
1 CTGCTGCCTCCGCTTGCCTCG
*
1769521 TTGCTGCCTCCGCTTGCCTCG
1 CTGCTGCCTCCGCTTGCCTCG
*
1769542 TTGCTGCCTCC
1 CTGCTGCCTCC
1769553 ACTTTAAGTT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 50 1.00
ACGTcount: A:0.00, C:0.45, G:0.22, T:0.34
Consensus pattern (21 bp):
CTGCTGCCTCCGCTTGCCTCG
Found at i:1769509 original size:11 final size:11
Alignment explanation
Indices: 1769493--1769551 Score: 54
Period size: 11 Copynumber: 5.5 Consensus size: 11
1769483 TTCCTTCGCT
1769493 TGCCTCGCTGC
1 TGCCTCGCTGC
1769504 TGCCTC-C-GC
1 TGCCTCGCTGC
*
1769513 TTGCCTCGTTGC
1 -TGCCTCGCTGC
1769525 TGCCTC-C-GC
1 TGCCTCGCTGC
*
1769534 TTGCCTCGTTGC
1 -TGCCTCGCTGC
1769546 TGCCTC
1 TGCCTC
1769552 CACTTTAAGT
Statistics
Matches: 39, Mismatches: 3, Indels: 12
0.72 0.06 0.22
Matches are distributed among these distances:
9 4 0.10
10 13 0.33
11 18 0.46
12 4 0.10
ACGTcount: A:0.00, C:0.44, G:0.24, T:0.32
Consensus pattern (11 bp):
TGCCTCGCTGC
Found at i:1769653 original size:66 final size:66
Alignment explanation
Indices: 1769547--1769695 Score: 253
Period size: 66 Copynumber: 2.3 Consensus size: 66
1769537 CCTCGTTGCT
* *
1769547 GCCTCCACTTTAAGTTGTAGATGGAGTTCTTCATATTTTTTTTGAGACTCTGCTTCTCTCACTGC
1 GCCTCCTCTTTAAGTTGTAGATGGAGTTCATCATATTTTTTTTGAGACTCTGCTTCTCTCACTGC
1769612 A
66 A
* * *
1769613 GCCTCCTCTTTAAGTTTTAGATGGAGTTCATCATATTTTTTTTGAGCCTCTGCTTCTCTCGCTGC
1 GCCTCCTCTTTAAGTTGTAGATGGAGTTCATCATATTTTTTTTGAGACTCTGCTTCTCTCACTGC
1769678 A
66 A
1769679 GCCTCCTCTTTAAGTTG
1 GCCTCCTCTTTAAGTTG
1769696 AGCAATTTGC
Statistics
Matches: 77, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
66 77 1.00
ACGTcount: A:0.16, C:0.24, G:0.17, T:0.43
Consensus pattern (66 bp):
GCCTCCTCTTTAAGTTGTAGATGGAGTTCATCATATTTTTTTTGAGACTCTGCTTCTCTCACTGC
A
Found at i:1771028 original size:8 final size:8
Alignment explanation
Indices: 1771015--1771108 Score: 65
Period size: 8 Copynumber: 11.8 Consensus size: 8
1771005 CTGTTTTTAT
1771015 TAATTAAA
1 TAATTAAA
1771023 TAATTAAA
1 TAATTAAA
*
1771031 T-ATTTAA
1 TAATTAAA
1771038 T--TTAATA
1 TAATTAA-A
1771045 TAATTAAA
1 TAATTAAA
1771053 TAATTAAA
1 TAATTAAA
* *
1771061 T-CTT--T
1 TAATTAAA
1771066 TCAATTAAA
1 T-AATTAAA
1771075 TAATTAAA
1 TAATTAAA
1771083 TAAGCTTAAA
1 TAA--TTAAA
1771093 TAATTATATA
1 TAATTA-A-A
1771103 TAATTA
1 TAATTA
1771109 TTTACGACCA
Statistics
Matches: 69, Mismatches: 6, Indels: 20
0.73 0.06 0.21
Matches are distributed among these distances:
5 1 0.01
6 3 0.04
7 12 0.17
8 32 0.46
9 6 0.09
10 15 0.22
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.44
Consensus pattern (8 bp):
TAATTAAA
Found at i:1771049 original size:30 final size:29
Alignment explanation
Indices: 1771015--1771094 Score: 99
Period size: 30 Copynumber: 2.6 Consensus size: 29
1771005 CTGTTTTTAT
1771015 TAATTAAATAATTAAATATTT-AATTTAATA
1 TAATTAAATAATTAAATATTTCAA-TTAA-A
*
1771045 TAATTAAATAATTAAATCTTTTCAATTAAA
1 TAATTAAATAATTAAAT-ATTTCAATTAAA
1771075 TAATTAAATAAGCTTAAATA
1 TAATTAAATAA--TTAAATA
1771095 ATTATATATA
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
30 29 0.66
31 7 0.16
32 8 0.18
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.42
Consensus pattern (29 bp):
TAATTAAATAATTAAATATTTCAATTAAA
Found at i:1771050 original size:22 final size:20
Alignment explanation
Indices: 1771013--1771059 Score: 67
Period size: 22 Copynumber: 2.2 Consensus size: 20
1771003 GGCTGTTTTT
1771013 ATTAATTAAATAATTAAATA
1 ATTAATTAAATAATTAAATA
*
1771033 TTTAATTTAATATAATTAAATA
1 ATTAA-TTAA-ATAATTAAATA
1771055 ATTAA
1 ATTAA
1771060 ATCTTTTCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 4 0.17
21 4 0.17
22 15 0.65
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
ATTAATTAAATAATTAAATA
Found at i:1771180 original size:18 final size:17
Alignment explanation
Indices: 1771159--1771284 Score: 81
Period size: 18 Copynumber: 7.7 Consensus size: 17
1771149 ATTAAAAATT
1771159 TTAATATAATTATTTACC
1 TTAATATAATTATTTA-C
1771177 TTAATATAATTA---A-
1 TTAATATAATTATTTAC
* * *
1771190 ATAAT-TAAATATTTAAT
1 TTAATATAATTATTT-AC
1771207 TTAATATAATTATTTAC
1 TTAATATAATTATTTAC
** *
1771224 TTAAATATAATTAAATAA
1 TT-AATATAATTATTTAC
* *
1771242 TTAA-AT-CTT-TTAAC
1 TTAATATAATTATTTAC
1771256 TT-ATATAATTATTTAC
1 TTAATATAATTATTTAC
1771272 TTTAATATAATTA
1 -TTAATATAATTA
1771285 AATAATTAAA
Statistics
Matches: 81, Mismatches: 15, Indels: 24
0.68 0.12 0.20
Matches are distributed among these distances:
12 5 0.06
13 5 0.06
14 5 0.06
15 5 0.06
16 7 0.09
17 11 0.14
18 43 0.53
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (17 bp):
TTAATATAATTATTTAC
Found at i:1771215 original size:48 final size:49
Alignment explanation
Indices: 1771158--1771307 Score: 225
Period size: 48 Copynumber: 3.1 Consensus size: 49
1771148 AATTAAAAAT
1771158 TTTAATATAATTATTTACCTTAATATAATTAAATAATTAAAT-ATTTAA
1 TTTAATATAATTATTTACCTTAATATAATTAAATAATTAAATCATTTAA
*
1771206 TTTAATATAATTATTTA-CTTAAATATAATTAAATAATTAAATCTTTTAA
1 TTTAATATAATTATTTACCTT-AATATAATTAAATAATTAAATCATTTAA
* * *
1771255 CTT-ATATAATTATTTACTTTAATATAATTAAATAATTAAATCTTTTAA
1 TTTAATATAATTATTTACCTTAATATAATTAAATAATTAAATCATTTAA
*
1771303 CTTAA
1 TTTAA
1771308 ATATTTAATT
Statistics
Matches: 95, Mismatches: 3, Indels: 7
0.90 0.03 0.07
Matches are distributed among these distances:
47 3 0.03
48 82 0.86
49 10 0.11
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (49 bp):
TTTAATATAATTATTTACCTTAATATAATTAAATAATTAAATCATTTAA
Found at i:1771378 original size:18 final size:18
Alignment explanation
Indices: 1771357--1771403 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
1771347 ATTAAACATG
1771357 ATTAAATAATTTAATATA
1 ATTAAATAATTTAATATA
** *
1771375 ATTATTTAGTTTAATATA
1 ATTAAATAATTTAATATA
1771393 ATTAAATAATT
1 ATTAAATAATT
1771404 ATATCTTTTA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (18 bp):
ATTAAATAATTTAATATA
Found at i:1771413 original size:26 final size:27
Alignment explanation
Indices: 1771358--1771416 Score: 68
Period size: 26 Copynumber: 2.2 Consensus size: 27
1771348 TTAAACATGA
*
1771358 TTAAATAATTTAATATAATTATTTAGT
1 TTAAATAATTTAATATAATTATATAGT
**
1771385 TTAATATAA-TTAA-ATAATTATATCTT
1 TTAA-ATAATTTAATATAATTATATAGT
1771411 TTAAAT
1 TTAAAT
1771417 TGAAAAGAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
25 2 0.07
26 14 0.50
27 8 0.29
28 4 0.14
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (27 bp):
TTAAATAATTTAATATAATTATATAGT
Found at i:1771673 original size:14 final size:14
Alignment explanation
Indices: 1771654--1771683 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
1771644 AAGATAGGTT
1771654 CAATTATATATTCC
1 CAATTATATATTCC
1771668 CAATTATATATTCC
1 CAATTATATATTCC
1771682 CA
1 CA
1771684 TTCAACAGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.37, C:0.23, G:0.00, T:0.40
Consensus pattern (14 bp):
CAATTATATATTCC
Found at i:1772461 original size:12 final size:12
Alignment explanation
Indices: 1772444--1772481 Score: 76
Period size: 12 Copynumber: 3.2 Consensus size: 12
1772434 TTACACTACC
1772444 AATGAAAGAAGT
1 AATGAAAGAAGT
1772456 AATGAAAGAAGT
1 AATGAAAGAAGT
1772468 AATGAAAGAAGT
1 AATGAAAGAAGT
1772480 AA
1 AA
1772482 CAGATTCAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.61, C:0.00, G:0.24, T:0.16
Consensus pattern (12 bp):
AATGAAAGAAGT
Found at i:1773602 original size:41 final size:41
Alignment explanation
Indices: 1773557--1773816 Score: 290
Period size: 41 Copynumber: 6.3 Consensus size: 41
1773547 AAATGATCCT
1773557 ACCTTTAGCGGCGCTTGAGGGAAAGCGCCGCTAATGACCAG
1 ACCTTTAGCGGCGCTTGAGGGAAAGCGCCGCTAATGACCAG
* * * *
1773598 ACCTTTTAGTGGCGCTTTAGGGAAAGCGCCGCTAATGATCAT
1 ACC-TTTAGCGGCGCTTGAGGGAAAGCGCCGCTAATGACCAG
* ** * * *
1773640 ACCTTTAGCGGCACTTGAGTTAAAGCGCCGCTAATTACAAT
1 ACCTTTAGCGGCGCTTGAGGGAAAGCGCCGCTAATGACCAG
* **
1773681 ACCTTTAGCGGCGCATT-AGAGAAAGCGCCGCTAATGACTTG
1 ACCTTTAGCGGCGC-TTGAGGGAAAGCGCCGCTAATGACCAG
* ** *
1773722 AACTTTAGCGGCGCTTGAGATAAAGCGCCGCTAATTA-CATG
1 ACCTTTAGCGGCGCTTGAGGGAAAGCGCCGCTAATGACCA-G
* * *
1773763 ATCTTTAGCGGCGCTTGTGGGTAAAGCGCCGCTAATGACCCG
1 ACCTTTAGCGGCGCTTGAGGG-AAAGCGCCGCTAATGACCAG
1773805 ACCTTTAGCGGC
1 ACCTTTAGCGGC
1773817 ACTTTTGTTA
Statistics
Matches: 182, Mismatches: 31, Indels: 11
0.81 0.14 0.05
Matches are distributed among these distances:
40 2 0.01
41 113 0.62
42 66 0.36
43 1 0.01
ACGTcount: A:0.25, C:0.25, G:0.27, T:0.24
Consensus pattern (41 bp):
ACCTTTAGCGGCGCTTGAGGGAAAGCGCCGCTAATGACCAG
Found at i:1773739 original size:82 final size:82
Alignment explanation
Indices: 1773557--1773879 Score: 327
Period size: 82 Copynumber: 3.9 Consensus size: 82
1773547 AAATGATCCT
* ** * * * * *
1773557 ACCTTTAGCGGCGCTTGAGGGAAAGCGCCGCTAATGACCAGACCTTTTAGTGGCGCTTTAG-GGA
1 ACCTTTAGCGGCACTTGAGTTAAAGCGCCGCTAATTA-CATACC-TTTAGCGGCGCATTAGAGAA
1773621 AAGCGCCGCTAATGATCAT-
64 AAGCGCCGCTAATGA-CATG
1773640 ACCTTTAGCGGCACTTGAGTTAAAGCGCCGCTAATTACAATACCTTTAGCGGCGCATTAGAG-AA
1 ACCTTTAGCGGCACTTGAGTTAAAGCGCCGCTAATTAC-ATACCTTTAGCGGCGCATTAGAGAAA
*
1773704 AGCGCCGCTAATGACTTG
65 AGCGCCGCTAATGACATG
* * * * * * *
1773722 AACTTTAGCGGCGCTTGAGATAAAGCGCCGCTAATTACATGATCTTTAGCGGCGC-TTGTGGGTA
1 ACCTTTAGCGGCACTTGAGTTAAAGCGCCGCTAATTACAT-ACCTTTAGCGGCGCATT-AGAGAA
**
1773786 AAGCGCCGCTAATGACCCG
64 AAGCGCCGCTAATGACATG
** * * *
1773805 ACCTTTAGCGGCACTTTTGTT-AAGCGCCGCTAA-TGCTTTACCTTTTGCGGCGCATTA-AGAAA
1 ACCTTTAGCGGCACTTGAGTTAAAGCGCCGCTAATTAC-ATACCTTTAGCGGCGCATTAGAGAAA
1773867 AGCGCCGCTAATG
65 AGCGCCGCTAATG
1773880 CTTTACCTTT
Statistics
Matches: 204, Mismatches: 28, Indels: 19
0.81 0.11 0.08
Matches are distributed among these distances:
80 16 0.08
81 20 0.10
82 96 0.47
83 72 0.35
ACGTcount: A:0.25, C:0.24, G:0.26, T:0.25
Consensus pattern (82 bp):
ACCTTTAGCGGCACTTGAGTTAAAGCGCCGCTAATTACATACCTTTAGCGGCGCATTAGAGAAAA
GCGCCGCTAATGACATG
Found at i:1773834 original size:123 final size:122
Alignment explanation
Indices: 1773557--1773879 Score: 330
Period size: 124 Copynumber: 2.6 Consensus size: 122
1773547 AAATGATCCT
* * ** * * *
1773557 ACCTTTAGCGGCGC-TTGAGGGAAAGCGCCGCTAATGACCAGACCTTTTAGTGGCGCTTTAGGGA
1 ACCTTTAGCGGCACATT-AGAGAAAGCGCCGCTAATGACTTGACC-TTTAGCGGCGC-TTAAGAA
* * *
1773621 AAGCGCCGCTAATGATCATACCTTTAGCGGCACTTGAGTTAAAGCGCCGCTAATTACAAT
63 AAGCGCCGCTAATGATCATACCTTTAGCGGCACTTGAGGTAAAGCGCCGCTAATGACAAG
* * *
1773681 ACCTTTAGCGGCGCATTAGAGAAAGCGCCGCTAATGACTTGAACTTTAGCGGCGCTTGAGATAAA
1 ACCTTTAGCGGCACATTAGAGAAAGCGCCGCTAATGACTTGACCTTTAGCGGCGCTTAAGA-AAA
* * * * **
1773746 GCGCCGCTAATTA-CATGATCTTTAGCGGCGCTTGTGGGTAAAGCGCCGCTAATGACCCG
65 GCGCCGCTAATGATCAT-ACCTTTAGCGGCACTTG-AGGTAAAGCGCCGCTAATGACAAG
* * ** * *
1773805 ACCTTTAGCGGCACTTTTG-TTAAGCGCCGCTAATG-CTTTACCTTTTGCGGCGCATTAAGAAAA
1 ACCTTTAGCGGCACATTAGAGAAAGCGCCGCTAATGACTTGACCTTTAGCGGCGC-TTAAGAAAA
1773868 GCGCCGCTAATG
65 GCGCCGCTAATG
1773880 CTTTACCTTT
Statistics
Matches: 167, Mismatches: 27, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
122 35 0.21
123 59 0.35
124 71 0.43
125 2 0.01
ACGTcount: A:0.25, C:0.24, G:0.26, T:0.25
Consensus pattern (122 bp):
ACCTTTAGCGGCACATTAGAGAAAGCGCCGCTAATGACTTGACCTTTAGCGGCGCTTAAGAAAAG
CGCCGCTAATGATCATACCTTTAGCGGCACTTGAGGTAAAGCGCCGCTAATGACAAG
Found at i:1774660 original size:18 final size:19
Alignment explanation
Indices: 1774611--1774662 Score: 70
Period size: 19 Copynumber: 2.8 Consensus size: 19
1774601 TACAAAATAT
* *
1774611 TTCAAAATATTTTTCAAAA
1 TTCAAAATATTTATAAAAA
1774630 TTCAAAATATTTATAAAAA
1 TTCAAAATATTTATAAAAA
*
1774649 TTCTAAAT-TTTATA
1 TTCAAAATATTTATA
1774663 TATTTTTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
18 6 0.20
19 24 0.80
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (19 bp):
TTCAAAATATTTATAAAAA
Found at i:1774707 original size:29 final size:30
Alignment explanation
Indices: 1774665--1774734 Score: 74
Period size: 30 Copynumber: 2.4 Consensus size: 30
1774655 ATTTTATATA
*
1774665 TTTTTAAAATTATA-AAA-AAAATTAAAAT
1 TTTTTAAAAATATACAAATAAAATTAAAAT
* *
1774693 TTTTTAAAGAATATACAAATAAAGTT-AAAG
1 TTTTTAAA-AATATACAAATAAAATTAAAAT
*
1774723 TTTTAAAAAATA
1 TTTTTAAAAATA
1774735 ATTTTAAGGA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
28 8 0.23
29 9 0.26
30 13 0.37
31 5 0.14
ACGTcount: A:0.57, C:0.01, G:0.04, T:0.37
Consensus pattern (30 bp):
TTTTTAAAAATATACAAATAAAATTAAAAT
Found at i:1786060 original size:37 final size:37
Alignment explanation
Indices: 1786010--1786113 Score: 199
Period size: 37 Copynumber: 2.8 Consensus size: 37
1786000 ACTTAGCCTT
*
1786010 GAGTGGTATTAGTCAAATAGCTATTATTGTGAGTCTG
1 GAGTGGTGTTAGTCAAATAGCTATTATTGTGAGTCTG
1786047 GAGTGGTGTTAGTCAAATAGCTATTATTGTGAGTCTG
1 GAGTGGTGTTAGTCAAATAGCTATTATTGTGAGTCTG
1786084 GAGTGGTGTTAGTCAAATAGCTATTATTGT
1 GAGTGGTGTTAGTCAAATAGCTATTATTGT
1786114 ACAGAAGATG
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
37 66 1.00
ACGTcount: A:0.26, C:0.08, G:0.28, T:0.38
Consensus pattern (37 bp):
GAGTGGTGTTAGTCAAATAGCTATTATTGTGAGTCTG
Found at i:1791235 original size:11 final size:12
Alignment explanation
Indices: 1791208--1791237 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
1791198 TTATATTTAT
1791208 ATTAAATAACTA
1 ATTAAATAACTA
1791220 ATTAAATAAC-A
1 ATTAAATAACTA
1791231 ATTAAAT
1 ATTAAAT
1791238 TTATTATTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 8 0.44
12 10 0.56
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (12 bp):
ATTAAATAACTA
Found at i:1791331 original size:17 final size:17
Alignment explanation
Indices: 1791311--1791362 Score: 59
Period size: 17 Copynumber: 3.1 Consensus size: 17
1791301 TTTAAAAGTT
1791311 ATATTTAATATAATAAA
1 ATATTTAATATAATAAA
* * * *
1791328 ATATTTATTATATTTAT
1 ATATTTAATATAATAAA
*
1791345 TTATTTAATATAATAAA
1 ATATTTAATATAATAAA
1791362 A
1 A
1791363 AAAATTATTA
Statistics
Matches: 25, Mismatches: 10, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
ATATTTAATATAATAAA
Found at i:1791352 original size:34 final size:35
Alignment explanation
Indices: 1791312--1791380 Score: 113
Period size: 35 Copynumber: 2.0 Consensus size: 35
1791302 TTAAAAGTTA
* *
1791312 TATTTAATATAAT-AAAATATTTATTATATTTATT
1 TATTTAATATAATAAAAAAAATTATTATATTTATT
1791346 TATTTAATATAATAAAAAAAATTATTATATTTATT
1 TATTTAATATAATAAAAAAAATTATTATATTTATT
1791381 GTAGTGATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 13 0.41
35 19 0.59
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (35 bp):
TATTTAATATAATAAAAAAAATTATTATATTTATT
Found at i:1794647 original size:28 final size:26
Alignment explanation
Indices: 1794616--1794690 Score: 71
Period size: 28 Copynumber: 2.7 Consensus size: 26
1794606 TAGACATTCA
1794616 AGGGTAAAATGGTAATTTTGCAAGTTTT
1 AGGGTAAAAT-GTAATTTTGCAAG-TTT
*
1794644 AGGGTTAAAATAG-AATTTTTGGAAGTTT
1 AGGG-TAAAAT-GTAA-TTTTGCAAGTTT
*
1794672 GGGGTAAAAATGTAATTTT
1 AGGGT-AAAATGTAATTTT
1794691 TAGAGGTTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
27 6 0.15
28 19 0.47
29 15 0.38
ACGTcount: A:0.35, C:0.01, G:0.25, T:0.39
Consensus pattern (26 bp):
AGGGTAAAATGTAATTTTGCAAGTTT
Found at i:1794711 original size:87 final size:88
Alignment explanation
Indices: 1794620--1794779 Score: 227
Period size: 87 Copynumber: 1.8 Consensus size: 88
1794610 CATTCAAGGG
* * *
1794620 TAAAATGGTAA-TTTTGCAAGTTTTAGGGTTAAAATAGAATTTTTGGAAGTTT-GGGGTAAAAAT
1 TAAAATGG-AATTTTTGCAAATTTAAGGGTAAAAATAGAATTTTTGGAAGTTTCGGGGTAAAAAT
1794683 GTA-ATTTTTAGAGGTTTTGGGGTT
65 G-AGATTTTTAGAGGTTTTGGGGTT
* * *
1794707 TAAAATGGAATTTTTGGAAATTTAAGGGTAAAAATGGGATTTTTGGAAGTTTCGGGGTAAAAATG
1 TAAAATGGAATTTTTGCAAATTTAAGGGTAAAAATAGAATTTTTGGAAGTTTCGGGGTAAAAATG
1794772 AGATTTTT
66 AGATTTTT
1794780 GGATAGTTTA
Statistics
Matches: 64, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
86 2 0.03
87 44 0.69
88 18 0.28
ACGTcount: A:0.33, C:0.01, G:0.26, T:0.39
Consensus pattern (88 bp):
TAAAATGGAATTTTTGCAAATTTAAGGGTAAAAATAGAATTTTTGGAAGTTTCGGGGTAAAAATG
AGATTTTTAGAGGTTTTGGGGTT
Found at i:1794722 original size:58 final size:57
Alignment explanation
Indices: 1794570--1794789 Score: 191
Period size: 58 Copynumber: 3.8 Consensus size: 57
1794560 GTAAAACGAT
* * *
1794570 AATTTTT-GAAAGTTTTGGGGTTAAAAATGGAGTTTTTAGACA-TTCAAGGGT-AAAATGG
1 AATTTTTAG-AAGTTTTGGGGTT-AAAAT-GAATTTTTGGA-AGTTTAAGGGTAAAAATGG
* * *
1794628 TAA-TTTT-GCAAGTTTTAGGGTTAAAATAGAATTTTTGGAAGTTT-GGGGTAAAAATGT
1 -AATTTTTAG-AAGTTTTGGGGTTAAAAT-GAATTTTTGGAAGTTTAAGGGTAAAAATGG
* *
1794685 AATTTTTAGAGGTTTTGGGGTTTAAAATGGAATTTTTGGAAATTTAAGGGTAAAAATGG
1 AATTTTTAGAAGTTTTGGGG-TTAAAAT-GAATTTTTGGAAGTTTAAGGGTAAAAATGG
* * * *
1794744 GATTTTTGGAAGTTTCGGGGTAAAAATGAGATTTTTGGATAGTTTA
1 AATTTTTAGAAGTTTTGGGGTTAAAATGA-ATTTTTGGA-AGTTTA
1794790 GGGACTTGTA
Statistics
Matches: 133, Mismatches: 20, Indels: 16
0.79 0.12 0.09
Matches are distributed among these distances:
56 7 0.05
57 37 0.28
58 55 0.41
59 34 0.26
ACGTcount: A:0.33, C:0.02, G:0.26, T:0.39
Consensus pattern (57 bp):
AATTTTTAGAAGTTTTGGGGTTAAAATGAATTTTTGGAAGTTTAAGGGTAAAAATGG
Found at i:1794781 original size:29 final size:29
Alignment explanation
Indices: 1794571--1794788 Score: 146
Period size: 29 Copynumber: 7.5 Consensus size: 29
1794561 TAAAACGATA
*
1794571 ATTTTTGAAAGTTTTGGGGTTAAAAATG-G
1 ATTTTTGGAAGTTTTGGGG-TAAAAATGAG
* ***
1794600 AGTTTTTAGACA-TTCAAGGGT-AAAATG-G
1 A-TTTTTGGA-AGTTTTGGGGTAAAAATGAG
* * * *
1794628 TAATTTTGCAAGTTTTAGGGTTAAAAT-AG
1 -ATTTTTGGAAGTTTTGGGGTAAAAATGAG
1794657 AATTTTTGGAAG-TTTGGGGTAAAAATGTA-
1 -ATTTTTGGAAGTTTTGGGGTAAAAATG-AG
* * *
1794686 ATTTTTAGAGGTTTTGGGGTTTAAAATG-G
1 ATTTTTGGAAGTTTTGGGG-TAAAAATGAG
* ** *
1794715 AATTTTTGGAAATTTAAGGGTAAAAATGGG
1 -ATTTTTGGAAGTTTTGGGGTAAAAATGAG
*
1794745 ATTTTTGGAAGTTTCGGGGTAAAAATGAG
1 ATTTTTGGAAGTTTTGGGGTAAAAATGAG
1794774 ATTTTTGGATAGTTT
1 ATTTTTGGA-AGTTT
1794789 AGGGACTTGT
Statistics
Matches: 147, Mismatches: 28, Indels: 27
0.73 0.14 0.13
Matches are distributed among these distances:
27 1 0.01
28 40 0.27
29 66 0.45
30 39 0.27
31 1 0.01
ACGTcount: A:0.32, C:0.02, G:0.27, T:0.39
Consensus pattern (29 bp):
ATTTTTGGAAGTTTTGGGGTAAAAATGAG
Found at i:1796171 original size:17 final size:17
Alignment explanation
Indices: 1796149--1796183 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1796139 TTAATTTAAT
1796149 TTTAATTTAAAAATAAA
1 TTTAATTTAAAAATAAA
* *
1796166 TTTAATTTTAAAGTAAA
1 TTTAATTTAAAAATAAA
1796183 T
1 T
1796184 CCAAACTCAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (17 bp):
TTTAATTTAAAAATAAA
Found at i:1796202 original size:34 final size:34
Alignment explanation
Indices: 1796158--1796224 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 34
1796148 TTTTAATTTA
*
1796158 AAAATAAATTT-AATTTTAAAGTAAATCCAAACTC
1 AAAATAAATTTGAA-TTTAAAATAAATCCAAACTC
* *
1796192 AAAATGAATTTGAATTTAAAATAAATTCAAACT
1 AAAATAAATTTGAATTTAAAATAAATCCAAACT
1796225 TATTTAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 27 0.93
35 2 0.07
ACGTcount: A:0.54, C:0.09, G:0.04, T:0.33
Consensus pattern (34 bp):
AAAATAAATTTGAATTTAAAATAAATCCAAACTC
Found at i:1796218 original size:17 final size:16
Alignment explanation
Indices: 1796149--1796218 Score: 50
Period size: 17 Copynumber: 4.1 Consensus size: 16
1796139 TTAATTTAAT
1796149 TTTAATTTAAAAATAAA
1 TTTAATTT-AAAATAAA
*
1796166 TTTAATTTTAAAGTAAA
1 TTTAA-TTTAAAATAAA
** * * *
1796183 TCCAAACTCAAAATGAA
1 T-TTAATTTAAAATAAA
1796200 TTTGAATTTAAAATAAA
1 TTT-AATTTAAAATAAA
1796217 TT
1 TT
1796219 CAAACTTATT
Statistics
Matches: 38, Mismatches: 12, Indels: 6
0.68 0.21 0.11
Matches are distributed among these distances:
17 33 0.87
18 5 0.13
ACGTcount: A:0.51, C:0.06, G:0.04, T:0.39
Consensus pattern (16 bp):
TTTAATTTAAAATAAA
Found at i:1805880 original size:19 final size:17
Alignment explanation
Indices: 1805854--1805899 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 17
1805844 CTTATAACTC
*
1805854 TTTTTTTTCTGTTTTCTT
1 TTTTTTTTCT-TTTTCCT
1805872 TTCTTTTTTCTTTTTCCT
1 TT-TTTTTTCTTTTTCCT
1805890 TTTTTTTTCT
1 TTTTTTTTCT
1805900 AGGCCTGCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 8 0.31
18 10 0.38
19 8 0.31
ACGTcount: A:0.00, C:0.15, G:0.02, T:0.83
Consensus pattern (17 bp):
TTTTTTTTCTTTTTCCT
Found at i:1807279 original size:17 final size:17
Alignment explanation
Indices: 1807257--1807291 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1807247 TTTGTTAATT
* *
1807257 ATTAATTAAATTATTTA
1 ATTAATAAAATCATTTA
1807274 ATTAATAAAATCATTTA
1 ATTAATAAAATCATTTA
1807291 A
1 A
1807292 AATATAATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (17 bp):
ATTAATAAAATCATTTA
Found at i:1807304 original size:27 final size:26
Alignment explanation
Indices: 1807274--1807325 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
1807264 AAATTATTTA
1807274 ATTAATAAAATCATTTAAAATATAATT
1 ATTAATAAAAT-ATTTAAAATATAATT
* * *
1807301 ATTAATTAAATGTTTGAAATATAAT
1 ATTAATAAAATATTTAAAATATAAT
1807326 GGTTGATTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 12 0.55
27 10 0.45
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.42
Consensus pattern (26 bp):
ATTAATAAAATATTTAAAATATAATT
Found at i:1816840 original size:23 final size:24
Alignment explanation
Indices: 1816814--1816864 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 24
1816804 TATTAATATA
*
1816814 ATACGTTTAAGCTCGTCAGCATG-
1 ATACATTTAAGCTCGTCAGCATGT
*
1816837 ATACATTTACGCTCGTCAGCATGT
1 ATACATTTAAGCTCGTCAGCATGT
1816861 ATAC
1 ATAC
1816865 TAGTAAATGT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 21 0.84
24 4 0.16
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (24 bp):
ATACATTTAAGCTCGTCAGCATGT
Found at i:1816893 original size:23 final size:23
Alignment explanation
Indices: 1816867--1816922 Score: 85
Period size: 23 Copynumber: 2.4 Consensus size: 23
1816857 ATGTATACTA
1816867 GTAAATGTATCATGCTGACGAGC
1 GTAAATGTATCATGCTGACGAGC
*
1816890 GTAAATGTATCATGCTGATGAGC
1 GTAAATGTATCATGCTGACGAGC
* *
1816913 TTAAACGTAT
1 GTAAATGTAT
1816923 TATATTAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.32, C:0.14, G:0.23, T:0.30
Consensus pattern (23 bp):
GTAAATGTATCATGCTGACGAGC
Found at i:1827854 original size:24 final size:24
Alignment explanation
Indices: 1827827--1827890 Score: 76
Period size: 24 Copynumber: 2.7 Consensus size: 24
1827817 ACTCTGTCTA
* *
1827827 GGCTCGAATGAACTAACTTATCTG
1 GGCTCGAATGAGCTAACCTATCTG
*
1827851 GGCTCCTAA-GAGCTAACCTATCTG
1 GGCT-CGAATGAGCTAACCTATCTG
*
1827875 GGCTCGTATGAGCTAA
1 GGCTCGAATGAGCTAA
1827891 TTTTGTCTGG
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
23 2 0.06
24 28 0.85
25 3 0.09
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (24 bp):
GGCTCGAATGAGCTAACCTATCTG
Found at i:1837427 original size:28 final size:28
Alignment explanation
Indices: 1837396--1837457 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 28
1837386 AAAACGGGAC
*
1837396 TTTTGGA-TACTCGGGGG-CAAAATCGTAA
1 TTTTGGACT-CTCGGGGGAAAAAAT-GTAA
*
1837424 TTTTTGACTCTCGGGGGAAAAAATGTAA
1 TTTTGGACTCTCGGGGGAAAAAATGTAA
1837452 TTTTGG
1 TTTTGG
1837458 GAAAATTTAG
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
28 23 0.79
29 6 0.21
ACGTcount: A:0.27, C:0.11, G:0.27, T:0.34
Consensus pattern (28 bp):
TTTTGGACTCTCGGGGGAAAAAATGTAA
Found at i:1837512 original size:59 final size:58
Alignment explanation
Indices: 1837443--1837807 Score: 361
Period size: 59 Copynumber: 6.2 Consensus size: 58
1837433 CTCGGGGGAA
1837443 AAAAT-GTAATTTTGGGAAAATTTAGGGTTAAAAAT-GAGATTTT-GAAAGGTTTAGGGGT
1 AAAATGGTAATTTTGGGAAAA-TTAGGGTTAAAAATGGA-ATTTTGGAAA-GTTTAGGGGT
*** * * * * **
1837501 AAAACAATAATTTTTGGTGAAACTGA-GGTTAAAAATGGGATTTTGGAAAGCTCGGGGGT
1 AAAATGGTAA-TTTTGG-GAAAATTAGGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGT
* * * * *
1837560 AAAACGGTAATTTTTGGTG-AACTTGGGGTTAAAAATGGAATTCTGGAAAGTTTGGGGGT
1 AAAATGGTAA-TTTTGG-GAAAATTAGGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGT
*
1837619 AAAATGGTAATTTTAGGTG-AAA-TCGAGGTTAAAAAT-GAGATTTTGGAAAGTTTAGGGGT
1 AAAATGGTAATTTT-GG-GAAAATTAG-GGTTAAAAATGGA-ATTTTGGAAAGTTTAGGGGT
* * * *
1837678 AAAATGGTAATTTTTGGTAAAATCAGGGTTAAAAGTGGAATTTTGGAAAGTTTGGGGGT
1 AAAATGGTAA-TTTTGGGAAAATTAGGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGT
*
1837737 AAAATGGTAATTTT-TGATGAAATTAGGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGT
1 AAAATGGTAATTTTGGGA--AAATTAGGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGT
1837796 AAAATGGTAATT
1 AAAATGGTAATT
1837808 GTTGAAAGTT
Statistics
Matches: 261, Mismatches: 31, Indels: 29
0.81 0.10 0.09
Matches are distributed among these distances:
57 1 0.00
58 20 0.08
59 216 0.83
60 20 0.08
61 4 0.02
ACGTcount: A:0.36, C:0.02, G:0.29, T:0.33
Consensus pattern (58 bp):
AAAATGGTAATTTTGGGAAAATTAGGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGT
Found at i:1837572 original size:29 final size:29
Alignment explanation
Indices: 1837532--1837847 Score: 183
Period size: 29 Copynumber: 10.8 Consensus size: 29
1837522 ACTGAGGTTA
* * *
1837532 AAAATGG-GATTTTGGAAAGCTCGGGGGT
1 AAAATGGTAATTTTGGAAAGTTTGGGGGT
* * * *
1837560 AAAACGGTAATTTTTGGTGAA-CTTGGGGTT
1 AAAATGGTAA-TTTTGG-AAAGTTTGGGGGT
*
1837590 AAAAATGG-AATTCTGGAAAGTTTGGGGGT
1 -AAAATGGTAATTTTGGAAAGTTTGGGGGT
* * *
1837619 AAAATGGTAATTTTAGGTGAAA--TCGAGGTT
1 AAAATGGTAATTTT--G-GAAAGTTTGGGGGT
*
1837649 AAAAAT-G-AGATTTTGGAAAGTTTAGGGGT
1 -AAAATGGTA-ATTTTGGAAAGTTTGGGGGT
* ** *
1837678 AAAATGGTAATTTTTGGTAAA-ATCAGGGTT
1 AAAATGGTAA-TTTTGG-AAAGTTTGGGGGT
1837708 AAAAGTGG-AATTTTGGAAAGTTTGGGGGT
1 AAAA-TGGTAATTTTGGAAAGTTTGGGGGT
* *
1837737 AAAATGGTAATTTTTGATGAAA--TTAGGGTT
1 AAAATGGTAA-TTTTG--GAAAGTTTGGGGGT
*
1837767 AAAAATGG-AATTTTGGAAAGTTTAGGGGT
1 -AAAATGGTAATTTTGGAAAGTTTGGGGGT
*
1837796 AAAATGGTAATTGTT-GAAAGTTTCGGGGT
1 AAAATGGTAATT-TTGGAAAGTTTGGGGGT
*
1837825 CAAAAT-GTAATTTTTGGATAGTT
1 -AAAATGGTAA-TTTTGGAAAGTT
1837848 CAAGGACCTA
Statistics
Matches: 227, Mismatches: 30, Indels: 60
0.72 0.09 0.19
Matches are distributed among these distances:
27 8 0.04
28 34 0.15
29 77 0.34
30 73 0.32
31 27 0.12
32 8 0.04
ACGTcount: A:0.34, C:0.03, G:0.30, T:0.34
Consensus pattern (29 bp):
AAAATGGTAATTTTGGAAAGTTTGGGGGT
Found at i:1837748 original size:177 final size:177
Alignment explanation
Indices: 1837468--1837807 Score: 513
Period size: 177 Copynumber: 1.9 Consensus size: 177
1837458 GAAAATTTAG
* *
1837468 GGTTAAAAATGAGATTTTGAAAGGTTTAGGGGTAAAACAATAATTTTTGGTGAAACTGAGGTTAA
1 GGTTAAAAATGAGATTTTGAAAGGTTTAGGGGTAAAACAATAATTTTTGGTAAAACAGAGGTTAA
* * * *
1837533 AAATGGGATTTTGGAAAGCTCGGGGGTAAAACGGTAATTTTTGGTGAACTTGGGGTTAAAAATGG
66 AAATGGAATTTTGGAAAGCTCGGGGGTAAAACGGTAATTTTTGATGAAATTAGGGTTAAAAATGG
*
1837598 AATTCTGGAAAGTTTGGGGGTAAAATGGTAATTTTAGGTGAAATCGA
131 AATTCTGGAAAGTTTAGGGGTAAAATGGTAATTTTAGGTGAAATCGA
***
1837645 GGTTAAAAATGAGATTTTGGAAA-GTTTAGGGGTAAAATGGTAATTTTTGGTAAAATCAG-GGTT
1 GGTTAAAAATGAGATTTT-GAAAGGTTTAGGGGTAAAACAATAATTTTTGGTAAAA-CAGAGGTT
* * * *
1837708 AAAAGTGGAATTTTGGAAAGTTTGGGGGTAAAATGGTAATTTTTGATGAAATTAGGGTTAAAAAT
64 AAAAATGGAATTTTGGAAAGCTCGGGGGTAAAACGGTAATTTTTGATGAAATTAGGGTTAAAAAT
*
1837773 GGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATT
129 GGAATTCTGGAAAGTTTAGGGGTAAAATGGTAATT
1837808 GTTGAAAGTT
Statistics
Matches: 146, Mismatches: 15, Indels: 4
0.88 0.09 0.02
Matches are distributed among these distances:
177 140 0.96
178 6 0.04
ACGTcount: A:0.35, C:0.03, G:0.29, T:0.33
Consensus pattern (177 bp):
GGTTAAAAATGAGATTTTGAAAGGTTTAGGGGTAAAACAATAATTTTTGGTAAAACAGAGGTTAA
AAATGGAATTTTGGAAAGCTCGGGGGTAAAACGGTAATTTTTGATGAAATTAGGGTTAAAAATGG
AATTCTGGAAAGTTTAGGGGTAAAATGGTAATTTTAGGTGAAATCGA
Found at i:1837787 original size:118 final size:117
Alignment explanation
Indices: 1837443--1837807 Score: 461
Period size: 118 Copynumber: 3.1 Consensus size: 117
1837433 CTCGGGGGAA
* *
1837443 AAAAT-GTAA-TTTTGGGAAAATTTAGGGTTAAAAAT-GAGATTTT-GAAAGGTTTAGGGGTAAA
1 AAAATGGTAATTTTTGGTAAAA-TTAGGGTTAAAAATGGA-ATTTTGGAAA-GTTTGGGGGTAAA
*** * * **
1837504 ACAATAATTTTTGGTGAAACTGAGGTTAAAAATGGGATTTTGGAAAGCTCGGGGGT
63 ATGGTAATTTTTGGTGAAA-TGAGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGT
* * * * *
1837560 AAAACGGTAATTTTTGGTGAACTTGGGGTTAAAAATGGAATTCTGGAAAGTTTGGGGGTAAAATG
1 AAAATGGTAATTTTTGGTAAAATTAGGGTTAAAAATGGAATTTTGGAAAGTTTGGGGGTAAAATG
*
1837625 GTAATTTTAGGTGAAATCGAGGTTAAAAAT-GAGATTTTGGAAAGTTTAGGGGT
66 GTAATTTTTGGTGAAAT-GAGGTTAAAAATGGA-ATTTTGGAAAGTTTAGGGGT
* *
1837678 AAAATGGTAATTTTTGGTAAAATCAGGGTTAAAAGTGGAATTTTGGAAAGTTTGGGGGTAAAATG
1 AAAATGGTAATTTTTGGTAAAATTAGGGTTAAAAATGGAATTTTGGAAAGTTTGGGGGTAAAATG
* *
1837743 GTAATTTTTGATGAAATTAGGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGT
66 GTAATTTTTGGTGAAATGA-GGTTAAAAATGGAATTTTGGAAAGTTTAGGGGT
1837796 AAAATGGTAATT
1 AAAATGGTAATT
1837808 GTTGAAAGTT
Statistics
Matches: 215, Mismatches: 25, Indels: 15
0.84 0.10 0.06
Matches are distributed among these distances:
117 7 0.03
118 192 0.89
119 16 0.07
ACGTcount: A:0.36, C:0.02, G:0.29, T:0.33
Consensus pattern (117 bp):
AAAATGGTAATTTTTGGTAAAATTAGGGTTAAAAATGGAATTTTGGAAAGTTTGGGGGTAAAATG
GTAATTTTTGGTGAAATGAGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGT
Found at i:1837840 original size:59 final size:56
Alignment explanation
Indices: 1837530--1837847 Score: 282
Period size: 59 Copynumber: 5.4 Consensus size: 56
1837520 AAACTGAGGT
* * ** * *
1837530 TAAAAATGGGATTTTGGAAAGCTCGGGGGTAAAACGGTAATTTTTGGTGAACTT-GGGG
1 TAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGGTAA-TTTT--TGAAATTCGGGG
* * *
1837588 TTAAAAATGGAATTCTGGAAAGTTTGGGGGTAAAATGGTAATTTTAGGTGAAA-TCGAGGT
1 -TAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTT---TGAAATTCG-GGG
* *
1837648 TAAAAAT-GAGATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTTGGTAAAATCAGGGT
1 TAAAAATGGA-ATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTT-G-AAATTC-GGGG
* * * *
1837707 TAAAAGTGGAATTTTGGAAAGTTTGGGGGTAAAATGGTAATTTTTGATGAAATTAGGGT
1 TAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGGTAA-TTTT--TGAAATTCGGGG
*
1837766 TAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTGTTGAAAGTTTCGGGG
1 TAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTTGAAA--TTCGGGG
* * *
1837824 TCAAAATGTAATTTTTGGATAGTT
1 TAAAAATGGAA-TTTTGGAAAGTT
1837848 CAAGGACCTA
Statistics
Matches: 223, Mismatches: 21, Indels: 30
0.81 0.08 0.11
Matches are distributed among these distances:
56 6 0.03
57 1 0.00
58 27 0.12
59 174 0.78
60 13 0.06
61 1 0.00
62 1 0.00
ACGTcount: A:0.34, C:0.03, G:0.30, T:0.34
Consensus pattern (56 bp):
TAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTTGAAATTCGGGG
Found at i:1839848 original size:17 final size:17
Alignment explanation
Indices: 1839821--1839904 Score: 87
Period size: 17 Copynumber: 4.8 Consensus size: 17
1839811 TTAAATTTTC
1839821 ATTTCAAAATAAATTTAA
1 ATTT-AAAATAAATTTAA
1839839 ATTTAAAATAAATTTAA
1 ATTTAAAATAAATTTAA
* ** * *
1839856 ACTCCAAACAAGTTTTAA
1 ATTTAAAATAA-ATTTAA
*
1839874 ATTTATAATAAATTTAA
1 ATTTAAAATAAATTTAA
*
1839891 ATTTAAAATGAATT
1 ATTTAAAATAAATT
1839905 AAAAATCTAA
Statistics
Matches: 52, Mismatches: 13, Indels: 3
0.76 0.19 0.04
Matches are distributed among these distances:
17 37 0.71
18 15 0.29
ACGTcount: A:0.52, C:0.06, G:0.02, T:0.39
Consensus pattern (17 bp):
ATTTAAAATAAATTTAA
Found at i:1840670 original size:91 final size:91
Alignment explanation
Indices: 1840551--1840719 Score: 268
Period size: 91 Copynumber: 1.9 Consensus size: 91
1840541 TTGTGTCGAA
* *
1840551 GCTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGATTTGCTATCCAACTTTACTAT-AAC
1 GCTTCATCTAGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACT-TCAAC
1840615 TTCAAAAGGATAGGGATTAACGTTGAT
65 TTCAAAAGGATAGGGATTAACGTTGAT
* * *
1840642 GCTTCATCTAGCTCTTACTTCAATTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTTCAATT
1 GCTTCATCTAGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTTCAACT
*
1840707 TCAAGAGGATAGG
66 TCAAAAGGATAGG
1840720 AAATGATCTT
Statistics
Matches: 71, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
90 1 0.01
91 70 0.99
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.33
Consensus pattern (91 bp):
GCTTCATCTAGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTTCAACT
TCAAAAGGATAGGGATTAACGTTGAT
Found at i:1840780 original size:76 final size:76
Alignment explanation
Indices: 1840647--1841718 Score: 1788
Period size: 76 Copynumber: 14.1 Consensus size: 76
1840637 TTGATGCTTC
* * *
1840647 ATCTAGCTCTTACTTCAATTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTTCAATTTCAAG
1 ATCTTGCTCTTACTTCAATTTC--AGAGATAAAGACTTGTTATCCAGCTTTACTTCAATTTCAAG
1840712 AGGATAGGAAATG
64 AGGATAGGAAATG
* * *
1840725 ATCTTGCTCTTACTTCAATTTCAGAGATGAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAG
1 ATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAGCTTTACTTCAATTTCAAGAG
1840790 GATAGGAAATG
66 GATAGGAAATG
* * *
1840801 ATCTTGCTCTTACTTCAATTTCAGAGATGAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAG
1 ATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAGCTTTACTTCAATTTCAAGAG
1840866 GATAGGAAATG
66 GATAGGAAATG
* *
1840877 ATCTTGTTCTTACTTCAATTTCAGAGATGAAGACTTGTTATCCAGCTTTACTTCAATTTCAAGAG
1 ATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAGCTTTACTTCAATTTCAAGAG
1840942 GATAGGAAATG
66 GATAGGAAATG
*
1840953 ATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAGCTTTACTTCAATTTCAAGAG
1 ATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAGCTTTACTTCAATTTCAAGAG
1841018 GATAGGAAATG
66 GATAGGAAATG
* * * * *
1841029 ATCTTACTATTACTTCAATTTCAGAGATGAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAG
1 ATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAGCTTTACTTCAATTTCAAGAG
1841094 GATAGGAAATG
66 GATAGGAAATG
* * *
1841105 ATCTTGCTCTTACTTCAATTTCAGAGATGAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAG
1 ATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAGCTTTACTTCAATTTCAAGAG
1841170 GATAGGAAATG
66 GATAGGAAATG
1841181 ATCTTGCTCTTACTTCAATTTCAGAGATGAAA-ACTTGTTATCCAGCTTTACTTCAATTTCAAGA
1 ATCTTGCTCTTACTTCAATTTCAGAGAT-AAAGACTTGTTATCCAGCTTTACTTCAATTTCAAGA
1841245 GGATAGGAAATG
65 GGATAGGAAATG
* * *
1841257 ATCTTGCTATTACTTCAATTTCAGAGATAAAGACTTGATATTCAGCTTTACTTCAATTTCAAGAG
1 ATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAGCTTTACTTCAATTTCAAGAG
1841322 GATAGGAAATG
66 GATAGGAAATG
* * *
1841333 ATCTTACTCTTACTTCAATTTCAAAGATAAAGACTTGATATCCAGCTTTACTTCAATTTCAAGAG
1 ATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAGCTTTACTTCAATTTCAAGAG
1841398 GATAGGAAATG
66 GATAGGAAATG
* *
1841409 ATCTTACTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAGCTTTACTTCAATTTCAAGAG
1 ATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAGCTTTACTTCAATTTCAAGAG
1841474 GATAGGAAATG
66 GATAGGAAATG
* * *
1841485 ATCTTACTCTTACTTCAATTTCATAGATAAAGACTTGATATCCAGCTTTACTTCAATTTCAAGAG
1 ATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAGCTTTACTTCAATTTCAAGAG
1841550 GATAGGAAATG
66 GATAGGAAATG
1841561 ATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAGCTTTACTTCAATTTCAAGAG
1 ATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAGCTTTACTTCAATTTCAAGAG
*
1841626 AAT-GGAAAATG
66 GATAGG-AAATG
* *
1841637 ATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAG
1 ATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAGCTTTACTTCAATTTCAAGAG
1841702 GATAGGAAATG
66 GATAGGAAATG
1841713 ATCTTG
1 ATCTTG
1841719 GTGCTTCATC
Statistics
Matches: 953, Mismatches: 37, Indels: 10
0.95 0.04 0.01
Matches are distributed among these distances:
75 5 0.01
76 923 0.97
77 4 0.00
78 21 0.02
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (76 bp):
ATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAGCTTTACTTCAATTTCAAGAG
GATAGGAAATG
Found at i:1842163 original size:50 final size:51
Alignment explanation
Indices: 1842107--1842233 Score: 175
Period size: 51 Copynumber: 2.5 Consensus size: 51
1842097 GCGATATTGA
* * *
1842107 ATCTGCCGTTGCGGGCTTAGATCTTTCCCGTC-GTGTCTTCGTGGTACTAG
1 ATCTGCCGTTGCGGTCTTAGATCTTTCCCGTCTGTATCTTCGTGGCACTAG
* * * *
1842157 ATCTGCCGTTGCGATCTTAGATCTTTCCCTTCTGTATCTTTGTGGCACTGG
1 ATCTGCCGTTGCGGTCTTAGATCTTTCCCGTCTGTATCTTCGTGGCACTAG
*
1842208 ATCTGCTGTTGCGGTCTTAGATCTTT
1 ATCTGCCGTTGCGGTCTTAGATCTTT
1842234 TCGGTCCATG
Statistics
Matches: 67, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
50 29 0.43
51 38 0.57
ACGTcount: A:0.11, C:0.24, G:0.24, T:0.40
Consensus pattern (51 bp):
ATCTGCCGTTGCGGTCTTAGATCTTTCCCGTCTGTATCTTCGTGGCACTAG
Found at i:1842277 original size:101 final size:98
Alignment explanation
Indices: 1842063--1842480 Score: 385
Period size: 101 Copynumber: 4.2 Consensus size: 98
1842053 TTCATGTATC
* * * * * * *
1842063 GCCATTGCGACTTAGACCTTTCCCTTTTGTCTTTGCGATATTGAATCTGCCGTTGCGGGCTTAGA
1 GCCATTGCGACTTAGACCTTTCCCTTCTGTTTTTGCGGTACTGGATCTG-CATTGCGGTCTTAGA
* * * * * *
1842128 TCTTTCCCGT-CGTG-TCTTCGTGGTACTA-GATCT
65 TCTTTTCCTTCCATGCT-TTTGAGGTAC-ACGGTCT
* * * * *
1842161 GCCGTTGCGATCTTAGATCTTTCCCTTCTGTATCTTTGTGGCACTGGATCTGCTGTTGCGGTCTT
1 GCCATTGCGA-CTTAGACCTTTCCCTTCTGT-T-TTTGCGGTACTGGATCTGC-ATTGCGGTCTT
** *
1842226 AGATCTTTTCGGTCCATGCTTTTGAGGTACACGGTCC
62 AGATCTTTTCCTTCCATGCTTTTGAGGTACACGGTCT
* *
1842263 GCAATTGCGACTTAGACCTTTCCCTTTTCTGTTTTTACGGTACTGGATCTGGCATTGCGGTCTTA
1 GCCATTGCGACTTAGACCTTTCCC--TTCTGTTTTTGCGGTACTGGATCT-GCATTGCGGTCTTA
* *
1842328 GATCTTTCCCTTCCATGCTTTTGAGGTACACGATCT
63 GATCTTTTCCTTCCATGCTTTTGAGGTACACGGTCT
* * * ** *
1842364 GCCGTTGCGACTTAGACCTTTCCCTTTTGTGTTTTTGCGGTACTAGATCCACCATTGCGGTTTTA
1 GCCATTGCGACTTAGACCTTTCCC--TTCTGTTTTTGCGGTACTGGAT-CTGCATTGCGGTCTTA
* *
1842429 GATC-TTTCCTTTCATGCTTCTGAGGTACACGGTCT
63 GATCTTTTCCTTCCATGCTTTTGAGGTACACGGTCT
*
1842464 GCCATTGTGACTTAGAC
1 GCCATTGCGACTTAGAC
1842481 ATCTCCTTGT
Statistics
Matches: 266, Mismatches: 43, Indels: 20
0.81 0.13 0.06
Matches are distributed among these distances:
98 9 0.03
99 18 0.07
100 43 0.16
101 163 0.61
102 26 0.10
103 7 0.03
ACGTcount: A:0.14, C:0.25, G:0.22, T:0.39
Consensus pattern (98 bp):
GCCATTGCGACTTAGACCTTTCCCTTCTGTTTTTGCGGTACTGGATCTGCATTGCGGTCTTAGAT
CTTTTCCTTCCATGCTTTTGAGGTACACGGTCT
Found at i:1842335 original size:51 final size:51
Alignment explanation
Indices: 1842273--1842437 Score: 158
Period size: 51 Copynumber: 3.3 Consensus size: 51
1842263 GCAATTGCGA
* *
1842273 CTTAGACCTTTCCCTTTTCTGTTTTTACGGTACTGGATCTGGCATTGCGGT
1 CTTAGACCTTTCCCTTTTCTGTTTTTACGGTACTAGATCTGCCATTGCGGT
* * * * *
1842324 CTTAGATCTTTCCC-TTCCATGCTTTTGA-GGTAC-ACGATCTGCCGTTGC-GA
1 CTTAGACCTTTCCCTTTTC-TG-TTTTTACGGTACTA-GATCTGCCATTGCGGT
* * **
1842374 CTTAGACCTTTCCCTTTTGTGTTTTTGCGGTACTAGATCCACCATTGCGGT
1 CTTAGACCTTTCCCTTTTCTGTTTTTACGGTACTAGATCTGCCATTGCGGT
* *
1842425 TTTAGATCTTTCC
1 CTTAGACCTTTCC
1842438 TTTCATGCTT
Statistics
Matches: 89, Mismatches: 18, Indels: 14
0.74 0.15 0.12
Matches are distributed among these distances:
49 4 0.04
50 34 0.38
51 46 0.52
52 5 0.06
ACGTcount: A:0.14, C:0.25, G:0.19, T:0.41
Consensus pattern (51 bp):
CTTAGACCTTTCCCTTTTCTGTTTTTACGGTACTAGATCTGCCATTGCGGT
Found at i:1842422 original size:50 final size:50
Alignment explanation
Indices: 1842063--1842480 Score: 177
Period size: 50 Copynumber: 8.3 Consensus size: 50
1842053 TTCATGTATC
* * *
1842063 GCCATTGCGACTTAGACCTTTCCC-TTT-TGTCTTTGCGATA-TTGAATCT
1 GCCATTGCGACTTAGACCTTTCCCTTTTATGTTTTTGCGGTACTAG-ATCT
* * * * ** * * *
1842111 GCCGTTGCGGGCTTAGATCTTTCCC-GTCGTGTCTTCGTGGTACTAGATCT
1 GCCATTGC-GACTTAGACCTTTCCCTTTTATGTTTTTGCGGTACTAGATCT
* * * * * * * * *
1842161 GCCGTTGCGATCTTAGATCTTTCCCTTCTGTATCTTTGTGGCACTGGATCT
1 GCCATTGCGA-CTTAGACCTTTCCCTTTTATGTTTTTGCGGTACTAGATCT
** * * * ** ** * * * *
1842212 GCTGTTGCGGTCTTAGATCTTTTCGGTCCATGCTTTTGAGGTAC-ACGGTCC
1 GCCATTGC-GACTTAGACCTTTCCCTTTTATGTTTTTGCGGTACTA-GATCT
* * * *
1842263 GCAATTGCGACTTAGACCTTTCCCTTTTCTGTTTTTACGGTACTGGATCT
1 GCCATTGCGACTTAGACCTTTCCCTTTTATGTTTTTGCGGTACTAGATCT
* * * ** * *
1842313 GGCATTGCGGTCTTAGATCTTTCCCTTCCATGCTTTTGAGGTAC-ACGATCT
1 GCCATTGC-GACTTAGACCTTTCCCTTTTATGTTTTTGCGGTACTA-GATCT
* * *
1842364 GCCGTTGCGACTTAGACCTTTCCCTTTTGTGTTTTTGCGGTACTAGATCC
1 GCCATTGCGACTTAGACCTTTCCCTTTTATGTTTTTGCGGTACTAGATCT
* ** * * * * * *
1842414 ACCATTGCGGTTTTAGATCTTT-CCTTTCATGCTTCTGAGGTAC-ACGGTCT
1 GCCATTGC-GACTTAGACCTTTCCCTTTTATGTTTTTGCGGTACTA-GATCT
*
1842464 GCCATTGTGACTTAGAC
1 GCCATTGCGACTTAGAC
1842481 ATCTCCTTGT
Statistics
Matches: 271, Mismatches: 86, Indels: 25
0.71 0.23 0.07
Matches are distributed among these distances:
48 7 0.03
49 23 0.08
50 132 0.49
51 108 0.40
52 1 0.00
ACGTcount: A:0.14, C:0.25, G:0.22, T:0.39
Consensus pattern (50 bp):
GCCATTGCGACTTAGACCTTTCCCTTTTATGTTTTTGCGGTACTAGATCT
Found at i:1854495 original size:59 final size:59
Alignment explanation
Indices: 1854432--1854826 Score: 467
Period size: 59 Copynumber: 6.8 Consensus size: 59
1854422 GAAAATTTAG
* * *
1854432 GGTTAAAAAT-GAGATTTT-GAAAGGTTTAAGGGTAAAATAGTAATTTTTTGTGAAATCGA
1 GGTTAAAAATGGA-ATTTTGGAAA-GTTTAGGGGTAAAATGGTAATTTTTGGTGAAATCGA
* * * * *
1854491 GGTTAAAAATGGGATTTTGGAAAGCTT-GAGGGTAAAACGGTAATTTTTGGTGAACTCGG
1 GGTTAAAAATGGAATTTTGGAAAGTTTAG-GGGTAAAATGGTAATTTTTGGTGAAATCGA
** *
1854550 GGTTAAAAATGGAATTTTGGAAAGTTTA--CCT---A---TAATTTTAGGTGAAATCGA
1 GGTTAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTTGGTGAAATCGA
**
1854601 GGTTAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTTAATGAAATCGA
1 GGTTAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTTGGTGAAATCGA
* * * *
1854660 GGTTAAAAAT-AAGATTTTAGAAAGTTTAGGGGTAAAATGGTAATTTTTGGTAAAAT-TA
1 GGTTAAAAATGGA-ATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTTGGTGAAATCGA
* * *
1854718 GGGTTAAAAGTGGAATTTTGGAAAGTTTAGGGGTAAGATGGTAATTTTTGGTGAAATCGG
1 -GGTTAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTTGGTGAAATCGA
1854778 GGTT-AAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTTGG
1 GGTTAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTTGG
1854827 AAGTTTAGGG
Statistics
Matches: 285, Mismatches: 35, Indels: 33
0.81 0.10 0.09
Matches are distributed among these distances:
51 44 0.15
53 1 0.00
54 1 0.00
56 1 0.00
57 1 0.00
58 45 0.16
59 186 0.65
60 6 0.02
ACGTcount: A:0.36, C:0.03, G:0.27, T:0.34
Consensus pattern (59 bp):
GGTTAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTTGGTGAAATCGA
Found at i:1854566 original size:30 final size:30
Alignment explanation
Indices: 1854473--1854567 Score: 72
Period size: 30 Copynumber: 3.2 Consensus size: 30
1854463 GTAAAATAGT
* * *
1854473 AATTTTTTGTGAAATCGAGGTTAAAAATGG
1 AATTTTTGGTGAACTCGGGGTTAAAAATGG
* * * *
1854503 GA-TTTTGG-AAAGCTTGAGGG-T-AAAACGG
1 AATTTTTGGTGAA-CTCG-GGGTTAAAAATGG
1854531 TAATTTTTGGTGAACTCGGGGTTAAAAATGG
1 -AATTTTTGGTGAACTCGGGGTTAAAAATGG
1854562 AATTTT
1 AATTTT
1854568 GGAAAGTTTA
Statistics
Matches: 47, Mismatches: 11, Indels: 14
0.65 0.15 0.19
Matches are distributed among these distances:
28 8 0.17
29 12 0.26
30 19 0.40
31 8 0.17
ACGTcount: A:0.33, C:0.05, G:0.27, T:0.35
Consensus pattern (30 bp):
AATTTTTGGTGAACTCGGGGTTAAAAATGG
Found at i:1854594 original size:51 final size:51
Alignment explanation
Indices: 1854531--1854628 Score: 169
Period size: 51 Copynumber: 1.9 Consensus size: 51
1854521 GGTAAAACGG
* * *
1854531 TAATTTTTGGTGAACTCGGGGTTAAAAATGGAATTTTGGAAAGTTTACCTA
1 TAATTTTAGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTACCTA
1854582 TAATTTTAGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTA
1 TAATTTTAGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTA
1854629 GGGGTAAAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 44 1.00
ACGTcount: A:0.35, C:0.05, G:0.23, T:0.37
Consensus pattern (51 bp):
TAATTTTAGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTACCTA
Done.