Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007987.1 Hibiscus syriacus cultivar Beakdansim tig00110432_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 872063
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 1 of 5
Found at i:1516 original size:33 final size:32
Alignment explanation
Indices: 1473--1582 Score: 170
Period size: 31 Copynumber: 3.4 Consensus size: 32
1463 TTTTGGTTGA
1473 AATGAAAATCGCAACGAGAGAATCGCAACGCG
1 AATGAAAATCGCAACGAGAGAATCGCAACGCG
* *
1505 AGATGACAATCGC-AC-CGAGAATCGCAACGCG
1 A-ATGAAAATCGCAACGAGAGAATCGCAACGCG
1536 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
1 -AATGAAAATCGCAACGAGAGAATCGCAACGCG
1569 AATGAAAATCGCAA
1 AATGAAAATCGCAA
1583 TGCGATTTTG
Statistics
Matches: 70, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
31 25 0.36
32 20 0.29
33 25 0.36
ACGTcount: A:0.44, C:0.23, G:0.24, T:0.10
Consensus pattern (32 bp):
AATGAAAATCGCAACGAGAGAATCGCAACGCG
Found at i:1517 original size:19 final size:18
Alignment explanation
Indices: 1478--1587 Score: 70
Period size: 14 Copynumber: 6.8 Consensus size: 18
1468 GTTGAAATGA
1478 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
1493 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
1510 ACAATCGC-AC-C--GA-G
1 A-AATCGCAACGCGAGATG
*
1524 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
1541 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
1557 -AATCGCAACGCGA-ATG
1 AAATCGCAACGCGAGATG
*
1573 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
1588 TTTTGGTTTC
Statistics
Matches: 75, Mismatches: 3, Indels: 31
0.69 0.03 0.28
Matches are distributed among these distances:
12 6 0.08
13 2 0.03
14 18 0.24
15 3 0.04
16 11 0.15
17 7 0.09
18 14 0.19
19 14 0.19
ACGTcount: A:0.42, C:0.24, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:1618 original size:14 final size:14
Alignment explanation
Indices: 1599--1653 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
1589 TTTGGTTTCG
1599 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1613 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
1632 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1646 CGTTGCGA
1 CGTTGCGA
1654 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.25, G:0.24, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1631 original size:33 final size:33
Alignment explanation
Indices: 1583--1653 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
1573 AAAATCGCAA
**
1583 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1616 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1649 TGCGA
1 TGCGA
1654 CAGTCATTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.08, C:0.23, G:0.25, T:0.44
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:1661 original size:33 final size:33
Alignment explanation
Indices: 1594--1675 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
1584 GCGATTTTGG
***
1594 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
1627 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
*
1660 TTCTCTCGTTGCGATT
1 TT-TCGCGTTGCGATT
1676 TTCATTTATC
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 32 0.73
34 12 0.27
ACGTcount: A:0.10, C:0.26, G:0.22, T:0.43
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
Found at i:1680 original size:20 final size:20
Alignment explanation
Indices: 1606--1694 Score: 75
Period size: 20 Copynumber: 4.8 Consensus size: 20
1596 TCGCGTTGCG
1606 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
1626 ATT-TCGCGTTGCG------
1 ATTCTCTCGTTGCGATTTTC
***
1639 ATTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTC
1659 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
1679 ATTTATCTCGTTGCGA
1 A-TTCTCTCGTTGCGA
1695 CTCTTCTGCA
Statistics
Matches: 55, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
13 3 0.05
14 9 0.16
19 9 0.16
20 21 0.38
21 13 0.24
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.44
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:1809 original size:32 final size:33
Alignment explanation
Indices: 1773--1842 Score: 106
Period size: 32 Copynumber: 2.2 Consensus size: 33
1763 AATACTAACT
* *
1773 TGAAAATCGCAACGAGAGAATAG-CACGCGAAA
1 TGAAAATCGCAACGACAGAATAGTAACGCGAAA
*
1805 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGTAACGCGAAA
1838 TGAAA
1 TGAAA
1843 TCTAAGTGAA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 21 0.62
33 13 0.38
ACGTcount: A:0.47, C:0.19, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGTAACGCGAAA
Found at i:2071 original size:22 final size:21
Alignment explanation
Indices: 2020--2073 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
2010 TGGTTGTGAG
**
2020 GGATTTCGCCGGAGATGGGAC
1 GGATTTCTTCGGAGATGGGAC
**
2041 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGAT-GGGAC
2063 GGATTTCTTCG
1 GGATTTCTTCG
2074 CCGTAGAGAG
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
21 12 0.46
22 14 0.54
ACGTcount: A:0.20, C:0.17, G:0.39, T:0.24
Consensus pattern (21 bp):
GGATTTCTTCGGAGATGGGAC
Found at i:2244 original size:20 final size:20
Alignment explanation
Indices: 2219--2411 Score: 219
Period size: 20 Copynumber: 9.6 Consensus size: 20
2209 CTTTAAATAT
2219 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
2239 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
2261 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
2280 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
2300 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
2320 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
2340 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
2360 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
2380 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
2400 CGCGTTGCGATT
1 CGCGTTGCGATT
2412 ATGGAAAATC
Statistics
Matches: 146, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 127 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:2406 original size:60 final size:60
Alignment explanation
Indices: 2219--2411 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
2209 CTTTAAATAT
**
2219 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
2280 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
2340 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
2400 CGCGTTGCGATT
1 CGCGTTGCGATT
2412 ATGGAAAATC
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 83 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:2492 original size:20 final size:20
Alignment explanation
Indices: 2467--2518 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
2457 AAGAATCGCG
*
2467 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
2487 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
2507 TTGCGATTCTGG
1 TTGCGATTCTGG
2519 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:14419 original size:62 final size:61
Alignment explanation
Indices: 14302--14426 Score: 137
Period size: 62 Copynumber: 2.0 Consensus size: 61
14292 TAACCTAAAG
* * ** * *
14302 GAACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCGTGGGGCCTATCTAA
1 GAACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAA
* *
14363 GAACAATCTTAGGGCC-GCAGGGCCTACCCGAGA-ATGATCTCAGGGCCGCAGAGCCTACCTAA
1 GAAC-ATCTTAGGGCCTG-AGAGCCTACCCAAGATA-GATCTCAGGGCCGCAGAGCCTACCTAA
14425 GA
1 GA
14427 GTCACATTAG
Statistics
Matches: 53, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
61 6 0.11
62 47 0.89
ACGTcount: A:0.26, C:0.27, G:0.29, T:0.18
Consensus pattern (61 bp):
GAACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAA
Found at i:17277 original size:13 final size:13
Alignment explanation
Indices: 17259--17292 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
17249 GGTCAACACC
*
17259 GGTCAACGGGTTA
1 GGTCAACGGGTCA
*
17272 GGTCAACGGGTCG
1 GGTCAACGGGTCA
17285 GGTCAACG
1 GGTCAACG
17293 AGTCGGGTCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.21, C:0.21, G:0.41, T:0.18
Consensus pattern (13 bp):
GGTCAACGGGTCA
Found at i:17297 original size:13 final size:13
Alignment explanation
Indices: 17272--17301 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
17262 CAACGGGTTA
*
17272 GGTCAACGGGTCG
1 GGTCAACGAGTCG
17285 GGTCAACGAGTCG
1 GGTCAACGAGTCG
17298 GGTC
1 GGTC
17302 GGGTGAACGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.17, C:0.23, G:0.43, T:0.17
Consensus pattern (13 bp):
GGTCAACGAGTCG
Found at i:17299 original size:18 final size:18
Alignment explanation
Indices: 17278--17323 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
17268 GTTAGGTCAA
17278 CGGGTCGGGTCAACGAGT
1 CGGGTCGGGTCAACGAGT
*
17296 CGGGTCGGGTGAACGAGT
1 CGGGTCGGGTCAACGAGT
*
17314 CCGGTCGGGT
1 CGGGTCGGGT
17324 TATAACCGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.13, C:0.22, G:0.48, T:0.17
Consensus pattern (18 bp):
CGGGTCGGGTCAACGAGT
Found at i:46958 original size:33 final size:34
Alignment explanation
Indices: 46921--46990 Score: 124
Period size: 34 Copynumber: 2.1 Consensus size: 34
46911 TTTTTCTAGG
*
46921 AGGGTTAGAGTGT-ATGTGTTTCTTATGTAATTC
1 AGGGTTAGAGTGTAATGTGTATCTTATGTAATTC
46954 AGGGTTAGAGTGTAATGTGTATCTTATGTAATTC
1 AGGGTTAGAGTGTAATGTGTATCTTATGTAATTC
46988 AGG
1 AGG
46991 TTTATTAATA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
33 13 0.37
34 22 0.63
ACGTcount: A:0.24, C:0.06, G:0.29, T:0.41
Consensus pattern (34 bp):
AGGGTTAGAGTGTAATGTGTATCTTATGTAATTC
Found at i:58520 original size:18 final size:19
Alignment explanation
Indices: 58484--58524 Score: 66
Period size: 20 Copynumber: 2.2 Consensus size: 19
58474 TTCTCAAACA
58484 AAGTCCTAAGACTCTGTTCC
1 AAGTCCTAAGAC-CTGTTCC
58504 AAGTCCTAAGA-CTGTTCC
1 AAGTCCTAAGACCTGTTCC
58522 AAG
1 AAG
58525 CCATAGAGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 10 0.48
20 11 0.52
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.27
Consensus pattern (19 bp):
AAGTCCTAAGACCTGTTCC
Found at i:66913 original size:29 final size:29
Alignment explanation
Indices: 66878--66959 Score: 128
Period size: 29 Copynumber: 2.8 Consensus size: 29
66868 AAACTAAATT
* *
66878 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAAGTAAA
*
66907 GATGTCATTGCTTACATCATTTAAGTAAT
1 GATGTCATTGCTTACATCATTTAAGTAAA
66936 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
66960 GTTAGCTGAG
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
29 44 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.11, T:0.41
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAAGTAAA
Found at i:71680 original size:29 final size:29
Alignment explanation
Indices: 71645--71726 Score: 128
Period size: 29 Copynumber: 2.8 Consensus size: 29
71635 AAACTAAATT
* *
71645 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAAGTAAA
*
71674 GATGTCATTGCTTACATCATTTAAGTAAT
1 GATGTCATTGCTTACATCATTTAAGTAAA
71703 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
71727 GTTAGGTGAG
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
29 44 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.11, T:0.41
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAAGTAAA
Found at i:75680 original size:60 final size:60
Alignment explanation
Indices: 75605--75719 Score: 153
Period size: 60 Copynumber: 1.9 Consensus size: 60
75595 TATGACTCTT
* * *
75605 ATTTTAAATTGGTCCT-ATAATTTTTAAATA-TTCTAATTTCACCCCTAAACTATGATTATC
1 ATTTTAAATTAGTCCTCA-AATTTTTAAACATTTC-AATTTCACCCCTAAAATATGATTATC
* *
75665 ATTTTAGATTAGTCCTCAAATTTTTAAACATTTCAATTTCATCCCTAAAATATGA
1 ATTTTAAATTAGTCCTCAAATTTTTAAACATTTCAATTTCACCCCTAAAATATGA
75720 CTTGTTTTGA
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
60 44 0.92
61 4 0.08
ACGTcount: A:0.35, C:0.17, G:0.05, T:0.43
Consensus pattern (60 bp):
ATTTTAAATTAGTCCTCAAATTTTTAAACATTTCAATTTCACCCCTAAAATATGATTATC
Found at i:76667 original size:60 final size:60
Alignment explanation
Indices: 76602--76714 Score: 176
Period size: 60 Copynumber: 1.9 Consensus size: 60
76592 GTCAGACGAC
*
76602 CATTTTGTAACTTTTAATAGTCGA-GAGACTCAACAAAGCAACT-TCCTATAGTCATGGGAT
1 CATTTTATAACTTTTAATAGTC-ATGAGACTCAACAAAGCAA-TATCCTATAGTCATGGGAT
*
76662 CATTTTATAACTTTTAATAGTCATGGGACTCAACAAAGCAATATCCTATAGTC
1 CATTTTATAACTTTTAATAGTCATGAGACTCAACAAAGCAATATCCTATAGTC
76715 GGGAGACCAT
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
59 2 0.04
60 47 0.96
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.33
Consensus pattern (60 bp):
CATTTTATAACTTTTAATAGTCATGAGACTCAACAAAGCAATATCCTATAGTCATGGGAT
Found at i:76726 original size:60 final size:60
Alignment explanation
Indices: 76589--76726 Score: 174
Period size: 60 Copynumber: 2.3 Consensus size: 60
76579 AACATAATGA
** *
76589 ATAGTCAGACGACCATTTTGTAACTTTTAATAGTCGAGAGACTCAACAAAGCAACTTCCT
1 ATAGTCAGGGGACCATTTTATAACTTTTAATAGTCGAGAGACTCAACAAAGCAACTTCCT
* * *
76649 ATAGTCATGGGATCATTTTATAACTTTTAATAGTC-ATGGGACTCAACAAAGCAA-TATCCT
1 ATAGTCAGGGGACCATTTTATAACTTTTAATAGTCGA-GAGACTCAACAAAGCAACT-TCCT
76709 ATAGTC-GGGAGACCATTT
1 ATAGTCAGGG-GACCATTT
76727 GTGTACTTCG
Statistics
Matches: 67, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
59 4 0.06
60 63 0.94
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Consensus pattern (60 bp):
ATAGTCAGGGGACCATTTTATAACTTTTAATAGTCGAGAGACTCAACAAAGCAACTTCCT
Found at i:78733 original size:2 final size:2
Alignment explanation
Indices: 78726--78752 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
78716 CTGTACAATA
78726 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
78753 ACAGTAATCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:79000 original size:266 final size:266
Alignment explanation
Indices: 78475--79012 Score: 988
Period size: 269 Copynumber: 2.0 Consensus size: 266
78465 TTTTCAAAAC
*
78475 TATATATATATAACAGTAATCAAATCACACACGCATATATGGTAAAGGAAAGTTATAATTAAAAG
1 TATATATATATAACAGTAATCAAATCACACAAGCATATATGGTAAAGGAAAGTTATAATTAAAAG
78540 TTAATTTCTAACTGTTCTAGTTTTATTGCATAGCGACTGTCTTAAAAAGACTTTGGATCGTGCTT
66 TTAATTTCTAACTGTTCTAGTTTTATTGCATAGCGACTGTCTTAAAAAGACTTTGGATCGTGCTT
*
78605 TCCTCTTCCTTTTTTCATCTATAGGAAATCCGTAAAGTGTTGATCGTGTAGGTTGAATATGACTA
131 TCCTCTTCCTTTTTTCATCTATAGGAAATCCGTAAAGTGTTGATCGTGTAGGTAGAATATGACTA
*
78670 TAACAATTATCATGTGATATATCATCTCATACATGGTCAAATAAAGCTGTACAATAATATATATA
196 TAACAATTATCATGTGATAAATCATCTCATACATGGTCAAATAAAGCTGTACAATAATATATATA
78735 TATATA
261 TATATA
* *
78741 TATATATATATAACAGTAATCAAATCACACAAGCATATATGGTAAAGGGATGTTATAATTAAAAG
1 TATATATATATAACAGTAATCAAATCACACAAGCATATATGGTAAAGGAAAGTTATAATTAAAAG
78806 TTAATTTCTAACTGTTCTAGTTTTATTGCATAGCGACTAGTCTTAAAAAGACTCTTTGGATCGTG
66 TTAATTTCTAACTGTTCTAGTTTTATTGCATAGCGACT-GTCTTAAAAAGA--CTTTGGATCGTG
78871 CTTTCCTCTTCCTTTTTTCATCTATAGGAAATCCGTAAAGTGTTGATCGTGTAGGTAGAATATGA
128 CTTTCCTCTTCCTTTTTTCATCTATAGGAAATCCGTAAAGTGTTGATCGTGTAGGTAGAATATGA
*
78936 CTATAACAATTATCATGTGATAAATCATCTCATATAT-GTCAAATAAAGCTGTACAATAATATAT
193 CTATAACAATTATCATGTGATAAATCATCTCATACATGGTCAAATAAAGCTGTACAATAATATAT
79000 ATATATATA
258 ATATATATA
79009 TATA
1 TATA
79013 ACGTGCGGTA
Statistics
Matches: 263, Mismatches: 6, Indels: 4
0.96 0.02 0.01
Matches are distributed among these distances:
266 100 0.38
267 12 0.05
268 40 0.15
269 111 0.42
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.37
Consensus pattern (266 bp):
TATATATATATAACAGTAATCAAATCACACAAGCATATATGGTAAAGGAAAGTTATAATTAAAAG
TTAATTTCTAACTGTTCTAGTTTTATTGCATAGCGACTGTCTTAAAAAGACTTTGGATCGTGCTT
TCCTCTTCCTTTTTTCATCTATAGGAAATCCGTAAAGTGTTGATCGTGTAGGTAGAATATGACTA
TAACAATTATCATGTGATAAATCATCTCATACATGGTCAAATAAAGCTGTACAATAATATATATA
TATATA
Found at i:79127 original size:14 final size:15
Alignment explanation
Indices: 79103--79135 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
79093 TGCGTTTGGT
79103 TTACGGAATGTAAGA
1 TTACGGAATGTAAGA
79118 TTAC-GAATGTAAGA
1 TTACGGAATGTAAGA
79132 TTAC
1 TTAC
79136 CAGTGGGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 14 0.78
15 4 0.22
ACGTcount: A:0.39, C:0.09, G:0.21, T:0.30
Consensus pattern (15 bp):
TTACGGAATGTAAGA
Found at i:82944 original size:21 final size:21
Alignment explanation
Indices: 82920--82959 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
82910 TTTATTTTAT
82920 AACTTTATTTCAATTATCGTA
1 AACTTTATTTCAATTATCGTA
*
82941 AACTTTGTTTCAATTATCG
1 AACTTTATTTCAATTATCG
82960 AACTTGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.47
Consensus pattern (21 bp):
AACTTTATTTCAATTATCGTA
Found at i:83033 original size:32 final size:32
Alignment explanation
Indices: 82954--83050 Score: 151
Period size: 33 Copynumber: 3.0 Consensus size: 32
82944 TTTGTTTCAA
82954 TTATCGAACTTGAAG-TTTTAAGTATTTGAAT
1 TTATCGAACTTGAAGTTTTTAAGTATTTGAAT
82985 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
* * *
83018 TTATCAAACTTGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTTGAAGTTTTTAAGTATTTGAAT
83050 T
1 T
83051 ATGTTGAGTT
Statistics
Matches: 61, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
31 11 0.18
32 24 0.39
33 26 0.43
ACGTcount: A:0.33, C:0.07, G:0.14, T:0.45
Consensus pattern (32 bp):
TTATCGAACTTGAAGTTTTTAAGTATTTGAAT
Found at i:83079 original size:13 final size:13
Alignment explanation
Indices: 83036--83090 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
83026 CTTGAAGTAT
83036 TTAAGTATTTCAA
1 TTAAGTATTTCAA
* *
83049 TTATGTTGAGTT-AA
1 TTAAG-T-ATTTCAA
83063 TTAAGTATTTCAA
1 TTAAGTATTTCAA
*
83076 TTAAGTATTTGAA
1 TTAAGTATTTCAA
83089 TT
1 TT
83091 TATCGAACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.49
Consensus pattern (13 bp):
TTAAGTATTTCAA
Found at i:83655 original size:15 final size:17
Alignment explanation
Indices: 83629--83660 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
83619 TTCTATGGGA
83629 AAAAACCGGAT-CGGAT
1 AAAAACCGGATCCGGAT
83645 AAAAACC-GATCCGGAT
1 AAAAACCGGATCCGGAT
83661 CGGATTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.20
16 12 0.80
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (17 bp):
AAAAACCGGATCCGGAT
Found at i:86058 original size:2 final size:2
Alignment explanation
Indices: 86051--86094 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
86041 TTTCAAAGCA
86051 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
86093 AT
1 AT
86095 TTGCATGTGT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:92430 original size:2 final size:2
Alignment explanation
Indices: 92415--92447 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
92405 TAGTTTCTCT
92415 TA TA -A TA TA T- TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
92448 TCTGTGTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 27 0.93
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:98534 original size:53 final size:55
Alignment explanation
Indices: 98415--98611 Score: 328
Period size: 54 Copynumber: 3.6 Consensus size: 55
98405 TCAAATGACG
* * *
98415 GTCTGCTCCCTATTCTTTCATGGAGTATAAGACTCGAACAATCTTCAGT-AACGT
1 GTCTGCTCCCTATTCGTTCAGGGAGTATAAGACTCGAATAATCTTCAGTAAACGT
* *
98469 GTCTGCTCCCTATTC-TTCAGGGAGTATAAGACTCGAGTAATCTTCACTAAACGT
1 GTCTGCTCCCTATTCGTTCAGGGAGTATAAGACTCGAATAATCTTCAGTAAACGT
98523 GTCTGCT-CCTATTCGTTCAGGGAGTATAAGACTCGAATAATCTTCAGTAAACGT
1 GTCTGCTCCCTATTCGTTCAGGGAGTATAAGACTCGAATAATCTTCAGTAAACGT
98577 GTCTGCTCCCTATTCGTTCAGGGAGTATAAGACTC
1 GTCTGCTCCCTATTCGTTCAGGGAGTATAAGACTC
98612 CTTCAGAGAT
Statistics
Matches: 134, Mismatches: 6, Indels: 5
0.92 0.04 0.03
Matches are distributed among these distances:
53 36 0.27
54 71 0.53
55 27 0.20
ACGTcount: A:0.25, C:0.23, G:0.19, T:0.32
Consensus pattern (55 bp):
GTCTGCTCCCTATTCGTTCAGGGAGTATAAGACTCGAATAATCTTCAGTAAACGT
Found at i:98536 original size:107 final size:110
Alignment explanation
Indices: 98415--98611 Score: 346
Period size: 107 Copynumber: 1.8 Consensus size: 110
98405 TCAAATGACG
* *
98415 GTCTGCTCCCTATTCTTTCATGGAGTATAAGACTCGAACAATCTTCAGT-AACGTGTCTGCTCCC
1 GTCTGCTCCCTATTCGTTCAGGGAGTATAAGACTCGAACAATCTTCAGTAAACGTGTCTGCTCCC
98479 TATTC-TTCAGGGAGTATAAGACTCGAGTAATCTTCACTAAACGT
66 TATTCGTTCAGGGAGTATAAGACTCGAGTAATCTTCACTAAACGT
*
98523 GTCTGCT-CCTATTCGTTCAGGGAGTATAAGACTCGAATAATCTTCAGTAAACGTGTCTGCTCCC
1 GTCTGCTCCCTATTCGTTCAGGGAGTATAAGACTCGAACAATCTTCAGTAAACGTGTCTGCTCCC
98587 TATTCGTTCAGGGAGTATAAGACTC
66 TATTCGTTCAGGGAGTATAAGACTC
98612 CTTCAGAGAT
Statistics
Matches: 84, Mismatches: 3, Indels: 3
0.93 0.03 0.03
Matches are distributed among these distances:
107 38 0.45
108 27 0.32
109 19 0.23
ACGTcount: A:0.25, C:0.23, G:0.19, T:0.32
Consensus pattern (110 bp):
GTCTGCTCCCTATTCGTTCAGGGAGTATAAGACTCGAACAATCTTCAGTAAACGTGTCTGCTCCC
TATTCGTTCAGGGAGTATAAGACTCGAGTAATCTTCACTAAACGT
Found at i:98804 original size:50 final size:51
Alignment explanation
Indices: 98650--99031 Score: 676
Period size: 51 Copynumber: 7.7 Consensus size: 51
98640 CAATAAACAG
*
98650 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
1 GTCCGCTCCCTATTCTTTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
*
98701 GTCCGCTCCCTATTCTTTCAGAGAGTACAGGACTCAATCTTCAACGAACTT
1 GTCCGCTCCCTATTCTTTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
98752 GTCCGCTCCCTATTCTTTCAGAGA-TATAGGACTCAATCTTCAACGAACTT
1 GTCCGCTCCCTATTCTTTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
98802 GTCCGCTCCCTATTCTTTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
1 GTCCGCTCCCTATTCTTTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
98853 GTCCGCT-CCTATTCTTTCAGAGAGTATAGGA--C--TCTTCAACGAACTT
1 GTCCGCTCCCTATTCTTTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
98899 GTCCGCT-CCTATTCTTTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
1 GTCCGCTCCCTATTCTTTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
98949 GTCCGCTCCCTATTCTTTCAGAGAGTATAGGACTCAATC-TCAACGAACTT
1 GTCCGCTCCCTATTCTTTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
98999 GTCCGCTCCC--TTCTTTCAGAGAGTATAGGACTC
1 GTCCGCTCCCTATTCTTTCAGAGAGTATAGGACTC
99032 TTCAACGAAC
Statistics
Matches: 322, Mismatches: 3, Indels: 15
0.95 0.01 0.04
Matches are distributed among these distances:
46 45 0.14
48 25 0.08
50 115 0.36
51 137 0.43
ACGTcount: A:0.25, C:0.28, G:0.16, T:0.31
Consensus pattern (51 bp):
GTCCGCTCCCTATTCTTTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
Found at i:98810 original size:101 final size:102
Alignment explanation
Indices: 98650--99031 Score: 676
Period size: 101 Copynumber: 3.8 Consensus size: 102
98640 CAATAAACAG
*
98650 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCGCTCCCTATT
1 GTCCGCTCCCTATTCTTTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCGCTCCCTATT
*
98715 CTTTCAGAGAGTACAGGACTCAATCTTCAACGAACTT
66 CTTTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
98752 GTCCGCTCCCTATTCTTTCAGAGA-TATAGGACTCAATCTTCAACGAACTTGTCCGCTCCCTATT
1 GTCCGCTCCCTATTCTTTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCGCTCCCTATT
98816 CTTTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
66 CTTTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
98853 GTCCGCT-CCTATTCTTTCAGAGAGTATAGGA--C--TCTTCAACGAACTTGTCCGCT-CCTATT
1 GTCCGCTCCCTATTCTTTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCGCTCCCTATT
98912 CTTTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
66 CTTTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
98949 GTCCGCTCCCTATTCTTTCAGAGAGTATAGGACTCAATC-TCAACGAACTTGTCCGCTCCC--TT
1 GTCCGCTCCCTATTCTTTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCGCTCCCTATT
99011 CTTTCAGAGAGTATAGGACTC
66 CTTTCAGAGAGTATAGGACTC
99032 TTCAACGAAC
Statistics
Matches: 271, Mismatches: 2, Indels: 17
0.93 0.01 0.06
Matches are distributed among these distances:
96 50 0.18
97 45 0.17
99 25 0.09
100 34 0.13
101 94 0.35
102 23 0.08
ACGTcount: A:0.25, C:0.28, G:0.16, T:0.31
Consensus pattern (102 bp):
GTCCGCTCCCTATTCTTTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCGCTCCCTATT
CTTTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
Found at i:100376 original size:27 final size:26
Alignment explanation
Indices: 100346--100468 Score: 85
Period size: 27 Copynumber: 4.6 Consensus size: 26
100336 TTGAACCCTC
100346 CTTTTATTTCTCTTTTTTCATTTTTCT
1 CTTTT-TTTCTCTTTTTTCATTTTTCT
* *
100373 CTTTTCCTTC-CTTTTTCCATTTTTTCT
1 CTTTT-TTTCTCTTTTTTCA-TTTTTCT
*
100400 CTTCTTTTTTTCTTTTCGTT--TTTTTCCAT
1 CTT-TTTTTCTCTTTT--TTCATTTTT-C-T
*
100429 CATTTTTTCT-TTTTTCTCATTTTT-T
1 CTTTTTTTCTCTTTTT-TCATTTTTCT
*
100454 CTTCTTTTCTCTTTT
1 CTTTTTTTCTCTTTT
100469 ATTTCTTCTT
Statistics
Matches: 75, Mismatches: 10, Indels: 23
0.69 0.09 0.21
Matches are distributed among these distances:
25 10 0.13
26 13 0.17
27 29 0.39
28 19 0.25
29 3 0.04
30 1 0.01
ACGTcount: A:0.05, C:0.22, G:0.01, T:0.72
Consensus pattern (26 bp):
CTTTTTTTCTCTTTTTTCATTTTTCT
Found at i:100389 original size:18 final size:18
Alignment explanation
Indices: 100352--100416 Score: 55
Period size: 18 Copynumber: 3.6 Consensus size: 18
100342 CCTCCTTTTA
*
100352 TTTCTCTTTT--TTCATT
1 TTTCTCTTTTCCTTCCTT
100368 TTTCTCTTTTCCTTCCTT
1 TTTCTCTTTTCCTTCCTT
*
100386 TTTCCATTTTTTCTCTT-CTT
1 TTT-C-TCTTTTC-CTTCCTT
*
100406 TTTTTCTTTTC
1 TTTCTCTTTTC
100417 GTTTTTTTCC
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
16 10 0.25
18 14 0.35
19 1 0.03
20 12 0.30
21 3 0.08
ACGTcount: A:0.03, C:0.25, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTCTCTTTTCCTTCCTT
Found at i:100421 original size:14 final size:13
Alignment explanation
Indices: 100392--100438 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 13
100382 CCTTTTTCCA
100392 TTTTTTCTCTTCT
1 TTTTTTCTCTTCT
*
100405 TTTTTTCTTTTCGT
1 TTTTTTCTCTTC-T
* *
100419 TTTTTTC-CATCA
1 TTTTTTCTCTTCT
100431 TTTTTTCT
1 TTTTTTCT
100439 TTTTTCTCAT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
12 7 0.25
13 13 0.46
14 8 0.29
ACGTcount: A:0.04, C:0.19, G:0.02, T:0.74
Consensus pattern (13 bp):
TTTTTTCTCTTCT
Found at i:100441 original size:20 final size:19
Alignment explanation
Indices: 100412--100475 Score: 62
Period size: 18 Copynumber: 3.4 Consensus size: 19
100402 TCTTTTTTTC
100412 TTTTCGTTTTTTTCCATCATT
1 TTTTC-TTTTTTTCC-TCATT
100433 TTTTC-TTTTTT-CTCATT
1 TTTTCTTTTTTTCCTCATT
* *
100450 TTTTCTTCTTTT-CTCTTT
1 TTTTCTTTTTTTCCTCATT
100468 TATTTCTT
1 T-TTTCTT
100476 CTTCAAGCAA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
17 10 0.26
18 12 0.31
19 12 0.31
21 5 0.13
ACGTcount: A:0.06, C:0.19, G:0.02, T:0.73
Consensus pattern (19 bp):
TTTTCTTTTTTTCCTCATT
Found at i:100442 original size:46 final size:47
Alignment explanation
Indices: 100374--100462 Score: 119
Period size: 46 Copynumber: 1.9 Consensus size: 47
100364 CATTTTTCTC
* * *
100374 TTTTCCTTCCTTTTTCCATTTTTTCTC-TTCTTTTTTTCTTTTCGTTT
1 TTTTCCATCATTTTTCCATTTTTTCTCATT-TTTTCTTCTTTTCGTTT
*
100421 TTTTCCATCATTTTTTC-TTTTTTCTCATTTTTTCTTCTTTTC
1 TTTTCCATCATTTTTCCATTTTTTCTCATTTTTTCTTCTTTTC
100463 TCTTTTATTT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
46 21 0.57
47 16 0.43
ACGTcount: A:0.04, C:0.22, G:0.01, T:0.72
Consensus pattern (47 bp):
TTTTCCATCATTTTTCCATTTTTTCTCATTTTTTCTTCTTTTCGTTT
Found at i:100473 original size:19 final size:18
Alignment explanation
Indices: 100428--100478 Score: 77
Period size: 17 Copynumber: 2.8 Consensus size: 18
100418 TTTTTTTCCA
100428 TCATTTTTTCTT-TTTTC
1 TCATTTTTTCTTCTTTTC
100445 TCATTTTTTCTTCTTTTC
1 TCATTTTTTCTTCTTTTC
*
100463 TCTTTTATTTCTTCTT
1 TCATTT-TTTCTTCTT
100479 CAAGCAAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
17 12 0.39
18 10 0.32
19 9 0.29
ACGTcount: A:0.06, C:0.20, G:0.00, T:0.75
Consensus pattern (18 bp):
TCATTTTTTCTTCTTTTC
Found at i:101960 original size:51 final size:51
Alignment explanation
Indices: 101516--102338 Score: 848
Period size: 51 Copynumber: 15.6 Consensus size: 51
101506 TGACGGGTCT
* *** * *
101516 GCTCCCTATTCTTTCATG-GAGTATAAGACTCGAACAATCTTCAGTAAACGTGTCT
1 GCTCCCTATTCTTTCA-GAGAGTATAGGACT----CAATCTTCAACGAACTTGTCC
* * * * * *
101571 GCTCCCTATTCATTCAGGGAGTATAAGACTCGAGTAATCTTC-ACTAAACGTGTCT
1 GCTCCCTATTCTTTCAGAGAGTATAGGACTC----AATCTTCAAC-GAACTTGTCC
* * * *** * *
101626 GCTCCCTATTCGTTCAGGGAGTATAAGACTCGAATAATCTTCAGTAAACGTGTCT
1 GCTCCCTATTCTTTCAGAGAGTATAGGACTC----AATCTTCAACGAACTTGTCC
* * * ** **
101681 GCTCCCTATTCGTTCAGGGAGTATAAGACTCGAACAATCTTCATAAAAACGGGTCC
1 GCTCCCTATTCTTTCAGAGAGTATAGGACT----CAATCTTCA-ACGAACTTGTCC
* * * ** **
101737 GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAATAAAACGGGTCC
1 GCTCCCTATTCTTTCAGAGAGTATAGGACT----CAATCTTCAA-CGAACTTGTCC
* * * ** **
101793 GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAAAATCTTCAATAAAACGGGTCC
1 GCTCCCTATTCTTTCAGAGAGTATAGGACTC----AATCTTCAA-CGAACTTGTCC
* * * ** **
101849 GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAAAATCTTCAATAAACAGGTCC
1 GCTCCCTATTCTTTCAGAGAGTATAGGACTC----AATCTTCAACGAACTTGTCC
*
101904 GCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCC
1 GCTCCCTATTCTTTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCC
*
101955 GCTCCCTATTCTTTCAGAGAGTACAGGACTCAATCTTCAACGAACTTGTCC
1 GCTCCCTATTCTTTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCC
102006 GCTCCCTATTCTTTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCC
1 GCTCCCTATTCTTTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCC
*
102057 GCTCCCTATTCTTTCAGAGAGTATAGGACTCAATCTTCAATGAACTTGTCC
1 GCTCCCTATTCTTTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCC
102108 GCTCCCTATTCTTTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCC
1 GCTCCCTATTCTTTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCC
102159 GCTCCCTATTCTTTCAGAGAGTATAGGA--C--TCTTCAACGAACTTGTCC
1 GCTCCCTATTCTTTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCC
102206 GCTCCCTATTCTTTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCC
1 GCTCCCTATTCTTTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCC
102257 GCTCCCTATTCTTTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCC
1 GCTCCCTATTCTTTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCC
102308 GCTCCCTATTCTTTCAGAGAGTATAGGACTC
1 GCTCCCTATTCTTTCAGAGAGTATAGGACTC
102339 TTCAACGAAC
Statistics
Matches: 717, Mismatches: 30, Indels: 46
0.90 0.04 0.06
Matches are distributed among these distances:
47 46 0.06
49 2 0.00
51 344 0.48
52 1 0.00
54 1 0.00
55 170 0.24
56 152 0.21
59 1 0.00
ACGTcount: A:0.28, C:0.26, G:0.17, T:0.30
Consensus pattern (51 bp):
GCTCCCTATTCTTTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCC
Found at i:102279 original size:149 final size:149
Alignment explanation
Indices: 101900--102349 Score: 837
Period size: 149 Copynumber: 3.0 Consensus size: 149
101890 CAATAAACAG
*
101900 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCGCTCCCTATT
1 GTCCGCTCCCTATTCTTTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCGCTCCCTATT
*
101965 CTTTCAGAGAGTACAGGACTCAATCTTCAACGAACTTGTCCGCTCCCTATTCTTTCAGAGAGTAT
66 CTTTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCGCTCCCTATTCTTTCAGAGAGTAT
102030 AGGACTCAATCTTCAACGAACTT
131 AGGA--C--TCTTCAACGAACTT
*
102053 GTCCGCTCCCTATTCTTTCAGAGAGTATAGGACTCAATCTTCAATGAACTTGTCCGCTCCCTATT
1 GTCCGCTCCCTATTCTTTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCGCTCCCTATT
102118 CTTTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCGCTCCCTATTCTTTCAGAGAGTAT
66 CTTTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCGCTCCCTATTCTTTCAGAGAGTAT
102183 AGGACTCTTCAACGAACTT
131 AGGACTCTTCAACGAACTT
102202 GTCCGCTCCCTATTCTTTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCGCTCCCTATT
1 GTCCGCTCCCTATTCTTTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCGCTCCCTATT
102267 CTTTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCGCTCCCTATTCTTTCAGAGAGTAT
66 CTTTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCGCTCCCTATTCTTTCAGAGAGTAT
102332 AGGACTCTTCAACGAACT
131 AGGACTCTTCAACGAACT
102350 AATTTGCTTC
Statistics
Matches: 293, Mismatches: 4, Indels: 4
0.97 0.01 0.01
Matches are distributed among these distances:
149 161 0.55
151 1 0.00
153 131 0.45
ACGTcount: A:0.25, C:0.28, G:0.16, T:0.31
Consensus pattern (149 bp):
GTCCGCTCCCTATTCTTTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCGCTCCCTATT
CTTTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCGCTCCCTATTCTTTCAGAGAGTAT
AGGACTCTTCAACGAACTT
Found at i:103693 original size:27 final size:26
Alignment explanation
Indices: 103663--103785 Score: 85
Period size: 27 Copynumber: 4.6 Consensus size: 26
103653 TTGAACCCTC
103663 CTTTTATTTCTCTTTTTTCATTTTTCT
1 CTTTT-TTTCTCTTTTTTCATTTTTCT
* *
103690 CTTTTCCTTC-CTTTTTCCATTTTTTCT
1 CTTTT-TTTCTCTTTTTTCA-TTTTTCT
*
103717 CTTCTTTTTTTCTTTTCGTT--TTTTTCCAT
1 CTT-TTTTTCTCTTTT--TTCATTTTT-C-T
*
103746 CATTTTTTCT-TTTTTCTCATTTTT-T
1 CTTTTTTTCTCTTTTT-TCATTTTTCT
*
103771 CTTCTTTTCTCTTTT
1 CTTTTTTTCTCTTTT
103786 ATTTCTTCTT
Statistics
Matches: 75, Mismatches: 10, Indels: 23
0.69 0.09 0.21
Matches are distributed among these distances:
25 10 0.13
26 13 0.17
27 29 0.39
28 19 0.25
29 3 0.04
30 1 0.01
ACGTcount: A:0.05, C:0.22, G:0.01, T:0.72
Consensus pattern (26 bp):
CTTTTTTTCTCTTTTTTCATTTTTCT
Found at i:103706 original size:18 final size:18
Alignment explanation
Indices: 103669--103733 Score: 55
Period size: 18 Copynumber: 3.6 Consensus size: 18
103659 CCTCCTTTTA
*
103669 TTTCTCTTTT--TTCATT
1 TTTCTCTTTTCCTTCCTT
103685 TTTCTCTTTTCCTTCCTT
1 TTTCTCTTTTCCTTCCTT
*
103703 TTTCCATTTTTTCTCTT-CTT
1 TTT-C-TCTTTTC-CTTCCTT
*
103723 TTTTTCTTTTC
1 TTTCTCTTTTC
103734 GTTTTTTTCC
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
16 10 0.25
18 14 0.35
19 1 0.03
20 12 0.30
21 3 0.08
ACGTcount: A:0.03, C:0.25, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTCTCTTTTCCTTCCTT
Found at i:103738 original size:14 final size:13
Alignment explanation
Indices: 103709--103755 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 13
103699 CCTTTTTCCA
103709 TTTTTTCTCTTCT
1 TTTTTTCTCTTCT
*
103722 TTTTTTCTTTTCGT
1 TTTTTTCTCTTC-T
* *
103736 TTTTTTC-CATCA
1 TTTTTTCTCTTCT
103748 TTTTTTCT
1 TTTTTTCT
103756 TTTTTCTCAT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
12 7 0.25
13 13 0.46
14 8 0.29
ACGTcount: A:0.04, C:0.19, G:0.02, T:0.74
Consensus pattern (13 bp):
TTTTTTCTCTTCT
Found at i:103758 original size:20 final size:19
Alignment explanation
Indices: 103729--103792 Score: 62
Period size: 18 Copynumber: 3.4 Consensus size: 19
103719 TCTTTTTTTC
103729 TTTTCGTTTTTTTCCATCATT
1 TTTTC-TTTTTTTCC-TCATT
103750 TTTTC-TTTTTT-CTCATT
1 TTTTCTTTTTTTCCTCATT
* *
103767 TTTTCTTCTTTT-CTCTTT
1 TTTTCTTTTTTTCCTCATT
103785 TATTTCTT
1 T-TTTCTT
103793 CTTCAAGCAA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
17 10 0.26
18 12 0.31
19 12 0.31
21 5 0.13
ACGTcount: A:0.06, C:0.19, G:0.02, T:0.73
Consensus pattern (19 bp):
TTTTCTTTTTTTCCTCATT
Found at i:103759 original size:46 final size:47
Alignment explanation
Indices: 103691--103779 Score: 119
Period size: 46 Copynumber: 1.9 Consensus size: 47
103681 CATTTTTCTC
* * *
103691 TTTTCCTTCCTTTTTCCATTTTTTCTC-TTCTTTTTTTCTTTTCGTTT
1 TTTTCCATCATTTTTCCATTTTTTCTCATT-TTTTCTTCTTTTCGTTT
*
103738 TTTTCCATCATTTTTTC-TTTTTTCTCATTTTTTCTTCTTTTC
1 TTTTCCATCATTTTTCCATTTTTTCTCATTTTTTCTTCTTTTC
103780 TCTTTTATTT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
46 21 0.57
47 16 0.43
ACGTcount: A:0.04, C:0.22, G:0.01, T:0.72
Consensus pattern (47 bp):
TTTTCCATCATTTTTCCATTTTTTCTCATTTTTTCTTCTTTTCGTTT
Found at i:103790 original size:19 final size:18
Alignment explanation
Indices: 103745--103795 Score: 77
Period size: 17 Copynumber: 2.8 Consensus size: 18
103735 TTTTTTTCCA
103745 TCATTTTTTCTT-TTTTC
1 TCATTTTTTCTTCTTTTC
103762 TCATTTTTTCTTCTTTTC
1 TCATTTTTTCTTCTTTTC
*
103780 TCTTTTATTTCTTCTT
1 TCATTT-TTTCTTCTT
103796 CAAGCAAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
17 12 0.39
18 10 0.32
19 9 0.29
ACGTcount: A:0.06, C:0.20, G:0.00, T:0.75
Consensus pattern (18 bp):
TCATTTTTTCTTCTTTTC
Found at i:113507 original size:44 final size:47
Alignment explanation
Indices: 113443--113539 Score: 146
Period size: 44 Copynumber: 2.1 Consensus size: 47
113433 TGTTATCCAT
113443 AAAAAGAAATCCTAACCGCATGATATCTAATTCGCATGC-TTATTC-
1 AAAAAGAAATCCTAACCGCATGATATCTAATTCGCATGCATTATTCG
* *
113488 AAAAATAAA-CCTAACCGCATGATATCTAGTTCGCATGCATTTATTCG
1 AAAAAGAAATCCTAACCGCATGATATCTAATTCGCATGCA-TTATTCG
113535 AAAAA
1 AAAAA
113540 ACGAAAATAA
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
44 28 0.60
45 8 0.17
46 6 0.13
47 5 0.11
ACGTcount: A:0.40, C:0.21, G:0.11, T:0.28
Consensus pattern (47 bp):
AAAAAGAAATCCTAACCGCATGATATCTAATTCGCATGCATTATTCG
Found at i:117493 original size:42 final size:41
Alignment explanation
Indices: 117433--117512 Score: 108
Period size: 42 Copynumber: 1.9 Consensus size: 41
117423 CAGTAAATTG
** *
117433 CCAAACTATTGCAGCGTTTTTAAAATAAACGCCATTAAAATA
1 CCAAACTATTGCAGCGTTTCCAAAA-AAACGCCACTAAAATA
117475 CCAAACTATTGC-GACGTTTCCAAAAAAACGCCACTAAA
1 CCAAACTATTGCAG-CGTTTCCAAAAAAACGCCACTAAA
117513 GTATGACTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
41 13 0.38
42 21 0.62
ACGTcount: A:0.42, C:0.24, G:0.10, T:0.24
Consensus pattern (41 bp):
CCAAACTATTGCAGCGTTTCCAAAAAAACGCCACTAAAATA
Found at i:120065 original size:18 final size:18
Alignment explanation
Indices: 120044--120100 Score: 78
Period size: 18 Copynumber: 3.1 Consensus size: 18
120034 TTTGTCCCGT
*
120044 AGGACCACTATGTCCTAA
1 AGGACCACTATGTCCCAA
* *
120062 AGGACCACTGTGTCCCGA
1 AGGACCACTATGTCCCAA
120080 AGGACCACTATGTCCCGAA
1 AGGACCACTATGTCCC-AA
120099 AG
1 AG
120101 ATCACTCCTT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
18 30 0.91
19 3 0.09
ACGTcount: A:0.30, C:0.30, G:0.23, T:0.18
Consensus pattern (18 bp):
AGGACCACTATGTCCCAA
Found at i:120106 original size:18 final size:18
Alignment explanation
Indices: 120036--120106 Score: 72
Period size: 18 Copynumber: 3.9 Consensus size: 18
120026 GCGTAGAATT
* *
120036 TGTCCCGTAGGACCACTA
1 TGTCCCGAAAGACCACTA
* *
120054 TGT-CCTAAAGGACCACTG
1 TGTCCCGAAA-GACCACTA
*
120072 TGTCCCGAAGGACCACTA
1 TGTCCCGAAAGACCACTA
*
120090 TGTCCCGAAAGATCACT
1 TGTCCCGAAAGACCACT
120107 CCTTAAGAAC
Statistics
Matches: 42, Mismatches: 9, Indels: 4
0.76 0.16 0.07
Matches are distributed among these distances:
17 3 0.07
18 35 0.83
19 4 0.10
ACGTcount: A:0.27, C:0.31, G:0.21, T:0.21
Consensus pattern (18 bp):
TGTCCCGAAAGACCACTA
Found at i:121032 original size:20 final size:20
Alignment explanation
Indices: 120997--121034 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
120987 TTCCCATTGA
*
120997 AGTGCATCGGTACATTCTAC
1 AGTGCATCGATACATTCTAC
*
121017 AGTGCATCGATGCATTCT
1 AGTGCATCGATACATTCT
121035 TTAACATGTG
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:0.24, C:0.24, G:0.21, T:0.32
Consensus pattern (20 bp):
AGTGCATCGATACATTCTAC
Found at i:122512 original size:23 final size:22
Alignment explanation
Indices: 122482--122541 Score: 75
Period size: 23 Copynumber: 2.7 Consensus size: 22
122472 CCGGGACAAA
122482 TATGTGATACTTCGGTGCAACCC
1 TATGTGATACTTCGGTGCAA-CC
* *
122505 TATGTGATATTTCGATGCAACC
1 TATGTGATACTTCGGTGCAACC
* *
122527 TATGTGGTCCTTCGG
1 TATGTGATACTTCGG
122542 GACAATTATA
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
22 13 0.42
23 18 0.58
ACGTcount: A:0.20, C:0.22, G:0.23, T:0.35
Consensus pattern (22 bp):
TATGTGATACTTCGGTGCAACC
Found at i:122540 original size:22 final size:23
Alignment explanation
Indices: 122482--122532 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
122472 CCGGGACAAA
*
122482 TATGTGATACTTCGGTGCAACCC
1 TATGTGATACTTCGATGCAACCC
*
122505 TATGTGATATTTCGATGCAA-CC
1 TATGTGATACTTCGATGCAACCC
122527 TATGTG
1 TATGTG
122533 GTCCTTCGGG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 8 0.31
23 18 0.69
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.35
Consensus pattern (23 bp):
TATGTGATACTTCGATGCAACCC
Found at i:123343 original size:12 final size:12
Alignment explanation
Indices: 123326--123356 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
123316 CAAGTTTAGT
123326 TTATTTCCGTCA
1 TTATTTCCGTCA
123338 TTATTTCCGTCA
1 TTATTTCCGTCA
123350 TTATTTC
1 TTATTTC
123357 TTTCTTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.16, C:0.23, G:0.06, T:0.55
Consensus pattern (12 bp):
TTATTTCCGTCA
Found at i:127109 original size:116 final size:116
Alignment explanation
Indices: 126891--127101 Score: 316
Period size: 116 Copynumber: 1.8 Consensus size: 116
126881 ATTTATATAA
*
126891 TAAAATAAAATGATAGAATCTAATTATATTGTGTAAAATATTTTAATTTTATATAAATTTAACAT
1 TAAAATAAAATGATAGAATCTAATTATATTGTGTAAAATATTTTAATTTTACATAAATTTAACAT
* *
126956 CGTTGAATTAATAGAGATAAACAATTGAGAGAAAAAATGAAAGATATTCAT
66 CGTTGAATTAATAGAAATAAACAACTGAGAGAAAAAATGAAAGATATTCAT
* * *
127007 TAAAATAAAATGATAGGATCTAATTATATTAG-GTAAAATATTTTAATTTTACATAGATTTAATA
1 TAAAATAAAATGATAGAATCTAATTATATT-GTGTAAAATATTTTAATTTTACATAAATTTAACA
** * *
127071 TTTTTGAATTACTAGAAATAAATAACTGAGA
65 TCGTTGAATTAATAGAAATAAACAACTGAGA
127102 TTAAAAATAA
Statistics
Matches: 84, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
116 83 0.99
117 1 0.01
ACGTcount: A:0.48, C:0.04, G:0.11, T:0.37
Consensus pattern (116 bp):
TAAAATAAAATGATAGAATCTAATTATATTGTGTAAAATATTTTAATTTTACATAAATTTAACAT
CGTTGAATTAATAGAAATAAACAACTGAGAGAAAAAATGAAAGATATTCAT
Found at i:129425 original size:33 final size:30
Alignment explanation
Indices: 129369--129431 Score: 81
Period size: 33 Copynumber: 2.0 Consensus size: 30
129359 AAAAAAATTC
*
129369 TCTAAATATTACCCATATTATTAAATTTTA
1 TCTAAATATTACCCATATAATTAAATTTTA
*
129399 TCTAAATATTATCCATCATATAATTAACTTTTA
1 TCTAAATATTA-CC--CATATAATTAAATTTTA
129432 AATATGATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
30 11 0.39
31 2 0.07
33 15 0.54
ACGTcount: A:0.40, C:0.14, G:0.00, T:0.46
Consensus pattern (30 bp):
TCTAAATATTACCCATATAATTAAATTTTA
Found at i:132117 original size:25 final size:25
Alignment explanation
Indices: 132069--132117 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 25
132059 AATATTAGAC
132069 AACATAAATGATTATTTTTTTTATAA
1 AACATAAATGA-TATTTTTTTTATAA
132095 AACATAAATGA-ATTTTTTATTAT
1 AACATAAATGATATTTTTT-TTAT
132118 TATGTTTGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 7 0.32
25 4 0.18
26 11 0.50
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.49
Consensus pattern (25 bp):
AACATAAATGATATTTTTTTTATAA
Found at i:142257 original size:25 final size:24
Alignment explanation
Indices: 142213--142269 Score: 62
Period size: 23 Copynumber: 2.3 Consensus size: 24
142203 ACTTTAGGGA
* *
142213 TTATATAAAAAGAAATAAAT-ATT
1 TTATATAAAAAAAAAAAAATAATT
142236 TTATATAAAAATTAAAAAAAATCAATT
1 TTATATAAAAA--AAAAAAAAT-AATT
142263 TTATATA
1 TTATATA
142270 TTTTAAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 11 0.39
25 7 0.25
27 10 0.36
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (24 bp):
TTATATAAAAAAAAAAAAATAATT
Found at i:148946 original size:21 final size:19
Alignment explanation
Indices: 148916--148955 Score: 53
Period size: 21 Copynumber: 2.0 Consensus size: 19
148906 ACCACTTAAG
148916 TAAATAATTTCTAAATTATAA
1 TAAATAATTT-T-AATTATAA
*
148937 TAAATCATTTTAATTATAA
1 TAAATAATTTTAATTATAA
148956 AATAGCTTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 8 0.44
20 1 0.06
21 9 0.50
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (19 bp):
TAAATAATTTTAATTATAA
Found at i:150150 original size:112 final size:110
Alignment explanation
Indices: 149972--150194 Score: 403
Period size: 112 Copynumber: 2.0 Consensus size: 110
149962 TTCACTTTAG
149972 TGTCATCTTATTGAACATCTCATGAGCTTTTGTTCCAAACCGTGTGTTTTTCCGATGCCCGCTTG
1 TGTCATCTTATTGAACATCTCATGAGCTTTTGTTCCAAACCGTGTGTTTTTCCGATGCCCGCTTG
150037 TTG-TTGACGAAATGCCTGTGAAAACTAATTTCACTTGGAACACCC
66 TTGTTTGACGAAATGCCTGTGAAAACT-ATTTCACTTGGAACACCC
150082 TGTCATCTTATTGAACAATCTCATGAGCTTTTGTTCCAAAACCGTGTGTTTTTCCGATGCCCGCT
1 TGTCATCTTATTGAAC-ATCTCATGAGCTTTTGTTCC-AAACCGTGTGTTTTTCCGATGCCCGCT
*
150147 TGTTGTTTGACGAACTGCCTGTGAAAACTATTTCACTTGGAACACCC
64 TGTTGTTTGACGAAATGCCTGTGAAAACTATTTCACTTGGAACACCC
150194 T
1 T
150195 TTTATCAGCT
Statistics
Matches: 109, Mismatches: 1, Indels: 4
0.96 0.01 0.04
Matches are distributed among these distances:
110 16 0.15
111 20 0.18
112 51 0.47
113 22 0.20
ACGTcount: A:0.22, C:0.24, G:0.18, T:0.36
Consensus pattern (110 bp):
TGTCATCTTATTGAACATCTCATGAGCTTTTGTTCCAAACCGTGTGTTTTTCCGATGCCCGCTTG
TTGTTTGACGAAATGCCTGTGAAAACTATTTCACTTGGAACACCC
Found at i:160191 original size:410 final size:408
Alignment explanation
Indices: 159480--160466 Score: 1270
Period size: 410 Copynumber: 2.4 Consensus size: 408
159470 TCAAGCTTTC
*
159480 GATCTTGA-CTCTCCATTAGCATGTTGGAATTCACATTCTTTTCT-TGTTTCGAGATCTGCAAAT
1 GATCTTGACCT-TCCATTTGCATGTTGGAATTCACA--C--TTCTATGTTTCGAGATCTGCAAAT
* * *
159543 GT-TGTCCAATCAATGGTACCTCGGGTATCATAGTTTTAACTTCAATGGCCTGAATAACAGGCTC
61 -TCTGTCCAATCAATGGCACCTCGGGTATCATAGTTTCAACTTCAATGGCTTGAATAACAGGCTC
* * *
159607 ATCTTCTACCAACATGTCCCTTTCTTCAATC--CTCCATGACCTGAACCATTGAATGAATATGGT
125 ATCTTCCACCAACATGTCCCTTACTTCAA-CAACTCCATGACCTGAACCATTGAATGAACATGGT
* * * * * *
159670 TCCGCCATCTCCGACTTAACATTATTATTAACTATCTTAGCCTTCAATACAGACTTTTCAGTAAT
189 TCCACCATATCCGACTTAACATTATCATCAACTATATTAGCCTTCAATACAGACTATTCAGTAAT
* * * ** * * *
159735 TGGCATAGGATCAGCAGAAATAGAATCAGATTTCACTTGAAACCCTGAAATGGGGTTGATTTCTG
254 TAGCATAGGACCAGCAGAAATACAATCAGATTTCACTTGAAACCCTGAAACAGGGCTAATTTCAG
* * * *
159800 ATACCTGATTGTTCATAGCAGAAGAGCCATACATGTCCTCCTCATTCTCCAACTGAACCTTGGGA
319 ATACCTGATTGTTCAAAGCAGAAGAACCACACATGTCATCCTCATTCTCCAACTGAACCTTGGGA
* *
159865 CCCTCATTCTCAACTTGGGGCATTG
384 CCCTCATTCTCAACTCGAGGCATTG
*
159890 GATCTTGACCTTCCATTTGCATGTTGGAATTCACACGTTCTAGTAGTTTCGAGATCCGCAAATTC
1 GATCTTGACCTTCCATTTGCATGTTGGAATTCACAC-TTCTA-T-GTTTCGAGATCTGCAAATTC
*
159955 TGTCCAATCAATGGCACCTTGGGTATCATAGTTTCAACTTCAATGGCTTGAATAACAGGCTCATC
63 TGTCCAATCAATGGCACCTCGGGTATCATAGTTTCAACTTCAATGGCTTGAATAACAGGCTCATC
* * * *
160020 TTCCATCAACACGTCCCTTACTTCAACAACCCCATGACCTGAACCATTGGATGAACATGGTTCCA
128 TTCCACCAACATGTCCCTTACTTCAACAACTCCATGACCTGAACCATTGAATGAACATGGTTCCA
* * * * * *
160085 CCATATCCGACTTAACATTATCATCAACTATATTATCCTT-AGTGCTGTCTATTCAGTATTTAGC
193 CCATATCCGACTTAACATTATCATCAACTATATTAGCCTTCAATACAGACTATTCAGTAATTAGC
* *
160149 ATAGGACCAGTAGAAATACAATCAGATTTCACTTGGAACCCTGAAACAGGGCTAATTTCAGATAC
258 ATAGGACCAGCAGAAATACAATCAGATTTCACTTGAAACCCTGAAACAGGGCTAATTTCAGATAC
* * *
160214 TTGATTGTTCAAAGCAGAAGAACCACGCATGTCATCCTCATTCTCCAACTGAGCCTTGGGACCCT
323 CTGATTGTTCAAAGCAGAAGAACCACACATGTCATCCTCATTCTCCAACTGAACCTTGGGACCCT
160279 CATTCTCAACTCGAGGCATTG
388 CATTCTCAACTCGAGGCATTG
* * * *
160300 GATCTTGACAC-TCCATTTGCATGTTGGAACTCACA-TTCTCATCTTGTTTCGAGCTATGCCAAT
1 GATCTTGAC-CTTCCATTTGCATGTTGGAATTCACACTTCT-A---TGTTTCGAGATCTGCAAAT
* * * * * *
160363 GCTGTCCAATCAATGGCACCTCAGGTATCATAGTTTCAACTACAGTGGTTTGAATAACTGGCTCA
61 TCTGTCCAATCAATGGCACCTCGGGTATCATAGTTTCAACTTCAATGGCTTGAATAACAGGCTCA
* * *
160428 TCTTTCACCAACATGGCCCTTCCTTCAACAACTCCATGA
126 TCTTCCACCAACATGTCCCTTACTTCAACAACTCCATGA
160467 AATTCAACTT
Statistics
Matches: 502, Mismatches: 64, Indels: 22
0.85 0.11 0.04
Matches are distributed among these distances:
407 4 0.01
408 5 0.01
409 4 0.01
410 418 0.83
411 71 0.14
ACGTcount: A:0.27, C:0.25, G:0.16, T:0.31
Consensus pattern (408 bp):
GATCTTGACCTTCCATTTGCATGTTGGAATTCACACTTCTATGTTTCGAGATCTGCAAATTCTGT
CCAATCAATGGCACCTCGGGTATCATAGTTTCAACTTCAATGGCTTGAATAACAGGCTCATCTTC
CACCAACATGTCCCTTACTTCAACAACTCCATGACCTGAACCATTGAATGAACATGGTTCCACCA
TATCCGACTTAACATTATCATCAACTATATTAGCCTTCAATACAGACTATTCAGTAATTAGCATA
GGACCAGCAGAAATACAATCAGATTTCACTTGAAACCCTGAAACAGGGCTAATTTCAGATACCTG
ATTGTTCAAAGCAGAAGAACCACACATGTCATCCTCATTCTCCAACTGAACCTTGGGACCCTCAT
TCTCAACTCGAGGCATTG
Found at i:165063 original size:3 final size:3
Alignment explanation
Indices: 165055--165140 Score: 165
Period size: 3 Copynumber: 29.0 Consensus size: 3
165045 TGGTCAGCGA
165055 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
165103 AAT AAT AAT AAT AAT AAT -AT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
165141 GCATTAGAAG
Statistics
Matches: 82, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
2 2 0.02
3 80 0.98
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:165772 original size:2 final size:2
Alignment explanation
Indices: 165765--165799 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
165755 ATAATGGATA
165765 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
165800 AATTGTAGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:168547 original size:21 final size:21
Alignment explanation
Indices: 168521--168560 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
168511 TCAATTGTGT
168521 ATCGATGCACTGCTACAGTGC
1 ATCGATGCACTGCTACAGTGC
168542 ATCGATGCACTGCTACAGT
1 ATCGATGCACTGCTACAGT
168561 AACTTCGGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (21 bp):
ATCGATGCACTGCTACAGTGC
Found at i:169267 original size:31 final size:31
Alignment explanation
Indices: 169232--169355 Score: 124
Period size: 31 Copynumber: 4.0 Consensus size: 31
169222 TCTCGGCAAC
* *
169232 TGTCCATAGGTCCCGAAGAACCTAGGTAAAT
1 TGTCCATATGTCCCGAAGAACATAGGTAAAT
* ** * *
169263 TGTCCATATGTTCCTTAGAACATAGGTATAC
1 TGTCCATATGTCCCGAAGAACATAGGTAAAT
* *
169294 TGTCCATATGTCTCGAA-AGACATAGGTAATT
1 TGTCCATATGTCCCGAAGA-ACATAGGTAAAT
* *
169325 CTGTCCATATGTTCCGGAGAACATAGGTAAA
1 -TGTCCATATGTCCCGAAGAACATAGGTAAA
169356 CCCTCGATTC
Statistics
Matches: 72, Mismatches: 18, Indels: 5
0.76 0.19 0.05
Matches are distributed among these distances:
30 1 0.01
31 46 0.64
32 24 0.33
33 1 0.01
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.29
Consensus pattern (31 bp):
TGTCCATATGTCCCGAAGAACATAGGTAAAT
Found at i:169346 original size:63 final size:62
Alignment explanation
Indices: 169230--169353 Score: 169
Period size: 62 Copynumber: 2.0 Consensus size: 62
169220 AATCTCGGCA
* **
169230 ACTGTCCATAGGTCCCGAAGAACCTAGGTAAATTGTCCATATGTTCCTTAGAACATAGGTAT
1 ACTGTCCATAGGTCCCGAAGAACATAGGTAAATTGTCCATATGTTCCGGAGAACATAGGTAT
* * *
169292 ACTGTCCATATGTCTCGAA-AGACATAGGTAATTCTGTCCATATGTTCCGGAGAACATAGGTA
1 ACTGTCCATAGGTCCCGAAGA-ACATAGGTAAAT-TGTCCATATGTTCCGGAGAACATAGGTA
169354 AACCCTCGAT
Statistics
Matches: 54, Mismatches: 6, Indels: 3
0.86 0.10 0.05
Matches are distributed among these distances:
61 1 0.02
62 27 0.50
63 26 0.48
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29
Consensus pattern (62 bp):
ACTGTCCATAGGTCCCGAAGAACATAGGTAAATTGTCCATATGTTCCGGAGAACATAGGTAT
Found at i:170141 original size:158 final size:158
Alignment explanation
Indices: 169853--170169 Score: 616
Period size: 158 Copynumber: 2.0 Consensus size: 158
169843 CACATAAGAA
169853 TCACCTTTTATATCTTATAGACATATCATTTACATACCTTTATCACATAGCTCGTATAATTTTTC
1 TCACCTTTTATATCTTATAGACATATCATTTACATACCTTTATCACATAGCTCGTATAATTTTTC
169918 CTGCATATTCATGTCACATAATGTATATGGTATGAACTCATATCATGTTTCATAATATGAAATGA
66 CTGCATATTCATGTCACATAATGTATATGGTATGAACTCATATCATGTTTCATAATATGAAATGA
169983 ATCATATATCAAAGTATTAAATCTAGTC
131 ATCATATATCAAAGTATTAAATCTAGTC
* *
170011 TCACCTTTTATATCTTATAGACGTATCATTTCCATACCTTTATCACATAGCTCGTATAATTTTTC
1 TCACCTTTTATATCTTATAGACATATCATTTACATACCTTTATCACATAGCTCGTATAATTTTTC
170076 CTGCATATTCATGTCACATAATGTATATGGTATGAACTCATATCATGTTTCATAATATGAAATGA
66 CTGCATATTCATGTCACATAATGTATATGGTATGAACTCATATCATGTTTCATAATATGAAATGA
170141 ATCATATATCAAAGTATTAAATCTAGTC
131 ATCATATATCAAAGTATTAAATCTAGTC
170169 T
1 T
170170 TATCACAAGT
Statistics
Matches: 157, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
158 157 1.00
ACGTcount: A:0.33, C:0.17, G:0.09, T:0.40
Consensus pattern (158 bp):
TCACCTTTTATATCTTATAGACATATCATTTACATACCTTTATCACATAGCTCGTATAATTTTTC
CTGCATATTCATGTCACATAATGTATATGGTATGAACTCATATCATGTTTCATAATATGAAATGA
ATCATATATCAAAGTATTAAATCTAGTC
Found at i:172191 original size:125 final size:125
Alignment explanation
Indices: 171969--172219 Score: 484
Period size: 125 Copynumber: 2.0 Consensus size: 125
171959 TGTTCTTTAA
171969 CTCTTTTAACTATTTCGATACATTCATTCTATGAGTTATAGAATTATAAAATTGAAAACATAACA
1 CTCTTTTAACTATTTCGATACATTCATTCTATGAGTTATAGAATTATAAAATTGAAAACATAACA
*
172034 ACATACTATTCCACATCATAAAATATTCTCTAATCTTATACAGGCACTCTCTGAGGTTTT
66 ACATACTATTCCACATCATAAAATATTCTCTAATCTTATACAGACACTCTCTGAGGTTTT
172094 CTCTTTTAACTATTTCGATACATTCATTCTATGAGTTATAGAATTATAAAATTGAAAACATAACA
1 CTCTTTTAACTATTTCGATACATTCATTCTATGAGTTATAGAATTATAAAATTGAAAACATAACA
*
172159 ACATATTATTCCACATCATAAAATATTCTCTAATCTTATACAGACACTCTCTGAGGTTTT
66 ACATACTATTCCACATCATAAAATATTCTCTAATCTTATACAGACACTCTCTGAGGTTTT
172219 C
1 C
172220 GCTCTTCTCC
Statistics
Matches: 124, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
125 124 1.00
ACGTcount: A:0.36, C:0.18, G:0.08, T:0.38
Consensus pattern (125 bp):
CTCTTTTAACTATTTCGATACATTCATTCTATGAGTTATAGAATTATAAAATTGAAAACATAACA
ACATACTATTCCACATCATAAAATATTCTCTAATCTTATACAGACACTCTCTGAGGTTTT
Found at i:172856 original size:12 final size:12
Alignment explanation
Indices: 172822--172878 Score: 73
Period size: 12 Copynumber: 4.9 Consensus size: 12
172812 GTATGAATAG
172822 TACCGTGAACAA
1 TACCGTGAACAA
* *
172834 TA--ATAAACAA
1 TACCGTGAACAA
172844 TACCGTGAACAA
1 TACCGTGAACAA
172856 TACCGTGAACAA
1 TACCGTGAACAA
*
172868 TACCATGAACA
1 TACCGTGAACA
172879 TTGAAAAATT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
10 8 0.21
12 30 0.79
ACGTcount: A:0.47, C:0.23, G:0.12, T:0.18
Consensus pattern (12 bp):
TACCGTGAACAA
Found at i:173743 original size:32 final size:32
Alignment explanation
Indices: 173665--173748 Score: 102
Period size: 32 Copynumber: 2.7 Consensus size: 32
173655 TAAGGTCTAT
173665 ATGTCCCGAAAGAC--AGGTAATTCTGTCCAC
1 ATGTCCCGAAAGACATAGGTAATTCTGTCCAC
* *
173695 ATGTCCCGAAAGACATATGTAATTCTGTCCAT
1 ATGTCCCGAAAGACATAGGTAATTCTGTCCAC
* *
173727 ATGTTCCG-TAGAACATAGGTAA
1 ATGTCCCGAAAG-ACATAGGTAA
173749 ACCCTCGACT
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
30 14 0.30
31 2 0.04
32 30 0.65
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.27
Consensus pattern (32 bp):
ATGTCCCGAAAGACATAGGTAATTCTGTCCAC
Found at i:175068 original size:26 final size:27
Alignment explanation
Indices: 175025--175075 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
175015 ATTCAGTTTC
** *
175025 AAATTCAACTTATCAACTCTTTTTCGG
1 AAATTCAACTTAAAAACTCATTTTCGG
175052 AAATTC-ACTTAAAAACTCATTTTC
1 AAATTCAACTTAAAAACTCATTTTC
175076 TTTAATCTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 15 0.71
27 6 0.29
ACGTcount: A:0.35, C:0.22, G:0.04, T:0.39
Consensus pattern (27 bp):
AAATTCAACTTAAAAACTCATTTTCGG
Found at i:182800 original size:15 final size:15
Alignment explanation
Indices: 182780--182810 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
182770 GCAAGGATAG
182780 GAGGTACATTGCACT
1 GAGGTACATTGCACT
182795 GAGGTACATTGCACT
1 GAGGTACATTGCACT
182810 G
1 G
182811 TAAAGAACTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.19, G:0.29, T:0.26
Consensus pattern (15 bp):
GAGGTACATTGCACT
Found at i:201439 original size:45 final size:45
Alignment explanation
Indices: 201369--201519 Score: 221
Period size: 45 Copynumber: 3.3 Consensus size: 45
201359 TTTATTTTCG
*
201369 TTTTTCGAATAAATGCATGCAAACTAGATATCATGCGGTTAGGTTTA
1 TTTTTTGAAT-AA-GCATGCAAACTAGATATCATGCGGTTAGGTTTA
*
201416 TTTTTTGAATAAGCATGCGAACTAGATATCATGCGGTTAGGTTTA
1 TTTTTTGAATAAGCATGCAAACTAGATATCATGCGGTTAGGTTTA
* * *
201461 TTTTTTGAATAAGCATGCAAATTAGATATCATACGGTTATGATTTA
1 TTTTTTGAATAAGCATGCAAACTAGATATCATGCGGTTA-GGTTTA
201507 TTTTTGTGAATAA
1 TTTTT-TGAATAA
201520 CAAAGCATGA
Statistics
Matches: 96, Mismatches: 6, Indels: 4
0.91 0.06 0.04
Matches are distributed among these distances:
45 68 0.71
46 12 0.12
47 16 0.17
ACGTcount: A:0.32, C:0.10, G:0.19, T:0.40
Consensus pattern (45 bp):
TTTTTTGAATAAGCATGCAAACTAGATATCATGCGGTTAGGTTTA
Found at i:221738 original size:12 final size:11
Alignment explanation
Indices: 221712--221764 Score: 79
Period size: 11 Copynumber: 4.7 Consensus size: 11
221702 CGCTTGAAGA
*
221712 AGAAATAAAAG
1 AGAAAAAAAAG
221723 AGAAAAAAAAG
1 AGAAAAAAAAG
221734 AAGAAAAAAAAG
1 -AGAAAAAAAAG
*
221746 AGAAAAAAATG
1 AGAAAAAAAAG
221757 AGAAAAAA
1 AGAAAAAA
221765 GAAAAAATGA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
11 28 0.72
12 11 0.28
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.04
Consensus pattern (11 bp):
AGAAAAAAAAG
Found at i:221738 original size:23 final size:22
Alignment explanation
Indices: 221708--221902 Score: 95
Period size: 23 Copynumber: 8.6 Consensus size: 22
221698 ATTTCGCTTG
221708 AAGAAGAAATAAAAGAGAAAAAA
1 AAGAAGAAATAAAA-AGAAAAAA
*
221731 AAGAAGAAA-AAAAAGAGAAAA
1 AAGAAGAAATAAAAAGAAAAAA
* *
221752 AA-ATGAGA-AAAAAG-AAAAA
1 AAGAAGAAATAAAAAGAAAAAA
* * **
221771 ATGATGGAAA-AAACGGGAAAAAAA
1 AAGA-AGAAATAAA-AAG-AAAAAA
**
221795 AAGAAGAAGA-AAATTGAAGAAAA
1 AAGAAGAA-ATAAAAAGAA-AAAA
221818 AATGAA-AAATGAAAAATGAAAAAA
1 AA-GAAGAAAT-AAAAA-GAAAAAA
*
221842 GAGAA-AAATGAAAAATGAAAAAA
1 AAGAAGAAAT-AAAAA-GAAAAAA
221865 AGAGAA-AAATGAAAAATG-AAAAA
1 A-AGAAGAAAT-AAAAA-GAAAAAA
221888 AAGAGAGAAATAAAA
1 AAGA-AGAAATAAAA
221903 GGAGGGTTCA
Statistics
Matches: 141, Mismatches: 17, Indels: 28
0.76 0.09 0.15
Matches are distributed among these distances:
19 5 0.04
20 11 0.08
21 15 0.11
22 11 0.08
23 53 0.38
24 43 0.30
25 3 0.02
ACGTcount: A:0.74, C:0.01, G:0.18, T:0.07
Consensus pattern (22 bp):
AAGAAGAAATAAAAAGAAAAAA
Found at i:221782 original size:20 final size:19
Alignment explanation
Indices: 221738--221794 Score: 53
Period size: 20 Copynumber: 2.9 Consensus size: 19
221728 AAAAAGAAGA
221738 AAAAAAAGAGAAAAAAATG
1 AAAAAAAGAGAAAAAAATG
*
221757 AGAAAAAAGA-AAAAATGATGG
1 A-AAAAAAGAGAAAAA-AAT-G
* *
221778 AAAAAACGGGAAAAAAA
1 AAAAAAAGAGAAAAAAA
221795 AAGAAGAAGA
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
19 6 0.20
20 17 0.57
21 7 0.23
ACGTcount: A:0.74, C:0.02, G:0.19, T:0.05
Consensus pattern (19 bp):
AAAAAAAGAGAAAAAAATG
Found at i:221817 original size:24 final size:24
Alignment explanation
Indices: 221787--221902 Score: 139
Period size: 24 Copynumber: 4.9 Consensus size: 24
221777 GAAAAAACGG
* *
221787 GAAAAAAAAAGAAGAA-GAAAATT
1 GAAAAAAAAAGAAAAATGAAAAAT
*
221810 GAAGAAAAAATGAAAAATGAAAAAT
1 GAA-AAAAAAAGAAAAATGAAAAAT
*
221835 G-AAAAAAGAGAAAAATGAAAAAT
1 GAAAAAAAAAGAAAAATGAAAAAT
*
221858 GAAAAAAAGAGAAAAATGAAAAAT
1 GAAAAAAAAAGAAAAATGAAAAAT
* *
221882 GAAAAAAAGAGAGAAAT-AAAA
1 GAAAAAAAAAGAAAAATGAAAA
221903 GGAGGGTTCA
Statistics
Matches: 84, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
23 27 0.32
24 50 0.60
25 7 0.08
ACGTcount: A:0.74, C:0.00, G:0.17, T:0.09
Consensus pattern (24 bp):
GAAAAAAAAAGAAAAATGAAAAAT
Found at i:221832 original size:6 final size:7
Alignment explanation
Indices: 221815--221887 Score: 83
Period size: 7 Copynumber: 9.7 Consensus size: 7
221805 AAATTGAAGA
221815 AAAAATG
1 AAAAATG
221822 AAAAATG
1 AAAAATG
221829 AAAAATG
1 AAAAATG
*
221836 AAAAAAGAG
1 -AAAAA-TG
221845 AAAAATG
1 AAAAATG
221852 AAAAATG
1 AAAAATG
*
221859 AAAAAAAGAG
1 --AAAAA-TG
221869 AAAAATG
1 AAAAATG
221876 AAAAATG
1 AAAAATG
221883 AAAAA
1 AAAAA
221888 AAGAGAGAAA
Statistics
Matches: 57, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
7 35 0.61
8 15 0.26
9 6 0.11
10 1 0.02
ACGTcount: A:0.75, C:0.00, G:0.15, T:0.10
Consensus pattern (7 bp):
AAAAATG
Found at i:221872 original size:47 final size:49
Alignment explanation
Indices: 221787--221902 Score: 152
Period size: 47 Copynumber: 2.4 Consensus size: 49
221777 GAAAAAACGG
* * *
221787 GAAAAAAAAAGAAGAA-GAAAATTGAAGAAAAAATGAAAAATGAAAAAT
1 GAAAAAAAGAGAAAAATGAAAAATGAAGAAAAAATGAAAAATGAAAAAT
221835 G-AAAAAAGAGAAAAATGAAAAATGAA-AAAAAGA-GAAAAATGAAAAAT
1 GAAAAAAAGAGAAAAATGAAAAATGAAGAAAAA-ATGAAAAATGAAAAAT
*
221882 GAAAAAAAGAGAGAAAT-AAAA
1 GAAAAAAAGAGAAAAATGAAAA
221903 GGAGGGTTCA
Statistics
Matches: 61, Mismatches: 4, Indels: 7
0.85 0.06 0.10
Matches are distributed among these distances:
47 36 0.59
48 25 0.41
ACGTcount: A:0.74, C:0.00, G:0.17, T:0.09
Consensus pattern (49 bp):
GAAAAAAAGAGAAAAATGAAAAATGAAGAAAAAATGAAAAATGAAAAAT
Found at i:223279 original size:51 final size:51
Alignment explanation
Indices: 223218--223580 Score: 485
Period size: 51 Copynumber: 6.9 Consensus size: 51
223208 AAATTCGTTT
223218 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
223269 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
223320 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
* *
223371 GTTGAAGATTTAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTT
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
* * **
223422 GTTGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTC
1 GTTGAAGA---TT-GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAG-TTC
* * * * *
223478 -ATGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACACGTTT
1 GTTGAAGA---TT-GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
* *
223532 GTTGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGAC
1 GTTGAAGA---TT-GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGAC
223581 CCGTTTTATG
Statistics
Matches: 294, Mismatches: 12, Indels: 8
0.94 0.04 0.03
Matches are distributed among these distances:
51 159 0.54
54 4 0.01
55 129 0.44
56 2 0.01
ACGTcount: A:0.29, C:0.15, G:0.28, T:0.28
Consensus pattern (51 bp):
GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
Found at i:223687 original size:55 final size:55
Alignment explanation
Indices: 223213--223717 Score: 532
Period size: 55 Copynumber: 9.5 Consensus size: 55
223203 GAAGCAAATT
*
223213 CGTTTGTTGAAGA---TT-GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
1 CGTTTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCGGACA
* * *
223264 AGTTCGTTGAAGA---TT-GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
1 CGTTTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCGGACA
* * *
223315 AGTTCGTTGAAGA---TT-GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
1 CGTTTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCGGACA
* * *
223366 AGTTCGTTGAAGA-T-TT--AGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
1 CGTTTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCGGACA
* * *
223417 AGTTTGTTGAAGATTGTTCGAGT-TCTATACTCTCTGAAGGAATAGAGAGCGGACC
1 CGTTTGTTGAAGATTGTTCGAGTCT-TATACTCTCTGAAGGAATAGGGAGCGGACA
** *
223472 CGTTTCATGAAGATTGTTCGAGT-TCTATACTCTCTGAAGGAATAGAGAGCGGACA
1 CGTTTGTTGAAGATTGTTCGAGTCT-TATACTCTCTGAAGGAATAGGGAGCGGACA
* *
223527 CGTTTGTTGAAGATTGTTCGAGT-TCTATACTCTCTGAAGGAATAGAGAGCGGACC
1 CGTTTGTTGAAGATTGTTCGAGTCT-TATACTCTCTGAAGGAATAGGGAGCGGACA
* * ** *
223582 CGTTT-TATGAAGATTGTTCGAGT-TCTATACTCCCTGAATGAATAGGGAGCATATA
1 CGTTTGT-TGAAGATTGTTCGAGTCT-TATACTCTCTGAAGGAATAGGGAGCGGACA
* * * *
223637 CGTTTGTTGAAGATTGTTCGAGTCTTATACTCCCTGAACGAATAGGGAGCAGACT
1 CGTTTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCGGACA
* * *
223692 CGTTAT-TCGAAGATTTTTCAAGTCTT
1 CGTT-TGTTGAAGATTGTTCGAGTCTT
223718 GCTTATCCTG
Statistics
Matches: 417, Mismatches: 27, Indels: 16
0.91 0.06 0.03
Matches are distributed among these distances:
51 160 0.38
52 3 0.01
53 2 0.00
54 1 0.00
55 248 0.59
56 3 0.01
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (55 bp):
CGTTTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCGGACA
Found at i:228149 original size:18 final size:17
Alignment explanation
Indices: 228139--228303 Score: 101
Period size: 18 Copynumber: 9.5 Consensus size: 17
228129 AGAAGAAATG
*
228139 AAAA-AAAAA-GAAAGA
1 AAAAGAAAAATGAAAAA
228154 AAAAG-AAAATGAAAAA
1 AAAAGAAAAATGAAAAA
*
228170 AAGAGCAAAAAT-AAAAGA
1 AAAAG-AAAAATGAAAA-A
*
228188 AAATGAAAAATGAGAAAA
1 AAAAGAAAAATGA-AAAA
* *
228206 AAATGAAAATGGTGAAAAA
1 AAAAGAAAA--ATGAAAAA
* *
228225 AAAAGAAATA-GAAGGAA
1 AAAAGAAAAATGAA-AAA
228242 AAAAGAAAAGA-GAAAATA
1 AAAAGAAAA-ATGAAAA-A
*
228260 AAAAAAAGAAAT-AAAAA
1 AAAAGAA-AAATGAAAAA
*
228277 AAAAGAAAAAAGAAAAA
1 AAAAGAAAAATGAAAAA
*
228294 GAAATGAAAA
1 -AAAAGAAAA
228304 GGGGGTTCAA
Statistics
Matches: 119, Mismatches: 15, Indels: 29
0.73 0.09 0.18
Matches are distributed among these distances:
15 8 0.07
16 15 0.13
17 33 0.28
18 44 0.37
19 16 0.13
20 3 0.03
ACGTcount: A:0.77, C:0.01, G:0.16, T:0.07
Consensus pattern (17 bp):
AAAAGAAAAATGAAAAA
Found at i:228159 original size:28 final size:27
Alignment explanation
Indices: 228128--228303 Score: 109
Period size: 26 Copynumber: 6.6 Consensus size: 27
228118 ATTTCGCTTG
228128 AAGAAGAAATGAAAAAAAAAGAAAGAAA
1 AAGAAGAAATGAAAAAAAAAGAAA-AAA
* *
228156 AAG-A-AAATGAAAAAAAGAGCAAAAAT
1 AAGAAGAAATGAAAAAAAAAG-AAAAAA
**
228182 AA-AAGAAAATG-AAAAATGAGAAAAAA
1 AAGAAG-AAATGAAAAAAAAAGAAAAAA
* * *
228208 ATGAA-AATGGTGAAAAAAAAAGAAATAGA
1 AAGAAGAA--ATGAAAAAAAAAGAAA-AAA
* * * *
228237 AGGAA-AAAAGAAAAGAGAAA-ATAAAA
1 AAGAAGAAATGAAAA-AAAAAGAAAAAA
228263 AA-AAGAAAT-AAAAAAAAAGAAAAAA
1 AAGAAGAAATGAAAAAAAAAGAAAAAA
*
228288 GAAAAAGAAATGAAAA
1 -AAGAAGAAATGAAAA
228304 GGGGGTTCAA
Statistics
Matches: 114, Mismatches: 19, Indels: 30
0.70 0.12 0.18
Matches are distributed among these distances:
24 4 0.04
25 13 0.11
26 33 0.29
27 30 0.26
28 26 0.23
29 8 0.07
ACGTcount: A:0.76, C:0.01, G:0.16, T:0.07
Consensus pattern (27 bp):
AAGAAGAAATGAAAAAAAAAGAAAAAA
Found at i:228196 original size:27 final size:28
Alignment explanation
Indices: 228134--228207 Score: 91
Period size: 27 Copynumber: 2.8 Consensus size: 28
228124 CTTGAAGAAG
* *
228134 AAATGAAAAAAAAAG-AAAGA-AAAAGA
1 AAATGAAAAAAAGAGAAAAAATAAAAGA
*
228160 AAATGAAAAAAAGAGCAAAAATAAAAGA
1 AAATGAAAAAAAGAGAAAAAATAAAAGA
*
228188 AAATG-AAAAATGAGAAAAAA
1 AAATGAAAAAAAGAGAAAAAA
228208 ATGAAAATGG
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
26 14 0.33
27 17 0.40
28 11 0.26
ACGTcount: A:0.77, C:0.01, G:0.15, T:0.07
Consensus pattern (28 bp):
AAATGAAAAAAAGAGAAAAAATAAAAGA
Found at i:228264 original size:14 final size:13
Alignment explanation
Indices: 228255--228303 Score: 64
Period size: 13 Copynumber: 3.6 Consensus size: 13
228245 AGAAAAGAGA
228255 AAATAAAAAAAAG
1 AAATAAAAAAAAG
228268 AAATAAAAAAAAAG
1 AAAT-AAAAAAAAG
228282 AAA-AAAGAAAAAG
1 AAATAAA-AAAAAG
228295 AAATGAAAA
1 AAAT-AAAA
228304 GGGGGTTCAA
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
12 3 0.09
13 13 0.41
14 13 0.41
15 3 0.09
ACGTcount: A:0.84, C:0.00, G:0.10, T:0.06
Consensus pattern (13 bp):
AAATAAAAAAAAG
Found at i:228267 original size:81 final size:79
Alignment explanation
Indices: 228137--228287 Score: 178
Period size: 81 Copynumber: 1.9 Consensus size: 79
228127 GAAGAAGAAA
* * * **
228137 TGAAAAAAAAAGAAAGAAAAAGAAAATGAAAAAAAGAGCAAAAATAAAAGAAAATGAAAAATGAG
1 TGAAAAAAAAAGAAAGAAAAAGAAAA-GAAAAAAAGAGAAAAAAAAAAAG-AAATAAAAAAAAAG
228202 AAAAAAATGAAAATGG
64 AAAAAAATGAAAATGG
* * * *
228218 TGAAAAAAAAAGAAATAGAAGGAAAA-AAGAAAAGAGAAAATAAAAAAAAGAAATAAAAAAAAAG
1 TGAAAAAAAAAGAAAGAAAAAGAAAAGAAAAAAAGAG-AAA-AAAAAAAAGAAATAAAAAAAAAG
228282 AAAAAA
64 AAAAAA
228288 GAAAAAGAAA
Statistics
Matches: 59, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
79 9 0.15
80 19 0.32
81 31 0.53
ACGTcount: A:0.76, C:0.01, G:0.16, T:0.07
Consensus pattern (79 bp):
TGAAAAAAAAAGAAAGAAAAAGAAAAGAAAAAAAGAGAAAAAAAAAAAGAAATAAAAAAAAAGAA
AAAAATGAAAATGG
Found at i:229623 original size:37 final size:36
Alignment explanation
Indices: 229569--229640 Score: 126
Period size: 37 Copynumber: 2.0 Consensus size: 36
229559 AAACAGGTCA
229569 ATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAACC
1 ATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAACC
*
229605 ATCTGTAAGCCTTCACGGAAGATTAGTGAAGCAAAC
1 ATCT-TAAGCCTTCACGGAAGAGTAGTGAAGCAAAC
229641 TCATTTTATG
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
36 4 0.12
37 30 0.88
ACGTcount: A:0.36, C:0.21, G:0.22, T:0.21
Consensus pattern (36 bp):
ATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAACC
Found at i:229702 original size:51 final size:52
Alignment explanation
Indices: 229642--229957 Score: 286
Period size: 51 Copynumber: 5.9 Consensus size: 52
229632 GAAGCAAACT
*
229642 CATTTTATGAAGA-TCGAGTCCTATACTCTCTGAAGCAATAGGGAGCAGACA
1 CATTTTATGAAGATTCGAGTCCTATACTCTCTGAAGGAATAGGGAGCAGACA
* *
229693 CATTTTATGAAGA-TCGAGTCTTATACTCTCTGAAGGAATAGGGAGCTGACA
1 CATTTTATGAAGATTCGAGTCCTATACTCTCTGAAGGAATAGGGAGCAGACA
* * * *
229744 CGTTTGT-TAAAGATT-GAGTCCTATACTCTCTGAAAGAATAGGGAGCGGAC-
1 CATTT-TATGAAGATTCGAGTCCTATACTCTCTGAAGGAATAGGGAGCAGACA
* * * * *
229794 C-TGTTTATTGAAGATTTTCTTAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACC
1 CAT-TTTA-TGAAGA--TTC-GAGTCCTATACTCTCTGAAGGAATAGGGAGCAGACA
* * * * * *
229850 CGTTTTATTGAAGATTGTTCAAGTCTTATACTCTTTGAATGAATAGAGAGCAGACA
1 CATTTTA-TGAAGA---TTCGAGTCCTATACTCTCTGAAGGAATAGGGAGCAGACA
*
229906 CATTTTATGAAGATTGTTCGAGTCTTATACT-TCCTGAAGGAATAGGGAGCAG
1 CATTTTATGAAGA---TTCGAGTCCTATACTCT-CTGAAGGAATAGGGAGCAG
229958 GCTCGTCATT
Statistics
Matches: 226, Mismatches: 26, Indels: 22
0.82 0.09 0.08
Matches are distributed among these distances:
49 2 0.01
50 3 0.01
51 94 0.42
52 2 0.01
53 2 0.01
54 1 0.00
55 70 0.31
56 47 0.21
57 5 0.02
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.31
Consensus pattern (52 bp):
CATTTTATGAAGATTCGAGTCCTATACTCTCTGAAGGAATAGGGAGCAGACA
Found at i:229935 original size:111 final size:104
Alignment explanation
Indices: 229651--229955 Score: 336
Period size: 111 Copynumber: 2.9 Consensus size: 104
229641 TCATTTTATG
*
229651 AAGATCGAGTCCTATACTCTCTGAAGCAATAGGGAGCAGACACATTTTATGAAGA---TCGAGTC
1 AAGATTGAGTCCTATACTCTCTGAAG-AATAGGGAGCAGACACATTTTATGAAGATTTTCGAGTC
* *
229713 TTATACTCTCTGAAGGAATAGGGAGCTGACACGTTTGTTA
65 TTATACTCTCTGAAGGAATAGGGAGCGGACACGTTTATTA
* *
229753 AAGATTGAGTCCTATACTCTCTGAAAGAATAGGGAGCGGAC-C-TGTTTATTGAAGATTTTCTTA
1 AAGATTGAGTCCTATACTCTCTG-AAGAATAGGGAGCAGACACAT-TTTA-TGAAGATTTTC-GA
* * *
229816 GT-TCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATTG
62 GTCT-TATACTCTCTGAAGGAATAGGGAGCGGACACG-TTTATTA
* * *
229860 AAGATTGTTCAAGTCTTATACTCTTTGAATGAATAGAGAGCAGACACATTTTATGAAGATTGTTC
1 AAGATTG----AGTCCTATACTCTCTGAA-GAATAGGGAGCAGACACATTTTATGAAGATT-TTC
229925 GAGTCTTATACT-TCCTGAAGGAATAGGGAGC
60 GAGTCTTATACTCT-CTGAAGGAATAGGGAGC
229956 AGGCTCGTCA
Statistics
Matches: 170, Mismatches: 14, Indels: 29
0.80 0.07 0.14
Matches are distributed among these distances:
100 1 0.01
101 5 0.03
102 41 0.24
103 3 0.02
105 3 0.02
106 32 0.19
107 12 0.07
110 3 0.02
111 60 0.35
112 9 0.05
113 1 0.01
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.31
Consensus pattern (104 bp):
AAGATTGAGTCCTATACTCTCTGAAGAATAGGGAGCAGACACATTTTATGAAGATTTTCGAGTCT
TATACTCTCTGAAGGAATAGGGAGCGGACACGTTTATTA
Found at i:230542 original size:31 final size:31
Alignment explanation
Indices: 230500--230560 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
230490 GTATTCTAAG
* *
230500 CACAAGTAGTGAATTTCGACAGCAATACTAT
1 CACAAGCAGTGAATTTCGAAAGCAATACTAT
* *
230531 CACAAGCAGTGAGTTTCGAAAGCTATACTA
1 CACAAGCAGTGAATTTCGAAAGCAATACTA
230561 GCAAATCATA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.25
Consensus pattern (31 bp):
CACAAGCAGTGAATTTCGAAAGCAATACTAT
Found at i:232640 original size:18 final size:17
Alignment explanation
Indices: 232614--232647 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
232604 CAAATACATG
*
232614 AAATGTGATGAACAAGTT
1 AAATCTGATGAA-AAGTT
232632 AAATCTGATGAAAAGT
1 AAATCTGATGAAAAGT
232648 AGATAAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.47, C:0.06, G:0.21, T:0.26
Consensus pattern (17 bp):
AAATCTGATGAAAAGTT
Found at i:234067 original size:70 final size:70
Alignment explanation
Indices: 233954--234089 Score: 254
Period size: 70 Copynumber: 1.9 Consensus size: 70
233944 ACTTTTGTTT
*
233954 CATTTTGGTACTTAAATTTTATGTCGTTTTAAAATCATGCATAATATTTAGTTTATGTTTTATTT
1 CATTTTGGTACTTAAATTTTATGTCGTTTCAAAATCATGCATAATATTTAGTTTATGTTTTATTT
234019 TTGGG
66 TTGGG
*
234024 CATTTTGGTACTTAAATTTTATGTCGTTTCAAAATCATGCATAATGTTTAGTTTATGTTTTATTT
1 CATTTTGGTACTTAAATTTTATGTCGTTTCAAAATCATGCATAATATTTAGTTTATGTTTTATTT
234089 T
66 T
234090 GGTAGCCCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
70 64 1.00
ACGTcount: A:0.26, C:0.08, G:0.13, T:0.53
Consensus pattern (70 bp):
CATTTTGGTACTTAAATTTTATGTCGTTTCAAAATCATGCATAATATTTAGTTTATGTTTTATTT
TTGGG
Found at i:237350 original size:3 final size:3
Alignment explanation
Indices: 237342--237374 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
237332 TGTTACAGAT
237342 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
237375 TTATGGTGAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:240451 original size:25 final size:24
Alignment explanation
Indices: 240423--240491 Score: 84
Period size: 24 Copynumber: 2.8 Consensus size: 24
240413 AACTCAAAAA
* * *
240423 AAAATTAGAAGTTCGATTGAAGCCT
1 AAAATTAG-AGCTCAATTGAAACCT
*
240448 AAAATTTGAGCTCAATTGAAACCT
1 AAAATTAGAGCTCAATTGAAACCT
*
240472 AAAATTTGAGCTCAATTGAA
1 AAAATTAGAGCTCAATTGAA
240492 GCGAAAGAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
24 33 0.82
25 7 0.17
ACGTcount: A:0.42, C:0.13, G:0.16, T:0.29
Consensus pattern (24 bp):
AAAATTAGAGCTCAATTGAAACCT
Found at i:240467 original size:24 final size:24
Alignment explanation
Indices: 240438--240493 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
240428 TAGAAGTTCG
240438 ATTGAAGCCTAAAATTTGAGCTCA
1 ATTGAAGCCTAAAATTTGAGCTCA
*
240462 ATTGAAACCTAAAATTTGAGCTCA
1 ATTGAAGCCTAAAATTTGAGCTCA
240486 ATTGAAGC
1 ATTGAAGC
240494 GAAAGAATAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.29
Consensus pattern (24 bp):
ATTGAAGCCTAAAATTTGAGCTCA
Found at i:246454 original size:63 final size:64
Alignment explanation
Indices: 246369--246540 Score: 215
Period size: 62 Copynumber: 2.7 Consensus size: 64
246359 TCCGATGGCG
* * * * *
246369 GCAACGACTGATTCCACATTAGGTGGTGAAGATCAGAGTCCTCAGACACC-TACGGTTCCGGGA
1 GCAACGACTGATTCAACATTAGGTGGTGAAGATCAGAGTCATCAGACACCAGACGATGCCGGGA
* * *
246432 GCGACGACTGATTCAACGTTAGGTGGTGAAGATCAGAGTCATC--ACACCAGATGATGCCGGGA
1 GCAACGACTGATTCAACATTAGGTGGTGAAGATCAGAGTCATCAGACACCAGACGATGCCGGGA
* * * *
246494 GCAACAAGTGATTCGATATTAGGTGGTGAAGATCAGAGTCATCAGAC
1 GCAACGACTGATTCAACATTAGGTGGTGAAGATCAGAGTCATCAGAC
246541 GCCGAAGATG
Statistics
Matches: 92, Mismatches: 14, Indels: 5
0.83 0.13 0.05
Matches are distributed among these distances:
61 5 0.05
62 46 0.50
63 39 0.42
64 2 0.02
ACGTcount: A:0.30, C:0.21, G:0.28, T:0.21
Consensus pattern (64 bp):
GCAACGACTGATTCAACATTAGGTGGTGAAGATCAGAGTCATCAGACACCAGACGATGCCGGGA
Found at i:252224 original size:20 final size:20
Alignment explanation
Indices: 252199--252241 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
252189 CGACATGACC
252199 TCATTTCTTGTTTTATACAA
1 TCATTTCTTGTTTTATACAA
252219 TCATTTCTTGTTTTATACAA
1 TCATTTCTTGTTTTATACAA
252239 TCA
1 TCA
252242 ACAAATATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.26, C:0.16, G:0.05, T:0.53
Consensus pattern (20 bp):
TCATTTCTTGTTTTATACAA
Found at i:260987 original size:22 final size:22
Alignment explanation
Indices: 260962--261020 Score: 82
Period size: 22 Copynumber: 2.6 Consensus size: 22
260952 AACCTCACTT
260962 AACAAACTAACTAATTAACAAC
1 AACAAACTAACTAATTAACAAC
* *
260984 AACAACCTAACTAATTATCAAC
1 AACAAACTAACTAATTAACAAC
*
261006 AACTTAACTAACTAA
1 AAC-AAACTAACTAA
261021 ATATCTGACA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
22 23 0.72
23 9 0.28
ACGTcount: A:0.54, C:0.24, G:0.00, T:0.22
Consensus pattern (22 bp):
AACAAACTAACTAATTAACAAC
Found at i:261036 original size:23 final size:22
Alignment explanation
Indices: 260966--261036 Score: 72
Period size: 22 Copynumber: 3.1 Consensus size: 22
260956 TCACTTAACA
* *
260966 AACTAACTAATTAACAACAAC-
1 AACTAACTAAATATCAACAACT
*
260987 AACCTAACTAATTATCAACAACTT
1 AA-CTAACTAAATATCAACAAC-T
*
261011 AACTAACTAAATATCTGACAACT
1 AACTAACTAAATATC-AACAACT
261034 AAC
1 AAC
261037 ACCCCCCTCA
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
21 2 0.05
22 18 0.42
23 16 0.37
24 7 0.16
ACGTcount: A:0.51, C:0.24, G:0.01, T:0.24
Consensus pattern (22 bp):
AACTAACTAAATATCAACAACT
Found at i:268303 original size:9 final size:10
Alignment explanation
Indices: 268283--268347 Score: 62
Period size: 10 Copynumber: 6.5 Consensus size: 10
268273 TTGAATTTAA
268283 AAAAAATCAT
1 AAAAAATCAT
268293 AAAAAAT-AT
1 AAAAAATCAT
*
268302 AAAAAATCAG
1 AAAAAATCAT
*
268312 AAAAAATACAAA
1 AAAAAAT-C-AT
*
268324 AAAAAAT-AC
1 AAAAAATCAT
*
268333 AAAAAATCAG
1 AAAAAATCAT
268343 AAAAA
1 AAAAA
268348 TTACAAAACA
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
9 17 0.36
10 21 0.45
11 1 0.02
12 8 0.17
ACGTcount: A:0.77, C:0.08, G:0.03, T:0.12
Consensus pattern (10 bp):
AAAAAATCAT
Found at i:268328 original size:31 final size:31
Alignment explanation
Indices: 268293--268355 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
268283 AAAAAATCAT
*
268293 AAAAAATATAAAAAATCAGAAAAAATACAAA
1 AAAAAATACAAAAAATCAGAAAAAATACAAA
*
268324 AAAAAATACAAAAAATCAGAAAAATTACAAA
1 AAAAAATACAAAAAATCAGAAAAAATACAAA
268355 A
1 A
268356 CAATTAATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.76, C:0.08, G:0.03, T:0.13
Consensus pattern (31 bp):
AAAAAATACAAAAAATCAGAAAAAATACAAA
Found at i:268355 original size:19 final size:19
Alignment explanation
Indices: 268283--268326 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
268273 TTGAATTTAA
* *
268283 AAAAAATCATAAAAAATAT
1 AAAAAATCAGAAAAAATAC
268302 AAAAAATCAGAAAAAATAC
1 AAAAAATCAGAAAAAATAC
268321 AAAAAA
1 AAAAAA
268327 AAATACAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.77, C:0.07, G:0.02, T:0.14
Consensus pattern (19 bp):
AAAAAATCAGAAAAAATAC
Found at i:268608 original size:15 final size:15
Alignment explanation
Indices: 268588--268617 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
268578 GGAGATGCCC
268588 TAAGTGGTTGTTGAA
1 TAAGTGGTTGTTGAA
268603 TAAGTGGTTGTTGAA
1 TAAGTGGTTGTTGAA
268618 AAATTTAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.33, T:0.40
Consensus pattern (15 bp):
TAAGTGGTTGTTGAA
Found at i:269680 original size:9 final size:8
Alignment explanation
Indices: 269665--269772 Score: 56
Period size: 9 Copynumber: 12.2 Consensus size: 8
269655 TAGAAATTAC
269665 AATAAAAA
1 AATAAAAA
269673 ACATAAAAGA
1 A-ATAAAA-A
*
269683 TATAATAAA
1 AATAA-AAA
269692 AATAAAATA
1 AATAAAA-A
*
269701 ATGTAACAAA
1 A-ATAA-AAA
*
269711 GAAAAAAAA
1 -AATAAAAA
* *
269720 AAGAAAAT
1 AATAAAAA
269728 AATAAAAGA
1 AATAAAA-A
269737 AAGTAAAAA
1 AA-TAAAAA
*
269746 AAT-CAAA
1 AATAAAAA
269753 AATAAAAA
1 AATAAAAA
269761 ATATAACAAA
1 A-ATAA-AAA
269771 AA
1 AA
269773 ATATATATAT
Statistics
Matches: 77, Mismatches: 11, Indels: 23
0.69 0.10 0.21
Matches are distributed among these distances:
7 6 0.08
8 20 0.26
9 30 0.39
10 18 0.23
11 3 0.04
ACGTcount: A:0.76, C:0.04, G:0.06, T:0.15
Consensus pattern (8 bp):
AATAAAAA
Found at i:269739 original size:28 final size:28
Alignment explanation
Indices: 269689--269747 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
269679 AAGATATAAT
* **
269689 AAAAATAAAATAATGTAACAAAGAAAAA
1 AAAAAGAAAATAATAAAACAAAGAAAAA
* *
269717 AAAAAGAAAATAATAAAAGAAAGTAAAA
1 AAAAAGAAAATAATAAAACAAAGAAAAA
269745 AAA
1 AAA
269748 TCAAAAATAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.78, C:0.02, G:0.08, T:0.12
Consensus pattern (28 bp):
AAAAAGAAAATAATAAAACAAAGAAAAA
Found at i:270260 original size:28 final size:27
Alignment explanation
Indices: 270207--270259 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
270197 ATAAATTAAG
* *
270207 TATTTTTTATTTCTAAAATTTATTTTA
1 TATTTTTAATTTCTAAAATATATTTTA
270234 TATTTTTAAATTTCTAAAATA-ATTTT
1 TATTTTT-AATTTCTAAAATATATTTT
270260 TTAAATTCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 12 0.52
28 11 0.48
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (27 bp):
TATTTTTAATTTCTAAAATATATTTTA
Found at i:283465 original size:46 final size:46
Alignment explanation
Indices: 283412--283536 Score: 198
Period size: 46 Copynumber: 2.7 Consensus size: 46
283402 AGAGTACTAG
*
283412 CTAAAATGTTACTTTTTCTACTGGAAATATTAATATC-GGACGCTAC
1 CTAAAATGTTACTTTTTCTACTGAAAATATTAATATCTGG-CGCTAC
283458 CTAAAATGTTACTTTTTCTACTGAAAATATTAATATCTGGCGCTAC
1 CTAAAATGTTACTTTTTCTACTGAAAATATTAATATCTGGCGCTAC
* * *
283504 TTAAAATGTTATTTTTTCTACCGAAAATATTAA
1 CTAAAATGTTACTTTTTCTACTGAAAATATTAA
283537 CATCAGAAAT
Statistics
Matches: 74, Mismatches: 4, Indels: 2
0.93 0.05 0.03
Matches are distributed among these distances:
46 72 0.97
47 2 0.03
ACGTcount: A:0.34, C:0.15, G:0.10, T:0.40
Consensus pattern (46 bp):
CTAAAATGTTACTTTTTCTACTGAAAATATTAATATCTGGCGCTAC
Found at i:294438 original size:2 final size:2
Alignment explanation
Indices: 294431--294460 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
294421 ATTATTCCAA
294431 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
294461 TGGATAAATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:304496 original size:19 final size:19
Alignment explanation
Indices: 304472--304508 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
304462 ATGACCAACA
304472 AAATCGCAATGCGATCTCT
1 AAATCGCAATGCGATCTCT
304491 AAATCGCAATGCGATCTC
1 AAATCGCAATGCGATCTC
304509 CAGTATCGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.24
Consensus pattern (19 bp):
AAATCGCAATGCGATCTCT
Found at i:304559 original size:20 final size:20
Alignment explanation
Indices: 304534--304606 Score: 76
Period size: 20 Copynumber: 3.6 Consensus size: 20
304524 GTTTACAGAT
*
304534 TCGCAACGCGATTTTGACTA
1 TCGCAACGCGATTATGACTA
* *
304554 TCGCAACGCGATAAT-ACAAAA
1 TCGCAACGCGATTATGAC--TA
* *
304575 TCGCAACGTGATTCTGACTA
1 TCGCAACGCGATTATGACTA
304595 TCGCAACGCGAT
1 TCGCAACGCGAT
304607 AATACAAAAT
Statistics
Matches: 42, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
19 2 0.05
20 25 0.60
21 13 0.31
22 2 0.05
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.23
Consensus pattern (20 bp):
TCGCAACGCGATTATGACTA
Found at i:304579 original size:21 final size:21
Alignment explanation
Indices: 304553--304627 Score: 82
Period size: 21 Copynumber: 3.6 Consensus size: 21
304543 GATTTTGACT
304553 ATCGCAACGCGATAATACAAA
1 ATCGCAACGCGATAATACAAA
* ** *
304574 ATCGCAACGTGATTCTGAC--T
1 ATCGCAACGCGATAAT-ACAAA
304594 ATCGCAACGCGATAATACAAA
1 ATCGCAACGCGATAATACAAA
*
304615 ATCGCAATGCGAT
1 ATCGCAACGCGAT
304628 TTTCAAAGCG
Statistics
Matches: 42, Mismatches: 9, Indels: 6
0.74 0.16 0.11
Matches are distributed among these distances:
19 2 0.05
20 13 0.31
21 25 0.60
22 2 0.05
ACGTcount: A:0.39, C:0.24, G:0.17, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGATAATACAAA
Found at i:304593 original size:41 final size:41
Alignment explanation
Indices: 304534--304628 Score: 163
Period size: 41 Copynumber: 2.3 Consensus size: 41
304524 GTTTACAGAT
*
304534 TCGCAACGCGATTTTGACTATCGCAACGCGATAATACAAAA
1 TCGCAACGCGATTCTGACTATCGCAACGCGATAATACAAAA
*
304575 TCGCAACGTGATTCTGACTATCGCAACGCGATAATACAAAA
1 TCGCAACGCGATTCTGACTATCGCAACGCGATAATACAAAA
*
304616 TCGCAATGCGATT
1 TCGCAACGCGATT
304629 TTCAAAGCGC
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 50 1.00
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (41 bp):
TCGCAACGCGATTCTGACTATCGCAACGCGATAATACAAAA
Found at i:305302 original size:20 final size:20
Alignment explanation
Indices: 305260--305302 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
305250 GATAGTCAAA
* *
305260 TTCGTGTTGCGATTTTCATT
1 TTCGTGTTGCGATTTTAAGT
305280 TTCGTGTTGCGATTTTAAGT
1 TTCGTGTTGCGATTTTAAGT
305300 TTC
1 TTC
305303 AGAAGCTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.12, C:0.14, G:0.21, T:0.53
Consensus pattern (20 bp):
TTCGTGTTGCGATTTTAAGT
Found at i:309049 original size:12 final size:12
Alignment explanation
Indices: 309028--309053 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
309018 TTGAGGAATA
309028 GGAGGAGGATTT
1 GGAGGAGGATTT
309040 GGAGGAGGATTT
1 GGAGGAGGATTT
309052 GG
1 GG
309054 TTGACGACTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.54, T:0.23
Consensus pattern (12 bp):
GGAGGAGGATTT
Found at i:318101 original size:18 final size:18
Alignment explanation
Indices: 318078--318113 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
318068 AGGAATGATA
318078 TGTGGTCCTTCGGGACAT
1 TGTGGTCCTTCGGGACAT
318096 TGTGGTCCTTCGGGACAT
1 TGTGGTCCTTCGGGACAT
318114 ATATGTATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.11, C:0.22, G:0.33, T:0.33
Consensus pattern (18 bp):
TGTGGTCCTTCGGGACAT
Found at i:318129 original size:121 final size:121
Alignment explanation
Indices: 317977--318216 Score: 462
Period size: 121 Copynumber: 2.0 Consensus size: 121
317967 AGGGTCTATA
*
317977 TGGTCCTTCGGGACATATATGTATTCTTTGGAATATGTGTGAAGTCTGGTGAGACACATACTTGA
1 TGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGA
318042 TCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACATTG
66 TCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACATTG
318098 TGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGA
1 TGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGA
*
318163 TCCCTATCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
66 TCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
318217 ATATGTATTC
Statistics
Matches: 117, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
121 117 1.00
ACGTcount: A:0.25, C:0.15, G:0.24, T:0.35
Consensus pattern (121 bp):
TGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGA
TCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACATTG
Found at i:318319 original size:103 final size:103
Alignment explanation
Indices: 318096--318311 Score: 423
Period size: 103 Copynumber: 2.1 Consensus size: 103
318086 TTCGGGACAT
318096 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
1 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
*
318161 GATCCCTATCATATGTATATGATTCTTAAGGAATGATA
66 GATCCCTAGCATATGTATATGATTCTTAAGGAATGATA
318199 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
1 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
318264 GATCCCTAGCATATGTATATGATTCTTAAGGAATGATA
66 GATCCCTAGCATATGTATATGATTCTTAAGGAATGATA
318302 TGTGGTCCTT
1 TGTGGTCCTT
318312 ATGGACATTA
Statistics
Matches: 112, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
103 112 1.00
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.36
Consensus pattern (103 bp):
TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
GATCCCTAGCATATGTATATGATTCTTAAGGAATGATA
Done.