Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007292.1 Hibiscus syriacus cultivar Beakdansim tig00019385_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: 122788
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:791 original size:13 final size:13
Alignment explanation
Indices: 773--797 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
763 GCACATCAAC
773 GGGTACTTCTGGG
1 GGGTACTTCTGGG
786 GGGTACTTCTGG
1 GGGTACTTCTGG
798 AGGTATATAT
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:0.08, C:0.16, G:0.44, T:0.32
Consensus pattern (13 bp):
GGGTACTTCTGGG
Found at i:10873 original size:54 final size:55
Alignment explanation
Indices: 10644--10874 Score: 311
Period size: 55 Copynumber: 4.2 Consensus size: 55
10634 TACTATCGAC
* * *
10644 ACTAAGTGTGCAAAACCACGGAATTCATAATATGTTTATGAAAGACCGTATTGGT
1 ACTAAGTGTGCAAAACCACAGAATTCATAATATGTTTATGAACGACCGTATCGGT
* * * * * *
10699 ACTAAGTGTACAAAACCAAAAAATTCATAATATGTTTATAAACGACCGTATCAGC
1 ACTAAGTGTGCAAAACCACAGAATTCATAATATGTTTATGAACGACCGTATCGGT
* * *
10754 ACTAAGTGTGCAAAACCACACAATTCATAATATATTTATGAACGACTGTATCGGT
1 ACTAAGTGTGCAAAACCACAGAATTCATAATATGTTTATGAACGACCGTATCGGT
* * *
10809 ACTAAATGTGC-AACCCACAGAATTCATAATATGTTTCTGAACGACCGTATCGGT
1 ACTAAGTGTGCAAAACCACAGAATTCATAATATGTTTATGAACGACCGTATCGGT
*
10863 ACTATGTGTGCA
1 ACTAAGTGTGCA
10875 TCCAAAGAAA
Statistics
Matches: 150, Mismatches: 25, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
54 47 0.31
55 103 0.69
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.28
Consensus pattern (55 bp):
ACTAAGTGTGCAAAACCACAGAATTCATAATATGTTTATGAACGACCGTATCGGT
Found at i:19464 original size:55 final size:55
Alignment explanation
Indices: 19376--19654 Score: 398
Period size: 55 Copynumber: 5.1 Consensus size: 55
19366 CTATGTGTAC
* * ** * *
19376 TATCGGCACTAACTGTGCAAAACCACGTAATTCATAAAATGTTTATGAATGACCG
1 TATCGACACTAAGTGTGCAAAACCACAAAATTCATAATATGTTTATGAACGACCG
* * * *
19431 TATGGGCACTAAGTGTGCAAAACCACAGAATTCATAATATGTTTATGAACGACCT
1 TATCGACACTAAGTGTGCAAAACCACAAAATTCATAATATGTTTATGAACGACCG
*
19486 TATCGACACTAAGTGTGCAAAACCACAAAATTCATAATATGTTTATGAACGACTG
1 TATCGACACTAAGTGTGCAAAACCACAAAATTCATAATATGTTTATGAACGACCG
* *
19541 TATCGAAACTAAGTGTGCAAAACCACAAAATTCATAATATATTTATGAACGACCG
1 TATCGACACTAAGTGTGCAAAACCACAAAATTCATAATATGTTTATGAACGACCG
* * * *
19596 CATCGACACTAAGTGTGC-AACCCACATAATTCATAATATGTTTATGAACGACTG
1 TATCGACACTAAGTGTGCAAAACCACAAAATTCATAATATGTTTATGAACGACCG
19650 TATCG
1 TATCG
19655 GTAGTACGTG
Statistics
Matches: 202, Mismatches: 22, Indels: 1
0.90 0.10 0.00
Matches are distributed among these distances:
54 36 0.18
55 166 0.82
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.27
Consensus pattern (55 bp):
TATCGACACTAAGTGTGCAAAACCACAAAATTCATAATATGTTTATGAACGACCG
Found at i:23025 original size:51 final size:51
Alignment explanation
Indices: 22953--23054 Score: 195
Period size: 51 Copynumber: 2.0 Consensus size: 51
22943 GAGGCCGAAA
22953 CTGTGATATGTCATTAGTTGAATTTGACTTGGGGATTAAAACCAGGTAGGC
1 CTGTGATATGTCATTAGTTGAATTTGACTTGGGGATTAAAACCAGGTAGGC
*
23004 CTGTGATATGTCATTAGTTGAATTTGACTTGGGGATTAAAACCATGTAGGC
1 CTGTGATATGTCATTAGTTGAATTTGACTTGGGGATTAAAACCAGGTAGGC
23055 TTCCAGAAGC
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.27, C:0.12, G:0.26, T:0.34
Consensus pattern (51 bp):
CTGTGATATGTCATTAGTTGAATTTGACTTGGGGATTAAAACCAGGTAGGC
Found at i:26363 original size:29 final size:30
Alignment explanation
Indices: 26318--26434 Score: 116
Period size: 29 Copynumber: 4.0 Consensus size: 30
26308 CTTCCCAGCA
* *
26318 TAGGTCGACATG-CCCTCCGGGCGACCTTG
1 TAGGTCGCCATGACACTCCGGGCGACCTTG
26347 TAGGTCGCCATGAC-CTCCGGGCGACCTTG
1 TAGGTCGCCATGACACTCCGGGCGACCTTG
* * * * * *
26376 TAGATCGCCATG-CACGCCAGGAGACATGG
1 TAGGTCGCCATGACACTCCGGGCGACCTTG
* *
26405 TAGGTCGCCATG-CACGCTGGGCGACCTTG
1 TAGGTCGCCATGACACTCCGGGCGACCTTG
26434 T
1 T
26435 CCTGTGCCCT
Statistics
Matches: 73, Mismatches: 13, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
28 1 0.01
29 71 0.97
30 1 0.01
ACGTcount: A:0.17, C:0.32, G:0.32, T:0.20
Consensus pattern (30 bp):
TAGGTCGCCATGACACTCCGGGCGACCTTG
Found at i:26511 original size:22 final size:22
Alignment explanation
Indices: 26480--26531 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
26470 CCCCACTGCA
26480 TGCA-GGCGACATCTTCCGACG
1 TGCATGGCGACATCTTCCGACG
*
26501 TGCATGGCGACCTCTTCCGACG
1 TGCATGGCGACATCTTCCGACG
26523 TGCATGGCG
1 TGCATGGCG
26532 CATGCAAAGC
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 4 0.14
22 25 0.86
ACGTcount: A:0.15, C:0.33, G:0.31, T:0.21
Consensus pattern (22 bp):
TGCATGGCGACATCTTCCGACG
Found at i:26570 original size:31 final size:31
Alignment explanation
Indices: 26535--26596 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
26525 CATGGCGCAT
26535 GCAAAGCTTCATCCTCTCACCACAGCTCGTA
1 GCAAAGCTTCATCCTCTCACCACAGCTCGTA
**
26566 GCAAAGCTTCATCCTCTTGCCACAGCTCGTA
1 GCAAAGCTTCATCCTCTCACCACAGCTCGTA
26597 TAGAACACTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.24, C:0.37, G:0.15, T:0.24
Consensus pattern (31 bp):
GCAAAGCTTCATCCTCTCACCACAGCTCGTA
Found at i:28059 original size:24 final size:24
Alignment explanation
Indices: 28015--28061 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
28005 TATAAATAAT
* *
28015 ATAATTAAATTTCAAAGATTAAAA
1 ATAATTAAATATCAAAAATTAAAA
28039 ATAATTAAATAAT-AAAAATTAAA
1 ATAATTAAAT-ATCAAAAATTAAA
28062 TGTACAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 19 0.95
25 1 0.05
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (24 bp):
ATAATTAAATATCAAAAATTAAAA
Found at i:28520 original size:32 final size:33
Alignment explanation
Indices: 28472--28534 Score: 92
Period size: 32 Copynumber: 1.9 Consensus size: 33
28462 ATTAGAACTC
*
28472 AAATACTTTAACTTTAGATATT-TTTAAAAATT
1 AAATACTTTAACTTTAGATATTGTATAAAAATT
* *
28504 AAATACTTTTATTTTAGATATTGTATAAAAA
1 AAATACTTTAACTTTAGATATTGTATAAAAA
28535 AACATAATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 20 0.74
33 7 0.26
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (33 bp):
AAATACTTTAACTTTAGATATTGTATAAAAATT
Found at i:29216 original size:21 final size:21
Alignment explanation
Indices: 29192--29238 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 21
29182 ATTCTGACTA
29192 TCGCATTGCGATTTCTCA-AAT
1 TCGCATTGCGATTT-TCATAAT
*
29213 TCGCGTTGCGATTTTCATAAT
1 TCGCATTGCGATTTTCATAAT
29234 TCGCA
1 TCGCA
29239 ATACGAATAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 3 0.13
21 20 0.87
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTCATAAT
Found at i:29296 original size:41 final size:41
Alignment explanation
Indices: 29234--29327 Score: 118
Period size: 41 Copynumber: 2.3 Consensus size: 41
29224 TTTTCATAAT
* * * *
29234 TCGCAATACGAA-TACGTAAATCGTAACGCGATTAAGTAAA
1 TCGCAATGCGAATTACGAAAATCGCAACGCGAATAAGTAAA
* * *
29274 TCGCAATGCGAATTAGGAAAATCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATTACGAAAATCGCAACGCGAATAAGTAAA
29315 TCGCAATGCGAAT
1 TCGCAATGCGAAT
29328 CTGACTATCG
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
40 11 0.24
41 35 0.76
ACGTcount: A:0.40, C:0.18, G:0.20, T:0.21
Consensus pattern (41 bp):
TCGCAATGCGAATTACGAAAATCGCAACGCGAATAAGTAAA
Found at i:29326 original size:20 final size:20
Alignment explanation
Indices: 29234--29327 Score: 116
Period size: 20 Copynumber: 4.7 Consensus size: 20
29224 TTTTCATAAT
*
29234 TCGCAATACGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* * * *
29254 TCGTAACGCGATTAAGTAAA
1 TCGCAATGCGAATACGTAAA
* *
29274 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAA-TACGTAAA
29295 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
29315 TCGCAATGCGAAT
1 TCGCAATGCGAAT
29328 CTGACTATCG
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
20 43 0.70
21 18 0.30
ACGTcount: A:0.40, C:0.18, G:0.20, T:0.21
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:29981 original size:33 final size:33
Alignment explanation
Indices: 29939--30001 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
29929 CAAAATCGCA
**
29939 TTGCGATTCTCTCGTTACGATTTTCATTTCATG
1 TTGCGATTCTCTCGTTACGATAGTCATTTCATG
*
29972 TTGCGATTCTCTCGTTGCGATAGTCATTTC
1 TTGCGATTCTCTCGTTACGATAGTCATTTC
30002 CGCGTTGCGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.46
Consensus pattern (33 bp):
TTGCGATTCTCTCGTTACGATAGTCATTTCATG
Found at i:30018 original size:20 final size:21
Alignment explanation
Indices: 29978--30041 Score: 78
Period size: 20 Copynumber: 3.1 Consensus size: 21
29968 CATGTTGCGA
* **
29978 TTCTCTCGTTGCGATAGTCAT
1 TTCTCGCGTTGCGATTTTCAT
29999 TTC-CGCGTTGCGATTTTCA-
1 TTCTCGCGTTGCGATTTTCAT
*
30018 TTCTCTCGTTGCGATTTTCAT
1 TTCTCGCGTTGCGATTTTCAT
30039 TTC
1 TTC
30042 AACCAAAAGA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
19 3 0.08
20 28 0.76
21 6 0.16
ACGTcount: A:0.11, C:0.25, G:0.17, T:0.47
Consensus pattern (21 bp):
TTCTCGCGTTGCGATTTTCAT
Found at i:31868 original size:17 final size:17
Alignment explanation
Indices: 31848--31889 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
31838 ATTCTGCTAA
*
31848 ACTGTGTATTCTTTAAC
1 ACTGTGAATTCTTTAAC
31865 ACTGTGAATTCTTTAAC
1 ACTGTGAATTCTTTAAC
31882 ACTGTGAA
1 ACTGTGAA
31890 GTTAGTATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.40
Consensus pattern (17 bp):
ACTGTGAATTCTTTAAC
Found at i:31928 original size:107 final size:110
Alignment explanation
Indices: 31770--31983 Score: 355
Period size: 111 Copynumber: 2.0 Consensus size: 110
31760 AAACTGTTTA
31770 TTAACACTGTGAAGTTAGTATTTGTCTTTTGTTTTGTCTTTTGGTTGAAGT-A-TT-TTCGGTTG
1 TTAACACTGTGAAGTTAGTATTTGTCTTTTGTTTTGTCTTTTGGTTGAAGTAATTTGTTCGGTTG
*
31832 CTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAATTCT
66 CTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTCTGAATTCT
*
31877 TTAACACTGTGAAGTTAGTATTTGTC-TTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGTT
1 TTAACACTGTGAAGTTAGTATTTGTCTTTTGTTTTGTCTTTTGGTTG-AAGT-AATTTGTTCGGT
*
31941 TGCTGCCAATTCTGCTAAACTGTGTATTCTTTAATACTCTGAA
64 TGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTCTGAA
31984 GTTAGTATTT
Statistics
Matches: 99, Mismatches: 3, Indels: 6
0.92 0.03 0.06
Matches are distributed among these distances:
106 20 0.20
107 30 0.30
109 1 0.01
110 2 0.02
111 46 0.46
ACGTcount: A:0.21, C:0.14, G:0.18, T:0.47
Consensus pattern (110 bp):
TTAACACTGTGAAGTTAGTATTTGTCTTTTGTTTTGTCTTTTGGTTGAAGTAATTTGTTCGGTTG
CTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTCTGAATTCT
Found at i:32154 original size:39 final size:35
Alignment explanation
Indices: 32111--32234 Score: 139
Period size: 33 Copynumber: 3.5 Consensus size: 35
32101 TCTTTTGGTT
*
32111 GAAATGAAAATTGCAACGAGAGAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAG-A-G--AATCGCAACGC
32150 GAAATGAAAATCGCAAC--GAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAGAATCGCAACGC
*
32183 GAAATGAAAATCGCAACGACA-A-AATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAGAATCGCAACGC
**
32216 GAAACCAAAAATCGCAACG
1 GAAA-TGAAAATCGCAACG
32235 CGAAACTAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 11
0.84 0.04 0.12
Matches are distributed among these distances:
33 43 0.55
34 13 0.17
35 2 0.03
36 1 0.01
37 3 0.04
39 16 0.21
ACGTcount: A:0.48, C:0.21, G:0.21, T:0.10
Consensus pattern (35 bp):
GAAATGAAAATCGCAACGAGAGAGAATCGCAACGC
Found at i:32157 original size:19 final size:19
Alignment explanation
Indices: 32111--32239 Score: 116
Period size: 20 Copynumber: 7.2 Consensus size: 19
32101 TCTTTTGGTT
* *
32111 GAAATGAAAATTGCAACGA
1 GAAATGAAAATCGCAACGC
32130 GAGAATGAAAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
32150 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
32167 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
32183 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
32200 G--A-CAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
**
32216 GAAACCAAAAATCGCAACGC
1 GAAA-TGAAAATCGCAACGC
32236 GAAA
1 GAAA
32240 CTAGAATCGT
Statistics
Matches: 92, Mismatches: 6, Indels: 23
0.76 0.05 0.19
Matches are distributed among these distances:
14 20 0.22
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 26 0.28
20 34 0.37
ACGTcount: A:0.49, C:0.21, G:0.21, T:0.09
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:32181 original size:33 final size:33
Alignment explanation
Indices: 32137--32234 Score: 151
Period size: 33 Copynumber: 2.9 Consensus size: 33
32127 CGAGAGAATG
*
32137 AAAATCGCAACGCGAAATGAAAATCGCAACGAG
1 AAAATCGCAACGCGAAATGAAAATCGCAACGAC
*
32170 AGAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAAATCGCAACGCGAAATGAAAATCGCAACGAC
**
32203 AAAATCGCAACGCGAAACCAAAAATCGCAACG
1 AAAATCGCAACGCGAAA-TGAAAATCGCAACG
32235 CGAAACTAGA
Statistics
Matches: 59, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
33 47 0.80
34 12 0.20
ACGTcount: A:0.48, C:0.24, G:0.19, T:0.08
Consensus pattern (33 bp):
AAAATCGCAACGCGAAATGAAAATCGCAACGAC
Found at i:32337 original size:19 final size:19
Alignment explanation
Indices: 32250--32329 Score: 89
Period size: 19 Copynumber: 4.4 Consensus size: 19
32240 CTAGAATCGT
**
32250 GTTGCGATTTTTGGTTTCGC
1 GTTGCGA-TTTTCATTTCGC
32270 GTTGCGATTTTCATTTCGC
1 GTTGCGATTTTCATTTCGC
*
32289 GTTGCGA--TTC-TAT--C
1 GTTGCGATTTTCATTTCGC
32303 GTTGCGATTTTCATTTCGC
1 GTTGCGATTTTCATTTCGC
32322 GTTGCGAT
1 GTTGCGAT
32330 AGTCATTTTT
Statistics
Matches: 51, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
14 8 0.16
16 5 0.10
17 5 0.10
19 26 0.51
20 7 0.14
ACGTcount: A:0.10, C:0.19, G:0.25, T:0.46
Consensus pattern (19 bp):
GTTGCGATTTTCATTTCGC
Found at i:32767 original size:21 final size:21
Alignment explanation
Indices: 32743--32809 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
32733 TCATTCCTCG
32743 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
32764 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
32785 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
32806 AGAG
1 AGAG
32810 CTCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:32767 original size:42 final size:42
Alignment explanation
Indices: 32691--32809 Score: 107
Period size: 42 Copynumber: 2.8 Consensus size: 42
32681 GACTCGCCTG
* * * * * * *
32691 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
*
32733 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
* * *
32775 TCA-TCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 TCATTCCTCG-AGA-GTCCCCTCCCACCGTTCAAGAG
32810 CTCGATTCAC
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 4 0.06
42 58 0.91
43 2 0.03
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.23
Consensus pattern (42 bp):
TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
Found at i:34179 original size:14 final size:14
Alignment explanation
Indices: 34160--34195 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
34150 ATTGTTTAAT
34160 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
34174 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
34188 TGATTTGT
1 TGATTTGT
34196 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:34318 original size:19 final size:19
Alignment explanation
Indices: 34302--34353 Score: 86
Period size: 19 Copynumber: 2.7 Consensus size: 19
34292 AAAAATGACT
*
34302 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
34321 ATCGCAACGCAAAATGAAA
1 ATCGCAACGCGAAATGAAA
34340 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
34354 CTAAATTCGT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.48, C:0.21, G:0.19, T:0.12
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:34406 original size:33 final size:33
Alignment explanation
Indices: 34364--34489 Score: 225
Period size: 33 Copynumber: 3.8 Consensus size: 33
34354 CTAAATTCGT
* *
34364 GTTGCGATTTTCATTTCGCTTTGCGATTCCCTC
1 GTTGCGATTTTCATTTCGCATTGCGATTCTCTC
34397 GTTGCGATTTTCATTTCGCATTGCGATTCTCTC
1 GTTGCGATTTTCATTTCGCATTGCGATTCTCTC
*
34430 GTTGCGATTTTAATTTCGCATTGCGATTCTCTC
1 GTTGCGATTTTCATTTCGCATTGCGATTCTCTC
34463 GTTGCGATTTTCATTTCGCATTGCGAT
1 GTTGCGATTTTCATTTCGCATTGCGAT
34490 AGTCATTTCC
Statistics
Matches: 89, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 89 1.00
ACGTcount: A:0.13, C:0.23, G:0.19, T:0.45
Consensus pattern (33 bp):
GTTGCGATTTTCATTTCGCATTGCGATTCTCTC
Found at i:34422 original size:19 final size:18
Alignment explanation
Indices: 34365--34509 Score: 89
Period size: 19 Copynumber: 8.4 Consensus size: 18
34355 TAAATTCGTG
34365 TTGCGATTTTCATTTCGC
1 TTGCGATTTTCATTTCGC
**
34383 TTTGCGA--TTC-CCTCG-
1 -TTGCGATTTTCATTTCGC
34398 TTGCGATTTTCATTTCGC
1 TTGCGATTTTCATTTCGC
*
34416 ATTGCGA--TTC-TCTCG-
1 -TTGCGATTTTCATTTCGC
*
34431 TTGCGATTTTAATTTCGC
1 TTGCGATTTTCATTTCGC
*
34449 ATTGCGA--TTC-TCTCG-
1 -TTGCGATTTTCATTTCGC
34464 TTGCGATTTTCATTTCGC
1 TTGCGATTTTCATTTCGC
**
34482 ATTGCGATAGTCATTTCCGC
1 -TTGCGATTTTCATTT-CGC
34502 GTTGCGAT
1 -TTGCGAT
34510 AGACATTAAG
Statistics
Matches: 97, Mismatches: 13, Indels: 31
0.69 0.09 0.22
Matches are distributed among these distances:
14 18 0.19
16 19 0.20
17 19 0.20
19 31 0.32
20 10 0.10
ACGTcount: A:0.13, C:0.23, G:0.19, T:0.44
Consensus pattern (18 bp):
TTGCGATTTTCATTTCGC
Found at i:34436 original size:14 final size:14
Alignment explanation
Indices: 34384--34471 Score: 50
Period size: 14 Copynumber: 5.6 Consensus size: 14
34374 TCATTTCGCT
*
34384 TTGCGATTCCCTCG
1 TTGCGATTCTCTCG
*
34398 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
34415 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
* *
34431 TTGCGATTTTAATTTCG
1 TTGCGA--TT-CTCTCG
34448 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
34464 TTGCGATT
1 TTGCGATT
34472 TTCATTTCGC
Statistics
Matches: 57, Mismatches: 7, Indels: 20
0.68 0.08 0.24
Matches are distributed among these distances:
14 20 0.35
16 13 0.23
17 12 0.21
19 12 0.21
ACGTcount: A:0.12, C:0.24, G:0.19, T:0.44
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:34508 original size:20 final size:20
Alignment explanation
Indices: 34462--34555 Score: 68
Period size: 20 Copynumber: 4.7 Consensus size: 20
34452 GCGATTCTCT
**
34462 CGTTGCGATTTTCATTT-CG
1 CGTTGCGATAGTCATTTCCG
*
34481 CATTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
* **
34501 CGTTGCGATAGACA-TTAAG
1 CGTTGCGATAGTCATTTCCG
*
34520 ATGATTGCGA-ACGTCATTTCCG
1 -CG-TTGCGATA-GTCATTTCCG
*
34542 TGTTGCGATAGTCA
1 CGTTGCGATAGTCA
34556 AATGAATGCC
Statistics
Matches: 58, Mismatches: 11, Indels: 11
0.73 0.14 0.14
Matches are distributed among these distances:
19 17 0.29
20 26 0.45
21 12 0.21
22 3 0.05
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:37992 original size:41 final size:40
Alignment explanation
Indices: 37946--38155 Score: 289
Period size: 41 Copynumber: 5.2 Consensus size: 40
37936 GCGATTTACT
* *
37946 AAATCGCAATGCGATTACGTAAATCG-AAGTGAGAATTAGGA
1 AAATCGCAATGCGATTACGTAAATCGCAA-TGCG-ATTACGA
*
37987 AAATCGCAATGCGATTACGTAAATCGCAATGCGAATTAGGA
1 AAATCGCAATGCGATTACGTAAATCGCAATGCG-ATTACGA
*
38028 AAATCGCAATGCGATTACGAAAATCGCAATGCGATTACGA
1 AAATCGCAATGCGATTACGTAAATCGCAATGCGATTACGA
* * *
38068 AAATTGCAATGCGAATTAGGAAAATCGCAATGCGATTACGA
1 AAATCGCAATGCG-ATTACGTAAATCGCAATGCGATTACGA
*
38109 AAATCGCAATGCGATTACGTAAATCGCAATGCGAATACG-
1 AAATCGCAATGCGATTACGTAAATCGCAATGCGATTACGA
*
38148 TAATCGCA
1 AAATCGCA
38156 TTTCCTAATT
Statistics
Matches: 157, Mismatches: 10, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
39 7 0.04
40 41 0.26
41 107 0.68
42 2 0.01
ACGTcount: A:0.40, C:0.17, G:0.21, T:0.21
Consensus pattern (40 bp):
AAATCGCAATGCGATTACGTAAATCGCAATGCGATTACGA
Found at i:38010 original size:61 final size:61
Alignment explanation
Indices: 37935--38144 Score: 309
Period size: 61 Copynumber: 3.4 Consensus size: 61
37925 AGAATCTCGT
* * *
37935 TGCGATTTAC-TAAATCGCAATGCG-ATTACGTAAATCG-AAGTGAGAATTAGGAAAATCGCAA
1 TGCGA-TTACGTAAATCGCAATGCGAATTACGAAAATCGCAA-TGCG-ATTACGAAAATCGCAA
*
37996 TGCGATTACGTAAATCGCAATGCGAATTAGGAAAATCGCAATGCGATTACGAAAATCGCAA
1 TGCGATTACGTAAATCGCAATGCGAATTACGAAAATCGCAATGCGATTACGAAAATCGCAA
* * *
38057 TGCGATTACGAAAATTGCAATGCGAATTAGGAAAATCGCAATGCGATTACGAAAATCGCAA
1 TGCGATTACGTAAATCGCAATGCGAATTACGAAAATCGCAATGCGATTACGAAAATCGCAA
38118 TGCGATTACGTAAATCGCAATGCGAAT
1 TGCGATTACGTAAATCGCAATGCGAAT
38145 ACGTAATCGC
Statistics
Matches: 138, Mismatches: 8, Indels: 6
0.91 0.05 0.04
Matches are distributed among these distances:
60 4 0.03
61 118 0.86
62 14 0.10
63 2 0.01
ACGTcount: A:0.39, C:0.17, G:0.21, T:0.23
Consensus pattern (61 bp):
TGCGATTACGTAAATCGCAATGCGAATTACGAAAATCGCAATGCGATTACGAAAATCGCAA
Found at i:38150 original size:20 final size:20
Alignment explanation
Indices: 37946--38147 Score: 280
Period size: 20 Copynumber: 9.9 Consensus size: 20
37936 GCGATTTACT
*
37946 AAATCGCAATGCGATTACGT
1 AAATCGCAATGCGATTACGA
* *
37966 AAATCG-AAGTGAGAATTAGGA
1 AAATCGCAA-TGCG-ATTACGA
*
37987 AAATCGCAATGCGATTACGT
1 AAATCGCAATGCGATTACGA
*
38007 AAATCGCAATGCGAATTAGGA
1 AAATCGCAATGCG-ATTACGA
38028 AAATCGCAATGCGATTACGA
1 AAATCGCAATGCGATTACGA
38048 AAATCGCAATGCGATTACGA
1 AAATCGCAATGCGATTACGA
* *
38068 AAATTGCAATGCGAATTAGGA
1 AAATCGCAATGCG-ATTACGA
38089 AAATCGCAATGCGATTACGA
1 AAATCGCAATGCGATTACGA
*
38109 AAATCGCAATGCGATTACGT
1 AAATCGCAATGCGATTACGA
*
38129 AAATCGCAATGCGAATACG
1 AAATCGCAATGCGATTACG
38148 TAATCGCATT
Statistics
Matches: 162, Mismatches: 15, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
19 2 0.01
20 108 0.67
21 50 0.31
22 2 0.01
ACGTcount: A:0.40, C:0.17, G:0.22, T:0.21
Consensus pattern (20 bp):
AAATCGCAATGCGATTACGA
Found at i:38212 original size:20 final size:20
Alignment explanation
Indices: 38163--38215 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
38153 GCATTTCCTA
38163 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
38183 AATCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
38203 ATTCGTATTGCGA
1 ATTCGCATTGCGA
38216 ATTAGGAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.23, C:0.19, G:0.21, T:0.38
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:38238 original size:21 final size:21
Alignment explanation
Indices: 38212--38257 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
38202 TATTCGTATT
38212 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* * *
38233 GCGAATTTGGGAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
38254 GCGA
1 GCGA
38258 TAGTCAGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.17, G:0.28, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:41185 original size:29 final size:31
Alignment explanation
Indices: 41153--41210 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
41143 AATTCGACAT
41153 AATAA-TATAA-ATATA-TCTTAAATATATAA
1 AATAATTATAATA-ATACTCTTAAATATATAA
*
41182 AATAATTATAATAATACTCTTATATATAT
1 AATAATTATAATAATACTCTTAAATATAT
41211 TAATTAGTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
29 5 0.20
30 8 0.32
31 12 0.48
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.41
Consensus pattern (31 bp):
AATAATTATAATAATACTCTTAAATATATAA
Found at i:43888 original size:26 final size:26
Alignment explanation
Indices: 43836--43889 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
43826 AACATTCATA
**
43836 ATAAACATCATATATATATATTCATG
1 ATAAACATCATATATATATAAACATG
*
43862 ATAACCATCATATATA-ATAAACAATG
1 ATAAACATCATATATATATAAAC-ATG
43888 AT
1 AT
43890 CAATGCATTC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 4 0.17
26 20 0.83
ACGTcount: A:0.50, C:0.13, G:0.04, T:0.33
Consensus pattern (26 bp):
ATAAACATCATATATATATAAACATG
Found at i:49191 original size:12 final size:12
Alignment explanation
Indices: 49174--49220 Score: 94
Period size: 12 Copynumber: 3.9 Consensus size: 12
49164 TTAACATTCG
49174 GGTACTGTTCAC
1 GGTACTGTTCAC
49186 GGTACTGTTCAC
1 GGTACTGTTCAC
49198 GGTACTGTTCAC
1 GGTACTGTTCAC
49210 GGTACTGTTCA
1 GGTACTGTTCA
49221 TTATTATTCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 35 1.00
ACGTcount: A:0.17, C:0.23, G:0.26, T:0.34
Consensus pattern (12 bp):
GGTACTGTTCAC
Found at i:49252 original size:22 final size:22
Alignment explanation
Indices: 49176--49252 Score: 73
Period size: 22 Copynumber: 3.4 Consensus size: 22
49166 AACATTCGGG
* *
49176 TACTGTTCACGGTACTGTTCACGG
1 TACTGTTCACAGTACTGTTCA--T
*
49200 TACTGTTCACGGTACTGTTCAT
1 TACTGTTCACAGTACTGTTCAT
* * * *
49222 TATTATTCACATTACTGTTTAT
1 TACTGTTCACAGTACTGTTCAT
49244 TACTGTTCA
1 TACTGTTCA
49253 TACCATATTT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
22 24 0.53
24 21 0.47
ACGTcount: A:0.21, C:0.21, G:0.16, T:0.43
Consensus pattern (22 bp):
TACTGTTCACAGTACTGTTCAT
Found at i:50110 original size:21 final size:21
Alignment explanation
Indices: 50086--50133 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
50076 ATAGAACAAA
*
50086 TGAAGCTAGAATATGTGAACT
1 TGAAGCTAGAATATGCGAACT
50107 TGAAGCTAGAATATGCGAACT
1 TGAAGCTAGAATATGCGAACT
50128 TGAAGC
1 TGAAGC
50134 AAGGGAGTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.38, C:0.12, G:0.25, T:0.25
Consensus pattern (21 bp):
TGAAGCTAGAATATGCGAACT
Found at i:53977 original size:2 final size:2
Alignment explanation
Indices: 53972--54023 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
53962 GTGTTGTGTG
53972 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
54014 AT AT AT AT AT
1 AT AT AT AT AT
54024 GTGTGTGTGT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:54028 original size:2 final size:2
Alignment explanation
Indices: 54023--54059 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
54013 TATATATATA
*
54023 TG TG TG TG TG TG TG TG TG TG TG TA TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
54060 ATGATTACAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.03, C:0.00, G:0.46, T:0.51
Consensus pattern (2 bp):
TG
Found at i:55292 original size:8 final size:8
Alignment explanation
Indices: 55262--55303 Score: 50
Period size: 8 Copynumber: 5.4 Consensus size: 8
55252 TATAAATATA
55262 ATATTCAT
1 ATATTCAT
* *
55270 ATAATAAT
1 ATATTCAT
55278 ATATT-AT
1 ATATTCAT
*
55285 ATATTTAT
1 ATATTCAT
55293 ATATTCAT
1 ATATTCAT
55301 ATA
1 ATA
55304 ACATAGATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
7 7 0.24
8 22 0.76
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (8 bp):
ATATTCAT
Found at i:55988 original size:36 final size:36
Alignment explanation
Indices: 55937--56362 Score: 307
Period size: 36 Copynumber: 12.1 Consensus size: 36
55927 AGCTTTTTTG
* * *
55937 TGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATT
1 TGTTTCAAGAAAAACTGTCTCAAGAGAGACAAAATT
55973 TGTTTCAAGAAAAACTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAGAAAAACTGTCTCAAGAGAGACAAAA-TT
* * * *
56010 AGTTCCAA-AAGAAACTTTCTCGAGAGAGACAAAATT
1 TGTTTCAAGAA-AAACTGTCTCAAGAGAGACAAAATT
* * * * *
56046 TGTTTAAAGGAAAACAGAT-TC-----A-A-ATATTT
1 TGTTTCAAGAAAAACTG-TCTCAAGAGAGACAAAATT
** * *
56075 TGTTTCAAGGGAAACTGTCTTAAGAGAGACAAGATT
1 TGTTTCAAGAAAAACTGTCTCAAGAGAGACAAAATT
**
56111 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGAAAAACTGTCTCAAGAGAGACAAAATT
* * * *
56147 TGTTTCAAGAGAAATTGTCTAAAGAGAGTCAAAACTT
1 TGTTTCAAGAAAAACTGTCTCAAGAGAGACAAAA-TT
* * * * *
56184 AGTTCCAA-AAGAAATTGTATCAAG-GAAGACGAAATT
1 TGTTTCAAGAA-AAACTGTCTCAAGAG-AGACAAAATT
* * *
56220 TGTTTCAAGGAAAACAGAT-TC-A-A-AG----ATTT
1 TGTTTCAAGAAAAACTG-TCTCAAGAGAGACAAAATT
** * *
56249 TGTTTCAAGGGAAATTGACTCAAGAGAGACAAAATT
1 TGTTTCAAGAAAAACTGTCTCAAGAGAGACAAAATT
*
56285 TGTTTTAAGAGAAAA-TGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGA-AAAACTGTCTCAAGAGAGACAAAATT
*
56321 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAGAAAAACTGTCTCAAGAGAGACAAAA-TT
56358 TGTTT
1 TGTTT
56363 TAAGTAAATC
Statistics
Matches: 309, Mismatches: 52, Indels: 57
0.74 0.12 0.14
Matches are distributed among these distances:
28 1 0.00
29 38 0.12
30 2 0.01
31 2 0.01
32 2 0.01
33 2 0.01
34 1 0.00
35 5 0.02
36 188 0.61
37 68 0.22
ACGTcount: A:0.42, C:0.12, G:0.19, T:0.27
Consensus pattern (36 bp):
TGTTTCAAGAAAAACTGTCTCAAGAGAGACAAAATT
Found at i:56036 original size:37 final size:37
Alignment explanation
Indices: 55942--56045 Score: 124
Period size: 37 Copynumber: 2.9 Consensus size: 37
55932 TTTTGTGTTT
* * *
55942 CAAG-AGAAACTATCTCAAGGGAGACAAAATTTGTTT
1 CAAGAAGAAACTATCTCAAGAGAGACAAAATTAGTTC
*
55978 CAAGAA-AAACTGTCTCAAGAGAGACAAAACTTAGTTC
1 CAAGAAGAAACTATCTCAAGAGAGACAAAA-TTAGTTC
* *
56015 CAA-AAGAAACTTTCTCGAGAGAGACAAAATT
1 CAAGAAGAAACTATCTCAAGAGAGACAAAATT
56046 TGTTTAAAGG
Statistics
Matches: 59, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
36 29 0.49
37 30 0.51
ACGTcount: A:0.45, C:0.16, G:0.17, T:0.21
Consensus pattern (37 bp):
CAAGAAGAAACTATCTCAAGAGAGACAAAATTAGTTC
Found at i:56232 original size:174 final size:174
Alignment explanation
Indices: 55937--56357 Score: 648
Period size: 174 Copynumber: 2.4 Consensus size: 174
55927 AGCTTTTTTG
* * *
55937 TGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTGTTTCAAGAAAAACTGTCTCAAGAGAGA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGA
* *
56002 CAAAACTTAGTTCCAAAAGAAACTTTCTCGAGAGAGACAAAATTTGTTTAAAGGAAAACAGATTC
66 CAAAACTTAGTTCCAAAAGAAACTTTATCAAGAGAGACAAAATTTGTTTAAAGGAAAACAGATTC
* * * *
56067 AAATATTTTGTTTCAAGGGAAACTGTCTTAAGAGAGACAAGATT
131 AAAGATTTTGTTTCAAGGGAAACTGACTCAAGAGAGACAAAATT
* * * *
56111 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAATTGTCTAAAGAGAGT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGA
* *
56176 CAAAACTTAGTTCCAAAAGAAA-TTGTATCAAG-GAAGACGAAATTTGTTTCAAGGAAAACAGAT
66 CAAAACTTAGTTCCAAAAGAAACTT-TATCAAGAG-AGACAAAATTTGTTTAAAGGAAAACAGAT
*
56239 TCAAAGATTTTGTTTCAAGGGAAATTGACTCAAGAGAGACAAAATT
129 TCAAAGATTTTGTTTCAAGGGAAACTGACTCAAGAGAGACAAAATT
* *
56285 TGTTTTAAGAGAAAATGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGA
56350 CAAAACTT
66 CAAAACTT
56358 TGTTTTAAGT
Statistics
Matches: 223, Mismatches: 22, Indels: 4
0.90 0.09 0.02
Matches are distributed among these distances:
173 3 0.01
174 220 0.99
ACGTcount: A:0.42, C:0.12, G:0.19, T:0.26
Consensus pattern (174 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGA
CAAAACTTAGTTCCAAAAGAAACTTTATCAAGAGAGACAAAATTTGTTTAAAGGAAAACAGATTC
AAAGATTTTGTTTCAAGGGAAACTGACTCAAGAGAGACAAAATT
Found at i:56251 original size:138 final size:137
Alignment explanation
Indices: 56105--56362 Score: 367
Period size: 138 Copynumber: 1.9 Consensus size: 137
56095 TAAGAGAGAC
* *
56105 AAGATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAATTGTCTAAA
1 AAGATTTGTTTCAAGGGAAACTGACTCAAGAGAGACAAAATTTGTTTCAAGAGAAAATGTCTAAA
* * *
56170 GAGAGTCAAAACTTAGTTCCAAAAGAAATTGTATCAAG-GAAGACGAAA-TTTGTTTCAAGGAAA
66 GAGAGACAAAA-TTAGTTCCAAAAGAAACTGTATCAAGAG-AGACAAAACTTTGTTTCAAGGAAA
56233 ACAGATTCA
129 ACAGATTCA
* * *
56242 AAGATTTTGTTTCAAGGGAAATTGACTCAAGAGAGACAAAATTTGTTTTAAGAGAAAATGTCTCA
1 AAGA-TTTGTTTCAAGGGAAACTGACTCAAGAGAGACAAAATTTGTTTCAAGAGAAAATGTCTAA
* * * *
56307 AGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTT
65 AGAGAGACAAAATTAGTTCCAAAAGAAACTGTATCAAGAGAGACAAAACTTTGTTT
56363 TAAGTAAATC
Statistics
Matches: 106, Mismatches: 12, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
137 32 0.30
138 74 0.70
ACGTcount: A:0.41, C:0.11, G:0.20, T:0.28
Consensus pattern (137 bp):
AAGATTTGTTTCAAGGGAAACTGACTCAAGAGAGACAAAATTTGTTTCAAGAGAAAATGTCTAAA
GAGAGACAAAATTAGTTCCAAAAGAAACTGTATCAAGAGAGACAAAACTTTGTTTCAAGGAAAAC
AGATTCA
Found at i:56295 original size:21 final size:21
Alignment explanation
Indices: 56268--56332 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 21
56258 GGAAATTGAC
56268 TCAAGAGAGACAAAATTTGTT
1 TCAAGAGAGACAAAATTTGTT
* *
56289 T-TA-AGAG--AAAA--TGTC
1 TCAAGAGAGACAAAATTTGTT
56304 TCAAGAGAGACAAAATTTGTT
1 TCAAGAGAGACAAAATTTGTT
56325 TCAAGAGA
1 TCAAGAGA
56333 AACTGTCTCA
Statistics
Matches: 34, Mismatches: 4, Indels: 12
0.68 0.08 0.24
Matches are distributed among these distances:
15 4 0.12
16 1 0.03
17 8 0.24
19 8 0.24
20 1 0.03
21 12 0.35
ACGTcount: A:0.45, C:0.09, G:0.20, T:0.26
Consensus pattern (21 bp):
TCAAGAGAGACAAAATTTGTT
Found at i:56331 original size:19 final size:19
Alignment explanation
Indices: 56273--56332 Score: 56
Period size: 19 Copynumber: 3.3 Consensus size: 19
56263 TTGACTCAAG
*
56273 AGAGACAAAATTTGTTTTA
1 AGAGACAAAATTTGTTTCA
*
56292 AGAG--AAAA--TGTCTCAA
1 AGAGACAAAATTTGTTTC-A
56308 GAGAGACAAAATTTGTTTCA
1 -AGAGACAAAATTTGTTTCA
56328 AGAGA
1 AGAGA
56333 AACTGTCTCA
Statistics
Matches: 32, Mismatches: 3, Indels: 12
0.68 0.06 0.26
Matches are distributed among these distances:
15 4 0.12
16 1 0.03
17 8 0.25
19 13 0.41
20 1 0.03
21 5 0.16
ACGTcount: A:0.45, C:0.08, G:0.20, T:0.27
Consensus pattern (19 bp):
AGAGACAAAATTTGTTTCA
Found at i:57894 original size:95 final size:95
Alignment explanation
Indices: 57731--57909 Score: 295
Period size: 95 Copynumber: 1.9 Consensus size: 95
57721 TGTAAATACA
* * * * * *
57731 TTTATCAAGTTAGCTGAATCTTATCCATAAAGCCGGGGCGTTTAACCAATTGCTTTATAGGGACA
1 TTTATCAAGCTAGCTGAATATTATCCATAAAGCCGGGACATTTAACCAATTGCTCTAGAGGGACA
57796 ACTCAAGCTTTATTGTATAGTATAATCACC
66 ACTCAAGCTTTATTGTATAGTATAATCACC
*
57826 TTTATCAGGCTAGCTGAATATTATCCATAAAGCCGGGACATTTAACCAATTGCTCTAGAGGGACA
1 TTTATCAAGCTAGCTGAATATTATCCATAAAGCCGGGACATTTAACCAATTGCTCTAGAGGGACA
57891 ACTCAAGCTTTATTGTATA
66 ACTCAAGCTTTATTGTATA
57910 TAAATAATAT
Statistics
Matches: 77, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
95 77 1.00
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.32
Consensus pattern (95 bp):
TTTATCAAGCTAGCTGAATATTATCCATAAAGCCGGGACATTTAACCAATTGCTCTAGAGGGACA
ACTCAAGCTTTATTGTATAGTATAATCACC
Found at i:60153 original size:18 final size:20
Alignment explanation
Indices: 60127--60164 Score: 53
Period size: 18 Copynumber: 2.0 Consensus size: 20
60117 AAGAGACAAA
60127 ATATCTTGAC-AG-CTTCTG
1 ATATCTTGACTAGTCTTCTG
*
60145 ATATGTTGACTAGTCTTCTG
1 ATATCTTGACTAGTCTTCTG
60165 CCTTCGTCTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 9 0.53
19 2 0.12
20 6 0.35
ACGTcount: A:0.21, C:0.18, G:0.18, T:0.42
Consensus pattern (20 bp):
ATATCTTGACTAGTCTTCTG
Found at i:60814 original size:21 final size:19
Alignment explanation
Indices: 60781--60824 Score: 52
Period size: 21 Copynumber: 2.2 Consensus size: 19
60771 AAAAGTTAGC
*
60781 AAAATAAAAATGATAAAAT
1 AAAATAAAAATGATAAAAG
*
60800 AAAATAAATAAATGATGAAAG
1 AAAAT-AA-AAATGATAAAAG
60821 AAAA
1 AAAA
60825 AATGAAAAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.24
20 2 0.10
21 14 0.67
ACGTcount: A:0.73, C:0.00, G:0.09, T:0.18
Consensus pattern (19 bp):
AAAATAAAAATGATAAAAG
Found at i:60826 original size:23 final size:19
Alignment explanation
Indices: 60781--60832 Score: 50
Period size: 23 Copynumber: 2.5 Consensus size: 19
60771 AAAAGTTAGC
*
60781 AAAATAAAAATGATAAAAT
1 AAAATAAAAATGATAAAAA
60800 AAAATAAATAAATGATGAAAGAA
1 AAAAT-AA-AAATGAT-AAA-AA
60823 AAAATGAAAA
1 AAAAT-AAAA
60833 GTAGAAAGAC
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
19 5 0.19
20 2 0.07
21 7 0.26
22 5 0.19
23 8 0.30
ACGTcount: A:0.73, C:0.00, G:0.10, T:0.17
Consensus pattern (19 bp):
AAAATAAAAATGATAAAAA
Found at i:61802 original size:14 final size:14
Alignment explanation
Indices: 61723--61802 Score: 56
Period size: 14 Copynumber: 5.4 Consensus size: 14
61713 AAAGACGTTA
*
61723 AAAAAGAAAATAAAT
1 AAAAA-AAAAGAAAT
*
61738 AAATTAAAAAG-AAT
1 AAA-AAAAAAGAAAT
* *
61752 AAAATAAAGGAAAT
1 AAAAAAAAAGAAAT
61766 AAAAATGAAAATGAAA-
1 AAAAA--AAAA-GAAAT
61782 AATAAAAAAAGAAAT
1 AA-AAAAAAAGAAAT
61797 AAAAAA
1 AAAAAA
61803 GGTAGATAAG
Statistics
Matches: 51, Mismatches: 7, Indels: 15
0.70 0.10 0.21
Matches are distributed among these distances:
13 4 0.08
14 21 0.41
15 13 0.25
16 6 0.12
17 7 0.14
ACGTcount: A:0.78, C:0.00, G:0.09, T:0.14
Consensus pattern (14 bp):
AAAAAAAAAGAAAT
Found at i:61802 original size:19 final size:21
Alignment explanation
Indices: 61708--61799 Score: 73
Period size: 21 Copynumber: 4.4 Consensus size: 21
61698 AAATACCCCC
** *
61708 AAAATAAAGACGTTAAAAAAG
1 AAAATAAAGAAATAAAAAAAG
* *
61729 AAAATAAATAAATTAAAAAGAAT
1 AAAATAAAGAAA-TAAAAA-AAG
*
61752 AAAATAAAGGAAAT-AAAAATG
1 AAAATAAA-GAAATAAAAAAAG
*
61773 AAAATGAA-AAATAAAAAAAG
1 AAAATAAAGAAATAAAAAAAG
61793 -AAATAAA
1 AAAATAAA
61800 AAAGGTAGAT
Statistics
Matches: 56, Mismatches: 11, Indels: 10
0.73 0.14 0.13
Matches are distributed among these distances:
19 10 0.18
20 6 0.11
21 17 0.30
22 9 0.16
23 11 0.20
24 3 0.05
ACGTcount: A:0.74, C:0.01, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATAAAGAAATAAAAAAAG
Found at i:61941 original size:21 final size:22
Alignment explanation
Indices: 61917--61988 Score: 55
Period size: 21 Copynumber: 3.4 Consensus size: 22
61907 AAAGACAAAA
61917 AAAAGTGAATAAATAAATGAA-
1 AAAAGTGAATAAATAAATGAAG
* *
61938 AAAAATG-ATAAAGAAA-GCAAG
1 AAAAGTGAATAAATAAATG-AAG
* *
61959 AAAA-T-AGATAAATAAATAAAT
1 AAAAGTGA-ATAAATAAATGAAG
61980 AAAAGTGAA
1 AAAAGTGAA
61989 AAAAATACAA
Statistics
Matches: 39, Mismatches: 5, Indels: 13
0.68 0.09 0.23
Matches are distributed among these distances:
19 1 0.03
20 11 0.28
21 24 0.62
22 2 0.05
23 1 0.03
ACGTcount: A:0.68, C:0.01, G:0.14, T:0.17
Consensus pattern (22 bp):
AAAAGTGAATAAATAAATGAAG
Found at i:62061 original size:13 final size:13
Alignment explanation
Indices: 62043--62144 Score: 50
Period size: 13 Copynumber: 7.6 Consensus size: 13
62033 TCATATATAG
62043 AATAAAATAAATA
1 AATAAAATAAATA
*
62056 AATAAATATATATA
1 AATAAA-ATAAATA
* *
62070 CATATAAT-AATA
1 AATAAAATAAATA
* *
62082 ATATATAATATAT-
1 A-ATAAAATAAATA
62095 AATAAAA-AAACGTA
1 AATAAAATAAA--TA
* *
62109 ATAAAAAATAAAAA
1 A-ATAAAATAAATA
62123 AATAAAA-AAACTA
1 AATAAAATAAA-TA
62136 AATACAAAT
1 AATA-AAAT
62145 TGAATTTAAC
Statistics
Matches: 66, Mismatches: 12, Indels: 20
0.67 0.12 0.20
Matches are distributed among these distances:
11 2 0.03
12 11 0.17
13 27 0.41
14 18 0.27
15 5 0.08
16 3 0.05
ACGTcount: A:0.70, C:0.04, G:0.01, T:0.25
Consensus pattern (13 bp):
AATAAAATAAATA
Found at i:62064 original size:26 final size:28
Alignment explanation
Indices: 62035--62095 Score: 74
Period size: 26 Copynumber: 2.2 Consensus size: 28
62025 TGTACTAATC
62035 ATATATAGA-ATAAAATAAATAA-ATA-A
1 ATATATAGACATAAAAT-AATAATATATA
* *
62061 ATATATATACATATAATAATAATATATA
1 ATATATAGACATAAAATAATAATATATA
62089 ATATATA
1 ATATATA
62096 ATAAAAAAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
26 13 0.43
27 9 0.30
28 8 0.27
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (28 bp):
ATATATAGACATAAAATAATAATATATA
Found at i:63399 original size:21 final size:21
Alignment explanation
Indices: 63370--63472 Score: 131
Period size: 21 Copynumber: 5.0 Consensus size: 21
63360 AGTCGAGGGT
* *
63370 TACAATGGTCCTTCGGGATAA
1 TACAGTGGTCCTTCGGGACAA
*
63391 TACAGTGGTCTTTCGGGACAA
1 TACAGTGGTCCTTCGGGACAA
*
63412 TACAGTGGTCCTTCAGGACAA
1 TACAGTGGTCCTTCGGGACAA
*
63433 TACAGTGGTCCTACGGGAC-A
1 TACAGTGGTCCTTCGGGACAA
*
63453 T--AGTGGTTCTTCGGGACAA
1 TACAGTGGTCCTTCGGGACAA
63472 T
1 T
63473 TTTCAGTGCC
Statistics
Matches: 72, Mismatches: 9, Indels: 4
0.85 0.11 0.05
Matches are distributed among these distances:
18 14 0.19
19 2 0.03
20 2 0.03
21 54 0.75
ACGTcount: A:0.25, C:0.20, G:0.27, T:0.27
Consensus pattern (21 bp):
TACAGTGGTCCTTCGGGACAA
Found at i:63459 original size:18 final size:18
Alignment explanation
Indices: 63436--63470 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
63426 AGGACAATAC
63436 AGTGGTCCTACGGGACAT
1 AGTGGTCCTACGGGACAT
* *
63454 AGTGGTTCTTCGGGACA
1 AGTGGTCCTACGGGACA
63471 ATTTTCAGTG
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:0.20, C:0.20, G:0.34, T:0.26
Consensus pattern (18 bp):
AGTGGTCCTACGGGACAT
Found at i:68919 original size:23 final size:22
Alignment explanation
Indices: 68889--68988 Score: 118
Period size: 21 Copynumber: 4.5 Consensus size: 22
68879 ACGATCAGGA
68889 GGGTATCGATACAC-ATTAAAAGG
1 GGGTATCGATAC-CTATTAAAA-G
*
68912 GGGTATCGATACCTATT-CAAG
1 GGGTATCGATACCTATTAAAAG
68933 GGGTATCGATACCTATTCAAAAG
1 GGGTATCGATACCTATT-AAAAG
*
68956 GGGTATCGATA-C-ATGTATAAG
1 GGGTATCGATACCTAT-TAAAAG
68977 GGGTATCGATAC
1 GGGTATCGATAC
68989 TTTATGCACA
Statistics
Matches: 69, Mismatches: 3, Indels: 11
0.83 0.04 0.13
Matches are distributed among these distances:
21 35 0.51
22 5 0.07
23 29 0.42
ACGTcount: A:0.33, C:0.15, G:0.26, T:0.26
Consensus pattern (22 bp):
GGGTATCGATACCTATTAAAAG
Found at i:68937 original size:21 final size:21
Alignment explanation
Indices: 68868--68988 Score: 106
Period size: 21 Copynumber: 5.6 Consensus size: 21
68858 AACCCGACAG
* *
68868 GGGGTATCGATA-CGA-TCAG
1 GGGGTATCGATACCTATTCAA
*
68887 GAGGGTATCGATACAC-ATTAAAA
1 G-GGGTATCGATAC-CTATT-CAA
68910 GGGGGTATCGATACCTATTCAA
1 -GGGGTATCGATACCTATTCAA
68932 GGGGTATCGATACCTATTCAAAA
1 GGGGTATCGATACCTATTC--AA
* *
68955 GGGGTATCGATACATGTAT-AA
1 GGGGTATCGATACCTAT-TCAA
68976 GGGGTATCGATAC
1 GGGGTATCGATAC
68989 TTTATGCACA
Statistics
Matches: 87, Mismatches: 5, Indels: 18
0.79 0.05 0.16
Matches are distributed among these distances:
19 1 0.01
20 11 0.13
21 35 0.40
22 5 0.06
23 33 0.38
24 2 0.02
ACGTcount: A:0.32, C:0.15, G:0.28, T:0.25
Consensus pattern (21 bp):
GGGGTATCGATACCTATTCAA
Found at i:68959 original size:44 final size:44
Alignment explanation
Indices: 68866--68988 Score: 139
Period size: 44 Copynumber: 2.8 Consensus size: 44
68856 TAAACCCGAC
* *
68866 AGGGGGTATCGATA-CGA-TCAGGAGGGTATCGATACACATTAAA
1 AGGGGGTATCGATACCTATTCAAG-GGGTATCGATACACATTAAA
68909 AGGGGGTATCGATACCTATTCAAGGGGTATCGATAC-CTATTCAAA
1 AGGGGGTATCGATACCTATTCAAGGGGTATCGATACAC-ATT-AAA
* *
68954 A-GGGGTATCGATACATGTAT-AAGGGGTATCGATAC
1 AGGGGGTATCGATACCTAT-TCAAGGGGTATCGATAC
68989 TTTATGCACA
Statistics
Matches: 71, Mismatches: 4, Indels: 9
0.85 0.05 0.11
Matches are distributed among these distances:
43 15 0.21
44 47 0.66
45 9 0.13
ACGTcount: A:0.33, C:0.15, G:0.28, T:0.24
Consensus pattern (44 bp):
AGGGGGTATCGATACCTATTCAAGGGGTATCGATACACATTAAA
Found at i:74591 original size:279 final size:279
Alignment explanation
Indices: 74055--74613 Score: 867
Period size: 279 Copynumber: 2.0 Consensus size: 279
74045 CTCTGGTACC
*
74055 AATTGTTGAGTTAATTGATCGACGAATCGGCCAAGAGGGGGTAAATTGGCAATAAAAATTTTGGT
1 AATTGTTGAGTTAATCGATCGACGAATCGGCCAAGAGGGGGTAAATTGGCAATAAAAATTTTGGT
* * * *
74120 GTAAGCTTTTGCATAAAATAAAAAGTAATTGCACAGCGATTTAGAGTGGTTCGACTTTCTCAACC
66 GGAAGCTTTTGCAGAAAATAAAAAGTAATTGCACAGCGATTTACAGTGGTTCGACTTTCTCAAAC
*
74185 AAAGTCTACGTCCTCTACCTTAGCTATCCACACTAAGGATTTTCCAACAAATTCACTAATTTGTT
131 AAAGTCTACGTCCACTACCTTAGCTATCCACACTAAGGATTTTCCAACAAATTCACTAATTTGTT
* * * *
74250 ATTTCTTTTAAGGACAAAGAGTAACCTTACAACTCCCTCAAGAATTATACCTCAATTCTTGAGCA
196 ATTTCTTTTAAGGACAAAGAGTAACCTTACAACTCCCTCAAGAAGTATACCCCAACTCTTGAGAA
74315 CACTC-TCTCCCAAAGAGA
261 CACTCTTCTCCCAAAGAGA
* *
74333 AATTGTTGAGTTAATCGAAT-GACGAAATTGGCCAAGAGGGGGGTGAATTGGCAATAAAAATTTT
1 AATTGTTGAGTTAATCG-ATCGACG-AATCGGCCAAGA-GGGGGTAAATTGGCAATAAAAATTTT
*
74397 -GTGGAAGCTTTTGCAGAAAATTGAAAA-TAATTGCACAGCGATTTACAGTGGTTCGACTTTCTC
63 GGTGGAAGCTTTTGCAGAAAA-TAAAAAGTAATTGCACAGCGATTTACAGTGGTTCGACTTTCTC
74460 AAACAAAGTCTACGTCCACTACCTTAGCTATCCACACTAAGGATTTTCCAACAAATTCACTAATT
127 AAACAAAGTCTACGTCCACTACCTTAGCTATCCACACTAAGGATTTTCCAACAAATTCACTAATT
* * * *
74525 TGTTCTTTCTTTTGAGGCCAAAGAGATAACCTTACAATTCCCTCAAG-AGTATACCCCAACTCTT
192 TGTTATTTCTTTTAAGGACAAAGAG-TAACCTTACAACTCCCTCAAGAAGTATACCCCAACTCTT
* *
74589 GAGAACACTCTTTTCTCAAAGAGA
256 GAGAACACTCTTCTCCCAAAGAGA
74613 A
1 A
74614 GATTACAAAT
Statistics
Matches: 256, Mismatches: 19, Indels: 10
0.90 0.07 0.04
Matches are distributed among these distances:
278 20 0.08
279 174 0.68
280 62 0.24
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (279 bp):
AATTGTTGAGTTAATCGATCGACGAATCGGCCAAGAGGGGGTAAATTGGCAATAAAAATTTTGGT
GGAAGCTTTTGCAGAAAATAAAAAGTAATTGCACAGCGATTTACAGTGGTTCGACTTTCTCAAAC
AAAGTCTACGTCCACTACCTTAGCTATCCACACTAAGGATTTTCCAACAAATTCACTAATTTGTT
ATTTCTTTTAAGGACAAAGAGTAACCTTACAACTCCCTCAAGAAGTATACCCCAACTCTTGAGAA
CACTCTTCTCCCAAAGAGA
Found at i:75148 original size:75 final size:75
Alignment explanation
Indices: 75059--75235 Score: 246
Period size: 75 Copynumber: 2.3 Consensus size: 75
75049 CCCCCTGGGG
* ** *
75059 TGGGGGAATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAACAAAAATGTTTAGGGGGGAATCA
1 TGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAACAAAAACATTCAGGGGGGAATCA
75124 GTTCCTCCTA
66 GTTCCTCCTA
* * * * *
75134 TGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAGCCAAACCATTCAGGGGGGAATCG
1 TGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAACAAAAACATTCAGGGGGGAATCA
75199 GTTCCTCCTA
66 GTTCCTCCTA
*
75209 TGGGGGGGAATCGGTTCCCTCTGAGCA
1 T--GGGGGAATCGGTTCCCTCCGAGCA
75236 ATCTGTAATT
Statistics
Matches: 90, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
75 67 0.74
77 23 0.26
ACGTcount: A:0.22, C:0.24, G:0.31, T:0.24
Consensus pattern (75 bp):
TGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAACAAAAACATTCAGGGGGGAATCA
GTTCCTCCTA
Found at i:75612 original size:19 final size:19
Alignment explanation
Indices: 75588--75626 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
75578 TGTTTTCATG
75588 TAAAACATTTAACACTTAT
1 TAAAACATTTAACACTTAT
75607 TAAAACATTTAACACTTAT
1 TAAAACATTTAACACTTAT
75626 T
1 T
75627 CTTCTCCCCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.46, C:0.15, G:0.00, T:0.38
Consensus pattern (19 bp):
TAAAACATTTAACACTTAT
Found at i:77896 original size:21 final size:21
Alignment explanation
Indices: 77870--77909 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
77860 CAGAACCCCA
*
77870 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
77891 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
77910 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:81800 original size:22 final size:21
Alignment explanation
Indices: 81758--81797 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
81748 GAGTTTGTTT
*
81758 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
81779 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
81798 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:83890 original size:75 final size:75
Alignment explanation
Indices: 83718--83920 Score: 264
Period size: 74 Copynumber: 2.7 Consensus size: 75
83708 GACCGTTGAA
* * ** * *
83718 CAGGGGGGAATCGGTACCCCCTGGGGGGGAATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAA
1 CAGGGGGGAATCGGTTCCTCCTATGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAA
**
83783 CAAAAATGTT
66 CAAAAACATT
* *
83793 TA-GGGGGAATCGGTTCCTCCTATGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAG
1 CAGGGGGGAATCGGTTCCTCCTATGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAA
* *
83857 CCAAACCATT
66 CAAAAACATT
* *
83867 CAGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCTGAGCAATCTG
1 CAGGGGGGAATCGGTTCCTCCTAT-GGGGGAATCGGTTCCCTCCGAGCATTCTG
83921 TAATTTTTGG
Statistics
Matches: 111, Mismatches: 15, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
74 62 0.56
75 22 0.20
76 27 0.24
ACGTcount: A:0.21, C:0.25, G:0.32, T:0.23
Consensus pattern (75 bp):
CAGGGGGGAATCGGTTCCTCCTATGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAA
CAAAAACATT
Found at i:84589 original size:21 final size:19
Alignment explanation
Indices: 84563--84637 Score: 80
Period size: 22 Copynumber: 3.7 Consensus size: 19
84553 ATATGTCTGA
84563 GGGTATCGGTACCTCCTGAGG
1 GGGTATCGGTACCT--TGAGG
84584 GGGTATCGGTACCATTGCATGG
1 GGGTATCGGTACC-TTG-A-GG
*
84606 GGGTATCGATACCTATG-GG
1 GGGTATCGGTACCT-TGAGG
84625 GGGTATCGGTACC
1 GGGTATCGGTACC
84638 ATCCCAGCAT
Statistics
Matches: 48, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
19 14 0.29
20 2 0.04
21 15 0.31
22 17 0.35
ACGTcount: A:0.17, C:0.20, G:0.37, T:0.25
Consensus pattern (19 bp):
GGGTATCGGTACCTTGAGG
Found at i:90024 original size:59 final size:60
Alignment explanation
Indices: 89932--90062 Score: 158
Period size: 59 Copynumber: 2.2 Consensus size: 60
89922 TATGATTCAG
* * * *
89932 TCCTTTAAATTTTTATTTATGCTATTGTAGTCCTTC-AAGTTTCTATTTTTGCTATTTTAG
1 TCCTTTAAGTTTTTATTTATGCTATTGTAGTCC-TCAAAGTTTCCATTTGTGCTATTTTAA
* * * * *
89992 TTCTTTAAGTTTTT-TTTTTGCTATTTTGGTCCTCAAAGTTTCCGTTTGTGCTATTTTAA
1 TCCTTTAAGTTTTTATTTATGCTATTGTAGTCCTCAAAGTTTCCATTTGTGCTATTTTAA
90051 TCCTTTAAGTTT
1 TCCTTTAAGTTT
90063 CTGTTAATCA
Statistics
Matches: 60, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
58 2 0.03
59 46 0.77
60 12 0.20
ACGTcount: A:0.18, C:0.14, G:0.11, T:0.57
Consensus pattern (60 bp):
TCCTTTAAGTTTTTATTTATGCTATTGTAGTCCTCAAAGTTTCCATTTGTGCTATTTTAA
Found at i:90063 original size:30 final size:30
Alignment explanation
Indices: 89930--90064 Score: 137
Period size: 30 Copynumber: 4.5 Consensus size: 30
89920 TTTATGATTC
* * * *
89930 AGTCCTTTAAATTTTTATTTATGCTATTGT
1 AGTCCTTTAAGTTTCTATTTTTGCTATTTT
*
89960 AGTCCTTCAAGTTTCTATTTTTGCTATTTT
1 AGTCCTTTAAGTTTCTATTTTTGCTATTTT
* *
89990 AGTTCTTTAAGTTT-TTTTTTTGCTATTTT
1 AGTCCTTTAAGTTTCTATTTTTGCTATTTT
* ** ** *
90019 GGTCCTCAAAGTTTCCGTTTGTGCTATTTT
1 AGTCCTTTAAGTTTCTATTTTTGCTATTTT
*
90049 AATCCTTTAAGTTTCT
1 AGTCCTTTAAGTTTCT
90065 GTTAATCATA
Statistics
Matches: 84, Mismatches: 20, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
29 24 0.29
30 60 0.71
ACGTcount: A:0.18, C:0.14, G:0.12, T:0.56
Consensus pattern (30 bp):
AGTCCTTTAAGTTTCTATTTTTGCTATTTT
Found at i:91314 original size:17 final size:17
Alignment explanation
Indices: 91288--91329 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
91278 TGCTTTACTC
*
91288 TCGTAAGAATTTATTAT
1 TCGTATGAATTTATTAT
91305 TCGTATGAATTTATTAT
1 TCGTATGAATTTATTAT
*
91322 TTGTATGA
1 TCGTATGA
91330 GTTTTATCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.31, C:0.05, G:0.14, T:0.50
Consensus pattern (17 bp):
TCGTATGAATTTATTAT
Found at i:92454 original size:21 final size:20
Alignment explanation
Indices: 92416--92455 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
92406 AATTAATATT
*
92416 TTTGCATATGCATTTGCATC
1 TTTGCATATGCATCTGCATC
*
92436 TTTGCATTTTGCATCTGCAT
1 TTTGCA-TATGCATCTGCAT
92456 TTCATTCGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.17, C:0.20, G:0.15, T:0.47
Consensus pattern (20 bp):
TTTGCATATGCATCTGCATC
Found at i:93760 original size:35 final size:36
Alignment explanation
Indices: 93712--93790 Score: 96
Period size: 35 Copynumber: 2.3 Consensus size: 36
93702 TGCGAAGATC
93712 AAATCAAA-A-CAAAT-AGA-AAAGAAGCGAAAGAAAA
1 AAATCAAAGAGCAAATAAGAGAAA-AAGC-AAAGAAAA
*
93746 AAA-CAAAGAGCAAATAAGAGAAAAATCAAAGAAAA
1 AAATCAAAGAGCAAATAAGAGAAAAAGCAAAGAAAA
93781 AAATCAAAGA
1 AAATCAAAGA
93791 AAAAGAACAA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
33 4 0.10
34 4 0.10
35 16 0.41
36 12 0.31
37 3 0.08
ACGTcount: A:0.71, C:0.09, G:0.14, T:0.06
Consensus pattern (36 bp):
AAATCAAAGAGCAAATAAGAGAAAAAGCAAAGAAAA
Found at i:93806 original size:14 final size:13
Alignment explanation
Indices: 93761--93794 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
93751 AAGAGCAAAT
*
93761 AAGAGAAAAATCA
1 AAGAAAAAAATCA
93774 AAGAAAAAAATCA
1 AAGAAAAAAATCA
93787 AAGAAAAA
1 AAGAAAAA
93795 GAACAAAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.76, C:0.06, G:0.12, T:0.06
Consensus pattern (13 bp):
AAGAAAAAAATCA
Found at i:95561 original size:134 final size:134
Alignment explanation
Indices: 95339--95652 Score: 441
Period size: 134 Copynumber: 2.3 Consensus size: 134
95329 TGGTGTATCA
*
95339 TCCTCATCACGTAAGAACCGTGTCATCCCCCGACCAGACCTCCTCATCACATAGGAGCCATGTCA
1 TCCTCATCACGTAAGAACCGTGTCATCCCCCGACCAAACCTCCTCATCACATAGGAGCCATGTCA
* *
95404 CCCCTAGATAACCAGTCGTCCTCATCACGTAGGAACTGTGTTATCACCCTTCCTAAAGATGGCAT
66 CCCCTAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCCTTCCTAAAGATGGCAT
95469 GTTG
131 GTTG
* * ** * *
95473 TCCTCATCACGTAGGAATCGTGTCATCCCCCGACCAAACCTCCTCATCATGTAGGAGTCGTGTCA
1 TCCTCATCACGTAAGAACCGTGTCATCCCCCGACCAAACCTCCTCATCACATAGGAGCCATGTCA
*
95538 CCCCTAGATAACCAGCCGTCCTCATCGCGTAGGAACCGTGTTATCACCCTTCCTAAAGATGGCCA
66 CCCCTAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCCTTCCTAAAGATGG-CA
***
95603 -GAAC
130 TGTTG
* * * * * *
95607 TCTTCATCACGTATGAGCCGTGTCATCCACCGACCATATCTCCTCA
1 TCCTCATCACGTAAGAACCGTGTCATCCCCCGACCAAACCTCCTCA
95653 CCAAGTAAGA
Statistics
Matches: 159, Mismatches: 20, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
134 157 0.99
135 2 0.01
ACGTcount: A:0.25, C:0.34, G:0.17, T:0.24
Consensus pattern (134 bp):
TCCTCATCACGTAAGAACCGTGTCATCCCCCGACCAAACCTCCTCATCACATAGGAGCCATGTCA
CCCCTAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCCTTCCTAAAGATGGCAT
GTTG
Found at i:95887 original size:3 final size:3
Alignment explanation
Indices: 95870--95906 Score: 58
Period size: 3 Copynumber: 12.3 Consensus size: 3
95860 TCTACAAAAA
95870 TAT TAAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
95907 TATATTGTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.06
3 27 0.84
4 3 0.09
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:97356 original size:30 final size:30
Alignment explanation
Indices: 97322--97498 Score: 132
Period size: 30 Copynumber: 6.0 Consensus size: 30
97312 TATGATTCAA
* *
97322 TCCTTTAAATTTTTGTTTGTTCTATTTTAG
1 TCCTTTAAATTTCTATTTGTTCTATTTTAG
* *
97352 TCCTTCAAGTTTCTATTT-TTGCTATTTTAG
1 TCCTTTAAATTTCTATTTGTT-CTATTTTAG
* * * *
97382 TCTTTTAAGTTTCTATTTTTTCTATTTTGG
1 TCCTTTAAATTTCTATTTGTTCTATTTTAG
* * *
97412 T-CATCAAAGTTTCTATTTGTGCTATTTTAG
1 TCCTTTAAA-TTTCTATTTGTTCTATTTTAG
* ** *
97442 TCCTTTAAGTTT-T-TGTTAATCATATTATAG
1 TCCTTTAAATTTCTAT-TTGTTC-TATTTTAG
*
97472 TCCTTTAAATTT-TA-TTGCTCTATTTTA
1 TCCTTTAAATTTCTATTTGTTCTATTTTA
97499 ATCCCTTATA
Statistics
Matches: 115, Mismatches: 25, Indels: 16
0.74 0.16 0.10
Matches are distributed among these distances:
28 7 0.06
29 13 0.11
30 89 0.77
31 6 0.05
ACGTcount: A:0.20, C:0.12, G:0.10, T:0.58
Consensus pattern (30 bp):
TCCTTTAAATTTCTATTTGTTCTATTTTAG
Found at i:97405 original size:60 final size:60
Alignment explanation
Indices: 97322--97453 Score: 176
Period size: 60 Copynumber: 2.2 Consensus size: 60
97312 TATGATTCAA
* * * * * *
97322 TCCTTTAAATTTTTGTTTGTTCTATTTTAGTCCTTC-AAGTTTCTATTTTTGCTATTTTAG
1 TCCTTTAAGTTTCTATTTTTTCTATTTTAGT-CATCAAAGTTTCTATTTGTGCTATTTTAG
* *
97382 TCTTTTAAGTTTCTATTTTTTCTATTTTGGTCATCAAAGTTTCTATTTGTGCTATTTTAG
1 TCCTTTAAGTTTCTATTTTTTCTATTTTAGTCATCAAAGTTTCTATTTGTGCTATTTTAG
97442 TCCTTTAAGTTT
1 TCCTTTAAGTTT
97454 TTGTTAATCA
Statistics
Matches: 62, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
59 3 0.05
60 59 0.95
ACGTcount: A:0.17, C:0.13, G:0.11, T:0.59
Consensus pattern (60 bp):
TCCTTTAAGTTTCTATTTTTTCTATTTTAGTCATCAAAGTTTCTATTTGTGCTATTTTAG
Found at i:103297 original size:24 final size:24
Alignment explanation
Indices: 103243--103297 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
103233 CTACTACTGG
* * *
103243 TGTCTCCTCTCAACAAGAACAGTT
1 TGTCTCTTCTCAACAAGAACAATC
*
103267 TGCCTCTTCTCAACAAGAACAATC
1 TGTCTCTTCTCAACAAGAACAATC
103291 TGTCTCT
1 TGTCTCT
103298 ACTGAGCAAG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.27, C:0.31, G:0.11, T:0.31
Consensus pattern (24 bp):
TGTCTCTTCTCAACAAGAACAATC
Found at i:105669 original size:18 final size:21
Alignment explanation
Indices: 105652--105695 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 21
105642 CTTTAAATTT
105652 TTTC-ATATTT-ATTTATTTA
1 TTTCAATATTTCATTTATTTA
105671 TTTCAAATATTTCATTTATTTA
1 TTTC-AATATTTCATTTATTTA
105693 TTT
1 TTT
105696 TACATACCCT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 4 0.18
21 6 0.27
22 12 0.55
ACGTcount: A:0.27, C:0.07, G:0.00, T:0.66
Consensus pattern (21 bp):
TTTCAATATTTCATTTATTTA
Found at i:105876 original size:26 final size:24
Alignment explanation
Indices: 105831--105878 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 24
105821 AAAATATTCA
**
105831 AATTTTTTTATTTTTTGTATCACT
1 AATTTTTTTATTTTCAGTATCACT
105855 AATTTATTTTATTTTACAGTATCA
1 AATTT-TTTTATTTT-CAGTATCA
105879 AATACCCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 5 0.25
25 9 0.45
26 6 0.30
ACGTcount: A:0.27, C:0.08, G:0.04, T:0.60
Consensus pattern (24 bp):
AATTTTTTTATTTTCAGTATCACT
Found at i:109615 original size:62 final size:63
Alignment explanation
Indices: 109548--109667 Score: 158
Period size: 62 Copynumber: 1.9 Consensus size: 63
109538 TAACATTATC
*
109548 TTTTAAATTTAAAATATT-AAATAG-ATATATATT-CCTTTTATTATTCAAA-TTAAAAAATATT
1 TTTT-AATTTAAAATATTCAAA-AGTATATA-ATTACCTTTTAATATTCAAAGTTAAAAAATATT
109609 A
63 A
* *
109610 TTTTAATTTTAAATATTCAAAAGTATATAATTATCTTTTAATATTCAAAGTTAAAAAA
1 TTTTAATTTAAAATATTCAAAAGTATATAATTACCTTTTAATATTCAAAGTTAAAAAA
109668 ACAACACATA
Statistics
Matches: 51, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
61 17 0.33
62 26 0.51
63 8 0.16
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.46
Consensus pattern (63 bp):
TTTTAATTTAAAATATTCAAAAGTATATAATTACCTTTTAATATTCAAAGTTAAAAAATATTA
Found at i:122022 original size:12 final size:12
Alignment explanation
Indices: 122005--122029 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
121995 CATGTACTAA
122005 CTTGTTTCATTT
1 CTTGTTTCATTT
122017 CTTGTTTCATTT
1 CTTGTTTCATTT
122029 C
1 C
122030 ATTTTGATAT
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:0.08, C:0.20, G:0.08, T:0.64
Consensus pattern (12 bp):
CTTGTTTCATTT
Done.