Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002284.1 Hibiscus syriacus cultivar Beakdansim tig00004648_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: 59683
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:2551 original size:28 final size:28
Alignment explanation
Indices: 2499--2567 Score: 131
Period size: 28 Copynumber: 2.5 Consensus size: 28
2489 CCCATCTTTA
2499 TAAGGTTTAGAG-TAATGTGATAGGATT
1 TAAGGTTTAGAGTTAATGTGATAGGATT
2526 TAAGGTTTAGAGTTAATGTGATAGGATT
1 TAAGGTTTAGAGTTAATGTGATAGGATT
2554 TAAGGTTTAGAGTT
1 TAAGGTTTAGAGTT
2568 TAGGATTTAT
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
27 12 0.29
28 29 0.71
ACGTcount: A:0.32, C:0.00, G:0.29, T:0.39
Consensus pattern (28 bp):
TAAGGTTTAGAGTTAATGTGATAGGATT
Found at i:2621 original size:26 final size:25
Alignment explanation
Indices: 2582--2631 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
2572 ATTTATGTAA
* * *
2582 TAAGGTTTAGGGTTTAGGGTTATGTT
1 TAAGGTATAAGGTTTA-AGTTATGTT
2608 TAAGGTATAAGGTTTAAGTTATGT
1 TAAGGTATAAGGTTTAAGTTATGT
2632 ACATGAATGT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 7 0.33
26 14 0.67
ACGTcount: A:0.26, C:0.00, G:0.30, T:0.44
Consensus pattern (25 bp):
TAAGGTATAAGGTTTAAGTTATGTT
Found at i:10064 original size:21 final size:21
Alignment explanation
Indices: 10022--10064 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
10012 TTTCTCGGCT
* *
10022 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
*
10043 AGGGGAATCGATACCCCCTCA
1 AGGGGAATCGATACCCACTCA
10064 A
1 A
10065 ACGAACCAGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:10137 original size:23 final size:22
Alignment explanation
Indices: 10093--10137 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
10083 AATCTCATAG
* *
10093 GGGAACTGATTCCCCCACAGGA
1 GGGAACCGATTCCCCCAAAGGA
10115 GGGAACCGATTCCCCCTAAAGGA
1 GGGAACCGATTCCCCC-AAAGGA
10138 AAATTATGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.29, C:0.31, G:0.27, T:0.13
Consensus pattern (22 bp):
GGGAACCGATTCCCCCAAAGGA
Found at i:11645 original size:103 final size:103
Alignment explanation
Indices: 11426--11646 Score: 361
Period size: 103 Copynumber: 2.1 Consensus size: 103
11416 GGGTCTACGC
*
11426 GGTCCTTGGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
1 GGTCCTTAGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
* *
11491 CCTTGGCATATGTATATGATTCTTAAGGAATGATATGT
66 CCCTAGCATATGTATATGATTCTTAAGGAATGATATGT
* * * *
11529 GGTTCTTCGGGACATATATGTATTTTTTGGAACATGTGTGAAGTCTGGTGAGACATATACTTGAT
1 GGTCCTTAGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
*
11594 CCCTAGTATATGTATATGATTCTTAAGGAATGATATGT
66 CCCTAGCATATGTATATGATTCTTAAGGAATGATATGT
*
11632 GGTCCTTATGGACAT
1 GGTCCTTAGGGACAT
11647 TATTATATGG
Statistics
Matches: 108, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
103 108 1.00
ACGTcount: A:0.26, C:0.12, G:0.24, T:0.37
Consensus pattern (103 bp):
GGTCCTTAGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
CCCTAGCATATGTATATGATTCTTAAGGAATGATATGT
Found at i:11690 original size:23 final size:23
Alignment explanation
Indices: 11655--11722 Score: 77
Period size: 23 Copynumber: 3.0 Consensus size: 23
11645 ATTATTATAT
11655 GGCACTACT-GTGCAATTCTACGC
1 GGCACT-CTGGTGCAATTCTACGC
**
11678 GGCACTCTGGTGCAATTCTACAT
1 GGCACTCTGGTGCAATTCTACGC
*
11701 GGCACT-TCGGTGCAATTATACG
1 GGCACTCT-GGTGCAATTCTACG
11723 AGCTGTGGTG
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
22 3 0.08
23 36 0.92
ACGTcount: A:0.22, C:0.26, G:0.24, T:0.28
Consensus pattern (23 bp):
GGCACTCTGGTGCAATTCTACGC
Found at i:18472 original size:2 final size:2
Alignment explanation
Indices: 18467--18511 Score: 65
Period size: 2 Copynumber: 23.0 Consensus size: 2
18457 ACACACACAC
* *
18467 AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT A- AC 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
18508 AT AT
1 AT AT
18512 TTATGAAGGG
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:18601 original size:14 final size:14
Alignment explanation
Indices: 18582--18609 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
18572 TAAGCAAGTA
18582 AAAAAGTAAAAGAT
1 AAAAAGTAAAAGAT
18596 AAAAAGTAAAAGAT
1 AAAAAGTAAAAGAT
18610 GCACAAGTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.71, C:0.00, G:0.14, T:0.14
Consensus pattern (14 bp):
AAAAAGTAAAAGAT
Found at i:23048 original size:37 final size:37
Alignment explanation
Indices: 23007--23119 Score: 167
Period size: 37 Copynumber: 3.1 Consensus size: 37
22997 AACATAACGT
23007 TAGAGTTTTACTAGTATTCAAACTCCTAAAAATATGA
1 TAGAGTTTTACTAGTATTCAAACTCCTAAAAATATGA
23044 TAGAGTTTTACTA-TGATTCAAACTCCTAAAAATATGA
1 TAGAGTTTTACTAGT-ATTCAAACTCCTAAAAATATGA
* * *
23081 TTGAGTTTTACTAAG-ATTCAAACTTCTAAAAATAGGA
1 TAGAGTTTTACT-AGTATTCAAACTCCTAAAAATATGA
23118 TA
1 TA
23120 CATAAGCATT
Statistics
Matches: 69, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
36 1 0.01
37 67 0.97
38 1 0.01
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.35
Consensus pattern (37 bp):
TAGAGTTTTACTAGTATTCAAACTCCTAAAAATATGA
Found at i:23536 original size:28 final size:26
Alignment explanation
Indices: 23487--23567 Score: 78
Period size: 28 Copynumber: 3.1 Consensus size: 26
23477 TTCTTTACTA
*
23487 TTATTATTATATATACTTTATTATTATT
1 TTATT-TT-TATATAATTTATTATTATT
*
23515 ATTATCTTTTATATATTTTATT-TT-TT
1 -TTAT-TTTTATATAATTTATTATTATT
*
23541 TTATTTTT-TTTAATTTATTATTATT
1 TTATTTTTATATAATTTATTATTATT
23566 TT
1 TT
23568 TTAAAACATT
Statistics
Matches: 46, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
23 9 0.20
24 6 0.13
25 8 0.17
26 2 0.04
27 2 0.04
28 12 0.26
29 6 0.13
30 1 0.02
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (26 bp):
TTATTTTTATATAATTTATTATTATT
Found at i:23964 original size:21 final size:22
Alignment explanation
Indices: 23935--23987 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
23925 ATTCTAACTA
23935 TCGCATTGCGATTTTCC-AAAT
1 TCGCATTGCGATTTTCCTAAAT
*
23956 TCGCGTTGCGATTTTCCTAAA-
1 TCGCATTGCGATTTTCCTAAAT
*
23977 TCGCAATGCGA
1 TCGCATTGCGA
23988 ATACGTAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 25 0.89
22 3 0.11
ACGTcount: A:0.23, C:0.25, G:0.19, T:0.34
Consensus pattern (22 bp):
TCGCATTGCGATTTTCCTAAAT
Found at i:23998 original size:20 final size:20
Alignment explanation
Indices: 23973--24067 Score: 147
Period size: 20 Copynumber: 4.8 Consensus size: 20
23963 GCGATTTTCC
23973 TAAATCGCAATGCGAATACG
1 TAAATCGCAATGCGAATACG
23993 TAAATCGCAATGCGAATACG
1 TAAATCGCAATGCGAATACG
24013 TAAATCGCAATGCGAATACG
1 TAAATCGCAATGCGAATACG
* *
24033 TAAATCGCAACGCGAAT-CT
1 TAAATCGCAATGCGAATACG
*
24052 TACTATCGCAATGCGA
1 TA-AATCGCAATGCGA
24068 TTTACATAGC
Statistics
Matches: 70, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
19 3 0.04
20 67 0.96
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.21
Consensus pattern (20 bp):
TAAATCGCAATGCGAATACG
Found at i:24270 original size:22 final size:22
Alignment explanation
Indices: 24245--24310 Score: 105
Period size: 22 Copynumber: 3.0 Consensus size: 22
24235 GGCGACATTT
24245 GTCCCCATCTCCGACGAAATCA
1 GTCCCCATCTCCGACGAAATCA
*
24267 GTCCCCATCTCCGACGATATCA
1 GTCCCCATCTCCGACGAAATCA
* *
24289 GTCTCCATCTCCGGCGAAATCA
1 GTCCCCATCTCCGACGAAATCA
24311 TTCACGGTCA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.24, C:0.39, G:0.15, T:0.21
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCA
Found at i:24706 original size:20 final size:20
Alignment explanation
Indices: 24681--24727 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
24671 GATTCTTGCA
24681 TTGCGATAGTCAAATTCGCG
1 TTGCGATAGTCAAATTCGCG
** *
24701 TTGCGATAGTCATTTTCGTG
1 TTGCGATAGTCAAATTCGCG
24721 TTGCGAT
1 TTGCGAT
24728 TTTCATTTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.19, C:0.17, G:0.26, T:0.38
Consensus pattern (20 bp):
TTGCGATAGTCAAATTCGCG
Found at i:24733 original size:20 final size:20
Alignment explanation
Indices: 24695--24749 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
24685 GATAGTCAAA
* **
24695 TTCGCGTTGCGATAGTCATT
1 TTCGTGTTGCGATTTTCATT
24715 TTCGTGTTGCGATTTTCATT
1 TTCGTGTTGCGATTTTCATT
24735 TTCGTGTTGCGATTT
1 TTCGTGTTGCGATTT
24750 AAAGTTTCAG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.11, C:0.16, G:0.24, T:0.49
Consensus pattern (20 bp):
TTCGTGTTGCGATTTTCATT
Found at i:24757 original size:20 final size:20
Alignment explanation
Indices: 24714--24757 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
24704 CGATAGTCAT
** *
24714 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTAAAG
24734 TTTCGTGTTGCGATTTAAAG
1 TTTCGTGTTGCGATTTAAAG
24754 TTTC
1 TTTC
24758 AGAAACTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.14, C:0.14, G:0.20, T:0.52
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTAAAG
Found at i:26645 original size:20 final size:20
Alignment explanation
Indices: 26620--26671 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
26610 ATAATAGTTT
*
26620 ACTATCGCAATGCGAAAATG
1 ACTATCGCAACGCGAAAATG
26640 ACTATCGCAACGCGAAAATG
1 ACTATCGCAACGCGAAAATG
26660 ACTATCGCAACG
1 ACTATCGCAACG
26672 AGAGAATCGC
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:0.38, C:0.25, G:0.19, T:0.17
Consensus pattern (20 bp):
ACTATCGCAACGCGAAAATG
Found at i:26735 original size:20 final size:20
Alignment explanation
Indices: 26710--26758 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
26700 CAACAACAAA
26710 ATCGCAACGCAAAAATGACT
1 ATCGCAACGCAAAAATGACT
* * **
26730 ATCGCAATGCGAATTTGACT
1 ATCGCAACGCAAAAATGACT
26750 ATCGCAACG
1 ATCGCAACG
26759 AAAGAATCGC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.37, C:0.24, G:0.18, T:0.20
Consensus pattern (20 bp):
ATCGCAACGCAAAAATGACT
Found at i:26769 original size:87 final size:87
Alignment explanation
Indices: 26623--26788 Score: 269
Period size: 87 Copynumber: 1.9 Consensus size: 87
26613 ATAGTTTACT
* * * *
26623 ATCGCAATGCGAAAATGACTATCGCAACGCGAAAATGACTATCGCAACGAGAGAATCGCAATGTG
1 ATCGCAACGCAAAAATGACTATCGCAACGCGAAAATGACTATCGCAACGAAAGAATCGCAATGCG
26688 AAATGAAAATCGCAACAACAAA
66 AAATGAAAATCGCAACAACAAA
* **
26710 ATCGCAACGCAAAAATGACTATCGCAATGCGAATTTGACTATCGCAACGAAAGAATCGCAATGCG
1 ATCGCAACGCAAAAATGACTATCGCAACGCGAAAATGACTATCGCAACGAAAGAATCGCAATGCG
26775 AAATGAAAATCGCA
66 AAATGAAAATCGCA
26789 TTGCGATAGT
Statistics
Matches: 72, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
87 72 1.00
ACGTcount: A:0.43, C:0.21, G:0.19, T:0.16
Consensus pattern (87 bp):
ATCGCAACGCAAAAATGACTATCGCAACGCGAAAATGACTATCGCAACGAAAGAATCGCAATGCG
AAATGAAAATCGCAACAACAAA
Found at i:27360 original size:18 final size:19
Alignment explanation
Indices: 27321--27362 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 19
27311 CTCACCTGTC
27321 ATCGTTCAAGAGGCCTCCCCT
1 ATCGTTCAAGAGG-C-CCCCT
27342 ATCGTTCAAGAGG-CCCCT
1 ATCGTTCAAGAGGCCCCCT
27360 ATC
1 ATC
27363 ATCCCTCAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
21 13 0.62
ACGTcount: A:0.21, C:0.36, G:0.19, T:0.24
Consensus pattern (19 bp):
ATCGTTCAAGAGGCCCCCT
Found at i:29079 original size:33 final size:34
Alignment explanation
Indices: 29022--29117 Score: 140
Period size: 33 Copynumber: 2.9 Consensus size: 34
29012 ACTAAATTGG
29022 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
* *
29056 CGTTGTGATTTTCA-TTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
** *
29089 CGTTGCGATAGTCATTTTCGCGTTGCGAT
1 CGTTGCGATTTTCATTTTCGCATTGCGAT
29118 AGTCAATTCC
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
33 29 0.53
34 26 0.47
ACGTcount: A:0.14, C:0.22, G:0.21, T:0.44
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
Found at i:29114 original size:20 final size:20
Alignment explanation
Indices: 29089--29196 Score: 122
Period size: 20 Copynumber: 5.7 Consensus size: 20
29079 GCGATTCTCT
*
29089 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTCCG
* *
29109 CGTTGCGATAGTCAATTCCA
1 CGTTGCGATAGTCATTTCCG
29129 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
29149 TGTTGCGATAGTCATATT-CG
1 CGTTGCGATAGTCAT-TTCCG
29169 CGTT--G-T-G--ATTTCCG
1 CGTTGCGATAGTCATTTCCG
29183 CGTTGCGATAGTCA
1 CGTTGCGATAGTCA
29197 AATGAATGTC
Statistics
Matches: 73, Mismatches: 7, Indels: 16
0.76 0.07 0.17
Matches are distributed among these distances:
13 2 0.03
14 8 0.11
16 2 0.03
17 2 0.03
18 2 0.03
20 55 0.75
21 2 0.03
ACGTcount: A:0.18, C:0.21, G:0.25, T:0.36
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:31639 original size:24 final size:24
Alignment explanation
Indices: 31600--31677 Score: 129
Period size: 24 Copynumber: 3.2 Consensus size: 24
31590 CTGAAAAATC
* *
31600 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGGGTATTGACCAAG
*
31624 ATCAAAGTCTGGGTATTGACCAAG
1 ATCAAAGTCCGGGTATTGACCAAG
31648 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGGGTATTGACCAAG
31672 ATCAAA
1 ATCAAA
31678 TTTCAAATAC
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 50 1.00
ACGTcount: A:0.38, C:0.19, G:0.21, T:0.22
Consensus pattern (24 bp):
ATCAAAGTCCGGGTATTGACCAAG
Found at i:32541 original size:20 final size:20
Alignment explanation
Indices: 32516--32582 Score: 116
Period size: 20 Copynumber: 3.4 Consensus size: 20
32506 AAATTCAGTA
32516 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCTCG
32536 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCTCG
* *
32556 TTGCGATAGTCAGATTCGCG
1 TTGCGATAGTCAGAATCTCG
32576 TTGCGAT
1 TTGCGAT
32583 TTACATATTC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.22, C:0.19, G:0.27, T:0.31
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCTCG
Found at i:32592 original size:20 final size:20
Alignment explanation
Indices: 32569--32621 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
32559 CGATAGTCAG
32569 ATTCGCGTTGCGATTTACAT
1 ATTCGCGTTGCGATTTACAT
* *
32589 ATTCGTGTTGCGATTTACGT
1 ATTCGCGTTGCGATTTACAT
*
32609 ATTCGCATTGCGA
1 ATTCGCGTTGCGA
32622 ATTAGGAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.40
Consensus pattern (20 bp):
ATTCGCGTTGCGATTTACAT
Found at i:32642 original size:21 final size:21
Alignment explanation
Indices: 32618--32663 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
32608 TATTCGCATT
32618 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* * *
32639 GCGAATTTGGAAAATTGCAAT
1 GCGAATTAGGAAAATCGCAAC
32660 GCGA
1 GCGA
32664 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:0.39, C:0.15, G:0.26, T:0.20
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:32982 original size:17 final size:19
Alignment explanation
Indices: 32944--32983 Score: 57
Period size: 17 Copynumber: 2.2 Consensus size: 19
32934 CTATTTCTTT
*
32944 TTTATTTTTATTCATTATC
1 TTTATTTTTATTCATCATC
32963 TTTATTTTT-TT-ATCATC
1 TTTATTTTTATTCATCATC
32980 TTTA
1 TTTA
32984 CATTTGTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 9 0.45
18 2 0.10
19 9 0.45
ACGTcount: A:0.20, C:0.10, G:0.00, T:0.70
Consensus pattern (19 bp):
TTTATTTTTATTCATCATC
Found at i:33926 original size:17 final size:17
Alignment explanation
Indices: 33904--33940 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
33894 TAATGGGCTT
*
33904 AGGACTAAGGGTTTGGC
1 AGGACTAAGGGTTTCGC
33921 AGGACTAAGGGTTTCGC
1 AGGACTAAGGGTTTCGC
33938 AGG
1 AGG
33941 CCCAAGGGGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.24, C:0.14, G:0.41, T:0.22
Consensus pattern (17 bp):
AGGACTAAGGGTTTCGC
Found at i:33947 original size:17 final size:17
Alignment explanation
Indices: 33904--33948 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
33894 TAATGGGCTT
* *
33904 AGGACTAAGGGTTTGGC
1 AGGACCAAGGGTTTCGC
*
33921 AGGACTAAGGGTTTCGC
1 AGGACCAAGGGTTTCGC
*
33938 AGGCCCAAGGG
1 AGGACCAAGGG
33949 GGCACCAGCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.24, C:0.18, G:0.40, T:0.18
Consensus pattern (17 bp):
AGGACCAAGGGTTTCGC
Found at i:37137 original size:95 final size:96
Alignment explanation
Indices: 36965--37212 Score: 294
Period size: 95 Copynumber: 2.7 Consensus size: 96
36955 AGATTATAAT
* *
36965 ATTATATATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGTTTTA
1 ATTATATATATACAATAAAGCTTGAGCTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTA
* *
37030 TGGATAATATTCAGCTAGCCTGATAAAGGTG
66 TGGATAAGATTCAGCTAACCTGATAAAGGTG
* *
37061 ATTATA-ATATACAATAAAGCTTGAGCTGTCCCTCTA-AGGCAATTGGTTAAACTCCTCGGCTTT
1 ATTATATATATACAATAAAGCTTGAGCTGTCCCTCTAGA-GCAATTGGTTAAACGCCCCGGCTTT
37124 ATGGATAAGATTCAGCTAACCTGATACAA-GTG
65 ATGGATAAGATTCAGCTAACCTGATA-AAGGTG
* *
37156 ------T-T-TAC-AT--A--TTGAGTTATCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTA
1 ATTATATATATACAATAAAGCTTGAGCTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTA
37208 TGGAT
66 TGGAT
37213 TCAGCTAGCC
Statistics
Matches: 138, Mismatches: 10, Indels: 21
0.82 0.06 0.12
Matches are distributed among these distances:
83 43 0.31
84 1 0.01
85 1 0.01
87 2 0.01
88 3 0.02
89 1 0.01
94 1 0.01
95 78 0.57
96 8 0.06
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (96 bp):
ATTATATATATACAATAAAGCTTGAGCTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTA
TGGATAAGATTCAGCTAACCTGATAAAGGTG
Found at i:38511 original size:84 final size:84
Alignment explanation
Indices: 38369--39395 Score: 931
Period size: 84 Copynumber: 12.4 Consensus size: 84
38359 TCAGTCAGTC
* * **
38369 AAGACCTTCGAGTTCGACTGCGCTCAGCTCCAAGGCATATCATTTTAAGCATAACTTAAGTCGAG
1 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAG
*
38434 AAGGGTTATCTGCCAATAA
66 AAGGGTTATCTGCCAACAA
* * *
38453 AAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCATTTGTAGCATAGCTTAAGTCGAG
1 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAG
38518 AAGGGTTATCTGCC-A-AA
66 AAGGGTTATCTGCCAACAA
* * * * * * * * * *
38535 AA-ACC-TCGAGTTCGATTACACTCAGCTTCGAGGGTACATCATTTACAACATAACTCAAGGCTA
1 AAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTGCAGCATAACTTAAGTCGA
* ** * *
38598 GAAGGGTTATCGGTGACCGA
65 GAAGGGTTATCTGCCAACAA
* * * *
38618 AAGACCTTCGAGTTCGACTACGCTCAACTCCAAGGCATATCATTTTGTAGCATAACTTAAGTTGA
1 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCA-TTTGCAGCATAACTTAAGTCGA
*
38683 GAAGGGTTATCTGCCAACCA
65 GAAGGGTTATCTGCCAACAA
* * * *
38703 AAGACCTTCGAGTTTGACTACGATCAACTCCAAGGCACATCATTTACAGCATAACTTAAGTCGAG
1 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAG
38768 AAGGGTTATCTG-C--C-A
66 AAGGGTTATCTGCCAACAA
* * * * * * * * * * * *
38783 AAGACCCTCGAGTTCAATTACACTCAGATTCGAGGGCACATCATTTACATCATAACTCAAGGCTA
1 AAGACCTTCGAGTTCGACTACGCTCAG-CTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGA
* ** *
38848 GAAGGGTTATATGTGACCAA
65 GAAGGGTTATCTGCCAACAA
* *
38868 AAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTCGAG
1 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAG
*
38933 AAGGGTTATCTGCCAACCA
66 AAGGGTTATCTGCCAACAA
* * *
38952 AAGACCTTCGAGTTCGACTATGATCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAG
1 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAG
* *
39017 AAGGGCTATCT----ACCA
66 AAGGGTTATCTGCCAACAA
* * * ** * * * * * * *
39032 AAGACCCTCGAGTTCAATTACATTCAGCTTCGAGGGCATATCATTTACAACATAACTCAATGT-T
1 AAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTGCAGCATAACTTAA-GTCG
* ** *
39096 AGAAGGGCTATCTGTGACCAA
64 AGAAGGGTTATCTGCCAACAA
* * * *
39117 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAATGCGCATCATTTGCAACGTAACTTAAGTCGAG
1 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAG
* *
39182 AATGGCTATCTG-C--C-A
66 AAGGGTTATCTGCCAACAA
* * * * * * * * *
39197 AAGATCCTT-GAGTTCGATTACACTCAACTTCGACGGCGCATCATTTACAACATAA-TTCAAGGC
1 AAGA-CCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTGCAGCATAACTT-AAGTC
* ** * * *
39260 TAGAATAGTTATTTGTCACCAA
63 GAGAAGGGTTATCTGCCAACAA
* * * *
39282 AAGACCTTCGAGTTCGACTACGCTAAGCTCCAAGGCACATCTTTTGCAGTATAACTTAAGTCGAT
1 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAG
* **
39347 AAGGGCTATCTGCCAACCG
66 AAGGGTTATCTGCCAACAA
* *
39366 AAGACCTTCGAGTTCGATTACACTCAGCTC
1 AAGACCTTCGAGTTCGACTACGCTCAGCTC
39396 AGAGGCAAAT
Statistics
Matches: 756, Mismatches: 160, Indels: 54
0.78 0.16 0.06
Matches are distributed among these distances:
80 88 0.12
81 162 0.21
82 7 0.01
83 7 0.01
84 335 0.44
85 157 0.21
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (84 bp):
AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAG
AAGGGTTATCTGCCAACAA
Found at i:38651 original size:165 final size:165
Alignment explanation
Indices: 38372--39428 Score: 918
Period size: 165 Copynumber: 6.4 Consensus size: 165
38362 GTCAGTCAAG
* * * * * * * * *
38372 ACCTTCGAGTTCGACTGCGCTCAGC-TCCAAGGCATATCATTTTA-AGCATAACTTAAGTCGAGA
1 ACCTTCGAGTTCGATTACACTCAGCTTCGAAGGCACATCA-TTTACAACATAACTCAAGGCTAGA
*** ** * * *
38435 AGGGTTATCTGCCAATAAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCATTTGT
65 AGGGTTATC-GGTGACCAAAGACCTTCGAGTTCGACTACGCTCAACTCCAAGGCACATCATTTGC
* *
38500 AGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAAAAA
129 AGCATAACTTAAGTCGAGAAGGGCTATCTGCCAAAAA
* *
38537 ACC-TCGAGTTCGATTACACTCAGCTTCGAGGGTACATCATTTACAACATAACTCAAGGCTAGAA
1 ACCTTCGAGTTCGATTACACTCAGCTTCGAAGGCACATCATTTACAACATAACTCAAGGCTAGAA
* *
38601 GGGTTATCGGTGACCGAAAGACCTTCGAGTTCGACTACGCTCAACTCCAAGGCATATCATTTTGT
66 GGGTTATCGGTGACC-AAAGACCTTCGAGTTCGACTACGCTCAACTCCAAGGCACATCA-TTTGC
* *
38666 AGCATAACTTAAGTTGAGAAGGGTTATCTGCCAACCAAA
129 AGCATAACTTAAGTCGAGAAGGGCTATCTGCCAA--AAA
* * * * * * * *
38705 GACCTTCGAGTTTGACTACGA-TCAAC-TCCAAGGCACATCATTTACAGCATAACTTAAGTCGAG
1 -ACCTTCGAGTTCGATTAC-ACTCAGCTTCGAAGGCACATCATTTACAACATAACTCAAGGCTAG
* * * * * * * *
38768 AAGGGTTATC--TG-CCAAAGACCCTCGAGTTCAATTACACTCAGATTCGAGGGCACATCATTTA
64 AAGGGTTATCGGTGACCAAAGACCTTCGAGTTCGACTACGCTCA-ACTCCAAGGCACATCATTTG
* * * * * * *
38830 CATCATAACTCAAGGCTAGAAGGGTTATATGTGACCAAAAG
128 CAGCATAACTTAAGTCGAGAAGGG--CTATCTG-CCAAAAA
* * * * * * * * * *
38871 ACCTTCGAGTTTGACTACGCTCAGC-TCCAAGGCATATCATTTGCAGCATAACTTAAGTCGAGAA
1 ACCTTCGAGTTCGATTACACTCAGCTTCGAAGGCACATCATTTACAACATAACTCAAGGCTAGAA
*** * * *
38935 GGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTATGATCAGCTCCAAGGCACATCATTTGCA
66 GGGTTATC-GGTGACCAAAGACCTTCGAGTTCGACTACGCTCAACTCCAAGGCACATCATTTGCA
* * *
39000 GCATAGCTTAAGTCGAGAAGGGCTATCTACC-AAAG
130 GCATAACTTAAGTCGAGAAGGGCTATCTGCCAAAAA
* * * * * * *
39035 ACCCTCGAGTTCAATTACATTCAGCTTCGAGGGCATATCATTTACAACATAACTCAATGTTAGAA
1 ACCTTCGAGTTCGATTACACTCAGCTTCGAAGGCACATCATTTACAACATAACTCAAGGCTAGAA
* * * * *
39100 GGGCTATCTGTGACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAATGCGCATCATTTGCA
66 GGGTTATCGGTGACC-AAAGACCTTCGAGTTCGACTACGCTCAACTCCAAGGCACATCATTTGCA
* * * *
39165 ACGTAACTTAAGTCGAGAATGGCTATCTGCCAAAGA
130 GCATAACTTAAGTCGAGAAGGGCTATCTGCCAAAAA
* * * * *
39201 TCCTT-GAGTTCGATTACACTCAACTTCGACGGCGCATCATTTACAACATAATTCAAGGCTAGAA
1 ACCTTCGAGTTCGATTACACTCAGCTTCGAAGGCACATCATTTACAACATAACTCAAGGCTAGAA
** ** * *
39265 TAGTTATTTGTCACCAAAAGACCTTCGAGTTCGACTACGCT-AAGCTCCAAGGCACATCTTTTGC
66 GGGTTATCGGTGACC-AAAGACCTTCGAGTTCGACTACGCTCAA-CTCCAAGGCACATCATTTGC
* * *
39329 AGTATAACTTAAGTCGATAAGGGCTATCTGCCAACCGAAG
129 AGCATAACTTAAGTCGAGAAGGGCTATCTGCCAA---AAA
* * *
39369 ACCTTCGAGTTCGATTACACTCAGC-TC-AGAGGCAAATCAAATTTACAGCATAGCTCAAGG
1 ACCTTCGAGTTCGATTACACTCAGCTTCGA-AGGCACATC--ATTTACAACATAACTCAAGG
39429 AAAGAATGAC
Statistics
Matches: 723, Mismatches: 140, Indels: 53
0.79 0.15 0.06
Matches are distributed among these distances:
164 51 0.07
165 430 0.59
166 62 0.09
167 8 0.01
168 54 0.07
169 84 0.12
170 33 0.05
171 1 0.00
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (165 bp):
ACCTTCGAGTTCGATTACACTCAGCTTCGAAGGCACATCATTTACAACATAACTCAAGGCTAGAA
GGGTTATCGGTGACCAAAGACCTTCGAGTTCGACTACGCTCAACTCCAAGGCACATCATTTGCAG
CATAACTTAAGTCGAGAAGGGCTATCTGCCAAAAA
Found at i:39047 original size:249 final size:249
Alignment explanation
Indices: 38369--39197 Score: 1298
Period size: 249 Copynumber: 3.3 Consensus size: 249
38359 TCAGTCAGTC
* **
38369 AAGACCTTCGAGTTCGACTGCGCTCAGCTCCAAGGCATATCATTTTAAGCATAACTTAAGTCGAG
1 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTCGAG
** *
38434 AAGGGTTATCTGCCAATAAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCATTTG
66 AAGGGTTATCTGCCAACCAAAGACCTTCGAGTTTGACTACGATCAGCTCCAAGGCACATCATTTG
* * * *
38499 TAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAAAAAACCTCGAGTTCGATTACACTCAGCTTC
131 CAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAAAGACCCTCGAGTTCAATTACACTCAGCTTC
* * *
38564 GAGGGTACATCATTTACAACATAACTCAAGGCTAGAAGGGTTATCGGTGACCGA
196 GAGGGCACATCATTTACAACATAACTCAAGGCTAGAAGGGTTATCTGTGACCAA
* * *
38618 AAGACCTTCGAGTTCGACTACGCTCAACTCCAAGGCATATCATTTTGTAGCATAACTTAAGTTGA
1 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCA-TTTGCAGCATAACTTAAGTCGA
*
38683 GAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTTGACTACGATCAACTCCAAGGCACATCATTT
65 GAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTTGACTACGATCAGCTCCAAGGCACATCATTT
* * *
38748 ACAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAAAGACCCTCGAGTTCAATTACACTCAGATT
130 GCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAAAGACCCTCGAGTTCAATTACACTCAGCTT
* *
38813 CGAGGGCACATCATTTACATCATAACTCAAGGCTAGAAGGGTTATATGTGACCAA
195 CGAGGGCACATCATTTACAACATAACTCAAGGCTAGAAGGGTTATCTGTGACCAA
*
38868 AAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTCGAG
1 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTCGAG
* *
38933 AAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTATGATCAGCTCCAAGGCACATCATTTG
66 AAGGGTTATCTGCCAACCAAAGACCTTCGAGTTTGACTACGATCAGCTCCAAGGCACATCATTTG
* * *
38998 CAGCATAGCTTAAGTCGAGAAGGGCTATCTACCAAAGACCCTCGAGTTCAATTACATTCAGCTTC
131 CAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAAAGACCCTCGAGTTCAATTACACTCAGCTTC
* * * *
39063 GAGGGCATATCATTTACAACATAACTCAATGTTAGAAGGGCTATCTGTGACCAA
196 GAGGGCACATCATTTACAACATAACTCAAGGCTAGAAGGGTTATCTGTGACCAA
* ** * *
39117 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAATGCGCATCATTTGCAACGTAACTTAAGTCGAG
1 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTCGAG
* *
39182 AATGGCTATCTGCCAA
66 AAGGGTTATCTGCCAA
39198 AGATCCTTGA
Statistics
Matches: 531, Mismatches: 48, Indels: 2
0.91 0.08 0.00
Matches are distributed among these distances:
249 303 0.57
250 228 0.43
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (249 bp):
AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTCGAG
AAGGGTTATCTGCCAACCAAAGACCTTCGAGTTTGACTACGATCAGCTCCAAGGCACATCATTTG
CAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAAAGACCCTCGAGTTCAATTACACTCAGCTTC
GAGGGCACATCATTTACAACATAACTCAAGGCTAGAAGGGTTATCTGTGACCAA
Found at i:39243 original size:414 final size:418
Alignment explanation
Indices: 38451--39428 Score: 1212
Period size: 414 Copynumber: 2.4 Consensus size: 418
38441 ATCTGCCAAT
* *
38451 AAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCATTTGTAGCATAGCTTAAGTCG
1 AAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCG
* * * *
38516 AGAAGGGTTATCTGCCAA--AAA-ACC-TCGAGTTCGATTACACTCAGCTTCGAGGGTACATCAT
66 AGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACACTCAGCTTCCAAGGCACATCAT
* * * * *
38577 TTACAACATAACTCAAGGCTAGAAGGGTTATCGGTGACCGAAAGACCTTCGAGTTCGACTACGCT
131 TTACAACATAACTCAAGGCGAGAAGGGCTATC-GTGACCGAAAGACCCTCGAGTTCAACTACACT
** * * *
38642 CAACTCCAAGGCATATCATTTTGTAGCATAACTTAAGTTGAGAAGGGTTATCTGCCAACCAAAGA
195 CAACTCCAAGGCATATCATTTTACAACATAACTCAAGTTGAGAAGGGCTATCTGCCAACCAAAGA
* *
38707 CCTTCGAGTTTGACTACGATCAACTCCAAGGCACATCATTTACAGCATAACTTAAGTCGAGAAGG
260 CCTTCGAGTTCGACTACGATCAACTCCAAGGCACATCATTTACAACATAACTTAAGTCGAGAAGG
* * *
38772 GTTATCTGCCAAAGACCCTCGAGTTCAATTACACTCAGATTCGAGGGCACATCATTTACATCATA
325 GCTATCTGCCAAAGACCCTCGAGTTCAATTACACTCAGATTCGACGGCACATCATTTACAACATA
* *
38837 ACTCAAGGCTAGAAGGGTTATATGTGACC
390 ACTCAAGGCTAGAAGAGTTATATGTCACC
*
38866 AAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTCG
1 AAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCG
*
38931 AGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTATGA-TCAGC-TCCAAGGCACATCA
66 AGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTA-CACTCAGCTTCCAAGGCACATCA
* * * * * * *
38994 TTTGCAGCATAGCTTAAGTCGAGAAGGGCTATC-T-ACC-AAAGACCCTCGAGTTCAATTACATT
130 TTTACAACATAACTCAAGGCGAGAAGGGCTATCGTGACCGAAAGACCCTCGAGTTCAACTACACT
* * * **
39056 CAGCTTCGAGGGCATATCA-TTTACAACATAACTCAATGTT-AGAAGGGCTATCTG-TGACCAAA
195 CAAC-TCCAAGGCATATCATTTTACAACATAACTCAA-GTTGAGAAGGGCTATCTGCCAACC-AA
* * * * * *
39118 AGACCTTCGAGTTCGACTACGCTCAGCTCCAATGCGCATCATTTGCAACGTAACTTAAGTCGAGA
257 AGACCTTCGAGTTCGACTACGATCAACTCCAAGGCACATCATTTACAACATAACTTAAGTCGAGA
* * * * *
39183 ATGGCTATCTGCCAAAGATCCTTGAGTTCGATTACACTCA-ACTTCGACGGCGCATCATTTACAA
322 AGGGCTATCTGCCAAAGACCCTCGAGTTCAATTACACTCAGA-TTCGACGGCACATCATTTACAA
* * *
39247 CATAATTCAAGGCTAGAATAGTTATTTGTCACC
386 CATAACTCAAGGCTAGAAGAGTTATATGTCACC
* * * *
39280 AAAAGACCTTCGAGTTCGACTACGCTAAGCTCCAAGGCACATCTTTTGCAGTATAACTTAAGTCG
1 AAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCG
* * * * *
39345 ATAAGGGCTATCTGCCAACCGAAGACCTTCGAGTTCGATTACACTCAGC-T-CAGAGGCAAATCA
66 AGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACACTCAGCTTCCA-AGGCACATC-
* *
39408 AATTTACAGCATAGCTCAAGG
129 -ATTTACAACATAACTCAAGG
39429 AAAGAATGAC
Statistics
Matches: 485, Mismatches: 65, Indels: 25
0.84 0.11 0.04
Matches are distributed among these distances:
413 7 0.01
414 301 0.62
415 98 0.20
416 18 0.04
417 3 0.01
418 40 0.08
419 17 0.04
420 1 0.00
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.25
Consensus pattern (418 bp):
AAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCG
AGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACACTCAGCTTCCAAGGCACATCAT
TTACAACATAACTCAAGGCGAGAAGGGCTATCGTGACCGAAAGACCCTCGAGTTCAACTACACTC
AACTCCAAGGCATATCATTTTACAACATAACTCAAGTTGAGAAGGGCTATCTGCCAACCAAAGAC
CTTCGAGTTCGACTACGATCAACTCCAAGGCACATCATTTACAACATAACTTAAGTCGAGAAGGG
CTATCTGCCAAAGACCCTCGAGTTCAATTACACTCAGATTCGACGGCACATCATTTACAACATAA
CTCAAGGCTAGAAGAGTTATATGTCACC
Found at i:39830 original size:37 final size:37
Alignment explanation
Indices: 39789--39974 Score: 336
Period size: 37 Copynumber: 5.0 Consensus size: 37
39779 AACATAACGT
39789 TAGAGTTTTACTATGATTCAAACTCCTAAAAATATGA
1 TAGAGTTTTACTATGATTCAAACTCCTAAAAATATGA
39826 TAGAGTTTTACTATGATTCAAACTCCTAAAAATATGA
1 TAGAGTTTTACTATGATTCAAACTCCTAAAAATATGA
* *
39863 TAGAGTTTTACGAAGATTCAAACTCCTAAAAATATGA
1 TAGAGTTTTACTATGATTCAAACTCCTAAAAATATGA
*
39900 TAGAGTTTTACTATGATTCAAACTCGTAAAAATATGA
1 TAGAGTTTTACTATGATTCAAACTCCTAAAAATATGA
*
39937 TAGAGTTTTACTAAGATTCAAACTCCTAAAAATATGA
1 TAGAGTTTTACTATGATTCAAACTCCTAAAAATATGA
39974 T
1 T
39975 TCATAAGCAT
Statistics
Matches: 142, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 142 1.00
ACGTcount: A:0.41, C:0.13, G:0.12, T:0.34
Consensus pattern (37 bp):
TAGAGTTTTACTATGATTCAAACTCCTAAAAATATGA
Found at i:40394 original size:19 final size:19
Alignment explanation
Indices: 40355--40410 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
40345 ATATACTTCA
* *
40355 TTATTATTATTATTATCTT
1 TTATTATTATTATTTTTTT
*
40374 TTA-TATGTTTTATTTTTTT
1 TTATTAT-TATTATTTTTTT
40393 TTATTATTATTATTTTTT
1 TTATTATTATTATTTTTT
40411 AAAACATATT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
18 3 0.10
19 25 0.81
20 3 0.10
ACGTcount: A:0.21, C:0.02, G:0.02, T:0.75
Consensus pattern (19 bp):
TTATTATTATTATTTTTTT
Found at i:40402 original size:16 final size:16
Alignment explanation
Indices: 40358--40411 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
40348 TACTTCATTA
40358 TTATTATTATTATCTTTT
1 TTATTATTATT-T-TTTT
* *
40376 ATATGTTTTATTTTTTT
1 TTAT-TATTATTTTTTT
*
40393 TTATTATTATTATTTT
1 TTATTATTATTTTTTT
40409 TTA
1 TTA
40412 AAACATATTA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
16 13 0.43
17 7 0.23
18 4 0.13
19 6 0.20
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.74
Consensus pattern (16 bp):
TTATTATTATTTTTTT
Found at i:40529 original size:2 final size:2
Alignment explanation
Indices: 40522--40547 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
40512 ATTACTATTT
40522 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
40548 ATTTTTCCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:40607 original size:8 final size:8
Alignment explanation
Indices: 40594--40618 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
40584 TATTTATTAT
40594 TACATATA
1 TACATATA
40602 TACATATA
1 TACATATA
40610 TACATATA
1 TACATATA
40618 T
1 T
40619 TTTATTTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.40
Consensus pattern (8 bp):
TACATATA
Found at i:40936 original size:17 final size:18
Alignment explanation
Indices: 40906--40949 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
40896 TTCTTATTCC
* *
40906 TTTATTTTGGTTATT-TT
1 TTTATTTTCGTTATTCTA
*
40923 TTTATTTTCTTTATTCTA
1 TTTATTTTCGTTATTCTA
40941 TTTATTTTC
1 TTTATTTTC
40950 ATTCTTTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 13 0.57
18 10 0.43
ACGTcount: A:0.14, C:0.07, G:0.05, T:0.75
Consensus pattern (18 bp):
TTTATTTTCGTTATTCTA
Found at i:51432 original size:17 final size:18
Alignment explanation
Indices: 51393--51432 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
51383 AGATACGTAA
*
51393 AATTTTATATTAAAAGAT
1 AATTTTATAATAAAAGAT
*
51411 AATTTTTTAATAAAAG-T
1 AATTTTATAATAAAAGAT
51428 AATTT
1 AATTT
51433 AATTTTTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (18 bp):
AATTTTATAATAAAAGAT
Found at i:54091 original size:22 final size:21
Alignment explanation
Indices: 54040--54092 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 21
54030 GTATCTTCAT
54040 TTCGTTTATGTTTACGAACAA
1 TTCGTTTATGTTTACGAACAA
** *
54061 TCTTTTTTATGTTTATGAACAA
1 T-TCGTTTATGTTTACGAACAA
54083 GTTCGTTTAT
1 -TTCGTTTAT
54093 CGACTTATTC
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
21 1 0.04
22 23 0.92
23 1 0.04
ACGTcount: A:0.25, C:0.11, G:0.13, T:0.51
Consensus pattern (21 bp):
TTCGTTTATGTTTACGAACAA
Found at i:54134 original size:37 final size:37
Alignment explanation
Indices: 54085--54157 Score: 110
Period size: 37 Copynumber: 2.0 Consensus size: 37
54075 ATGAACAAGT
*
54085 TCGTTTATCGACTTATTCATTTATGTTCACAAACAAA
1 TCGTTTATCGACTCATTCATTTATGTTCACAAACAAA
* * *
54122 TCGTTTATCGACTCGTTCATTTATGTTTATAAACAA
1 TCGTTTATCGACTCATTCATTTATGTTCACAAACAA
54158 CTTGTCTATT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.30, C:0.18, G:0.10, T:0.42
Consensus pattern (37 bp):
TCGTTTATCGACTCATTCATTTATGTTCACAAACAAA
Found at i:54962 original size:17 final size:17
Alignment explanation
Indices: 54937--54975 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
54927 ATTTTGATTC
*
54937 TTTTCCTTTGCTTTTAA
1 TTTTTCTTTGCTTTTAA
*
54954 TTTTTCTTTGCTTTTGA
1 TTTTTCTTTGCTTTTAA
54971 TTTTT
1 TTTTT
54976 TTCTGATAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.08, C:0.13, G:0.08, T:0.72
Consensus pattern (17 bp):
TTTTTCTTTGCTTTTAA
Done.