Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003145.1 Hibiscus syriacus cultivar Beakdansim tig00006617_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: 79030
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:4294 original size:13 final size:13
Alignment explanation
Indices: 4276--4301 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4266 ATATTTAGTT
4276 ATTTTTTTATTTA
1 ATTTTTTTATTTA
4289 ATTTTTTTATTTA
1 ATTTTTTTATTTA
4302 CAAATAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (13 bp):
ATTTTTTTATTTA
Found at i:5550 original size:16 final size:17
Alignment explanation
Indices: 5525--5558 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
5515 CCGATGTGTC
5525 ACATTGACTTTT-CAAA
1 ACATTGACTTTTACAAA
*
5541 ACATTTACTTTTACAAA
1 ACATTGACTTTTACAAA
5558 A
1 A
5559 GAATGAAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.41, C:0.18, G:0.03, T:0.38
Consensus pattern (17 bp):
ACATTGACTTTTACAAA
Found at i:6236 original size:22 final size:22
Alignment explanation
Indices: 6211--6272 Score: 106
Period size: 22 Copynumber: 2.8 Consensus size: 22
6201 GTGAAATTTA
6211 TCCCGAATGACCTATGTATATG
1 TCCCGAATGACCTATGTATATG
6233 TCCCGAATGACCTATGTATATG
1 TCCCGAATGACCTATGTATATG
* *
6255 TCCCAAAGGACCTATGTA
1 TCCCGAATGACCTATGTA
6273 ACCCTCGACT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (22 bp):
TCCCGAATGACCTATGTATATG
Found at i:7193 original size:21 final size:21
Alignment explanation
Indices: 7142--7195 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 21
7132 TTGCCTTATG
* * *
7142 GTATCGATACTCTTTCAGCAA
1 GTATCGATACCCTTTAAACAA
** *
7163 GTATTTATACCCTTTAAACCA
1 GTATCGATACCCTTTAAACAA
7184 GTATCGATACCC
1 GTATCGATACCC
7196 ATGCCCCAAT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.30, C:0.26, G:0.11, T:0.33
Consensus pattern (21 bp):
GTATCGATACCCTTTAAACAA
Found at i:9441 original size:16 final size:15
Alignment explanation
Indices: 9412--9493 Score: 76
Period size: 15 Copynumber: 5.4 Consensus size: 15
9402 GATAATGTTT
*
9412 CGTGAAACTGTTCTA
1 CGTGAAAATGTTCTA
9427 CGTGAAAAATGTTCTA
1 CGTG-AAAATGTTCTA
* *
9443 CATGAAAATGTTGTA
1 CGTGAAAATGTTCTA
** *
9458 TATGAAAATGTGCTA
1 CGTGAAAATGTTCTA
*
9473 AGTGAAAA-GATTCTA
1 CGTGAAAATG-TTCTA
9488 CGTGAA
1 CGTGAA
9494 GATACATTAT
Statistics
Matches: 55, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
14 1 0.02
15 41 0.75
16 13 0.24
ACGTcount: A:0.38, C:0.11, G:0.21, T:0.30
Consensus pattern (15 bp):
CGTGAAAATGTTCTA
Found at i:9737 original size:23 final size:23
Alignment explanation
Indices: 9625--9745 Score: 161
Period size: 23 Copynumber: 5.2 Consensus size: 23
9615 GAGTTGTGGG
*
9625 TTCTATGTGGTCATTCGGGATAA
1 TTCTATGTGGTCCTTCGGGATAA
* * *
9648 ATCTAAGTGGTCCTTCGGGACAA
1 TTCTATGTGGTCCTTCGGGATAA
* *
9671 TTCTATGTAGTCCTTCGGGACAA
1 TTCTATGTGGTCCTTCGGGATAA
9694 TTCTATGTGGTCCTTCGGGATAA
1 TTCTATGTGGTCCTTCGGGATAA
**
9717 TTCTATGTGGTCCTTTAGGATGAA
1 TTCTATGTGGTCCTTCGGGAT-AA
9741 TTCTA
1 TTCTA
9746 CATGGTTCTT
Statistics
Matches: 86, Mismatches: 11, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
23 79 0.92
24 7 0.08
ACGTcount: A:0.21, C:0.17, G:0.24, T:0.37
Consensus pattern (23 bp):
TTCTATGTGGTCCTTCGGGATAA
Found at i:9756 original size:24 final size:23
Alignment explanation
Indices: 9692--9756 Score: 58
Period size: 23 Copynumber: 2.8 Consensus size: 23
9682 CCTTCGGGAC
** **
9692 AATTCTATGTGGTCCTTCGGGAT
1 AATTCTACATGGTCCTTTAGGAT
**
9715 AATTCTATGTGGTCCTTTAGGAT
1 AATTCTACATGGTCCTTTAGGAT
*
9738 GAATTCTACATGGTTCTTT
1 -AATTCTACATGGTCCTTT
9757 CGGACAAATC
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
23 21 0.58
24 15 0.42
ACGTcount: A:0.20, C:0.15, G:0.22, T:0.43
Consensus pattern (23 bp):
AATTCTACATGGTCCTTTAGGAT
Found at i:15060 original size:15 final size:15
Alignment explanation
Indices: 15023--15067 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
15013 TATATGTTAT
15023 TATATTTTATATGA-
1 TATATTTTATATGAG
* *
15037 AAGTGTTTTATATGAG
1 TA-TATTTTATATGAG
15053 TATATTTTATATGAG
1 TATATTTTATATGAG
15068 GGCTTTATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
14 1 0.04
15 23 0.92
16 1 0.04
ACGTcount: A:0.33, C:0.00, G:0.16, T:0.51
Consensus pattern (15 bp):
TATATTTTATATGAG
Found at i:15085 original size:28 final size:28
Alignment explanation
Indices: 15024--15097 Score: 76
Period size: 30 Copynumber: 2.5 Consensus size: 28
15014 ATATGTTATT
* * *
15024 ATATTTTATATGAAAGTGTTTTATATGAGT
1 ATATTTTATATG--AGGGCTTTATATGAGA
*
15054 ATATTTTATATGAGGGCTTTATATGCGA
1 ATATTTTATATGAGGGCTTTATATGAGA
15082 ATATGTTTTATATGAG
1 ATA--TTTTATATGAG
15098 TAAATTGATA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
28 15 0.39
30 23 0.61
ACGTcount: A:0.31, C:0.03, G:0.19, T:0.47
Consensus pattern (28 bp):
ATATTTTATATGAGGGCTTTATATGAGA
Found at i:15496 original size:23 final size:24
Alignment explanation
Indices: 15470--15514 Score: 83
Period size: 23 Copynumber: 1.9 Consensus size: 24
15460 AAAATATATT
15470 TGGTCCTTCGAGAC-AATTCTATA
1 TGGTCCTTCGAGACAAATTCTATA
15493 TGGTCCTTCGAGACAAATTCTA
1 TGGTCCTTCGAGACAAATTCTA
15515 CGCGTTCCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
23 14 0.67
24 7 0.33
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.33
Consensus pattern (24 bp):
TGGTCCTTCGAGACAAATTCTATA
Found at i:15523 original size:24 final size:24
Alignment explanation
Indices: 15471--15538 Score: 77
Period size: 24 Copynumber: 2.9 Consensus size: 24
15461 AAATATATTT
* *
15471 GGTCCTTCGAGAC-AATTCTATAT
1 GGTCCTTCGAGACAAATTCTACAC
*
15494 GGTCCTTCGAGACAAATTCTACGC
1 GGTCCTTCGAGACAAATTCTACAC
* *
15518 GTTCCTTCGGGACAAA-TCTAC
1 GGTCCTTCGAGACAAATTCTAC
15539 TTTTGTGCAA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
23 18 0.46
24 21 0.54
ACGTcount: A:0.25, C:0.26, G:0.19, T:0.29
Consensus pattern (24 bp):
GGTCCTTCGAGACAAATTCTACAC
Found at i:17190 original size:60 final size:60
Alignment explanation
Indices: 17096--17208 Score: 138
Period size: 60 Copynumber: 1.9 Consensus size: 60
17086 CCACTCTATT
* * * * * * *
17096 GACATTTAGGTCGAACAAGTTGGTAGTTGCATGCCTTCCC-CTTGAACTTGAAGACATCTC
1 GACATTGAGGTCGAAAAAGCTCGCAGTTGAATGCC-TCCCTCTGGAACTTGAAGACATCTC
*
17156 GACATTGAGGTCGAAAAAGCTCGCAGTTGAATGCCTCCCTCTGGAGCTTGAAG
1 GACATTGAGGTCGAAAAAGCTCGCAGTTGAATGCCTCCCTCTGGAACTTGAAG
17209 GTATCGTGTC
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
59 4 0.09
60 40 0.91
ACGTcount: A:0.26, C:0.23, G:0.25, T:0.27
Consensus pattern (60 bp):
GACATTGAGGTCGAAAAAGCTCGCAGTTGAATGCCTCCCTCTGGAACTTGAAGACATCTC
Found at i:20925 original size:60 final size:60
Alignment explanation
Indices: 20801--20939 Score: 149
Period size: 60 Copynumber: 2.3 Consensus size: 60
20791 GTATGTACGT
* * * *
20801 ATAGTTTGAGATGAAATTGGATTGTTCAAAATGTTTGGAGACCAATTTAGAATAATGATG
1 ATAGTTTGGGATGAAATTGAAATGTTCAAAATGTTTGGAGACCAATTTAGAATAATGATC
* * *
20861 ATAGTTTGGGGATGAAATTGAAATGTTCAAAA-GTTTTGG-GACTAATTTAGGATGATTG-TC
1 ATAGTTT-GGGATGAAATTGAAATGTTCAAAATG-TTTGGAGACCAATTTAGAAT-AATGATC
*
20921 ATAGTTTATGGATGAAATT
1 ATAGTTT-GGGATGAAATT
20940 AAAACATTTA
Statistics
Matches: 67, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
60 38 0.57
61 29 0.43
ACGTcount: A:0.35, C:0.04, G:0.24, T:0.37
Consensus pattern (60 bp):
ATAGTTTGGGATGAAATTGAAATGTTCAAAATGTTTGGAGACCAATTTAGAATAATGATC
Found at i:21464 original size:21 final size:21
Alignment explanation
Indices: 21434--21728 Score: 141
Period size: 21 Copynumber: 14.0 Consensus size: 21
21424 GATTTACATA
* *
21434 TTCGCATTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
*
21455 TTCGCGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
* * *
21476 TTCGCGTTGCGATTTATTCTAAA
1 TTCGCGTTGCGA--TAGTCCAAG
* *
21499 TT--CGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
21520 TT--CGTTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
*
21539 TTCGCGTTGCGATTTATTCCAAG
1 TTCGCGTTGCGA--TAGTCCAAG
*
21562 TT--CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
* *
21581 TTCGCGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
* * *
21604 TT--CGTTGCAATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
* *
21625 TT--CGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
* *
21646 TTCGTGTTGCGATTTATTCCAAG
1 TTCGCGTTGCGA--TAGTCCAAG
* *
21669 TT--CATTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
* *
21688 TTCGCGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
21711 TT--CGTTGCGATAGTCCAA
1 TTCGCGTTGCGATAGTCCAA
21729 AATCACAACG
Statistics
Matches: 232, Mismatches: 26, Indels: 34
0.79 0.09 0.12
Matches are distributed among these distances:
19 34 0.15
21 145 0.62
23 53 0.23
ACGTcount: A:0.22, C:0.19, G:0.21, T:0.37
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTCCAAG
Found at i:21486 original size:42 final size:41
Alignment explanation
Indices: 21440--21611 Score: 188
Period size: 42 Copynumber: 4.1 Consensus size: 41
21430 CATATTCGCA
* *
21440 TTGCGATAGTCGAAGTTCGCGTTGCGA-TAGTCGAAGTTCGCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTATTCCAAGTT--CG
* * * *
21482 TTGCGATTTATTCTAAATT--CGTTGCGATTTATTCCAAATTCG
1 TTGCGA--TAGTCGAAGTTCGCGTTGCGA-TTATTCCAAGTTCG
*
21524 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGA-TTATTCCAAGTTCG
*
21566 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGA-TTATTCCAAGTTCG
21608 TTGC
1 TTGC
21612 AATTTATTCC
Statistics
Matches: 112, Mismatches: 12, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
40 8 0.07
42 88 0.79
44 16 0.14
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.37
Consensus pattern (41 bp):
TTGCGATAGTCGAAGTTCGCGTTGCGATTATTCCAAGTTCG
Found at i:21526 original size:63 final size:61
Alignment explanation
Indices: 21459--21728 Score: 260
Period size: 63 Copynumber: 4.3 Consensus size: 61
21449 TCGAAGTTCG
* *
21459 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCTAAATTCGTTGCGATTTATTCCAAATT
1 CGTTGCGATAGTCCAAGTT--CGTTGCGATTTATTCCAAATTCGTTGCGATTTATTCCAAATT
* * * *
21522 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGA--TAGTCGAAGTT
1 CGTTGCGATAGTCCAAGTT--CGTTGCGATTTATTCCAAATTCGTTGCGATTTATTCCAAATT
* * *
21583 CGCGTTGCGATTTATTCCAAATTCGTTGCAATTTATTCCAAATTCGTTGCGATTTATTCCAAATT
1 --CGTTGCGA--TAGTCCAAGTTCGTTGCGATTTATTCCAAATTCGTTGCGATTTATTCCAAATT
* * * * *
21648 CGTGTTGCGATTTATTCCAAGTTCATTGCGA--TAGTCGAAGTTCGCGTTGCGATTTATTCCAAA
1 C--GTTGCGA--TAGTCCAAGTTCGTTGCGATTTATTCCAAATT--CGTTGCGATTTATTCCAAA
21711 TT
60 TT
21713 CGTTGCGATAGTCCAA
1 CGTTGCGATAGTCCAA
21729 AATCACAACG
Statistics
Matches: 177, Mismatches: 20, Indels: 22
0.81 0.09 0.10
Matches are distributed among these distances:
61 15 0.08
63 98 0.55
65 64 0.36
ACGTcount: A:0.22, C:0.19, G:0.21, T:0.38
Consensus pattern (61 bp):
CGTTGCGATAGTCCAAGTTCGTTGCGATTTATTCCAAATTCGTTGCGATTTATTCCAAATT
Found at i:21631 original size:42 final size:42
Alignment explanation
Indices: 21480--21721 Score: 253
Period size: 42 Copynumber: 5.7 Consensus size: 42
21470 TCGAAGTTCG
*
21480 CGTTGCGATTTATTCTAAATTCGTTGCGATTTATTCCAAATT
1 CGTTGCGATTTATTCCAAATTCGTTGCGATTTATTCCAAATT
* * *
21522 CGTTGCGA--TAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTT
1 CGTTGCGATTTATTCCAAATT--CGTTGCGATTTATTCCAAATT
* * *
21564 CGTTGCGA--TAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
1 CGTTGCGATTTATTCCAAATT--CGTTGCGATTTATTCCAAATT
*
21606 CGTTGCAATTTATTCCAAATTCGTTGCGATTTATTCCAAATT
1 CGTTGCGATTTATTCCAAATTCGTTGCGATTTATTCCAAATT
* * * * *
21648 CGTGTTGCGATTTATTCCAAGTTCATTGCGA--TAGTCGAAGTT
1 C--GTTGCGATTTATTCCAAATTCGTTGCGATTTATTCCAAATT
21690 CGCGTTGCGATTTATTCCAAATTCGTTGCGAT
1 --CGTTGCGATTTATTCCAAATTCGTTGCGAT
21722 AGTCCAAAAT
Statistics
Matches: 173, Mismatches: 18, Indels: 17
0.83 0.09 0.08
Matches are distributed among these distances:
40 8 0.05
42 131 0.76
44 34 0.20
ACGTcount: A:0.22, C:0.19, G:0.20, T:0.39
Consensus pattern (42 bp):
CGTTGCGATTTATTCCAAATTCGTTGCGATTTATTCCAAATT
Found at i:22467 original size:21 final size:21
Alignment explanation
Indices: 22441--22512 Score: 85
Period size: 21 Copynumber: 3.4 Consensus size: 21
22431 ATTTTGGACT
22441 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAATTTGGAATAA
* * *
22462 ATCGCAACGCGAACTTCGACT--
1 ATCGCAA--CGAATTTGGAATAA
22483 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAATTTGGAATAA
22504 ATCGCAACG
1 ATCGCAACG
22513 CGGACTTCGA
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
19 9 0.22
21 23 0.56
23 9 0.22
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.21
Consensus pattern (21 bp):
ATCGCAACGAATTTGGAATAA
Found at i:22496 original size:42 final size:42
Alignment explanation
Indices: 22437--22568 Score: 232
Period size: 42 Copynumber: 3.2 Consensus size: 42
22427 TGCGATTTTG
22437 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
*
22479 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGGACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
*
22521 GACTATCGCAACGAATTTGG-A-AAATCGCAACGCGAACTTG
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
22561 GACTATCG
1 GACTATCG
22569 TAATGCAAAT
Statistics
Matches: 87, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
40 25 0.29
41 1 0.01
42 61 0.70
ACGTcount: A:0.34, C:0.23, G:0.21, T:0.21
Consensus pattern (42 bp):
GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
Found at i:22528 original size:21 final size:21
Alignment explanation
Indices: 22462--22568 Score: 87
Period size: 21 Copynumber: 5.2 Consensus size: 21
22452 TTTGGAATAA
22462 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
* * *
22483 ATCGCAA--CGAATTTGGAAT
1 ATCGCAACGCGAACTTCGACT
*
22502 AAATCGCAACGCGGACTTCGACT
1 --ATCGCAACGCGAACTTCGACT
* * **
22525 ATCGCAA--CGAATTTGGAAA
1 ATCGCAACGCGAACTTCGACT
*
22544 ATCGCAACGCGAACTTGGACT
1 ATCGCAACGCGAACTTCGACT
22565 ATCG
1 ATCG
22569 TAATGCAAAT
Statistics
Matches: 65, Mismatches: 15, Indels: 12
0.71 0.16 0.13
Matches are distributed among these distances:
19 23 0.35
21 34 0.52
23 8 0.12
ACGTcount: A:0.33, C:0.25, G:0.21, T:0.21
Consensus pattern (21 bp):
ATCGCAACGCGAACTTCGACT
Found at i:22704 original size:20 final size:21
Alignment explanation
Indices: 22622--22929 Score: 98
Period size: 21 Copynumber: 14.1 Consensus size: 21
22612 TTGCGATAGT
* * *
22622 CGAATTTGGAAAATCGCAAAG
1 CGAACTTGGAATATCGCAATG
*
22643 CGAACTT-CAACTATCGCAATG
1 CGAACTTGGAA-TATCGCAATG
*
22664 CGAACTTGGAATATTGCAATG
1 CGAACTTGGAATATCGCAATG
*
22685 CGAA-TATGTAA-ATCGCAATG
1 CGAACT-TGGAATATCGCAATG
* * *
22705 CGATA-GTCGAAGT-TCGCGTTGCGATAG
1 CGA-ACTTGGAA-TAT--C---GCAAT-G
* * *
22732 TCGAATTTGGAAAATCGCAACG
1 -CGAACTTGGAATATCGCAATG
* * *
22754 CGAACTTCGACTATCGCAACG
1 CGAACTTGGAATATCGCAATG
* *
22775 CGAACTTCGACTATCGCAATG
1 CGAACTTGGAATATCGCAATG
*
22796 CGAA-TATGTAA-ATCGCAATG
1 CGAACT-TGGAATATCGCAATG
* *
22816 CGATA-GTCGAAGT-TCGCATTGCGATAG
1 CGA-ACTTGGAA-TATCGCA-----AT-G
* * *
22843 TCGAATTTGGAAAATCGCAACG
1 -CGAACTTGGAATATCGCAATG
* *
22865 CGAACTTCGACTATCGCAATG
1 CGAACTTGGAATATCGCAATG
*
22886 CGAACTTGGACTATCGCAATG
1 CGAACTTGGAATATCGCAATG
*
22907 CGAA-TATGTAA-ATCGCAATG
1 CGAACT-TGGAATATCGCAATG
22927 CGA
1 CGA
22930 TAGTCGAAGT
Statistics
Matches: 218, Mismatches: 40, Indels: 59
0.69 0.13 0.19
Matches are distributed among these distances:
20 46 0.21
21 132 0.61
22 4 0.02
23 5 0.02
26 7 0.03
27 4 0.02
28 20 0.09
ACGTcount: A:0.33, C:0.21, G:0.23, T:0.24
Consensus pattern (21 bp):
CGAACTTGGAATATCGCAATG
Found at i:22738 original size:111 final size:111
Alignment explanation
Indices: 22544--22950 Score: 706
Period size: 111 Copynumber: 3.7 Consensus size: 111
22534 AATTTGGAAA
* * *
22544 ATCGCAACGCGAACTTGGACTATCGTAATGCAAATATGTAAATCGCATTGCGATAGTCGAAGTTC
1 ATCGCAACGCGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGAAGTTC
* * *
22609 GTATTGCGATAGTCGAATTTGGAAAATCGCAAAGCGAACTTCAACT
66 GCATTGCGATAGTCGAATTTGGAAAATCGCAACGCGAACTTCGACT
* * *
22655 ATCGCAATGCGAACTTGGAATATTGCAATGCGAATATGTAAATCGCAATGCGATAGTCGAAGTTC
1 ATCGCAACGCGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGAAGTTC
*
22720 GCGTTGCGATAGTCGAATTTGGAAAATCGCAACGCGAACTTCGACT
66 GCATTGCGATAGTCGAATTTGGAAAATCGCAACGCGAACTTCGACT
*
22766 ATCGCAACGCGAACTTCGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGAAGTTC
1 ATCGCAACGCGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGAAGTTC
22831 GCATTGCGATAGTCGAATTTGGAAAATCGCAACGCGAACTTCGACT
66 GCATTGCGATAGTCGAATTTGGAAAATCGCAACGCGAACTTCGACT
*
22877 ATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGAAGTTC
1 ATCGCAACGCGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGAAGTTC
22942 GCATTGCGA
66 GCATTGCGA
22951 ATCTGGAAAC
Statistics
Matches: 279, Mismatches: 17, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
111 279 1.00
ACGTcount: A:0.32, C:0.20, G:0.23, T:0.25
Consensus pattern (111 bp):
ATCGCAACGCGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGAAGTTC
GCATTGCGATAGTCGAATTTGGAAAATCGCAACGCGAACTTCGACT
Found at i:22923 original size:90 final size:89
Alignment explanation
Indices: 22766--22937 Score: 242
Period size: 90 Copynumber: 1.9 Consensus size: 89
22756 AACTTCGACT
* *
22766 ATCGCAACGCGAACTTCGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGAAGTTC
1 ATCGCAACGCGAACTTCGACTATCGCAATGCGAATATGGAAATCGCAATGCGATAGTC-AAGATC
*
22831 GCATTGCGATAGTCGAATTTGGAAA
65 GCAATGCGATAGTCGAATTTGGAAA
*
22856 ATCGCAACGCGAACTTCGACTATCGCAATGCGAACT-TGGACTATCGCAATGCGAATATGT-AA-
1 ATCGCAACGCGAACTTCGACTATCGCAATGCGAA-TATGGA-AATCGCAATGCG-ATA-GTCAAG
22918 ATCGCAATGCGATAGTCGAA
62 ATCGCAATGCGATAGTCGAA
22938 GTTCGCATTG
Statistics
Matches: 74, Mismatches: 4, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
90 55 0.74
91 14 0.19
92 3 0.04
93 2 0.03
ACGTcount: A:0.33, C:0.22, G:0.23, T:0.23
Consensus pattern (89 bp):
ATCGCAACGCGAACTTCGACTATCGCAATGCGAATATGGAAATCGCAATGCGATAGTCAAGATCG
CAATGCGATAGTCGAATTTGGAAA
Found at i:33727 original size:30 final size:30
Alignment explanation
Indices: 33676--33734 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
33666 AGCAACAAGC
*
33676 TTAACGAGCAATGAGTCGAGCAACAATTTTT
1 TTAACGAGCAATGAATCGAGCAA-AATTTTT
*
33707 TTAACTAGC-ATGAATCGAGCAAAATTTT
1 TTAACGAGCAATGAATCGAGCAAAATTTT
33735 AATGGGTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 6 0.23
30 12 0.46
31 8 0.31
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.31
Consensus pattern (30 bp):
TTAACGAGCAATGAATCGAGCAAAATTTTT
Found at i:39516 original size:2 final size:2
Alignment explanation
Indices: 39509--39559 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
39499 GTAGGTATCG
39509 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
39551 AT AT AT AT A
1 AT AT AT AT A
39560 AGTATACATA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:40200 original size:75 final size:75
Alignment explanation
Indices: 40019--40201 Score: 242
Period size: 75 Copynumber: 2.4 Consensus size: 75
40009 CTTATCCTGT
*** * *
40019 TAAAATAAAATAGGTGCTACCTATTATATTAAACTACCTACCGGTTTGTTTGAAAGTTACTAATA
1 TAAAATAAAATAGACACTACCTATTATGTTAAAATACCTACCGGTTTGTTTGAAAGTTACTAATA
40084 ATGTAAACGG
66 ATGTAAACGG
* * * * * *
40094 TAAAATAAAATAGGCATTACATGTTACGTTAAAATACCTATCGGTTTGTTT-AAAGGTTACTAAT
1 TAAAATAAAATAGACACTACCTATTATGTTAAAATACCTACCGGTTTGTTTGAAA-GTTACTAAT
40158 AATGTAAACGG
65 AATGTAAACGG
*
40169 TAAAATAAAATATACACTACCTATTATGTTAAA
1 TAAAATAAAATAGACACTACCTATTATGTTAAA
40202 CAGGCACTAC
Statistics
Matches: 92, Mismatches: 15, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
74 3 0.03
75 89 0.97
ACGTcount: A:0.42, C:0.12, G:0.13, T:0.33
Consensus pattern (75 bp):
TAAAATAAAATAGACACTACCTATTATGTTAAAATACCTACCGGTTTGTTTGAAAGTTACTAATA
ATGTAAACGG
Found at i:40329 original size:173 final size:173
Alignment explanation
Indices: 40035--40348 Score: 461
Period size: 173 Copynumber: 1.8 Consensus size: 173
40025 AAAATAGGTG
* * *
40035 CTACCTATTATATTAAACTACCTACCGGTTTGTTTGAAAGTTACTAATAATGTAAACGGTAAAAT
1 CTACCTATTACATTAAACTACCTACCGGTTTGTTTGAAAGTTAATAATAATGTAAACAGTAAAAT
* * * *
40100 AAAATAGGCATTACATGTTACGTTAAAATACCTATCGGTTTGTTTAAAGGTTACTAATAATGTAA
66 AAAATAGGCACTACATATTACGTCAAAATACCTAACGGTTTGTTTAAAGGTTACTAATAATGTAA
40165 ACGGTAAAATAAAATATACACTACCTATTATGTTAAACAGGCA
131 ACGGTAAAATAAAATATACACTACCTATTATGTTAAACAGGCA
* * * *
40208 CTACCTATTACATTAAATTATCTACTGGTTTGTTT-AAGTGTTAATAATAATGTAAACAGTAAAA
1 CTACCTATTACATTAAACTACCTACCGGTTTGTTTGAA-AGTTAATAATAATGTAAACAGTAAAA
* * * *
40272 TAAAATAGGCGCTATC-TATTACGTCAAAATGCCTAACTGTTTGTTTAAAGTTTACTAATAATGT
65 TAAAATAGGCACTA-CATATTACGTCAAAATACCTAACGGTTTGTTTAAAGGTTACTAATAATGT
40336 AAACGGTAAAATA
129 AAACGGTAAAATA
40349 TATACAATTT
Statistics
Matches: 124, Mismatches: 15, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
172 2 0.02
173 121 0.98
174 1 0.01
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.34
Consensus pattern (173 bp):
CTACCTATTACATTAAACTACCTACCGGTTTGTTTGAAAGTTAATAATAATGTAAACAGTAAAAT
AAAATAGGCACTACATATTACGTCAAAATACCTAACGGTTTGTTTAAAGGTTACTAATAATGTAA
ACGGTAAAATAAAATATACACTACCTATTATGTTAAACAGGCA
Found at i:40595 original size:38 final size:38
Alignment explanation
Indices: 40544--40617 Score: 121
Period size: 38 Copynumber: 1.9 Consensus size: 38
40534 AAGATATGGA
* *
40544 TATTTACTCTAAAAGTATGAATATTCTAAAGGTTAAGT
1 TATTTACTCTAAAAGTACGAATACTCTAAAGGTTAAGT
*
40582 TATTTACTCTAAAAGTACGGATACTCTAAAGGTTAA
1 TATTTACTCTAAAAGTACGAATACTCTAAAGGTTAA
40618 TGATAATGTA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.36
Consensus pattern (38 bp):
TATTTACTCTAAAAGTACGAATACTCTAAAGGTTAAGT
Found at i:41112 original size:108 final size:108
Alignment explanation
Indices: 40818--41339 Score: 422
Period size: 108 Copynumber: 4.7 Consensus size: 108
40808 ATTGGGCGCA
* * * * * * * *
40818 ACCTAGTATGTTAATATTTATTTATAACAAAATAA-TAAATTAACATATTTTGTTGTCGTGGGTT
1 ACCTAATATGTTGATA-ATATTAATAACAAATTAAGT-AATTAACATATTTTGTTATCGTCGGAT
* * * * *
40882 TTCGAAGGCCCCATTAACTTAAACTTTGTTAATATTTTAGGCGCA
64 TTCTAAGGCCCCATCAACTTAAACTTTGATAATATTTTAGACGCT
* * *
40927 ACCTAATATGTTGATAATATTAATAACAAAATAAATAATTAACATATTTTGTTATCGTCGGACTT
1 ACCTAATATGTTGATAATATTAATAACAAATTAAGTAATTAACATATTTTGTTATCGTCGGATTT
* *
40992 CTAAGACCCCATCAACTTAAACTTTGATAATATTTTAGGCGCT
66 CTAAGGCCCCATCAACTTAAACTTTGATAATATTTTAGACGCT
* *
41035 ACCTAATATGTTGATAATATTAATAACAATTTAAGTAATTAACCTATTTTGTTATCGTCGGATTT
1 ACCTAATATGTTGATAATATTAATAACAAATTAAGTAATTAACATATTTTGTTATCGTCGGATTT
* * * ** * * * * * *
41100 TTAAAGCTCCATCTGCTTTAAAAAGGCGCTACCT-ATTACATTAAATAAACACT
66 CTAAGGCCCCATCAAC-TT--AAA----CT--TTGATAATATT--TTAGACGCT
* ** * * * *** * * *
41153 ACTTGTTATGTT-ATTATGGTTGATAA-TGTTTCCAGTAATTAACCTATTTTGTTATCGTCAGAT
1 ACCTAATATGTTGATAAT-ATTAATAACAAATT-AAGTAATTAACATATTTTGTTATCGTCGGAT
* * *
41216 TTCTAAGGCTCCATCAGCTTAAACTTTGGTAATATTTTAGACGCT
64 TTCTAAGGCCCCATCAACTTAAACTTTGATAATATTTTAGACGCT
* * * * *
41261 ACATAATTTGTTGATAATATTGATAAAAAATGAAGTAATTAACATATTTTGTTATCGTCGGATTT
1 ACCTAATATGTTGATAATATTAATAACAAATTAAGTAATTAACATATTTTGTTATCGTCGGATTT
41326 CTAAGGCCCCATCA
66 CTAAGGCCCCATCA
41340 TCTTTAAAAA
Statistics
Matches: 331, Mismatches: 65, Indels: 35
0.77 0.15 0.08
Matches are distributed among these distances:
108 213 0.64
109 23 0.07
110 5 0.02
111 5 0.02
115 5 0.02
116 6 0.02
117 10 0.03
118 64 0.19
ACGTcount: A:0.34, C:0.15, G:0.13, T:0.39
Consensus pattern (108 bp):
ACCTAATATGTTGATAATATTAATAACAAATTAAGTAATTAACATATTTTGTTATCGTCGGATTT
CTAAGGCCCCATCAACTTAAACTTTGATAATATTTTAGACGCT
Found at i:41240 original size:226 final size:226
Alignment explanation
Indices: 40962--41421 Score: 643
Period size: 226 Copynumber: 2.0 Consensus size: 226
40952 ACAAAATAAA
*
40962 TAATTAACATATTTTGTTATCGTCGGACTTCTAAGACCCCATCAACTTAAACTTTGATAATATTT
1 TAATTAACATATTTTGTTATCGTCAGACTTCTAAGACCCCATCAACTTAAACTTTGATAATATTT
* * * * * *
41027 TAGGCGCTACCTAATATGTTGATAATATTAATAACAATTTAAGTAATTAACCTATTTTGTTATCG
66 TAGACGCTACATAATATGTTGATAATATTAATAAAAAATGAAGTAATTAACATATTTTGTTATCG
* * * *
41092 TCGGATTTTTAAAGCTCCATC-TGCTTTAAAAAGGCGCTACCTATTACATTAAATAAACACTACT
131 TCGGATTTCTAAAGCCCCATCAT-CTTTAAAAAGGCGCTACATATTACATTAAATAAACACTACC
* *
41156 TGTTATGTTATTATGGTTGATAATGTTTCCAG
195 TGTTATGTTATTATGATTGATAATATTTCCAG
* * * * * *
41188 TAATTAACCTATTTTGTTATCGTCAGATTTCTAAGGCTCCATCAGCTTAAACTTTGGTAATATTT
1 TAATTAACATATTTTGTTATCGTCAGACTTCTAAGACCCCATCAACTTAAACTTTGATAATATTT
* *
41253 TAGACGCTACATAATTTGTTGATAATATTGATAAAAAATGAAGTAATTAACATATTTTGTTATCG
66 TAGACGCTACATAATATGTTGATAATATTAATAAAAAATGAAGTAATTAACATATTTTGTTATCG
* * * * * * *
41318 TCGGATTTCTAAGGCCCCATCATCTTTAAAAATGTGCTACATATTACGTTACATAAGCGCTACCT
131 TCGGATTTCTAAAGCCCCATCATCTTTAAAAAGGCGCTACATATTACATTAAATAAACACTACCT
*
41383 GTTATGTTATTATGATTGATAATATTTTCAG
196 GTTATGTTATTATGATTGATAATATTTCCAG
41414 TAATTAAC
1 TAATTAAC
41422 TAGTTATGTT
Statistics
Matches: 204, Mismatches: 29, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
226 203 1.00
227 1 0.00
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.40
Consensus pattern (226 bp):
TAATTAACATATTTTGTTATCGTCAGACTTCTAAGACCCCATCAACTTAAACTTTGATAATATTT
TAGACGCTACATAATATGTTGATAATATTAATAAAAAATGAAGTAATTAACATATTTTGTTATCG
TCGGATTTCTAAAGCCCCATCATCTTTAAAAAGGCGCTACATATTACATTAAATAAACACTACCT
GTTATGTTATTATGATTGATAATATTTCCAG
Found at i:42040 original size:6 final size:6
Alignment explanation
Indices: 42029--42064 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
42019 GAGAGTAGGG
42029 GATGAA GATGAA GATGAA GATGAA GATGAA GATGAA
1 GATGAA GATGAA GATGAA GATGAA GATGAA GATGAA
42065 ATTAAAAGTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.33, T:0.17
Consensus pattern (6 bp):
GATGAA
Found at i:48636 original size:50 final size:51
Alignment explanation
Indices: 48571--48673 Score: 174
Period size: 51 Copynumber: 2.0 Consensus size: 51
48561 TATTTTGACT
48571 TTCAACTTTTCATTTTAAAG-AAAAAAATCTTCTATTTGAAATGTTAATCG
1 TTCAACTTTTCATTTTAAAGAAAAAAAATCTTCTATTTGAAATGTTAATCG
*
48621 TTCAACATTTT-ATTTTAAAGAAAAAAAATCTTCTATTTGGAATGTTAATCG
1 TTCAAC-TTTTCATTTTAAAGAAAAAAAATCTTCTATTTGAAATGTTAATCG
48672 TT
1 TT
48674 TGTTGACTAA
Statistics
Matches: 50, Mismatches: 1, Indels: 3
0.93 0.02 0.06
Matches are distributed among these distances:
50 15 0.30
51 35 0.70
ACGTcount: A:0.38, C:0.11, G:0.09, T:0.43
Consensus pattern (51 bp):
TTCAACTTTTCATTTTAAAGAAAAAAAATCTTCTATTTGAAATGTTAATCG
Found at i:50804 original size:33 final size:33
Alignment explanation
Indices: 50766--50873 Score: 135
Period size: 33 Copynumber: 3.3 Consensus size: 33
50756 CTCCCTCCTT
* *
50766 ATGGTGAAGATGATCGTCCTGTTCCTCATGGTC
1 ATGGTGATGATGATCGTCCTCTTCCTCATGGTC
*
50799 ATGGTGATGATGATCGTCCTCTTCCTCATTGTC
1 ATGGTGATGATGATCGTCCTCTTCCTCATGGTC
* * * **
50832 ATGGTCATGATGATCTTCCTCATGGTCATGGTC
1 ATGGTGATGATGATCGTCCTCTTCCTCATGGTC
*
50865 ATGATGATG
1 ATGGTGATG
50874 GTGGTGATGA
Statistics
Matches: 64, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 64 1.00
ACGTcount: A:0.19, C:0.20, G:0.25, T:0.36
Consensus pattern (33 bp):
ATGGTGATGATGATCGTCCTCTTCCTCATGGTC
Found at i:50818 original size:27 final size:28
Alignment explanation
Indices: 50788--50872 Score: 91
Period size: 27 Copynumber: 2.9 Consensus size: 28
50778 ATCGTCCTGT
*
50788 TCCTCATGGTCATGGTGATGATGATCGTCCTC
1 TCCTCATGGTCATGGTCATGATGATCG----C
* *
50820 TTCCTCATTGTCATGGTCATGATGATC-T
1 -TCCTCATGGTCATGGTCATGATGATCGC
50848 TCCTCATGGTCATGGTCATGATGAT
1 TCCTCATGGTCATGGTCATGATGAT
50873 GGTGGTGATG
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
27 24 0.50
33 24 0.50
ACGTcount: A:0.18, C:0.22, G:0.22, T:0.38
Consensus pattern (28 bp):
TCCTCATGGTCATGGTCATGATGATCGC
Found at i:50875 original size:39 final size:39
Alignment explanation
Indices: 50832--50906 Score: 96
Period size: 39 Copynumber: 1.9 Consensus size: 39
50822 CCTCATTGTC
* * *
50832 ATGGTCATGATGATCTTCCTCATGGTCATGGTCATGATG
1 ATGGTCATGATGATCATCCTCACGGTCATGATCATGATG
** *
50871 ATGGTGGTGATGATCATCCTCACGGTCTTGATCATG
1 ATGGTCATGATGATCATCCTCACGGTCATGATCATG
50907 GTGCTTAAAC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
39 30 1.00
ACGTcount: A:0.20, C:0.19, G:0.27, T:0.35
Consensus pattern (39 bp):
ATGGTCATGATGATCATCCTCACGGTCATGATCATGATG
Found at i:52353 original size:2 final size:2
Alignment explanation
Indices: 52346--52420 Score: 150
Period size: 2 Copynumber: 37.5 Consensus size: 2
52336 TTATGCAGTT
52346 TA TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA TA
52388 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
52421 GGTTTTCAGA
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 73 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:63021 original size:64 final size:65
Alignment explanation
Indices: 62897--63032 Score: 179
Period size: 64 Copynumber: 2.1 Consensus size: 65
62887 CATACCCATT
* * **
62897 TCGAATGCATTTTGTGTACCGATGCACAATCCATGCATCGGTGCACTCTTGAATATTTTG-AACA
1 TCGAATGCATTTTATGTACCGATGCACAATCCATGCATCGATGCACTCCAGAATATTTTGAAACA
**
62961 TCGAATGCATTTTATGTACCGATGCAC-ATACCATGCATCGATGCACTCCAGGTTCA-TTTGAAA
1 TCGAATGCATTTTATGTACCGATGCACAAT-CCATGCATCGATGCACTCCAGAAT-ATTTTGAAA
63024 CA
64 CA
63026 TCGAATG
1 TCGAATG
63033 TAATTAGTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
63 2 0.03
64 49 0.78
65 12 0.19
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31
Consensus pattern (65 bp):
TCGAATGCATTTTATGTACCGATGCACAATCCATGCATCGATGCACTCCAGAATATTTTGAAACA
Found at i:64960 original size:21 final size:21
Alignment explanation
Indices: 64935--64974 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
64925 AAGACTTTAT
64935 TTTCAAAATACAAAAATGATA
1 TTTCAAAATACAAAAATGATA
**
64956 TTTCAAAATTGAAAAATGA
1 TTTCAAAATACAAAAATGA
64975 AAATAGTCTT
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:0.55, C:0.07, G:0.07, T:0.30
Consensus pattern (21 bp):
TTTCAAAATACAAAAATGATA
Found at i:68877 original size:44 final size:44
Alignment explanation
Indices: 68820--68938 Score: 118
Period size: 44 Copynumber: 2.7 Consensus size: 44
68810 GACAGTGTAT
*
68820 CGATGCATCCCTTGAATGTGCATCGATACACCATGAAGGTGCAC
1 CGATGCATTCCTTGAATGTGCATCGATACACCATGAAGGTGCAC
* * * * * *
68864 CGATGCATTCCTTGAAGGTGCACCGATGCATTCCTTGAATGTGCAT
1 CGATGCATTCCTTGAATGTGCATCGATACA--CCATGAAGGTGCAC
* *
68910 CGATGCACT-C-TG-CTGTGCATCGATACACC
1 CGATGCATTCCTTGAATGTGCATCGATACACC
68939 CATCGGGTTT
Statistics
Matches: 61, Mismatches: 12, Indels: 7
0.76 0.15 0.09
Matches are distributed among these distances:
41 2 0.03
43 11 0.18
44 28 0.46
45 1 0.02
46 19 0.31
ACGTcount: A:0.24, C:0.28, G:0.23, T:0.26
Consensus pattern (44 bp):
CGATGCATTCCTTGAATGTGCATCGATACACCATGAAGGTGCAC
Found at i:68883 original size:23 final size:23
Alignment explanation
Indices: 68820--68916 Score: 117
Period size: 23 Copynumber: 4.3 Consensus size: 23
68810 GACAGTGTAT
* * *
68820 CGATGCATCCCTTGAATGTGCAT
1 CGATGCATTCCTTGAAGGTGCAC
* *
68843 CGATACA--CCATGAAGGTGCAC
1 CGATGCATTCCTTGAAGGTGCAC
68864 CGATGCATTCCTTGAAGGTGCAC
1 CGATGCATTCCTTGAAGGTGCAC
* *
68887 CGATGCATTCCTTGAATGTGCAT
1 CGATGCATTCCTTGAAGGTGCAC
68910 CGATGCA
1 CGATGCA
68917 CTCTGCTGTG
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
21 17 0.27
23 47 0.73
ACGTcount: A:0.25, C:0.26, G:0.24, T:0.26
Consensus pattern (23 bp):
CGATGCATTCCTTGAAGGTGCAC
Found at i:71228 original size:13 final size:13
Alignment explanation
Indices: 71198--71231 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
71188 AGGGGGAGTA
*
71198 ATTTTCAAAATTT
1 ATTTTCAAAATCT
71211 A-TTTCAAAATCT
1 ATTTTCAAAATCT
71223 ATTTTCAAA
1 ATTTTCAAA
71232 GAAAATCCTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.41, C:0.12, G:0.00, T:0.47
Consensus pattern (13 bp):
ATTTTCAAAATCT
Done.