Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A07
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: 92880876
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2857347 characters in sequence are not A, C, G, or T
File 290 of 290
Found at i:92727613 original size:7 final size:7
Alignment explanation
Indices: 92727603--92727671 Score: 93
Period size: 7 Copynumber: 9.9 Consensus size: 7
92727593 TAGGGTTAAA
92727603 GGGTTTG
1 GGGTTTG
92727610 GGGTTTG
1 GGGTTTG
**
92727617 AAGTTTG
1 GGGTTTG
*
92727624 GGGTTTA
1 GGGTTTG
92727631 GGGTTTG
1 GGGTTTG
92727638 GGGTTTG
1 GGGTTTG
92727645 GGGTTTG
1 GGGTTTG
*
92727652 GGGTTTA
1 GGGTTTG
*
92727659 GGGTTTA
1 GGGTTTG
92727666 GGGTTT
1 GGGTTT
92727672 TAAGGTTTTA
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
7 55 1.00
ACGTcount: A:0.07, C:0.00, G:0.49, T:0.43
Consensus pattern (7 bp):
GGGTTTG
Found at i:92737708 original size:10 final size:10
Alignment explanation
Indices: 92737670--92737701 Score: 64
Period size: 10 Copynumber: 3.2 Consensus size: 10
92737660 AAATCGAGTT
92737670 AAAAGAAAAA
1 AAAAGAAAAA
92737680 AAAAGAAAAA
1 AAAAGAAAAA
92737690 AAAAGAAAAA
1 AAAAGAAAAA
92737700 AA
1 AA
92737702 GTGAAAATTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (10 bp):
AAAAGAAAAA
Found at i:92738579 original size:14 final size:13
Alignment explanation
Indices: 92738560--92738597 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
92738550 AATAGTGAGA
92738560 GAAAAAGAAAA-T
1 GAAAAAGAAAATT
92738572 GAAGAAAAGAAAATT
1 G-A-AAAAGAAAATT
92738587 GAAAAAGAAAA
1 GAAAAAGAAAA
92738598 AGATGTTGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 10 0.43
14 10 0.43
15 2 0.09
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (13 bp):
GAAAAAGAAAATT
Found at i:92740660 original size:140 final size:140
Alignment explanation
Indices: 92740408--92740687 Score: 515
Period size: 140 Copynumber: 2.0 Consensus size: 140
92740398 GAAGGGGGGA
92740408 TGATGTGACCACGCCCCAAGCCCCATCAAGTCCTCGTCTTGATTCCCTCGAGCTTCCAAAGGGAC
1 TGATGTGACCACGCCCCAAGCCCCATCAAGTCCTCGTCTTGATTCCCTCGAGCTTCCAAAGGGAC
*
92740473 AAATGAACCGAGCTAGGTCCAAGCGATTTCATGAACTTGTTTCAGCTTTATTGTTCAAGTTTTGG
66 AAATGAACCGAGCTAGGTCCAAGCGATTTCATGAACTTGTTTCAGCTTTATTGTTCAAGTTTTAG
92740538 AAGGAGAATC
131 AAGGAGAATC
92740548 TGATGTGACCACGCCCCAAGCCCCATCAAGTCCTCGTCTTGATTCCCTCGAGCTTCCAAAGGGAC
1 TGATGTGACCACGCCCCAAGCCCCATCAAGTCCTCGTCTTGATTCCCTCGAGCTTCCAAAGGGAC
* * * *
92740613 CAATGACCCGAGCTAGGTCCAAGCGATTTCATGAAGTTGTTTCAGCTTTGTTGTTCAAGTTTTAG
66 AAATGAACCGAGCTAGGTCCAAGCGATTTCATGAACTTGTTTCAGCTTTATTGTTCAAGTTTTAG
92740678 AAGGAGAATC
131 AAGGAGAATC
92740688 AGCTTTTTGA
Statistics
Matches: 135, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
140 135 1.00
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.27
Consensus pattern (140 bp):
TGATGTGACCACGCCCCAAGCCCCATCAAGTCCTCGTCTTGATTCCCTCGAGCTTCCAAAGGGAC
AAATGAACCGAGCTAGGTCCAAGCGATTTCATGAACTTGTTTCAGCTTTATTGTTCAAGTTTTAG
AAGGAGAATC
Found at i:92740814 original size:10 final size:10
Alignment explanation
Indices: 92740798--92740855 Score: 64
Period size: 10 Copynumber: 5.7 Consensus size: 10
92740788 CAACTCCGAC
92740798 CAGCTCAATT
1 CAGCTCAATT
* *
92740808 GAGCTCATTT
1 CAGCTCAATT
92740818 CAGCTCAA-T
1 CAGCTCAATT
92740827 CGAGCTCAATT
1 C-AGCTCAATT
*
92740838 TAGCTACAATT
1 CAGCT-CAATT
92740849 CAGCTCA
1 CAGCTCA
92740856 TTTATTTTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 2 0.05
10 27 0.69
11 10 0.26
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:92740821 original size:20 final size:20
Alignment explanation
Indices: 92740798--92740858 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
92740788 CAACTCCGAC
92740798 CAGCTCAATTGAGCTCATTT
1 CAGCTCAATTGAGCTCATTT
*
92740818 CAGCTCAATCGAGCTCAATTT
1 CAGCTCAATTGAGCTC-ATTT
*
92740839 -AGCTACAATTCAGCTCATTT
1 CAGCT-CAATTGAGCTCATTT
92740859 ATTTTATTGG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (20 bp):
CAGCTCAATTGAGCTCATTT
Found at i:92746070 original size:20 final size:21
Alignment explanation
Indices: 92746032--92746079 Score: 71
Period size: 20 Copynumber: 2.3 Consensus size: 21
92746022 AAATGAACTG
92746032 AAACGAGCTAAATTCGAGCTC
1 AAACGAGCTAAATTCGAGCTC
*
92746053 AAACGAGCTGAA-TCGAGCTC
1 AAACGAGCTAAATTCGAGCTC
*
92746073 AAGCGAG
1 AAACGAG
92746080 ATGATTTGAG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 14 0.56
21 11 0.44
ACGTcount: A:0.38, C:0.23, G:0.25, T:0.15
Consensus pattern (21 bp):
AAACGAGCTAAATTCGAGCTC
Found at i:92746091 original size:20 final size:20
Alignment explanation
Indices: 92746045--92746083 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
92746035 CGAGCTAAAT
*
92746045 TCGAGCTCAAACGAGCTGAA
1 TCGAGCTCAAACGAGATGAA
*
92746065 TCGAGCTCAAGCGAGATGA
1 TCGAGCTCAAACGAGATGA
92746084 TTTGAGCTGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.23, G:0.28, T:0.15
Consensus pattern (20 bp):
TCGAGCTCAAACGAGATGAA
Found at i:92746579 original size:18 final size:17
Alignment explanation
Indices: 92746558--92746612 Score: 65
Period size: 18 Copynumber: 3.1 Consensus size: 17
92746548 GAGAAAAACA
92746558 AAAACAAAATTGAAAAAG
1 AAAA-AAAATTGAAAAAG
**
92746576 AAAAAGAAATTGATCAAG
1 AAAAA-AAATTGAAAAAG
92746594 AAAAGAAAATTGAAAAAG
1 AAAA-AAAATTGAAAAAG
92746612 A
1 A
92746613 GAGTGAGTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
17 1 0.03
18 29 0.94
19 1 0.03
ACGTcount: A:0.69, C:0.04, G:0.15, T:0.13
Consensus pattern (17 bp):
AAAAAAAATTGAAAAAG
Found at i:92748493 original size:11 final size:13
Alignment explanation
Indices: 92748465--92748497 Score: 52
Period size: 11 Copynumber: 2.7 Consensus size: 13
92748455 TGCAATTTCT
92748465 TTTTCTTTCTTCG
1 TTTTCTTTCTTCG
92748478 TTTTCTTT-TT-G
1 TTTTCTTTCTTCG
92748489 TTTTCTTTC
1 TTTTCTTTC
92748498 AATTTCTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 9 0.47
12 2 0.11
13 8 0.42
ACGTcount: A:0.00, C:0.18, G:0.06, T:0.76
Consensus pattern (13 bp):
TTTTCTTTCTTCG
Found at i:92749541 original size:11 final size:11
Alignment explanation
Indices: 92749504--92749550 Score: 51
Period size: 11 Copynumber: 4.3 Consensus size: 11
92749494 CTCGCAAGAC
*
92749504 TTTTCACTTTT
1 TTTTTACTTTT
**
92749515 TTTTTAACTTGA
1 TTTTT-ACTTTT
92749527 TTTTTACTTTT
1 TTTTTACTTTT
92749538 TTTTT-CTTTT
1 TTTTTACTTTT
92749548 TTT
1 TTT
92749551 GCTCACTTCT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
10 8 0.27
11 13 0.43
12 9 0.30
ACGTcount: A:0.11, C:0.11, G:0.02, T:0.77
Consensus pattern (11 bp):
TTTTTACTTTT
Found at i:92751115 original size:20 final size:20
Alignment explanation
Indices: 92751092--92751138 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
92751082 GGGTTAAGAT
*
92751092 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
92751112 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
92751132 TGAGCTG
1 TGAGCTG
92751139 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:92752521 original size:30 final size:29
Alignment explanation
Indices: 92752476--92752560 Score: 109
Period size: 30 Copynumber: 2.8 Consensus size: 29
92752466 TTCTTTTGTT
*
92752476 TCAATTTCTTTTTCATCTTCTTTTTCACTC
1 TCAATTTCTTTTTCAT-TTCTTTTTCAATC
92752506 TCAAATTTC-TTTTCATTCTCTTTTTCAATC
1 TC-AATTTCTTTTTCATT-TCTTTTTCAATC
*
92752536 TCATTTTCTTTTTCATTTTCTTTTT
1 TCAATTTCTTTTTCA-TTTCTTTTT
92752561 GATTTTCAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
29 6 0.12
30 35 0.71
31 8 0.16
ACGTcount: A:0.14, C:0.22, G:0.00, T:0.64
Consensus pattern (29 bp):
TCAATTTCTTTTTCATTTCTTTTTCAATC
Found at i:92752551 original size:12 final size:12
Alignment explanation
Indices: 92752536--92752567 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
92752526 TTTTTCAATC
92752536 TCATTTTCTTTT
1 TCATTTTCTTTT
92752548 TCATTTTCTTTT
1 TCATTTTCTTTT
*
92752560 TGATTTTC
1 TCATTTTC
92752568 AAAGGCTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.09, C:0.16, G:0.03, T:0.72
Consensus pattern (12 bp):
TCATTTTCTTTT
Found at i:92752560 original size:18 final size:18
Alignment explanation
Indices: 92752511--92752559 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
92752501 CACTCTCAAA
*
92752511 TTTC-TTTTCATTCTCTT
1 TTTCATTTTCATTTTCTT
* *
92752528 TTTCAATCTCATTTTCTT
1 TTTCATTTTCATTTTCTT
92752546 TTTCATTTTC-TTTT
1 TTTCATTTTCATTTT
92752560 TGATTTTCAA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
17 8 0.31
18 18 0.69
ACGTcount: A:0.10, C:0.20, G:0.00, T:0.69
Consensus pattern (18 bp):
TTTCATTTTCATTTTCTT
Found at i:92752578 original size:12 final size:12
Alignment explanation
Indices: 92752563--92752591 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
92752553 TTCTTTTTGA
92752563 TTTTCAAAGGCT
1 TTTTCAAAGGCT
92752575 TTTTCAAAGGCT
1 TTTTCAAAGGCT
92752587 TTTTC
1 TTTTC
92752592 GAGTTCTCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.21, C:0.17, G:0.14, T:0.48
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:92752647 original size:5 final size:5
Alignment explanation
Indices: 92752637--92752693 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
92752627 CTCTTGCCTC
*
92752637 TCTTT TCTTT T-TATT TCATTT TCTTT T-TCT TCTTT TGCTTTT TCTTT
1 TCTTT TCTTT TCT-TT TC-TTT TCTTT TCTTT TCTTT T-C-TTT TCTTT
92752684 TCTTT TCTTT
1 TCTTT TCTTT
92752694 GTTTTCTCTT
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
4 4 0.09
5 29 0.66
6 6 0.14
7 5 0.11
ACGTcount: A:0.04, C:0.18, G:0.02, T:0.77
Consensus pattern (5 bp):
TCTTT
Found at i:92752677 original size:15 final size:14
Alignment explanation
Indices: 92752637--92752693 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
92752627 CTCTTGCCTC
*
92752637 TCTTTTCTTTTTATT
1 TCTTTTCTTTTT-CT
92752652 TCATTTTCTTTTTCT
1 TC-TTTTCTTTTTCT
92752667 TCTTTTGCTTTTTCTTT
1 TCTTTT-CTTTTTC--T
92752684 TCTTTTCTTT
1 TCTTTTCTTT
92752694 GTTTTCTCTT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
14 4 0.11
15 12 0.32
16 14 0.38
17 7 0.19
ACGTcount: A:0.04, C:0.18, G:0.02, T:0.77
Consensus pattern (14 bp):
TCTTTTCTTTTTCT
Found at i:92752694 original size:21 final size:21
Alignment explanation
Indices: 92752637--92752704 Score: 61
Period size: 21 Copynumber: 3.2 Consensus size: 21
92752627 CTCTTGCCTC
* *
92752637 TCTTTTCTTTT-TATTTCATTT
1 TCTTTTCTTTTCT-TTGCTTTT
*
92752658 TCTTTT-TCTTCTTTTGCTTTT
1 TCTTTTCTTTTC-TTTGCTTTT
92752679 TCTTTTCTTTTCTTTG-TTTT
1 TCTTTTCTTTTCTTTGCTTTT
92752699 CTCTTT
1 -TCTTT
92752705 ACAAGAATGT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
20 7 0.18
21 27 0.69
22 5 0.13
ACGTcount: A:0.03, C:0.18, G:0.03, T:0.76
Consensus pattern (21 bp):
TCTTTTCTTTTCTTTGCTTTT
Found at i:92755195 original size:23 final size:22
Alignment explanation
Indices: 92755143--92755195 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
92755133 TCCACGTCTT
*
92755143 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
92755165 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
92755188 TTTCTTTT
1 TTTCTTTT
92755196 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:92758421 original size:10 final size:10
Alignment explanation
Indices: 92758408--92758447 Score: 62
Period size: 10 Copynumber: 3.9 Consensus size: 10
92758398 TTTTCAGATT
92758408 TTTTTTTGAA
1 TTTTTTTGAA
*
92758418 TTTTTTTTGCA
1 -TTTTTTTGAA
92758429 TTTTTTTGAA
1 TTTTTTTGAA
92758439 TTTTTTTGA
1 TTTTTTTGA
92758448 CTTGTATAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
10 18 0.67
11 9 0.33
ACGTcount: A:0.15, C:0.03, G:0.10, T:0.72
Consensus pattern (10 bp):
TTTTTTTGAA
Found at i:92758421 original size:11 final size:11
Alignment explanation
Indices: 92758407--92758445 Score: 62
Period size: 11 Copynumber: 3.6 Consensus size: 11
92758397 TTTTTCAGAT
92758407 TTTTTTTTGAA
1 TTTTTTTTGAA
*
92758418 TTTTTTTTGCA
1 TTTTTTTTGAA
92758429 -TTTTTTTGAA
1 TTTTTTTTGAA
92758439 TTTTTTT
1 TTTTTTT
92758446 GACTTGTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 9 0.36
11 16 0.64
ACGTcount: A:0.13, C:0.03, G:0.08, T:0.77
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:92759590 original size:22 final size:22
Alignment explanation
Indices: 92759560--92759606 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
92759550 TTTGGTATTT
92759560 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
92759582 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
92759604 GGG
1 GGG
92759607 TTCAAAAAGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.32, C:0.04, G:0.40, T:0.23
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:92763895 original size:17 final size:17
Alignment explanation
Indices: 92763870--92763923 Score: 63
Period size: 17 Copynumber: 3.2 Consensus size: 17
92763860 TCTCTTTTCA
*
92763870 TTCTCTTTTTTTGAATT
1 TTCTTTTTTTTTGAATT
* *
92763887 TTCTTTTTTTTTCATTT
1 TTCTTTTTTTTTGAATT
* *
92763904 TTCTTTTCTTTTGTATT
1 TTCTTTTTTTTTGAATT
92763921 TTC
1 TTC
92763924 GCTCTTTTCT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.07, C:0.13, G:0.04, T:0.76
Consensus pattern (17 bp):
TTCTTTTTTTTTGAATT
Found at i:92768585 original size:18 final size:18
Alignment explanation
Indices: 92768562--92768596 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
92768552 TTTTTCTTTT
92768562 TCAATTT-TTTTCTCAATC
1 TCAATTTCTTTT-TCAATC
92768580 TCAATTTCTTTTTCAAT
1 TCAATTTCTTTTTCAAT
92768597 TTTCTTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.23, C:0.20, G:0.00, T:0.57
Consensus pattern (18 bp):
TCAATTTCTTTTTCAATC
Found at i:92769536 original size:14 final size:13
Alignment explanation
Indices: 92769493--92769529 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
92769483 AAATACTTCG
92769493 ATTTTTTTTTTGA
1 ATTTTTTTTTTGA
*
92769506 ATTTTTTTTTTGG
1 ATTTTTTTTTTGA
92769519 ATTTTTTTTTT
1 ATTTTTTTTTT
92769530 CAAATTTCCT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.11, C:0.00, G:0.08, T:0.81
Consensus pattern (13 bp):
ATTTTTTTTTTGA
Found at i:92771424 original size:24 final size:23
Alignment explanation
Indices: 92771370--92771425 Score: 58
Period size: 24 Copynumber: 2.4 Consensus size: 23
92771360 GATTAATTAA
**
92771370 GAAATGGTATTTGGTTTTGGTAC
1 GAAATGGTATTTGGAATTGGTAC
***
92771393 GTTTTGGTATTTGGGAATTGGTAC
1 GAAATGGTATTT-GGAATTGGTAC
92771417 GAAATGGTA
1 GAAATGGTA
92771426 AGGGTTCAAA
Statistics
Matches: 24, Mismatches: 8, Indels: 1
0.73 0.24 0.03
Matches are distributed among these distances:
23 9 0.38
24 15 0.62
ACGTcount: A:0.23, C:0.04, G:0.32, T:0.41
Consensus pattern (23 bp):
GAAATGGTATTTGGAATTGGTAC
Found at i:92773701 original size:30 final size:30
Alignment explanation
Indices: 92773667--92773763 Score: 99
Period size: 30 Copynumber: 3.2 Consensus size: 30
92773657 TAAACTAAAA
92773667 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * *
92773697 TGAGCTGAGGC-TAAACTCGTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
* *
92773727 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
92773757 TGAGCTA
1 TGAGCTA
92773764 GGAGTGAGCT
Statistics
Matches: 52, Mismatches: 12, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
29 2 0.04
30 44 0.85
31 6 0.12
ACGTcount: A:0.28, C:0.14, G:0.30, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:92774392 original size:19 final size:19
Alignment explanation
Indices: 92774368--92774404 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
92774358 TACTACAACA
92774368 ATTTAAGTTGTCTTAGTTC
1 ATTTAAGTTGTCTTAGTTC
*
92774387 ATTTAATTTGTCTTAGTT
1 ATTTAAGTTGTCTTAGTT
92774405 TAATGCATGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.08, G:0.14, T:0.57
Consensus pattern (19 bp):
ATTTAAGTTGTCTTAGTTC
Found at i:92776722 original size:19 final size:19
Alignment explanation
Indices: 92776699--92776774 Score: 75
Period size: 20 Copynumber: 3.8 Consensus size: 19
92776689 TAAAAATTTG
92776699 AAAAAATAAAAAAAAGTATC
1 AAAAAATAAAAAAAAGT-TC
92776719 AAAAAA-ACAAAAAAA-TTC
1 AAAAAATA-AAAAAAAGTTC
*
92776737 AAAAAATCCAAAAAAAAGTTA
1 AAAAAAT--AAAAAAAAGTTC
92776758 AAAAAATTAGAAAAAAA
1 AAAAAA-TA-AAAAAAA
92776775 ACCTTGAAAA
Statistics
Matches: 48, Mismatches: 1, Indels: 13
0.77 0.02 0.21
Matches are distributed among these distances:
18 8 0.17
19 2 0.04
20 21 0.44
21 16 0.33
22 1 0.02
ACGTcount: A:0.76, C:0.07, G:0.04, T:0.13
Consensus pattern (19 bp):
AAAAAATAAAAAAAAGTTC
Found at i:92776723 original size:21 final size:20
Alignment explanation
Indices: 92776699--92776774 Score: 70
Period size: 21 Copynumber: 3.8 Consensus size: 20
92776689 TAAAAATTTG
92776699 AAAAAATAAAAAAAAGTATCA
1 AAAAAATAAAAAAAAGT-TCA
*
92776720 AAAAAA-CAAAAAAA-TTC-
1 AAAAAATAAAAAAAAGTTCA
92776737 AAAAAATCCAAAAAAAAGTT-A
1 AAAAAAT--AAAAAAAAGTTCA
92776758 AAAAAATTAGAAAAAAA
1 AAAAAA-TA-AAAAAAA
92776775 ACCTTGAAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 14
0.74 0.03 0.23
Matches are distributed among these distances:
17 6 0.13
18 2 0.04
19 1 0.02
20 15 0.33
21 21 0.46
22 1 0.02
ACGTcount: A:0.76, C:0.07, G:0.04, T:0.13
Consensus pattern (20 bp):
AAAAAATAAAAAAAAGTTCA
Found at i:92778857 original size:30 final size:30
Alignment explanation
Indices: 92778823--92778919 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
92778813 TAAACTAAAA
92778823 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
92778853 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
* *
92778883 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
92778913 TGAGCTA
1 TGAGCTA
92778920 GAAGTGAGCT
Statistics
Matches: 50, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
29 2 0.04
30 42 0.84
31 6 0.12
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:92779327 original size:54 final size:54
Alignment explanation
Indices: 92779245--92779356 Score: 224
Period size: 54 Copynumber: 2.1 Consensus size: 54
92779235 TCAAAGGAGT
92779245 CAAATTCAAATGTGTTCGATAGTTCATAAAATATTCATTCAATCGAACATATGC
1 CAAATTCAAATGTGTTCGATAGTTCATAAAATATTCATTCAATCGAACATATGC
92779299 CAAATTCAAATGTGTTCGATAGTTCATAAAATATTCATTCAATCGAACATATGC
1 CAAATTCAAATGTGTTCGATAGTTCATAAAATATTCATTCAATCGAACATATGC
92779353 CAAA
1 CAAA
92779357 AATCTCAATT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 58 1.00
ACGTcount: A:0.40, C:0.17, G:0.11, T:0.32
Consensus pattern (54 bp):
CAAATTCAAATGTGTTCGATAGTTCATAAAATATTCATTCAATCGAACATATGC
Found at i:92781106 original size:30 final size:30
Alignment explanation
Indices: 92781072--92781138 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
92781062 TTTTTCATCT
*
92781072 TCTTTTTCACTCTCAAATTTC-TTTTCGTTC
1 TCTTTTTCAATCTC-AATTTCATTTTCGTTC
* * *
92781102 TCTTTTTCAATCTCATTTTCATTTTCTTTT
1 TCTTTTTCAATCTCAATTTCATTTTCGTTC
92781132 TCTTTTT
1 TCTTTTT
92781139 GCTTTTCAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 5 0.16
30 27 0.84
ACGTcount: A:0.12, C:0.22, G:0.01, T:0.64
Consensus pattern (30 bp):
TCTTTTTCAATCTCAATTTCATTTTCGTTC
Found at i:92781156 original size:12 final size:12
Alignment explanation
Indices: 92781141--92781171 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
92781131 TTCTTTTTGC
92781141 TTTTCAAAGGCT
1 TTTTCAAAGGCT
92781153 TTTTCAAAGGCT
1 TTTTCAAAGGCT
92781165 TTTTCAA
1 TTTTCAA
92781172 GTCCTCTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:92781242 original size:6 final size:6
Alignment explanation
Indices: 92781233--92781287 Score: 66
Period size: 6 Copynumber: 10.0 Consensus size: 6
92781223 TTCTTTTTAA
*
92781233 TTCTTT TTCTTT TTC--- TTCTTT TTCTTT TTCTTT TGCTTT TTC-TT
1 TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT
92781277 TTC-TT TTCTTT
1 TTCTTT TTCTTT
92781288 GTTTTCTCTT
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
3 3 0.07
5 10 0.23
6 30 0.70
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.80
Consensus pattern (6 bp):
TTCTTT
Found at i:92781243 original size:21 final size:19
Alignment explanation
Indices: 92781219--92781294 Score: 77
Period size: 21 Copynumber: 3.8 Consensus size: 19
92781209 CTCTTGCCTC
92781219 TCTTTTCTTTTTAATTCTTTT
1 TCTTTTCTTTTT--TTCTTTT
92781240 TCTTTTTCTTCTTTTTCTTTT
1 TC-TTTTCTT-TTTTTCTTTT
92781261 TCTTTTGC--TTTTTC-TTT
1 TCTTTT-CTTTTTTTCTTTT
92781278 TCTTTTCTTTGTTTTCT
1 TCTTTTCTTT-TTTTCT
92781295 CTTTACAAGA
Statistics
Matches: 48, Mismatches: 0, Indels: 15
0.76 0.00 0.24
Matches are distributed among these distances:
16 1 0.02
17 9 0.19
18 7 0.15
19 5 0.10
20 4 0.08
21 12 0.25
22 7 0.15
23 3 0.06
ACGTcount: A:0.03, C:0.17, G:0.03, T:0.78
Consensus pattern (19 bp):
TCTTTTCTTTTTTTCTTTT
Found at i:92781262 original size:15 final size:15
Alignment explanation
Indices: 92781221--92781278 Score: 71
Period size: 15 Copynumber: 3.6 Consensus size: 15
92781211 CTTGCCTCTC
*
92781221 TTTTCTTTTTAATTCT
1 TTTTCTTTTT-CTTCT
92781237 TTTTCTTTTTCTTCT
1 TTTTCTTTTTCTTCT
92781252 TTTTCTTTTTCTTTTGCT
1 TTTTCTTTTTC--TT-CT
92781270 TTTTCTTTT
1 TTTTCTTTT
92781279 CTTTTCTTTG
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
15 15 0.39
16 10 0.26
17 2 0.05
18 11 0.29
ACGTcount: A:0.03, C:0.16, G:0.02, T:0.79
Consensus pattern (15 bp):
TTTTCTTTTTCTTCT
Found at i:92781263 original size:27 final size:28
Alignment explanation
Indices: 92781233--92781287 Score: 85
Period size: 27 Copynumber: 2.0 Consensus size: 28
92781223 TTCTTTTTAA
*
92781233 TTCTTTTTCTTTTTCTTCT-TTTTCTTT
1 TTCTTTTGCTTTTTCTTCTCTTTTCTTT
*
92781260 TTCTTTTGCTTTTTCTTTTCTTTTCTTT
1 TTCTTTTGCTTTTTCTTCTCTTTTCTTT
92781288 GTTTTCTCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 17 0.68
28 8 0.32
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.80
Consensus pattern (28 bp):
TTCTTTTGCTTTTTCTTCTCTTTTCTTT
Found at i:92783231 original size:30 final size:31
Alignment explanation
Indices: 92783197--92783293 Score: 101
Period size: 30 Copynumber: 3.2 Consensus size: 31
92783187 AGCTCACTCC
*
92783197 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* * * * *
92783227 TAGCTCAAC-TTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* *
92783257 CAGCTCAACTTT-AGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
92783287 TAGCTCA
1 TAGCTCA
92783294 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
30 47 0.92
31 4 0.08
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (31 bp):
TAGCTCAACTTTCAGCTCACGAGCTAAACCT
Found at i:92785638 original size:23 final size:22
Alignment explanation
Indices: 92785602--92785666 Score: 94
Period size: 23 Copynumber: 2.9 Consensus size: 22
92785592 GACACCATTT
*
92785602 AAAACATGCATTAAATTCGGCC
1 AAAACATACATTAAATTCGGCC
*
92785624 AGAAACATACTTTAAATTCGGCC
1 A-AAACATACATTAAATTCGGCC
92785647 AAAGACATACATTAAATTCG
1 AAA-ACATACATTAAATTCG
92785667 TCTGGAAAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
22 3 0.08
23 35 0.92
ACGTcount: A:0.43, C:0.20, G:0.12, T:0.25
Consensus pattern (22 bp):
AAAACATACATTAAATTCGGCC
Found at i:92785904 original size:13 final size:13
Alignment explanation
Indices: 92785888--92785922 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
92785878 TTTAAACAAA
*
92785888 TTAATTAACTTAT
1 TTAATTAACTAAT
92785901 TTAATTAACTAAT
1 TTAATTAACTAAT
*
92785914 TTAACTAAC
1 TTAATTAAC
92785923 AGCAACTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.43, C:0.11, G:0.00, T:0.46
Consensus pattern (13 bp):
TTAATTAACTAAT
Found at i:92786010 original size:20 final size:20
Alignment explanation
Indices: 92785985--92786039 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
92785975 ACAAGTTAAA
* *
92785985 TTGAGCTTGAATGAGCTGAC
1 TTGAGCTCGAATGAGCTAAC
*
92786005 TTGAGCACGAATGAGCTAAC
1 TTGAGCTCGAATGAGCTAAC
92786025 TTGAGCTCGAATGAG
1 TTGAGCTCGAATGAG
92786040 TTGAACCACA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.25
Consensus pattern (20 bp):
TTGAGCTCGAATGAGCTAAC
Found at i:92787348 original size:15 final size:16
Alignment explanation
Indices: 92787309--92787349 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
92787299 AACAACACTC
92787309 CTTTCTTTTTCACTTT
1 CTTTCTTTTTCACTTT
* *
92787325 C-ATCCTTTTCA-TTT
1 CTTTCTTTTTCACTTT
92787339 CTTTCTTTTTC
1 CTTTCTTTTTC
92787350 CAACTCATTT
Statistics
Matches: 20, Mismatches: 4, Indels: 3
0.74 0.15 0.11
Matches are distributed among these distances:
14 4 0.20
15 15 0.75
16 1 0.05
ACGTcount: A:0.07, C:0.27, G:0.00, T:0.66
Consensus pattern (16 bp):
CTTTCTTTTTCACTTT
Found at i:92787542 original size:17 final size:15
Alignment explanation
Indices: 92787505--92787545 Score: 55
Period size: 15 Copynumber: 2.5 Consensus size: 15
92787495 TATCTCCCAC
92787505 TCATCTTCTTTTTCTT
1 TCAT-TTCTTTTTCTT
92787521 TCATTTCTTTTTCATGT
1 TCATTTCTTTTTC-T-T
92787538 TCATTTCT
1 TCATTTCT
92787546 CGCTCGCGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 9 0.39
16 5 0.22
17 9 0.39
ACGTcount: A:0.10, C:0.22, G:0.02, T:0.66
Consensus pattern (15 bp):
TCATTTCTTTTTCTT
Found at i:92788542 original size:13 final size:13
Alignment explanation
Indices: 92788526--92788568 Score: 86
Period size: 13 Copynumber: 3.3 Consensus size: 13
92788516 ATTGAATACA
92788526 TTTTTTGAATTTT
1 TTTTTTGAATTTT
92788539 TTTTTTGAATTTT
1 TTTTTTGAATTTT
92788552 TTTTTTGAATTTT
1 TTTTTTGAATTTT
92788565 TTTT
1 TTTT
92788569 CCTTTTTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 30 1.00
ACGTcount: A:0.14, C:0.00, G:0.07, T:0.79
Consensus pattern (13 bp):
TTTTTTGAATTTT
Found at i:92789462 original size:15 final size:15
Alignment explanation
Indices: 92789444--92789473 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
92789434 TTTTTTTCGA
92789444 TTTTTTTT-TGAATT
1 TTTTTTTTCTGAATT
92789458 TTTTTTTTCTGAATT
1 TTTTTTTTCTGAATT
92789473 T
1 T
92789474 CTTATCTCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.13, C:0.03, G:0.07, T:0.77
Consensus pattern (15 bp):
TTTTTTTTCTGAATT
Found at i:92793045 original size:17 final size:17
Alignment explanation
Indices: 92793003--92793045 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
92792993 TGCACTTAAG
*
92793003 CCATTCATGCATTTTAT
1 CCATTCATGCATTTGAT
*
92793020 -CATCCCATGCATTTGAT
1 CCAT-TCATGCATTTGAT
92793037 CCATTCATG
1 CCATTCATG
92793046 GACTAGCCTT
Statistics
Matches: 21, Mismatches: 3, Indels: 4
0.75 0.11 0.14
Matches are distributed among these distances:
16 3 0.14
17 15 0.71
18 3 0.14
ACGTcount: A:0.23, C:0.28, G:0.09, T:0.40
Consensus pattern (17 bp):
CCATTCATGCATTTGAT
Found at i:92794415 original size:20 final size:20
Alignment explanation
Indices: 92794369--92794415 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
92794359 AGCTCGTTTC
*
92794369 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
92794389 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
92794409 CAGCTCA
1 CAGCTCA
92794416 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:92800681 original size:1 final size:1
Alignment explanation
Indices: 92800640--92800666 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
92800630 TTCAAAATTC
92800640 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
92800667 GAAGTGACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:92801814 original size:48 final size:47
Alignment explanation
Indices: 92801735--92801840 Score: 135
Period size: 48 Copynumber: 2.2 Consensus size: 47
92801725 GAGTGTCATG
*
92801735 GAAAAAGAAATTGAGATTGAAAAAGGATGTGA-AAAAGAGAAAGAAATC
1 GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAA-AGAAA-AAATC
* *
92801783 GAAAAAGAAATTGAGATTGAACAAAAG-TGTGAGGAAAAAGAGAAAATT
1 GAAAAAGAAATTGAGATTGAA-AAAAGATGTGA-GAAAAAGAAAAAATC
92801831 GAAAAAGAAA
1 GAAAAAGAAA
92801841 GAAAAGACAA
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.59, C:0.02, G:0.25, T:0.14
Consensus pattern (47 bp):
GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAAAGAAAAAATC
Found at i:92803556 original size:20 final size:20
Alignment explanation
Indices: 92803510--92803556 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
92803500 AGCTCGTTTC
*
92803510 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
92803530 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
92803550 CAGCTCA
1 CAGCTCA
92803557 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:92808861 original size:30 final size:30
Alignment explanation
Indices: 92808766--92808862 Score: 88
Period size: 30 Copynumber: 3.2 Consensus size: 30
92808756 AGCTCACTCC
*
92808766 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTT-AGCTCACGAGCTAAACCT
* * * * * *
92808796 TAGCTCAACTTCAGCTTAGGAGTTTATCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* * *
92808826 CAGCTCAACTTTAGCTCATGAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
92808856 TAGCTCA
1 TAGCTCA
92808863 TTTTAGTTTA
Statistics
Matches: 50, Mismatches: 16, Indels: 2
0.74 0.24 0.03
Matches are distributed among these distances:
30 46 0.92
31 4 0.08
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.30
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:92810907 original size:10 final size:10
Alignment explanation
Indices: 92810894--92810938 Score: 63
Period size: 10 Copynumber: 4.4 Consensus size: 10
92810884 AAAAGAAATT
92810894 AGCTGAAACG
1 AGCTGAAACG
*
92810904 AGCTGAAATCA
1 AGCTGAAA-CG
*
92810915 AGCTCAAACG
1 AGCTGAAACG
92810925 AGCTGAAACG
1 AGCTGAAACG
92810935 AGCT
1 AGCT
92810939 CAAGTGAGCT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
10 22 0.73
11 8 0.27
ACGTcount: A:0.40, C:0.22, G:0.24, T:0.13
Consensus pattern (10 bp):
AGCTGAAACG
Found at i:92810947 original size:20 final size:21
Alignment explanation
Indices: 92810894--92810950 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 21
92810884 AAAAGAAATT
*
92810894 AGCTGAAACGAGCTGAAATCA
1 AGCTCAAACGAGCTGAAATCA
*
92810915 AGCTCAAACGAGCTGAAA-CG
1 AGCTCAAACGAGCTGAAATCA
**
92810935 AGCTCAAGTGAGCTGA
1 AGCTCAAACGAGCTGA
92810951 TTGGAGCTGA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 15 0.47
21 17 0.53
ACGTcount: A:0.39, C:0.21, G:0.26, T:0.14
Consensus pattern (21 bp):
AGCTCAAACGAGCTGAAATCA
Found at i:92813964 original size:22 final size:22
Alignment explanation
Indices: 92813936--92813979 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
92813926 TTTTGAACCA
92813936 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
92813958 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
92813980 AAATACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.25, C:0.36, G:0.05, T:0.34
Consensus pattern (22 bp):
TTACCATTTCGTACCAAATCCC
Found at i:92816174 original size:20 final size:20
Alignment explanation
Indices: 92816128--92816175 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
92816118 AGTAAGCTCG
92816128 GTTGAGCTCAAATGAGCTGA
1 GTTGAGCTCAAATGAGCTGA
*** *
92816148 AACGAGCTTAAATGAGCTGA
1 GTTGAGCTCAAATGAGCTGA
92816168 GTTGAGCT
1 GTTGAGCT
92816176 GGACGGAGCT
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.31, C:0.15, G:0.29, T:0.25
Consensus pattern (20 bp):
GTTGAGCTCAAATGAGCTGA
Found at i:92817786 original size:18 final size:19
Alignment explanation
Indices: 92817763--92817801 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
92817753 TTTATCTCAA
*
92817763 TTTCTTTTTC-CACTCTTT
1 TTTCTTGTTCACACTCTTT
*
92817781 TTTCTTGTTCACATTCTTT
1 TTTCTTGTTCACACTCTTT
92817800 TT
1 TT
92817802 CTCTCTCAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.08, C:0.23, G:0.03, T:0.67
Consensus pattern (19 bp):
TTTCTTGTTCACACTCTTT
Found at i:92817840 original size:18 final size:17
Alignment explanation
Indices: 92817818--92817866 Score: 62
Period size: 18 Copynumber: 2.8 Consensus size: 17
92817808 CAAACTCTTT
92817818 TTCATTCTCTTTTTCAA
1 TTCATTCTCTTTTTCAA
* *
92817835 TCTCATTTTCTTTTTCAC
1 T-TCATTCTCTTTTTCAA
*
92817853 TTCAATCTCTTTTT
1 TTCATTCTCTTTTT
92817867 TTTTTCTTTC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
17 12 0.44
18 15 0.56
ACGTcount: A:0.14, C:0.24, G:0.00, T:0.61
Consensus pattern (17 bp):
TTCATTCTCTTTTTCAA
Found at i:92817858 original size:23 final size:22
Alignment explanation
Indices: 92817830--92817872 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
92817820 CATTCTCTTT
92817830 TTCAATCTCATTTTCTTTTTCAC
1 TTCAATCTC-TTTTCTTTTTCAC
*
92817853 TTCAATCTCTTTTTTTTTTC
1 TTCAATCTCTTTTCTTTTTC
92817873 TTTCATTTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.14, C:0.23, G:0.00, T:0.63
Consensus pattern (22 bp):
TTCAATCTCTTTTCTTTTTCAC
Found at i:92825575 original size:20 final size:20
Alignment explanation
Indices: 92825529--92825576 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
92825519 AGTAAGCTCG
92825529 GTTGAGCTCAAACGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
*** * *
92825549 AACGAGCTTAAATGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
92825569 GTTGAGCT
1 GTTGAGCT
92825577 GGACGGAGCT
Statistics
Matches: 20, Mismatches: 8, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.31, C:0.17, G:0.29, T:0.23
Consensus pattern (20 bp):
GTTGAGCTCAAACGAGCTGA
Found at i:92825720 original size:30 final size:30
Alignment explanation
Indices: 92825686--92825745 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
92825676 CTTTAATACG
92825686 AACTTTGGCAAAATTAC-CATTTTGCCCCTA
1 AACTTTGGCAAAATTACAC-TTTTGCCCCTA
* *
92825716 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGCAAAATTACACTTTTGCCCCTA
92825746 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 26 0.96
31 1 0.04
ACGTcount: A:0.28, C:0.27, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGCAAAATTACACTTTTGCCCCTA
Found at i:92836886 original size:22 final size:22
Alignment explanation
Indices: 92836858--92836901 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
92836848 TTTTGAACCA
92836858 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
92836880 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
92836902 AAATACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.25, C:0.36, G:0.05, T:0.34
Consensus pattern (22 bp):
TTACCATTTCGTACCAAATCCC
Found at i:92838298 original size:13 final size:13
Alignment explanation
Indices: 92838280--92838324 Score: 65
Period size: 14 Copynumber: 3.5 Consensus size: 13
92838270 TTGTAGATTC
92838280 AAAAAAATTG-AA
1 AAAAAAATTGAAA
*
92838292 AAAAAAATCGAAA
1 AAAAAAATTGAAA
92838305 AAAAAAATTTGAAA
1 AAAAAAA-TTGAAA
92838319 AAAAAA
1 AAAAAA
92838325 TTGCATACGG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
12 9 0.31
13 9 0.31
14 11 0.38
ACGTcount: A:0.78, C:0.02, G:0.07, T:0.13
Consensus pattern (13 bp):
AAAAAAATTGAAA
Found at i:92838325 original size:13 final size:12
Alignment explanation
Indices: 92838280--92838327 Score: 69
Period size: 13 Copynumber: 3.8 Consensus size: 12
92838270 TTGTAGATTC
92838280 AAAAAAATTGAA
1 AAAAAAATTGAA
*
92838292 AAAAAAATCGAAA
1 AAAAAAATTG-AA
92838305 AAAAAAATTTGAA
1 AAAAAAA-TTGAA
92838318 AAAAAAATTG
1 AAAAAAATTG
92838328 CATACGGTCT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
12 12 0.38
13 18 0.56
14 2 0.06
ACGTcount: A:0.73, C:0.02, G:0.08, T:0.17
Consensus pattern (12 bp):
AAAAAAATTGAA
Found at i:92853577 original size:18 final size:18
Alignment explanation
Indices: 92853538--92853579 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
92853528 TACACTCGTT
*
92853538 TTTTCTTCACTCTTTTTG
1 TTTTCTTCACTCTTTTTC
*
92853556 TTTTCTTGA-TCTTTATTC
1 TTTTCTTCACTCTTT-TTC
92853574 TTTTCT
1 TTTTCT
92853580 CTCATTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.07, C:0.19, G:0.05, T:0.69
Consensus pattern (18 bp):
TTTTCTTCACTCTTTTTC
Found at i:92854638 original size:18 final size:18
Alignment explanation
Indices: 92854615--92854651 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
92854605 GCACCGGCTA
*
92854615 TTTTTTTGTTTGATTCTT
1 TTTTTTTGTTTCATTCTT
92854633 TTTTTTTGTTTCATTCTT
1 TTTTTTTGTTTCATTCTT
92854651 T
1 T
92854652 GATTGTCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.05, C:0.08, G:0.08, T:0.78
Consensus pattern (18 bp):
TTTTTTTGTTTCATTCTT
Found at i:92855523 original size:15 final size:15
Alignment explanation
Indices: 92855503--92855534 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
92855493 TTGTACTATG
92855503 AGATAAATAAATTTT
1 AGATAAATAAATTTT
92855518 AGATAAATAAATTTT
1 AGATAAATAAATTTT
92855533 AG
1 AG
92855535 TGAAGAAAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.09, T:0.38
Consensus pattern (15 bp):
AGATAAATAAATTTT
Found at i:92859172 original size:23 final size:22
Alignment explanation
Indices: 92859121--92859172 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
92859111 CCTCGTCTTT
*
92859121 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
92859143 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
92859166 TTCTTTT
1 TTCTTTT
92859173 TCAATTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:92863852 original size:41 final size:41
Alignment explanation
Indices: 92863790--92863900 Score: 134
Period size: 46 Copynumber: 2.6 Consensus size: 41
92863780 TTTTTCCTTA
*
92863790 TACT-ATTACAACATCTATTCCATTCAACCAAACAATTGAAT
1 TACTGATTACAGC-TCTATTCCATTCAACCAAACAATTGAAT
* *
92863831 TATTGATTACAGCTCTATTCCATTCCATTCAACCAAACTATTGAAT
1 TACTGATTACAGCTC---T--ATTCCATTCAACCAAACAATTGAAT
92863877 TACTGATTACAGCTCTATTCCATT
1 TACTGATTACAGCTCTATTCCATT
92863901 ACAGCTCTAT
Statistics
Matches: 60, Mismatches: 4, Indels: 12
0.79 0.05 0.16
Matches are distributed among these distances:
41 13 0.22
42 7 0.12
43 1 0.02
44 1 0.02
46 38 0.63
ACGTcount: A:0.34, C:0.24, G:0.05, T:0.36
Consensus pattern (41 bp):
TACTGATTACAGCTCTATTCCATTCAACCAAACAATTGAAT
Found at i:92863858 original size:46 final size:46
Alignment explanation
Indices: 92863806--92863900 Score: 172
Period size: 46 Copynumber: 2.1 Consensus size: 46
92863796 TACAACATCT
*
92863806 ATTCCATTCAACCAAACAATTGAATTATTGATTACAGCTCTATTCC
1 ATTCCATTCAACCAAACAATTGAATTACTGATTACAGCTCTATTCC
*
92863852 ATTCCATTCAACCAAACTATTGAATTACTGATTACAGCTCTATTCC
1 ATTCCATTCAACCAAACAATTGAATTACTGATTACAGCTCTATTCC
92863898 ATT
1 ATT
92863901 ACAGCTCTAT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.34, C:0.24, G:0.06, T:0.36
Consensus pattern (46 bp):
ATTCCATTCAACCAAACAATTGAATTACTGATTACAGCTCTATTCC
Found at i:92863903 original size:16 final size:16
Alignment explanation
Indices: 92863882--92863936 Score: 83
Period size: 16 Copynumber: 3.4 Consensus size: 16
92863872 TGAATTACTG
*
92863882 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTCA
92863898 ATTACAGCTCTATTCA
1 ATTACAGCTCTATTCA
* *
92863914 ATTACAGCCCTATTCT
1 ATTACAGCTCTATTCA
92863930 ATTACAG
1 ATTACAG
92863937 TGAACCAAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.29, C:0.27, G:0.07, T:0.36
Consensus pattern (16 bp):
ATTACAGCTCTATTCA
Found at i:92866760 original size:104 final size:105
Alignment explanation
Indices: 92866514--92866781 Score: 450
Period size: 104 Copynumber: 2.6 Consensus size: 105
92866504 TTGTATATAA
** *
92866514 AGGGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGGTGCTATGTGCG-TGATCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGAT-ATCCACCATATCT
92866578 TTGAAATGTGAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
65 TTGAAATGTGAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
*
92866619 AGGGGTTGCTAAGTGCTGATTCCCCGGTTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
92866684 TGAAATGTG-AAAGGGGGTTGCTATGTGCTGATTCCCCCG
66 TGAAATGTGAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
** *
92866723 AGGGGTTGCTAAGTGCTGATTCCCCGATTCAGCGGTGGTGCTAAGTGCGAGATCCACCA
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCA
92866782 ATAACGGTTA
Statistics
Matches: 154, Mismatches: 8, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
104 85 0.55
105 68 0.44
106 1 0.01
ACGTcount: A:0.19, C:0.21, G:0.31, T:0.30
Consensus pattern (105 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
TGAAATGTGAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
Found at i:92873243 original size:23 final size:22
Alignment explanation
Indices: 92873192--92873243 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
92873182 CCTCGTCTTT
*
92873192 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
92873214 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
92873237 TTCTTTT
1 TTCTTTT
92873244 TCACTCTCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:92876109 original size:14 final size:14
Alignment explanation
Indices: 92876080--92876115 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
92876070 AATGTGAACT
92876080 TAATTAAAACATAGC
1 TAATT-AAACATAGC
*
92876095 TAATTAAAGATAGC
1 TAATTAAACATAGC
92876109 TAATTAA
1 TAATTAA
92876116 TGAACTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 15 0.75
15 5 0.25
ACGTcount: A:0.53, C:0.08, G:0.08, T:0.31
Consensus pattern (14 bp):
TAATTAAACATAGC
Found at i:92877441 original size:46 final size:46
Alignment explanation
Indices: 92877376--92877785 Score: 497
Period size: 46 Copynumber: 9.0 Consensus size: 46
92877366 TTATCTTCGA
* * * *
92877376 CATGATGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCA-TTTCATGT
* * ** *
92877422 CAGGTTGCCATGGAATCTTTCAACCATGGTCTTGTTTATTTCATGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGT
* * **
92877468 --TGCATTGCCATGGTATCTTTCAACCATGGTCTTATTCATTCCCCGT
1 CATG--TTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGT
* * *
92877514 CATGTTGCCAT-GTATCTTTCAACCAT-GTCTTACACATTTTATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGT
* * *
92877558 CCTGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGT
*
92877604 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGT
*** * * *
92877650 TGCGTTGCCATAGTATCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGT
* *
92877696 CATGTTGCTATGGTATCTTTCAACCATGGTCTTATTCATTTCATGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGT
*
92877742 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCAT
92877786 TTTAGAAAGC
Statistics
Matches: 310, Mismatches: 47, Indels: 14
0.84 0.13 0.04
Matches are distributed among these distances:
44 22 0.07
45 34 0.11
46 252 0.81
48 2 0.01
ACGTcount: A:0.21, C:0.23, G:0.14, T:0.41
Consensus pattern (46 bp):
CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGT
Done.