Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D06
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: 68668488
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1920000 characters in sequence are not A, C, G, or T
File 120 of 230
Found at i:34880796 original size:15 final size:15
Alignment explanation
Indices: 34880772--34880803 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
34880762 CTTAATTTCA
*
34880772 TTAGTTTAATTTAAC
1 TTAGTCTAATTTAAC
34880787 TTAGTCTAATTTAAC
1 TTAGTCTAATTTAAC
34880802 TT
1 TT
34880804 CTACAAGTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.31, C:0.09, G:0.06, T:0.53
Consensus pattern (15 bp):
TTAGTCTAATTTAAC
Found at i:34882530 original size:29 final size:30
Alignment explanation
Indices: 34882477--34882546 Score: 88
Period size: 29 Copynumber: 2.4 Consensus size: 30
34882467 ATAGCCGAAG
* * *
34882477 CCATCCTTTTTCATAGTTAGATGGTTGTCA
1 CCATCCCTTTTAATAGTTAGATGGTCGTCA
*
34882507 CCATCCCTTTTAATTGTT-GATGGTCGTCA
1 CCATCCCTTTTAATAGTTAGATGGTCGTCA
*
34882536 CCATCTCTTTT
1 CCATCCCTTTT
34882547 CATAATCAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
29 20 0.57
30 15 0.43
ACGTcount: A:0.17, C:0.24, G:0.14, T:0.44
Consensus pattern (30 bp):
CCATCCCTTTTAATAGTTAGATGGTCGTCA
Found at i:34891434 original size:30 final size:29
Alignment explanation
Indices: 34891400--34891622 Score: 147
Period size: 29 Copynumber: 7.6 Consensus size: 29
34891390 TAACCAAAGT
34891400 TATCCCTTTTCATAGTTTGATAGTCGAAGC
1 TATCCCTTTTCATA-TTTGATAGTCGAAGC
* * *
34891430 TATCCCTTTTAATAATTTGATGGTCGTTA-C
1 TATCCCTTTTCAT-ATTTGATAGTCG-AAGC
* * * *
34891460 CAT-CCTTTTCCATTGTTTGA-AGGCCGTCA-C
1 TATCCCTTTT-CA-TATTTGATA-GTCG-AAGC
* *
34891490 CATCCCTTTTCATAGTTTGATGGTC-ATTA-C
1 TATCCCTTTTCATA-TTTGATAGTCGA--AGC
* * * * *
34891520 CATCCCTTTTCATAATCGATAGCCAAAGC
1 TATCCCTTTTCATATTTGATAGTCGAAGC
34891549 TATCCCTTTTCATATTTGATAG-CTGAAGC
1 TATCCCTTTTCATATTTGATAGTC-GAAGC
34891578 TATCCCTTTTCATATTTGATAG-CTGAAGC
1 TATCCCTTTTCATATTTGATAGTC-GAAGC
*
34891607 TATCCTTTTTCATATT
1 TATCCCTTTTCATATT
34891623 CAATAACCAA
Statistics
Matches: 158, Mismatches: 22, Indels: 27
0.76 0.11 0.13
Matches are distributed among these distances:
28 2 0.01
29 81 0.51
30 66 0.42
31 9 0.06
ACGTcount: A:0.23, C:0.23, G:0.13, T:0.41
Consensus pattern (29 bp):
TATCCCTTTTCATATTTGATAGTCGAAGC
Found at i:34891478 original size:60 final size:60
Alignment explanation
Indices: 34891401--34891620 Score: 186
Period size: 60 Copynumber: 3.7 Consensus size: 60
34891391 AACCAAAGTT
* * * *
34891401 ATCCCTTTTCATAGTTTGATAGTCGAAGCTATCCCTTTTAATAATTTGATGGTCGTTACC
1 ATCCCTTTTCATTGTTTGATAGCCGAAGCTATCCCTTTTCATAATTTGATGGTCATTACC
* * *
34891461 AT-CCTTTTCCATTGTTTGA-AGGCCGTCA-CCATCCCTTTTCATAGTTTGATGGTCATTACC
1 ATCCCTTTT-CATTGTTTGATA-GCCG-AAGCTATCCCTTTTCATAATTTGATGGTCATTACC
** * * * * *
34891521 ATCCCTTTTCA-TAATCGATAGCCAAAGCTATCCCTTTTCAT-ATTTGATAG-C-TGAAGCT
1 ATCCCTTTTCATTGTTTGATAGCCGAAGCTATCCCTTTTCATAATTTGATGGTCAT-TA-CC
* * *
34891579 ATCCCTTTTCA-TATTTGATAGCTGAAGCTATCCTTTTTCATA
1 ATCCCTTTTCATTGTTTGATAGCCGAAGCTATCCCTTTTCATA
34891621 TTCAATAACC
Statistics
Matches: 129, Mismatches: 22, Indels: 19
0.76 0.13 0.11
Matches are distributed among these distances:
56 1 0.01
57 2 0.02
58 45 0.35
59 27 0.21
60 47 0.36
61 7 0.05
ACGTcount: A:0.23, C:0.23, G:0.13, T:0.40
Consensus pattern (60 bp):
ATCCCTTTTCATTGTTTGATAGCCGAAGCTATCCCTTTTCATAATTTGATGGTCATTACC
Found at i:34891569 original size:29 final size:29
Alignment explanation
Indices: 34891521--34891644 Score: 158
Period size: 29 Copynumber: 4.3 Consensus size: 29
34891511 GGTCATTACC
*
34891521 ATCCCTTTTCATAATCGATAGCCAAAGCT
1 ATCCCTTTTCATATTCGATAGCCAAAGCT
* **
34891550 ATCCCTTTTCATATTTGATAGCTGAAGCT
1 ATCCCTTTTCATATTCGATAGCCAAAGCT
* **
34891579 ATCCCTTTTCATATTTGATAGCTGAAGCT
1 ATCCCTTTTCATATTCGATAGCCAAAGCT
* * *
34891608 ATCCTTTTTCATATTCAATAACCAAAGCT
1 ATCCCTTTTCATATTCGATAGCCAAAGCT
34891637 ATCCCTTT
1 ATCCCTTT
34891645 GCATTCATCG
Statistics
Matches: 84, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 84 1.00
ACGTcount: A:0.27, C:0.24, G:0.10, T:0.39
Consensus pattern (29 bp):
ATCCCTTTTCATATTCGATAGCCAAAGCT
Found at i:34894686 original size:16 final size:17
Alignment explanation
Indices: 34894654--34894686 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
34894644 TTTAGATCAA
*
34894654 GAAAATTGAAGAAAATG
1 GAAAATTGAACAAAATG
34894671 GAAAATT-AACAAAATG
1 GAAAATTGAACAAAATG
34894687 CCCCTGAACT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.61, C:0.03, G:0.18, T:0.18
Consensus pattern (17 bp):
GAAAATTGAACAAAATG
Found at i:34894985 original size:87 final size:87
Alignment explanation
Indices: 34894835--34895102 Score: 387
Period size: 87 Copynumber: 3.1 Consensus size: 87
34894825 CCCTCAGATA
* *
34894835 ATGAAAAGGGATAGCTTC-AGCTATCGATTATGAAAAGGGATGGTGACGACCATCAAGTTTGAAA
1 ATGAAAAGGGATAGCTTCGA-CTATCGATTATGAAAAGGGATGGTGACGACCATCAACTATGAAA
* * *
34894899 AGGTATAGCTTCGGCTATCAAAT
65 AGGGATAGCTTCGACTATCAACT
*
34894922 ATGAAAAGGGATAGCTTCGACTATCGATTATGAAAATGGATGGTGACGACCATCAACTATGAAAA
1 ATGAAAAGGGATAGCTTCGACTATCGATTATGAAAAGGGATGGTGACGACCATCAACTATGAAAA
* * *
34894987 GGGAT-GGTGACGACCATCAACT
66 GGGATAGCT-TCGACTATCAACT
* * *
34895009 ATGAAAAGGGATAGCTTCGACTATCGACTATGAAAAGGGATGGTGACAACCATCGACTATGAAAA
1 ATGAAAAGGGATAGCTTCGACTATCGATTATGAAAAGGGATGGTGACGACCATCAACTATGAAAA
*
34895074 GGGATAGCTTCGACTATCGACT
66 GGGATAGCTTCGACTATCAACT
34895096 ATGAAAA
1 ATGAAAA
34895103 AAGATGGTTT
Statistics
Matches: 161, Mismatches: 17, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
86 2 0.01
87 156 0.97
88 3 0.02
ACGTcount: A:0.37, C:0.15, G:0.25, T:0.23
Consensus pattern (87 bp):
ATGAAAAGGGATAGCTTCGACTATCGATTATGAAAAGGGATGGTGACGACCATCAACTATGAAAA
GGGATAGCTTCGACTATCAACT
Found at i:34895092 original size:29 final size:29
Alignment explanation
Indices: 34894835--34895102 Score: 231
Period size: 29 Copynumber: 9.2 Consensus size: 29
34894825 CCCTCAGATA
*
34894835 ATGAAAAGGGATAGCTTC-AGCTATCGATT
1 ATGAAAAGGGATAGCTTCGA-CTATCGACT
* * * * *
34894864 ATGAAAAGGGAT-GGTGACGACCATCAAGT
1 ATGAAAAGGGATAGCT-TCGACTATCGACT
* * * * *
34894893 TTGAAAAGGTATAGCTTCGGCTATCAAAT
1 ATGAAAAGGGATAGCTTCGACTATCGACT
*
34894922 ATGAAAAGGGATAGCTTCGACTATCGATT
1 ATGAAAAGGGATAGCTTCGACTATCGACT
* * * * *
34894951 ATGAAAATGGAT-GGTGACGACCATCAACT
1 ATGAAAAGGGATAGCT-TCGACTATCGACT
* * * *
34894980 ATGAAAAGGGAT-GGTGACGACCATCAACT
1 ATGAAAAGGGATAGCT-TCGACTATCGACT
34895009 ATGAAAAGGGATAGCTTCGACTATCGACT
1 ATGAAAAGGGATAGCTTCGACTATCGACT
* * * *
34895038 ATGAAAAGGGAT-GGTGACAACCATCGACT
1 ATGAAAAGGGATAGCT-TCGACTATCGACT
34895067 ATGAAAAGGGATAGCTTCGACTATCGACT
1 ATGAAAAGGGATAGCTTCGACTATCGACT
34895096 ATGAAAA
1 ATGAAAA
34895103 AAGATGGTTT
Statistics
Matches: 196, Mismatches: 36, Indels: 14
0.80 0.15 0.06
Matches are distributed among these distances:
28 6 0.03
29 183 0.93
30 7 0.04
ACGTcount: A:0.37, C:0.15, G:0.25, T:0.23
Consensus pattern (29 bp):
ATGAAAAGGGATAGCTTCGACTATCGACT
Found at i:34895110 original size:58 final size:58
Alignment explanation
Indices: 34894835--34895102 Score: 317
Period size: 58 Copynumber: 4.6 Consensus size: 58
34894825 CCCTCAGATA
* *
34894835 ATGAAAAGGGATAGCTTC-AGCTATCGATTATGAAAAGGGATGGTGACGACCATCAAGT
1 ATGAAAAGGGATAGCTTCGA-CTATCGACTATGAAAAGGGATGGTGACGACCATCAACT
* * * * * * * * * *
34894893 TTGAAAAGGTATAGCTTCGGCTATCAAATATGAAAAGGGATAGCT-TCGACTATCGATT
1 ATGAAAAGGGATAGCTTCGACTATCGACTATGAAAAGGGAT-GGTGACGACCATCAACT
* * * * *
34894951 ATGAAAATGGAT-GGTGACGACCATCAACTATGAAAAGGGATGGTGACGACCATCAACT
1 ATGAAAAGGGATAGCT-TCGACTATCGACTATGAAAAGGGATGGTGACGACCATCAACT
* *
34895009 ATGAAAAGGGATAGCTTCGACTATCGACTATGAAAAGGGATGGTGACAACCATCGACT
1 ATGAAAAGGGATAGCTTCGACTATCGACTATGAAAAGGGATGGTGACGACCATCAACT
34895067 ATGAAAAGGGATAGCTTCGACTATCGACTATGAAAA
1 ATGAAAAGGGATAGCTTCGACTATCGACTATGAAAA
34895103 AAGATGGTTT
Statistics
Matches: 175, Mismatches: 30, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
57 4 0.02
58 167 0.95
59 4 0.02
ACGTcount: A:0.37, C:0.15, G:0.25, T:0.23
Consensus pattern (58 bp):
ATGAAAAGGGATAGCTTCGACTATCGACTATGAAAAGGGATGGTGACGACCATCAACT
Found at i:34899272 original size:25 final size:24
Alignment explanation
Indices: 34899215--34899349 Score: 108
Period size: 25 Copynumber: 5.5 Consensus size: 24
34899205 CCACAACTCA
* * *
34899215 TGTGAGCATACCAATTTACAGGTCA
1 TGTGAGCATACCGA-TTACAGCTCG
**
34899240 TGAAAGCATACCGATCTACAGCTCG
1 TGTGAGCATACCGAT-TACAGCTCG
*** * *
34899265 TGTGAGCATAAATATTATAGGTCG
1 TGTGAGCATACCGATTACAGCTCG
*
34899289 TGAGAGCATACCGATCTACAGCTCG
1 TGTGAGCATACCGAT-TACAGCTCG
*
34899314 AGTGAGCATACCGATTCACAGCTCG
1 TGTGAGCATACCGATT-ACAGCTCG
* *
34899339 TATAAGCATAC
1 TGTGAGCATAC
34899350 ATGTACAAGA
Statistics
Matches: 84, Mismatches: 23, Indels: 6
0.74 0.20 0.05
Matches are distributed among these distances:
24 20 0.24
25 64 0.76
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.24
Consensus pattern (24 bp):
TGTGAGCATACCGATTACAGCTCG
Found at i:34899297 original size:49 final size:49
Alignment explanation
Indices: 34899215--34899324 Score: 159
Period size: 49 Copynumber: 2.2 Consensus size: 49
34899205 CCACAACTCA
34899215 TGTGAGCATACCAATTTACAGGTCATGAAAGCATACCGATCTACAGCTCG
1 TGTGAGCATA-CAATTTACAGGTCATGAAAGCATACCGATCTACAGCTCG
* * *
34899265 TGTGAGCATA-AATATTATAGGTCGTGAGAGCATACCGATCTACAGCTCG
1 TGTGAGCATACAAT-TTACAGGTCATGAAAGCATACCGATCTACAGCTCG
*
34899314 AGTGAGCATAC
1 TGTGAGCATAC
34899325 CGATTCACAG
Statistics
Matches: 54, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
48 3 0.06
49 41 0.76
50 10 0.19
ACGTcount: A:0.32, C:0.21, G:0.23, T:0.25
Consensus pattern (49 bp):
TGTGAGCATACAATTTACAGGTCATGAAAGCATACCGATCTACAGCTCG
Found at i:34900139 original size:14 final size:14
Alignment explanation
Indices: 34900120--34900148 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
34900110 TTTGTAAGAT
34900120 TATGGTTTCATGAA
1 TATGGTTTCATGAA
34900134 TATGGTTTCATGAA
1 TATGGTTTCATGAA
34900148 T
1 T
34900149 CTTACGATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.07, G:0.21, T:0.45
Consensus pattern (14 bp):
TATGGTTTCATGAA
Found at i:34909493 original size:25 final size:25
Alignment explanation
Indices: 34909459--34909553 Score: 93
Period size: 25 Copynumber: 3.8 Consensus size: 25
34909449 GCAGACACAC
* *
34909459 TACAGCTCGT-ATGAGCTTACCTATT
1 TACAGCTCGTGA-GAGCATACCGATT
34909484 TACAGCTCGTGAGAGCATACCGATT
1 TACAGCTCGTGAGAGCATACCGATT
* ** *
34909509 TGCAGCTCAAGAAAGCATACCGATT
1 TACAGCTCGTGAGAGCATACCGATT
* * *
34909534 CACAGCTTGTGTGAGCATAC
1 TACAGCTCGTGAGAGCATAC
34909554 ATGTACTAGA
Statistics
Matches: 56, Mismatches: 13, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
25 55 0.98
26 1 0.02
ACGTcount: A:0.28, C:0.24, G:0.21, T:0.26
Consensus pattern (25 bp):
TACAGCTCGTGAGAGCATACCGATT
Found at i:34915949 original size:67 final size:67
Alignment explanation
Indices: 34915840--34915973 Score: 241
Period size: 67 Copynumber: 2.0 Consensus size: 67
34915830 AAAACTTATC
34915840 GAGTCTGTTTTCACATGAAAGAAACAATGTAGGAAAAGGAATTACATATTATGAGATATTTGAAT
1 GAGTCTGTTTTCACATGAAAGAAACAATGTAGGAAAAGGAATTACATATTATGAGATATTTGAAT
34915905 TT
66 TT
* * *
34915907 GAGTCTGTTTTCACATGAAAGAAACAATGTAGGCAAATGAATTATATATTATGAGATATTTGAAT
1 GAGTCTGTTTTCACATGAAAGAAACAATGTAGGAAAAGGAATTACATATTATGAGATATTTGAAT
34915972 TT
66 TT
34915974 TAGTGAGATA
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
67 64 1.00
ACGTcount: A:0.40, C:0.07, G:0.19, T:0.34
Consensus pattern (67 bp):
GAGTCTGTTTTCACATGAAAGAAACAATGTAGGAAAAGGAATTACATATTATGAGATATTTGAAT
TT
Found at i:34927652 original size:14 final size:14
Alignment explanation
Indices: 34927633--34927660 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
34927623 CCAATTTATT
34927633 AATGAATTATTAAA
1 AATGAATTATTAAA
34927647 AATGAATTATTAAA
1 AATGAATTATTAAA
34927661 TATAACTTTA
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:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (14 bp):
AATGAATTATTAAA
Found at i:34933470 original size:27 final size:27
Alignment explanation
Indices: 34933440--34933617 Score: 137
Period size: 27 Copynumber: 6.6 Consensus size: 27
34933430 ATATTGAGCC
* *
34933440 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* * * *
34933467 CGCACATTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
* *
34933494 CGCACACTTAGTGCTACATAGTCAAACC
1 CGCACACTTAGTGCTACATAATC-AACT
** ** *
34933522 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
34933549 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* *
34933576 CGCACACTTAGTGCAACA-AAGT-AGAAT
1 CGCACACTTAGTGCTACATAA-TCA-ACT
34933603 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
34933618 GTACAATTTA
Statistics
Matches: 121, Mismatches: 25, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
26 2 0.02
27 96 0.79
28 23 0.19
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:34933552 original size:55 final size:54
Alignment explanation
Indices: 34933440--34933617 Score: 164
Period size: 54 Copynumber: 3.3 Consensus size: 54
34933430 ATATTGAGCC
* * * * *
34933440 CGCACACTCAGTGCTATATAATCAACTCGCACATTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACCCGCACACTTAGTGCCACATAATCAAAT
* * ** *
34933494 CGCACACTTAGTGCTACATAGTCAAACCCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATC-AACCCGCACACTTAGTGCCACATAATCAAAT
* *** *
34933549 CGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACA-AAGT-AGAAT
1 CGCACACTTAGTGCTA-CATAATCAACCCGCACACTTAGTGCCACATAA-TCA-AAT
34933603 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
34933618 GTACAATTTA
Statistics
Matches: 100, Mismatches: 19, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
53 1 0.01
54 55 0.55
55 44 0.44
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (54 bp):
CGCACACTTAGTGCTACATAATCAACCCGCACACTTAGTGCCACATAATCAAAT
Found at i:34941476 original size:27 final size:27
Alignment explanation
Indices: 34941446--34941623 Score: 137
Period size: 27 Copynumber: 6.6 Consensus size: 27
34941436 ATATTGAGCC
* *
34941446 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* * * *
34941473 CGCACATTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
* *
34941500 CGCACACTTAGTGCTACATAGTCAAACC
1 CGCACACTTAGTGCTACATAATC-AACT
** ** *
34941528 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
34941555 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* *
34941582 CGCACACTTAGTGCAACA-AAGT-AGAAT
1 CGCACACTTAGTGCTACATAA-TCA-ACT
34941609 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
34941624 GTACAATTTA
Statistics
Matches: 121, Mismatches: 25, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
26 2 0.02
27 96 0.79
28 23 0.19
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:34941558 original size:55 final size:54
Alignment explanation
Indices: 34941446--34941623 Score: 164
Period size: 54 Copynumber: 3.3 Consensus size: 54
34941436 ATATTGAGCC
* * * * *
34941446 CGCACACTCAGTGCTATATAATCAACTCGCACATTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACCCGCACACTTAGTGCCACATAATCAAAT
* * ** *
34941500 CGCACACTTAGTGCTACATAGTCAAACCCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATC-AACCCGCACACTTAGTGCCACATAATCAAAT
* *** *
34941555 CGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACA-AAGT-AGAAT
1 CGCACACTTAGTGCTA-CATAATCAACCCGCACACTTAGTGCCACATAA-TCA-AAT
34941609 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
34941624 GTACAATTTA
Statistics
Matches: 100, Mismatches: 19, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
53 1 0.01
54 55 0.55
55 44 0.44
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (54 bp):
CGCACACTTAGTGCTACATAATCAACCCGCACACTTAGTGCCACATAATCAAAT
Found at i:34951598 original size:14 final size:15
Alignment explanation
Indices: 34951568--34951601 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
34951558 CTGTTTAGGG
*
34951568 TTTCATTTCTATCCA
1 TTTCATTGCTATCCA
34951583 TTTCATTGCT-TCCA
1 TTTCATTGCTATCCA
34951597 TTTCA
1 TTTCA
34951602 CTTTTCTTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.18, C:0.26, G:0.03, T:0.53
Consensus pattern (15 bp):
TTTCATTGCTATCCA
Found at i:34953335 original size:17 final size:17
Alignment explanation
Indices: 34953315--34953407 Score: 83
Period size: 17 Copynumber: 5.9 Consensus size: 17
34953305 TTATTTTCTA
34953315 TATAAGTTTTCTAAATT
1 TATAAGTTTTCTAAATT
34953332 TATAAGTTTTCT-AA--
1 TATAAGTTTTCTAAATT
*
34953346 -ATAATTTTTCTAAATT
1 TATAAGTTTTCTAAATT
* * *
34953362 TATTAGTATT-AAAATT
1 TATAAGTTTTCTAAATT
* *
34953378 TATCAG-TAT-TAAATT
1 TATAAGTTTTCTAAATT
34953393 TATAAGTTTTCTAAA
1 TATAAGTTTTCTAAA
34953408 AAAGTGTTCT
Statistics
Matches: 59, Mismatches: 11, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
13 10 0.17
14 2 0.03
15 11 0.19
16 14 0.24
17 22 0.37
ACGTcount: A:0.39, C:0.05, G:0.05, T:0.51
Consensus pattern (17 bp):
TATAAGTTTTCTAAATT
Found at i:34953343 original size:30 final size:30
Alignment explanation
Indices: 34953308--34953425 Score: 107
Period size: 30 Copynumber: 3.9 Consensus size: 30
34953298 TATTGTTTTA
*
34953308 TTTTCTATATAAGTTTTCTAAATTTATAAG
1 TTTTCTAAATAAGTTTTCTAAATTTATAAG
* *
34953338 TTTTCTAAATAATTTTTCTAAATTTATTAG
1 TTTTCTAAATAAGTTTTCTAAATTTATAAG
* * *
34953368 TATT-AAAATTTATCAG-TAT-TAAATTTATAAG
1 TTTTCTAAA--TA--AGTTTTCTAAATTTATAAG
* *
34953399 TTTTCTAAAAAAGTGTTCTAAATTTAT
1 TTTTCTAAATAAGTTTTCTAAATTTAT
34953426 TATTAATAAA
Statistics
Matches: 68, Mismatches: 13, Indels: 14
0.72 0.14 0.15
Matches are distributed among these distances:
28 2 0.03
29 4 0.06
30 40 0.59
31 16 0.24
32 5 0.07
33 1 0.01
ACGTcount: A:0.37, C:0.06, G:0.06, T:0.51
Consensus pattern (30 bp):
TTTTCTAAATAAGTTTTCTAAATTTATAAG
Found at i:34953358 original size:13 final size:13
Alignment explanation
Indices: 34953308--34953360 Score: 52
Period size: 13 Copynumber: 3.8 Consensus size: 13
34953298 TATTGTTTTA
*
34953308 TTTTCTATATAAG
1 TTTTCTAAATAAG
34953321 TTTTCTAAATTTATAAG
1 TTTTCT-AA---ATAAG
*
34953338 TTTTCTAAATAAT
1 TTTTCTAAATAAG
34953351 TTTTCTAAAT
1 TTTTCTAAAT
34953361 TTATTAGTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
13 20 0.59
14 1 0.03
16 2 0.06
17 11 0.32
ACGTcount: A:0.34, C:0.08, G:0.04, T:0.55
Consensus pattern (13 bp):
TTTTCTAAATAAG
Found at i:34953391 original size:15 final size:15
Alignment explanation
Indices: 34953356--34953395 Score: 62
Period size: 16 Copynumber: 2.6 Consensus size: 15
34953346 ATAATTTTTC
*
34953356 TAAATTTATTAGTAT
1 TAAATTTATCAGTAT
34953371 TAAAATTTATCAGTAT
1 T-AAATTTATCAGTAT
34953387 TAAATTTAT
1 TAAATTTAT
34953396 AAGTTTTCTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 9 0.39
16 14 0.61
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (15 bp):
TAAATTTATCAGTAT
Found at i:34953398 original size:61 final size:61
Alignment explanation
Indices: 34953326--34953473 Score: 215
Period size: 61 Copynumber: 2.4 Consensus size: 61
34953316 ATAAGTTTTC
* * *
34953326 TAAATTTATAAGTTTTCTAAATAATTTTTCTAAATTTATTAGTATTAAAATTTATCAGTAT
1 TAAATTTATAAGTTTTCTAAATAATTGTTCTAAATTTATTAGTAATAAAATTTATAAGTAT
* * *
34953387 TAAATTTATAAGTTTTCTAAAAAAGTGTTCTAAATTTATTATTAATAAAATTTATAAGTAT
1 TAAATTTATAAGTTTTCTAAATAATTGTTCTAAATTTATTAGTAATAAAATTTATAAGTAT
* * *
34953448 CAATTTTATAATTTTTCTAAATAATT
1 TAAATTTATAAGTTTTCTAAATAATT
34953474 ATATATTTTT
Statistics
Matches: 76, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
61 76 1.00
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.49
Consensus pattern (61 bp):
TAAATTTATAAGTTTTCTAAATAATTGTTCTAAATTTATTAGTAATAAAATTTATAAGTAT
Found at i:34953668 original size:21 final size:21
Alignment explanation
Indices: 34953642--34953718 Score: 68
Period size: 21 Copynumber: 3.7 Consensus size: 21
34953632 TAACATAATA
* *
34953642 CATAACTTATAT-ATAAGCTTG
1 CATAACTTACATAATAA-CTTC
34953663 CATAACTTACATAATAACTTC
1 CATAACTTACATAATAACTTC
** *
34953684 CATAACTTA-ATACACCACTTA
1 CATAACTTACATA-ATAACTTC
*
34953705 AATAACTTACATAA
1 CATAACTTACATAA
34953719 CTTACATAGC
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
20 3 0.06
21 37 0.79
22 7 0.15
ACGTcount: A:0.44, C:0.21, G:0.03, T:0.32
Consensus pattern (21 bp):
CATAACTTACATAATAACTTC
Found at i:34953718 original size:9 final size:9
Alignment explanation
Indices: 34953700--34954168 Score: 158
Period size: 9 Copynumber: 54.3 Consensus size: 9
34953690 TTAATACACC
*
34953700 ACTTAAATA
1 ACTTACATA
34953709 ACTTACATA
1 ACTTACATA
34953718 ACTTACATA
1 ACTTACATA
*
34953727 GCTTACATA
1 ACTTACATA
*
34953736 AC-T-CATT
1 ACTTACATA
34953743 ACTTACATA
1 ACTTACATA
*
34953752 ACATACATA
1 ACTTACATA
**
34953761 AAATAC--A
1 ACTTACATA
34953768 ACTTACATA
1 ACTTACATA
*
34953777 TCTTACATA
1 ACTTACATA
34953786 A--TACATA
1 ACTTACATA
*
34953793 ACTTACAGA
1 ACTTACATA
* *
34953802 AATTAAATA
1 ACTTACATA
* *
34953811 ACCTGCATA
1 ACTTACATA
*
34953820 A--AACATA
1 ACTTACATA
* *
34953827 GCCTACATA
1 ACTTACATA
*
34953836 ACTTATATA
1 ACTTACATA
* *
34953845 GCTTTCATA
1 ACTTACATA
**
34953854 AAGTAC--A
1 ACTTACATA
34953861 ACTTACATA
1 ACTTACATA
**
34953870 TTTTACATAAA
1 ACTTACAT--A
34953881 ACTTACATA
1 ACTTACATA
34953890 A--TACATA
1 ACTTACATA
*
34953897 ACTTAC-TT
1 ACTTACATA
**
34953905 ACATAATACAGC
1 AC-T--TACATA
*
34953917 ACTTACACA
1 ACTTACATA
*
34953926 ACTTAAATA
1 ACTTACATA
*
34953935 ACTTGCATA
1 ACTTACATA
34953944 A--TACATA
1 ACTTACATA
34953951 GAC-TACATA
1 -ACTTACATA
*
34953960 ACTTA-ATTTG
1 ACTTACA--TA
*
34953970 CCTTACATA
1 ACTTACATA
34953979 A--TACA-A
1 ACTTACATA
*
34953985 CACTTACACA
1 -ACTTACATA
*
34953995 ACTTAAATA
1 ACTTACATA
*
34954004 ACTTGCATA
1 ACTTACATA
34954013 A--TACA-A
1 ACTTACATA
*
34954019 AGCCTACATA
1 A-CTTACATA
*
34954029 ACTTA-ATTTG
1 ACTTACA--TA
*
34954039 CCTTACATA
1 ACTTACATA
**
34954048 A--TACAGC
1 ACTTACATA
34954055 ACTTACATA
1 ACTTACATA
34954064 ACTTACATA
1 ACTTACATA
**
34954073 GGTTACATA
1 ACTTACATA
34954082 A--TACATA
1 ACTTACATA
*
34954089 ACTTAAATA
1 ACTTACATA
*
34954098 ACTTATATA
1 ACTTACATA
34954107 A--TACATA
1 ACTTACATA
34954114 ACTTACATA
1 ACTTACATA
* *
34954123 ATTTACTTA
1 ACTTACATA
34954132 A--TACATA
1 ACTTACATA
* *
34954139 A-ATATATA
1 ACTTACATA
* *
34954147 TCATATCATA
1 ACTTA-CATA
34954157 ACTTACATA
1 ACTTACATA
34954166 ACT
1 ACT
34954169 CATTTAATTT
Statistics
Matches: 335, Mismatches: 81, Indels: 88
0.66 0.16 0.17
Matches are distributed among these distances:
6 3 0.01
7 70 0.21
8 15 0.04
9 213 0.64
10 19 0.06
11 13 0.04
12 2 0.01
ACGTcount: A:0.45, C:0.20, G:0.03, T:0.32
Consensus pattern (9 bp):
ACTTACATA
Found at i:34953749 original size:16 final size:17
Alignment explanation
Indices: 34953700--34953799 Score: 73
Period size: 16 Copynumber: 5.9 Consensus size: 17
34953690 TTAATACACC
*
34953700 ACTTAAATAACTTACAT
1 ACTTACATAACTTACAT
*
34953717 AACTTACATAGCTTACAT
1 -ACTTACATAACTTACAT
*
34953735 AAC-T-CATTACTTACAT
1 -ACTTACATAACTTACAT
* **
34953751 AACATACATAAAATACA-
1 -ACTTACATAACTTACAT
*
34953768 ACTTACATATCTTACAT
1 ACTTACATAACTTACAT
*
34953785 A-ATACATAACTTACA
1 ACTTACATAACTTACA
34953800 GAAATTAAAT
Statistics
Matches: 66, Mismatches: 13, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
16 37 0.56
17 3 0.05
18 26 0.39
ACGTcount: A:0.46, C:0.21, G:0.01, T:0.32
Consensus pattern (17 bp):
ACTTACATAACTTACAT
Found at i:34953795 original size:25 final size:25
Alignment explanation
Indices: 34953712--34953799 Score: 97
Period size: 25 Copynumber: 3.5 Consensus size: 25
34953702 TTAAATAACT
*
34953712 TACATAACTTACATAGCTTACATAA
1 TACATAACTTACATAACTTACATAA
* *
34953737 CT-CATTACTTACATAACATACATAA
1 -TACATAACTTACATAACTTACATAA
* * * *
34953762 AATACAACTTACATATCTTACATAA
1 TACATAACTTACATAACTTACATAA
34953787 TACATAACTTACA
1 TACATAACTTACA
34953800 GAAATTAAAT
Statistics
Matches: 49, Mismatches: 12, Indels: 3
0.77 0.19 0.05
Matches are distributed among these distances:
25 48 0.98
26 1 0.02
ACGTcount: A:0.45, C:0.22, G:0.01, T:0.32
Consensus pattern (25 bp):
TACATAACTTACATAACTTACATAA
Found at i:34953920 original size:20 final size:20
Alignment explanation
Indices: 34953881--34953922 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
34953871 TTTACATAAA
*
34953881 ACTTACATAATACATAACTT
1 ACTTACATAATACAGAACTT
*
34953901 ACTTACATAATACAGCACTT
1 ACTTACATAATACAGAACTT
34953921 AC
1 AC
34953923 ACAACTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.43, C:0.24, G:0.02, T:0.31
Consensus pattern (20 bp):
ACTTACATAATACAGAACTT
Found at i:34953946 original size:34 final size:34
Alignment explanation
Indices: 34953901--34954114 Score: 170
Period size: 34 Copynumber: 6.3 Consensus size: 34
34953891 TACATAACTT
*
34953901 ACTTACATAATACAGCACTTACACAACTTAAATA
1 ACTTACATAATACAGCACTTACATAACTTAAATA
* * *
34953935 ACTTGCATAATACATAG-AC-TACATAACTTAATTTG
1 ACTTACATAATAC--AGCACTTACATAACTTAA-ATA
* * *
34953970 CCTTACATAATACAACACTTACACAACTTAAATA
1 ACTTACATAATACAGCACTTACATAACTTAAATA
* * *
34954004 ACTTGCATAATACAAAGC-C-TACATAACTTAATTTG
1 ACTTACATAATAC--AGCACTTACATAACTTAA-ATA
* *
34954039 CCTTACATAATACAGCACTTACATAACTTACATA
1 ACTTACATAATACAGCACTTACATAACTTAAATA
** ** * *
34954073 GGTTACATAATACATAACTTAAATAACTTATATA
1 ACTTACATAATACAGCACTTACATAACTTAAATA
34954107 A--TACATAA
1 ACTTACATAA
34954115 CTTACATAAT
Statistics
Matches: 142, Mismatches: 28, Indels: 22
0.74 0.15 0.11
Matches are distributed among these distances:
32 7 0.05
33 4 0.03
34 78 0.55
35 49 0.35
36 4 0.03
ACGTcount: A:0.44, C:0.21, G:0.05, T:0.30
Consensus pattern (34 bp):
ACTTACATAATACAGCACTTACATAACTTAAATA
Found at i:34953983 original size:69 final size:69
Alignment explanation
Indices: 34953902--34954102 Score: 305
Period size: 69 Copynumber: 2.9 Consensus size: 69
34953892 ACATAACTTA
34953902 CTTACATAATACAGCACTTACACAACTTAAATAACTTGCATAATACATAGACTACATAACTTAAT
1 CTTACATAATACAGCACTTACACAACTTAAATAACTTGCATAATACATAGACTACATAACTTAAT
34953967 TTGC
66 TTGC
* * *
34953971 CTTACATAATACAACACTTACACAACTTAAATAACTTGCATAATACAAAGCCTACATAACTTAAT
1 CTTACATAATACAGCACTTACACAACTTAAATAACTTGCATAATACATAGACTACATAACTTAAT
34954036 TTGC
66 TTGC
* * ** * *
34954040 CTTACATAATACAGCACTTACATAACTTACATAGGTTACATAATACATA-ACTTAAATAACTTA
1 CTTACATAATACAGCACTTACACAACTTAAATAACTTGCATAATACATAGAC-TACATAACTTA
34954103 TATAATACAT
Statistics
Matches: 119, Mismatches: 12, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
68 1 0.01
69 118 0.99
ACGTcount: A:0.43, C:0.21, G:0.05, T:0.30
Consensus pattern (69 bp):
CTTACATAATACAGCACTTACACAACTTAAATAACTTGCATAATACATAGACTACATAACTTAAT
TTGC
Found at i:34954086 original size:25 final size:25
Alignment explanation
Indices: 34954058--34954139 Score: 110
Period size: 25 Copynumber: 3.3 Consensus size: 25
34954048 ATACAGCACT
**
34954058 TACATAACTTACATAGGTTACATAA
1 TACATAACTTACATAACTTACATAA
* *
34954083 TACATAACTTAAATAACTTATATAA
1 TACATAACTTACATAACTTACATAA
* *
34954108 TACATAACTTACATAATTTACTTAA
1 TACATAACTTACATAACTTACATAA
34954133 TACATAA
1 TACATAA
34954140 ATATATATCA
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 49 1.00
ACGTcount: A:0.48, C:0.15, G:0.02, T:0.35
Consensus pattern (25 bp):
TACATAACTTACATAACTTACATAA
Found at i:34959720 original size:66 final size:65
Alignment explanation
Indices: 34959613--34959782 Score: 225
Period size: 66 Copynumber: 2.6 Consensus size: 65
34959603 GAACAAATTA
* * * *
34959613 CACAACTTAAAACGGAGGCAGCATCGAGAGAAGCTGAGGTTCAA-AAAAGATATGAAGAACTCCA
1 CACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAG-TATGAAGAACTCCA
*
34959677 T
65 G
*
34959678 CTACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACGAAAGTATGAAGAACTCCA
1 C-ACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAGTATGAAGAACTCCA
34959743 G
65 G
* * * *
34959744 CGCAGCTTAAAGCAGATGCGGCAGCGAGAGAAGCAGAGG
1 CACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGG
34959783 CTGCAGTGAG
Statistics
Matches: 93, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
65 35 0.38
66 54 0.58
67 4 0.04
ACGTcount: A:0.39, C:0.19, G:0.28, T:0.14
Consensus pattern (65 bp):
CACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAGTATGAAGAACTCCAG
Found at i:34959778 original size:21 final size:21
Alignment explanation
Indices: 34959753--34959823 Score: 97
Period size: 21 Copynumber: 3.4 Consensus size: 21
34959743 GCGCAGCTTA
* * *
34959753 AAGCAGATGCGGCAGCGAGAG
1 AAGCAGAGGCTGCAGCGAGGG
*
34959774 AAGCAGAGGCTGCAGTGAGGG
1 AAGCAGAGGCTGCAGCGAGGG
*
34959795 AAGTAGAGGCTGCAGCGAGGG
1 AAGCAGAGGCTGCAGCGAGGG
34959816 AAGCAGAG
1 AAGCAGAG
34959824 CAGCGTAGAA
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 43 1.00
ACGTcount: A:0.32, C:0.15, G:0.45, T:0.07
Consensus pattern (21 bp):
AAGCAGAGGCTGCAGCGAGGG
Found at i:34960304 original size:86 final size:86
Alignment explanation
Indices: 34960154--34960333 Score: 208
Period size: 86 Copynumber: 2.1 Consensus size: 86
34960144 TTTTCAAAAA
*
34960154 CGCCACTAAAGGTCATGGTCATTTGCGGCGTTTGTAGAAAAAGCGTCGCTAAAGATCAGAGTCTT
1 CGCCGCTAAAGGTCATGGTCATTTGCGGCGTTTGTAGAAAAAGCGTCGCTAAAGATCAGAGTCTT
*
34960219 TAGCAGCGTTTGT-TTGGAAAG
66 TAGCAGCGTTTGTGGT-GAAAG
* * * * *
34960240 CGCCGCTAAAGGTCATTGTC-TTTAGTGGCGTTTTTCAG-ATAAGCGTTGCTAAA-AGTCATG-G
1 CGCCGCTAAAGGTCATGGTCATTT-GCGGCGTTTGT-AGAAAAAGCGTCGCTAAAGA-TCA-GAG
*
34960301 TCTTTAGCGGCGTTTGTGGTGAAAG
62 TCTTTAGCAGCGTTTGTGGTGAAAG
34960326 CGCCGCTA
1 CGCCGCTA
34960334 CAGTTAGCGA
Statistics
Matches: 81, Mismatches: 8, Indels: 10
0.82 0.08 0.10
Matches are distributed among these distances:
85 4 0.05
86 73 0.90
87 4 0.05
ACGTcount: A:0.23, C:0.18, G:0.28, T:0.30
Consensus pattern (86 bp):
CGCCGCTAAAGGTCATGGTCATTTGCGGCGTTTGTAGAAAAAGCGTCGCTAAAGATCAGAGTCTT
TAGCAGCGTTTGTGGTGAAAG
Found at i:34960327 original size:43 final size:42
Alignment explanation
Indices: 34960159--34960333 Score: 142
Period size: 43 Copynumber: 4.1 Consensus size: 42
34960149 AAAAACGCCA
* *
34960159 CTAAAGGTCATGGTCATTT-GCGGCGTTTGTAGAAAAAGCGTCG
1 CTAAAAGTCATGGTC-TTTAGCGGCGTTTGT-GAGAAAGCGTCG
* *
34960202 CT-AAAGATCA-GAGTCTTTAGCAGCGTTTGTTTG-GAAAGCGCCG
1 CTAAAAG-TCATG-GTCTTTAGCGGCGTTTG--TGAGAAAGCGTCG
* * * * * *
34960245 CTAAAGGTCATTGTCTTTAGTGGCGTTTTTCAGATAAGCGTTG
1 CTAAAAGTCATGGTCTTTAGCGGCGTTTGTGAGA-AAGCGTCG
* *
34960288 CTAAAAGTCATGGTCTTTAGCGGCGTTTGTGGTGAAAGCGCCG
1 CTAAAAGTCATGGTCTTTAGCGGCGTTTGT-GAGAAAGCGTCG
34960331 CTA
1 CTA
34960334 CAGTTAGCGA
Statistics
Matches: 102, Mismatches: 20, Indels: 20
0.72 0.14 0.14
Matches are distributed among these distances:
41 1 0.01
42 9 0.09
43 85 0.83
44 6 0.06
45 1 0.01
ACGTcount: A:0.23, C:0.17, G:0.29, T:0.31
Consensus pattern (42 bp):
CTAAAAGTCATGGTCTTTAGCGGCGTTTGTGAGAAAGCGTCG
Found at i:34965154 original size:16 final size:16
Alignment explanation
Indices: 34965129--34965165 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
34965119 TAGTAATAAA
34965129 TACATAGATAAAATGT
1 TACATAGATAAAATGT
*
34965145 TACATGGATAAAATGT
1 TACATAGATAAAATGT
34965161 TACAT
1 TACAT
34965166 TTCATAATGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.46, C:0.08, G:0.14, T:0.32
Consensus pattern (16 bp):
TACATAGATAAAATGT
Found at i:34982459 original size:80 final size:79
Alignment explanation
Indices: 34982375--34982546 Score: 220
Period size: 79 Copynumber: 2.2 Consensus size: 79
34982365 GGACTAAGAT
*
34982375 CCGAAGGCATTTGTGCGAGATA-CAAATTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACT
1 CCGAAGGCATTTGTGCGAGATATCAAA-TCCGGGTTAAGCCCCGAAGG-CATTGTGCGAGATACT
* *
34982439 AAATCCGGGTTAAGTC
64 AAAACCGGGCTAAGTC
* * * * * * *
34982455 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATATCAAATCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAA
*
34982520 AACCGGGCTATGTC
66 AACCGGGCTAAGTC
34982534 CCGAAGGCATTTG
1 CCGAAGGCATTTG
34982547 AACGAGGAGC
Statistics
Matches: 79, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
79 38 0.48
80 38 0.48
81 3 0.04
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATATCAAATCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAA
AACCGGGCTAAGTC
Found at i:34982526 original size:39 final size:39
Alignment explanation
Indices: 34982322--34982544 Score: 209
Period size: 40 Copynumber: 5.6 Consensus size: 39
34982312 TTGAATGCTG
* * * * *
34982322 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTA-AGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGA-T-ACTAAA
**
34982362 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATAC-AAA
1 TCCGGGTTAAG-TCCCGAAGGCA-TTGTGCGAGATACTAAA
* *
34982401 TTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAA
1 -TCCGGGTTAAGTCCCGAAGG-CATTGTGCGAGATACTAAA
* *
34982442 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGATACTAAA
* * *
34982482 TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGATACTAAA
* * *
34982521 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
34982545 TGAACGAGGA
Statistics
Matches: 157, Mismatches: 18, Indels: 17
0.82 0.09 0.09
Matches are distributed among these distances:
39 40 0.25
40 103 0.66
41 13 0.08
42 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.26
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGATACTAAA
Found at i:34982564 original size:79 final size:80
Alignment explanation
Indices: 34982402--34982579 Score: 191
Period size: 79 Copynumber: 2.2 Consensus size: 80
34982392 AGATACAAAT
* * * *
34982402 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
** * *
34982467 GTGCGAGTTATTAAA
66 GAACGAGTGACTAAA
* * * * *
34982482 TCCGGGTTATGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
*
34982546 GAACGAG-GAGCTATA
66 GAACGAGTGA-CTAAA
*
34982561 TCC-GGTTAAATCCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
34982580 TACGTGATTT
Statistics
Matches: 81, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
78 15 0.19
79 48 0.59
80 18 0.22
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
GAACGAGTGACTAAA
Found at i:34987821 original size:27 final size:27
Alignment explanation
Indices: 34987790--34987967 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
34987780 TAAATTGTAC
34987790 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
34987817 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
34987843 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
34987871 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
34987899 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
34987926 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
34987953 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
34987968 GGCTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:34987904 original size:82 final size:81
Alignment explanation
Indices: 34987791--34987946 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
34987781 AAATTGTACA
* *
34987791 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
34987855 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
34987872 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
34987937 TGCGAGTTGA
65 TGCGAATTGA
34987947 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:34987958 original size:82 final size:81
Alignment explanation
Indices: 34987787--34987967 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
34987777 GATTAAATTG
* *
34987787 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
34987852 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
34987868 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
34987932 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
34987950 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
34987968 GGCTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:34987978 original size:27 final size:27
Alignment explanation
Indices: 34987872--34987978 Score: 70
Period size: 27 Copynumber: 3.9 Consensus size: 27
34987862 TGACCATGCG
* * * *
34987872 GCACTAAGTGTGCGAGTTTGACTATGTA
1 GCACTAAGTGTGCGAG-CTCAATATATA
** * * **
34987900 GCACTAAGTGTGCGATTTGATTACGTA
1 GCACTAAGTGTGCGAGCTCAATATATA
* * *
34987927 GCACTAAGTGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGAGCTCAATATATA
* *
34987954 GCACTGAGTGTGCGGGCTCAATATA
1 GCACTAAGTGTGCGAGCTCAATATA
34987979 CATTCGTGAA
Statistics
Matches: 68, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
27 53 0.78
28 15 0.22
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.31
Consensus pattern (27 bp):
GCACTAAGTGTGCGAGCTCAATATATA
Found at i:34990590 original size:21 final size:19
Alignment explanation
Indices: 34990561--34990617 Score: 51
Period size: 22 Copynumber: 2.7 Consensus size: 19
34990551 AAAAAAATTG
34990561 AAATATTGAAAAAGAATAAAGA
1 AAAT-TTGAAAAA-AA-AAAGA
34990583 AAATTTGAAGTAAAAAAAAGA
1 AAATTTGAA--AAAAAAAAGA
*
34990604 AGGATTTGAAAAAA
1 A-AATTTGAAAAAA
34990618 TTTGAGTTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
20 4 0.13
21 11 0.35
22 13 0.42
23 3 0.10
ACGTcount: A:0.65, C:0.00, G:0.16, T:0.19
Consensus pattern (19 bp):
AAATTTGAAAAAAAAAAGA
Found at i:34992773 original size:16 final size:18
Alignment explanation
Indices: 34992735--34992776 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
34992725 GTTTACAAAT
*
34992735 AAGAAAGAAAATGAGAGTA
1 AAGAAAAAAAATGAGAG-A
34992754 AAGAAAAAAAAT-AGAG-
1 AAGAAAAAAAATGAGAGA
34992770 AAGAAAA
1 AAGAAAA
34992777 GTGAAAAGGT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 7 0.32
18 4 0.18
19 11 0.50
ACGTcount: A:0.71, C:0.00, G:0.21, T:0.07
Consensus pattern (18 bp):
AAGAAAAAAAATGAGAGA
Found at i:34992916 original size:17 final size:17
Alignment explanation
Indices: 34992894--34992929 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
34992884 ATTGGAAGAA
34992894 AAAATATTGAGTTGATT
1 AAAATATTGAGTTGATT
34992911 AAAATATTGAGTTGATT
1 AAAATATTGAGTTGATT
34992928 AA
1 AA
34992930 TGAGAGGAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.17, T:0.39
Consensus pattern (17 bp):
AAAATATTGAGTTGATT
Found at i:34997486 original size:151 final size:151
Alignment explanation
Indices: 34997202--34997495 Score: 453
Period size: 151 Copynumber: 1.9 Consensus size: 151
34997192 TTCACGAGTT
* * *
34997202 TGCTCACACAAGCTGTCAGTCTTTTGTTACTACTCAGTGCTGCTCACACAAGCTATCAGGTATCC
1 TGCTCACACAAGCTGTCAGTCATTCGTCACTACTCAGTGCTGCTCACACAAGCTATCAGGTATCC
* *
34997267 GCAACATATGCCGGTATACCCAGCCACTGGTAGAACTTAAGACCAGCACCTGATTACACATTAAT
66 GCAACATATGCCGGTATACCCAGCCACTGGTAGAACTTAAGACCAGCACCCGAATACACATTAAT
*
34997332 CACAGTTTCACATCACGGGCC
131 CACAATTTCACATCACGGGCC
* *
34997353 TGCTCACACAAGCTGTCAGTCATTCGTCACTACTCAGTGCTGCTCACACAAGCTGTCAGGTATCT
1 TGCTCACACAAGCTGTCAGTCATTCGTCACTACTCAGTGCTGCTCACACAAGCTATCAGGTATCC
* * * * * * *
34997418 GTAACATATGCCGGTATACCCAGCCACTGGTAGAACTTATGACTAGCGCCCGAATCCACTTTATT
66 GCAACATATGCCGGTATACCCAGCCACTGGTAGAACTTAAGACCAGCACCCGAATACACATTAAT
34997483 CACAATTTCACAT
131 CACAATTTCACAT
34997496 AGATCTCTAA
Statistics
Matches: 128, Mismatches: 15, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
151 128 1.00
ACGTcount: A:0.27, C:0.30, G:0.17, T:0.26
Consensus pattern (151 bp):
TGCTCACACAAGCTGTCAGTCATTCGTCACTACTCAGTGCTGCTCACACAAGCTATCAGGTATCC
GCAACATATGCCGGTATACCCAGCCACTGGTAGAACTTAAGACCAGCACCCGAATACACATTAAT
CACAATTTCACATCACGGGCC
Found at i:35002471 original size:5 final size:5
Alignment explanation
Indices: 35002461--35002489 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
35002451 CACATGCTCT
35002461 TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
35002490 TCACAAGCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTC
Found at i:35021558 original size:22 final size:22
Alignment explanation
Indices: 35021515--35021558 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
35021505 GAAAATGATC
**
35021515 AAAATTAATCAAAATTTGACAT
1 AAAATTAATCAAAATTAAACAT
*
35021537 AAAATTAATTAAAATTAAACAT
1 AAAATTAATCAAAATTAAACAT
35021559 GTTCATAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.59, C:0.07, G:0.02, T:0.32
Consensus pattern (22 bp):
AAAATTAATCAAAATTAAACAT
Found at i:35025113 original size:30 final size:31
Alignment explanation
Indices: 35025055--35025114 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
35025045 GCCTTTTGAA
* *
35025055 AATATTTACAAAAAAATGACATCTAATTTTT
1 AATATTTACAAAAAAATGACACCAAATTTTT
35025086 AATATTTACAAAAAGAAT-A-ACCAAATTTT
1 AATATTTACAAAAA-AATGACACCAAATTTT
35025115 GAAAATAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 8 0.31
31 15 0.58
32 3 0.12
ACGTcount: A:0.52, C:0.10, G:0.03, T:0.35
Consensus pattern (31 bp):
AATATTTACAAAAAAATGACACCAAATTTTT
Found at i:35032871 original size:22 final size:22
Alignment explanation
Indices: 35032828--35032871 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
35032818 AAAAATAATC
**
35032828 AAAACTAATCAAAATTTGACAT
1 AAAACTAATCAAAATTCAACAT
* *
35032850 AAAATTAATTAAAATTCAACAT
1 AAAACTAATCAAAATTCAACAT
35032872 GTTCATAATT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.57, C:0.11, G:0.02, T:0.30
Consensus pattern (22 bp):
AAAACTAATCAAAATTCAACAT
Found at i:35038711 original size:19 final size:19
Alignment explanation
Indices: 35038687--35038723 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
35038677 TGGAAATGTC
* *
35038687 ATTTCCATTTTCATTTTTT
1 ATTTCCAATTCCATTTTTT
35038706 ATTTCCAATTCCATTTTT
1 ATTTCCAATTCCATTTTT
35038724 GGAAATATAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.19, C:0.19, G:0.00, T:0.62
Consensus pattern (19 bp):
ATTTCCAATTCCATTTTTT
Found at i:35039246 original size:66 final size:66
Alignment explanation
Indices: 35039140--35039271 Score: 169
Period size: 66 Copynumber: 2.0 Consensus size: 66
35039130 CTTATTACAT
*
35039140 TAATGTCGCTACATGAGTTAATCCCAGATTGCATTCAGAATTGTT-GCCGCACTTGACAGCTGTC
1 TAATGTCGCTACATGAGTTAATCCCAGATTACATTCAGAATT-TTCGCCGCACTTGACAGCTGTC
35039204 TG
65 TG
* * * ** *
35039206 TAATGTTGCTGCATGAGTTAATTCCAGATTAC-TTCCAGAATTTTCGTTGCACTTGATAGCTGTC
1 TAATGTCGCTACATGAGTTAATCCCAGATTACATT-CAGAATTTTCGCCGCACTTGACAGCTGTC
35039270 TG
65 TG
35039272 GATAAGAACT
Statistics
Matches: 57, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
65 4 0.07
66 53 0.93
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.36
Consensus pattern (66 bp):
TAATGTCGCTACATGAGTTAATCCCAGATTACATTCAGAATTTTCGCCGCACTTGACAGCTGTCT
G
Found at i:35048235 original size:41 final size:37
Alignment explanation
Indices: 35048140--35048236 Score: 104
Period size: 38 Copynumber: 2.5 Consensus size: 37
35048130 TACAATCACT
* *
35048140 TTAATATTAAATTAATATAATATTTATCTTGATAAATA
1 TTAA-ATTAAATTAATATAATATTTATCTAGATAAACA
* *
35048178 TTATAATCAAAATAATATAATATTTATCTAAAAGATAAACA
1 TTA-AATTAAATTAATATAATATTTATCT---AGATAAACA
35048219 TTAAATTAAATTTAATAT
1 TTAAATTAAA-TTAATAT
35048237 TAAACCATTA
Statistics
Matches: 48, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
38 25 0.52
39 1 0.02
40 6 0.12
41 16 0.33
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.42
Consensus pattern (37 bp):
TTAAATTAAATTAATATAATATTTATCTAGATAAACA
Found at i:35050120 original size:27 final size:27
Alignment explanation
Indices: 35050052--35050121 Score: 79
Period size: 27 Copynumber: 2.6 Consensus size: 27
35050042 CACACGTGAA
* *
35050052 CACCAACTCGCCGAGCCTACTGGAGAT
1 CACCAACTCGCCAAGCCTACTGGAGAC
**
35050079 CACCAACTCATCAAGCCTACT-GACGAC
1 CACCAACTCGCCAAGCCTACTGGA-GAC
*
35050106 CACCAACTTGCCAAGC
1 CACCAACTCGCCAAGC
35050122 GCCAAACTCC
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
26 2 0.06
27 33 0.94
ACGTcount: A:0.30, C:0.40, G:0.16, T:0.14
Consensus pattern (27 bp):
CACCAACTCGCCAAGCCTACTGGAGAC
Found at i:35050746 original size:12 final size:12
Alignment explanation
Indices: 35050718--35050750 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
35050708 CTTCGTTATT
35050718 TTTATG-TTTTC
1 TTTATGTTTTTC
35050729 -TTATGTTTTTC
1 TTTATGTTTTTC
35050740 TTTATGTTTTT
1 TTTATGTTTTT
35050751 ATTTGCAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 5 0.25
11 5 0.25
12 10 0.50
ACGTcount: A:0.09, C:0.06, G:0.09, T:0.76
Consensus pattern (12 bp):
TTTATGTTTTTC
Found at i:35056984 original size:16 final size:16
Alignment explanation
Indices: 35056963--35056994 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
35056953 GTTTCGTTGC
*
35056963 TAATTTTACTTTTTCA
1 TAATTTCACTTTTTCA
35056979 TAATTTCACTTTTTCA
1 TAATTTCACTTTTTCA
35056995 CTTTCAATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.16, G:0.00, T:0.59
Consensus pattern (16 bp):
TAATTTCACTTTTTCA
Found at i:35057427 original size:101 final size:101
Alignment explanation
Indices: 35057215--35057438 Score: 231
Period size: 101 Copynumber: 2.2 Consensus size: 101
35057205 AATGATACCG
* * *
35057215 GTTCACATAGTAGCCTACACATAGTACTACACATGTGACCATCACTAACCGATACACGTAATATC
1 GTTCACATAGTAGCCTACACATAGTACTACAAATGCGACCATCACTAACCGATACACGTAATAGC
* *
35057280 CTGTACATAATACTACACACGTGATCGAAGCTATCT
66 CTGCACATAATACTACACACGTGATCCAAGCTATCT
* * * * * * *
35057316 GGTACGCATAGTAGCCTGCACATAGTACTACAAATGCGACCTATCA-T-TCTGGTACACGTAGTA
1 -GTTCACATAGTAGCCTACACATAGTACTACAAATGCGACC-ATCACTAACCGATACACGTAATA
* * *
35057379 GCCTGCACATAGTACTACACACGTGA-CCATTGCTTTTACT
64 GCCTGCACATAATACTACACACGTGATCCA-AGC-TAT-CT
*
35057419 -TTCACATAGTGGCCTACACA
1 GTTCACATAGTAGCCTACACA
35057439 CAGACCATGC
Statistics
Matches: 99, Mismatches: 19, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
100 2 0.02
101 53 0.54
102 38 0.38
103 6 0.06
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.26
Consensus pattern (101 bp):
GTTCACATAGTAGCCTACACATAGTACTACAAATGCGACCATCACTAACCGATACACGTAATAGC
CTGCACATAATACTACACACGTGATCCAAGCTATCT
Found at i:35060648 original size:20 final size:20
Alignment explanation
Indices: 35060595--35060648 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 20
35060585 GCTGAAAGTA
*
35060595 AGCTCAGTTGAGCTCAAACG
1 AGCTGAGTTGAGCTCAAACG
**** *
35060615 AGCTGAAACAAGCTCAAATG
1 AGCTGAGTTGAGCTCAAACG
35060635 AGCTGAGTTGAGCT
1 AGCTGAGTTGAGCT
35060649 GGACGGTGCT
Statistics
Matches: 24, Mismatches: 10, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.33, C:0.20, G:0.26, T:0.20
Consensus pattern (20 bp):
AGCTGAGTTGAGCTCAAACG
Found at i:35062320 original size:11 final size:12
Alignment explanation
Indices: 35062290--35062321 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
35062280 TTTCACTCTT
35062290 CTCTTTTTCAAA
1 CTCTTTTTCAAA
35062302 CTCTTTTTCAAA
1 CTCTTTTTCAAA
*
35062314 TTCTTTTT
1 CTCTTTTT
35062322 TGGCTTTTTC
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:0.19, C:0.22, G:0.00, T:0.59
Consensus pattern (12 bp):
CTCTTTTTCAAA
Found at i:35062333 original size:27 final size:27
Alignment explanation
Indices: 35062303--35062364 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
35062293 TTTTTCAAAC
*
35062303 TCTTTTTCAA-ATTCTTTT-TTGGCTTTT
1 TCTTTTTCAATATTCTTTTCTT--CATTT
*
35062330 TCTTTTTCAATTTTCTTTTCTTCATTT
1 TCTTTTTCAATATTCTTTTCTTCATTT
35062357 TCTTTTTC
1 TCTTTTTC
35062365 TCTCACTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
27 22 0.71
28 7 0.23
29 2 0.06
ACGTcount: A:0.10, C:0.18, G:0.03, T:0.69
Consensus pattern (27 bp):
TCTTTTTCAATATTCTTTTCTTCATTT
Found at i:35062343 original size:13 final size:12
Alignment explanation
Indices: 35062327--35062446 Score: 63
Period size: 12 Copynumber: 10.0 Consensus size: 12
35062317 TTTTTTGGCT
35062327 TTTTCTTTTTCAA
1 TTTTCTTTTTC-A
35062340 TTTTCTTTTCTTCA
1 TTTTC-TTT-TTCA
35062354 TTTTCTTTTTC-
1 TTTTCTTTTTCA
** *
35062365 TCTCACTTTTTTGA
1 T-TTTC-TTTTTCA
35062379 -TTTCTTTTTC-
1 TTTTCTTTTTCA
** *
35062389 TTTTGCAATTTCT
1 TTTT-CTTTTTCA
*
35062402 TTTTCTTTTTCG
1 TTTTCTTTTTCA
*
35062414 TTTTCTTTTT-G
1 TTTTCTTTTTCA
35062425 TTTTC--TTTCA
1 TTTTCTTTTTCA
*
35062435 ATTTCTTTTTCA
1 TTTTCTTTTTCA
35062447 ATCTCTTTCT
Statistics
Matches: 83, Mismatches: 13, Indels: 23
0.70 0.11 0.19
Matches are distributed among these distances:
9 3 0.04
10 4 0.05
11 15 0.18
12 32 0.39
13 17 0.20
14 9 0.11
15 3 0.04
ACGTcount: A:0.08, C:0.17, G:0.03, T:0.71
Consensus pattern (12 bp):
TTTTCTTTTTCA
Found at i:35062356 original size:14 final size:14
Alignment explanation
Indices: 35062327--35062363 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
35062317 TTTTTTGGCT
35062327 TTTTC-TTTTTCAA
1 TTTTCTTTTTTCAA
35062340 TTTTCTTTTCTTC-A
1 TTTTCTTTT-TTCAA
35062354 TTTTCTTTTT
1 TTTTCTTTTT
35062364 CTCTCACTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 6 0.27
14 13 0.59
15 3 0.14
ACGTcount: A:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTTCTTTTTTCAA
Found at i:35062445 original size:6 final size:6
Alignment explanation
Indices: 35062325--35062432 Score: 67
Period size: 6 Copynumber: 17.7 Consensus size: 6
35062315 TCTTTTTTGG
* * * **
35062325 CTTTTT CTTTTT CAATTTT CTTTTCTT CATTTT CTTTTT CTCTCA CTTTTT
1 CTTTTT CTTTTT C-TTTTT C-TTT-TT CTTTTT CTTTTT CTTTTT CTTTTT
* * ** *
35062376 -TGATTT CTTTTT CTTTTG CAATTT CTTTTT CTTTTT CGTTTT CTTTTT
1 CT-TTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
*
35062424 -GTTTT CTTT
1 CTTTTT CTTT
35062433 CAATTTCTTT
Statistics
Matches: 74, Mismatches: 23, Indels: 10
0.69 0.21 0.09
Matches are distributed among these distances:
5 5 0.07
6 56 0.76
7 10 0.14
8 3 0.04
ACGTcount: A:0.06, C:0.18, G:0.04, T:0.72
Consensus pattern (6 bp):
CTTTTT
Found at i:35063524 original size:36 final size:37
Alignment explanation
Indices: 35063450--35063524 Score: 100
Period size: 36 Copynumber: 2.0 Consensus size: 37
35063440 GCAAGACTTT
35063450 TCACTTTTTTTTTCTTCTTTTTTTAACTCGATTTTTTTG
1 TCACTTTTTTTTTCTTCTTTTTTT-A-TCGATTTTTTTG
*
35063489 TCACTTCTTTTTTTTTTC-TTTTTT-TCGATTTTTTTG
1 TCACTT-TTTTTTTCTTCTTTTTTTATCGATTTTTTTG
35063525 AATTTTTTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
36 12 0.35
39 12 0.35
40 10 0.29
ACGTcount: A:0.08, C:0.15, G:0.05, T:0.72
Consensus pattern (37 bp):
TCACTTTTTTTTTCTTCTTTTTTTATCGATTTTTTTG
Found at i:35063532 original size:12 final size:12
Alignment explanation
Indices: 35063517--35063541 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
35063507 TTTTTTTCGA
35063517 TTTTTTTGAATT
1 TTTTTTTGAATT
35063529 TTTTTTTGAATT
1 TTTTTTTGAATT
35063541 T
1 T
35063542 CTTCTCTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.00, G:0.08, T:0.76
Consensus pattern (12 bp):
TTTTTTTGAATT
Found at i:35065115 original size:20 final size:20
Alignment explanation
Indices: 35065062--35065115 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 20
35065052 GCTGAAAGTA
*
35065062 AGCTCAGTTGAGCTCAAACG
1 AGCTGAGTTGAGCTCAAACG
**** *
35065082 AGCTGAAACAAGCTCAAATG
1 AGCTGAGTTGAGCTCAAACG
35065102 AGCTGAGTTGAGCT
1 AGCTGAGTTGAGCT
35065116 GGACGGTGCT
Statistics
Matches: 24, Mismatches: 10, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.33, C:0.20, G:0.26, T:0.20
Consensus pattern (20 bp):
AGCTGAGTTGAGCTCAAACG
Found at i:35066323 original size:28 final size:27
Alignment explanation
Indices: 35066282--35066350 Score: 84
Period size: 28 Copynumber: 2.5 Consensus size: 27
35066272 GTTTTCACAA
*
35066282 ATTTAAAATTTAATCGATTTATTTTTT
1 ATTTAAAATTTAATCCATTTATTTTTT
* *
35066309 ATTTAAATATTTAATCCTTTTATTTTTAA
1 ATTTAAA-ATTTAATCCATTTATTTTT-T
*
35066338 ATTTTAAATTTAA
1 ATTTAAAATTTAA
35066351 ATTTAATTGT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
27 7 0.19
28 23 0.64
29 6 0.17
ACGTcount: A:0.36, C:0.04, G:0.01, T:0.58
Consensus pattern (27 bp):
ATTTAAAATTTAATCCATTTATTTTTT
Found at i:35076470 original size:31 final size:30
Alignment explanation
Indices: 35076432--35076496 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 30
35076422 AATACAAAGA
* *
35076432 ATTCTTTCATTACTCAATACATTTTCATTC
1 ATTCTTTCAATACTCAATACAGTTTCATTC
* *
35076462 TATTCTTTCAATACTTAGTACAGTTTCATTC
1 -ATTCTTTCAATACTCAATACAGTTTCATTC
35076493 ATTC
1 ATTC
35076497 AATACACAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 4 0.13
31 26 0.87
ACGTcount: A:0.26, C:0.22, G:0.03, T:0.49
Consensus pattern (30 bp):
ATTCTTTCAATACTCAATACAGTTTCATTC
Found at i:35076930 original size:7 final size:7
Alignment explanation
Indices: 35076918--35076951 Score: 52
Period size: 7 Copynumber: 4.9 Consensus size: 7
35076908 TGAACAAAAG
35076918 AATTTTA
1 AATTTTA
35076925 AATTTTA
1 AATTTTA
35076932 AATTTTA
1 AATTTTA
35076939 AATTATT-
1 AATT-TTA
35076946 AATTTT
1 AATTTT
35076952 TTTCAAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
6 2 0.08
7 22 0.85
8 2 0.08
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (7 bp):
AATTTTA
Found at i:35079437 original size:16 final size:16
Alignment explanation
Indices: 35079410--35079480 Score: 97
Period size: 16 Copynumber: 4.4 Consensus size: 16
35079400 GTTTGGTTCA
35079410 CTGTAATGGAATAGAG
1 CTGTAATGGAATAGAG
* *
35079426 CTATAATTGAATAGAG
1 CTGTAATGGAATAGAG
*
35079442 CTGTAATTGAATAGAG
1 CTGTAATGGAATAGAG
* *
35079458 TTGTAATGGAATAAAG
1 CTGTAATGGAATAGAG
35079474 CTGTAAT
1 CTGTAAT
35079481 CAGTAATTCA
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 48 1.00
ACGTcount: A:0.39, C:0.06, G:0.24, T:0.31
Consensus pattern (16 bp):
CTGTAATGGAATAGAG
Found at i:35079796 original size:22 final size:24
Alignment explanation
Indices: 35079757--35079810 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 24
35079747 TAAATATTAT
* *
35079757 TTATTT-ATTTTATCAATACAT-A
1 TTATTTAATTTAATCAATAAATAA
35079779 TTATTTAATTTAAT-AATAAATAA
1 TTATTTAATTTAATCAATAAATAA
*
35079802 TAATTTAAT
1 TTATTTAAT
35079811 CATATTTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 12 0.44
23 15 0.56
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (24 bp):
TTATTTAATTTAATCAATAAATAA
Found at i:35082623 original size:13 final size:13
Alignment explanation
Indices: 35082602--35082631 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
35082592 ATCAAAAGGC
35082602 CTCTATATTTTCT
1 CTCTATATTTTCT
*
35082615 CTCTCTATTTTCT
1 CTCTATATTTTCT
35082628 CTCT
1 CTCT
35082632 TTTTTGTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.10, C:0.30, G:0.00, T:0.60
Consensus pattern (13 bp):
CTCTATATTTTCT
Found at i:35084884 original size:17 final size:18
Alignment explanation
Indices: 35084862--35084895 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
35084852 AAAACTAAAA
*
35084862 TTAAAAGTAA-AAGAAAG
1 TTAAAAGAAATAAGAAAG
35084879 TTAAAAGAAATAAGAAA
1 TTAAAAGAAATAAGAAA
35084896 AAATAATAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.68, C:0.00, G:0.15, T:0.18
Consensus pattern (18 bp):
TTAAAAGAAATAAGAAAG
Found at i:35087181 original size:23 final size:23
Alignment explanation
Indices: 35087155--35087253 Score: 180
Period size: 23 Copynumber: 4.3 Consensus size: 23
35087145 AGTGTTATTG
*
35087155 ATCAGTGGTAACTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
35087178 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
35087201 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
35087224 TTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
35087247 ATCAGTG
1 ATCAGTG
35087254 TGGCACTTAT
Statistics
Matches: 73, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 73 1.00
ACGTcount: A:0.22, C:0.21, G:0.25, T:0.31
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:35087426 original size:38 final size:37
Alignment explanation
Indices: 35087383--35087454 Score: 101
Period size: 38 Copynumber: 1.9 Consensus size: 37
35087373 ATGTGTGGAA
*
35087383 TTGAATTGAATATTGACTTGAAA-ATGAAAAAGTGAGTT
1 TTGAATTGAATAGTGA-TT-AAATATGAAAAAGTGAGTT
*
35087421 TTGAATTGAATAGTGATTAAATGTGAAAAAGTGA
1 TTGAATTGAATAGTGATTAAATATGAAAAAGTGA
35087455 AATTATGAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
36 3 0.10
37 13 0.42
38 15 0.48
ACGTcount: A:0.43, C:0.01, G:0.22, T:0.33
Consensus pattern (37 bp):
TTGAATTGAATAGTGATTAAATATGAAAAAGTGAGTT
Found at i:35096299 original size:30 final size:30
Alignment explanation
Indices: 35096242--35096300 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
35096232 TGCCTTTGAA
* *
35096242 AATATTTACAAAAAGAGACATCTAATTTTT
1 AATATTTACAAAAAGAGACAGCAAATTTTT
35096272 AATATTTACAAAAAGAG-CAAGCAAATTTT
1 AATATTTACAAAAAGAGAC-AGCAAATTTT
35096301 GAAAATAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 1 0.04
30 25 0.96
ACGTcount: A:0.49, C:0.10, G:0.08, T:0.32
Consensus pattern (30 bp):
AATATTTACAAAAAGAGACAGCAAATTTTT
Found at i:35097166 original size:14 final size:13
Alignment explanation
Indices: 35097149--35097179 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
35097139 CGAGTATGCC
35097149 TTTGATCTCTTTA
1 TTTGATCTCTTTA
35097162 GTTTGATCTCTTTA
1 -TTTGATCTCTTTA
35097176 TTTG
1 TTTG
35097180 CCAGTTCAGC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.24
14 13 0.76
ACGTcount: A:0.13, C:0.13, G:0.13, T:0.61
Consensus pattern (13 bp):
TTTGATCTCTTTA
Found at i:35106792 original size:43 final size:43
Alignment explanation
Indices: 35106708--35106806 Score: 117
Period size: 43 Copynumber: 2.3 Consensus size: 43
35106698 CCTGTTCTTT
* ** * *
35106708 CGATGATGCACTATGCGTGCCAGTATATTTTGATGGGTTTATC
1 CGATGATGCACTACGCGTGCCAGTATATTTCCATCGATTTATC
* *
35106751 CGATGATGCACTACGTGTGCCAGTATATTTCCTTCGATTTATC
1 CGATGATGCACTACGCGTGCCAGTATATTTCCATCGATTTATC
**
35106794 TAATGATGCACTA
1 CGATGATGCACTA
35106807 TAGTGCTAGA
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 47 1.00
ACGTcount: A:0.23, C:0.19, G:0.21, T:0.36
Consensus pattern (43 bp):
CGATGATGCACTACGCGTGCCAGTATATTTCCATCGATTTATC
Found at i:35117126 original size:20 final size:21
Alignment explanation
Indices: 35117101--35117139 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
35117091 AATGAAATAG
35117101 ATTTACTAA-AATTA-AACACA
1 ATTTAC-AACAATTATAACACA
35117121 ATTTACAACAATTATAACA
1 ATTTACAACAATTATAACA
35117140 TAAATAAACT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 2 0.12
20 11 0.65
21 4 0.24
ACGTcount: A:0.54, C:0.15, G:0.00, T:0.31
Consensus pattern (21 bp):
ATTTACAACAATTATAACACA
Found at i:35119341 original size:36 final size:36
Alignment explanation
Indices: 35119294--35119363 Score: 131
Period size: 36 Copynumber: 1.9 Consensus size: 36
35119284 AACATTCATT
*
35119294 TATTAAAACATACTTATGAAATAAATGATTAAAACA
1 TATTAAAACATACTTATGAAAGAAATGATTAAAACA
35119330 TATTAAAACATACTTATGAAAGAAATGATTAAAA
1 TATTAAAACATACTTATGAAAGAAATGATTAAAA
35119364 TATACTTGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.56, C:0.07, G:0.07, T:0.30
Consensus pattern (36 bp):
TATTAAAACATACTTATGAAAGAAATGATTAAAACA
Found at i:35119379 original size:24 final size:26
Alignment explanation
Indices: 35119331--35119379 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
35119321 ATTAAAACAT
*
35119331 ATTAAAACATACTTATGAAAGAAATG
1 ATTAAAACATACTTATGAAAAAAATG
*
35119357 ATTAAAATATAC-T-TGAAAAAAAT
1 ATTAAAACATACTTATGAAAAAAAT
35119380 TTAAAAGTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 9 0.43
25 1 0.05
26 11 0.52
ACGTcount: A:0.57, C:0.06, G:0.08, T:0.29
Consensus pattern (26 bp):
ATTAAAACATACTTATGAAAAAAATG
Found at i:35124207 original size:6 final size:7
Alignment explanation
Indices: 35124180--35124206 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
35124170 TATAATTATA
35124180 ATTTTTT
1 ATTTTTT
35124187 ATTTTTT
1 ATTTTTT
35124194 ATTTTTT
1 ATTTTTT
35124201 ATTTTT
1 ATTTTT
35124207 AGACATTTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (7 bp):
ATTTTTT
Found at i:35125910 original size:29 final size:28
Alignment explanation
Indices: 35125848--35125910 Score: 72
Period size: 29 Copynumber: 2.2 Consensus size: 28
35125838 TTAAATTTAG
* *
35125848 AGTTATTTTTTAATTTTATATATAATTT
1 AGTTATTTTTTAATTTTACATATAAATT
* * *
35125876 ATTTATTTTATTATTTTTACATGTAAATT
1 AGTTATTTT-TTAATTTTACATATAAATT
35125905 AGTTAT
1 AGTTAT
35125911 CAAATCCAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
28 8 0.29
29 20 0.71
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.62
Consensus pattern (28 bp):
AGTTATTTTTTAATTTTACATATAAATT
Found at i:35133082 original size:25 final size:25
Alignment explanation
Indices: 35133048--35133105 Score: 116
Period size: 25 Copynumber: 2.3 Consensus size: 25
35133038 AAATTATTAT
35133048 TTAGTTTTCATATTTGATTTCGCTC
1 TTAGTTTTCATATTTGATTTCGCTC
35133073 TTAGTTTTCATATTTGATTTCGCTC
1 TTAGTTTTCATATTTGATTTCGCTC
35133098 TTAGTTTT
1 TTAGTTTT
35133106 TTACCTAGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.16, C:0.14, G:0.12, T:0.59
Consensus pattern (25 bp):
TTAGTTTTCATATTTGATTTCGCTC
Found at i:35137043 original size:47 final size:47
Alignment explanation
Indices: 35136974--35137068 Score: 181
Period size: 47 Copynumber: 2.0 Consensus size: 47
35136964 TGTGTGATTG
*
35136974 TTTTATGCTTTTCTAGGAAGATAATTGGTTAAAGCTAGGTGTATAGA
1 TTTTATGCTTTTCCAGGAAGATAATTGGTTAAAGCTAGGTGTATAGA
35137021 TTTTATGCTTTTCCAGGAAGATAATTGGTTAAAGCTAGGTGTATAGA
1 TTTTATGCTTTTCCAGGAAGATAATTGGTTAAAGCTAGGTGTATAGA
35137068 T
1 T
35137069 ATGACGCTTT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.29, C:0.07, G:0.23, T:0.40
Consensus pattern (47 bp):
TTTTATGCTTTTCCAGGAAGATAATTGGTTAAAGCTAGGTGTATAGA
Found at i:35137078 original size:47 final size:47
Alignment explanation
Indices: 35136980--35137078 Score: 162
Period size: 47 Copynumber: 2.1 Consensus size: 47
35136970 ATTGTTTTAT
* * * *
35136980 GCTTTTCTAGGAAGATAATTGGTTAAAGCTAGGTGTATAGATTTTAT
1 GCTTTTCCAGGAAGATAATTGGTTAAAGCTAGGTGTATAGATATGAC
35137027 GCTTTTCCAGGAAGATAATTGGTTAAAGCTAGGTGTATAGATATGAC
1 GCTTTTCCAGGAAGATAATTGGTTAAAGCTAGGTGTATAGATATGAC
35137074 GCTTT
1 GCTTT
35137079 ACTTTTTTGT
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.37
Consensus pattern (47 bp):
GCTTTTCCAGGAAGATAATTGGTTAAAGCTAGGTGTATAGATATGAC
Found at i:35137448 original size:23 final size:23
Alignment explanation
Indices: 35137418--35137461 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
35137408 GAATGTGGTG
35137418 GTTGTGGATAACTAGGATTGTTA
1 GTTGTGGATAACTAGGATTGTTA
**
35137441 GTTGTGGATATTTAGGATTGT
1 GTTGTGGATAACTAGGATTGT
35137462 ATGTCTGTCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.23, C:0.02, G:0.32, T:0.43
Consensus pattern (23 bp):
GTTGTGGATAACTAGGATTGTTA
Found at i:35142030 original size:27 final size:25
Alignment explanation
Indices: 35141953--35142030 Score: 93
Period size: 26 Copynumber: 3.0 Consensus size: 25
35141943 TTTCTCACCC
*
35141953 CAATTTTACCCTAATAAAATTTTGA
1 CAATTTTACCCTGATAAAATTTTGA
* *
35141978 CAATTTTACTCTTGGTAAAATTTTGA
1 CAATTTTAC-CCTGATAAAATTTTGA
*
35142004 CGATTTTAAACCCTGATAAAATTTTGA
1 CAATTTT--ACCCTGATAAAATTTTGA
35142031 GAAAATTCAT
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
25 9 0.20
26 19 0.43
27 14 0.32
28 2 0.05
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.41
Consensus pattern (25 bp):
CAATTTTACCCTGATAAAATTTTGA
Found at i:35142306 original size:9 final size:10
Alignment explanation
Indices: 35142279--35142319 Score: 52
Period size: 10 Copynumber: 4.4 Consensus size: 10
35142269 CTGAATGTTT
*
35142279 TTCATTTCTC
1 TTCATTTCTA
35142289 TT--TTTCTA
1 TTCATTTCTA
35142297 TTCA-TTCTA
1 TTCATTTCTA
35142306 TTCATTTCTA
1 TTCATTTCTA
35142316 TTCA
1 TTCA
35142320 AACACGCAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
8 7 0.26
9 9 0.33
10 11 0.41
ACGTcount: A:0.17, C:0.22, G:0.00, T:0.61
Consensus pattern (10 bp):
TTCATTTCTA
Found at i:35144683 original size:30 final size:29
Alignment explanation
Indices: 35144487--35144696 Score: 251
Period size: 29 Copynumber: 7.2 Consensus size: 29
35144477 ATATCGACGC
35144487 CCATCGAATATGAAAAGGGATGGTTTCGA
1 CCATCGAATATGAAAAGGGATGGTTTCGA
* * **
35144516 CCATCAAATATGAAAAGGGATGCTGACGA
1 CCATCGAATATGAAAAGGGATGGTTTCGA
* * * *
35144545 CCATCAAATAAGAAAAGGGGTAGTTTCGA
1 CCATCGAATATGAAAAGGGATGGTTTCGA
*
35144574 CCATC-AAGTATGAAAAGGGATGGTTTCTA
1 CCATCGAA-TATGAAAAGGGATGGTTTCGA
* **
35144603 CCATCGAATATGAAAAAGGATGGTGACGA
1 CCATCGAATATGAAAAGGGATGGTTTCGA
35144632 CCATCGAATATGAAAAGGGATGGTTTCGA
1 CCATCGAATATGAAAAGGGATGGTTTCGA
* * * *
35144661 CCATTGATTAAAGAAAATGGATGGTTTCGA
1 CCATCGAAT-ATGAAAAGGGATGGTTTCGA
35144691 CCATCG
1 CCATCG
35144697 TTTAGCACAC
Statistics
Matches: 152, Mismatches: 26, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
28 2 0.01
29 125 0.82
30 25 0.16
ACGTcount: A:0.37, C:0.15, G:0.25, T:0.23
Consensus pattern (29 bp):
CCATCGAATATGAAAAGGGATGGTTTCGA
Found at i:35149539 original size:75 final size:75
Alignment explanation
Indices: 35149407--35149549 Score: 180
Period size: 75 Copynumber: 1.9 Consensus size: 75
35149397 GCTTACATAT
* * * * * * *
35149407 ATGTATATGTTCTTTTATTGAATTTAGGAAGGACATTTATATAAGTTTATATGAGATTTGATTAT
1 ATGTATATGTTCTTGTAATGAATTTAAGAAGGAAATTTATATAAGTATATAGGAGATTCGATTAT
35149472 GCAGGTATAC
66 GCAGGTATAC
* * *
35149482 ATGTATATGTTCTTGTAATGAATTTAAGTATGAAATTTATATATGTATA-AGGAAGATTCGATTA
1 ATGTATATGTTCTTGTAATGAATTTAAGAAGGAAATTTATATAAGTATATAGG-AGATTCGATTA
35149546 TGCA
65 TGCA
35149550 TATATATTCA
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
74 2 0.04
75 55 0.96
ACGTcount: A:0.34, C:0.05, G:0.18, T:0.43
Consensus pattern (75 bp):
ATGTATATGTTCTTGTAATGAATTTAAGAAGGAAATTTATATAAGTATATAGGAGATTCGATTAT
GCAGGTATAC
Found at i:35149727 original size:41 final size:41
Alignment explanation
Indices: 35149641--35149734 Score: 100
Period size: 41 Copynumber: 2.3 Consensus size: 41
35149631 TCAGATTTAC
* * * * * *
35149641 GTCTAGCAGGTTTGATGCCGGTGAAATATTTAAGACTTTAT
1 GTCTAGCAGGCTTAATGCCAGTGAAAAATTTAAGACTATAA
*
35149682 GTCTAGCAGGCTTAATGCCAGTGAAACAATTT-GGACTATAA
1 GTCTAGCAGGCTTAATGCCAGTGAAA-AATTTAAGACTATAA
*
35149723 GTCTAACAGGCT
1 GTCTAGCAGGCT
35149735 AAAAGCCGAT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
41 40 0.91
42 4 0.09
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.31
Consensus pattern (41 bp):
GTCTAGCAGGCTTAATGCCAGTGAAAAATTTAAGACTATAA
Found at i:35149939 original size:69 final size:67
Alignment explanation
Indices: 35149859--35150074 Score: 233
Period size: 63 Copynumber: 3.2 Consensus size: 67
35149849 TTGAAGAATA
* * * *
35149859 TGTATACACATTCGGTGATAATACTTGTTAGGCATATTTATATATGTATTTAGCTATTCATGTTT
1 TGTATATACATTCGGTGATAATATTTGTTA-GCATATTTATATA-GCATTCAGCTATTCATGTTT
35149924 AAAG
64 AAAG
* * *
35149928 TGTATATACATTCGGTGATAATATTTGTT---ATGTGTATA-AGCATTCGGCTATTCATGTTTAA
1 TGTATATACATTCGGTGATAATATTTGTTAGCATATTTATATAGCATTCAGCTATTCATGTTTAA
35149989 AG
66 AG
* * *
35149991 TGTGTATACATTCGATGATAATATTTGTTAAGCATATATGTATATACACATTCAGCTATTCATGT
1 TGTATATACATTCGGTGATAATATTTGTT-AGCATAT-T-TATATA-GCATTCAGCTATTCATG-
*
35150056 TTTAAAT
61 TTTAAAG
*
35150063 TGTATATGCATT
1 TGTATATACATT
35150075 TGACTATATG
Statistics
Matches: 122, Mismatches: 16, Indels: 15
0.80 0.10 0.10
Matches are distributed among these distances:
63 48 0.39
64 1 0.01
65 7 0.06
67 3 0.02
69 31 0.25
70 1 0.01
71 15 0.12
72 16 0.13
ACGTcount: A:0.31, C:0.10, G:0.16, T:0.44
Consensus pattern (67 bp):
TGTATATACATTCGGTGATAATATTTGTTAGCATATTTATATAGCATTCAGCTATTCATGTTTAA
AG
Found at i:35149964 original size:32 final size:32
Alignment explanation
Indices: 35149925--35150022 Score: 89
Period size: 32 Copynumber: 3.1 Consensus size: 32
35149915 TTCATGTTTA
35149925 AAGTGTATATACATTCGGTGATAATATTTGTT
1 AAGTGTATATACATTCGGTGATAATATTTGTT
* *
35149957 ATGTGTATA-AGCATTCGGCT-AT--TCATGTT-TA
1 AAGTGTATATA-CATTCGG-TGATAAT-AT-TTGTT
* *
35149988 AAGTGTGTATACATTCGATGATAATATTTGTT
1 AAGTGTATATACATTCGGTGATAATATTTGTT
35150020 AAG
1 AAG
35150023 CATATATGTA
Statistics
Matches: 51, Mismatches: 6, Indels: 18
0.68 0.08 0.24
Matches are distributed among these distances:
30 2 0.04
31 21 0.41
32 26 0.51
33 2 0.04
ACGTcount: A:0.31, C:0.08, G:0.19, T:0.42
Consensus pattern (32 bp):
AAGTGTATATACATTCGGTGATAATATTTGTT
Found at i:35152410 original size:39 final size:38
Alignment explanation
Indices: 35152356--35152466 Score: 132
Period size: 39 Copynumber: 2.9 Consensus size: 38
35152346 AGTTTGAGTC
35152356 TTTAATTATGTCATAATTTGAACATCATTAATATGAGAT
1 TTTAATTATGTCATAATTTGAACATCATTAATA-GAGAT
* * * * *
35152395 TTTAATTATGTCATAATCTGAACAACATTAGTAGGGGT
1 TTTAATTATGTCATAATTTGAACATCATTAATAGAGAT
* * *
35152433 TTTAATTATGTCATAGTTTAGGACATCTTTAATA
1 TTTAATTATGTCATAATTT-GAACATCATTAATA
35152467 CATGTTTTAA
Statistics
Matches: 60, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
38 20 0.33
39 40 0.67
ACGTcount: A:0.35, C:0.09, G:0.14, T:0.42
Consensus pattern (38 bp):
TTTAATTATGTCATAATTTGAACATCATTAATAGAGAT
Found at i:35158088 original size:14 final size:15
Alignment explanation
Indices: 35158069--35158109 Score: 57
Period size: 14 Copynumber: 2.7 Consensus size: 15
35158059 GTTGTAAAGT
35158069 TTTATTTTTATTTA-
1 TTTATTTTTATTTAG
*
35158083 TTTATTTTTACTTAG
1 TTTATTTTTATTTAG
35158098 TTTAATTTTTAT
1 TTT-ATTTTTAT
35158110 GTAAATATTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
14 13 0.57
15 3 0.13
16 7 0.30
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.73
Consensus pattern (15 bp):
TTTATTTTTATTTAG
Found at i:35166247 original size:11 final size:12
Alignment explanation
Indices: 35166231--35166264 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
35166221 AAATTTTTGA
35166231 ACGAAATTTT-C
1 ACGAAATTTTCC
35166242 ACGAAATATTTCC
1 ACGAAAT-TTTCC
35166255 ACGAAATTTT
1 ACGAAATTTT
35166265 AGGCCATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 7 0.33
12 6 0.29
13 8 0.38
ACGTcount: A:0.38, C:0.18, G:0.09, T:0.35
Consensus pattern (12 bp):
ACGAAATTTTCC
Found at i:35166435 original size:39 final size:39
Alignment explanation
Indices: 35166381--35166497 Score: 128
Period size: 39 Copynumber: 3.0 Consensus size: 39
35166371 TAATTTAGTT
* *
35166381 TGAATATTCAATTATGTCATAATTTGAACATCATTAATA
1 TGAATTTTTAATTATGTCATAATTTGAACATCATTAATA
* *
35166420 TGAATTTTTAATTATGTCATAATCTGAACAACATTAATA
1 TGAATTTTTAATTATGTCATAATTTGAACATCATTAATA
* ** * * *
35166459 AG-GGTTTTAATTATGTCATAGTTTAGGACATCTTTAATA
1 TGAATTTTTAATTATGTCATAATTT-GAACATCATTAATA
35166498 CATGTTTTAA
Statistics
Matches: 65, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
38 18 0.28
39 47 0.72
ACGTcount: A:0.38, C:0.09, G:0.11, T:0.42
Consensus pattern (39 bp):
TGAATTTTTAATTATGTCATAATTTGAACATCATTAATA
Found at i:35169751 original size:27 final size:27
Alignment explanation
Indices: 35169720--35169897 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
35169710 TAAATTGTAC
35169720 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
35169747 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
35169773 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
35169801 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
35169829 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
35169856 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
35169883 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
35169898 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:35169834 original size:82 final size:81
Alignment explanation
Indices: 35169721--35169876 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
35169711 AAATTGTACA
* *
35169721 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
35169785 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
35169802 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
35169867 TGCGAGTTGA
65 TGCGAATTGA
35169877 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:35169888 original size:82 final size:81
Alignment explanation
Indices: 35169717--35169897 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
35169707 GATTAAATTG
* *
35169717 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
35169782 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
35169798 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
35169862 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
35169880 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
35169898 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:35177931 original size:27 final size:27
Alignment explanation
Indices: 35177900--35178076 Score: 187
Period size: 27 Copynumber: 6.6 Consensus size: 27
35177890 TAAATTGTAC
*
35177900 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGAATATGT
* **
35177927 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGAATATGT
* ** *
35177953 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGAATATGT
*
35177981 GGCACTAAGTGTGCGAGTTTGAATAT-T
1 AGCACTAAGTGTGCGA-TTTGAATATGT
* *
35178008 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGAATATGT
* * *
35178035 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGAATATGT
*
35178062 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
35178077 GACTCAATAT
Statistics
Matches: 126, Mismatches: 20, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
26 7 0.06
27 113 0.90
28 6 0.05
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGAATATGT
Found at i:35178013 original size:81 final size:81
Alignment explanation
Indices: 35177901--35178055 Score: 215
Period size: 81 Copynumber: 1.9 Consensus size: 81
35177891 AAATTGTACA
* * *
35177901 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGAATATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
35177965 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
35177982 GCACTAAGTGTGCGAGTTTGAATAT-TAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGAATATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
35178046 TGCGAGTTGA
65 TGCGAATTGA
35178056 TTATATAGCA
Statistics
Matches: 65, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
81 56 0.86
82 9 0.14
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGAATATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:35178067 original size:81 final size:81
Alignment explanation
Indices: 35177897--35178076 Score: 211
Period size: 81 Copynumber: 2.2 Consensus size: 81
35177887 GATTAAATTG
* * *
35177897 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGAATATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
35177962 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
35177978 TGCGGCACTAAGTGTGCGAGTTTGAATAT-TAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGAATATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
35178041 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
35178059 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
35178077 GACTCAATAT
Statistics
Matches: 82, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
80 1 0.01
81 73 0.89
82 8 0.10
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGAATATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:35180866 original size:14 final size:14
Alignment explanation
Indices: 35180847--35180898 Score: 68
Period size: 14 Copynumber: 3.6 Consensus size: 14
35180837 TAATAGACAC
*
35180847 AATTTTAACAAATA
1 AATTTTAACAATTA
35180861 AATTTTAACAATGTTA
1 AATTTTAACAA--TTA
*
35180877 AATATTAACAATTA
1 AATTTTAACAATTA
35180891 AATTTTAA
1 AATTTTAA
35180899 TTTTTAAACT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
14 21 0.64
16 12 0.36
ACGTcount: A:0.52, C:0.06, G:0.02, T:0.40
Consensus pattern (14 bp):
AATTTTAACAATTA
Found at i:35181440 original size:11 final size:11
Alignment explanation
Indices: 35181423--35181460 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
35181413 TTTTTAATCA
35181423 AATATATATTT
1 AATATATATTT
* *
35181434 TATATATATTA
1 AATATATATTT
35181445 AATATATATTT
1 AATATATATTT
35181456 AATAT
1 AATAT
35181461 GGGCCGGGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (11 bp):
AATATATATTT
Found at i:35184503 original size:24 final size:23
Alignment explanation
Indices: 35184434--35184504 Score: 72
Period size: 24 Copynumber: 3.0 Consensus size: 23
35184424 TAATAATAAA
35184434 ATATATATATATGAAAAAAA-ATGC
1 ATATATAT-TAT-AAAAAAATATGC
* * *
35184458 ACATGTATTTATAAAAATATATGC
1 ATATATA-TTATAAAAAAATATGC
35184482 ATATATATTATAAAAGAAATATG
1 ATATATATTATAAAA-AAATATG
35184505 TATGTACATG
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
23 14 0.37
24 23 0.61
25 1 0.03
ACGTcount: A:0.54, C:0.04, G:0.08, T:0.34
Consensus pattern (23 bp):
ATATATATTATAAAAAAATATGC
Found at i:35186116 original size:43 final size:41
Alignment explanation
Indices: 35186008--35186116 Score: 132
Period size: 40 Copynumber: 2.6 Consensus size: 41
35185998 TTCTTCTATT
*
35186008 TGCTCCACTGCAACTTCAGGGAGATAAGACTATATGTGATC
1 TGCTCCACTGCAACTTCAGGGAGATAAGACTATATGTAATC
* * *
35186049 TGCT-CTCTGCAACTTCAGAGAGATAAGATCTATGATTTAATCC
1 TGCTCCACTGCAACTTCAGGGAGATAAGA-CTAT-ATGTAAT-C
*
35186092 T-CTCCACTGTAACTTCAGGGAGATA
1 TGCTCCACTGCAACTTCAGGGAGATA
35186117 GGATTTTTTA
Statistics
Matches: 57, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
40 22 0.39
41 8 0.14
42 7 0.12
43 20 0.35
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.29
Consensus pattern (41 bp):
TGCTCCACTGCAACTTCAGGGAGATAAGACTATATGTAATC
Found at i:35186581 original size:88 final size:88
Alignment explanation
Indices: 35186432--35186866 Score: 691
Period size: 88 Copynumber: 5.0 Consensus size: 88
35186422 AAGACTGATG
** * *
35186432 TCTTCGATCTGCTT-TGCTACCAGTACAGGAAGGCAAGATCTG-TCATTTTCGACCTACTCCACT
1 TCTTCGATCTGCTTCT-CTGTCAGTACAGGAAGGCAAGATCTGCT-ATTTTCAACCTGCTCCACT
*
35186495 GCTGCCCAGGGAGACAAGGCTGGTA
64 ACTGCCCAGGGAGACAAGGCTGGTA
*
35186520 TCTTCGATCTGCTTCTCTGTCAGTACAGGAAGGCAAGATCTACTATTTTCAACCTGCTCCACTAC
1 TCTTCGATCTGCTTCTCTGTCAGTACAGGAAGGCAAGATCTGCTATTTTCAACCTGCTCCACTAC
35186585 TGCCCAGGGAGACAAGGCTGGTA
66 TGCCCAGGGAGACAAGGCTGGTA
*
35186608 TCTTCGA-CTTGCTTCTCTGTCAGTACAGGAAGGAAAGATCTGCTATTTTCAACCTGCTCCACTA
1 TCTTCGATC-TGCTTCTCTGTCAGTACAGGAAGGCAAGATCTGCTATTTTCAACCTGCTCCACTA
*
35186672 CTGCCCAGGGGGACAAGGCTGGTA
65 CTGCCCAGGGAGACAAGGCTGGTA
* *
35186696 TCTTCGATCTGCTTCTCTGTCAGTACAGGAAGGCAAGATCTGCTATTTTGAAGCTGCTCCACTAC
1 TCTTCGATCTGCTTCTCTGTCAGTACAGGAAGGCAAGATCTGCTATTTTCAACCTGCTCCACTAC
*
35186761 TGCCCAGGGGGACAAGGCTGGTA
66 TGCCCAGGGAGACAAGGCTGGTA
*
35186784 TCTTCGATCTGCTTCTCTGTCAGTACAGGAAGGCAAGATCTGCTA-TTTCAACCTACTCCACTAC
1 TCTTCGATCTGCTTCTCTGTCAGTACAGGAAGGCAAGATCTGCTATTTTCAACCTGCTCCACTAC
*
35186848 -GCCTAGGGAGACAAGGCTG
66 TGCCCAGGGAGACAAGGCTG
35186867 AAGTTTTACC
Statistics
Matches: 326, Mismatches: 17, Indels: 10
0.92 0.05 0.03
Matches are distributed among these distances:
86 17 0.05
87 17 0.05
88 289 0.89
89 3 0.01
ACGTcount: A:0.23, C:0.27, G:0.23, T:0.27
Consensus pattern (88 bp):
TCTTCGATCTGCTTCTCTGTCAGTACAGGAAGGCAAGATCTGCTATTTTCAACCTGCTCCACTAC
TGCCCAGGGAGACAAGGCTGGTA
Found at i:35193284 original size:22 final size:22
Alignment explanation
Indices: 35193259--35193307 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
35193249 ATAAAGAAAA
* *
35193259 AAAATATGCGTATATACATTAT
1 AAAATATGCGGAAATACATTAT
*
35193281 AAAATATGCGGAAATATATTAT
1 AAAATATGCGGAAATACATTAT
35193303 AAAAT
1 AAAAT
35193308 GTTGAAAAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.51, C:0.06, G:0.10, T:0.33
Consensus pattern (22 bp):
AAAATATGCGGAAATACATTAT
Found at i:35194188 original size:19 final size:20
Alignment explanation
Indices: 35194164--35194210 Score: 64
Period size: 17 Copynumber: 2.5 Consensus size: 20
35194154 AAATTTCTTC
*
35194164 TTTTCTTTTTTTCGTAC-TT
1 TTTTCTTTTTTTCATACATT
35194183 TTTTC--TTTTTCATACATT
1 TTTTCTTTTTTTCATACATT
35194201 TTTTCTTTTT
1 TTTTCTTTTT
35194211 ACACTTTTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
17 9 0.38
18 7 0.29
19 5 0.21
20 3 0.12
ACGTcount: A:0.09, C:0.15, G:0.02, T:0.74
Consensus pattern (20 bp):
TTTTCTTTTTTTCATACATT
Found at i:35194191 original size:17 final size:18
Alignment explanation
Indices: 35194171--35194210 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
35194161 TTCTTTTCTT
*
35194171 TTTTTCGTAC-TTTTTTC
1 TTTTTCATACATTTTTTC
35194188 TTTTTCATACATTTTTTC
1 TTTTTCATACATTTTTTC
35194206 TTTTT
1 TTTTT
35194211 ACACTTTTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 9 0.43
18 12 0.57
ACGTcount: A:0.10, C:0.15, G:0.03, T:0.72
Consensus pattern (18 bp):
TTTTTCATACATTTTTTC
Found at i:35194219 original size:17 final size:18
Alignment explanation
Indices: 35194181--35194219 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
35194171 TTTTTCGTAC
*
35194181 TTTTTTCTTTTTCATACA
1 TTTTTTCTTTTTCACACA
35194199 TTTTTTCTTTTT-ACAC-
1 TTTTTTCTTTTTCACACA
35194215 TTTTT
1 TTTTT
35194220 CCTGATCTCC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 5 0.25
17 3 0.15
18 12 0.60
ACGTcount: A:0.13, C:0.15, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTTTTCTTTTTCACACA
Found at i:35195171 original size:9 final size:9
Alignment explanation
Indices: 35195159--35195225 Score: 91
Period size: 9 Copynumber: 7.4 Consensus size: 9
35195149 TTTTGTTAAA
35195159 AATTAACCG
1 AATTAACCG
35195168 AATTAACCG
1 AATTAACCG
35195177 AATT-ACCTG
1 AATTAACC-G
*
35195186 AATTAATCG
1 AATTAACCG
*
35195195 AATTACCCG
1 AATTAACCG
*
35195204 AATTAATCG
1 AATTAACCG
35195213 AATTAACCG
1 AATTAACCG
35195222 AATT
1 AATT
35195226 GAATCACTAC
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
8 3 0.06
9 45 0.90
10 2 0.04
ACGTcount: A:0.42, C:0.19, G:0.10, T:0.28
Consensus pattern (9 bp):
AATTAACCG
Found at i:35195351 original size:18 final size:18
Alignment explanation
Indices: 35195328--35195371 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
35195318 AATTTTTATG
*
35195328 ATTGGGTTGGGTTGGATA
1 ATTGGGTTGGGTTGAATA
35195346 ATTGGGTTGGGTTGAATA
1 ATTGGGTTGGGTTGAATA
*
35195364 CTTGGGTT
1 ATTGGGTT
35195372 TGGATTGGGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.16, C:0.02, G:0.41, T:0.41
Consensus pattern (18 bp):
ATTGGGTTGGGTTGAATA
Found at i:35195959 original size:24 final size:24
Alignment explanation
Indices: 35195926--35195973 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
35195916 AATTTAACAT
*
35195926 CATATAAACATTATCATATATCTA
1 CATATAAACATTACCATATATCTA
*
35195950 CATATGAACATTACCATATATCTA
1 CATATAAACATTACCATATATCTA
35195974 TGCCTTGACT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (24 bp):
CATATAAACATTACCATATATCTA
Found at i:35208014 original size:13 final size:13
Alignment explanation
Indices: 35207996--35208021 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
35207986 AATTAAAAAT
35207996 TATTGAAGATAAA
1 TATTGAAGATAAA
35208009 TATTGAAGATAAA
1 TATTGAAGATAAA
35208022 AAAAATAGAA
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:0.54, C:0.00, G:0.15, T:0.31
Consensus pattern (13 bp):
TATTGAAGATAAA
Done.