Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A09
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: 81831061
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 3560000 characters in sequence are not A, C, G, or T
File 130 of 259
Found at i:42163050 original size:682 final size:682
Alignment explanation
Indices: 42161738--42163102 Score: 2329
Period size: 682 Copynumber: 2.0 Consensus size: 682
42161728 GTGGTCAGGT
*
42161738 CGTGTGATCACACACGCCCGTATCTCGACCCCATGTAACTCTCTGACTTGTAACCCATGAACTAA
1 CGTGTGATCACACACGCCCGTATCTCGACCCCATGTAACTCTCTGACTTGTAACCCATGAACAAA
* *
42161803 TTAAGATCACACGGCCAAGTCACACACCCGTGTGCTAGGCCATGCGGAAAATTAATTTTCATAAA
66 TTAAGATCACACAGCCAAGTCACACACCCGTGTGCTAGGCCATGCGAAAAATTAATTTTCATAAA
* **
42161868 ATAGGTGCAGACTTCACACGGCCAGGGCACACGCCCGTGTTCGAGGTCGTGCCGTCTACATGGCT
131 ATAGGTGCAAACTTCACACGGCCAGGGCACACGCCCGTGTTCGAGGTCGTGCCGTCTACACAGCT
* * *
42161933 GAGGCACACTCCCATGTCTCTTCCCGTGTGCTCAATTCTGAGTATTCTGTTTCTCAAAATTAAGG
196 GAGACACACGCCCATGTCTCTGCCCGTGTGCTCAATTCTGAGTATTCTGTTTCTCAAAATTAAGG
* *
42161998 TGCAGGGGACACATGGCCAACACACATTCCCATGGGACAGGCCATGTGTCACACACAGTCTAGAC
261 TGCAGGGGACACATGGCCAACACACATCCCCATGGGACAGGCCATGTATCACACACAGTCTAGAC
* *
42162063 ACATGCACATGTGTCTACCCGTGTGGACAAAATAAAGGCTATTTACCAAGTCATTTGCCACCTTA
326 ACATACACATGTGTCTACCCGTGTGGACAAAATAAAGGCTATTTACCAAGTCATTTGCCACCCTA
* * **
42162128 ATTCACACATACACTTACACCAATTAAAAGGCACAAAACATAATATACTTAGGCAATGAAACATC
391 ATTCACACATACACTTAAACCAATTAAAAGACACAAAACATAATATACTTAGGCAACCAAACATC
* * * *
42162193 CATAATTATGACCTACACATGCCAATACAATATCAGCATCGATCATACTCACAATATTTATTATG
456 CACAATTATGACCTACACATGCCAATACAATATCAACATCGATCATACTCACAATACTTATTATA
* * *
42162258 CTCTAACTCAATCATGCAAATTTCCAGTCATCAAGCCTCAATTAACTACTTTCAAGTTACCTAAT
521 CCCTAAATCAATCATGCAAATTTCCAATCATCAAGCCTCAATTAACTACTTTCAAGTTACCTAAT
*
42162323 TGTACACAAATTTATCATCTCATCAATAGATCACATTTCCAAACATTTCACTTTCATGCTATAAA
586 TGTACACAAATTTATCATCTCATCAATAGATCACATTTCCAAACATTTCACTTTCATGATATAAA
42162388 TCACTTTCCATCATACACCAAGCATACCATGA
651 TCACTTTCCATCATACACCAAGCATACCATGA
* * *
42162420 CGTGTGGTCACACATGCCCGTATCTCGACCCCATGTAACTCTCTGACTTGTAACCCATGAGCAAA
1 CGTGTGATCACACACGCCCGTATCTCGACCCCATGTAACTCTCTGACTTGTAACCCATGAACAAA
* *
42162485 TTAAGATCACACAGCCAAGTCACACACCTGTGTGCTAGGCTATGCGAAAAATTAATTTTCAT-AA
66 TTAAGATCACACAGCCAAGTCACACACCCGTGTGCTAGGCCATGCGAAAAATTAATTTTCATAAA
42162549 ATAAGGTGCAAACTTCACACGGCCAGGGCACACGCCCGTGTTCGAGG-CTGTGCCGTCTACACAG
131 AT-AGGTGCAAACTTCACACGGCCAGGGCACACGCCCGTGTTCGAGGTC-GTGCCGTCTACACAG
* * *
42162613 CTGAGACACACGCCCGTGTCTCTGCCCGTGTGCTCAATTCTGAGTATTTTGTTTCTCAAAATTAG
194 CTGAGACACACGCCCATGTCTCTGCCCGTGTGCTCAATTCTGAGTATTCTGTTTCTCAAAATTAA
* *
42162678 GGTGCAGGGGGCACATGGCCAACACACATCCCCATGGGACAGGCCGTGTATCACACACAGTCTAG
259 GGTGCAGGGGACACATGGCCAACACACATCCCCATGGGACAGGCCATGTATCACACACAGTCTAG
* *
42162743 ACACATACACGTGTGTCTACCCTTGTGGACAAAATAAAGGCTATTTACCAAGTCATTTGCCACCC
324 ACACATACACATGTGTCTACCCGTGTGGACAAAATAAAGGCTATTTACCAAGTCATTTGCCACCC
42162808 TAATTCACACATACACTTAAACCAATTAAAAGACACAAAACATAATATACTTAGGCAACCAAACA
389 TAATTCACACATACACTTAAACCAATTAAAAGACACAAAACATAATATACTTAGGCAACCAAACA
42162873 TCCACAATTATGACCTACACATGCCAATACAATATCAACATCGATCATACTCACAATACTTATTA
454 TCCACAATTATGACCTACACATGCCAATACAATATCAACATCGATCATACTCACAATACTTATTA
42162938 TACCCTAAATCAATCATGCAAATTTCCAATCATCAAGCCTCAATTAACTACTTTCAAGTTACCTA
519 TACCCTAAATCAATCATGCAAATTTCCAATCATCAAGCCTCAATTAACTACTTTCAAGTTACCTA
* ***
42163003 ATTGTACATAAATTTATCATCTCATCAATCTTTCACATTTCCAAACATTTCACTTTCATGATATA
584 ATTGTACACAAATTTATCATCTCATCAATAGATCACATTTCCAAACATTTCACTTTCATGATATA
42163068 AATCACTTTCCATCATACACCAAGCATACCATGA
649 AATCACTTTCCATCATACACCAAGCATACCATGA
42163102 C
1 C
42163103 TATAACACCA
Statistics
Matches: 640, Mismatches: 41, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
681 5 0.01
682 635 0.99
ACGTcount: A:0.32, C:0.27, G:0.14, T:0.26
Consensus pattern (682 bp):
CGTGTGATCACACACGCCCGTATCTCGACCCCATGTAACTCTCTGACTTGTAACCCATGAACAAA
TTAAGATCACACAGCCAAGTCACACACCCGTGTGCTAGGCCATGCGAAAAATTAATTTTCATAAA
ATAGGTGCAAACTTCACACGGCCAGGGCACACGCCCGTGTTCGAGGTCGTGCCGTCTACACAGCT
GAGACACACGCCCATGTCTCTGCCCGTGTGCTCAATTCTGAGTATTCTGTTTCTCAAAATTAAGG
TGCAGGGGACACATGGCCAACACACATCCCCATGGGACAGGCCATGTATCACACACAGTCTAGAC
ACATACACATGTGTCTACCCGTGTGGACAAAATAAAGGCTATTTACCAAGTCATTTGCCACCCTA
ATTCACACATACACTTAAACCAATTAAAAGACACAAAACATAATATACTTAGGCAACCAAACATC
CACAATTATGACCTACACATGCCAATACAATATCAACATCGATCATACTCACAATACTTATTATA
CCCTAAATCAATCATGCAAATTTCCAATCATCAAGCCTCAATTAACTACTTTCAAGTTACCTAAT
TGTACACAAATTTATCATCTCATCAATAGATCACATTTCCAAACATTTCACTTTCATGATATAAA
TCACTTTCCATCATACACCAAGCATACCATGA
Found at i:42170733 original size:26 final size:26
Alignment explanation
Indices: 42170704--42170753 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
42170694 TATTTTGAGT
*
42170704 AATT-AGGACTAAATTGCAAAATAATA
1 AATTGAGGACTAAAATG-AAAATAATA
42170730 AATTGAGGACTAAAATGAAAATAA
1 AATTGAGGACTAAAATGAAAATAA
42170754 ATGAAATGTG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 11 0.50
27 11 0.50
ACGTcount: A:0.56, C:0.06, G:0.14, T:0.24
Consensus pattern (26 bp):
AATTGAGGACTAAAATGAAAATAATA
Found at i:42171665 original size:50 final size:50
Alignment explanation
Indices: 42171574--42171912 Score: 439
Period size: 50 Copynumber: 7.0 Consensus size: 50
42171564 TTTGACCACA
**
42171574 TAGGTAAGTACATATGTGATG-TATATTGAACCTTGTGTATTCGGCCATG
1 TAGGTAAGTATTTATGTGATGATATATTGAACCTTGTGTATTCGGCCATG
* *
42171623 TAGGTAAGTATTTATGTGATGATATATTGAAGCTTGTTTATTCGGCCATG
1 TAGGTAAGTATTTATGTGATGATATATTGAACCTTGTGTATTCGGCCATG
* *
42171673 TAGGTAAGTATTTATGTGATGATAAATTGAACCTTCTGTATTCGGCC---
1 TAGGTAAGTATTTATGTGATGATATATTGAACCTTGTGTATTCGGCCATG
* *
42171720 -----AAGTATTTATGTGATGATATATTGAACCTTCTGTATTCAGCCATG
1 TAGGTAAGTATTTATGTGATGATATATTGAACCTTGTGTATTCGGCCATG
42171765 TAGGTAAGTATTTATGTGATGATATATTGAACCTTGTGTATTCGGCCATG
1 TAGGTAAGTATTTATGTGATGATATATTGAACCTTGTGTATTCGGCCATG
* * * *
42171815 TAGGTAAGTATTCATGTGATGATATATTGAACCTTGTATATTTGGCCATA
1 TAGGTAAGTATTTATGTGATGATATATTGAACCTTGTGTATTCGGCCATG
* * **
42171865 T-GAGTATGTATTTATGTGATGATATACTTG-ATCTTGCATATTCGGCCA
1 TAG-GTAAGTATTTATGTGATGATATA-TTGAACCTTGTGTATTCGGCCA
42171913 AATGAATGGT
Statistics
Matches: 258, Mismatches: 21, Indels: 21
0.86 0.07 0.07
Matches are distributed among these distances:
42 40 0.16
49 20 0.08
50 195 0.76
51 3 0.01
ACGTcount: A:0.27, C:0.11, G:0.22, T:0.40
Consensus pattern (50 bp):
TAGGTAAGTATTTATGTGATGATATATTGAACCTTGTGTATTCGGCCATG
Found at i:42171737 original size:92 final size:92
Alignment explanation
Indices: 42171628--42171888 Score: 344
Period size: 92 Copynumber: 2.8 Consensus size: 92
42171618 CCATGTAGGT
* *
42171628 AAGTATTTATGTGATGATATATTGAAGCTTGTTTATTCGGCCATGTAGGTAAGTATTTATGTGAT
1 AAGTATTTATGTGATGATATATTGAACCTTGTATATTCGGCCATGTAGGTAAGTATTTATGTGAT
42171693 GATAAATTGAACCTTCTGTATTCGGCC
66 GATAAATTGAACCTTCTGTATTCGGCC
* * *
42171720 AAGTATTTATGTGATGATATATTGAACCTTCTGTATTCAGCCATGTAGGTAAGTATTTATGTGAT
1 AAGTATTTATGTGATGATATATTGAACCTTGTATATTCGGCCATGTAGGTAAGTATTTATGTGAT
* *
42171785 GATATATTGAACCTTGTGTATTCGGCC
66 GATAAATTGAACCTTCTGTATTCGGCC
* * *
42171812 ATGTAGGTAAGTATTCATGTGATGATATATTGAACCTTGTATATTTGGCCATAT-GAGTATGTAT
1 A---A-GT-A-T-TT-ATGTGATGATATATTGAACCTTGTATATTCGGCCATGTAG-GTAAGTAT
42171876 TTATGTGATGATA
57 TTATGTGATGATA
42171889 TACTTGATCT
Statistics
Matches: 148, Mismatches: 12, Indels: 10
0.87 0.07 0.06
Matches are distributed among these distances:
92 87 0.59
95 1 0.01
96 2 0.01
97 1 0.01
98 1 0.01
99 3 0.02
100 53 0.36
ACGTcount: A:0.28, C:0.10, G:0.21, T:0.41
Consensus pattern (92 bp):
AAGTATTTATGTGATGATATATTGAACCTTGTATATTCGGCCATGTAGGTAAGTATTTATGTGAT
GATAAATTGAACCTTCTGTATTCGGCC
Found at i:42171763 original size:142 final size:141
Alignment explanation
Indices: 42171586--42171849 Score: 465
Period size: 142 Copynumber: 1.9 Consensus size: 141
42171576 GGTAAGTACA
* *
42171586 TATGTGATGTATATTGAACCTTGTGTATTCGGCCATGTAGGTAAGTATTTATGTGATGATATATT
1 TATGTGATGTATATTGAACCTTCTGTATTCAGCCATGTAGGTAAGTATTTATGTGATGATATATT
* * *
42171651 GAAGCTTGTTTATTCGGCCATGTAGGTAAGTATTTATGTGATGATAAATTGAACCTTCTGTATTC
66 GAACCTTGTGTATTCGGCCATGTAGGTAAGTATTCATGTGATGATAAATTGAACCTTCTGTATTC
42171716 GGCCAAGTATT
131 GGCCAAGTATT
42171727 TATGTGATGATATATTGAACCTTCTGTATTCAGCCATGTAGGTAAGTATTTATGTGATGATATAT
1 TATGTGATG-TATATTGAACCTTCTGTATTCAGCCATGTAGGTAAGTATTTATGTGATGATATAT
*
42171792 TGAACCTTGTGTATTCGGCCATGTAGGTAAGTATTCATGTGATGATATATTGAACCTT
65 TGAACCTTGTGTATTCGGCCATGTAGGTAAGTATTCATGTGATGATAAATTGAACCTT
42171850 GTATATTTGG
Statistics
Matches: 116, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
141 9 0.08
142 107 0.92
ACGTcount: A:0.27, C:0.11, G:0.22, T:0.40
Consensus pattern (141 bp):
TATGTGATGTATATTGAACCTTCTGTATTCAGCCATGTAGGTAAGTATTTATGTGATGATATATT
GAACCTTGTGTATTCGGCCATGTAGGTAAGTATTCATGTGATGATAAATTGAACCTTCTGTATTC
GGCCAAGTATT
Found at i:42178617 original size:9 final size:9
Alignment explanation
Indices: 42178603--42178641 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
42178593 ACATATACTC
42178603 CTTTTTTTT
1 CTTTTTTTT
*
42178612 CTTTTTCTT
1 CTTTTTTTT
*
42178621 -TTTTTTCT
1 CTTTTTTTT
42178629 CTTTTTTTT
1 CTTTTTTTT
42178638 CTTT
1 CTTT
42178642 CAAGATCATT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
8 6 0.24
9 19 0.76
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (9 bp):
CTTTTTTTT
Found at i:42178623 original size:15 final size:16
Alignment explanation
Indices: 42178603--42178642 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
42178593 ACATATACTC
42178603 CTTTTTTTTCT-TTTT
1 CTTTTTTTTCTCTTTT
42178618 CTTTTTTTTCTCTTTT
1 CTTTTTTTTCTCTTTT
*
42178634 -TTTTCTTTC
1 CTTTTTTTTC
42178643 AAGATCATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 19 0.83
16 4 0.17
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.82
Consensus pattern (16 bp):
CTTTTTTTTCTCTTTT
Found at i:42181358 original size:77 final size:77
Alignment explanation
Indices: 42181265--42181423 Score: 221
Period size: 77 Copynumber: 2.1 Consensus size: 77
42181255 ACTGGGAGCA
* * * * * *
42181265 AGCTGTTGGCTGTTGGCGCACG-CGAGCTGGAGCTAGAAGTAGGCCTGGTGTGTGCGACAGTAGC
1 AGCTGTTGGCTATTGGCGCACGAGGA-CTGGAGCTAGAAGCAAGCCTGGCGTGTGCGACAGTAAC
42181329 AGCGTACATATGG
65 AGCGTACATATGG
*
42181342 AGCTGTTGGCTATTGGCGCACGAGGACTGGAGCTAGAAGCAAGCCTGGCGTGTGCGGCAGTAACA
1 AGCTGTTGGCTATTGGCGCACGAGGACTGGAGCTAGAAGCAAGCCTGGCGTGTGCGACAGTAACA
* *
42181407 GCGTGCATGTGG
66 GCGTACATATGG
42181419 AGCTG
1 AGCTG
42181424 CTAGCCGAAT
Statistics
Matches: 72, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
77 70 0.97
78 2 0.03
ACGTcount: A:0.20, C:0.20, G:0.39, T:0.21
Consensus pattern (77 bp):
AGCTGTTGGCTATTGGCGCACGAGGACTGGAGCTAGAAGCAAGCCTGGCGTGTGCGACAGTAACA
GCGTACATATGG
Found at i:42192378 original size:19 final size:19
Alignment explanation
Indices: 42192356--42192410 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
42192346 TAATAGTATT
42192356 TTATTAATTTAATTTTAAA
1 TTATTAATTTAATTTTAAA
*
42192375 TTATT-ATCTTAATATTAAA
1 TTATTAAT-TTAATTTTAAA
42192394 -T-TTAATTTAATGTTTAA
1 TTATTAATTTAAT-TTTAA
42192411 TAAACATTCT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
17 7 0.23
18 9 0.29
19 15 0.48
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (19 bp):
TTATTAATTTAATTTTAAA
Found at i:42194782 original size:43 final size:43
Alignment explanation
Indices: 42194713--42194839 Score: 211
Period size: 42 Copynumber: 3.0 Consensus size: 43
42194703 ATATGCAACG
*
42194713 CCGCTAAAGACCAGGACTTTTAGCGGCGCTTTTTTAAAAAACA
1 CCGCTAAAGACCAGGACTTTTCGCGGCGCTTTTTTAAAAAACA
* * *
42194756 CCGCTAAAGACCAGGACCTTTCGCGGCGCTTTTAT-AAAAACG
1 CCGCTAAAGACCAGGACTTTTCGCGGCGCTTTTTTAAAAAACA
42194798 CCGCTAAAGACCAGGACTTTTCGCGGCGCTTTTTTAAAAAAC
1 CCGCTAAAGACCAGGACTTTTCGCGGCGCTTTTTTAAAAAAC
42194840 GCCATGAATT
Statistics
Matches: 77, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
42 39 0.51
43 38 0.49
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (43 bp):
CCGCTAAAGACCAGGACTTTTCGCGGCGCTTTTTTAAAAAACA
Found at i:42194808 original size:42 final size:43
Alignment explanation
Indices: 42194709--42194842 Score: 225
Period size: 43 Copynumber: 3.1 Consensus size: 43
42194699 CATTATATGC
*
42194709 AACGCCGCTAAAGACCAGGACTTTTAGCGGCGCTTTTTTAAAA
1 AACGCCGCTAAAGACCAGGACTTTTCGCGGCGCTTTTTTAAAA
* * *
42194752 AACACCGCTAAAGACCAGGACCTTTCGCGGCGCTTTTAT-AAA
1 AACGCCGCTAAAGACCAGGACTTTTCGCGGCGCTTTTTTAAAA
42194794 AACGCCGCTAAAGACCAGGACTTTTCGCGGCGCTTTTTTAAAA
1 AACGCCGCTAAAGACCAGGACTTTTCGCGGCGCTTTTTTAAAA
42194837 AACGCC
1 AACGCC
42194843 ATGAATTTGC
Statistics
Matches: 83, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
42 39 0.47
43 44 0.53
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.23
Consensus pattern (43 bp):
AACGCCGCTAAAGACCAGGACTTTTCGCGGCGCTTTTTTAAAA
Found at i:42199465 original size:41 final size:41
Alignment explanation
Indices: 42199421--42199619 Score: 206
Period size: 41 Copynumber: 4.9 Consensus size: 41
42199411 GTTATACGAC
* * * *
42199421 TTTTAGCGGCATTTTACCAAAAGCGCCGCTAATGCTCCGGC
1 TTTTAGCGGCGTTTTACCAAAAACGCCGCTATTGCTCCGGT
* * ** *
42199462 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTTTGTT
1 TTTTAGCGGCGTTTTACCAAAAACGCCGCTATTGCTCCGGT
* * * **
42199503 TTTTAGTGGCGTTTTACCAAAAACGCAGCTATTTCT-CTAT
1 TTTTAGCGGCGTTTTACCAAAAACGCCGCTATTGCTCCGGT
* * *
42199543 TTTTAGAGGCGTTTTAACAAAAAACGCCGGTATTGCTCC-GT
1 TTTTAGCGGCGTTTT-ACCAAAAACGCCGCTATTGCTCCGGT
*
42199584 TTTTAGCGGCGTTTTA-CTAAAACGCCGCTATTGCTC
1 TTTTAGCGGCGTTTTACCAAAAACGCCGCTATTGCTC
42199620 TGTGTTTTAC
Statistics
Matches: 133, Mismatches: 23, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
39 17 0.13
40 16 0.12
41 99 0.74
42 1 0.01
ACGTcount: A:0.23, C:0.23, G:0.20, T:0.34
Consensus pattern (41 bp):
TTTTAGCGGCGTTTTACCAAAAACGCCGCTATTGCTCCGGT
Found at i:42200001 original size:43 final size:42
Alignment explanation
Indices: 42199954--42200073 Score: 145
Period size: 43 Copynumber: 2.8 Consensus size: 42
42199944 AATGCCAACA
* * *
42199954 TCCCAGACGTGGTATTACATGTAATCAGATATCGATGCC-ACTG
1 TCCCAGACGTGGTCTTACACG-AATCACATATCGATGCCGA-TG
42199997 TCCCAGACAG-GGTCTTACACGAATCACATATACGATGCCGATG
1 TCCCAGAC-GTGGTCTTACACGAATCACATAT-CGATGCCGATG
*
42200040 TCCCAGACATGGTCTTACACGCAATCACATATCG
1 TCCCAGACGTGGTCTTACACG-AATCACATATCG
42200074 TAAATCCTAT
Statistics
Matches: 68, Mismatches: 4, Indels: 10
0.83 0.05 0.12
Matches are distributed among these distances:
42 9 0.13
43 47 0.69
44 12 0.18
ACGTcount: A:0.29, C:0.28, G:0.19, T:0.24
Consensus pattern (42 bp):
TCCCAGACGTGGTCTTACACGAATCACATATCGATGCCGATG
Found at i:42203200 original size:16 final size:16
Alignment explanation
Indices: 42203179--42203209 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
42203169 TTTTCTTGGA
42203179 TTTCATGTAATATTTT
1 TTTCATGTAATATTTT
*
42203195 TTTCATGTCATATTT
1 TTTCATGTAATATTT
42203210 CCATATCATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.10, G:0.06, T:0.61
Consensus pattern (16 bp):
TTTCATGTAATATTTT
Found at i:42204099 original size:67 final size:67
Alignment explanation
Indices: 42204025--42204151 Score: 227
Period size: 67 Copynumber: 1.9 Consensus size: 67
42204015 GTCTATCTAG
* * *
42204025 ATCTATACGAGTGAATTTAACATTAATTTATCATTTTTTACATTCATATGGACTAAATTTAACAT
1 ATCTATACAAGTAAATTTAACATTAATTTATCATATTTTACATTCATATGGACTAAATTTAACAT
42204090 TA
66 TA
42204092 ATCTATACAAGTAAATTTAACATTAATTTATCATATTTTACATTCATATGGACTAAATTT
1 ATCTATACAAGTAAATTTAACATTAATTTATCATATTTTACATTCATATGGACTAAATTT
42204152 TCATCCTAGG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
67 57 1.00
ACGTcount: A:0.39, C:0.12, G:0.06, T:0.43
Consensus pattern (67 bp):
ATCTATACAAGTAAATTTAACATTAATTTATCATATTTTACATTCATATGGACTAAATTTAACAT
TA
Found at i:42207831 original size:19 final size:19
Alignment explanation
Indices: 42207809--42207851 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
42207799 ATTTTTACCC
42207809 TTAAATTAAAAATAAATTA
1 TTAAATTAAAAATAAATTA
* **
42207828 TTAAA-TGAAAATTTATTA
1 TTAAATTAAAAATAAATTA
42207846 TTAAAT
1 TTAAAT
42207852 AATATTTTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (19 bp):
TTAAATTAAAAATAAATTA
Found at i:42207860 original size:18 final size:18
Alignment explanation
Indices: 42207824--42207875 Score: 61
Period size: 18 Copynumber: 2.8 Consensus size: 18
42207814 TTAAAAATAA
*
42207824 ATTATTAAATGAA-AATTT
1 ATTATTAAAT-AATATTTT
42207842 ATTATTAAATAATATTTT
1 ATTATTAAATAATATTTT
*
42207860 AATATTATAATAATAT
1 ATTATTA-AATAATAT
42207876 GTAATAACAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
17 2 0.07
18 20 0.67
19 8 0.27
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (18 bp):
ATTATTAAATAATATTTT
Found at i:42207927 original size:19 final size:21
Alignment explanation
Indices: 42207903--42207958 Score: 71
Period size: 22 Copynumber: 2.7 Consensus size: 21
42207893 AATAGTTTTA
*
42207903 AATAACCTAT-TTAA-ATCTT
1 AATAACATATATTAATATCTT
42207922 AATAACATATATTAATATCTT
1 AATAACATATATTAATATCTT
*
42207943 AAAAATCATATATTAA
1 AATAA-CATATATTAA
42207959 AATAATATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
19 9 0.28
20 4 0.12
21 9 0.28
22 10 0.31
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (21 bp):
AATAACATATATTAATATCTT
Found at i:42207941 original size:21 final size:20
Alignment explanation
Indices: 42207903--42207959 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 20
42207893 AATAGTTTTA
*
42207903 AATAACCTAT-TTAAATCTT
1 AATAACATATATTAAATCTT
42207922 AATAACATATATTAATATCTT
1 AATAACATATATTAA-ATCTT
*
42207943 AAAAATCATATATTAAA
1 AATAA-CATATATTAAA
42207960 ATAATATTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.27
20 4 0.12
21 10 0.30
22 10 0.30
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.39
Consensus pattern (20 bp):
AATAACATATATTAAATCTT
Found at i:42211190 original size:3 final size:3
Alignment explanation
Indices: 42211182--42211227 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
42211172 TATAAATTGA
42211182 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
42211228 GATATAAACT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:42217076 original size:21 final size:22
Alignment explanation
Indices: 42217022--42217076 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
42217012 TAGGTAAGAC
**
42217022 ATTTTACGGGAATAAGAAAATA
1 ATTTTACGTTAATAAGAAAATA
** *
42217044 ATTTTATATTAATTAGAAAAT-
1 ATTTTACGTTAATAAGAAAATA
42217065 ATTTTACGTTAA
1 ATTTTACGTTAA
42217077 CCATCCTATT
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
21 10 0.38
22 16 0.62
ACGTcount: A:0.45, C:0.04, G:0.11, T:0.40
Consensus pattern (22 bp):
ATTTTACGTTAATAAGAAAATA
Found at i:42218525 original size:15 final size:15
Alignment explanation
Indices: 42218492--42218538 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 15
42218482 CTGAAAACTC
* *
42218492 TAAAATTTATA-AAA
1 TAAAATTAATATATA
42218506 TAAAATTAATATATA
1 TAAAATTAATATATA
*
42218521 TAAAATAAATATATA
1 TAAAATTAATATATA
42218536 TAA
1 TAA
42218539 TTGTTTAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
14 10 0.34
15 19 0.66
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (15 bp):
TAAAATTAATATATA
Found at i:42218558 original size:28 final size:27
Alignment explanation
Indices: 42218527--42218591 Score: 69
Period size: 28 Copynumber: 2.3 Consensus size: 27
42218517 TATATAAAAT
*
42218527 AAATATATATAA-TTGTTTAAAAAATTTA
1 AAATATATAGAACTT-TTTAAAAAA-TTA
*
42218555 AAATATGTCAGAACTTTTTAAAAAATTA
1 AAATATAT-AGAACTTTTTAAAAAATTA
*
42218583 AAAAATATA
1 AAATATATA
42218592 AAATATATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
27 1 0.03
28 16 0.52
29 12 0.39
30 2 0.06
ACGTcount: A:0.55, C:0.03, G:0.05, T:0.37
Consensus pattern (27 bp):
AAATATATAGAACTTTTTAAAAAATTA
Found at i:42222045 original size:22 final size:23
Alignment explanation
Indices: 42222020--42222065 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
42222010 CAACCAAATC
42222020 AATTCA-ACATATTT-TCAAGATA
1 AATTCATACATATTTAT-AAGATA
*
42222042 AATTCATGCATATTTATAAGATA
1 AATTCATACATATTTATAAGATA
42222065 A
1 A
42222066 CGTCATCACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
23 14 0.67
24 1 0.05
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.37
Consensus pattern (23 bp):
AATTCATACATATTTATAAGATA
Found at i:42222071 original size:23 final size:23
Alignment explanation
Indices: 42222027--42222071 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
42222017 ATCAATTCAA
*
42222027 CATATTTTCAAGATAAATTCATG
1 CATATTTTCAAGATAAAGTCATG
*
42222050 CATATTTAT-AAGATAACGTCAT
1 CATATTT-TCAAGATAAAGTCAT
42222072 CACATATCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (23 bp):
CATATTTTCAAGATAAAGTCATG
Found at i:42226931 original size:25 final size:24
Alignment explanation
Indices: 42226897--42226946 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 24
42226887 TATAACACTA
42226897 ATTATCATATTATTAAATTAATTT
1 ATTATCATATTATTAAATTAATTT
*
42226921 ATTATACATATTATTAATTTAATTT
1 ATTAT-CATATTATTAAATTAATTT
42226946 A
1 A
42226947 AATTTTATAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 5 0.21
25 19 0.79
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (24 bp):
ATTATCATATTATTAAATTAATTT
Found at i:42226954 original size:20 final size:20
Alignment explanation
Indices: 42226913--42226954 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
42226903 ATATTATTAA
*
42226913 ATTAATTTATTATACATATT
1 ATTAATTTATTATAAATATT
*
42226933 ATTAATTTAATT-TAAATTTT
1 ATTAATTT-ATTATAAATATT
42226953 AT
1 AT
42226955 AGATTTTGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 16 0.84
21 3 0.16
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (20 bp):
ATTAATTTATTATAAATATT
Found at i:42234366 original size:22 final size:20
Alignment explanation
Indices: 42234326--42234374 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
42234316 TAATTTAAAA
42234326 TATAAAAATTTATTAATATG
1 TATAAAAATTTATTAATATG
* *
42234346 TATATAAATTTATTAATATA
1 TATAAAAATTTATTAATATG
*
42234366 TGTAAAAAT
1 TATAAAAAT
42234375 AACTTTTACG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (20 bp):
TATAAAAATTTATTAATATG
Found at i:42234487 original size:20 final size:20
Alignment explanation
Indices: 42234462--42234501 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
42234452 AAATATTTTC
42234462 AGTAAATCATTTTCCAGAAA
1 AGTAAATCATTTTCCAGAAA
*
42234482 AGTAAATCGTTTTCCAGAAA
1 AGTAAATCATTTTCCAGAAA
42234502 TCATTTTCCG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.42, C:0.15, G:0.12, T:0.30
Consensus pattern (20 bp):
AGTAAATCATTTTCCAGAAA
Found at i:42247374 original size:22 final size:23
Alignment explanation
Indices: 42247334--42247397 Score: 69
Period size: 22 Copynumber: 2.8 Consensus size: 23
42247324 AATGGCAGCG
* *
42247334 AAACAACATAATAAACAACTA-CA
1 AAACAACACAAAAAACAAC-ACCA
*
42247357 AAACAACA-ATAAAACAACACCA
1 AAACAACACAAAAAACAACACCA
*
42247379 AATCAACACAAAAAACAAC
1 AAACAACACAAAAAACAAC
42247398 CTGCAAAATG
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
21 1 0.03
22 17 0.49
23 17 0.49
ACGTcount: A:0.67, C:0.25, G:0.00, T:0.08
Consensus pattern (23 bp):
AAACAACACAAAAAACAACACCA
Found at i:42263026 original size:22 final size:22
Alignment explanation
Indices: 42262987--42263045 Score: 82
Period size: 22 Copynumber: 2.6 Consensus size: 22
42262977 TAGCTCGTAT
42262987 GAGCTTACCGTTTTAGCTCTACA
1 GAGCTTACCG-TTTAGCTCTACA
*
42263010 GAGCTTACCGTTTAGCTCTTCA
1 GAGCTTACCGTTTAGCTCTACA
* *
42263032 TAGTTTACCGTTTA
1 GAGCTTACCGTTTA
42263046 TCAGCTCAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
22 23 0.70
23 10 0.30
ACGTcount: A:0.20, C:0.24, G:0.17, T:0.39
Consensus pattern (22 bp):
GAGCTTACCGTTTAGCTCTACA
Found at i:42267281 original size:39 final size:41
Alignment explanation
Indices: 42267199--42267281 Score: 107
Period size: 39 Copynumber: 2.1 Consensus size: 41
42267189 TATGCATATA
** *
42267199 GTATCTGAGATGGGCTAAGGCCCTAATTTATATCTGAGGCT
1 GTATCTGAGATGGGCTAAGGCCCTAAACTATATCTGAAGCT
* *
42267240 GTATCTGA-ATGGGCTAAGG-CCTAAACTGTATCTGAATCT
1 GTATCTGAGATGGGCTAAGGCCCTAAACTATATCTGAAGCT
42267279 GTA
1 GTA
42267282 ATGGGCTTAG
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
39 18 0.49
40 11 0.30
41 8 0.22
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.31
Consensus pattern (41 bp):
GTATCTGAGATGGGCTAAGGCCCTAAACTATATCTGAAGCT
Found at i:42273673 original size:7 final size:7
Alignment explanation
Indices: 42273657--42273698 Score: 57
Period size: 7 Copynumber: 6.0 Consensus size: 7
42273647 ATTTAAAAAA
42273657 AATTGAG
1 AATTGAG
*
42273664 AATTGGG
1 AATTGAG
42273671 AATTGAG
1 AATTGAG
*
42273678 GATTGAG
1 AATTGAG
42273685 AATTGAG
1 AATTGAG
*
42273692 GATTGAG
1 AATTGAG
42273699 TTAAAAAGAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.36, C:0.00, G:0.36, T:0.29
Consensus pattern (7 bp):
AATTGAG
Found at i:42273676 original size:14 final size:14
Alignment explanation
Indices: 42273657--42273698 Score: 66
Period size: 14 Copynumber: 3.0 Consensus size: 14
42273647 ATTTAAAAAA
* *
42273657 AATTGAGAATTGGG
1 AATTGAGGATTGAG
42273671 AATTGAGGATTGAG
1 AATTGAGGATTGAG
42273685 AATTGAGGATTGAG
1 AATTGAGGATTGAG
42273699 TTAAAAAGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.36, C:0.00, G:0.36, T:0.29
Consensus pattern (14 bp):
AATTGAGGATTGAG
Found at i:42273682 original size:21 final size:21
Alignment explanation
Indices: 42273658--42273698 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
42273648 TTTAAAAAAA
42273658 ATTGAGAATTG-GGAATTGAGG
1 ATTGAGAATTGAGG-ATTGAGG
42273679 ATTGAGAATTGAGGATTGAG
1 ATTGAGAATTGAGGATTGAG
42273699 TTAAAAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.89
22 2 0.11
ACGTcount: A:0.34, C:0.00, G:0.37, T:0.29
Consensus pattern (21 bp):
ATTGAGAATTGAGGATTGAGG
Found at i:42288488 original size:30 final size:30
Alignment explanation
Indices: 42288430--42288502 Score: 76
Period size: 30 Copynumber: 2.4 Consensus size: 30
42288420 TTTGTTAATG
* * **
42288430 AATAAGTAATTTAATATATTTATTTTTAAA
1 AATAAATAATTTAAAATATTTAAATTTAAA
* *
42288460 TAAT-ATTAATTTAAAATTTTTAAATTTAAA
1 -AATAAATAATTTAAAATATTTAAATTTAAA
42288490 AATAAATAATTTA
1 AATAAATAATTTA
42288503 TTTCAAAATT
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
29 3 0.09
30 29 0.83
31 3 0.09
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (30 bp):
AATAAATAATTTAAAATATTTAAATTTAAA
Found at i:42288815 original size:33 final size:33
Alignment explanation
Indices: 42288778--42288852 Score: 132
Period size: 33 Copynumber: 2.3 Consensus size: 33
42288768 GATGTTCATT
* *
42288778 GATAAATAATGTGCCTCGTTAAAACCTTACTAA
1 GATAAAAAATCTGCCTCGTTAAAACCTTACTAA
42288811 GATAAAAAATCTGCCTCGTTAAAACCTTACTAA
1 GATAAAAAATCTGCCTCGTTAAAACCTTACTAA
42288844 GATAAAAAA
1 GATAAAAAA
42288853 ATCTTAGTGA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.45, C:0.17, G:0.11, T:0.27
Consensus pattern (33 bp):
GATAAAAAATCTGCCTCGTTAAAACCTTACTAA
Found at i:42291697 original size:25 final size:26
Alignment explanation
Indices: 42291669--42291718 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 26
42291659 CAACAAAACT
* *
42291669 AAAATCTAACCTA-AAAAGAAAAGAG
1 AAAACCTAAACTAGAAAAGAAAAGAG
*
42291694 AAAACCTAAACTAGAAATGAAAAGA
1 AAAACCTAAACTAGAAAAGAAAAGA
42291719 ACAAAAAAGG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 11 0.52
26 10 0.48
ACGTcount: A:0.64, C:0.12, G:0.12, T:0.12
Consensus pattern (26 bp):
AAAACCTAAACTAGAAAAGAAAAGAG
Found at i:42298720 original size:27 final size:25
Alignment explanation
Indices: 42298677--42298734 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 25
42298667 AAATTATAAA
*
42298677 AAAATTTAATATTTATTTTAAAATAT-
1 AAAA-TTAATATTTATTATAAAA-ATC
42298703 AAAATTAATATTAATATTATAAAAATC
1 AAAATTAATATT--TATTATAAAAATC
42298730 AAAAT
1 AAAAT
42298735 ATAAGAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
25 8 0.29
26 6 0.21
27 14 0.50
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (25 bp):
AAAATTAATATTTATTATAAAAATC
Found at i:42302175 original size:129 final size:129
Alignment explanation
Indices: 42301938--42302189 Score: 355
Period size: 129 Copynumber: 2.0 Consensus size: 129
42301928 ATTTATTTAA
** ** *
42301938 AAATTCTTTAAAACGAAGGCGGTGTTCGATATTTGGCAATTCGCGGAATCGTGCTCTAACATGCT
1 AAATTCTCCAAAACGAAGGCAATGTTCGATATTTGGCAATTCGCGGAATCGTGCCCTAACATGCT
*
42302003 GGGTTGCAATTCCTCGTTTGCTCAAAATAATTGAATGTCCCTTTAGAATTTCATTCATGCGTTT
66 GGGTTGCAATTCCTCGTTTGCTCAAAATAATTGAATGTCCCTTTAGAATTTCACTCATGCGTTT
* * *
42302067 AAATTCTCCAAAACGAAGGCAATGTTCGATGTTTGGCAATTCGGGGAATCGTGCCCTATCATGCT
1 AAATTCTCCAAAACGAAGGCAATGTTCGATATTTGGCAATTCGCGGAATCGTGCCCTAACATGCT
* * * *
42302132 GGGTTGTAATTTCCT-GTTTGTTCAAAATGATTGAA-GATTCCTTTAGAATTTCACTCAT
66 GGGTTGCAA-TTCCTCGTTTGCTCAAAATAATTGAATG-TCCCTTTAGAATTTCACTCAT
42302190 ATTCTCTAAA
Statistics
Matches: 108, Mismatches: 13, Indels: 4
0.86 0.10 0.03
Matches are distributed among these distances:
128 1 0.01
129 102 0.94
130 5 0.05
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.35
Consensus pattern (129 bp):
AAATTCTCCAAAACGAAGGCAATGTTCGATATTTGGCAATTCGCGGAATCGTGCCCTAACATGCT
GGGTTGCAATTCCTCGTTTGCTCAAAATAATTGAATGTCCCTTTAGAATTTCACTCATGCGTTT
Found at i:42329748 original size:28 final size:28
Alignment explanation
Indices: 42329715--42329776 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 28
42329705 CCACAAATAC
* *
42329715 AGGTTCATAATTAGGGCTCGCACATGTA
1 AGGTTCACAACTAGGGCTCGCACATGTA
* * * *
42329743 GGGTTCGCACCTAGGGTTCGCACATGTA
1 AGGTTCACAACTAGGGCTCGCACATGTA
42329771 AGGTTC
1 AGGTTC
42329777 GCGTATGCGT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.23, C:0.21, G:0.29, T:0.27
Consensus pattern (28 bp):
AGGTTCACAACTAGGGCTCGCACATGTA
Found at i:42329750 original size:15 final size:15
Alignment explanation
Indices: 42329726--42329778 Score: 65
Period size: 15 Copynumber: 3.7 Consensus size: 15
42329716 GGTTCATAAT
*
42329726 TAGGGCTCGCACATG
1 TAGGGTTCGCACATG
*
42329741 TAGGGTTCGCAC--C
1 TAGGGTTCGCACATG
42329754 TAGGGTTCGCACATG
1 TAGGGTTCGCACATG
*
42329769 TAAGGTTCGC
1 TAGGGTTCGC
42329779 GTATGCGTGT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
13 12 0.38
15 20 0.62
ACGTcount: A:0.19, C:0.25, G:0.32, T:0.25
Consensus pattern (15 bp):
TAGGGTTCGCACATG
Found at i:42329759 original size:13 final size:13
Alignment explanation
Indices: 42329741--42329765 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42329731 CTCGCACATG
42329741 TAGGGTTCGCACC
1 TAGGGTTCGCACC
42329754 TAGGGTTCGCAC
1 TAGGGTTCGCAC
42329766 ATGTAAGGTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.28, G:0.32, T:0.24
Consensus pattern (13 bp):
TAGGGTTCGCACC
Found at i:42329841 original size:21 final size:20
Alignment explanation
Indices: 42329815--42329868 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 20
42329805 GACATATATA
42329815 AGGTTCGCATAAAAAGCACAT
1 AGGTTCGCATAAAAA-CACAT
* * *
42329836 AGGTTCACATAAATACATAT
1 AGGTTCGCATAAAAACACAT
42329856 AGGGTTCGCATAA
1 A-GGTTCGCATAA
42329869 CATGGCTCGT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 5 0.18
21 23 0.82
ACGTcount: A:0.41, C:0.17, G:0.19, T:0.24
Consensus pattern (20 bp):
AGGTTCGCATAAAAACACAT
Found at i:42330105 original size:25 final size:25
Alignment explanation
Indices: 42330077--42330129 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
42330067 TTATGACTCG
*
42330077 CATGTGACAAACAACAGGTGACACA
1 CATGTAACAAACAACAGGTGACACA
* ** *
42330102 CATGTAATATTCAACAGGTGACTCA
1 CATGTAACAAACAACAGGTGACACA
42330127 CAT
1 CAT
42330130 ATACAACAAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.40, C:0.23, G:0.17, T:0.21
Consensus pattern (25 bp):
CATGTAACAAACAACAGGTGACACA
Found at i:42331421 original size:48 final size:48
Alignment explanation
Indices: 42331350--42331446 Score: 194
Period size: 48 Copynumber: 2.0 Consensus size: 48
42331340 TATATAGGGA
42331350 TGCCAATAACTAGCATATTTCGCCTTTGTTTTTCTCTGAGTTCTTCCC
1 TGCCAATAACTAGCATATTTCGCCTTTGTTTTTCTCTGAGTTCTTCCC
42331398 TGCCAATAACTAGCATATTTCGCCTTTGTTTTTCTCTGAGTTCTTCCC
1 TGCCAATAACTAGCATATTTCGCCTTTGTTTTTCTCTGAGTTCTTCCC
42331446 T
1 T
42331447 TAGTCTCTGG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.16, C:0.27, G:0.12, T:0.44
Consensus pattern (48 bp):
TGCCAATAACTAGCATATTTCGCCTTTGTTTTTCTCTGAGTTCTTCCC
Found at i:42334918 original size:27 final size:26
Alignment explanation
Indices: 42334883--42334994 Score: 118
Period size: 27 Copynumber: 4.2 Consensus size: 26
42334873 AGCATGGCTG
* *
42334883 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
*
42334909 CCAGATACAGATAACCGTGGCAGAGCCA
1 CCAGA-ACAGATAA-TGTGGCAGAGCCA
*
42334937 CCAGAACAGATATATGTGGTAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* *
42334964 CCA-AATCAGATAATTGTGGCATAGCAA
1 CCAGAA-CAGATAA-TGTGGCAGAGCCA
42334991 CCAG
1 CCAG
42334995 GACGCTTCCT
Statistics
Matches: 72, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
26 8 0.11
27 48 0.67
28 16 0.22
ACGTcount: A:0.38, C:0.22, G:0.23, T:0.16
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:42334947 original size:54 final size:54
Alignment explanation
Indices: 42334883--42334994 Score: 136
Period size: 54 Copynumber: 2.1 Consensus size: 54
42334873 AGCATGGCTG
* * *
42334883 CCAGAACAGATA-ATGTGACAGAGTCACCAGATACAGATAACCGTGGCAGAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAAAT-CAGATAACCGTGGCAGAGCAA
** ** *
42334937 CCAGAACAGATATATGTGGTAGAGCCACCAAATCAGATAATTGTGGCATAGCAA
1 CCAGAACAGATATATGTGACAGAGCCACCAAATCAGATAACCGTGGCAGAGCAA
42334991 CCAG
1 CCAG
42334995 GACGCTTCCT
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
54 33 0.67
55 16 0.33
ACGTcount: A:0.38, C:0.22, G:0.23, T:0.16
Consensus pattern (54 bp):
CCAGAACAGATATATGTGACAGAGCCACCAAATCAGATAACCGTGGCAGAGCAA
Found at i:42341798 original size:16 final size:16
Alignment explanation
Indices: 42341773--42341804 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
42341763 CAATCTTTAT
*
42341773 AAAATTTTTATTTTCG
1 AAAATCTTTATTTTCG
42341789 AAAATCTTTATTTTCG
1 AAAATCTTTATTTTCG
42341805 TAAACCCATT
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:0.31, C:0.09, G:0.06, T:0.53
Consensus pattern (16 bp):
AAAATCTTTATTTTCG
Found at i:42342844 original size:27 final size:27
Alignment explanation
Indices: 42342805--42342883 Score: 99
Period size: 27 Copynumber: 3.0 Consensus size: 27
42342795 GTCATTAGAT
*
42342805 ACAGA-AATCGTGGCAGAGCCACCAGA
1 ACAGATAATTGTGGCAGAGCCACCAGA
*
42342831 ACAGAT-ATATGTGGTAGAGCCACCAGA
1 ACAGATAAT-TGTGGCAGAGCCACCAGA
* *
42342858 TCAGATAATTGTGGCATAGCCACCAG
1 ACAGATAATTGTGGCAGAGCCACCAG
42342884 GACGCTTCCT
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
26 7 0.16
27 36 0.80
28 2 0.04
ACGTcount: A:0.35, C:0.23, G:0.25, T:0.16
Consensus pattern (27 bp):
ACAGATAATTGTGGCAGAGCCACCAGA
Found at i:42345162 original size:29 final size:29
Alignment explanation
Indices: 42345128--42345198 Score: 133
Period size: 29 Copynumber: 2.4 Consensus size: 29
42345118 TGAGAACTTA
42345128 TGATATGTGAGCCTTTATGGCTGAATCTC
1 TGATATGTGAGCCTTTATGGCTGAATCTC
*
42345157 TGATATATGAGCCTTTATGGCTGAATCTC
1 TGATATGTGAGCCTTTATGGCTGAATCTC
42345186 TGATATGTGAGCC
1 TGATATGTGAGCC
42345199 CGTCTAGCGA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.23, C:0.17, G:0.24, T:0.37
Consensus pattern (29 bp):
TGATATGTGAGCCTTTATGGCTGAATCTC
Found at i:42345328 original size:65 final size:65
Alignment explanation
Indices: 42345205--42345336 Score: 167
Period size: 65 Copynumber: 2.0 Consensus size: 65
42345195 AGCCCGTCTA
* * * * *
42345205 GCGAAGATTGTTTGAATGCAAGTTGGTGTCTTAATAGTTGTTCCTGTTACATGTGTGCCCTTGTG
1 GCGAAGATTGTTTGAATGCAAGTGGGTGTCTTAATAGCTATTCATGATACATGTGTGCCCTTGTG
* * * *
42345270 GCGAAGATTGTTTGAATGCAGGTGGGTGTCTTAATGGCTATCTGATGATGCATG-GTGCCCTTGT
1 GCGAAGATTGTTTGAATGCAAGTGGGTGTCTTAATAGCTAT-TCATGATACATGTGTGCCCTTGT
42345334 G
65 G
42345335 GC
1 GC
42345337 TATATGTTGA
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
65 49 0.86
66 8 0.14
ACGTcount: A:0.18, C:0.14, G:0.31, T:0.36
Consensus pattern (65 bp):
GCGAAGATTGTTTGAATGCAAGTGGGTGTCTTAATAGCTATTCATGATACATGTGTGCCCTTGTG
Found at i:42360006 original size:30 final size:31
Alignment explanation
Indices: 42359966--42360024 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
42359956 ATCTATTTAC
* *
42359966 TTTCCTCCAAAATTTTTACTCC-CTCCCACT
1 TTTCCACCAAAACTTTTACTCCTCTCCCACT
*
42359996 TTTCCACCAAAACTTTTATTCCTCTCCCA
1 TTTCCACCAAAACTTTTACTCCTCTCCCA
42360025 TCCCACCCCC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 19 0.76
31 6 0.24
ACGTcount: A:0.22, C:0.39, G:0.00, T:0.39
Consensus pattern (31 bp):
TTTCCACCAAAACTTTTACTCCTCTCCCACT
Found at i:42360148 original size:125 final size:127
Alignment explanation
Indices: 42360002--42360237 Score: 345
Period size: 125 Copynumber: 1.9 Consensus size: 127
42359992 CACTTTTCCA
* * * * **
42360002 CCAAAACTTTTATTCCTCTCCCATCCCACCCCCCTTCTA-CCCAAACTCATCCCCTCC-CCCCCC
1 CCAAAACGTTTACTCCCCTCCCATCCCACCCCCCTTCTACCCCAAACCCA-CCCC-CCACCCCAA
* *
42360065 TTTTTTTTAATATT-TCC-CCCCAAAATTTTACTCCTTCAACCCCCAAAACTTTTTATTTTCTC
64 ATTTTTTTAATATTCTCCTCCCCAAAATTTTACTCCCTCAACCCCCAAAACTTTTTATTTTCTC
*
42360127 CCAAAACGTTTACTCCCCTCCCATTCCACCCCCCTTCTACCCCAAACCCACCCCCCACCCCAAAT
1 CCAAAACGTTTACTCCCCTCCCATCCCACCCCCCTTCTACCCCAAACCCACCCCCCACCCCAAAT
42360192 TTTTTTAATATTCTCCTCCCCAAAATTTTACTCCCTCAACCCCCAA
66 TTTTTTAATATTCTCCTCCCCAAAATTTTACTCCCTCAACCCCCAA
42360238 TTTTTTTTTA
Statistics
Matches: 98, Mismatches: 9, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
124 2 0.02
125 56 0.57
126 12 0.12
127 28 0.29
ACGTcount: A:0.23, C:0.46, G:0.00, T:0.31
Consensus pattern (127 bp):
CCAAAACGTTTACTCCCCTCCCATCCCACCCCCCTTCTACCCCAAACCCACCCCCCACCCCAAAT
TTTTTTAATATTCTCCTCCCCAAAATTTTACTCCCTCAACCCCCAAAACTTTTTATTTTCTC
Found at i:42360810 original size:30 final size:30
Alignment explanation
Indices: 42360774--42360842 Score: 111
Period size: 30 Copynumber: 2.3 Consensus size: 30
42360764 TATATTTGAT
*
42360774 TCGATTCGATTGAATTACATCTCATTCGAC
1 TCGATTCGATTGAATTACATCTCACTCGAC
* *
42360804 TCGATTCGATTGAATTCCATCTCACTCGGC
1 TCGATTCGATTGAATTACATCTCACTCGAC
42360834 TCGATTCGA
1 TCGATTCGA
42360843 GAAAATTTCA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.23, C:0.26, G:0.16, T:0.35
Consensus pattern (30 bp):
TCGATTCGATTGAATTACATCTCACTCGAC
Found at i:42361007 original size:17 final size:18
Alignment explanation
Indices: 42360974--42361007 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
42360964 TAGAAGTATT
42360974 AATAATTATACATTTAAA
1 AATAATTATACATTTAAA
*
42360992 AATATTTATA-ATTTAA
1 AATAATTATACATTTAA
42361008 TATAAGTTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (18 bp):
AATAATTATACATTTAAA
Found at i:42364520 original size:39 final size:38
Alignment explanation
Indices: 42364465--42364540 Score: 91
Period size: 39 Copynumber: 2.0 Consensus size: 38
42364455 AGTATCAATT
42364465 TCACATTTTATCTTTAAGATAATTTTT-ATTTAAAAAA
1 TCACATTTTATCTTTAAGATAATTTTTAATTTAAAAAA
* * * *
42364502 TCACATTTTTTACATTTAATATATTTTTTAATTTCAAAA
1 TCACATTTTAT-C-TTTAAGATAATTTTTAATTTAAAAA
42364541 TACATAGTGA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
37 10 0.31
38 1 0.03
39 13 0.41
40 8 0.25
ACGTcount: A:0.38, C:0.09, G:0.01, T:0.51
Consensus pattern (38 bp):
TCACATTTTATCTTTAAGATAATTTTTAATTTAAAAAA
Found at i:42365276 original size:13 final size:12
Alignment explanation
Indices: 42365252--42365279 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
42365242 AATAGTCATC
42365252 TATCAGTTTTTT
1 TATCAGTTTTTT
42365264 TATCAGTTTTTT
1 TATCAGTTTTTT
42365276 TATC
1 TATC
42365280 TTTATTATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.18, C:0.11, G:0.07, T:0.64
Consensus pattern (12 bp):
TATCAGTTTTTT
Found at i:42365415 original size:15 final size:15
Alignment explanation
Indices: 42365395--42365426 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
42365385 GGTAACGTTG
42365395 TAACTAAGGGTTGAA
1 TAACTAAGGGTTGAA
42365410 TAACTAAGGGTTGAA
1 TAACTAAGGGTTGAA
42365425 TA
1 TA
42365427 CAAAATTAAT
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:0.41, C:0.06, G:0.25, T:0.28
Consensus pattern (15 bp):
TAACTAAGGGTTGAA
Found at i:42368022 original size:41 final size:40
Alignment explanation
Indices: 42367957--42368051 Score: 109
Period size: 41 Copynumber: 2.3 Consensus size: 40
42367947 ATAATAAATC
*
42367957 AAATATATTTAAAACAAATATTAAAATAAGAAACAAATAAA
1 AAATATA-ATAAAACAAATATTAAAATAAGAAACAAATAAA
* * * * * *
42367998 AAATGATACTAAAACAATTCTTAAAATAATACACAAATTAA
1 AAAT-ATAATAAAACAAATATTAAAATAAGAAACAAATAAA
42368039 AAATATAATAAAA
1 AAATATAATAAAA
42368052 AGTGATTATA
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
40 8 0.17
41 35 0.76
42 3 0.07
ACGTcount: A:0.65, C:0.07, G:0.02, T:0.25
Consensus pattern (40 bp):
AAATATAATAAAACAAATATTAAAATAAGAAACAAATAAA
Found at i:42368102 original size:28 final size:27
Alignment explanation
Indices: 42368034--42368102 Score: 75
Period size: 28 Copynumber: 2.5 Consensus size: 27
42368024 TAATACACAA
* * *
42368034 ATTAAAAATATAATAAAAAGTGATTAT
1 ATTAAAAATAAAATAAAAAGTAAATAT
* *
42368061 ATTAAAATTGAAAATAAAATGTAAATAT
1 ATTAAAAAT-AAAATAAAAAGTAAATAT
42368089 GATTAAAAATAAAA
1 -ATTAAAAATAAAA
42368103 AATATATATA
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
27 8 0.24
28 18 0.53
29 8 0.24
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.30
Consensus pattern (27 bp):
ATTAAAAATAAAATAAAAAGTAAATAT
Found at i:42376417 original size:3 final size:3
Alignment explanation
Indices: 42376409--42376434 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
42376399 GTGATAGAAA
42376409 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
42376435 CCTTCATCCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:42379315 original size:19 final size:18
Alignment explanation
Indices: 42379267--42379307 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
42379257 TTTTAAAAGG
* *
42379267 AAAACAAATGAATTTTAA
1 AAAACAAATGAATCTAAA
42379285 AAAACAAATGAATCTAAA
1 AAAACAAATGAATCTAAA
42379303 AAAAC
1 AAAAC
42379308 TTAATGAAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.66, C:0.10, G:0.05, T:0.20
Consensus pattern (18 bp):
AAAACAAATGAATCTAAA
Found at i:42381296 original size:17 final size:18
Alignment explanation
Indices: 42381264--42381298 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
42381254 ATAATTTTTA
42381264 AATGTGTCTAAATTAATT
1 AATGTGTCTAAATTAATT
*
42381282 AATGTG-CTGAATTAATT
1 AATGTGTCTAAATTAATT
42381299 TGTGTGTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.37, C:0.06, G:0.14, T:0.43
Consensus pattern (18 bp):
AATGTGTCTAAATTAATT
Found at i:42385843 original size:27 final size:27
Alignment explanation
Indices: 42385813--42385866 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
42385803 GCTTCTTGTG
42385813 TTAGCTTCTTTTCAGATTTCGCTAAAT
1 TTAGCTTCTTTTCAGATTTCGCTAAAT
42385840 TTAGCTTCTTTTCAGATTTCGCTAAAT
1 TTAGCTTCTTTTCAGATTTCGCTAAAT
42385867 CTTTTCCACT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.22, C:0.19, G:0.11, T:0.48
Consensus pattern (27 bp):
TTAGCTTCTTTTCAGATTTCGCTAAAT
Found at i:42389782 original size:74 final size:74
Alignment explanation
Indices: 42389683--42389825 Score: 205
Period size: 74 Copynumber: 1.9 Consensus size: 74
42389673 TAGTGCTAGG
* * * * *
42389683 CGCAAATATTGTTAGTAAATCCAACTAGAGCTGGGCTCACTATTTATTCGTCGGTTTATCCGACC
1 CGCAAATACTATTAGTAAATCCAACTAGAGCTGGGCTCACAAATTATTCGTCGGTTTACCCGACC
42389748 AGCGCCGGA
66 AGCGCCGGA
* * * *
42389757 CGCAAATACTATTGGTATATCCAACTAGAGCTGGGCTCACAAATTATTTGTCGGTTTACCCGACT
1 CGCAAATACTATTAGTAAATCCAACTAGAGCTGGGCTCACAAATTATTCGTCGGTTTACCCGACC
42389822 AGCG
66 AGCG
42389826 TTGAGCACAA
Statistics
Matches: 60, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
74 60 1.00
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.29
Consensus pattern (74 bp):
CGCAAATACTATTAGTAAATCCAACTAGAGCTGGGCTCACAAATTATTCGTCGGTTTACCCGACC
AGCGCCGGA
Found at i:42398509 original size:31 final size:30
Alignment explanation
Indices: 42398474--42398545 Score: 76
Period size: 29 Copynumber: 2.4 Consensus size: 30
42398464 ATTATTAAAG
* *
42398474 TAAAATTATACTTTGACCTTTTTTA-AAATTA
1 TAAAATTATAATTT-A-ATTTTTTATAAATTA
42398505 TAAAAATT-TAATTTAATTTTTTATAAATTA
1 T-AAAATTATAATTTAATTTTTTATAAATTA
*
42398535 TAAAAATATAA
1 TAAAATTATAA
42398546 ACTATAAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
29 12 0.34
30 11 0.31
31 6 0.17
32 6 0.17
ACGTcount: A:0.47, C:0.04, G:0.01, T:0.47
Consensus pattern (30 bp):
TAAAATTATAATTTAATTTTTTATAAATTA
Found at i:42398546 original size:15 final size:15
Alignment explanation
Indices: 42398526--42398555 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
42398516 TTTAATTTTT
*
42398526 TATAAATTATAAAAA
1 TATAAACTATAAAAA
42398541 TATAAACTATAAAAA
1 TATAAACTATAAAAA
42398556 ATTCAAATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (15 bp):
TATAAACTATAAAAA
Found at i:42409482 original size:52 final size:48
Alignment explanation
Indices: 42409420--42409612 Score: 187
Period size: 47 Copynumber: 4.0 Consensus size: 48
42409410 GAAATGTGAT
* * *
42409420 TTCCGTATAAGACCATAGCTGGGCTATGGCTTCGGAGAAATGTGATTTGTGC
1 TTCCGTATAAGACCATAGCTGGGATATGGCATC-GAG---TGTGATATGTGC
* *
42409472 TTCCGTATAAGACCATATCCGGGATATGGCATCG-GTGTGATATGTGC
1 TTCCGTATAAGACCATAGCTGGGATATGGCATCGAGTGTGATATGTGC
* * *
42409519 TACTGTATAAGACCATATCTGGGATATGGCATC-AGTGTGATATGTG-
1 TTCCGTATAAGACCATAGCTGGGATATGGCATCGAGTGTGATATGTGC
* * ** *
42409565 ATCCGTATAAGACCATGGCTGGTCTATGGCCTCG-GTATGTGATATGTG
1 TTCCGTATAAGACCATAGCTGGGATATGGCATCGAG--TGTGATATGTG
42409613 ACTATGTGCA
Statistics
Matches: 121, Mismatches: 16, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
46 26 0.21
47 53 0.44
48 11 0.09
50 1 0.01
51 1 0.01
52 29 0.24
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.31
Consensus pattern (48 bp):
TTCCGTATAAGACCATAGCTGGGATATGGCATCGAGTGTGATATGTGC
Found at i:42413436 original size:27 final size:27
Alignment explanation
Indices: 42413406--42413583 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
42413396 ATATTGAGTC
* * * *
42413406 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
42413433 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
42413460 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
42413488 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
42413515 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
42413542 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
42413569 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
42413584 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:42413545 original size:82 final size:81
Alignment explanation
Indices: 42413427--42413582 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
42413417 TGCTATATAA
* *
42413427 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
42413492 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
42413509 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
42413573 CACTTAGTGC
65 CACTTAGTGC
42413583 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:42415668 original size:29 final size:28
Alignment explanation
Indices: 42415636--42415730 Score: 84
Period size: 29 Copynumber: 3.2 Consensus size: 28
42415626 TTGAGATACT
42415636 AAATTGAACCTAAAAAAAGTTTAGGTACC
1 AAATTGAA-CTAAAAAAAGTTTAGGTACC
* *
42415665 AAATTAAGAA-AAAAATACCAAGTTAAGGTACC
1 AAATT--GAACTAAAA-A--AAGTTTAGGTACC
**
42415697 AAATTGGGCTTAAAAAAAGTTTAGGTACC
1 AAATTGAAC-TAAAAAAAGTTTAGGTACC
42415726 AAATT
1 AAATT
42415731 AAGAAAAAAT
Statistics
Matches: 53, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
29 26 0.49
30 2 0.04
31 4 0.08
32 21 0.40
ACGTcount: A:0.49, C:0.12, G:0.15, T:0.24
Consensus pattern (28 bp):
AAATTGAACTAAAAAAAGTTTAGGTACC
Found at i:42415718 original size:61 final size:60
Alignment explanation
Indices: 42415646--42415800 Score: 215
Period size: 59 Copynumber: 2.6 Consensus size: 60
42415636 AAATTGAACC
* *
42415646 TAAAAAAAGTTTAGGTACCAAATTAAGAAAAAAATACCAAGTTAAGGTACCAAATTGGGCT
1 TAAAAAAAGTTTAGGTACCAAATTAAGAAAAAAATACCAAGTTAAGATACCAAATTAGG-T
** *
42415707 TAAAAAAAGTTTAGGTACCAAATTAAG-AAAAAATGTCAAGTTCAGATACCAAATTAGGT
1 TAAAAAAAGTTTAGGTACCAAATTAAGAAAAAAATACCAAGTTAAGATACCAAATTAGGT
* * *
42415766 AAAAAAAAGTTTAGGTACTAAATT-AGAACAAAATA
1 TAAAAAAAGTTTAGGTACCAAATTAAGAAAAAAATA
42415801 GTAAGTTGAA
Statistics
Matches: 84, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
58 2 0.02
59 29 0.35
60 26 0.31
61 27 0.32
ACGTcount: A:0.52, C:0.10, G:0.15, T:0.24
Consensus pattern (60 bp):
TAAAAAAAGTTTAGGTACCAAATTAAGAAAAAAATACCAAGTTAAGATACCAAATTAGGT
Found at i:42427303 original size:26 final size:26
Alignment explanation
Indices: 42427274--42427332 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 26
42427264 TACCCCTAGC
* * *
42427274 AAAATTTTAATGATTTTACCTTTGGT
1 AAAATTTTAACGATGTTACCTTTAGT
* *
42427300 AAAATTTTGACGATGTTGCCTTTAGT
1 AAAATTTTAACGATGTTACCTTTAGT
42427326 AAAATTT
1 AAAATTT
42427333 CAAGAAAATA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.32, C:0.08, G:0.14, T:0.46
Consensus pattern (26 bp):
AAAATTTTAACGATGTTACCTTTAGT
Found at i:42436051 original size:27 final size:27
Alignment explanation
Indices: 42436020--42436197 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
42436010 TAAATTGTAC
42436020 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
42436047 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
42436073 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
42436101 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
42436129 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
42436156 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
42436183 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
42436198 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:42436134 original size:82 final size:81
Alignment explanation
Indices: 42436021--42436176 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
42436011 AAATTGTACA
* *
42436021 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
42436085 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
42436102 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
42436167 TGCGAGTTGA
65 TGCGAATTGA
42436177 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:42436188 original size:82 final size:81
Alignment explanation
Indices: 42436017--42436197 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
42436007 GATTAAATTG
* *
42436017 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
42436082 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
42436098 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
42436162 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
42436180 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
42436198 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:42440898 original size:50 final size:50
Alignment explanation
Indices: 42440768--42441009 Score: 283
Period size: 50 Copynumber: 4.8 Consensus size: 50
42440758 AGCCGAAGCT
* * * * *
42440768 ATCTGATACGCATAGTAGCCTGCACTTAGTACTACACATGCGACC-AACA
1 ATCTGATACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAACC
* * *
42440817 ATCCGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTCACC
1 ATCTGATACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAACC
* * *
42440867 ATCTGATACACGTAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGTC
1 ATCTGATACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAA-CC
* * * *
42440918 AT-TGAGTACGCATAGTAGCCTGCACTTAGTACTACACATGTGACTTAA-C
1 ATCTGA-TACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAACC
* *
42440967 AGTATGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTG
1 A-TCTGATACACGTAGTAGCCTGCACTTAGTACTACACACGTG
42441010 TACTCACAAT
Statistics
Matches: 164, Mismatches: 24, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
49 41 0.25
50 82 0.50
51 41 0.25
ACGTcount: A:0.29, C:0.27, G:0.19, T:0.25
Consensus pattern (50 bp):
ATCTGATACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAACC
Found at i:42451165 original size:16 final size:17
Alignment explanation
Indices: 42451132--42451166 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
42451122 AGAAATAATA
*
42451132 ATATGTAAAATTTAAAT
1 ATATGTAAAATATAAAT
42451149 ATATGTAAAA-ATAAAT
1 ATATGTAAAATATAAAT
42451165 AT
1 AT
42451167 TAAAAATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (17 bp):
ATATGTAAAATATAAAT
Found at i:42455640 original size:15 final size:15
Alignment explanation
Indices: 42455615--42455647 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
42455605 AATTGTTTTC
42455615 AAAAATAAAAATAATA
1 AAAAATAAAAATAA-A
42455631 AAAAAT-AAAATAAA
1 AAAAATAAAAATAAA
42455645 AAA
1 AAA
42455648 CAAAAAGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.24
15 7 0.41
16 6 0.35
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (15 bp):
AAAAATAAAAATAAA
Found at i:42458449 original size:56 final size:56
Alignment explanation
Indices: 42458379--42458491 Score: 181
Period size: 56 Copynumber: 2.0 Consensus size: 56
42458369 GAAGAATCCC
* * *
42458379 TATAATCAAGGATTGACTCAATCCTAAAGAAAGAAAGAAATAAAATCTCATCAAAT
1 TATAATCAAAGATTGACCCAATCCTAAAGAAAAAAAGAAATAAAATCTCATCAAAT
* *
42458435 TATAATTAAAGATTGACCCCATCCTAAAGAAAAAAAGAAATAAAATCTCATCAAAT
1 TATAATCAAAGATTGACCCAATCCTAAAGAAAAAAAGAAATAAAATCTCATCAAAT
42458491 T
1 T
42458492 TGTCTCAATT
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
56 52 1.00
ACGTcount: A:0.52, C:0.15, G:0.09, T:0.24
Consensus pattern (56 bp):
TATAATCAAAGATTGACCCAATCCTAAAGAAAAAAAGAAATAAAATCTCATCAAAT
Found at i:42459860 original size:13 final size:15
Alignment explanation
Indices: 42459842--42459873 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
42459832 TTATATACTA
42459842 TTTTATTA-A-TAGT
1 TTTTATTATATTAGT
42459855 TTTTATTATATTAGT
1 TTTTATTATATTAGT
42459870 TTTT
1 TTTT
42459874 GAATTTCTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 8 0.47
14 1 0.06
15 8 0.47
ACGTcount: A:0.25, C:0.00, G:0.06, T:0.69
Consensus pattern (15 bp):
TTTTATTATATTAGT
Found at i:42459949 original size:13 final size:13
Alignment explanation
Indices: 42459931--42459956 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
42459921 TTCGTTAATC
42459931 GCCTAAATCATTT
1 GCCTAAATCATTT
42459944 GCCTAAATCATTT
1 GCCTAAATCATTT
42459957 CTATATATTA
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:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (13 bp):
GCCTAAATCATTT
Found at i:42465196 original size:47 final size:47
Alignment explanation
Indices: 42465110--42465232 Score: 135
Period size: 47 Copynumber: 2.6 Consensus size: 47
42465100 GAGATGTAAG
***
42465110 CCAGTGTAAGACATGTCTGGGACAT-GCATCGGTTATGAGATGAT-AA
1 CCAGTGTAAGACATGTCTGGGACATGGCATCAACTATGAGAT-ATGAA
* *
42465156 TCAGTGTAAGATCATGTCTGGGACATGGCATCAACT-TGAGATATGAG
1 CCAGTGTAAGA-CATGTCTGGGACATGGCATCAACTATGAGATATGAA
* *
42465203 CCAGTATAAGACCATGTCTAGGACATGGCA
1 CCAGTGTAAGA-CATGTCTGGGACATGGCA
42465233 CCGATACCTT
Statistics
Matches: 65, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
46 12 0.18
47 47 0.72
48 6 0.09
ACGTcount: A:0.31, C:0.17, G:0.27, T:0.25
Consensus pattern (47 bp):
CCAGTGTAAGACATGTCTGGGACATGGCATCAACTATGAGATATGAA
Found at i:42467942 original size:48 final size:46
Alignment explanation
Indices: 42467837--42468041 Score: 166
Period size: 46 Copynumber: 4.4 Consensus size: 46
42467827 TATGTGTGCT
* ** *
42467837 AGTGTAAGACATGTCTGGGACATGCATTAGCCAT--AGCATGA-GAGCC
1 AGTGTAAGACATGTTTGGGACATGCATCGGCC-TCGAG-AT-ATAAGCC
* *
42467883 AGTGTAAGACATGTTTGGGGCATGCATGGGCCTCGAGATATTTAAGCC
1 AGTGTAAGACATGTTTGGGACATGCATCGGCCTCGAGATA--TAAGCC
* * * * * * *
42467931 AGTGTAAGACATGTCTGGGACATGCATCTGCATTGAGACGA-GAGCT
1 AGTGTAAGACATGTTTGGGACATGCATCGGCCTCGAGA-TATAAGCC
* *
42467977 AGTGTAAGACATGTTTGGGACATGCATCGGCCTCGTGATATACAAGCT
1 AGTGTAAGACATGTTTGGGACATGCATCGGCCTCGAGATAT--AAGCC
*
42468025 AGTGTAAGACCTGTTTG
1 AGTGTAAGACATGTTTG
42468042 AGTCATGGCA
Statistics
Matches: 128, Mismatches: 22, Indels: 16
0.77 0.13 0.10
Matches are distributed among these distances:
45 3 0.02
46 66 0.52
47 2 0.02
48 56 0.44
49 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.26
Consensus pattern (46 bp):
AGTGTAAGACATGTTTGGGACATGCATCGGCCTCGAGATATAAGCC
Found at i:42467986 original size:94 final size:94
Alignment explanation
Indices: 42467837--42468140 Score: 294
Period size: 94 Copynumber: 3.2 Consensus size: 94
42467827 TATGTGTGCT
*
42467837 AGTGTAAGACATGTCTGGGACATGCATTAGCCATAGCATGAGAGCCAGTGTAAGACATGTTTGGG
1 AGTGTAAGACATGTCTGGGACATGCATTAGCCATAGCACGAGAGCCAGTGTAAGACATGTTTGGG
* * **
42467902 GCATGCATGGGCCTCGAGATATTTAAGCC
66 ACATGCATCGGCCTCGAGATATACAAGCC
*
42467931 AGTGTAAGACATGTCTGGGACATGCATCT-G-CATTGAG-ACGAGAGCTAGTGTAAGACATGTTT
1 AGTGTAAGACATGTCTGGGACATGCAT-TAGCCA-T-AGCACGAGAGCCAGTGTAAGACATGTTT
* *
42467993 GGGACATGCATCGGCCTCGTGATATACAAGCT
63 GGGACATGCATCGGCCTCGAGATATACAAGCC
* * * * * * * * *
42468025 AGTGTAAGACCTGTTTGAGTCATGGCATCAACACCAATAG-ATGAGAGCCAGTGTAAGACCTGTC
1 AGTGTAAGACATGTCTGGGACAT-GCAT-TA-GCC-ATAGCACGAGAGCCAGTGTAAGACATGTT
* **
42468089 TAGGACATGGCATCGGCCTCGCTATATGA-AAGCC
62 TGGGACAT-GCATCGGCCTCGAGATAT-ACAAGCC
*
42468123 AGTGTAACATCATGTCTG
1 AGTGTAAGA-CATGTCTG
42468141 AGGCATGGCG
Statistics
Matches: 174, Mismatches: 25, Indels: 17
0.81 0.12 0.08
Matches are distributed among these distances:
93 2 0.01
94 97 0.56
95 8 0.05
97 29 0.17
98 30 0.17
99 8 0.05
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.25
Consensus pattern (94 bp):
AGTGTAAGACATGTCTGGGACATGCATTAGCCATAGCACGAGAGCCAGTGTAAGACATGTTTGGG
ACATGCATCGGCCTCGAGATATACAAGCC
Found at i:42468123 original size:49 final size:47
Alignment explanation
Indices: 42467837--42468140 Score: 195
Period size: 48 Copynumber: 6.4 Consensus size: 47
42467827 TATGTGTGCT
** * * *
42467837 AGTGTAAGACATGTCTGGGACATGCATTAG-C-CATAGCATGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGTA-TATGAAAGCC
* * * * **
42467883 AGTGTAAGACATGTTTGGGGCATGCATGGGCCTCGAGATATTTAAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCG-TATATGAAAGCC
* * * * * * *
42467931 AGTGTAAGACATGTCTGGGACATGCATCTGCATTG-AGACGAGAGCT
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGTATATGAAAGCC
* *
42467977 AGTGTAAGACATGTTTGGGACATGCATCGGCCTCGTGATAT-ACAAGCT
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGT-ATATGA-AAGCC
* * * * ** * * *
42468025 AGTGTAAGACCTGTTTGAGTCATGGCATCAACAC-CAATAGATGAGAGCC
1 AGTGTAAGACATGTCTGGGACAT-GCATCGGC-CTC-GTATATGAAAGCC
* *
42468074 AGTGTAAGACCTGTCTAGGACATGGCATCGGCCTCGCTATATGAAAGCC
1 AGTGTAAGACATGTCTGGGACAT-GCATCGGCCTCG-TATATGAAAGCC
*
42468123 AGTGTAACATCATGTCTG
1 AGTGTAAGA-CATGTCTG
42468141 AGGCATGGCG
Statistics
Matches: 195, Mismatches: 50, Indels: 22
0.73 0.19 0.08
Matches are distributed among these distances:
46 62 0.32
47 2 0.01
48 63 0.32
49 59 0.30
50 9 0.05
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.25
Consensus pattern (47 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGTATATGAAAGCC
Found at i:42469813 original size:14 final size:14
Alignment explanation
Indices: 42469794--42469825 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
42469784 GGCTCCCGCT
42469794 GACCTCATCTAAGA
1 GACCTCATCTAAGA
42469808 GACCTCATCTAAGA
1 GACCTCATCTAAGA
42469822 GACC
1 GACC
42469826 GAGAGAGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.34, C:0.31, G:0.16, T:0.19
Consensus pattern (14 bp):
GACCTCATCTAAGA
Found at i:42474491 original size:30 final size:30
Alignment explanation
Indices: 42474452--42474508 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
42474442 ATCGATTTTC
**
42474452 AAGTATAGGGTTAAAATGGTCATTTTGTGA
1 AAGTATAGGGGCAAAATGGTCATTTTGTGA
*
42474482 AAGTCTAGGGGCAAAATGGTCATTTTG
1 AAGTATAGGGGCAAAATGGTCATTTTG
42474509 CCCAATTATG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.32, C:0.07, G:0.28, T:0.33
Consensus pattern (30 bp):
AAGTATAGGGGCAAAATGGTCATTTTGTGA
Found at i:42474903 original size:48 final size:45
Alignment explanation
Indices: 42474846--42475014 Score: 144
Period size: 48 Copynumber: 3.6 Consensus size: 45
42474836 TGATATGTGT
* *
42474846 GCTAATGTAAGACATGTCTGGGACATGCATGGGACTCGAGATATTTAA
1 GCTAGTGTAAGACATGTCTGGGACATGCAT-CGACTCGAGATA--TAA
* * * * * * *
42474894 GCCAGTGTAAGACATATCTAGGAAATGCATCTG-CATTGAGACGA-GA
1 GCTAGTGTAAGACATGTCTGGGACATGCATC-GAC-TCGAGA-TATAA
* *
42474940 GCTAGTGTAAGACATGTCTGGGACATGCATCAACCTCGTGATATACAA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGA-CTCGAGATAT--AA
42474988 GCTAGTGTAAGACATGTCTGGGACATG
1 GCTAGTGTAAGACATGTCTGGGACATG
42475015 GCGTTAGCTT
Statistics
Matches: 95, Mismatches: 18, Indels: 16
0.74 0.14 0.12
Matches are distributed among these distances:
45 1 0.01
46 32 0.34
47 2 0.02
48 59 0.62
49 1 0.01
ACGTcount: A:0.31, C:0.17, G:0.27, T:0.25
Consensus pattern (45 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCGACTCGAGATATAA
Found at i:42474968 original size:46 final size:46
Alignment explanation
Indices: 42474892--42475014 Score: 124
Period size: 46 Copynumber: 2.6 Consensus size: 46
42474882 CGAGATATTT
* * * * **
42474892 AAGCCAGTGTAAGACATATCTAGGAAATGCATCTGCAT-TG-AGAC
1 AAGCTAGTGTAAGACATGTCTGGGACATGCATCAACATCTGAAGAC
* *
42474936 GAGAGCTAGTGTAAGACATGTCTGGGACATGCATCAACCTCGTGATATAC
1 -A-AGCTAGTGTAAGACATGTCTGGGACATGCATCAACATC-TGA-AGAC
42474986 AAGCTAGTGTAAGACATGTCTGGGACATG
1 AAGCTAGTGTAAGACATGTCTGGGACATG
42475015 GCGTTAGCTT
Statistics
Matches: 65, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
45 1 0.02
46 30 0.46
48 30 0.46
49 1 0.02
50 3 0.05
ACGTcount: A:0.33, C:0.18, G:0.26, T:0.24
Consensus pattern (46 bp):
AAGCTAGTGTAAGACATGTCTGGGACATGCATCAACATCTGAAGAC
Found at i:42479425 original size:24 final size:21
Alignment explanation
Indices: 42479379--42479419 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
42479369 CTGCTCTGCT
42479379 CTGCCTCCCTCGCTGCTGCCG
1 CTGCCTCCCTCGCTGCTGCCG
*
42479400 CTGCCTCCCTCTCTGCTGCC
1 CTGCCTCCCTCGCTGCTGCC
42479420 TCCGCTCTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.00, C:0.54, G:0.20, T:0.27
Consensus pattern (21 bp):
CTGCCTCCCTCGCTGCTGCCG
Found at i:42484866 original size:9 final size:9
Alignment explanation
Indices: 42484852--42484923 Score: 69
Period size: 9 Copynumber: 8.2 Consensus size: 9
42484842 TAAGTACAAT
42484852 TAAGTTATG
1 TAAGTTATG
42484861 TAAGTTATG
1 TAAGTTATG
* * *
42484870 ATATGATATA
1 -TAAGTTATG
*
42484880 T-ATTTATG
1 TAAGTTATG
42484888 T-A-TTATG
1 TAAGTTATG
42484895 TAAGTTATG
1 TAAGTTATG
*
42484904 TAAATTATG
1 TAAGTTATG
42484913 TAAGTTATG
1 TAAGTTATG
42484922 TA
1 TA
42484924 TTATGTACGA
Statistics
Matches: 51, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
7 6 0.12
8 6 0.12
9 33 0.65
10 6 0.12
ACGTcount: A:0.36, C:0.00, G:0.17, T:0.47
Consensus pattern (9 bp):
TAAGTTATG
Found at i:42484894 original size:34 final size:34
Alignment explanation
Indices: 42484856--42484930 Score: 98
Period size: 34 Copynumber: 2.2 Consensus size: 34
42484846 TACAATTAAG
* *
42484856 TTATGTAAGTTATG-ATATGATATATATTTATGTA
1 TTATGTAAGTTATGTAAATGATATA-AGTTATGTA
* *
42484890 TTATGTAAGTTATGTAAATTATGTAAGTTATGTA
1 TTATGTAAGTTATGTAAATGATATAAGTTATGTA
42484924 TTATGTA
1 TTATGTA
42484931 CGACATAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
34 29 0.81
35 7 0.19
ACGTcount: A:0.35, C:0.00, G:0.16, T:0.49
Consensus pattern (34 bp):
TTATGTAAGTTATGTAAATGATATAAGTTATGTA
Found at i:42485070 original size:9 final size:9
Alignment explanation
Indices: 42485056--42485196 Score: 66
Period size: 9 Copynumber: 15.7 Consensus size: 9
42485046 TGTGTTAATT
42485056 TTATGTAAA
1 TTATGTAAA
*
42485065 TTATGTAAG
1 TTATGTAAA
42485074 TTATG-AAA
1 TTATGTAAA
*
42485082 TTTGATCTTTAAA
1 -TT-A--TGTAAA
*
42485095 TTATGTAAG
1 TTATGTAAA
*
42485104 TCATGT--A
1 TTATGTAAA
42485111 TTATGTAAGA
1 TTATGTAA-A
42485121 -TATGT--A
1 TTATGTAAA
*
42485127 TTATGTAAG
1 TTATGTAAA
42485136 TTATG-AAA
1 TTATGTAAA
*
42485144 TTCAAACTTTAAA
1 TT---A-TGTAAA
*
42485157 TTATGTAAG
1 TTATGTAAA
42485166 TTATGT--A
1 TTATGTAAA
42485173 TTATGTAAA
1 TTATGTAAA
*
42485182 TTAAGTAAA
1 TTATGTAAA
42485191 TTATGT
1 TTATGT
42485197 GAGTTGCTGG
Statistics
Matches: 98, Mismatches: 16, Indels: 36
0.65 0.11 0.24
Matches are distributed among these distances:
6 1 0.01
7 16 0.16
8 6 0.06
9 58 0.59
10 3 0.03
11 2 0.02
12 4 0.04
13 8 0.08
ACGTcount: A:0.38, C:0.03, G:0.14, T:0.45
Consensus pattern (9 bp):
TTATGTAAA
Found at i:42485095 original size:30 final size:30
Alignment explanation
Indices: 42485061--42485170 Score: 100
Period size: 30 Copynumber: 3.6 Consensus size: 30
42485051 TAATTTTATG
*
42485061 TAAATTATGTAAGTTATGAAATTTGATCTT
1 TAAATTATGTAAGTTATGAAATTAGATCTT
* * * *
42485091 TAAATTATGTAAGTCATGTATTATGTAAGATATG
1 TAAATTATGTAAGTTATG-A-AAT-T-AGATCTT
*
42485125 T--ATTATGTAAGTTATGAAATTCA-AACTT
1 TAAATTATGTAAGTTATGAAATT-AGATCTT
42485153 TAAATTATGTAAGTTATG
1 TAAATTATGTAAGTTATG
42485171 TATTATGTAA
Statistics
Matches: 63, Mismatches: 11, Indels: 12
0.73 0.13 0.14
Matches are distributed among these distances:
28 3 0.05
29 2 0.03
30 34 0.54
31 2 0.03
32 16 0.25
33 1 0.02
34 5 0.08
ACGTcount: A:0.38, C:0.04, G:0.15, T:0.44
Consensus pattern (30 bp):
TAAATTATGTAAGTTATGAAATTAGATCTT
Found at i:42485140 original size:16 final size:16
Alignment explanation
Indices: 42485094--42485180 Score: 79
Period size: 16 Copynumber: 5.6 Consensus size: 16
42485084 TGATCTTTAA
*
42485094 ATTATGTAAGTCATGT
1 ATTATGTAAGTTATGT
*
42485110 ATTATGTAAGATATGT
1 ATTATGTAAGTTATGT
*
42485126 ATTATGTAAGTTATGA
1 ATTATGTAAGTTATGT
* ** * **
42485142 AAT-TCAAACTT-TAA
1 ATTATGTAAGTTATGT
42485156 ATTATGTAAGTTATGT
1 ATTATGTAAGTTATGT
42485172 ATTATGTAA
1 ATTATGTAA
42485181 ATTAAGTAAA
Statistics
Matches: 54, Mismatches: 15, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
14 4 0.07
15 10 0.19
16 40 0.74
ACGTcount: A:0.38, C:0.03, G:0.15, T:0.44
Consensus pattern (16 bp):
ATTATGTAAGTTATGT
Found at i:42485140 original size:62 final size:62
Alignment explanation
Indices: 42485064--42485180 Score: 198
Period size: 62 Copynumber: 1.9 Consensus size: 62
42485054 TTTTATGTAA
** *
42485064 ATTATGTAAGTTATGAAATTTGATCTTTAAATTATGTAAGTCATGTATTATGTAAGATATGT
1 ATTATGTAAGTTATGAAATTCAAACTTTAAATTATGTAAGTCATGTATTATGTAAGATATGT
*
42485126 ATTATGTAAGTTATGAAATTCAAACTTTAAATTATGTAAGTTATGTATTATGTAA
1 ATTATGTAAGTTATGAAATTCAAACTTTAAATTATGTAAGTCATGTATTATGTAA
42485181 ATTAAGTAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
62 51 1.00
ACGTcount: A:0.38, C:0.03, G:0.15, T:0.44
Consensus pattern (62 bp):
ATTATGTAAGTTATGAAATTCAAACTTTAAATTATGTAAGTCATGTATTATGTAAGATATGT
Found at i:42485402 original size:99 final size:99
Alignment explanation
Indices: 42485295--42485677 Score: 651
Period size: 99 Copynumber: 3.9 Consensus size: 99
42485285 AATTAAAGTG
42485295 AAATAAAAT-AGAATATTTAAAATAAAACTTTAAATACAATTTAATTTAATTAGGTAATGTTAAA
1 AAATAAAATGA-AATATTTAAAATAAAACTTTAAATACAATTTAATTTAATTAGGTAATGTTAAA
42485359 ATAAAATAAAATATTGAAAATATTTTTCGTGATTC
65 ATAAAATAAAATATTGAAAATATTTTTCGTGATTC
* * *
42485394 AAAAAAAATGAAATATTTACAATAAAACTTTGAATACAATTTAATTTAATTAGGTAATGTTAAAA
1 AAATAAAATGAAATATTTAAAATAAAACTTTAAATACAATTTAATTTAATTAGGTAATGTTAAAA
*
42485459 TAAAATAAAATATTGAAATTATTTTTCGTGATTC
66 TAAAATAAAATATTGAAAATATTTTTCGTGATTC
*
42485493 AAATTAAATGAAATATTTAAAATAAAACTTTAAATACAATTTAATTTAATTAGGTAATGTTAAAA
1 AAATAAAATGAAATATTTAAAATAAAACTTTAAATACAATTTAATTTAATTAGGTAATGTTAAAA
* * *
42485558 TAAAATAAAACATTGAAATTATTTTTTGTGATTC
66 TAAAATAAAATATTGAAAATATTTTTCGTGATTC
* *
42485592 AAATTAAATGAAATATTTAAAATAAAACTTTAAATACGATTTAATTTAATTAGGTAATGTTAAAA
1 AAATAAAATGAAATATTTAAAATAAAACTTTAAATACAATTTAATTTAATTAGGTAATGTTAAAA
*
42485657 TAAAATAAAATATTTAAAATA
66 TAAAATAAAATATTGAAAATA
42485678 AAATAAAATA
Statistics
Matches: 269, Mismatches: 14, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
99 268 1.00
100 1 0.00
ACGTcount: A:0.51, C:0.04, G:0.07, T:0.38
Consensus pattern (99 bp):
AAATAAAATGAAATATTTAAAATAAAACTTTAAATACAATTTAATTTAATTAGGTAATGTTAAAA
TAAAATAAAATATTGAAAATATTTTTCGTGATTC
Found at i:42485617 original size:56 final size:56
Alignment explanation
Indices: 42485552--42485732 Score: 184
Period size: 56 Copynumber: 3.1 Consensus size: 56
42485542 TTAGGTAATG
* * *
42485552 TTAAAATAAAATAAAACATTGAAATTATTTTTTGTGATTCAAATTAAATGAAATAT
1 TTAAAATAAAATAAAACATTAAAATTATTTTTTGTGATTCAAATAAAATAAAATAT
* * * ** * *
42485608 TTAAAATAAAACTTTAAATACGATTTAATTTA-ATTAGGTAATGTTAAAATAAAATAAAATAT
1 TTAAAATAAAA---TAAA-AC-ATTAAAATTATTTTTTGTGA--TTCAAATAAAATAAAATAT
* *
42485670 TTAAAATAAAATAAAATATTAAAATTATTTTTTGTGATTCAAAAAAAATAAAATAT
1 TTAAAATAAAATAAAACATTAAAATTATTTTTTGTGATTCAAATAAAATAAAATAT
42485726 TTAAAAT
1 TTAAAAT
42485733 GAAACTTTAA
Statistics
Matches: 99, Mismatches: 18, Indels: 16
0.74 0.14 0.12
Matches are distributed among these distances:
56 35 0.35
57 8 0.08
58 6 0.06
59 8 0.08
60 7 0.07
61 8 0.08
62 27 0.27
ACGTcount: A:0.54, C:0.03, G:0.06, T:0.38
Consensus pattern (56 bp):
TTAAAATAAAATAAAACATTAAAATTATTTTTTGTGATTCAAATAAAATAAAATAT
Found at i:42485668 original size:62 final size:60
Alignment explanation
Indices: 42485592--42485784 Score: 200
Period size: 62 Copynumber: 3.2 Consensus size: 60
42485582 TTTGTGATTC
* * *
42485592 AAATTAAATGAAATATTTAAAATAAAACTTTAAATACGATTTAATTTAATTAGGTAATGTTA
1 AAATAAAATAAAATATTTAAAATAAAACTTTAAATA-AATTTAATTTAATTAGGTAAT-TTA
** * * * *
42485654 AAATAAAATAAAATATTTAAAATAAAA-TAAAATATTAAAATT-ATTT--TT-TGTGATTCA
1 AAATAAAATAAAATATTTAAAATAAAACTTTAA-A-TAAATTTAATTTAATTAGGTAATTTA
*
42485711 AAA-AAAATAAAATATTTAAAATGAAACTTTAAATATAATTTAATTTAATTAGGTAATTTGA
1 AAATAAAATAAAATATTTAAAATAAAACTTTAAATA-AATTTAATTTAATTAGGTAATTT-A
42485772 AAATAAAATAAAA
1 AAATAAAATAAAA
42485785 GATAACAAAA
Statistics
Matches: 105, Mismatches: 16, Indels: 20
0.74 0.11 0.14
Matches are distributed among these distances:
55 2 0.02
56 27 0.26
57 12 0.11
58 4 0.04
59 4 0.04
60 5 0.05
61 11 0.10
62 38 0.36
63 2 0.02
ACGTcount: A:0.55, C:0.02, G:0.06, T:0.37
Consensus pattern (60 bp):
AAATAAAATAAAATATTTAAAATAAAACTTTAAATAAATTTAATTTAATTAGGTAATTTA
Found at i:42485682 original size:118 final size:118
Alignment explanation
Indices: 42485552--42485784 Score: 378
Period size: 118 Copynumber: 2.0 Consensus size: 118
42485542 TTAGGTAATG
* ** *
42485552 TTAAAATAAAATAAAACATTGAAATTATTTTTTGTGATTCAAATTAAATGAAATATTTAAAATAA
1 TTAAAATAAAATAAAACATTAAAATTATTTTTTGTGATTCAAAAAAAATAAAATATTTAAAATAA
*
42485617 AACTTTAAATACGATTTAATTTAATTAGGTAATGTT-AAAATAAAATAAAATAT
66 AACTTTAAATACAATTTAATTTAATTAGGTAAT-TTGAAAATAAAATAAAATAT
* *
42485670 TTAAAATAAAATAAAATATTAAAATTATTTTTTGTGATTCAAAAAAAATAAAATATTTAAAATGA
1 TTAAAATAAAATAAAACATTAAAATTATTTTTTGTGATTCAAAAAAAATAAAATATTTAAAATAA
*
42485735 AACTTTAAATATAATTTAATTTAATTAGGTAATTTGAAAATAAAATAAAA
66 AACTTTAAATACAATTTAATTTAATTAGGTAATTTGAAAATAAAATAAAA
42485785 GATAACAAAA
Statistics
Matches: 106, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
117 2 0.02
118 104 0.98
ACGTcount: A:0.54, C:0.03, G:0.06, T:0.38
Consensus pattern (118 bp):
TTAAAATAAAATAAAACATTAAAATTATTTTTTGTGATTCAAAAAAAATAAAATATTTAAAATAA
AACTTTAAATACAATTTAATTTAATTAGGTAATTTGAAAATAAAATAAAATAT
Found at i:42485693 original size:18 final size:19
Alignment explanation
Indices: 42485651--42485694 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
42485641 TTAGGTAATG
42485651 TTAAAATAAAATAAAATAT
1 TTAAAATAAAATAAAATAT
42485670 TTAAAATAAAATAAAATA-
1 TTAAAATAAAATAAAATAT
42485688 TTAAAAT
1 TTAAAAT
42485695 TATTTTTTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 7 0.28
19 18 0.72
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (19 bp):
TTAAAATAAAATAAAATAT
Found at i:42485978 original size:87 final size:87
Alignment explanation
Indices: 42485881--42486057 Score: 354
Period size: 87 Copynumber: 2.0 Consensus size: 87
42485871 AAGTTTAATT
42485881 TTTTGGGTTGTTCCTAGAGTCCATGATTTTGTACAATTACCGTCGTTACTACTAAAAATTGCTAT
1 TTTTGGGTTGTTCCTAGAGTCCATGATTTTGTACAATTACCGTCGTTACTACTAAAAATTGCTAT
42485946 GATATAGGCAAGTTTGTCATAC
66 GATATAGGCAAGTTTGTCATAC
42485968 TTTTGGGTTGTTCCTAGAGTCCATGATTTTGTACAATTACCGTCGTTACTACTAAAAATTGCTAT
1 TTTTGGGTTGTTCCTAGAGTCCATGATTTTGTACAATTACCGTCGTTACTACTAAAAATTGCTAT
42486033 GATATAGGCAAGTTTGTCATAC
66 GATATAGGCAAGTTTGTCATAC
42486055 TTT
1 TTT
42486058 CAGCTTTTCT
Statistics
Matches: 90, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
87 90 1.00
ACGTcount: A:0.26, C:0.16, G:0.18, T:0.40
Consensus pattern (87 bp):
TTTTGGGTTGTTCCTAGAGTCCATGATTTTGTACAATTACCGTCGTTACTACTAAAAATTGCTAT
GATATAGGCAAGTTTGTCATAC
Found at i:42488820 original size:12 final size:12
Alignment explanation
Indices: 42488803--42488828 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
42488793 CAAGTTAAAT
42488803 TAAGTCACCAAA
1 TAAGTCACCAAA
42488815 TAAGTCACCAAA
1 TAAGTCACCAAA
42488827 TA
1 TA
42488829 TGCAAATCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.23, G:0.08, T:0.19
Consensus pattern (12 bp):
TAAGTCACCAAA
Found at i:42491717 original size:40 final size:40
Alignment explanation
Indices: 42491632--42491717 Score: 127
Period size: 40 Copynumber: 2.1 Consensus size: 40
42491622 CTTTTGAGGT
* * * *
42491632 GATCTTTAGCGGCGTTTTTCAGAAAGCGCTGCTAATGCTC
1 GATCTTTAGCGGCGTTTTTCAAAAAGCGCCGCTAAAGATC
*
42491672 TATCTTTAGCGGCGTTTTTCAAAAAGCGCCGCTAAAGATC
1 GATCTTTAGCGGCGTTTTTCAAAAAGCGCCGCTAAAGATC
42491712 GATCTT
1 GATCTT
42491718 CTAAATAAAG
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.23, C:0.22, G:0.22, T:0.33
Consensus pattern (40 bp):
GATCTTTAGCGGCGTTTTTCAAAAAGCGCCGCTAAAGATC
Found at i:42491909 original size:94 final size:95
Alignment explanation
Indices: 42491734--42491916 Score: 244
Period size: 94 Copynumber: 1.9 Consensus size: 95
42491724 AAAGGGCGAT
* * * *
42491734 GTCGTTTTGGTCAACTATTTTTTGCGGTGCTTTTCAGAAAACGCCGCTAATGCTTGACATTTAGC
1 GTCGTTTTGGTCAACTATTTATTGCGGCGCTTTTCAAAAAACGCCACTAATGCTTGACATTTAGC
* ** *
42491799 GGTGCTTTTTTAAAAACGCTGCTAAAGATC
66 AGTGCTTTTGGAAAAACGCCGCTAAAGATC
* *
42491829 GTCGTTTTGTTCAACT-TTTATTGCGGCGCTTTTTAAAAAACGCCACTAATGCTTGATC-TTTAG
1 GTCGTTTTGGTCAACTATTTATTGCGGCGCTTTTCAAAAAACGCCACTAATGCTTGA-CATTTAG
*
42491892 CAGTGCTTTTGGGAAAACGCCGCTA
65 CAGTGCTTTTGGAAAAACGCCGCTA
42491917 CTGCTTTATC
Statistics
Matches: 76, Mismatches: 11, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
94 60 0.79
95 16 0.21
ACGTcount: A:0.23, C:0.20, G:0.21, T:0.37
Consensus pattern (95 bp):
GTCGTTTTGGTCAACTATTTATTGCGGCGCTTTTCAAAAAACGCCACTAATGCTTGACATTTAGC
AGTGCTTTTGGAAAAACGCCGCTAAAGATC
Found at i:42491973 original size:40 final size:40
Alignment explanation
Indices: 42491851--42491998 Score: 172
Period size: 40 Copynumber: 3.7 Consensus size: 40
42491841 AACTTTTATT
** * *
42491851 GCGGCGCTTTTTAAAAAACGCCACTAATGCTTGATCTTTA
1 GCGGCGCTTTTGGAAAAACGCCGCTAATGCTTTATCTTTA
* * * *
42491891 GCAGTGCTTTTGGGAAAACGCCGCTACTGCTTTATCTTTA
1 GCGGCGCTTTTGGAAAAACGCCGCTAATGCTTTATCTTTA
*
42491931 GCGGCGCTTTTGGTAAAACGCCGCTAATGCTTTATCTTTA
1 GCGGCGCTTTTGGAAAAACGCCGCTAATGCTTTATCTTTA
* * *
42491971 GCGGC-ATTTTCGAAAAAGCGCTGCTAAT
1 GCGGCGCTTTTGGAAAAA-CGCCGCTAAT
42491999 TCTCGATCTA
Statistics
Matches: 91, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
39 9 0.10
40 82 0.90
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.32
Consensus pattern (40 bp):
GCGGCGCTTTTGGAAAAACGCCGCTAATGCTTTATCTTTA
Found at i:42492015 original size:80 final size:80
Alignment explanation
Indices: 42491847--42492016 Score: 184
Period size: 80 Copynumber: 2.1 Consensus size: 80
42491837 GTTCAACTTT
* * *
42491847 TATTGCGGCGCTTTTTAAAAAACGCCACTAATGCTTGATCTTTAGCAGTGCTTTTGGGAAAACGC
1 TATTGCGGCGCTTTTGAAAAAACGCCACTAATGCTTGATCTTTAGCAGTGCTTTTCGAAAAACGC
* **
42491912 CGCTACTGCTTTATC
66 CGCTAATGCTCGATC
** * *
42491927 T-TTAGCGGCGCTTTTGGTAAAACGCCGCTAATGCTTTATCTTTAGC-G-GCATTTTCGAAAAAG
1 TATT-GCGGCGCTTTTGAAAAAACGCCACTAATGCTTGATCTTTAGCAGTGC-TTTTCGAAAAA-
* *
42491989 CGCTGCTAATTCTCGATC
63 CGCCGCTAATGCTCGATC
42492007 TATTGCGGCG
1 TATTGCGGCG
42492017 TTTGTTTCAT
Statistics
Matches: 74, Mismatches: 12, Indels: 8
0.79 0.13 0.09
Matches are distributed among these distances:
78 2 0.03
79 12 0.16
80 58 0.78
81 2 0.03
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.34
Consensus pattern (80 bp):
TATTGCGGCGCTTTTGAAAAAACGCCACTAATGCTTGATCTTTAGCAGTGCTTTTCGAAAAACGC
CGCTAATGCTCGATC
Found at i:42492038 original size:41 final size:41
Alignment explanation
Indices: 42491993--42492074 Score: 112
Period size: 41 Copynumber: 2.0 Consensus size: 41
42491983 AAAAAGCGCT
* *
42491993 GCTAATTCTCGATCTATTGCGGCGTTTGTT-TCATAAACGCC
1 GCTAATTCTCGACCTATTGCGGCGTTT-TTGTCACAAACGCC
* *
42492034 GCTAATTCTTGACCTTTTGCGGCGTTTTTGTCACAAACGCC
1 GCTAATTCTCGACCTATTGCGGCGTTTTTGTCACAAACGCC
42492075 ACTATAACTC
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
40 2 0.06
41 34 0.94
ACGTcount: A:0.18, C:0.26, G:0.20, T:0.37
Consensus pattern (41 bp):
GCTAATTCTCGACCTATTGCGGCGTTTTTGTCACAAACGCC
Found at i:42495673 original size:20 final size:20
Alignment explanation
Indices: 42495648--42495698 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
42495638 TATCAAAATA
*
42495648 ACACGGGCGTGTACCTGTAT
1 ACACGGGCGTGAACCTGTAT
42495668 ACACGGGCGTGAACCTGTAT
1 ACACGGGCGTGAACCTGTAT
42495688 ACACGGGCGTG
1 ACACGGGCGTG
42495699 GGAGAAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.22, C:0.25, G:0.33, T:0.20
Consensus pattern (20 bp):
ACACGGGCGTGAACCTGTAT
Found at i:42501833 original size:22 final size:22
Alignment explanation
Indices: 42501802--42501856 Score: 85
Period size: 22 Copynumber: 2.5 Consensus size: 22
42501792 GAATAGTACC
42501802 ACACGCCCGTGTGGCTTG-TGTG
1 ACACGCCCGTGTGGC-TGATGTG
*
42501824 ACACGTCCGTGTGGCTGATGTG
1 ACACGCCCGTGTGGCTGATGTG
42501846 ACACGCCCGTG
1 ACACGCCCGTG
42501857 AAGGGCTAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 2 0.07
22 28 0.93
ACGTcount: A:0.13, C:0.29, G:0.35, T:0.24
Consensus pattern (22 bp):
ACACGCCCGTGTGGCTGATGTG
Found at i:42516641 original size:27 final size:27
Alignment explanation
Indices: 42516610--42516683 Score: 96
Period size: 27 Copynumber: 2.7 Consensus size: 27
42516600 TTAGTTTACC
**
42516610 AAATTACTGAAATACCCTC-GACTTGTA
1 AAATTACCAAAATACCC-CTGACTTGTA
**
42516637 AAATTACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCCTGACTTGTA
42516664 AAATTACCAAAATACCCCTG
1 AAATTACCAAAATACCCCTG
42516684 TAGGGTAGAA
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
26 1 0.02
27 41 0.98
ACGTcount: A:0.39, C:0.24, G:0.09, T:0.27
Consensus pattern (27 bp):
AAATTACCAAAATACCCCTGACTTGTA
Found at i:42516695 original size:27 final size:27
Alignment explanation
Indices: 42516638--42516842 Score: 259
Period size: 27 Copynumber: 7.6 Consensus size: 27
42516628 CGACTTGTAA
* ** *
42516638 AATTACCAAAATACCCCTGGT-TTGTAA
1 AATTACCGAAATACCCCT-GTAGGGTAG
*
42516665 AATTACCAAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
42516692 AATTACTGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * *
42516719 AGTTAGCGAAATACCCTTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
42516746 AAATACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
42516773 AATTACTGAAATACCCTTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
42516800 AAATACCAAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
42516827 AATTACCGAGATACCC
1 AATTACCGAAATACCC
42516843 TTGTGGGCAA
Statistics
Matches: 154, Mismatches: 23, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
26 2 0.01
27 152 0.99
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.24
Consensus pattern (27 bp):
AATTACCGAAATACCCCTGTAGGGTAG
Found at i:42516969 original size:16 final size:16
Alignment explanation
Indices: 42516948--42516978 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
42516938 CAAATATGGG
*
42516948 CATGACATTTTGCATA
1 CATGACATGTTGCATA
42516964 CATGACATGTTGCAT
1 CATGACATGTTGCAT
42516979 GGGTGGGGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.35
Consensus pattern (16 bp):
CATGACATGTTGCATA
Found at i:42521054 original size:19 final size:20
Alignment explanation
Indices: 42521020--42521057 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
42521010 AGTCCTTACA
42521020 CTAAATTAACCTTAATTAAG
1 CTAAATTAACCTTAATTAAG
*
42521040 CTAAATTTA-CTTAATTAA
1 CTAAATTAACCTTAATTAA
42521058 AATCTAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.45, C:0.13, G:0.03, T:0.39
Consensus pattern (20 bp):
CTAAATTAACCTTAATTAAG
Found at i:42528444 original size:20 final size:21
Alignment explanation
Indices: 42528419--42528469 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 21
42528409 GTCCTTACAT
42528419 TAAATTAACCTTAATT-AATC
1 TAAATTAACCTTAATTAAATC
*
42528439 TAAATTTA-CTTAATTAAAATC
1 TAAATTAACCTTAATT-AAATC
42528460 T-AATTAACCT
1 TAAATTAACCT
42528470 CTCACTTAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
19 7 0.27
20 12 0.46
21 7 0.27
ACGTcount: A:0.45, C:0.14, G:0.00, T:0.41
Consensus pattern (21 bp):
TAAATTAACCTTAATTAAATC
Found at i:42532599 original size:47 final size:46
Alignment explanation
Indices: 42532513--42532612 Score: 114
Period size: 47 Copynumber: 2.2 Consensus size: 46
42532503 TATCTTAATC
* *
42532513 TAAGACACATTAAAAAGCTGTACTTATTATAACATATTAATTAAACT
1 TAAGACACATTAAAAAGCTGTACATAATATAACATATTAA-TAAACT
* * *
42532560 TAAGACACATTAAAATGTTGTA-ATAAT-TAACATGCATTAATAGACT
1 TAAGACACATTAAAAAGCTGTACATAATATAACAT--ATTAATAAACT
42532606 TAAGACA
1 TAAGACA
42532613 TATTTAAGAC
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
45 6 0.13
46 15 0.33
47 25 0.54
ACGTcount: A:0.47, C:0.12, G:0.09, T:0.32
Consensus pattern (46 bp):
TAAGACACATTAAAAAGCTGTACATAATATAACATATTAATAAACT
Found at i:42536717 original size:10 final size:10
Alignment explanation
Indices: 42536619--42536883 Score: 86
Period size: 10 Copynumber: 27.8 Consensus size: 10
42536609 TATAAAAGTC
42536619 ATAAAAAA-T
1 ATAAAAAATT
*
42536628 AT-AAAAATC
1 ATAAAAAATT
*
42536637 ATAAAATATT
1 ATAAAAAATT
*
42536647 AGTAAAATATT
1 A-TAAAAAATT
42536658 -TAAAAAAATT
1 AT-AAAAAATT
* **
42536668 TTAAAAAGCT
1 ATAAAAAATT
*
42536678 ATAAAATA-T
1 ATAAAAAATT
* *
42536687 ATTAAAGATT
1 ATAAAAAATT
42536697 -TAGATAAAATT
1 ATA-A-AAAATT
42536708 ATAAAAAATT
1 ATAAAAAATT
* *
42536718 CATAGAAACTT
1 -ATAAAAAATT
* **
42536729 AT-TAATTTT
1 ATAAAAAATT
*
42536738 ATAAAAACTT
1 ATAAAAAATT
42536748 AT-AAAAATT
1 ATAAAAAATT
*
42536757 ATAAACAA-T
1 ATAAAAAATT
* *
42536766 CTAATAAATT
1 ATAAAAAATT
42536776 ATAAAAAAATT
1 AT-AAAAAATT
42536787 -T-AAAAATT
1 ATAAAAAATT
42536795 CAT-AAAAATT
1 -ATAAAAAATT
* **
42536805 GT-AAGTATT
1 ATAAAAAATT
*
42536814 ATAATAAATT
1 ATAAAAAATT
*
42536824 AT-AAAAGTT
1 ATAAAAAATT
*
42536833 ATAATAAATT
1 ATAAAAAATT
42536843 AT-----ATT
1 ATAAAAAATT
*
42536848 ATGAAAAATT
1 ATAAAAAATT
42536858 -T-AAAAA-T
1 ATAAAAAATT
42536865 ATATAAAAATT
1 ATA-AAAAATT
42536876 ATAAAAAA
1 ATAAAAAA
42536884 GTCATTTATT
Statistics
Matches: 190, Mismatches: 39, Indels: 53
0.67 0.14 0.19
Matches are distributed among these distances:
5 5 0.03
7 1 0.01
8 18 0.09
9 48 0.25
10 81 0.43
11 35 0.18
12 2 0.01
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.34
Consensus pattern (10 bp):
ATAAAAAATT
Found at i:42536758 original size:19 final size:18
Alignment explanation
Indices: 42536608--42536882 Score: 134
Period size: 19 Copynumber: 14.5 Consensus size: 18
42536598 TTCATTTTTC
* *
42536608 TTATAAAAGTCATAAAAA
1 TTATAAAAATTATAAAAA
* *
42536626 ATATAAAAATCATAAAATA
1 TTATAAAAATTATAAAA-A
*
42536645 TTAGTAAAATATTTAAAAAAA
1 TTA-TAAAA-A-TTATAAAAA
* *
42536666 TTTTAAAAAGCTAT-AAAA
1 TTATAAAAA-TTATAAAAA
* *
42536684 TATATTAAAGATTTAGATAAAA
1 T-TA-TAAA-AATTATA-AAAA
*
42536706 TTATAAAAAATTCATAGAAAC
1 TTAT-AAAAATT-ATA-AAAA
* **
42536727 TTATTAATTTTATAAAAA
1 TTATAAAAATTATAAAAA
42536745 CTTATAAAAATTATAAACAA
1 -TTATAAAAATTATAAA-AA
*
42536765 TCTA-ATAAATTATAAAAAAA
1 T-TATAAAAATTAT--AAAAA
42536785 TT-TAAAAATTCATAAAAA
1 TTATAAAAATT-ATAAAAA
* **
42536803 TTGTAAGTATTATAATAAA
1 TTATAAAAATTATAA-AAA
*
42536822 TTATAAAAGTTATAATAAA
1 TTATAAAAATTATAA-AAA
42536841 TTAT----ATTATGAAAAA
1 TTATAAAAATTAT-AAAAA
42536856 TT-TAAAAATATATAAAAA
1 TTATAAAAAT-TATAAAAA
42536874 TTATAAAAA
1 TTATAAAAA
42536883 AGTCATTTAT
Statistics
Matches: 197, Mismatches: 33, Indels: 53
0.70 0.12 0.19
Matches are distributed among these distances:
14 1 0.01
15 9 0.05
16 2 0.01
18 43 0.22
19 76 0.39
20 33 0.17
21 22 0.11
22 11 0.06
ACGTcount: A:0.59, C:0.03, G:0.04, T:0.34
Consensus pattern (18 bp):
TTATAAAAATTATAAAAA
Done.