Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015267.1 Kokia drynarioides strain JFW-HI SEQ_130312, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 275530
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 225 characters in sequence are not A, C, G, or T
Found at i:1074 original size:19 final size:19
Alignment explanation
Indices: 1050--1088 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
1040 TAAACACGAG
*
1050 ATAGTCCACTGAGATAATA
1 ATAGTCCACTGAGACAATA
1069 ATAGTCCACTGAGACAATA
1 ATAGTCCACTGAGACAATA
1088 A
1 A
1089 ACACGGGGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.44, C:0.18, G:0.15, T:0.23
Consensus pattern (19 bp):
ATAGTCCACTGAGACAATA
Found at i:4194 original size:22 final size:19
Alignment explanation
Indices: 4164--4207 Score: 61
Period size: 22 Copynumber: 2.2 Consensus size: 19
4154 TCTTTCATGA
4164 TTAACTTAATTAATCACTTAT
1 TTAACTTAATTAATC-C-TAT
4185 TTAACCTTAATTAATCCTAT
1 TTAA-CTTAATTAATCCTAT
4205 TTA
1 TTA
4208 TAATCAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 6 0.27
21 5 0.23
22 11 0.50
ACGTcount: A:0.36, C:0.16, G:0.00, T:0.48
Consensus pattern (19 bp):
TTAACTTAATTAATCCTAT
Found at i:4608 original size:35 final size:35
Alignment explanation
Indices: 4557--4627 Score: 124
Period size: 35 Copynumber: 2.0 Consensus size: 35
4547 AAGAGTCTGC
*
4557 CACAGACTAAATAGTTTGAGAATACTCACTAAGAA
1 CACAGACTAAATAGTTTGAGAATACTCACCAAGAA
*
4592 CACATACTAAATAGTTTGAGAATACTCACCAAGAA
1 CACAGACTAAATAGTTTGAGAATACTCACCAAGAA
4627 C
1 C
4628 CTTTAAGAGG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.45, C:0.20, G:0.13, T:0.23
Consensus pattern (35 bp):
CACAGACTAAATAGTTTGAGAATACTCACCAAGAA
Found at i:20295 original size:17 final size:17
Alignment explanation
Indices: 20273--20305 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
20263 CAATATAATA
20273 ATAATAAATAATATATG
1 ATAATAAATAATATATG
*
20290 ATAATAATTAATATAT
1 ATAATAAATAATATAT
20306 TATGTATTAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (17 bp):
ATAATAAATAATATATG
Found at i:20309 original size:20 final size:20
Alignment explanation
Indices: 20265--20302 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
20255 ATTTTAACCA
*
20265 ATATAATAATAATAAATAAT
1 ATATGATAATAATAAATAAT
*
20285 ATATGATAATAATTAATA
1 ATATGATAATAATAAATA
20303 TATTATGTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (20 bp):
ATATGATAATAATAAATAAT
Found at i:23825 original size:29 final size:29
Alignment explanation
Indices: 23783--23841 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
23773 GCCACATGAG
23783 CGTGTGGGTCACACGAATTTATGTTAGAT
1 CGTGTGGGTCACACGAATTTATGTTAGAT
23812 CGTGTGGGTCACACGAATTTATGTTAGAT
1 CGTGTGGGTCACACGAATTTATGTTAGAT
23841 C
1 C
23842 ATGTAAGCCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.15, G:0.27, T:0.34
Consensus pattern (29 bp):
CGTGTGGGTCACACGAATTTATGTTAGAT
Found at i:23853 original size:29 final size:29
Alignment explanation
Indices: 23792--23855 Score: 92
Period size: 29 Copynumber: 2.2 Consensus size: 29
23782 GCGTGTGGGT
* ** *
23792 CACACGAATTTATGTTAGATCGTGTGGGT
1 CACACGAATTTATGTTAGATCATGTAAGC
23821 CACACGAATTTATGTTAGATCATGTAAGC
1 CACACGAATTTATGTTAGATCATGTAAGC
23850 CACACG
1 CACACG
23856 GGCTGAGTCA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.30
Consensus pattern (29 bp):
CACACGAATTTATGTTAGATCATGTAAGC
Found at i:29443 original size:14 final size:13
Alignment explanation
Indices: 29424--29455 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 13
29414 CAAATAAAAG
29424 AAAAATTAAAATGT
1 AAAAATTAAAAT-T
29438 AAAAATTAAAATT
1 AAAAATTAAAATT
29451 AAAAA
1 AAAAA
29456 CAAAAATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 6 0.33
14 12 0.67
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (13 bp):
AAAAATTAAAATT
Found at i:29461 original size:20 final size:20
Alignment explanation
Indices: 29438--29480 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
29428 ATTAAAATGT
29438 AAAA-ATTAAAATTAAAAACA
1 AAAATATTAAAA-TAAAAACA
*
29458 AAAATATTAAAATAAAAATA
1 AAAATATTAAAATAAAAACA
29478 AAA
1 AAA
29481 TGACTAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 14 0.67
21 7 0.33
ACGTcount: A:0.77, C:0.02, G:0.00, T:0.21
Consensus pattern (20 bp):
AAAATATTAAAATAAAAACA
Found at i:32973 original size:60 final size:60
Alignment explanation
Indices: 32880--33003 Score: 158
Period size: 60 Copynumber: 2.1 Consensus size: 60
32870 GGGATACCTA
* * * *
32880 GGCTGAGCACAAGGGCATGTGAATATACAATTTTGCATTTACAGGTGCATTGGTCACATG
1 GGCTGAGCACAAGGGCATGTGAATATACAATTTTGCAATTACAAGTGCAGTGGTCACACG
* * * * * *
32940 GGCTGGGCACACGGGCGTTTGAATATACTATTTTGCAATTACAAGTGTAGTGGTCACACG
1 GGCTGAGCACAAGGGCATGTGAATATACAATTTTGCAATTACAAGTGCAGTGGTCACACG
33000 GGCT
1 GGCT
33004 ATACACACGA
Statistics
Matches: 54, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
60 54 1.00
ACGTcount: A:0.26, C:0.18, G:0.28, T:0.28
Consensus pattern (60 bp):
GGCTGAGCACAAGGGCATGTGAATATACAATTTTGCAATTACAAGTGCAGTGGTCACACG
Found at i:37244 original size:28 final size:28
Alignment explanation
Indices: 37213--37275 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 28
37203 GAAATGTGAT
** *
37213 TTTTGGATGCTCGGGGG-TAAATCGATAA
1 TTTTGGACACTCGGGGGCAAAAT-GATAA
*
37241 TTTTGGACATTCGGGGGCAAAATGATAA
1 TTTTGGACACTCGGGGGCAAAATGATAA
37269 TTTTGGA
1 TTTTGGA
37276 AGGTTCGAGG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 26 0.87
29 4 0.13
ACGTcount: A:0.27, C:0.10, G:0.30, T:0.33
Consensus pattern (28 bp):
TTTTGGACACTCGGGGGCAAAATGATAA
Found at i:37366 original size:59 final size:57
Alignment explanation
Indices: 37259--37496 Score: 198
Period size: 59 Copynumber: 4.1 Consensus size: 57
37249 ATTCGGGGGC
* * * *
37259 AAAATGATAATTTTGGAAG-GTTC-GAGGTCAAAACTAAAATTTTTAGACATCTCGAGGT
1 AAAATGGTAATTTT-GAAGAGTTCAGA-GTTAAAAATAAAATTTTTAGACAT-TAGAGGT
* * *
37317 AAAATGGTAATTTCTGAAGAGTTTAGAATTAAAAATAAAATTTTTAGACATTTAGGGGT
1 AAAATGGTAATTT-TGAAGAGTTCAGAGTTAAAAATAAAATTTTTAGACA-TTAGAGGT
* * * * ** *
37376 AATATAGTAAATTTTGAA-AGGTTCAGGGTTAGAAATGGAATTTTTAGACATTTGAGGGT
1 AAAATGGT-AATTTTGAAGA-GTTCAGAGTTAAAAATAAAATTTTTAGACATTAGA-GGT
* *
37435 AAAATGGTAATTTTGGAATGA-TTCA-AGGTTAAAAATAGAATTTTTAGACATTAGGGGT
1 AAAATGGTAATTTT-GAA-GAGTTCAGA-GTTAAAAATAAAATTTTTAGACATTAGAGGT
37493 AAAA
1 AAAA
37497 AAAGTATTTT
Statistics
Matches: 145, Mismatches: 24, Indels: 22
0.76 0.13 0.12
Matches are distributed among these distances:
58 33 0.23
59 103 0.71
60 8 0.06
61 1 0.01
ACGTcount: A:0.40, C:0.05, G:0.21, T:0.34
Consensus pattern (57 bp):
AAAATGGTAATTTTGAAGAGTTCAGAGTTAAAAATAAAATTTTTAGACATTAGAGGT
Found at i:37446 original size:29 final size:30
Alignment explanation
Indices: 37408--37821 Score: 194
Period size: 30 Copynumber: 14.1 Consensus size: 30
37398 TCAGGGTTAG
*
37408 AAATGG-AATTTTTAGACATTTGAGGGT-A
1 AAATGGTAATTTTTAGAAATTTGAGGGTAA
* ** *
37436 AAATGGTAA-TTTTGGAATGATTCAAGGTTAA
1 AAATGGTAATTTTTAGAA--ATTTGAGGGTAA
* * *
37467 AAATAG-AATTTTTAGACATTAG-GGGTAA
1 AAATGGTAATTTTTAGAAATTTGAGGGTAA
** *
37495 AAAAAGTATTTTTTAGAAAATTTG-GGGTCAA
1 AAATGGTAATTTTTAG-AAATTTGAGGGT-AA
* * **
37526 AAATAG-AA-TTTTGGAAAGTTCAAGGGTAA
1 AAATGGTAATTTTTAGAAA-TTTGAGGGTAA
* * *
37555 AAAT-GTAATTTTT-GTAAAATTCAAGGTAAA
1 AAATGGTAATTTTTAG-AAATTTGAGGGT-AA
* * *
37585 AAATGG-AATTTTTAGATATTCGGGGGT-A
1 AAATGGTAATTTTTAGAAATTTGAGGGTAA
* * * *
37613 AAATGGTAA-TTTTGGAAGGATTCG-TGGTTA
1 AAATGGTAATTTTTAGAA--ATTTGAGGGTAA
*
37643 AAATGG-AATTTTTAGACATTT-AGGGGT-A
1 AAATGGTAATTTTTAGAAATTTGA-GGGTAA
* *
37671 AAATGGTAATTTTTGGAAAATTTGAGGTTAA
1 AAATGGTAATTTTTAG-AAATTTGAGGGTAA
* *
37702 AAATGG-AA-TTTTGGAAAGTTCGAGGGTAA
1 AAATGGTAATTTTTAGAAA-TTTGAGGGTAA
*
37731 AAAT-GTAATTTTTGGAAAATTT-AGGGTCAA
1 AAATGGTAATTTTTAG-AAATTTGAGGGT-AA
* *
37761 AAATGG-AA-TTTTGGAAAGTTTAAGGGTAA
1 AAATGGTAATTTTTAGAAA-TTTGAGGGTAA
* *
37790 CAAT-GTAATTTTTATAAATTTTG-GGGTAA
1 AAATGGTAATTTTTAGAAA-TTTGAGGGTAA
37819 AAA
1 AAA
37822 CAAAATTTTG
Statistics
Matches: 300, Mismatches: 49, Indels: 73
0.71 0.12 0.17
Matches are distributed among these distances:
28 57 0.19
29 102 0.34
30 108 0.36
31 33 0.11
ACGTcount: A:0.39, C:0.03, G:0.23, T:0.35
Consensus pattern (30 bp):
AAATGGTAATTTTTAGAAATTTGAGGGTAA
Found at i:37477 original size:88 final size:88
Alignment explanation
Indices: 37385--37801 Score: 313
Period size: 88 Copynumber: 4.7 Consensus size: 88
37375 TAATATAGTA
** * * *
37385 AATTTTGAAAGGTTCAGGGTTAGAAATGGAATTTTTAG-ACATTTGAGGGT-AAAATGGTAATTT
1 AATTTTGAAACATTCAGGGTAAAAAATGGAATTTTTAGAAAATTTGAGGGTAAAAATGG-AATTT
* *
37448 TGGAATGATTCAAGGTTAAAAATAG-
65 TGGAAAG-TTCAAGGGTAAAAAT-GT
* * * * * *
37473 AATTTTTAGACATT-AGGGGTAAAAAAAGTATTTTTTAGAAAATTTG-GGGTCAAAAATAGAATT
1 AATTTTGAAACATTCA-GGGTAAAAAATGGAATTTTTAGAAAATTTGAGGGT-AAAAATGGAATT
37536 TTGGAAAGTTCAAGGGTAAAAATGT
64 TTGGAAAGTTCAAGGGTAAAAATGT
* * * *
37561 AATTTTTGTAAA-ATTCAAGGTAAAAAATGGAATTTTTAG-ATATTCGGGGGT-AAAATGGTAAT
1 AA-TTTTG-AAACATTCAGGGTAAAAAATGGAATTTTTAGAAAATTTGAGGGTAAAAATGG-AAT
* * *
37623 TTTGGAAGGATTC--GTGGTTAAAATGG
63 TTTGGAAAG-TTCAAG-GGTAAAAATGT
* * * * *
37649 AATTTTTAGACATTTAGGGGT--AAAATGGTAATTTTTGGAAAATTTGAGGTTAAAAATGGAATT
1 AATTTTGAAACATTCA-GGGTAAAAAATGG-AATTTTTAGAAAATTTGAGGGTAAAAATGGAATT
*
37712 TTGGAAAGTTCGAGGGTAAAAATGT
64 TTGGAAAGTTCAAGGGTAAAAATGT
* * * * * * *
37737 AATTTTTGGAAA-ATTTAGGGTCAAAAATGGAA-TTTTGGAAAGTTTAAGGGTAACAATGTAATT
1 AA-TTTT-GAAACATTCAGGGTAAAAAATGGAATTTTTAGAAAATTTGAGGGTAAAAATGGAATT
37800 TT
64 TT
37802 TATAAATTTT
Statistics
Matches: 262, Mismatches: 44, Indels: 46
0.74 0.12 0.13
Matches are distributed among these distances:
86 9 0.03
87 28 0.11
88 139 0.53
89 68 0.26
90 18 0.07
ACGTcount: A:0.38, C:0.03, G:0.24, T:0.35
Consensus pattern (88 bp):
AATTTTGAAACATTCAGGGTAAAAAATGGAATTTTTAGAAAATTTGAGGGTAAAAATGGAATTTT
GGAAAGTTCAAGGGTAAAAATGT
Found at i:37477 original size:118 final size:116
Alignment explanation
Indices: 37267--37713 Score: 372
Period size: 118 Copynumber: 3.8 Consensus size: 116
37257 GCAAAATGAT
* * ** *
37267 AATTTTGGAAGGTTCGAGGTCAAAACTAAAATTTTTAGACATCTCGA-GGTAAAATGGTAATTTC
1 AATTTTGAAAGGTTCG-GGTTAAAA-TGGAATTTTTAGACAT-TCGAGGGTAAAATGGTAATTTT
* * * * *
37331 T-GAAGAGTT-TAGAATTAAAAATAAAATTTTTAGACATTTAGGGGTAATATAGTA
63 TGGAA-AATTCAAG-GTTAAAAATAGAATTTTTAGACATTTAGGGGTAAAATAGTA
*
37385 AATTTTGAAAGGTTCAGGGTTAGAAATGGAATTTTTAGACATTTGAGGGTAAAATGGTAA-TTTT
1 AATTTTGAAAGGTTC-GGGTTA-AAATGGAATTTTTAGACATTCGAGGGTAAAATGGTAATTTTT
* *
37449 GGAATGATTCAAGGTTAAAAATAGAATTTTTAGACA-TTAGGGGTAAAAAAAGTA
64 GGAA-AATTCAAGGTTAAAAATAGAATTTTTAGACATTTAGGGGT-AAAATAGTA
** ** * * * * * *
37503 TTTTTTAGAAAATTTGGGGTCAAAAATAGAA-TTTTGGAAAGTTCAAGGGTAAAAAT-GTAATTT
1 AATTTT-GAAAGGTTCGGGT-TAAAATGGAATTTTTAGACA-TTCGAGGGT-AAAATGGTAATTT
* * * * ** *
37566 TTGTAAAATTCAAGGTAAAAAATGGAATTTTTAGATATTCGGGGGTAAAATGGT-
62 TTGGAAAATTCAAGGTTAAAAATAGAATTTTTAGACATTTAGGGGTAAAATAGTA
* *
37620 AATTTTGGAAGGATTCGTGGTTAAAATGGAATTTTTAGACATT-TAGGGGTAAAATGGTAATTTT
1 AATTTTGAAAGG-TTCG-GGTTAAAATGGAATTTTTAGACATTCGA-GGGTAAAATGGTAATTTT
** *
37684 TGGAAAATTTGAGGTTAAAAATGGAATTTT
63 TGGAAAATTCAAGGTTAAAAATAGAATTTT
37714 GGAAAGTTCG
Statistics
Matches: 263, Mismatches: 49, Indels: 35
0.76 0.14 0.10
Matches are distributed among these distances:
116 9 0.03
117 76 0.29
118 147 0.56
119 31 0.12
ACGTcount: A:0.39, C:0.04, G:0.22, T:0.35
Consensus pattern (116 bp):
AATTTTGAAAGGTTCGGGTTAAAATGGAATTTTTAGACATTCGAGGGTAAAATGGTAATTTTTGG
AAAATTCAAGGTTAAAAATAGAATTTTTAGACATTTAGGGGTAAAATAGTA
Found at i:37528 original size:59 final size:59
Alignment explanation
Indices: 37408--37802 Score: 288
Period size: 59 Copynumber: 6.7 Consensus size: 59
37398 TCAGGGTTAG
* * * * ** *
37408 AAATGGAATTTTTAGACA-TTTGAGGGTAAAATGGTAA-TTTTGGAATGATTCAAGGTTAA
1 AAATGGAATTTTTAGAAAGTTAG-GGGTAAAAAGGTAATTTTTGGAA-AATTTGAGGTCAA
* * * * * *
37467 AAATAGAATTTTTAGACA-TTAGGGGTAAAAAAAGTATTTTTTAGAAAATTTGGGGTCAA
1 AAATGGAATTTTTAGAAAGTTAGGGGT-AAAAAGGTAATTTTTGGAAAATTTGAGGTCAA
* * * * * ** *
37526 AAATAGAA-TTTTGGAAAGTTCAAGGGTAAAAATGTAATTTTTGTAAAATTCAAGGTAAA
1 AAATGGAATTTTTAGAAAGTT-AGGGGTAAAAAGGTAATTTTTGGAAAATTTGAGGTCAA
* * * * * * *
37585 AAATGGAATTTTTAGATA-TTCGGGGGTAAAATGGTAA-TTTTGGAAGGATTCGTGGT-TA
1 AAATGGAATTTTTAGAAAGTT-AGGGGTAAAAAGGTAATTTTTGGAA-AATTTGAGGTCAA
* * * *
37643 AAATGGAATTTTTAGACATTTAGGGGTAAAATGGTAATTTTTGGAAAATTTGAGGTTAA
1 AAATGGAATTTTTAGAAAGTTAGGGGTAAAAAGGTAATTTTTGGAAAATTTGAGGTCAA
* * *
37702 AAATGGAA-TTTTGGAAAGTTCGAGGGTAAAAATGTAATTTTTGGAAAATTT-AGGGTCAA
1 AAATGGAATTTTTAGAAAGTTAG-GGGTAAAAAGGTAATTTTTGGAAAATTTGA-GGTCAA
* * * *
37761 AAATGGAA-TTTTGGAAAGTTTAAGGGTAACAATGTAATTTTT
1 AAATGGAATTTTTAGAAAG-TTAGGGGTAAAAAGGTAATTTTT
37803 ATAAATTTTG
Statistics
Matches: 274, Mismatches: 50, Indels: 24
0.79 0.14 0.07
Matches are distributed among these distances:
58 69 0.25
59 184 0.67
60 21 0.08
ACGTcount: A:0.39, C:0.03, G:0.23, T:0.35
Consensus pattern (59 bp):
AAATGGAATTTTTAGAAAGTTAGGGGTAAAAAGGTAATTTTTGGAAAATTTGAGGTCAA
Found at i:37636 original size:30 final size:30
Alignment explanation
Indices: 37602--37801 Score: 93
Period size: 29 Copynumber: 6.8 Consensus size: 30
37592 ATTTTTAGAT
*
37602 ATTCGGGGGTAAAATGGTAATTTTGGAAGG
1 ATTCGAGGGTAAAATGGTAATTTTGGAAGG
* * * *
37632 ATTCGTGGTTAAAATGG-AATTTT--TAGAC
1 ATTCGAGGGTAAAATGGTAATTTTGGAAG-G
* *
37660 ATT-TAGGGGTAAAATGGTAATTTTTGGAA-A
1 ATTCGA-GGGTAAAATGGTAA-TTTTGGAAGG
* * *
37690 ATTTGAGGTTAAAAATGG-AATTTTGGAAAG
1 ATTCGAGGGT-AAAATGGTAATTTTGGAAGG
*
37720 -TTCGAGGGTAAAAAT-GTAATTTTTGGAA-A
1 ATTCGAGGGT-AAAATGGTAA-TTTTGGAAGG
* *
37749 ATT-TAGGGTCAAAAATGG-AATTTTGGAAAG
1 ATTCGAGGGT--AAAATGGTAATTTTGGAAGG
**
37779 -TTTAAGGGTAACAAT-GTAATTTT
1 ATTCGAGGGTAA-AATGGTAATTTT
37802 TATAAATTTT
Statistics
Matches: 134, Mismatches: 18, Indels: 37
0.71 0.10 0.20
Matches are distributed among these distances:
27 2 0.01
28 17 0.13
29 55 0.41
30 50 0.37
31 9 0.07
32 1 0.01
ACGTcount: A:0.36, C:0.03, G:0.26, T:0.35
Consensus pattern (30 bp):
ATTCGAGGGTAAAATGGTAATTTTGGAAGG
Found at i:37838 original size:59 final size:59
Alignment explanation
Indices: 37489--37841 Score: 175
Period size: 59 Copynumber: 6.0 Consensus size: 59
37479 TAGACATTAG
* * * * * *
37489 GGGTAAAAAAAGTATTTTTTAGAAAATTTGGGGTCAAAAATAGAATTTTGGAAAGTTCAA
1 GGGT-AAAAATGTAATTTTTAGAAAATTTAGGGTCAAAAACAAAATTTTGGAAAGTTTAA
* * * ** * * * ***
37549 GGGTAAAAATGTAATTTTT-GTAAAATTCAAGGTAAAAAATGGAATTTTTAGATA-TTCGG
1 GGGTAAAAATGTAATTTTTAG-AAAATTTAGGGTCAAAAA-CAAAATTTTGGAAAGTTTAA
* * * * *** * * * *
37608 GGGT-AAAATGGTAA-TTTTGGAAGGA-TTCGTGGTTAAAATGGAATTTTTAGACA-TTTAG
1 GGGTAAAAAT-GTAATTTTTAGAA-AATTTAG-GGTCAAAAACAAAATTTTGGAAAGTTTAA
* * *** **
37666 GGGT-AAAATGGTAATTTTTGGAAAATTT-GAGGTTAAAAATGGAATTTTGGAAAGTTCGA
1 GGGTAAAAAT-GTAATTTTTAGAAAATTTAG-GGTCAAAAACAAAATTTTGGAAAGTTTAA
* ***
37725 GGGTAAAAATGTAATTTTTGGAAAATTTAGGGTCAAAAATGGAATTTTGGAAAGTTTAA
1 GGGTAAAAATGTAATTTTTAGAAAATTTAGGGTCAAAAACAAAATTTTGGAAAGTTTAA
* * * *
37784 GGGTAACAATGTAATTTTTATAAATTTTGGGGT-AAAAACAAAATTTTGGAAAAGTTTA
1 GGGTAAAAATGTAATTTTTAGAAAATTTAGGGTCAAAAACAAAATTTTGG-AAAGTTTA
37842 GGAGTTAAAA
Statistics
Matches: 236, Mismatches: 45, Indels: 25
0.77 0.15 0.08
Matches are distributed among these distances:
58 75 0.32
59 143 0.61
60 18 0.08
ACGTcount: A:0.39, C:0.03, G:0.23, T:0.35
Consensus pattern (59 bp):
GGGTAAAAATGTAATTTTTAGAAAATTTAGGGTCAAAAACAAAATTTTGGAAAGTTTAA
Found at i:39069 original size:19 final size:20
Alignment explanation
Indices: 39049--39099 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
39039 ACTAATATTA
39049 TTATTATTATCAAAAAATAT
1 TTATTATTATCAAAAAATAT
* *
39069 TTATTATTAT-TAAAATTAT
1 TTATTATTATCAAAAAATAT
39088 TTATTATTATCA
1 TTATTATTATCA
39100 CCATTATTGA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
19 17 0.63
20 10 0.37
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (20 bp):
TTATTATTATCAAAAAATAT
Found at i:39818 original size:17 final size:17
Alignment explanation
Indices: 39803--39898 Score: 84
Period size: 17 Copynumber: 5.5 Consensus size: 17
39793 TTAAAATTTT
39803 ATTTCAAAATAAATTTAA
1 ATTT-AAAATAAATTTAA
39821 ATTTAAAATAAATTTAA
1 ATTTAAAATAAATTTAA
* ** *
39838 ACTCCAAATAAGTCTTAA
1 ATTTAAAATAAAT-TTAA
*
39856 ATTTACAATAAATTTAA
1 ATTTAAAATAAATTTAA
* * * *
39873 ACTTGAAATGAATTAAA
1 ATTTAAAATAAATTTAA
*
39890 ATCTAAAAT
1 ATTTAAAAT
39899 TTTGATCCAA
Statistics
Matches: 60, Mismatches: 17, Indels: 3
0.75 0.21 0.04
Matches are distributed among these distances:
17 44 0.73
18 16 0.27
ACGTcount: A:0.53, C:0.08, G:0.03, T:0.35
Consensus pattern (17 bp):
ATTTAAAATAAATTTAA
Found at i:39866 original size:35 final size:34
Alignment explanation
Indices: 39809--39898 Score: 108
Period size: 35 Copynumber: 2.6 Consensus size: 34
39799 TTTTATTTCA
39809 AAATAAATTTAAATTTAAAATAAATTTAAACTCC
1 AAATAAATTTAAATTTAAAATAAATTTAAACTCC
* * **
39843 AAATAAGTCTTAAATTTACAATAAATTTAAACTTG
1 AAATAAAT-TTAAATTTAAAATAAATTTAAACTCC
* * *
39878 AAATGAATTAAAATCTAAAAT
1 AAATAAATTTAAATTTAAAAT
39899 TTTGATCCAA
Statistics
Matches: 46, Mismatches: 9, Indels: 2
0.81 0.16 0.04
Matches are distributed among these distances:
34 17 0.37
35 29 0.63
ACGTcount: A:0.54, C:0.08, G:0.03, T:0.34
Consensus pattern (34 bp):
AAATAAATTTAAATTTAAAATAAATTTAAACTCC
Found at i:40401 original size:49 final size:49
Alignment explanation
Indices: 40329--40685 Score: 350
Period size: 49 Copynumber: 7.3 Consensus size: 49
40319 TGGCCTAAAT
* * * *
40329 TTTCCTTTCATG-CTTCTAGGGTACTAGGTTCGCCATTGCAACTTAAACC
1 TTTCCCTTCATGTCTTCGA-GGTACTAGGTTCGCCGTTGCGACTTAAACC
** * * **
40378 TTTCCCTTTGTGTCTTCGTGGTACT-GGATTCGCCGTTGCGGCTTAAGTC
1 TTTCCCTTCATGTCTTCGAGGTACTAGG-TTCGCCGTTGCGACTTAAACC
* *
40427 TTTCCCTTCATGTC-TCTGAGGTACAAGGTTCGCCATTGCGACTTAAACC
1 TTTCCCTTCATGTCTTC-GAGGTACTAGGTTCGCCGTTGCGACTTAAACC
** * * *
40476 TTTCCCTTTGTGTCTTCGTGGTACT-GGATTCGCCGTTGCGGCTTAAATC
1 TTTCCCTTCATGTCTTCGAGGTACTAGG-TTCGCCGTTGCGACTTAAACC
* *
40525 TTTCCCTTCATGTC-TCTGAGGTACAAGGTTCGCCATTGCGACTTAAACC
1 TTTCCCTTCATGTCTTC-GAGGTACTAGGTTCGCCGTTGCGACTTAAACC
** * *
40574 TTTCCCTTTTGTGTCTTCGAGGTACTAGATTCGCCGTTGC-AGCTTAAATC
1 TTTCCC-TTCATGTCTTCGAGGTACTAGGTTCGCCGTTGCGA-CTTAAACC
* * *
40624 TTTCCCTTCATG-CTTTTGAGGTACAAGGTTCGCCGTTACGACTTAAACC
1 TTTCCCTTCATGTC-TTCGAGGTACTAGGTTCGCCGTTGCGACTTAAACC
*
40673 TTTCCCTCCATGT
1 TTTCCCTTCATGT
40686 TTCACGGTAT
Statistics
Matches: 248, Mismatches: 46, Indels: 27
0.77 0.14 0.08
Matches are distributed among these distances:
48 9 0.04
49 188 0.76
50 49 0.20
51 2 0.01
ACGTcount: A:0.16, C:0.27, G:0.20, T:0.37
Consensus pattern (49 bp):
TTTCCCTTCATGTCTTCGAGGTACTAGGTTCGCCGTTGCGACTTAAACC
Found at i:40647 original size:99 final size:98
Alignment explanation
Indices: 40308--40679 Score: 572
Period size: 98 Copynumber: 3.8 Consensus size: 98
40298 ATGGTAGTAA
* * * * *
40308 ATTCGCCGTTGTGGCCTAAAT-TTTCCTTTCATG-CTTCT-AGGGTACTAGGTTCGCCATTGCAA
1 ATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTC-TCTGA-GGTACAAGGTTCGCCATTGCGA
40370 CTTAAACCTTTCCCTTTGTGTCTTCGTGGTACTGG
64 CTTAAACCTTTCCCTTTGTGTCTTCGTGGTACTGG
*
40405 ATTCGCCGTTGCGGCTTAAGTCTTTCCCTTCATGTCTCTGAGGTACAAGGTTCGCCATTGCGACT
1 ATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTCTGAGGTACAAGGTTCGCCATTGCGACT
40470 TAAACCTTTCCCTTTGTGTCTTCGTGGTACTGG
66 TAAACCTTTCCCTTTGTGTCTTCGTGGTACTGG
40503 ATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTCTGAGGTACAAGGTTCGCCATTGCGACT
1 ATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTCTGAGGTACAAGGTTCGCCATTGCGACT
* *
40568 TAAACCTTTCCCTTTTGTGTCTTCGAGGTACTAG
66 TAAACCTTTCCC-TTTGTGTCTTCGTGGTACTGG
* * * *
40602 ATTCGCCGTTGCAGCTTAAATCTTTCCCTTCATG-CTTTTGAGGTACAAGGTTCGCCGTTACGAC
1 ATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTC-TCTGAGGTACAAGGTTCGCCATTGCGAC
40666 TTAAACCTTTCCCT
65 TTAAACCTTTCCCT
40680 CCATGTTTCA
Statistics
Matches: 257, Mismatches: 13, Indels: 9
0.92 0.05 0.03
Matches are distributed among these distances:
97 18 0.07
98 147 0.57
99 92 0.36
ACGTcount: A:0.16, C:0.26, G:0.20, T:0.37
Consensus pattern (98 bp):
ATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTCTGAGGTACAAGGTTCGCCATTGCGACT
TAAACCTTTCCCTTTGTGTCTTCGTGGTACTGG
Found at i:45415 original size:16 final size:16
Alignment explanation
Indices: 45394--45431 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
45384 TTTGGCTTGT
45394 ATCCCAACCTAAAATG
1 ATCCCAACCTAAAATG
45410 ATCCCAACCTAAAATG
1 ATCCCAACCTAAAATG
45426 ATCCCA
1 ATCCCA
45432 TTTTCCTAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.42, C:0.34, G:0.05, T:0.18
Consensus pattern (16 bp):
ATCCCAACCTAAAATG
Found at i:52651 original size:59 final size:57
Alignment explanation
Indices: 52533--52690 Score: 178
Period size: 59 Copynumber: 2.7 Consensus size: 57
52523 AAATCGATAA
** *
52533 TTTTAGACATCAAGGGTAAAATGGTAATTTTGGAAGGTTCAAGGTCAAAAATAGGAT
1 TTTTAGACATCCGGGGTAAAATGGTAATTTTGGAAGGTTCAAAGTCAAAAATAGGAT
* *
52590 TTTTAGACATCTCGGGGTAAAATGGTAATTTTTGG-AGAGTTCAAAATTC-AAAA-CGGAAT
1 TTTTAGACATC-CGGGGTAAAATGGTAA-TTTTGGAAG-GTTC-AAAGTCAAAAATAGG-AT
*
52649 TTTTAGACATCCGGGGGTAAAATGGCAAATTTTGGAAGGTTC
1 TTTTAGACATCC-GGGGTAAAATGG-TAATTTTGGAAGGTTC
52691 GGGGTGTAAA
Statistics
Matches: 87, Mismatches: 6, Indels: 14
0.81 0.06 0.13
Matches are distributed among these distances:
57 11 0.13
58 19 0.22
59 49 0.56
60 8 0.09
ACGTcount: A:0.35, C:0.09, G:0.25, T:0.31
Consensus pattern (57 bp):
TTTTAGACATCCGGGGTAAAATGGTAATTTTGGAAGGTTCAAAGTCAAAAATAGGAT
Found at i:52705 original size:23 final size:23
Alignment explanation
Indices: 52675--52718 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
52665 GTAAAATGGC
*
52675 AAATTTTGGAAGGTTCGGGGTGT
1 AAATTTTGAAAGGTTCGGGGTGT
52698 AAATTTTGAAAGGTTCGGGGT
1 AAATTTTGAAAGGTTCGGGGT
52719 TAGAAATGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.25, C:0.05, G:0.36, T:0.34
Consensus pattern (23 bp):
AAATTTTGAAAGGTTCGGGGTGT
Found at i:52836 original size:30 final size:28
Alignment explanation
Indices: 52801--52899 Score: 94
Period size: 28 Copynumber: 3.5 Consensus size: 28
52791 TTTAAACATT
* *
52801 AAAATGGTAATTTTGGAAATTTTGGGGTAA
1 AAAATGG-AATTTTGGAAAGTTTAGGG-AA
52831 AAAATGGAATTTTGGAAAGTTTAGGGAA
1 AAAATGGAATTTTGGAAAGTTTAGGGAA
* * **
52859 AAATAT--AATTTTTGGAAAATTCAGGTCA
1 AAA-ATGGAA-TTTTGGAAAGTTTAGGGAA
52887 AAAATGGAATTTT
1 AAAATGGAATTTT
52900 TAGATATCCA
Statistics
Matches: 59, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
27 4 0.07
28 27 0.46
29 21 0.36
30 7 0.12
ACGTcount: A:0.41, C:0.02, G:0.22, T:0.34
Consensus pattern (28 bp):
AAAATGGAATTTTGGAAAGTTTAGGGAA
Found at i:52841 original size:29 final size:28
Alignment explanation
Indices: 52801--52899 Score: 89
Period size: 29 Copynumber: 3.5 Consensus size: 28
52791 TTTAAACATT
*
52801 AAAATGGTAATTTTGGAAATTTTGGGGTAA
1 AAAATGG-AATTTTGGAAA-TTTAGGGTAA
52831 AAAATGGAATTTTGGAAAGTTTAGGG-AA
1 AAAATGGAATTTTGGAAA-TTTAGGGTAA
* *
52859 AAATAT--AATTTTTGGAAAATTCA-GGTCA
1 AAA-ATGGAA-TTTTGG-AAATTTAGGGTAA
52887 AAAATGGAATTTT
1 AAAATGGAATTTT
52900 TAGATATCCA
Statistics
Matches: 59, Mismatches: 4, Indels: 14
0.77 0.05 0.18
Matches are distributed among these distances:
27 6 0.10
28 22 0.37
29 24 0.41
30 7 0.12
ACGTcount: A:0.41, C:0.02, G:0.22, T:0.34
Consensus pattern (28 bp):
AAAATGGAATTTTGGAAATTTAGGGTAA
Found at i:52943 original size:29 final size:30
Alignment explanation
Indices: 52911--52989 Score: 92
Period size: 29 Copynumber: 2.7 Consensus size: 30
52901 AGATATCCAA
*
52911 GGGTAAAATGGTAATTTTTGA-AGGATTCGG
1 GGGTAAAATGGTAATTTTTGAGA-CATTCGG
* *
52941 GGTTAAAACGG-AATTTTT-AGACATTCGGG
1 GGGTAAAATGGTAATTTTTGAGACATTC-GG
52970 GGGTAAAATGGTAATTTTTG
1 GGGTAAAATGGTAATTTTTG
52990 GAAAATTTAA
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
28 5 0.12
29 19 0.47
30 16 0.40
ACGTcount: A:0.30, C:0.05, G:0.30, T:0.34
Consensus pattern (30 bp):
GGGTAAAATGGTAATTTTTGAGACATTCGG
Found at i:53008 original size:30 final size:28
Alignment explanation
Indices: 52971--53102 Score: 88
Period size: 29 Copynumber: 4.6 Consensus size: 28
52961 ACATTCGGGG
52971 GGTAAAATGGTAATTTTTGGAAAATTTAA
1 GGTAAAATGG-AATTTTTGGAAAATTTAA
* * **
53000 GGTCAAAATGGAA-TTTGGGAAAGTTCTGT
1 GGT-AAAATGGAATTTTTGGAAAATT-TAA
* ** *
53029 GGTAAAATGTAATTCATGGAAAATTTAG
1 GGTAAAATGGAATTTTTGGAAAATTTAA
* * *
53057 GGTTAAAAATGGAA-TTTTAGAAAGTTTAGG
1 GG-T-AAAATGGAATTTTTGGAAAATTTA-A
*
53087 GGTAAAATGTAATTTT
1 GGTAAAATGGAATTTT
53103 CAAAAAGTTA
Statistics
Matches: 79, Mismatches: 17, Indels: 14
0.72 0.15 0.13
Matches are distributed among these distances:
28 29 0.37
29 32 0.41
30 18 0.23
ACGTcount: A:0.39, C:0.02, G:0.24, T:0.35
Consensus pattern (28 bp):
GGTAAAATGGAATTTTTGGAAAATTTAA
Found at i:53013 original size:59 final size:58
Alignment explanation
Indices: 52864--53015 Score: 164
Period size: 59 Copynumber: 2.6 Consensus size: 58
52854 GGGAAAAATA
* *
52864 TAATTTTTGGAAAA-TTCAGGTCAAAAATGGAATTTTTAGATATCCAAGGGTAAAATGG
1 TAATTTTTGGAAAATTTAAGGTC-AAAATGGAATTTTTAGACATCCAAGGGTAAAATGG
* *** * * ***
52922 TAATTTTT-GAAGGATTCGGGGTTAAAACGGAATTTTTAGACATTCGGGGGGTAAAATGG
1 TAATTTTTGGAA-AATTTAAGGTCAAAATGGAATTTTTAGACA-TCCAAGGGTAAAATGG
52981 TAATTTTTGGAAAATTTAAGGTCAAAATGGAATTT
1 TAATTTTTGGAAAATTTAAGGTCAAAATGGAATTT
53016 GGGAAAGTTC
Statistics
Matches: 74, Mismatches: 16, Indels: 7
0.76 0.16 0.07
Matches are distributed among these distances:
57 3 0.04
58 26 0.35
59 42 0.57
60 3 0.04
ACGTcount: A:0.36, C:0.06, G:0.24, T:0.34
Consensus pattern (58 bp):
TAATTTTTGGAAAATTTAAGGTCAAAATGGAATTTTTAGACATCCAAGGGTAAAATGG
Found at i:53015 original size:29 final size:27
Alignment explanation
Indices: 52971--53143 Score: 103
Period size: 28 Copynumber: 6.0 Consensus size: 27
52961 ACATTCGGGG
52971 GGTAAAATGGTAATTTTTGGAAAATTTAA
1 GGTAAAATGG-AA-TTTTGGAAAATTTAA
* * **
53000 GGTCAAAATGGAATTTGGGAAAGTTCTGT
1 GGT-AAAATGGAATTTTGGAAAATT-TAA
* * *
53029 GGTAAAATGTAATTCATGGAAAATTTAG
1 GGTAAAATGGAATT-TTGGAAAATTTAA
* * *
53057 GGTTAAAAATGGAATTTTAGAAAGTTTAGG
1 GG-T-AAAATGGAATTTTGGAAAATTTA-A
* ** *
53087 GGTAAAATGTAATTTTCAAAAAGTTAGA
1 GGTAAAATGGAATTTTGGAAAATTTA-A
*
53115 GGTCAAAAATGAAATTTTGGAAAAGTTTA
1 GGT--AAAATGGAATTTTGGAAAA-TTTA
53144 GGGGTTAAAA
Statistics
Matches: 111, Mismatches: 24, Indels: 16
0.74 0.16 0.11
Matches are distributed among these distances:
28 45 0.41
29 27 0.24
30 36 0.32
31 3 0.03
ACGTcount: A:0.41, C:0.03, G:0.23, T:0.33
Consensus pattern (27 bp):
GGTAAAATGGAATTTTGGAAAATTTAA
Found at i:53069 original size:58 final size:57
Alignment explanation
Indices: 52969--53154 Score: 171
Period size: 58 Copynumber: 3.2 Consensus size: 57
52959 AGACATTCGG
** * *
52969 GGGGTAAAATGGTAATTTTTGGAAAATTTAAGGTCAAAATGGAATTTGGGAAAGTTCT-
1 GGGGTAAAAT-GTAATTCATGGAAAATTTAAGGTAAAAATGGAATTTGAGAAAGTT-TA
* * *
53027 GTGGTAAAATGTAATTCATGGAAAATTTAGGGTTAAAAATGGAATTTTAGAAAGTTTA
1 GGGGTAAAATGTAATTCATGGAAAATTTAAGG-TAAAAATGGAATTTGAGAAAGTTTA
* ** * *
53085 GGGGTAAAATGTAATT-TTCAAAAAGTTAGAGGTCAAAAATGAAATTTTG-GAAAAGTTTA
1 GGGGTAAAATGTAATTCATGGAAAATTTA-AGGT-AAAAATGGAA-TTTGAG-AAAGTTTA
53144 GGGGTTAAAAT
1 GGGG-TAAAAT
53155 ATGATTTTTG
Statistics
Matches: 106, Mismatches: 15, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
57 29 0.27
58 56 0.53
59 15 0.14
60 6 0.06
ACGTcount: A:0.40, C:0.03, G:0.25, T:0.32
Consensus pattern (57 bp):
GGGGTAAAATGTAATTCATGGAAAATTTAAGGTAAAAATGGAATTTGAGAAAGTTTA
Found at i:53154 original size:30 final size:30
Alignment explanation
Indices: 52968--53176 Score: 125
Period size: 30 Copynumber: 7.1 Consensus size: 30
52958 TAGACATTCG
*
52968 GGGGGTAAAATGGTAATTTTTGGAAAA-TTTA
1 GGGGTTAAAATGG-AA-TTTTGGAAAAGTTTA
* * *
52999 -AGGTCAAAATGGAA-TTTGGGAAAGTTCT-
1 GGGGTTAAAATGGAATTTTGGAAAAGTT-TA
* * *
53027 GTGG-TAAAATGTAATTCATGGAAAA-TTTA
1 GGGGTTAAAATGGAATT-TTGGAAAAGTTTA
*
53056 -GGGTTAAAAATGGAATTTTAG-AAAGTTTA
1 GGGGTT-AAAATGGAATTTTGGAAAAGTTTA
* **
53085 GGGG-TAAAATGTAATTTTCAAAAAG-TTA
1 GGGGTTAAAATGGAATTTTGGAAAAGTTTA
* * *
53113 GAGGTCAAAAATGAAATTTTGGAAAAGTTTA
1 GGGGT-TAAAATGGAATTTTGGAAAAGTTTA
* * *
53144 GGGGTTAAAATATGATTTTTGG-ATAGTTTA
1 GGGGTTAAAAT-GGAATTTTGGAAAAGTTTA
53174 GGG
1 GGG
53177 ACCTCGAAGG
Statistics
Matches: 136, Mismatches: 27, Indels: 31
0.70 0.14 0.16
Matches are distributed among these distances:
27 8 0.06
28 34 0.25
29 20 0.15
30 60 0.44
31 14 0.10
ACGTcount: A:0.38, C:0.02, G:0.26, T:0.33
Consensus pattern (30 bp):
GGGGTTAAAATGGAATTTTGGAAAAGTTTA
Found at i:53966 original size:35 final size:35
Alignment explanation
Indices: 53920--54000 Score: 162
Period size: 35 Copynumber: 2.3 Consensus size: 35
53910 TTTAAAACCC
53920 TTTTCCCTTTTCATTCTTTAAAAGATGATTTTGAT
1 TTTTCCCTTTTCATTCTTTAAAAGATGATTTTGAT
53955 TTTTCCCTTTTCATTCTTTAAAAGATGATTTTGAT
1 TTTTCCCTTTTCATTCTTTAAAAGATGATTTTGAT
53990 TTTTCCCTTTT
1 TTTTCCCTTTT
54001 TTTTAATAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 46 1.00
ACGTcount: A:0.20, C:0.16, G:0.07, T:0.57
Consensus pattern (35 bp):
TTTTCCCTTTTCATTCTTTAAAAGATGATTTTGAT
Found at i:54406 original size:19 final size:21
Alignment explanation
Indices: 54366--54417 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
54356 ACTAATATTA
54366 TTATTATTATCAAAAAAGTAT
1 TTATTATTATCAAAAAAGTAT
*
54387 TTATTATTAT-TAAAAA-TAT
1 TTATTATTATCAAAAAAGTAT
54406 TTATTATTATCA
1 TTATTATTATCA
54418 CCATTATTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 13 0.46
20 5 0.18
21 10 0.36
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.50
Consensus pattern (21 bp):
TTATTATTATCAAAAAAGTAT
Found at i:55142 original size:17 final size:17
Alignment explanation
Indices: 55127--55197 Score: 70
Period size: 17 Copynumber: 4.1 Consensus size: 17
55117 TTAAAATTTT
55127 ATTTCAAAATAAATTTAA
1 ATTT-AAAATAAATTTAA
55145 ATTTAAAATAAATTTAA
1 ATTTAAAATAAATTTAA
* ** *
55162 ACTCCAAATAAGTATTAA
1 ATTTAAAATAAAT-TTAA
**
55180 ATTTACTATAAATTTAA
1 ATTTAAAATAAATTTAA
55197 A
1 A
55198 CTTGAAATGA
Statistics
Matches: 42, Mismatches: 10, Indels: 3
0.76 0.18 0.05
Matches are distributed among these distances:
17 27 0.64
18 15 0.36
ACGTcount: A:0.54, C:0.07, G:0.01, T:0.38
Consensus pattern (17 bp):
ATTTAAAATAAATTTAA
Found at i:55191 original size:35 final size:34
Alignment explanation
Indices: 55133--55199 Score: 98
Period size: 35 Copynumber: 1.9 Consensus size: 34
55123 TTTTATTTCA
55133 AAATAAATTTAAATTTAAAATAAATTTAAACTCC
1 AAATAAATTTAAATTTAAAATAAATTTAAACTCC
* **
55167 AAATAAGTATTAAATTTACTATAAATTTAAACT
1 AAATAAAT-TTAAATTTAAAATAAATTTAAACT
55200 TGAAATGACT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 7 0.24
35 22 0.76
ACGTcount: A:0.54, C:0.07, G:0.01, T:0.37
Consensus pattern (34 bp):
AAATAAATTTAAATTTAAAATAAATTTAAACTCC
Found at i:65633 original size:24 final size:24
Alignment explanation
Indices: 65605--65673 Score: 86
Period size: 24 Copynumber: 2.9 Consensus size: 24
65595 TTTCTAGAAG
*
65605 ATTTAGTATTTATTAGTGTAATAT
1 ATTTAGCATTTATTAGTGTAATAT
***
65629 ATTTAGCATTTATTAGCAAAATAT
1 ATTTAGCATTTATTAGTGTAATAT
65653 ATTTCA-CATTTATTAGTGTAA
1 ATTT-AGCATTTATTAGTGTAA
65674 AAATCATTAT
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
24 36 0.97
25 1 0.03
ACGTcount: A:0.36, C:0.06, G:0.10, T:0.48
Consensus pattern (24 bp):
ATTTAGCATTTATTAGTGTAATAT
Found at i:67318 original size:96 final size:95
Alignment explanation
Indices: 67140--67322 Score: 246
Period size: 96 Copynumber: 1.9 Consensus size: 95
67130 GAAAAGGATG
* **
67140 TTCGATTATCTTGATTTGAGGAAAGGTTGCACCTAGTAAGTTAAGGCACAAATTTTCAGAATCGA
1 TTCGATTATCTTGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAAATTTTCAGAATCGA
* *
67205 AGATAAGGAAANNTTGCCTCGATTAAGGGTA
66 AGATAAAGAAA-ATTGCCTCGATTAAGGGTA
67236 TTCGATTAT-TTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAAATTTTC-GAAACT
1 TTCGATTATCTT-GATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAAATTTTCAG-AA-T
*
67299 CGAA-ATAAAAGAATATTGCCTCGA
63 CGAAGAT-AAAGAAAATTGCCTCGA
67323 ATTTAAAGTT
Statistics
Matches: 77, Mismatches: 6, Indels: 8
0.85 0.07 0.09
Matches are distributed among these distances:
95 3 0.04
96 64 0.83
97 10 0.13
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.30
Consensus pattern (95 bp):
TTCGATTATCTTGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAAATTTTCAGAATCGA
AGATAAAGAAAATTGCCTCGATTAAGGGTA
Found at i:67656 original size:59 final size:58
Alignment explanation
Indices: 67584--68022 Score: 459
Period size: 59 Copynumber: 7.5 Consensus size: 58
67574 CGAATTCTCG
* *
67584 GGGT-AAAATGGTAATTTTGGGAAG-TTCGGGGTTAAAAAATGGAATTTTTGGATA-TTCGG
1 GGGTAAAAATGG-AATTTTTGGAAGTTTCGGGG-T-AAAAATGGAATTTTTGGA-AGTTCGA
* ** ** *
67643 GGGT-AAAAGGGTAA-TTTT-GAGAGTTTCAAGGTCAAAAATGGAGA-AATTGGAGGTTCGA
1 GGGTAAAAATGG-AATTTTTGGA-AGTTTCGGGGT-AAAAATGGA-ATTTTTGGAAGTTCGA
* *
67701 GGGTAAAAATGGAATTTTTGGAAGTTTCGAGGTCAAAAATGGCATTTTTGGAAGTTCGA
1 GGGTAAAAATGGAATTTTTGGAAGTTTCGGGGT-AAAAATGGAATTTTTGGAAGTTCGA
*
67760 GGGTAAAAATGGAATTTTTGGAAG-TTCGGGGGTAAAAATGGATTTTTTGGAAGTTCGA
1 GGGTAAAAATGGAATTTTTGGAAGTTTC-GGGGTAAAAATGGAATTTTTGGAAGTTCGA
* ** * *
67818 GGGTAAAAATGGAATTTTTGGAAGCTTCGATGTCAAAAATGAAATTTTTGGAAGTTCAA
1 GGGTAAAAATGGAATTTTTGGAAGTTTCGGGGT-AAAAATGGAATTTTTGGAAGTTCGA
* * *
67877 GGGTAAAAATGGAATTTTTGGAAGTTTTGGGGTTGAAAATGGAATTTTTGAAAGTTTCGA
1 GGGTAAAAATGGAATTTTTGGAAGTTTCGGGG-TAAAAATGGAATTTTTGGAAG-TTCGA
*
67937 -GGTCAAAAATGGAATTTTAGGAAGTTT-GGTGGTAAAAATGGAATTTTTGGAAGTTCG-
1 GGGT-AAAAATGGAATTTTTGGAAGTTTCGG-GGTAAAAATGGAATTTTTGGAAGTTCGA
*
67994 GGCGTAAAAATGGAATTTTCGGACAGTTT
1 GG-GTAAAAATGGAATTTTTGGA-AGTTT
68023 AGGGACCTTC
Statistics
Matches: 327, Mismatches: 35, Indels: 36
0.82 0.09 0.09
Matches are distributed among these distances:
57 2 0.01
58 106 0.32
59 188 0.57
60 31 0.09
ACGTcount: A:0.33, C:0.05, G:0.30, T:0.32
Consensus pattern (58 bp):
GGGTAAAAATGGAATTTTTGGAAGTTTCGGGGTAAAAATGGAATTTTTGGAAGTTCGA
Found at i:67721 original size:29 final size:29
Alignment explanation
Indices: 67584--68021 Score: 427
Period size: 29 Copynumber: 14.9 Consensus size: 29
67574 CGAATTCTCG
*
67584 GGGT-AAAATGGTAATTTTGGGAAGTTCG-
1 GGGTAAAAATGG-AATTTTTGGAAGTTCGA
*
67612 GGGTTAAAAAATGGAATTTTTGGATA-TTCGG
1 GGG-T-AAAAATGGAATTTTTGGA-AGTTCGA
*
67643 GGGT-AAAAGGGTAA-TTTT-GAGAGTTTC-A
1 GGGTAAAAATGG-AATTTTTGGA-AG-TTCGA
* ** *
67671 AGGTCAAAAATGGAGA-AATTGGAGGTTCGA
1 GGGT-AAAAATGGA-ATTTTTGGAAGTTCGA
67701 GGGTAAAAATGGAATTTTTGGAAGTTTCGA
1 GGGTAAAAATGGAATTTTTGGAAG-TTCGA
*
67731 -GGTCAAAAATGGCATTTTTGGAAGTTCGA
1 GGGT-AAAAATGGAATTTTTGGAAGTTCGA
*
67760 GGGTAAAAATGGAATTTTTGGAAGTTCGG
1 GGGTAAAAATGGAATTTTTGGAAGTTCGA
*
67789 GGGTAAAAATGGATTTTTTGGAAGTTCGA
1 GGGTAAAAATGGAATTTTTGGAAGTTCGA
67818 GGGTAAAAATGGAATTTTTGGAAGCTTCGA
1 GGGTAAAAATGGAATTTTTGGAAG-TTCGA
* * *
67848 -TGTCAAAAATGAAATTTTTGGAAGTTCAA
1 GGGT-AAAAATGGAATTTTTGGAAGTTCGA
*
67877 GGGTAAAAATGGAATTTTTGGAAGTTTTG-
1 GGGTAAAAATGGAATTTTTGGAAG-TTCGA
* *
67906 GGGTTGAAAATGGAATTTTTGAAAGTTTCGA
1 GGG-TAAAAATGGAATTTTTGGAAG-TTCGA
* *
67937 -GGTCAAAAATGGAATTTTAGGAAGTTTG-
1 GGGT-AAAAATGGAATTTTTGGAAGTTCGA
67965 GTGGTAAAAATGGAATTTTTGGAAGTTCG-
1 G-GGTAAAAATGGAATTTTTGGAAGTTCGA
*
67994 GGCGTAAAAATGGAATTTTCGGACAGTT
1 GG-GTAAAAATGGAATTTTTGGA-AGTT
68022 TAGGGACCTT
Statistics
Matches: 346, Mismatches: 36, Indels: 54
0.79 0.08 0.12
Matches are distributed among these distances:
27 3 0.01
28 18 0.05
29 180 0.52
30 132 0.38
31 13 0.04
ACGTcount: A:0.33, C:0.05, G:0.30, T:0.32
Consensus pattern (29 bp):
GGGTAAAAATGGAATTTTTGGAAGTTCGA
Found at i:67739 original size:117 final size:116
Alignment explanation
Indices: 67584--68022 Score: 457
Period size: 117 Copynumber: 3.7 Consensus size: 116
67574 CGAATTCTCG
* * * *
67584 GGGT-AAAATGGTAATTTTGGGAAG-TTCGGGGTTAAAAAATGGAATTTTTGGATA-TTCGGGGG
1 GGGTAAAAATGG-AATTTTTGGAAGTTTCGAGG-TCAAAAATGGAATTTTTGGA-AGTTCGAGGG
* ** **
67646 T-AAAAGGGTAA-TTTT-GAGAGTTTCAAGGTCAAAAATGGAGAAATTGGAGGTTCGA
63 TAAAAATGG-AATTTTTGGA-AGTTTCGGGGT-AAAAATGGA-ATTTTGGAGGTTCGA
*
67701 GGGTAAAAATGGAATTTTTGGAAGTTTCGAGGTCAAAAATGGCATTTTTGGAAGTTCGAGGGTAA
1 GGGTAAAAATGGAATTTTTGGAAGTTTCGAGGTCAAAAATGGAATTTTTGGAAGTTCGAGGGTAA
* *
67766 AAATGGAATTTTTGGAAG-TTCGGGGGTAAAAATGGATTTTTTGGAAGTTCGA
66 AAATGGAATTTTTGGAAGTTTC-GGGGTAAAAATGGA-ATTTTGGAGGTTCGA
* * * *
67818 GGGTAAAAATGGAATTTTTGGAAGCTTCGATGTCAAAAATGAAATTTTTGGAAGTTCAAGGGTAA
1 GGGTAAAAATGGAATTTTTGGAAGTTTCGAGGTCAAAAATGGAATTTTTGGAAGTTCGAGGGTAA
* * * *
67883 AAATGGAATTTTTGGAAGTTTTGGGGTTGAAAATGGAATTTTTGAAAGTTTCGA
66 AAATGGAATTTTTGGAAGTTTCGGGG-TAAAAATGGAA-TTTTG-GAGGTTCGA
* * *
67937 -GGTCAAAAATGGAATTTTAGGAAGTTTGGTGGT-AAAAATGGAATTTTTGGAAGTTCG-GGCGT
1 GGGT-AAAAATGGAATTTTTGGAAGTTTCGAGGTCAAAAATGGAATTTTTGGAAGTTCGAGG-GT
*
67999 AAAAATGGAATTTTCGGACAGTTT
64 AAAAATGGAATTTTTGGA-AGTTT
68023 AGGGACCTTC
Statistics
Matches: 276, Mismatches: 32, Indels: 26
0.83 0.10 0.08
Matches are distributed among these distances:
116 1 0.00
117 150 0.54
118 88 0.32
119 37 0.13
ACGTcount: A:0.33, C:0.05, G:0.30, T:0.32
Consensus pattern (116 bp):
GGGTAAAAATGGAATTTTTGGAAGTTTCGAGGTCAAAAATGGAATTTTTGGAAGTTCGAGGGTAA
AAATGGAATTTTTGGAAGTTTCGGGGTAAAAATGGAATTTTGGAGGTTCGA
Found at i:69025 original size:15 final size:16
Alignment explanation
Indices: 69002--69040 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
68992 TACTAAAATA
69002 ATTAATATTAATA-TT
1 ATTAATATTAATAGTT
*
69017 ATTATTATTAATAGTT
1 ATTAATATTAATAGTT
69033 ATTGAATA
1 ATT-AATA
69041 AATTAAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 12 0.60
16 5 0.25
17 3 0.15
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (16 bp):
ATTAATATTAATAGTT
Found at i:69741 original size:24 final size:23
Alignment explanation
Indices: 69704--69750 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
69694 TTAGACTTTG
*
69704 ATTTAAATAGATTTAAACTTTAA
1 ATTTAAATAAATTTAAACTTTAA
*
69727 ATTTATAATAAATTTAAATTTTAA
1 ATTTA-AATAAATTTAAACTTTAA
69751 GTAAATTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 5 0.24
24 16 0.76
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (23 bp):
ATTTAAATAAATTTAAACTTTAA
Found at i:69742 original size:17 final size:17
Alignment explanation
Indices: 69717--69796 Score: 106
Period size: 17 Copynumber: 4.6 Consensus size: 17
69707 TAAATAGATT
*
69717 TAAACTTTAAATTTATAA
1 TAAA-TTTAAATTTAAAA
* *
69735 TAAATTTAAATTTTAAG
1 TAAATTTAAATTTAAAA
*
69752 TAAATTTAAAATTAAAA
1 TAAATTTAAATTTAAAA
*
69769 TAAATTTAATTTTAAAA
1 TAAATTTAAATTTAAAA
69786 TAAATTTAAAT
1 TAAATTTAAAT
69797 CTTGTTGGGC
Statistics
Matches: 53, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
17 49 0.92
18 4 0.08
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:69744 original size:6 final size:6
Alignment explanation
Indices: 69714--69796 Score: 59
Period size: 6 Copynumber: 14.3 Consensus size: 6
69704 ATTTAAATAG
* *
69714 ATTTAA ACTTTAA ATTTATA A--TAA ATTTAA ATTTTA A-GTAA ATTTAA
1 ATTTAA A-TTTAA ATTTA-A ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
* * * *
69761 AATTAA A-ATAA ATTTAA TTTTAA A-ATAA ATTTAA AT
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA AT
69797 CTTGTTGGGC
Statistics
Matches: 59, Mismatches: 11, Indels: 14
0.70 0.13 0.17
Matches are distributed among these distances:
4 2 0.03
5 13 0.22
6 36 0.61
7 8 0.14
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (6 bp):
ATTTAA
Found at i:71588 original size:21 final size:21
Alignment explanation
Indices: 71563--71604 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
71553 AATTAATTCA
71563 ATTGCTTCCCTTTATTCATAT
1 ATTGCTTCCCTTTATTCATAT
71584 ATTGCTTCCCTTTATTCATAT
1 ATTGCTTCCCTTTATTCATAT
71605 GCATGAGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.19, C:0.24, G:0.05, T:0.52
Consensus pattern (21 bp):
ATTGCTTCCCTTTATTCATAT
Found at i:79747 original size:20 final size:19
Alignment explanation
Indices: 79694--79751 Score: 57
Period size: 20 Copynumber: 3.1 Consensus size: 19
79684 CAATAGAATG
79694 AAAGAAAAT-AAAA-AAAA
1 AAAGAAAATGAAAAGAAAA
**
79711 AAAGAAAATGGGGAAGAAAA
1 AAAGAAAAT-GAAAAGAAAA
*
79731 GAAGAAAATCGAAAAGAAAA
1 AAAGAAAAT-GAAAAGAAAA
79751 A
1 A
79752 CACCAGAGAA
Statistics
Matches: 31, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
17 9 0.29
19 2 0.06
20 20 0.65
ACGTcount: A:0.74, C:0.02, G:0.19, T:0.05
Consensus pattern (19 bp):
AAAGAAAATGAAAAGAAAA
Found at i:81261 original size:17 final size:17
Alignment explanation
Indices: 81239--81275 Score: 67
Period size: 16 Copynumber: 2.2 Consensus size: 17
81229 TAATTATTTT
81239 TTAAAAATATTTT-AAA
1 TTAAAAATATTTTAAAA
81255 TTAAAAATATTTTAAAA
1 TTAAAAATATTTTAAAA
81272 TTAA
1 TTAA
81276 TTTAAAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 13 0.65
17 7 0.35
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TTAAAAATATTTTAAAA
Found at i:81269 original size:11 final size:11
Alignment explanation
Indices: 81255--81289 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
81245 ATATTTTAAA
*
81255 TTAAAAATATT
1 TTAAAATTATT
*
81266 TTAAAATTAAT
1 TTAAAATTATT
81277 TTAAAATTATT
1 TTAAAATTATT
81288 TT
1 TT
81290 TTAAATATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (11 bp):
TTAAAATTATT
Found at i:83003 original size:68 final size:67
Alignment explanation
Indices: 82884--83013 Score: 165
Period size: 68 Copynumber: 1.9 Consensus size: 67
82874 ATTTTAATAA
* *
82884 TTTAATATTAAATTTAATTTAATACTTATCTTAATAGTATTTTATTAATTTAATATTAAAATGAT
1 TTTAATAATAAATTTAATTTAATACTTATCTTAATA-TATTTTATAAATTTAATATTAAAATGAT
82949 TAT
65 TAT
* **
82952 TTTAATAATAAATTTAATTTCATGTTTATCGTT-AT-TATTTTAATAAGATTTAATATTAAAAT
1 TTTAATAATAAATTTAATTTAATACTTATC-TTAATATATTTT-ATAA-ATTTAATATTAAAAT
83014 TTAATCTATT
Statistics
Matches: 54, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
66 6 0.11
67 3 0.06
68 43 0.80
69 2 0.04
ACGTcount: A:0.41, C:0.03, G:0.04, T:0.52
Consensus pattern (67 bp):
TTTAATAATAAATTTAATTTAATACTTATCTTAATATATTTTATAAATTTAATATTAAAATGATT
AT
Found at i:86716 original size:23 final size:23
Alignment explanation
Indices: 86687--87062 Score: 509
Period size: 23 Copynumber: 16.3 Consensus size: 23
86677 CTTATATCTA
*
86687 TGCTTAAATATTAATATGATTTA
1 TGCTTAAATATTAATATGATTTG
** *
86710 TTATTAAATATTAATGTGATTTG
1 TGCTTAAATATTAATATGATTTG
* *
86733 TGCTTAAGTATTAATATGATTTA
1 TGCTTAAATATTAATATGATTTG
86756 TGCTTAAATATTAATATGATTTG
1 TGCTTAAATATTAATATGATTTG
* *
86779 TGCTCAAATATTAATGTGATTTG
1 TGCTTAAATATTAATATGATTTG
*
86802 TGCTTAAATATTTATATGATTTG
1 TGCTTAAATATTAATATGATTTG
* *
86825 TGCTCAAATATTAACATGATTTG
1 TGCTTAAATATTAATATGATTTG
* * *
86848 TGCTCAAATATTAATGTGATTTA
1 TGCTTAAATATTAATATGATTTG
*
86871 TGCTTAAATGTTAATATGATTTG
1 TGCTTAAATATTAATATGATTTG
* *
86894 TGCTCAAATATTAACATGATTTG
1 TGCTTAAATATTAATATGATTTG
* * *
86917 TGCTCAAATATTAATGTGATTTA
1 TGCTTAAATATTAATATGATTTG
86940 TGCTTAAATATTAATATGATTTG
1 TGCTTAAATATTAATATGATTTG
* * *
86963 TGCTCAAATATTAATGTGATTTA
1 TGCTTAAATATTAATATGATTTG
*
86986 TGCTTAAATATTAATTTGATTTG
1 TGCTTAAATATTAATATGATTTG
*
87009 TGCTTAAATATTAATATGATTTA
1 TGCTTAAATATTAATATGATTTG
* *
87032 TGATTAAATATTAATGTGATTTG
1 TGCTTAAATATTAATATGATTTG
87055 TGCTTAAA
1 TGCTTAAA
87063 GAATTAAGAT
Statistics
Matches: 306, Mismatches: 47, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 306 1.00
ACGTcount: A:0.34, C:0.06, G:0.13, T:0.46
Consensus pattern (23 bp):
TGCTTAAATATTAATATGATTTG
Found at i:90887 original size:63 final size:62
Alignment explanation
Indices: 90786--90951 Score: 266
Period size: 63 Copynumber: 2.7 Consensus size: 62
90776 TTCTTAGTAT
90786 TTTTATTTATTTATTTATTATTTTAT-AA-AT-ATAAATAAATATAAAATAATATTAATTTTG
1 TTTTA-TTATTTATTTATTATTTTATGAATATAATAAATAAATATAAAATAATATTAATTTTG
* *
90846 TTTTATTATTTATTTATTATTGTATGAATATAAATAAATAAATGTAAAATAATATTAATTTTG
1 TTTTATTATTTATTTATTATTTTATGAATAT-AATAAATAAATATAAAATAATATTAATTTTG
90909 TTTTATTATTTATTTATTATTTTATGAATATAGATAAATAAAT
1 TTTTATTATTTATTTATTATTTTATGAATATA-ATAAATAAAT
90952 TAATAAATAA
Statistics
Matches: 98, Mismatches: 3, Indels: 7
0.91 0.03 0.06
Matches are distributed among these distances:
59 19 0.19
60 7 0.07
61 2 0.02
62 1 0.01
63 69 0.70
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (62 bp):
TTTTATTATTTATTTATTATTTTATGAATATAATAAATAAATATAAAATAATATTAATTTTG
Found at i:93479 original size:31 final size:31
Alignment explanation
Indices: 93441--93506 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
93431 CATATGCATT
*
93441 CATTCATAAAATTCTGCTTCACATTTTCATG
1 CATTCATAAAATTCTGCGTCACATTTTCATG
* * *
93472 CATTCATAAAGTTTTGCGTCGCATTTTCATG
1 CATTCATAAAATTCTGCGTCACATTTTCATG
93503 CATT
1 CATT
93507 AAAAGTTTGA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.26, C:0.21, G:0.11, T:0.42
Consensus pattern (31 bp):
CATTCATAAAATTCTGCGTCACATTTTCATG
Found at i:98247 original size:50 final size:49
Alignment explanation
Indices: 98183--98298 Score: 128
Period size: 50 Copynumber: 2.3 Consensus size: 49
98173 ATCCTATACC
* * *
98183 CCTAAAGCTATAGAGGAATAGATTGAAGCAACG-ATGGTGAATCTCATAT-A
1 CCTAAAGCTGTAGAGGAACAGATTGAAG--ACGAATGGCGAATCTCAT-TCA
** *
98233 CCTAAAGCTGTAGAGGGGCAGATTGAAGATGTAATGGCGAATCTCATTCA
1 CCTAAAGCTGTAGAGGAACAGATTGAAGACG-AATGGCGAATCTCATTCA
98283 CCTAAAGCTGTAGAGG
1 CCTAAAGCTGTAGAGG
98299 GGTCAATTGA
Statistics
Matches: 57, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
48 2 0.04
49 1 0.02
50 54 0.95
ACGTcount: A:0.35, C:0.16, G:0.26, T:0.23
Consensus pattern (49 bp):
CCTAAAGCTGTAGAGGAACAGATTGAAGACGAATGGCGAATCTCATTCA
Found at i:98299 original size:50 final size:50
Alignment explanation
Indices: 98216--98310 Score: 149
Period size: 50 Copynumber: 1.9 Consensus size: 50
98206 TGAAGCAACG
*
98216 ATGGTGAATCTCATATACCTAAAGCTGTAGAGGGG-CAGATTGAAGATGTA
1 ATGGCGAATCTCATATACCTAAAGCTGTAGAGGGGTCA-ATTGAAGATGTA
98266 ATGGCGAATCTCAT-TCACCTAAAGCTGTAGAGGGGTCAATTGAAG
1 ATGGCGAATCTCATAT-ACCTAAAGCTGTAGAGGGGTCAATTGAAG
98311 TCGCAAGGAC
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
49 1 0.02
50 39 0.93
51 2 0.05
ACGTcount: A:0.33, C:0.15, G:0.27, T:0.25
Consensus pattern (50 bp):
ATGGCGAATCTCATATACCTAAAGCTGTAGAGGGGTCAATTGAAGATGTA
Found at i:98324 original size:50 final size:50
Alignment explanation
Indices: 98216--98360 Score: 147
Period size: 50 Copynumber: 2.9 Consensus size: 50
98206 TGAAGCAACG
* *
98216 ATGGTGAATCTCATATACCTAAAGCTGTAGAGGGGCAGATTGAAGATGTA
1 ATGGCGAATCTCATATACCTAAAGCTGTAGAGGGGCAGATTGAAGATGCA
98266 ATGGCGAATCTCAT-TCACCTAAAGCTGTAGAGGGGTCA-ATTGAAG-TCGCA
1 ATGGCGAATCTCATAT-ACCTAAAGCTGTAGAGGGG-CAGATTGAAGAT-GCA
* * * * * *
98316 A-GGACGAATCTTATGTTCCTAAAGCT-AAAATGGGCAGATTGAAGA
1 ATGG-CGAATCTCATATACCTAAAGCTGTAGAGGGGCAGATTGAAGA
98361 CCATCCGATC
Statistics
Matches: 81, Mismatches: 7, Indels: 14
0.79 0.07 0.14
Matches are distributed among these distances:
48 2 0.02
49 16 0.20
50 60 0.74
51 3 0.04
ACGTcount: A:0.34, C:0.15, G:0.26, T:0.25
Consensus pattern (50 bp):
ATGGCGAATCTCATATACCTAAAGCTGTAGAGGGGCAGATTGAAGATGCA
Found at i:98480 original size:79 final size:79
Alignment explanation
Indices: 98348--98734 Score: 540
Period size: 79 Copynumber: 4.9 Consensus size: 79
98338 AGCTAAAATG
** ** *
98348 GGCAGATTGAAGACCATCCGATCTCTTACATCGACCATGGGGCAGATTGAAGCAATTTAATTTTT
1 GGCAGATTGAAGACCATCCGATCTCTTACCCCGACCATGGGGCAGATTGAAGCAATCCAATCTTT
98413 TACCCTAACCAGAA
66 TACCCTAACCAGAA
* * * *
98427 GGCAGATTGAAGACCATCCGATCTCTTACCTCGACCATAGGGTAGATTAAAGCAATCCAATCTTT
1 GGCAGATTGAAGACCATCCGATCTCTTACCCCGACCATGGGGCAGATTGAAGCAATCCAATCTTT
*
98492 TACCCTAACCAGAG
66 TACCCTAACCAGAA
** **
98506 GGCAGATTGAAGGTCATATGATCTCTTACCCCGACCATGGGGCAGATTGAAGCAATCCAATCTTT
1 GGCAGATTGAAGACCATCCGATCTCTTACCCCGACCATGGGGCAGATTGAAGCAATCCAATCTTT
* *
98571 TACCCTGACTAGAA
66 TACCCTAACCAGAA
* * * * *
98585 GGCAGATTAAATAACATCCAATCTCTTACCCCGACCATGGGGCAGATTGAAGCAATCTAATCTTT
1 GGCAGATTGAAGACCATCCGATCTCTTACCCCGACCATGGGGCAGATTGAAGCAATCCAATCTTT
* * *
98650 TGCCTTAACCAGAG
66 TACCCTAACCAGAA
* *
98664 GGCAGATTGAAGACCATCCGATCTCTTACCCCGACCATGGGGCAGATTGAAACAGTCCAATCTTT
1 GGCAGATTGAAGACCATCCGATCTCTTACCCCGACCATGGGGCAGATTGAAGCAATCCAATCTTT
98729 TACCCT
66 TACCCT
98735 TAAAACTATA
Statistics
Matches: 267, Mismatches: 41, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
79 267 1.00
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.25
Consensus pattern (79 bp):
GGCAGATTGAAGACCATCCGATCTCTTACCCCGACCATGGGGCAGATTGAAGCAATCCAATCTTT
TACCCTAACCAGAA
Found at i:99343 original size:59 final size:62
Alignment explanation
Indices: 99263--99426 Score: 246
Period size: 63 Copynumber: 2.7 Consensus size: 62
99253 TTCTTATTAT
99263 TTTTATTTATTTATTTATTATTTTATGAATATAAATAAAT-A-TAAAATAATATTAATTTTG
1 TTTTATTTATTTATTTATTATTTTATGAATATAAATAAATAAGTAAAATAATATTAATTTTG
*
99323 TTTTA-TTATTTATTTATTATTGTATGAATATAAATAAATAAATGTAAAATAATATTAATTTTG
1 TTTTATTTATTTATTTATTATTTTATGAATATAAATAAAT-AA-GTAAAATAATATTAATTTTG
* * *
99386 TTTTATTTATTT-TTTATTATTTTATTAATATAGATATATAA
1 TTTTATTTATTTATTTATTATTTTATGAATATAAATAAATAA
99427 ATNNNNNNNN
Statistics
Matches: 94, Mismatches: 5, Indels: 8
0.88 0.05 0.07
Matches are distributed among these distances:
59 33 0.35
60 5 0.05
61 1 0.01
62 2 0.02
63 47 0.50
64 6 0.06
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.55
Consensus pattern (62 bp):
TTTTATTTATTTATTTATTATTTTATGAATATAAATAAATAAGTAAAATAATATTAATTTTG
Found at i:99544 original size:1 final size:1
Alignment explanation
Indices: 99538--99564 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
99528 NNNNNNNNNN
99538 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
99565 TATATATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:99569 original size:2 final size:2
Alignment explanation
Indices: 99564--99590 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
99554 AAAAAAAAAA
99564 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
99591 CACTATATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:103661 original size:21 final size:20
Alignment explanation
Indices: 103622--103663 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
103612 CCCAGTCTTC
*
103622 AAAAAATCAAAACATAACAA
1 AAAAAATCAAAACACAACAA
*
103642 AAAAAATCAAAATTACAACAA
1 AAAAAATCAAAA-CACAACAA
103663 A
1 A
103664 TTACTTCATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.74, C:0.14, G:0.00, T:0.12
Consensus pattern (20 bp):
AAAAAATCAAAACACAACAA
Found at i:105118 original size:15 final size:16
Alignment explanation
Indices: 105085--105123 Score: 55
Period size: 15 Copynumber: 2.5 Consensus size: 16
105075 ATACAGTAAA
105085 TATAATTTGATTATTT
1 TATAATTTGATTATTT
105101 TATAATTT-A-TATTTT
1 TATAATTTGATTA-TTT
105116 TATAATTT
1 TATAATTT
105124 TTAAAAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 2 0.09
15 12 0.55
16 8 0.36
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (16 bp):
TATAATTTGATTATTT
Found at i:105143 original size:20 final size:22
Alignment explanation
Indices: 105118--105166 Score: 66
Period size: 20 Copynumber: 2.3 Consensus size: 22
105108 TATATTTTTA
*
105118 TAATTTTTAA-AAAATTAAAT-
1 TAATTTTTAAGAAAATAAAATG
*
105138 TAATTTTTAAGGAAATAAAATG
1 TAATTTTTAAGAAAATAAAATG
105160 TAATTTT
1 TAATTTT
105167 ATTTTTATTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 10 0.40
21 8 0.32
22 7 0.28
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.45
Consensus pattern (22 bp):
TAATTTTTAAGAAAATAAAATG
Found at i:112084 original size:34 final size:34
Alignment explanation
Indices: 112041--112108 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
112031 TGAAAATACT
112041 TGTATTAGGAGTTAGATTGTATATTACTGCTCTA
1 TGTATTAGGAGTTAGATTGTATATTACTGCTCTA
112075 TGTATTAGGAGTTAGATTGTATATTACTGCTCTA
1 TGTATTAGGAGTTAGATTGTATATTACTGCTCTA
112109 CTCAAAAAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.26, C:0.09, G:0.21, T:0.44
Consensus pattern (34 bp):
TGTATTAGGAGTTAGATTGTATATTACTGCTCTA
Found at i:116169 original size:2 final size:2
Alignment explanation
Indices: 116162--116186 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
116152 TATGTCCAAT
116162 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
116187 TTTGGTGTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:117634 original size:24 final size:23
Alignment explanation
Indices: 117583--117641 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 23
117573 ACCTAGTGAG
*
117583 ATGCCTGGTGGGTTTCCAGGTGGA
1 ATGCCTGGT-GGTTTCCAGGTAGA
* *
117607 ATGCCTGGTGGTTTCCCTGGTAGT
1 ATGCCTGGTGGTTT-CCAGGTAGA
*
117631 ATGCCGGGTGG
1 ATGCCTGGTGG
117642 GATGCCTGGA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
23 5 0.17
24 25 0.83
ACGTcount: A:0.10, C:0.19, G:0.41, T:0.31
Consensus pattern (23 bp):
ATGCCTGGTGGTTTCCAGGTAGA
Found at i:120953 original size:64 final size:63
Alignment explanation
Indices: 120863--120987 Score: 153
Period size: 64 Copynumber: 2.0 Consensus size: 63
120853 GGGTTTGAAC
* **
120863 TTTTTTTTGTATAAGTTAGTCCCTGAACTTGATAATTGTTCCCATGTTAGGGCTTGAACTTTT
1 TTTTTTTTGTATAAGTTAGTCCCTGAACTTGACAATTGTTCCCACATTAGGGCTTGAACTTTT
** * * *
120926 TTTTTTTCTGT-TCAAGTTAGTTTCTGAACTTGGCAATTGTTCTCACATTAGGGCTTTAACTT
1 TTTTTTT-TGTAT-AAGTTAGTCCCTGAACTTGACAATTGTTCCCACATTAGGGCTTGAACTT
120988 AAGGGTTTTC
Statistics
Matches: 52, Mismatches: 8, Indels: 3
0.83 0.13 0.05
Matches are distributed among these distances:
63 8 0.15
64 44 0.85
ACGTcount: A:0.20, C:0.15, G:0.17, T:0.48
Consensus pattern (63 bp):
TTTTTTTTGTATAAGTTAGTCCCTGAACTTGACAATTGTTCCCACATTAGGGCTTGAACTTTT
Found at i:133148 original size:13 final size:13
Alignment explanation
Indices: 133130--133186 Score: 51
Period size: 15 Copynumber: 4.0 Consensus size: 13
133120 TTATATATTT
133130 TATAATTTTTTTA
1 TATAATTTTTTTA
133143 TATAATTTATTATTA
1 TATAATTT-TT-TTA
*
133158 TAAAATTATTTTTAA
1 TATAATT-TTTTT-A
*
133173 TTTAATATTTTTTA
1 TATAAT-TTTTTTA
133187 AATTATAAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 9
0.75 0.06 0.19
Matches are distributed among these distances:
13 8 0.22
14 5 0.14
15 21 0.58
16 2 0.06
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (13 bp):
TATAATTTTTTTA
Found at i:139637 original size:26 final size:26
Alignment explanation
Indices: 139604--139653 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
139594 AAAAATAATA
*
139604 TTACTATATTTTATGT-ATTTATTTAT
1 TTACTATATTATAT-TAATTTATTTAT
139630 TTACTATATTATATTAATTTATTT
1 TTACTATATTATATTAATTTATTT
139654 GTTAATCTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 1 0.05
26 21 0.95
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.64
Consensus pattern (26 bp):
TTACTATATTATATTAATTTATTTAT
Found at i:140127 original size:49 final size:49
Alignment explanation
Indices: 140051--140152 Score: 186
Period size: 49 Copynumber: 2.1 Consensus size: 49
140041 ATAGAAGGAA
* *
140051 TTAAGCATTCATATTTTTATATTGTGTTTAAAATTATTCATAATTTTTT
1 TTAAGCATTCATATTTTTATATCGTGTTTAAAACTATTCATAATTTTTT
140100 TTAAGCATTCATATTTTTATATCGTGTTTAAAACTATTCATAATTTTTT
1 TTAAGCATTCATATTTTTATATCGTGTTTAAAACTATTCATAATTTTTT
140149 TTAA
1 TTAA
140153 CTCATAAATG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 51 1.00
ACGTcount: A:0.31, C:0.08, G:0.06, T:0.55
Consensus pattern (49 bp):
TTAAGCATTCATATTTTTATATCGTGTTTAAAACTATTCATAATTTTTT
Found at i:144857 original size:21 final size:21
Alignment explanation
Indices: 144831--144876 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
144821 ATAAATTTAA
* *
144831 ATTTTAACTTGAA-TTTATTTT
1 ATTTTAA-TTAAATTTTAGTTT
144852 ATTTTAATTAAATTTTAGTTT
1 ATTTTAATTAAATTTTAGTTT
144873 ATTT
1 ATTT
144877 ATTTTACGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 4 0.18
21 18 0.82
ACGTcount: A:0.30, C:0.02, G:0.04, T:0.63
Consensus pattern (21 bp):
ATTTTAATTAAATTTTAGTTT
Found at i:145190 original size:14 final size:13
Alignment explanation
Indices: 145173--145220 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
145163 AAACTAAAAT
145173 ATTAAAATATAAA
1 ATTAAAATATAAA
* *
145186 GATTAAATTGATTAA
1 -ATTAAAAT-ATAAA
145201 ATTAAAATATAAAA
1 ATTAAAATAT-AAA
145215 ATTAAA
1 ATTAAA
145221 TACATAATTC
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
13 2 0.07
14 22 0.79
15 4 0.14
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.33
Consensus pattern (13 bp):
ATTAAAATATAAA
Found at i:145865 original size:8 final size:8
Alignment explanation
Indices: 145846--145901 Score: 58
Period size: 8 Copynumber: 6.6 Consensus size: 8
145836 AGTAAATCAT
145846 TTAAAGTTA
1 TTAAA-TTA
145855 TTAAATTA
1 TTAAATTA
* *
145863 TTAAAATG
1 TTAAATTA
*
145871 TTAAATCA
1 TTAAATTA
145879 TTTAAAGTTA
1 -TTAAA-TTA
145889 TTAAATTA
1 TTAAATTA
145897 TTAAA
1 TTAAA
145902 ATGTTTATGT
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
8 22 0.56
9 15 0.38
10 2 0.05
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (8 bp):
TTAAATTA
Found at i:145878 original size:34 final size:34
Alignment explanation
Indices: 145838--145906 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
145828 TTCTTTTGAG
145838 TAAATCATTTAAAGTTATTAAATTATTAAAATGT
1 TAAATCATTTAAAGTTATTAAATTATTAAAATGT
145872 TAAATCATTTAAAGTTATTAAATTATTAAAATGT
1 TAAATCATTTAAAGTTATTAAATTATTAAAATGT
145906 T
1 T
145907 TATGTTTCAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.45
Consensus pattern (34 bp):
TAAATCATTTAAAGTTATTAAATTATTAAAATGT
Found at i:161132 original size:30 final size:31
Alignment explanation
Indices: 161096--161165 Score: 124
Period size: 30 Copynumber: 2.3 Consensus size: 31
161086 TTGAAAGACT
*
161096 AAAATGAAATCACTCTAAAAATTGAGTGAC-
1 AAAATGAAATCACTATAAAAATTGAGTGACA
161126 AAAATGAAATCACTATAAAAATTGAGTGACA
1 AAAATGAAATCACTATAAAAATTGAGTGACA
161157 AAAATGAAA
1 AAAATGAAA
161166 GTGTAAACAT
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
30 29 0.76
31 9 0.24
ACGTcount: A:0.56, C:0.10, G:0.13, T:0.21
Consensus pattern (31 bp):
AAAATGAAATCACTATAAAAATTGAGTGACA
Found at i:162740 original size:22 final size:23
Alignment explanation
Indices: 162714--162775 Score: 83
Period size: 23 Copynumber: 2.7 Consensus size: 23
162704 TAAAAATGAT
162714 AAAATT-TCAATTTAATTAT-TTA
1 AAAATTAT-AATTTAATTATCTTA
* *
162736 AAAATTATATTTTTATTATCTTA
1 AAAATTATAATTTAATTATCTTA
162759 AAAATTATAATTTAATT
1 AAAATTATAATTTAATT
162776 TCAACACCCA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
22 15 0.44
23 19 0.56
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (23 bp):
AAAATTATAATTTAATTATCTTA
Found at i:179568 original size:11 final size:11
Alignment explanation
Indices: 179552--179576 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
179542 TTTCAACAAG
179552 CATCTTACTCA
1 CATCTTACTCA
179563 CATCTTACTCA
1 CATCTTACTCA
179574 CAT
1 CAT
179577 ATCAATCGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.36, G:0.00, T:0.36
Consensus pattern (11 bp):
CATCTTACTCA
Found at i:179972 original size:46 final size:46
Alignment explanation
Indices: 179919--180011 Score: 116
Period size: 46 Copynumber: 2.0 Consensus size: 46
179909 TCGACGCGAT
* * *
179919 ACATAATCT-AGGTTTTTAATTAGGCCAATCAACACTAATTGCCAAC
1 ACATAATCTGA-GTTCTTAATTAGGCCAAACAACACCAATTGCCAAC
* * *
179965 ACATAATCTGAGTTCTTCATTAGTCCAAACAACACCGATTGCCAAC
1 ACATAATCTGAGTTCTTAATTAGGCCAAACAACACCAATTGCCAAC
180011 A
1 A
180012 GAATGATAAC
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
46 39 0.98
47 1 0.03
ACGTcount: A:0.37, C:0.25, G:0.11, T:0.28
Consensus pattern (46 bp):
ACATAATCTGAGTTCTTAATTAGGCCAAACAACACCAATTGCCAAC
Found at i:185652 original size:103 final size:103
Alignment explanation
Indices: 185493--185687 Score: 309
Period size: 103 Copynumber: 1.9 Consensus size: 103
185483 TCTTTAATTA
* * ** *
185493 AAATTAATGTACTCAATTTTGTACATTTGTCCTACATGCATGCAACTTTATGTTTATTAGTCAAA
1 AAATTAATATACTCAATTTTGTACATTTATCCTACATGCATGCAACTAAATATTTATTAGTCAAA
*
185558 CCAAATCAATGAGCATTAAATTTAATTAAAGAGATTTT
66 CCAAACCAATGAGCATTAAATTTAATTAAAGAGATTTT
* *
185596 AAATTAATATACTCAATTTTGTACGTTTATCCTACATGCATGCAGCTAAATATTTATTAGTCAAA
1 AAATTAATATACTCAATTTTGTACATTTATCCTACATGCATGCAACTAAATATTTATTAGTCAAA
*
185661 CCAAACCAATGAGCATTAATTTTAATT
66 CCAAACCAATGAGCATTAAATTTAATT
185688 TTAATTTTGT
Statistics
Matches: 83, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
103 83 1.00
ACGTcount: A:0.37, C:0.15, G:0.10, T:0.38
Consensus pattern (103 bp):
AAATTAATATACTCAATTTTGTACATTTATCCTACATGCATGCAACTAAATATTTATTAGTCAAA
CCAAACCAATGAGCATTAAATTTAATTAAAGAGATTTT
Found at i:196133 original size:4 final size:4
Alignment explanation
Indices: 196124--196166 Score: 68
Period size: 4 Copynumber: 10.8 Consensus size: 4
196114 ATCAATTTTA
* *
196124 ACAT ACAT ACAT ACGT ACGT ACAT ACAT ACAT ACAT ACAT ACA
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACA
196167 CACACACACA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 37 1.00
ACGTcount: A:0.47, C:0.26, G:0.05, T:0.23
Consensus pattern (4 bp):
ACAT
Found at i:197209 original size:85 final size:85
Alignment explanation
Indices: 197110--197276 Score: 289
Period size: 85 Copynumber: 2.0 Consensus size: 85
197100 CCTAGTTAAA
* *
197110 TCTTTAAAATATTAATATTATATTAATTAAGTTTATTATTAGTATAAACATCAATTTAAATATTA
1 TCTTTAAAATATTAATATTATATCAATTAAGTATATTATTAGTATAAACATCAATTTAAATATTA
197175 AATGTCAATATAAATTTGAT
66 AATGTCAATATAAATTTGAT
* *
197195 TCTTTAAAATATTAATATTATATCAATTAAGTATATTATTAGTATAGACGTCAATTTAAATATTA
1 TCTTTAAAATATTAATATTATATCAATTAAGTATATTATTAGTATAAACATCAATTTAAATATTA
*
197260 AATGTCAATATGAATTT
66 AATGTCAATATAAATTT
197277 AATGTGGAAT
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
85 77 1.00
ACGTcount: A:0.44, C:0.05, G:0.06, T:0.45
Consensus pattern (85 bp):
TCTTTAAAATATTAATATTATATCAATTAAGTATATTATTAGTATAAACATCAATTTAAATATTA
AATGTCAATATAAATTTGAT
Found at i:216356 original size:56 final size:57
Alignment explanation
Indices: 216270--216399 Score: 142
Period size: 56 Copynumber: 2.4 Consensus size: 57
216260 AAATACGAAT
* * * * * *
216270 AAAAATAT-TTTTTT-GTGTCGCTTATGTCATGATCGACA-CATCTTTATCAAATAA
1 AAAAATATATTTTTTGGTGTAGCCTATATCATGACCGACACCACCTTTACCAAATAA
* * **
216324 AAATATATATTTTTTGGTGTAGCCTATATCATGGCCGACACCACCTTTACCTGATAA
1 AAAAATATATTTTTTGGTGTAGCCTATATCATGACCGACACCACCTTTACCAAATAA
216381 AAAAATAT-TTTTTTGGTGT
1 AAAAATATATTTTTTGGTGT
216400 CGTCATGCCA
Statistics
Matches: 62, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
54 7 0.11
55 6 0.10
56 30 0.48
57 19 0.31
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.40
Consensus pattern (57 bp):
AAAAATATATTTTTTGGTGTAGCCTATATCATGACCGACACCACCTTTACCAAATAA
Found at i:216420 original size:55 final size:56
Alignment explanation
Indices: 216320--216449 Score: 145
Period size: 56 Copynumber: 2.3 Consensus size: 56
216310 TCTTTATCAA
* * * *
216320 ATAAAAATATATATTTTTTGGTGTAGCCTATATCATGGCCGACACCACCTTTACCTG
1 ATAAAAAAATAT-TTTTTTGGTGTAGCCTATACCATGGCCAACACCACATTTACCTG
* * * * **
216377 ATAAAAAAATATTTTTTTGGTGTCGTC-ATGCCATGGCCAACACCTCATTTATTTG
1 ATAAAAAAATATTTTTTTGGTGTAGCCTATACCATGGCCAACACCACATTTACCTG
216432 ATAAAAAAAATATTTTTT
1 AT-AAAAAAATATTTTTT
216450 AGGTATTATT
Statistics
Matches: 62, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
55 23 0.37
56 28 0.45
57 11 0.18
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.38
Consensus pattern (56 bp):
ATAAAAAAATATTTTTTTGGTGTAGCCTATACCATGGCCAACACCACATTTACCTG
Found at i:217239 original size:21 final size:22
Alignment explanation
Indices: 217213--217342 Score: 93
Period size: 23 Copynumber: 5.7 Consensus size: 22
217203 ATACGGAACA
*
217213 AACAGAGAGTAC-CAAAGTACT
1 AACAGAGAGCACACAAAGTACT
* *
217234 AACAGAGAGCACA-TAAGTGCTGGGT
1 AACAGAGAGCACACAAAGTAC----T
* * *
217259 AACAGAGAACACACACAGTGCT
1 AACAGAGAGCACACAAAGTACT
*
217281 AAACAGAGAGTACACAAAGTACT
1 -AACAGAGAGCACACAAAGTACT
**
217304 AATCAGAGAGCACACAAAGTGTT
1 AA-CAGAGAGCACACAAAGTACT
*
217327 AATCAGAGAACACACA
1 AA-CAGAGAGCACACA
217343 CACTGCTAAT
Statistics
Matches: 87, Mismatches: 14, Indels: 14
0.76 0.12 0.12
Matches are distributed among these distances:
21 16 0.18
22 3 0.03
23 50 0.57
25 13 0.15
26 5 0.06
ACGTcount: A:0.46, C:0.20, G:0.21, T:0.13
Consensus pattern (22 bp):
AACAGAGAGCACACAAAGTACT
Found at i:217334 original size:69 final size:67
Alignment explanation
Indices: 217212--217351 Score: 194
Period size: 69 Copynumber: 2.0 Consensus size: 67
217202 TATACGGAAC
* *
217212 AAACAGAGAGTACCAAAGTACTAACAGAGAGCACATAAGTGCTGGGTAACAGAGAACACACACAG
1 AAACAGAGAGTACCAAAGTACTAACAGAGAGCACAAAAGTGCT--GTAACAGAGAACACACACAC
217277 TGCT
64 TGCT
217281 AAACAGAGAGTACACAAAGTACTAATCAGAGAGCACACAAAGTG-T-TAATCAGAGAACACACAC
1 AAACAGAGAGTAC-CAAAGTACTAA-CAGAGAGCACA-AAAGTGCTGTAA-CAGAGAACACACAC
217344 ACTGCT
62 ACTGCT
217350 AA
1 AA
217352 TAATAGAGAG
Statistics
Matches: 65, Mismatches: 2, Indels: 8
0.87 0.03 0.11
Matches are distributed among these distances:
68 3 0.05
69 34 0.52
70 11 0.17
71 12 0.18
72 5 0.08
ACGTcount: A:0.46, C:0.21, G:0.20, T:0.14
Consensus pattern (67 bp):
AAACAGAGAGTACCAAAGTACTAACAGAGAGCACAAAAGTGCTGTAACAGAGAACACACACACTG
CT
Found at i:217352 original size:23 final size:23
Alignment explanation
Indices: 217261--217352 Score: 103
Period size: 23 Copynumber: 4.0 Consensus size: 23
217251 TGCTGGGTAA
* *
217261 CAGAGAACACACACAGTGCTAAA
1 CAGAGAACACACAAAGTGCTAAT
** *
217284 CAGAGAGTACACAAAGTACTAAT
1 CAGAGAACACACAAAGTGCTAAT
* *
217307 CAGAGAGCACACAAAGTGTTAAT
1 CAGAGAACACACAAAGTGCTAAT
* *
217330 CAGAGAACACACACACTGCTAAT
1 CAGAGAACACACAAAGTGCTAAT
217353 AATAGAGAGC
Statistics
Matches: 57, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 57 1.00
ACGTcount: A:0.46, C:0.23, G:0.17, T:0.14
Consensus pattern (23 bp):
CAGAGAACACACAAAGTGCTAAT
Found at i:230981 original size:22 final size:25
Alignment explanation
Indices: 230948--231000 Score: 76
Period size: 23 Copynumber: 2.2 Consensus size: 25
230938 ATTAGATCAA
230948 AAAATAAATTA-TTATTT-T-TTATT
1 AAAA-AAATTATTTATTTATATTATT
230971 AAAAAAATTATTTATTTATATTATT
1 AAAAAAATTATTTATTTATATTATT
230996 AAAAA
1 AAAAA
231001 TTGATCTCTA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
22 6 0.22
23 10 0.37
24 1 0.04
25 10 0.37
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (25 bp):
AAAAAAATTATTTATTTATATTATT
Found at i:231002 original size:23 final size:21
Alignment explanation
Indices: 230953--231000 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 21
230943 ATCAAAAAAT
230953 AAATTATTATTTTTTATTAAAA
1 AAATTATTATTTTTTATT-AAA
230975 AAATTATTTATTTATATTATTAAA
1 AAATTA-TTATTT-T-TTATTAAA
230999 AA
1 AA
231001 TTGATCTCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 6 0.26
23 6 0.26
24 6 0.26
25 5 0.22
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
AAATTATTATTTTTTATTAAA
Found at i:231616 original size:3 final size:3
Alignment explanation
Indices: 231610--231641 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
231600 TATTTGGGTT
231610 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
231642 TTTAATTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:239319 original size:18 final size:18
Alignment explanation
Indices: 239296--239341 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
239286 CGACACGGAG
239296 GAGGAAGAAGAAGAACCA
1 GAGGAAGAAGAAGAACCA
* *
239314 GAGGAAGAAGAGGAGCCA
1 GAGGAAGAAGAAGAACCA
239332 GAGGAAGAAG
1 GAGGAAGAAG
239342 GAGTTCAAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.50, C:0.09, G:0.41, T:0.00
Consensus pattern (18 bp):
GAGGAAGAAGAAGAACCA
Found at i:250550 original size:14 final size:16
Alignment explanation
Indices: 250531--250567 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
250521 AAAATGTTAA
250531 TTAATT-AA-ATTTAT
1 TTAATTAAAGATTTAT
250545 TTAATTAAAGATTTAT
1 TTAATTAAAGATTTAT
250561 TCTAATT
1 T-TAATT
250568 CCATTTGGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 6 0.30
15 2 0.10
16 7 0.35
17 5 0.25
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (16 bp):
TTAATTAAAGATTTAT
Found at i:271296 original size:18 final size:17
Alignment explanation
Indices: 271262--271306 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
271252 TGTCACATCG
*
271262 ATAAATAATTTAAAATT
1 ATAAATAATTCAAAATT
271279 ATAAATATATTCAAAATT
1 ATAAATA-ATTCAAAATT
*
271297 CTATAATAAT
1 ATA-AATAAT
271307 AATAATTCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 7 0.29
18 13 0.54
19 4 0.17
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (17 bp):
ATAAATAATTCAAAATT
Found at i:273617 original size:4 final size:4
Alignment explanation
Indices: 273608--273636 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
273598 TCTTCTACTT
273608 AATA AATA AATA AATA AATA AATA AATA A
1 AATA AATA AATA AATA AATA AATA AATA A
273637 TTTTTTTGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AATA
Found at i:274261 original size:10 final size:11
Alignment explanation
Indices: 274232--274261 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
274222 TTAAAGCTTA
274232 AATTTAAATTG
1 AATTTAAATTG
274243 AATTTAAATTG
1 AATTTAAATTG
274254 AA-TTAAAT
1 AATTTAAAT
274262 AAGTTCAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 6 0.32
11 13 0.68
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (11 bp):
AATTTAAATTG
Found at i:275188 original size:26 final size:27
Alignment explanation
Indices: 275154--275207 Score: 83
Period size: 26 Copynumber: 2.0 Consensus size: 27
275144 TACCTGACAC
*
275154 CCAATGGAGGAACA-CGAGTGGCGGCA
1 CCAATGGAGGAACATCAAGTGGCGGCA
*
275180 CCAATGGAGGAATATCAAGTGGCGGCA
1 CCAATGGAGGAACATCAAGTGGCGGCA
275207 C
1 C
275208 TAAGGGGTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 13 0.52
27 12 0.48
ACGTcount: A:0.31, C:0.22, G:0.35, T:0.11
Consensus pattern (27 bp):
CCAATGGAGGAACATCAAGTGGCGGCA
Found at i:275413 original size:17 final size:16
Alignment explanation
Indices: 275387--275441 Score: 76
Period size: 17 Copynumber: 3.4 Consensus size: 16
275377 GGGAAAGAAA
*
275387 GAAAGGAAGAACGAGAG
1 GAAAGAAAGAA-GAGAG
275404 GAAAGAAAGAAGGAGAG
1 GAAAGAAAGAA-GAGAG
275421 GAAAGAAAGAAGA-AG
1 GAAAGAAAGAAGAGAG
275436 GAAAGA
1 GAAAGA
275442 TTTAAGTAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.22
16 2 0.06
17 26 0.72
ACGTcount: A:0.60, C:0.02, G:0.38, T:0.00
Consensus pattern (16 bp):
GAAAGAAAGAAGAGAG
Done.