Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A12
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: 102106374
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 3186644 characters in sequence are not A, C, G, or T
File 270 of 311
Found at i:89298039 original size:27 final size:27
Alignment explanation
Indices: 89297949--89298040 Score: 105
Period size: 27 Copynumber: 3.4 Consensus size: 27
89297939 ATGACACTAC
* *
89297949 TAAGCCGAATGCTTATCTTTTCCAAAA
1 TAAGTCGAATGCTCATCTTTTCCAAAA
*
89297976 T-AGGCTGAATGCTCATCTTTTCCAAAA
1 TAAGTC-GAATGCTCATCTTTTCCAAAA
* * * *
89298003 TAGGTTGAATGCTCCTCTTTTTCAAAA
1 TAAGTCGAATGCTCATCTTTTCCAAAA
89298030 TAAGTCGAATG
1 TAAGTCGAATG
89298041 TTCCTTTCAT
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
26 3 0.06
27 50 0.93
28 1 0.02
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.35
Consensus pattern (27 bp):
TAAGTCGAATGCTCATCTTTTCCAAAA
Found at i:89304306 original size:18 final size:18
Alignment explanation
Indices: 89304285--89304346 Score: 63
Period size: 18 Copynumber: 3.4 Consensus size: 18
89304275 TACTATTTAT
*
89304285 GTATACAGCATTATTCAC
1 GTATACAGCACTATTCAC
*
89304303 GTATACGGCACTATTCAC
1 GTATACAGCACTATTCAC
* * *
89304321 ATATAC-GATACTGTTCAC
1 GTATACAG-CACTATTCAC
89304339 GTATACAG
1 GTATACAG
89304347 TAGTTGGGAT
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
17 1 0.03
18 34 0.94
19 1 0.03
ACGTcount: A:0.32, C:0.23, G:0.15, T:0.31
Consensus pattern (18 bp):
GTATACAGCACTATTCAC
Found at i:89315888 original size:17 final size:17
Alignment explanation
Indices: 89315845--89315889 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
89315835 TATTATTTAT
*
89315845 TTATTATATTGTTGGAA
1 TTATAATATTGTTGGAA
*
89315862 TTGA-ATTATTGTTGGAA
1 TT-ATAATATTGTTGGAA
89315879 TTATAATATTG
1 TTATAATATTG
89315890 AATTGGATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
16 1 0.04
17 21 0.91
18 1 0.04
ACGTcount: A:0.31, C:0.00, G:0.18, T:0.51
Consensus pattern (17 bp):
TTATAATATTGTTGGAA
Found at i:89316595 original size:23 final size:21
Alignment explanation
Indices: 89316560--89316601 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
89316550 ACCAACTTAC
89316560 ATATTGGTATGAGAATGAGGT
1 ATATTGGTATGAGAATGAGGT
*
89316581 ATATTGTGATATGAGTATGAG
1 ATATTG-G-TATGAGAATGAG
89316602 TGTTATATGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 6 0.33
22 1 0.06
23 11 0.61
ACGTcount: A:0.33, C:0.00, G:0.31, T:0.36
Consensus pattern (21 bp):
ATATTGGTATGAGAATGAGGT
Found at i:89318098 original size:4 final size:4
Alignment explanation
Indices: 89318084--89318116 Score: 57
Period size: 4 Copynumber: 8.0 Consensus size: 4
89318074 AACAGGGGAA
89318084 AAAG AAAAG AAAG AAAG AAAG AAAG AAAG AAAG
1 AAAG -AAAG AAAG AAAG AAAG AAAG AAAG AAAG
89318117 GAAAATTTAG
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 24 0.86
5 4 0.14
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:89320297 original size:50 final size:50
Alignment explanation
Indices: 89320173--89320421 Score: 284
Period size: 50 Copynumber: 4.8 Consensus size: 50
89320163 GATAATAACA
* * ** * *
89320173 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGAT-GG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCAT-CTCGG
* *
89320224 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
89320274 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* *
89320324 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC---ATC-T-CGG
* *
89320379 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
89320422 TTACCCAAAT
Statistics
Matches: 170, Mismatches: 21, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
49 1 0.01
50 92 0.54
51 33 0.19
53 2 0.01
54 1 0.01
55 2 0.01
56 39 0.23
ACGTcount: A:0.20, C:0.29, G:0.24, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:89320351 original size:100 final size:104
Alignment explanation
Indices: 89320172--89320421 Score: 357
Period size: 100 Copynumber: 2.4 Consensus size: 104
89320162 TGATAATAAC
**
89320172 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGATGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCGTGATGGTGCCCATGCCATG
* *
89320237 TCCCAGACATGGTCTTATAGGGGACCTCTC-ATC-T-CGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
* *
89320274 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGT-CTCGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGAT-GGTGCCCATGCCATG
89320337 TCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCA--ATCTTAAGG
* *
89320379 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
89320422 TTACCCAAAT
Statistics
Matches: 133, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
99 1 0.01
100 50 0.38
101 36 0.27
103 3 0.02
104 1 0.01
105 2 0.02
106 40 0.30
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (104 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGATGGTGCCCATGCCATGT
CCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
Found at i:89320537 original size:13 final size:13
Alignment explanation
Indices: 89320516--89320547 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
89320506 GCTTGGATCA
*
89320516 TCATCAAATAAAT
1 TCATAAAATAAAT
89320529 TCATAAAATAAAT
1 TCATAAAATAAAT
89320542 TCATAA
1 TCATAA
89320548 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:89320794 original size:30 final size:30
Alignment explanation
Indices: 89320759--89320816 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
89320749 CCTCCACTCT
*
89320759 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
89320789 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
89320817 AAGGCTCGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.31, C:0.24, G:0.03, T:0.41
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:89327890 original size:50 final size:52
Alignment explanation
Indices: 89327765--89328014 Score: 276
Period size: 50 Copynumber: 4.8 Consensus size: 52
89327755 GATAATAACA
* * ** * *
89327765 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTTC-TCGTGATGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCGT-ACGG
* *
89327817 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATC-T-CGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCGTACGG
* * *
89327867 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTC-T-CGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCGTACGG
* * *
89327917 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC---ATCGTACGG
* *
89327972 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
89328015 TTACCCAAAT
Statistics
Matches: 170, Mismatches: 21, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
50 87 0.51
52 37 0.22
53 4 0.02
54 1 0.01
55 2 0.01
56 39 0.23
ACGTcount: A:0.20, C:0.29, G:0.24, T:0.26
Consensus pattern (52 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCGTACGG
Found at i:89327944 original size:100 final size:104
Alignment explanation
Indices: 89327764--89328014 Score: 359
Period size: 100 Copynumber: 2.4 Consensus size: 104
89327754 TGATAATAAC
*
89327764 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTTCTCGTGATGGTGCCCATGCCAT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA--TCTCTCGTGATGGTGCCCATGCCAT
* *
89327829 GTCCCAGACATGGTCTTATAGGGGACCTCTC-ATC-T-CGG
64 GTCCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
* * *
89327867 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGT-CTCGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATCTCTCGTGAT-GGTGCCCATGCCATG
89327930 TCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCA--ATCTTAAGG
*
89327972 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
89328015 TTACCCAAAT
Statistics
Matches: 133, Mismatches: 8, Indels: 11
0.88 0.05 0.07
Matches are distributed among these distances:
99 1 0.01
100 50 0.38
102 36 0.27
103 3 0.02
104 1 0.01
105 2 0.02
106 40 0.30
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (104 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATCTCTCGTGATGGTGCCCATGCCATGT
CCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
Found at i:89328130 original size:13 final size:13
Alignment explanation
Indices: 89328109--89328140 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
89328099 GCTTGGATCA
*
89328109 TCATCAAATAAAT
1 TCATAAAATAAAT
89328122 TCATAAAATAAAT
1 TCATAAAATAAAT
89328135 TCATAA
1 TCATAA
89328141 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:89328388 original size:30 final size:30
Alignment explanation
Indices: 89328353--89328410 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
89328343 CCTCGACTCT
*
89328353 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
89328383 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
89328411 AAGGCTCGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.31, C:0.24, G:0.03, T:0.41
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:89331913 original size:39 final size:39
Alignment explanation
Indices: 89331868--89332006 Score: 233
Period size: 39 Copynumber: 3.6 Consensus size: 39
89331858 ATGCAAGATA
89331868 CTGGAAATGTATCCGGGCTAAAGTCTCGCAGGCTTCGTG
1 CTGGAAATGTATCCGGGCTAAAGTCTCGCAGGCTTCGTG
*
89331907 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
1 CTGGAAATGTATCCGGGCTAAAGTCTCGCAGGCTTCGTG
* *
89331946 TTGGAAATGTATCCGGGCTAAAGTCTCGTAGGCTTCGTG
1 CTGGAAATGTATCCGGGCTAAAGTCTCGCAGGCTTCGTG
* *
89331985 CAGGAAATGTATCCGGCCTAAA
1 CTGGAAATGTATCCGGGCTAAA
89332007 ATCCCGTAAG
Statistics
Matches: 93, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 93 1.00
ACGTcount: A:0.23, C:0.22, G:0.29, T:0.25
Consensus pattern (39 bp):
CTGGAAATGTATCCGGGCTAAAGTCTCGCAGGCTTCGTG
Found at i:89336100 original size:16 final size:16
Alignment explanation
Indices: 89336079--89336110 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
89336069 TGAAATTCGC
89336079 TTAACAAAATAGTCCT
1 TTAACAAAATAGTCCT
89336095 TTAACAAAATAGTCCT
1 TTAACAAAATAGTCCT
89336111 AAAATATTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.19, G:0.06, T:0.31
Consensus pattern (16 bp):
TTAACAAAATAGTCCT
Found at i:89338764 original size:43 final size:42
Alignment explanation
Indices: 89338703--89338812 Score: 116
Period size: 42 Copynumber: 2.6 Consensus size: 42
89338693 CAATGCCAAC
*
89338703 GTCCCAGAC-GTGGTCTTACATGTAATCAAACATCGATA-CCACT
1 GTCCCAGACAG-GGTCTTACATGTAATCAAACA-CGA-AGACACT
* * *
89338746 GTCCCAGACAGGGTCTTACATGAAATCATATACGAAGACACT
1 GTCCCAGACAGGGTCTTACATGTAATCAAACACGAAGACACT
* * *
89338788 ATCCCAGACATGGTCTTACACGTAA
1 GTCCCAGACAGGGTCTTACATGTAA
89338813 AACAGAAGTC
Statistics
Matches: 57, Mismatches: 8, Indels: 5
0.81 0.11 0.07
Matches are distributed among these distances:
41 1 0.02
42 28 0.49
43 27 0.47
44 1 0.02
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (42 bp):
GTCCCAGACAGGGTCTTACATGTAATCAAACACGAAGACACT
Found at i:89338805 original size:42 final size:43
Alignment explanation
Indices: 89338704--89338807 Score: 122
Period size: 43 Copynumber: 2.4 Consensus size: 43
89338694 AATGCCAACG
* * * *
89338704 TCCCAGACGTGGTCTTACATGTAATCAAACATCGATACCACTG
1 TCCCAGACATGGTCTTACATGAAATCAAACATCGATAACACTA
* * *
89338747 TCCCAGACAGGGTCTTACATGAAATCATATA-CGA-AGACACTA
1 TCCCAGACATGGTCTTACATGAAATCAAACATCGATA-ACACTA
89338789 TCCCAGACATGGTCTTACA
1 TCCCAGACATGGTCTTACA
89338808 CGTAAAACAG
Statistics
Matches: 52, Mismatches: 8, Indels: 3
0.83 0.13 0.05
Matches are distributed among these distances:
41 1 0.02
42 25 0.48
43 26 0.50
ACGTcount: A:0.33, C:0.27, G:0.16, T:0.24
Consensus pattern (43 bp):
TCCCAGACATGGTCTTACATGAAATCAAACATCGATAACACTA
Found at i:89341202 original size:18 final size:17
Alignment explanation
Indices: 89341181--89341214 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
89341171 TAATTCTACT
89341181 CAAAAATAATTTTTGATC
1 CAAAAAT-ATTTTTGATC
*
89341199 CAAAAGTATTTTTGAT
1 CAAAAATATTTTTGAT
89341215 AAATAATGCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.41
Consensus pattern (17 bp):
CAAAAATATTTTTGATC
Found at i:89356059 original size:27 final size:25
Alignment explanation
Indices: 89356003--89356082 Score: 103
Period size: 25 Copynumber: 3.3 Consensus size: 25
89355993 ATTTTAACGC
*
89356003 GCTCTCTGATAATTAGCACGTTAGT
1 GCTCTCTGATAATTAGCACATTAGT
*
89356028 GCTCTCTGATTATTAGCACATTAGT
1 GCTCTCTGATAATTAGCACATTAGT
* *
89356053 GCTCTCTG-T--TTATCACATTTGT
1 GCTCTCTGATAATTAGCACATTAGT
89356075 GCTCTCTG
1 GCTCTCTG
89356083 TATAGCATTT
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
22 19 0.37
24 1 0.02
25 31 0.61
ACGTcount: A:0.19, C:0.23, G:0.17, T:0.41
Consensus pattern (25 bp):
GCTCTCTGATAATTAGCACATTAGT
Found at i:89356076 original size:22 final size:23
Alignment explanation
Indices: 89356003--89356101 Score: 103
Period size: 22 Copynumber: 4.2 Consensus size: 23
89355993 ATTTTAACGC
*
89356003 GCTCTCTGATAATTAGCACGTTAGT
1 GCTCTCTG-T-ATTAGCACATTAGT
89356028 GCTCTCTGATTATTAGCACATTAGT
1 GCTCTCTG--TATTAGCACATTAGT
* *
89356053 GCTCTCTGT-TTATCACATTTGT
1 GCTCTCTGTATTAGCACATTAGT
**
89356075 GCTCTCTGTA-TAGCATTTTAGT
1 GCTCTCTGTATTAGCACATTAGT
89356097 GCTCT
1 GCTCT
89356102 TTGTTCATTA
Statistics
Matches: 64, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
22 33 0.52
23 1 0.02
25 29 0.45
26 1 0.02
ACGTcount: A:0.19, C:0.21, G:0.17, T:0.42
Consensus pattern (23 bp):
GCTCTCTGTATTAGCACATTAGT
Found at i:89356971 original size:14 final size:16
Alignment explanation
Indices: 89356935--89356975 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
89356925 TTGATATAGT
89356935 TTTTAAATATATATGA
1 TTTTAAATATATATGA
*
89356951 TTTTAAATTTATAT-A
1 TTTTAAATATATATGA
89356966 -TTTAAATATA
1 TTTTAAATATA
89356976 GAATTAGTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
14 9 0.39
15 1 0.04
16 13 0.57
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (16 bp):
TTTTAAATATATATGA
Found at i:89366171 original size:2 final size:2
Alignment explanation
Indices: 89366164--89366212 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
89366154 ATTCATTATA
89366164 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
89366206 AG AG AG A
1 AG AG AG A
89366213 TTCAGAAGGG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:89370665 original size:2 final size:2
Alignment explanation
Indices: 89370658--89370683 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
89370648 AGTTTTAAAG
89370658 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
89370684 TGAAGTAGCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:89372237 original size:21 final size:23
Alignment explanation
Indices: 89372203--89372249 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
89372193 AACTTATCAA
*
89372203 TTTAAATATTATAA-TAAAAAAT
1 TTTAAATATCATAATTAAAAAAT
*
89372225 TTTAAA-ATCATAATTAAAACAT
1 TTTAAATATCATAATTAAAAAAT
89372247 TTT
1 TTT
89372250 TTTAACATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 6 0.27
22 16 0.73
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (23 bp):
TTTAAATATCATAATTAAAAAAT
Found at i:89376374 original size:25 final size:25
Alignment explanation
Indices: 89376317--89376374 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
89376307 CAACTCTTAC
* *
89376317 GAGCTTACCGATATTCAGCTCGTAT
1 GAGCTTACCGATATTCAGCTCGGAG
* * *
89376342 GAGTTTACCGTTATTCAGCTTGGAG
1 GAGCTTACCGATATTCAGCTCGGAG
89376367 GAGCTTAC
1 GAGCTTAC
89376375 TGTTTATCGC
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.22, C:0.21, G:0.24, T:0.33
Consensus pattern (25 bp):
GAGCTTACCGATATTCAGCTCGGAG
Found at i:89386130 original size:19 final size:21
Alignment explanation
Indices: 89386102--89386148 Score: 64
Period size: 19 Copynumber: 2.4 Consensus size: 21
89386092 GGTGAGAAAC
*
89386102 AAATTGAAATTTTT-T-ATTT
1 AAATTTAAATTTTTATAATTT
89386121 AAATTTAAATTTTTATAATTT
1 AAATTTAAATTTTTATAATTT
89386142 -AATTTAA
1 AAATTTAA
89386149 TTTAATTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 13 0.52
20 8 0.32
21 4 0.16
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (21 bp):
AAATTTAAATTTTTATAATTT
Found at i:89387472 original size:22 final size:23
Alignment explanation
Indices: 89387444--89387487 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
89387434 TAACAATATA
89387444 ATAAATATATAAATTT-ATTATC
1 ATAAATATATAAATTTAATTATC
*
89387466 ATAAATATATAAGTTTAATTAT
1 ATAAATATATAAATTTAATTAT
89387488 TATTTAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.45
Consensus pattern (23 bp):
ATAAATATATAAATTTAATTATC
Found at i:89392355 original size:3 final size:3
Alignment explanation
Indices: 89392347--89392717 Score: 154
Period size: 3 Copynumber: 122.7 Consensus size: 3
89392337 AATAACATAT
* * *
89392347 ATA ATA AT- ATG ACA ATA ATA ATA ACA ATA ATA ATAA ATAA ATAA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A AT-A AT-A ATA
* * *
89392394 ATG ATA ATA ATA ATA ATA ATA A-A GAAA ATA CA-G ATA A-A ATTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA -ATA ATA ATA A-TA ATA
* * * * * *
89392439 ATG ATA CTA ACGA AT- ATA AGTA ATA GTA GTA A-A AAA ATA ATAA ATA
1 ATA ATA ATA A-TA ATA ATA A-TA ATA ATA ATA ATA ATA ATA AT-A ATA
* * * * ** *
89392485 ATA ATA GTA ACA ATA ATG ATA ATAA ATA TTA GCA GTA A-A A-A ATA
1 ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA
** * * * *
89392529 ATA ATA GGA ATA ATA ATA ACA ATA ATA ATA GTA ATA ATA AGA ATA TTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * ** * * *
89392577 ATA TTA GTA TTA ATA ATA AGG ATA ATA GTA GAAA ATA AAA ATA A-A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA
* * * *
89392622 ATA AT- ATA GTA ATA ATA ATA A-A AGCA AAA ATA ATA GTA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA ATA ATA ATA
* * * *
89392666 ATG GTA AAA ATAA ATA GTA ATA ATA ATA ATA ATA ATA CA-A ATA ATAA
1 ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA AT-A
89392713 ATA AT
1 ATA AT
89392718 CTAAAGTTTG
Statistics
Matches: 274, Mismatches: 70, Indels: 48
0.70 0.18 0.12
Matches are distributed among these distances:
2 21 0.08
3 217 0.79
4 36 0.13
ACGTcount: A:0.62, C:0.03, G:0.08, T:0.28
Consensus pattern (3 bp):
ATA
Found at i:89392897 original size:3 final size:3
Alignment explanation
Indices: 89392884--89393022 Score: 79
Period size: 3 Copynumber: 46.0 Consensus size: 3
89392874 GAAAATATAC
* * *
89392884 AAT AGT AAT AAT AAT AAA AAGGT AAT AAT AAT -AT ATT AGAT AAT AAAT
1 AAT AAT AAT AAT AAT AAT AA--T AAT AAT AAT AAT AAT A-AT AAT -AAT
* * * * * ** *
89392932 AAT AAT AAT AAT AAC AGT AAT AA- AA- AAT GAT AAT AGT GAT GTT AGT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * *
89392978 AAT AAT AAT AAC AAT -AT ATT AAT AAT AAT AAT ATAT ATT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT
89393023 GACAATAACA
Statistics
Matches: 103, Mismatches: 25, Indels: 16
0.72 0.17 0.11
Matches are distributed among these distances:
2 8 0.08
3 85 0.83
4 8 0.08
5 2 0.02
ACGTcount: A:0.58, C:0.01, G:0.07, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:89392954 original size:28 final size:27
Alignment explanation
Indices: 89392892--89393022 Score: 72
Period size: 28 Copynumber: 4.7 Consensus size: 27
89392882 ACAATAGTAA
* *
89392892 TAATAATAAA-AAGGTAATAATAATATAT
1 TAATAATAAATAA--TAATAATAATACAG
89392920 TAGATAATAAATAATAATAATAATAACAG
1 TA-ATAATAAATAATAATAATAAT-ACAG
* * * * **
89392949 TAATAAAAAATGATAATAGTGATGTTAG
1 TAATAATAAATAATAATAATAAT-ACAG
*
89392977 TAATAAT-AATAACAATATATTAATA-A-
1 TAATAATAAATAATAATA-A-TAATACAG
* *
89393003 TAATAATATATATTAATAAT
1 TAATAATAAATAATAATAAT
89393023 GACAATAACA
Statistics
Matches: 79, Mismatches: 18, Indels: 15
0.71 0.16 0.13
Matches are distributed among these distances:
25 1 0.01
26 8 0.10
27 16 0.20
28 37 0.47
29 15 0.19
30 2 0.03
ACGTcount: A:0.58, C:0.02, G:0.07, T:0.34
Consensus pattern (27 bp):
TAATAATAAATAATAATAATAATACAG
Found at i:89393002 original size:17 final size:17
Alignment explanation
Indices: 89392980--89393029 Score: 64
Period size: 19 Copynumber: 2.8 Consensus size: 17
89392970 ATGTTAGTAA
89392980 TAATAATAACAATATAT
1 TAATAATAACAATATAT
*
89392997 TAATAATAATAATATATAT
1 TAATAATAA-CA-ATATAT
*
89393016 TAATAATGACAATA
1 TAATAATAACAATA
89393030 ACAGAAAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
17 12 0.43
18 2 0.07
19 14 0.50
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.36
Consensus pattern (17 bp):
TAATAATAACAATATAT
Found at i:89394681 original size:3 final size:3
Alignment explanation
Indices: 89394673--89394701 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
89394663 TTTTCGTAAA
89394673 TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
89394702 TTTAATAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:89396051 original size:13 final size:14
Alignment explanation
Indices: 89396007--89396049 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
89395997 AATCTTTAGT
*
89396007 TTTCCTT-TTTTTT
1 TTTCCTTATTTTTC
89396020 TTTCCTTATTTTTC
1 TTTCCTTATTTTTC
89396034 TTTCC-TATTCTTTC
1 TTTCCTTATT-TTTC
89396048 TT
1 TT
89396050 CCCCTGTTCG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
13 11 0.41
14 16 0.59
ACGTcount: A:0.05, C:0.21, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTCCTTATTTTTC
Found at i:89397315 original size:47 final size:47
Alignment explanation
Indices: 89397206--89397316 Score: 154
Period size: 47 Copynumber: 2.4 Consensus size: 47
89397196 CCGGGATAAG
*
89397206 CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACATTATAGTA
1 CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTATAGTA
* * *
89397253 CACAAAGTACTTCATCGGAACAAATCCGGAACTTTAACAGTAGTCG-A
1 CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTA-TAGTA
89397300 CACATAGTG-TCTCATCG
1 CACATAGTGCT-TCATCG
89397317 ACTCAATGTC
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
46 1 0.02
47 53 0.95
48 2 0.04
ACGTcount: A:0.35, C:0.23, G:0.16, T:0.25
Consensus pattern (47 bp):
CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTATAGTA
Found at i:89398096 original size:4 final size:4
Alignment explanation
Indices: 89398079--89398109 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
89398069 CCCTTTTCTA
*
89398079 TTTC TTTC TATC TTTC TTTC TTTC TTTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT
89398110 TTTTTAACTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.03, C:0.23, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTC
Found at i:89403242 original size:47 final size:47
Alignment explanation
Indices: 89403133--89403243 Score: 154
Period size: 47 Copynumber: 2.4 Consensus size: 47
89403123 CCGGGATAAG
*
89403133 CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACATTATAGTA
1 CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTATAGTA
* * *
89403180 CACAAAGTACTTCATCGGAACAAATCCGGAACTTTAACAGTAGTCG-A
1 CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTA-TAGTA
89403227 CACATAGTG-TCTCATCG
1 CACATAGTGCT-TCATCG
89403244 ACTCAATGTC
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
46 1 0.02
47 53 0.95
48 2 0.04
ACGTcount: A:0.35, C:0.23, G:0.16, T:0.25
Consensus pattern (47 bp):
CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTATAGTA
Found at i:89404697 original size:31 final size:31
Alignment explanation
Indices: 89404662--89404727 Score: 82
Period size: 31 Copynumber: 2.1 Consensus size: 31
89404652 TAATTAATAA
*
89404662 TTTTAATAA-TAATAA-ACATCTAATAAATATC
1 TTTTAATAATTAATAATACATAT-A-AAATATC
*
89404693 TTTTACTAATTAATAATACATATAAAATATC
1 TTTTAATAATTAATAATACATATAAAATATC
89404724 TTTT
1 TTTT
89404728 CGCTAATTGT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
31 19 0.61
32 7 0.23
33 5 0.16
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.44
Consensus pattern (31 bp):
TTTTAATAATTAATAATACATATAAAATATC
Found at i:89405321 original size:14 final size:14
Alignment explanation
Indices: 89405295--89405333 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
89405285 TTTCTTTTTA
89405295 AATTTTAAT-TATT
1 AATTTTAATATATT
*
89405308 AATTTTATTATATT
1 AATTTTAATATATT
*
89405322 ATTTTTAATATA
1 AATTTTAATATA
89405334 AATATAATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
13 8 0.36
14 14 0.64
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
AATTTTAATATATT
Found at i:89405343 original size:18 final size:16
Alignment explanation
Indices: 89405317--89405358 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
89405307 TAATTTTATT
*
89405317 ATATTATTTTTAATATAA
1 ATATAATTTTTAA-AT-A
89405335 ATATAA-TTTTAAATA
1 ATATAATTTTTAAATA
89405350 ATATAATTT
1 ATATAATTT
89405359 GTGTAAACAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 7 0.32
16 4 0.18
17 6 0.27
18 5 0.23
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
ATATAATTTTTAAATA
Found at i:89405354 original size:15 final size:17
Alignment explanation
Indices: 89405324--89405358 Score: 56
Period size: 15 Copynumber: 2.2 Consensus size: 17
89405314 ATTATATTAT
89405324 TTTTAATATAAATATAA
1 TTTTAATATAAATATAA
89405341 TTTTAA-AT-AATATAA
1 TTTTAATATAAATATAA
89405356 TTT
1 TTT
89405359 GTGTAAACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 10 0.56
16 2 0.11
17 6 0.33
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
TTTTAATATAAATATAA
Found at i:89409029 original size:3 final size:3
Alignment explanation
Indices: 89408983--89409011 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
89408973 TCTTATACTA
89408983 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
89409012 ATAGGGTGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:89413941 original size:17 final size:17
Alignment explanation
Indices: 89413913--89413945 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
89413903 TTATATATAA
89413913 TTTTTAATTTAAATTATT
1 TTTTTAATTT-AATTATT
89413931 TTTTTAA-TTAATTAT
1 TTTTTAATTTAATTAT
89413946 ATGAAAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 2 0.13
18 7 0.47
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTTTAATTTAATTATT
Found at i:89427672 original size:42 final size:42
Alignment explanation
Indices: 89427625--89427704 Score: 133
Period size: 42 Copynumber: 1.9 Consensus size: 42
89427615 GAAAAAGAAG
*
89427625 AAGAAATAATGATCATTGCTTAAATGCACTTAACATGGTATT
1 AAGAAATAATAATCATTGCTTAAATGCACTTAACATGGTATT
**
89427667 AAGAAATAATAATCATTGCTTATCTGCACTTAACATGG
1 AAGAAATAATAATCATTGCTTAAATGCACTTAACATGG
89427705 AGAATCTTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.33
Consensus pattern (42 bp):
AAGAAATAATAATCATTGCTTAAATGCACTTAACATGGTATT
Found at i:89439245 original size:53 final size:53
Alignment explanation
Indices: 89439089--89439254 Score: 205
Period size: 53 Copynumber: 3.1 Consensus size: 53
89439079 GACGAAAAAT
* **
89439089 ATGTGATAAGTGTG-C-CCGTTTAAGACCATAGGC-GGGCTATGGCATCGGTGCA
1 ATGTGATAA-TGTGACTCCGTATAAGACCATA-GCTGGGCTATGGCATCGGTATA
89439141 ATGTGATAATGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA
1 ATGTGATAATGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA
* * *
89439194 ATGTGATAATGTGATTCCGTATAAGACCAT-GTCTGGGATATGGCTTCGGTATGA
1 ATGTGATAATGTGACTCCGTATAAGACCATAG-CTGGGCTATGGCATCGGTAT-A
89439248 TATGTGA
1 -ATGTGA
89439255 ACCGTGTAAG
Statistics
Matches: 102, Mismatches: 6, Indels: 9
0.87 0.05 0.08
Matches are distributed among these distances:
51 4 0.04
52 13 0.13
53 78 0.76
54 1 0.01
55 6 0.06
ACGTcount: A:0.26, C:0.16, G:0.29, T:0.30
Consensus pattern (53 bp):
ATGTGATAATGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA
Found at i:89444868 original size:19 final size:19
Alignment explanation
Indices: 89444844--89444881 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
89444834 TTGGTCCAAA
89444844 ATCTTTGAC-CTTTTTAATC
1 ATCTTT-ACTCTTTTTAATC
89444863 ATCTTTACTTCTTTTTAAT
1 ATCTTTAC-TCTTTTTAAT
89444882 TCTTGACAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 2 0.12
19 6 0.35
20 9 0.53
ACGTcount: A:0.21, C:0.18, G:0.03, T:0.58
Consensus pattern (19 bp):
ATCTTTACTCTTTTTAATC
Found at i:89448024 original size:90 final size:90
Alignment explanation
Indices: 89447869--89448047 Score: 340
Period size: 90 Copynumber: 2.0 Consensus size: 90
89447859 TTTATCTTAC
89447869 CAAGGCCCATCACTTTGACAATGAAAAAAACCCACCATGTATCATTTGTCGGTTGTAAATCATGT
1 CAAGGCCCATCACTTTGACAATGAAAAAAACCCACCATGTATCATTTGTCGGTTGTAAATCATGT
89447934 CAATCTATCATTATGCATACCAAGT
66 CAATCTATCATTATGCATACCAAGT
* *
89447959 CAAGGCCCATCACTTTGACAATGAAAAAAGCCCACCATGTATCATTTGTCGGTTGTAAATTATGT
1 CAAGGCCCATCACTTTGACAATGAAAAAAACCCACCATGTATCATTTGTCGGTTGTAAATCATGT
89448024 CAATCTATCATTATGCATACCAAG
66 CAATCTATCATTATGCATACCAAG
89448048 AGGACTTTAT
Statistics
Matches: 87, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
90 87 1.00
ACGTcount: A:0.34, C:0.23, G:0.14, T:0.29
Consensus pattern (90 bp):
CAAGGCCCATCACTTTGACAATGAAAAAAACCCACCATGTATCATTTGTCGGTTGTAAATCATGT
CAATCTATCATTATGCATACCAAGT
Found at i:89452973 original size:27 final size:27
Alignment explanation
Indices: 89452936--89452988 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
89452926 AATGGTATAT
89452936 TTTTTCAACGGAAAACTTTTTTCTAAA
1 TTTTTCAACGGAAAACTTTTTTCTAAA
**
89452963 TTTTTCAACGGAAATTTTTTTTCTAA
1 TTTTTCAACGGAAAACTTTTTTCTAA
89452989 CATCTAAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.30, C:0.13, G:0.08, T:0.49
Consensus pattern (27 bp):
TTTTTCAACGGAAAACTTTTTTCTAAA
Found at i:89454042 original size:17 final size:18
Alignment explanation
Indices: 89454020--89454054 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
89454010 TCCCTAATTA
89454020 TTTTTTAAAATTT-CCCT
1 TTTTTTAAAATTTACCCT
*
89454037 TTTTTTCAAATTTACCCT
1 TTTTTTAAAATTTACCCT
89454055 CAAATATCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.23, C:0.20, G:0.00, T:0.57
Consensus pattern (18 bp):
TTTTTTAAAATTTACCCT
Found at i:89457457 original size:40 final size:40
Alignment explanation
Indices: 89457402--89457628 Score: 382
Period size: 40 Copynumber: 5.7 Consensus size: 40
89457392 CAATTGAGGA
*
89457402 TTATATCCGGGTTAAGTCCCGAAAGCATTCGTGCTGGTTG
1 TTATATCCGGGTTAAGTCCCGAAGGCATTCGTGCTGGTTG
*
89457442 TTATATCCGGGTTAAGTCTCGAAGGCATTCGTGCTGGTTG
1 TTATATCCGGGTTAAGTCCCGAAGGCATTCGTGCTGGTTG
89457482 TTATATCCGGGTTAAGTCCCGAAGGCATTCGTGCTGGTTG
1 TTATATCCGGGTTAAGTCCCGAAGGCATTCGTGCTGGTTG
*
89457522 TTATATCCAGGTTAAGTCCCGAAGGCATTCGTGCTGGTTG
1 TTATATCCGGGTTAAGTCCCGAAGGCATTCGTGCTGGTTG
* *
89457562 TTATATCTGGGTTAAGTCCCGAAGGCATTTGTGCTGGTTG
1 TTATATCCGGGTTAAGTCCCGAAGGCATTCGTGCTGGTTG
* * *
89457602 TTATATCCGGGCTAAATCTCGAAGGCA
1 TTATATCCGGGTTAAGTCCCGAAGGCA
89457629 ATTGGGTTGG
Statistics
Matches: 176, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 176 1.00
ACGTcount: A:0.20, C:0.19, G:0.28, T:0.33
Consensus pattern (40 bp):
TTATATCCGGGTTAAGTCCCGAAGGCATTCGTGCTGGTTG
Found at i:89458767 original size:40 final size:40
Alignment explanation
Indices: 89458712--89458794 Score: 139
Period size: 40 Copynumber: 2.1 Consensus size: 40
89458702 AGAGTGTAGT
* * *
89458712 GCATTTGTGCTGGTTGTTATATCCGGGTTAAGTTCCGAAG
1 GCATTTGTGCTGGTTGTTATATCCGGGCTAAATCCCGAAG
89458752 GCATTTGTGCTGGTTGTTATATCCGGGCTAAATCCCGAAG
1 GCATTTGTGCTGGTTGTTATATCCGGGCTAAATCCCGAAG
89458792 GCA
1 GCA
89458795 ATTGGGTTGG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.19, C:0.18, G:0.29, T:0.34
Consensus pattern (40 bp):
GCATTTGTGCTGGTTGTTATATCCGGGCTAAATCCCGAAG
Found at i:89460342 original size:53 final size:53
Alignment explanation
Indices: 89460261--89460411 Score: 214
Period size: 53 Copynumber: 2.8 Consensus size: 53
89460251 CTTACACGGT
* *
89460261 TCACATATCATACCGAAGCCATATCCCAGAC-ATGGTCTTATACGGAATCACATTA
1 TCACAT-T-ATACCGATGCCATAGCCCAG-CTATGGTCTTATACGGAATCACATTA
*
89460316 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAGTCACATTA
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
** *
89460369 TCACATTGCACCGATGCCATAGCCCAGCTATGGTCTTAAACGG
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGG
89460412 GCACACTTAT
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
52 1 0.01
53 81 0.91
54 1 0.01
55 6 0.07
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.26
Consensus pattern (53 bp):
TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
Found at i:89463026 original size:13 final size:13
Alignment explanation
Indices: 89463010--89463036 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
89463000 AAAATATGAA
89463010 AGCAAATTATGGT
1 AGCAAATTATGGT
89463023 AGCAAATTATGGT
1 AGCAAATTATGGT
89463036 A
1 A
89463037 TTAACACGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.07, G:0.22, T:0.30
Consensus pattern (13 bp):
AGCAAATTATGGT
Found at i:89463507 original size:11 final size:11
Alignment explanation
Indices: 89463491--89463535 Score: 54
Period size: 11 Copynumber: 3.9 Consensus size: 11
89463481 ATATAAAAGC
89463491 ATATACATAAT
1 ATATACATAAT
* *
89463502 ATATACAAAACGC
1 ATATACATAA--T
89463515 ATATACATAAT
1 ATATACATAAT
89463526 ATATACATAA
1 ATATACATAA
89463536 CGTACGAAAC
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
11 19 0.68
13 9 0.32
ACGTcount: A:0.56, C:0.13, G:0.02, T:0.29
Consensus pattern (11 bp):
ATATACATAAT
Found at i:89463518 original size:24 final size:24
Alignment explanation
Indices: 89463475--89463537 Score: 94
Period size: 24 Copynumber: 2.7 Consensus size: 24
89463465 AAATAGATAT
*
89463475 ATAATA-ATATAAAA-GCATATAC
1 ATAATATATACAAAACGCATATAC
89463497 ATAATATATACAAAACGCATATAC
1 ATAATATATACAAAACGCATATAC
*
89463521 ATAATATATACATAACG
1 ATAATATATACAAAACG
89463538 TACGAAACAA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
22 6 0.16
23 7 0.19
24 24 0.65
ACGTcount: A:0.56, C:0.13, G:0.05, T:0.27
Consensus pattern (24 bp):
ATAATATATACAAAACGCATATAC
Found at i:89463605 original size:17 final size:18
Alignment explanation
Indices: 89463570--89463608 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
89463560 ATATTAAAAC
*
89463570 ATATACATGACATACATA
1 ATATACATGACAAACATA
89463588 ATATACATGA-AAACATA
1 ATATACATGACAAACATA
89463605 ATAT
1 ATAT
89463609 GATATATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.54, C:0.13, G:0.05, T:0.28
Consensus pattern (18 bp):
ATATACATGACAAACATA
Found at i:89464015 original size:19 final size:20
Alignment explanation
Indices: 89463978--89464019 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
89463968 TAGTATTAAT
89463978 TAAAAATGTCTAAATAATAA
1 TAAAAATGTCTAAATAATAA
89463998 TAAAATATGT-TAAA-AATAA
1 TAAAA-ATGTCTAAATAATAA
89464017 TAA
1 TAA
89464020 TACAAGAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 8 0.38
20 9 0.43
21 4 0.19
ACGTcount: A:0.62, C:0.02, G:0.05, T:0.31
Consensus pattern (20 bp):
TAAAAATGTCTAAATAATAA
Found at i:89465530 original size:42 final size:43
Alignment explanation
Indices: 89465484--89465573 Score: 128
Period size: 43 Copynumber: 2.1 Consensus size: 43
89465474 TTTCCTAACC
*
89465484 GCTTAGGGGTTT-AGTTCTGTAAATTCAACCTGTTACCCTACT
1 GCTTAGGGGTTTAAGGTCTGTAAATTCAACCTGTTACCCTACT
*** *
89465526 GCTTAGGGGTTTAAGGTCTGTAAATTTGGCTTGTTACCCTACT
1 GCTTAGGGGTTTAAGGTCTGTAAATTCAACCTGTTACCCTACT
89465569 GCTTA
1 GCTTA
89465574 AAGGGTTAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
42 12 0.29
43 30 0.71
ACGTcount: A:0.20, C:0.19, G:0.22, T:0.39
Consensus pattern (43 bp):
GCTTAGGGGTTTAAGGTCTGTAAATTCAACCTGTTACCCTACT
Found at i:89465973 original size:44 final size:44
Alignment explanation
Indices: 89465912--89466066 Score: 152
Period size: 44 Copynumber: 3.5 Consensus size: 44
89465902 AAATTTGGCT
*
89465912 TGTTACCCTACTGCTTAGGGGGTTAAAGCTCATTATCTTCGATC
1 TGTTACCCTACTGCTTAGGGGGTTAAAGCTCATTAACTTCGATC
* * * * * * *
89465956 TGTTTCCCTACTGCTTAGGGTGAT-AAGATTTATGAACTTC-AGC
1 TGTTACCCTACTGCTTAGGGGGTTAAAG-CTCATTAACTTCGATC
* * **
89465999 TTGTTACCCTACTGCTTAGGAGGTTAAAGCTCGTTGCCTTCGATC
1 -TGTTACCCTACTGCTTAGGGGGTTAAAGCTCATTAACTTCGATC
* *
89466044 TGTTTCCCTACTGCTTATGGGGT
1 TGTTACCCTACTGCTTAGGGGGT
89466067 AAGATCTGTT
Statistics
Matches: 85, Mismatches: 22, Indels: 8
0.74 0.19 0.07
Matches are distributed among these distances:
43 5 0.06
44 75 0.88
45 5 0.06
ACGTcount: A:0.19, C:0.22, G:0.22, T:0.37
Consensus pattern (44 bp):
TGTTACCCTACTGCTTAGGGGGTTAAAGCTCATTAACTTCGATC
Found at i:89478308 original size:19 final size:18
Alignment explanation
Indices: 89478271--89478311 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
89478261 ATATTAAAAC
* *
89478271 ATATACATGACATACATA
1 ATATACATGAAAAACATA
89478289 ATATACATGATAAAACATA
1 ATATACATGA-AAAACATA
89478308 ATAT
1 ATAT
89478312 GATATTTACA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.54, C:0.12, G:0.05, T:0.29
Consensus pattern (18 bp):
ATATACATGAAAAACATA
Found at i:89478523 original size:21 final size:21
Alignment explanation
Indices: 89478472--89478523 Score: 52
Period size: 21 Copynumber: 2.4 Consensus size: 21
89478462 ATAATAACAA
*
89478472 TAATATATAAATGTATATGTAT
1 TAATAT-TAAATGTATATATAT
* *
89478494 TTATGTTAAA-GATATATATAT
1 TAATATTAAATG-TATATATAT
89478515 TAATATTAA
1 TAATATTAA
89478524 TAATAAATAT
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
20 1 0.04
21 19 0.79
22 4 0.17
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (21 bp):
TAATATTAAATGTATATATAT
Found at i:89478631 original size:23 final size:23
Alignment explanation
Indices: 89478605--89478651 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
89478595 ATATATTGGG
*
89478605 AACAACAATAATAATATATATAA
1 AACAACAATAAGAATATATATAA
*
89478628 AACAACTATAAGAATATATATAA
1 AACAACAATAAGAATATATATAA
89478651 A
1 A
89478652 GTATATACAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.64, C:0.09, G:0.02, T:0.26
Consensus pattern (23 bp):
AACAACAATAAGAATATATATAA
Found at i:89479871 original size:18 final size:18
Alignment explanation
Indices: 89479848--89479890 Score: 79
Period size: 17 Copynumber: 2.4 Consensus size: 18
89479838 GGGTTAGTGG
89479848 GTTTTGGGTAGGTTATTT
1 GTTTTGGGTAGGTTATTT
89479866 GTTTT-GGTAGGTTATTT
1 GTTTTGGGTAGGTTATTT
89479883 GTTTTGGG
1 GTTTTGGG
89479891 CCAAAAATTG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 17 0.71
18 7 0.29
ACGTcount: A:0.09, C:0.00, G:0.35, T:0.56
Consensus pattern (18 bp):
GTTTTGGGTAGGTTATTT
Found at i:89482132 original size:21 final size:21
Alignment explanation
Indices: 89482029--89482122 Score: 134
Period size: 21 Copynumber: 4.5 Consensus size: 21
89482019 TGAATATGCC
89482029 AACAGAAGCTTATAAGAGCTG
1 AACAGAAGCTTATAAGAGCTG
*
89482050 AACAGAAACTTATAAGAGCTG
1 AACAGAAGCTTATAAGAGCTG
* * *
89482071 AACAAAAACTTATAAGAGTTG
1 AACAGAAGCTTATAAGAGCTG
* *
89482092 AATAGAAGCTCATAAGAGCTG
1 AACAGAAGCTTATAAGAGCTG
89482113 AACAGAAGCT
1 AACAGAAGCT
89482123 CGAAAGAGCT
Statistics
Matches: 64, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 64 1.00
ACGTcount: A:0.47, C:0.14, G:0.20, T:0.19
Consensus pattern (21 bp):
AACAGAAGCTTATAAGAGCTG
Found at i:89483497 original size:19 final size:19
Alignment explanation
Indices: 89483473--89483510 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
89483463 CATAAGGATG
89483473 TGTAAGCCTCTATGGCTGA
1 TGTAAGCCTCTATGGCTGA
*
89483492 TGTAAGCCTCTGTGGCTGA
1 TGTAAGCCTCTATGGCTGA
89483511 GACCCATGGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.18, C:0.21, G:0.29, T:0.32
Consensus pattern (19 bp):
TGTAAGCCTCTATGGCTGA
Found at i:89485380 original size:31 final size:31
Alignment explanation
Indices: 89485342--89485403 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
89485332 GTAGATAAGT
89485342 TTTATGAATCATCCATGGAAAATTAGAAAAA
1 TTTATGAATCATCCATGGAAAATTAGAAAAA
*
89485373 TTTATGAATCATCCGTGGAAAATTAGAAAAA
1 TTTATGAATCATCCATGGAAAATTAGAAAAA
89485404 GTAAAGGATG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.47, C:0.10, G:0.15, T:0.29
Consensus pattern (31 bp):
TTTATGAATCATCCATGGAAAATTAGAAAAA
Found at i:89486383 original size:25 final size:25
Alignment explanation
Indices: 89486350--89486412 Score: 108
Period size: 25 Copynumber: 2.5 Consensus size: 25
89486340 AGTCCTTTCA
*
89486350 AGCTTCCCGTTATATGGTTCTTACG
1 AGCTTCCCGTTATATGATTCTTACG
89486375 AGCTTCCCGTTATATGATTCTTACG
1 AGCTTCCCGTTATATGATTCTTACG
*
89486400 AGCTTCTCGTTAT
1 AGCTTCCCGTTAT
89486413 TAGCTCTTCG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.17, C:0.24, G:0.17, T:0.41
Consensus pattern (25 bp):
AGCTTCCCGTTATATGATTCTTACG
Found at i:89486513 original size:26 final size:26
Alignment explanation
Indices: 89486478--89486552 Score: 80
Period size: 26 Copynumber: 2.9 Consensus size: 26
89486468 ACAGCTCTTA
* *
89486478 TGAGCGTCCCG-TTATATGGCTCTTCG
1 TGAGCTTCCCGATTA-AAGGCTCTTCG
*
89486504 TGAGCTTCCCGATTAAAGGCTCTTTG
1 TGAGCTTCCCGATTAAAGGCTCTTCG
** *
89486530 TGAGCTTCCTAATTAATGGCTCT
1 TGAGCTTCCCGATTAAAGGCTCT
89486553 CCAGAGCTTC
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
26 39 0.93
27 3 0.07
ACGTcount: A:0.17, C:0.24, G:0.23, T:0.36
Consensus pattern (26 bp):
TGAGCTTCCCGATTAAAGGCTCTTCG
Found at i:89486746 original size:25 final size:25
Alignment explanation
Indices: 89486664--89486746 Score: 103
Period size: 25 Copynumber: 3.3 Consensus size: 25
89486654 AGCTTTCTAA
**
89486664 ATATGGCTCTTATGAGCTTCCCGTT
1 ATATGGCTCAAATGAGCTTCCCGTT
* *
89486689 ATATGGCCCAAATAAGCTTCCCGTT
1 ATATGGCTCAAATGAGCTTCCCGTT
* * *
89486714 ACATGGCTCACATGAGCTTCCCGCT
1 ATATGGCTCAAATGAGCTTCCCGTT
89486739 ATATGGCT
1 ATATGGCT
89486747 TAAAAGAGTG
Statistics
Matches: 48, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 48 1.00
ACGTcount: A:0.22, C:0.28, G:0.19, T:0.31
Consensus pattern (25 bp):
ATATGGCTCAAATGAGCTTCCCGTT
Found at i:89488302 original size:51 final size:51
Alignment explanation
Indices: 89488221--89488319 Score: 180
Period size: 51 Copynumber: 1.9 Consensus size: 51
89488211 ATTATATGAA
89488221 ATGTCTGTTGATGCTCACTAAACTAACTAAAAATTCGACTAAGGCAAGCGC
1 ATGTCTGTTGATGCTCACTAAACTAACTAAAAATTCGACTAAGGCAAGCGC
* *
89488272 ATGTTTGTTGATGGTCACTAAACTAACTAAAAATTCGACTAAGGCAAG
1 ATGTCTGTTGATGCTCACTAAACTAACTAAAAATTCGACTAAGGCAAG
89488320 TGCACCTATC
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 46 1.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.27
Consensus pattern (51 bp):
ATGTCTGTTGATGCTCACTAAACTAACTAAAAATTCGACTAAGGCAAGCGC
Found at i:89490279 original size:53 final size:53
Alignment explanation
Indices: 89490125--89490290 Score: 212
Period size: 53 Copynumber: 3.1 Consensus size: 53
89490115 GACGAAAAAT
* * **
89490125 ATGTGATAAGTGTG-C-CCGTTTAAGACCATAGCTGGGCTATGGCATCAGTGCA
1 ATGTGATAA-TGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA
89490177 ATGTGATAATGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA
1 ATGTGATAATGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA
* * *
89490230 ATGTGATAATGTGATTCCGTATAAGACCAT-GTCTGGGATATGGCTTCGGTATGA
1 ATGTGATAATGTGACTCCGTATAAGACCATAG-CTGGGCTATGGCATCGGTAT-A
89490284 TATGTGA
1 -ATGTGA
89490291 ACCGTGTAAG
Statistics
Matches: 102, Mismatches: 7, Indels: 7
0.88 0.06 0.06
Matches are distributed among these distances:
51 4 0.04
52 11 0.11
53 80 0.78
54 1 0.01
55 6 0.06
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.30
Consensus pattern (53 bp):
ATGTGATAATGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA
Found at i:89494491 original size:10 final size:10
Alignment explanation
Indices: 89494478--89494519 Score: 57
Period size: 10 Copynumber: 4.2 Consensus size: 10
89494468 CATTTTCAAA
89494478 TTTTTTTTCT
1 TTTTTTTTCT
* *
89494488 TTTTCTTTCA
1 TTTTTTTTCT
89494498 TTTTTTTTCT
1 TTTTTTTTCT
*
89494508 TCTTTTTTCT
1 TTTTTTTTCT
89494518 TT
1 TT
89494520 CAAATCTGTT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.02, C:0.14, G:0.00, T:0.83
Consensus pattern (10 bp):
TTTTTTTTCT
Found at i:89494514 original size:24 final size:22
Alignment explanation
Indices: 89494478--89494521 Score: 70
Period size: 24 Copynumber: 1.9 Consensus size: 22
89494468 CATTTTCAAA
89494478 TTTTTTTTCTTTTTCTTTCATT
1 TTTTTTTTCTTTTTCTTTCATT
89494500 TTTTTTCTTCTTTTTTCTTTCA
1 TTTTTT-TTC-TTTTTCTTTCA
89494522 AATCTGTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 6 0.30
23 3 0.15
24 11 0.55
ACGTcount: A:0.05, C:0.16, G:0.00, T:0.80
Consensus pattern (22 bp):
TTTTTTTTCTTTTTCTTTCATT
Found at i:89494570 original size:15 final size:16
Alignment explanation
Indices: 89494540--89494573 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
89494530 ATATATATTT
89494540 AATAAATAAAAAGGAA
1 AATAAATAAAAAGGAA
*
89494556 AATAAA-AAAAGGGAA
1 AATAAATAAAAAGGAA
89494571 AAT
1 AAT
89494574 TTTTACCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.74, C:0.00, G:0.15, T:0.12
Consensus pattern (16 bp):
AATAAATAAAAAGGAA
Found at i:89495176 original size:15 final size:16
Alignment explanation
Indices: 89495156--89495190 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
89495146 CTTTTAATAT
89495156 TATTTAATATT-TTTA
1 TATTTAATATTATTTA
*
89495171 TATTTACTATTATTTA
1 TATTTAATATTATTTA
89495187 TATT
1 TATT
89495191 ATTATTAGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (16 bp):
TATTTAATATTATTTA
Found at i:89495176 original size:25 final size:24
Alignment explanation
Indices: 89495148--89495195 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
89495138 ATTAATTACT
*
89495148 TTTAATATTATTTAATATTTTTATA
1 TTTAATATTATTT-ATATTATTATA
*
89495173 TTTACTATTATTTATATTATTAT
1 TTTAATATTATTTATATTATTAT
89495196 TAGTATATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 9 0.43
25 12 0.57
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (24 bp):
TTTAATATTATTTATATTATTATA
Found at i:89495204 original size:14 final size:13
Alignment explanation
Indices: 89495178--89495409 Score: 54
Period size: 12 Copynumber: 18.1 Consensus size: 13
89495168 TTATATTTAC
89495178 TATTATT-TATAT
1 TATTATTATATAT
89495190 TATTATTAGTATATT
1 TATTATTA-TATA-T
*
89495205 TTTTATTATATAT
1 TATTATTATATAT
*
89495218 GTA-TA-TATCT-T
1 -TATTATTATATAT
*
89495229 TAATA-TATATAT
1 TATTATTATATAT
*
89495241 GTATATATTTATATAG
1 -TAT-TA-TTATATAT
89495257 TATTATTA-ATAGT
1 TATTATTATATA-T
* * *
89495270 TGTTTTTA-ACAT
1 TATTATTATATAT
89495282 TATTATTAT-T-T
1 TATTATTATATAT
*
89495293 CTAATATGTATATAT
1 -TATTAT-TATATAT
89495308 TATGTA--A-ATAT
1 TAT-TATTATATAT
89495319 T-TTA--ATACTA-
1 TATTATTATA-TAT
89495329 TATTATGTATATAT
1 TATTAT-TATATAT
89495343 T-TT-TTATATA-
1 TATTATTATATAT
* *
89495353 TGTTACGTATATAT
1 TATTA-TTATATAT
* *
89495367 ATATCTTTTAAATAT
1 -TAT-TATTATATAT
*
89495382 TA-TATTTTATAT
1 TATTATTATATAT
89495394 ATATTATGTATATAT
1 -TATTAT-TATATAT
89495409 T
1 T
89495410 TTTAATATCA
Statistics
Matches: 163, Mismatches: 24, Indels: 64
0.65 0.10 0.25
Matches are distributed among these distances:
9 3 0.02
10 6 0.04
11 26 0.16
12 36 0.22
13 31 0.19
14 26 0.16
15 28 0.17
16 7 0.04
ACGTcount: A:0.35, C:0.03, G:0.05, T:0.57
Consensus pattern (13 bp):
TATTATTATATAT
Found at i:89495214 original size:12 final size:14
Alignment explanation
Indices: 89495153--89495215 Score: 51
Period size: 15 Copynumber: 4.6 Consensus size: 14
89495143 TTACTTTTAA
*
89495153 TATTAT-TTAATAT
1 TATTATATTATTAT
* *
89495166 TTTTATATTTACTAT
1 TATTATA-TTATTAT
89495181 TATTTATATTATTAT
1 TA-TTATATTATTAT
*
89495196 TAGTATATT-TT-T
1 TATTATATTATTAT
89495208 TATTATAT
1 TATTATAT
89495216 ATGTATATAT
Statistics
Matches: 41, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
12 8 0.20
13 7 0.17
14 6 0.15
15 15 0.37
16 5 0.12
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (14 bp):
TATTATATTATTAT
Found at i:89495230 original size:21 final size:21
Alignment explanation
Indices: 89495189--89495248 Score: 72
Period size: 23 Copynumber: 2.9 Consensus size: 21
89495179 ATTATTTATA
*
89495189 TTATTAT-TA-GTATAT-TTT
1 TTATTATATATGTATATATCT
89495207 TTATTATATATGTATATATCT
1 TTATTATATATGTATATATCT
89495228 TTAATATATATATGTATATAT
1 TT-AT-TATATATGTATATAT
89495249 TTATATAGTA
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
18 7 0.19
19 2 0.06
20 6 0.17
21 4 0.11
22 2 0.06
23 15 0.42
ACGTcount: A:0.35, C:0.02, G:0.05, T:0.58
Consensus pattern (21 bp):
TTATTATATATGTATATATCT
Found at i:89495313 original size:11 final size:11
Alignment explanation
Indices: 89495297--89495409 Score: 54
Period size: 11 Copynumber: 10.1 Consensus size: 11
89495287 TTATTTCTAA
89495297 TATGTATATAT
1 TATGTATATAT
*
89495308 TATGTAAATAT
1 TATGTATATAT
* *
89495319 TTTAATACTATAT
1 TAT-GTA-TATAT
89495332 TATGTATATAT
1 TATGTATATAT
* *
89495343 TTTTTATATATGT
1 TATGTATATA--T
*
89495356 TACGTATATAT
1 TATGTATATAT
* * *
89495367 ATATCT-TTTAAA
1 -TATGTATAT-AT
89495379 TAT-TATAT-T
1 TATGTATATAT
*
89495388 T-TATATATAT
1 TATGTATATAT
89495398 TATGTATATAT
1 TATGTATATAT
89495409 T
1 T
89495410 TTTAATATCA
Statistics
Matches: 74, Mismatches: 18, Indels: 20
0.66 0.16 0.18
Matches are distributed among these distances:
8 1 0.01
9 6 0.08
10 3 0.04
11 42 0.57
12 8 0.11
13 14 0.19
ACGTcount: A:0.36, C:0.03, G:0.05, T:0.56
Consensus pattern (11 bp):
TATGTATATAT
Found at i:89495397 original size:16 final size:16
Alignment explanation
Indices: 89495360--89495400 Score: 52
Period size: 14 Copynumber: 2.8 Consensus size: 16
89495350 ATATGTTACG
*
89495360 TATATATA-TATCTTT
1 TATATATATTATATTT
89495375 TA-A-ATATTATATTT
1 TATATATATTATATTT
89495389 TATATATATTAT
1 TATATATATTAT
89495401 GTATATATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
13 3 0.14
14 9 0.41
15 3 0.14
16 7 0.32
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (16 bp):
TATATATATTATATTT
Found at i:89495407 original size:13 final size:13
Alignment explanation
Indices: 89495301--89495408 Score: 52
Period size: 13 Copynumber: 8.4 Consensus size: 13
89495291 TTCTAATATG
89495301 TATATATTATGTA
1 TATATATTATGTA
89495314 -A-ATATT-T-TAA
1 TATATATTATGT-A
89495324 TACTATATTATGTA
1 TA-TATATTATGTA
*
89495338 TATAT-TT-TTTA
1 TATATATTATGTA
* *
89495349 TATATGTTACGTA
1 TATATATTATGTA
* *
89495362 TATATATATCTTTTAAA
1 TATATAT-T-ATGT--A
89495379 TATTATATT-T-TA
1 TA-TATATTATGTA
89495391 TATATATTATGTA
1 TATATATTATGTA
89495404 TATAT
1 TATAT
89495409 TTTTAATATC
Statistics
Matches: 73, Mismatches: 7, Indels: 30
0.66 0.06 0.27
Matches are distributed among these distances:
9 1 0.01
10 2 0.03
11 20 0.27
12 9 0.12
13 23 0.32
14 6 0.08
15 3 0.04
17 4 0.05
18 5 0.07
ACGTcount: A:0.37, C:0.03, G:0.05, T:0.56
Consensus pattern (13 bp):
TATATATTATGTA
Found at i:89495510 original size:25 final size:25
Alignment explanation
Indices: 89495469--89495521 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
89495459 TTTTAATAAT
**
89495469 TATATTATGTATGTATTTTTAACAC
1 TATATTATGTACATATTTTTAACAC
*
89495494 TATATTATGTACATATTTTTAATAC
1 TATATTATGTACATATTTTTAACAC
89495519 TAT
1 TAT
89495522 GTATATACCT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.34, C:0.08, G:0.06, T:0.53
Consensus pattern (25 bp):
TATATTATGTACATATTTTTAACAC
Found at i:89495626 original size:18 final size:18
Alignment explanation
Indices: 89495588--89495622 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
89495578 TATATATCGT
*
89495588 TATTATTAGTTATTTTTA
1 TATTATTAGCTATTTTTA
89495606 TATTATTA-CTATTTTTA
1 TATTATTAGCTATTTTTA
89495623 ATATATATTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.66
Consensus pattern (18 bp):
TATTATTAGCTATTTTTA
Found at i:89496835 original size:15 final size:15
Alignment explanation
Indices: 89496815--89496847 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
89496805 AACACGACCA
89496815 AAAGCAAAAAGAGTG
1 AAAGCAAAAAGAGTG
89496830 AAAGCAAAAAGAGTG
1 AAAGCAAAAAGAGTG
89496845 AAA
1 AAA
89496848 AAAAAGGATC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.64, C:0.06, G:0.24, T:0.06
Consensus pattern (15 bp):
AAAGCAAAAAGAGTG
Found at i:89504744 original size:15 final size:16
Alignment explanation
Indices: 89504719--89504748 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
89504709 GCTAAATGTT
89504719 AAAAAGAGAAAAAAAA
1 AAAAAGAGAAAAAAAA
89504735 AAAAAG-GAAAAAAA
1 AAAAAGAGAAAAAAA
89504749 GGCTATTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (16 bp):
AAAAAGAGAAAAAAAA
Found at i:89509299 original size:16 final size:15
Alignment explanation
Indices: 89509274--89509317 Score: 65
Period size: 13 Copynumber: 3.0 Consensus size: 15
89509264 AATACTTAAG
89509274 TATATAATATAATAA
1 TATATAATATAATAA
89509289 TATATTAATATAAT-A
1 TATA-TAATATAATAA
89509304 -ATATAATATAATAA
1 TATATAATATAATAA
89509318 AACATAAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
13 9 0.33
14 4 0.15
15 5 0.19
16 9 0.33
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
TATATAATATAATAA
Found at i:89509317 original size:8 final size:8
Alignment explanation
Indices: 89509277--89509311 Score: 61
Period size: 8 Copynumber: 4.4 Consensus size: 8
89509267 ACTTAAGTAT
89509277 ATAATATA
1 ATAATATA
89509285 ATAATATA
1 ATAATATA
*
89509293 TTAATATA
1 ATAATATA
89509301 ATAATATA
1 ATAATATA
89509309 ATA
1 ATA
89509312 TAATAAAACA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (8 bp):
ATAATATA
Found at i:89509327 original size:16 final size:15
Alignment explanation
Indices: 89509275--89509328 Score: 60
Period size: 13 Copynumber: 3.7 Consensus size: 15
89509265 ATACTTAAGT
*
89509275 ATATAATATAATAAT
1 ATATAATATAATAAA
89509290 ATATTAATATAAT--A
1 ATA-TAATATAATAAA
89509304 ATATAATATAATAAA
1 ATATAATATAATAAA
*
89509319 ACATAA-ATAA
1 ATATAATATAA
89509329 ACTAAAGTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
13 9 0.26
14 7 0.21
15 9 0.26
16 9 0.26
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (15 bp):
ATATAATATAATAAA
Found at i:89509406 original size:9 final size:9
Alignment explanation
Indices: 89509392--89509420 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
89509382 AACAGGGGAC
89509392 AAAGAAAGA
1 AAAGAAAGA
89509401 AAAGAAAGA
1 AAAGAAAGA
89509410 AAA-AAAGA
1 AAAGAAAGA
89509418 AAA
1 AAA
89509421 TTAGGGATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 8 0.40
9 12 0.60
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (9 bp):
AAAGAAAGA
Found at i:89509723 original size:19 final size:19
Alignment explanation
Indices: 89509688--89509724 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
89509678 GAAAGAAATT
**
89509688 TGAAATTAGGGTTTTATGG
1 TGAAATTAGGGAGTTATGG
89509707 TGAAATTAGGGAGTTATG
1 TGAAATTAGGGAGTTATG
89509725 AAATTGGTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.30, C:0.00, G:0.32, T:0.38
Consensus pattern (19 bp):
TGAAATTAGGGAGTTATGG
Found at i:89510105 original size:5 final size:5
Alignment explanation
Indices: 89510090--89510134 Score: 54
Period size: 5 Copynumber: 8.6 Consensus size: 5
89510080 TAATTGTAGT
* *
89510090 ATTGAA ATTGA ATTGA GTTGA ATTGA ATTGT ATTGA ATTGGA ATT
1 ATTG-A ATTGA ATTGA ATTGA ATTGA ATTGA ATTGA ATT-GA ATT
89510135 TATAAGTTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
5 25 0.74
6 9 0.26
ACGTcount: A:0.36, C:0.00, G:0.22, T:0.42
Consensus pattern (5 bp):
ATTGA
Found at i:89510115 original size:15 final size:15
Alignment explanation
Indices: 89510088--89510134 Score: 60
Period size: 15 Copynumber: 3.0 Consensus size: 15
89510078 GATAATTGTA
89510088 GTATTGAAATTGAATT
1 GTATTG-AATTGAATT
89510104 G-AGTTGAATTGAATT
1 GTA-TTGAATTGAATT
89510119 GTATTGAATTGGAATT
1 GTATTGAATT-GAATT
89510135 TATAAGTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
15 18 0.64
16 10 0.36
ACGTcount: A:0.34, C:0.00, G:0.23, T:0.43
Consensus pattern (15 bp):
GTATTGAATTGAATT
Found at i:89511952 original size:15 final size:15
Alignment explanation
Indices: 89511932--89511965 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
89511922 TAACAAATAT
89511932 TTAATTTAACTAACA
1 TTAATTTAACTAACA
89511947 TTAATTTAACTAACA
1 TTAATTTAACTAACA
89511962 TTAA
1 TTAA
89511966 ACCAAAACGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (15 bp):
TTAATTTAACTAACA
Found at i:89515960 original size:13 final size:14
Alignment explanation
Indices: 89515942--89515970 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
89515932 ATAGTTTTGG
89515942 ATAAAAA-TTAAAT
1 ATAAAAATTTAAAT
89515955 ATAAAAATTTAAAT
1 ATAAAAATTTAAAT
89515969 AT
1 AT
89515971 TTTATTTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (14 bp):
ATAAAAATTTAAAT
Found at i:89519520 original size:7 final size:6
Alignment explanation
Indices: 89519490--89519551 Score: 54
Period size: 6 Copynumber: 9.7 Consensus size: 6
89519480 TCAAGGTTCG
* *
89519490 GGTTTA GGTTTA GGTTTG GGATTTA GGATTTTA AGTTT- GAGTTTA GGTTTAA
1 GGTTTA GGTTTA GGTTTA GG-TTTA GG--TTTA GGTTTA G-GTTTA GGTTT-A
89519542 GGTTTA GGTT
1 GGTTTA GGTT
89519552 AAAGAATTTA
Statistics
Matches: 46, Mismatches: 5, Indels: 10
0.75 0.08 0.16
Matches are distributed among these distances:
6 29 0.63
7 12 0.26
8 5 0.11
ACGTcount: A:0.19, C:0.00, G:0.32, T:0.48
Consensus pattern (6 bp):
GGTTTA
Found at i:89519534 original size:39 final size:39
Alignment explanation
Indices: 89519491--89519572 Score: 112
Period size: 39 Copynumber: 2.1 Consensus size: 39
89519481 CAAGGTTCGG
* * * *
89519491 GTTTAGGTTT-AGGTTTGGGATTTAGGATTTTAAGTTTGA
1 GTTTAGGTTTAAGGTTTAGG-TTAAAGAATTTAAGTTTGA
89519530 GTTTAGGTTTAAGGTTTAGGTTAAAGAATTTAAGTTTGA
1 GTTTAGGTTTAAGGTTTAGGTTAAAGAATTTAAGTTTGA
89519569 GTTT
1 GTTT
89519573 CAAGATTCGA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
39 30 0.79
40 8 0.21
ACGTcount: A:0.24, C:0.00, G:0.28, T:0.48
Consensus pattern (39 bp):
GTTTAGGTTTAAGGTTTAGGTTAAAGAATTTAAGTTTGA
Found at i:89519548 original size:13 final size:12
Alignment explanation
Indices: 89519490--89519551 Score: 54
Period size: 13 Copynumber: 4.8 Consensus size: 12
89519480 TCAAGGTTCG
89519490 GGTTTAGGTTTA
1 GGTTTAGGTTTA
*
89519502 GGTTTGGGATTTA
1 GGTTTAGG-TTTA
*
89519515 GGATTTTAAGTTT-
1 GG--TTTAGGTTTA
89519528 GAGTTTAGGTTTAA
1 G-GTTTAGGTTT-A
89519542 GGTTTAGGTT
1 GGTTTAGGTT
89519552 AAAGAATTTA
Statistics
Matches: 40, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
12 15 0.38
13 16 0.40
14 5 0.12
15 4 0.10
ACGTcount: A:0.19, C:0.00, G:0.32, T:0.48
Consensus pattern (12 bp):
GGTTTAGGTTTA
Found at i:89520463 original size:21 final size:21
Alignment explanation
Indices: 89520420--89520465 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
89520410 GATGAAGGAT
* *
89520420 GAAAACATGAAGCAAAGCGAC
1 GAAAACACGAAGCAAAGCAAC
*
89520441 GAAAACACGAAGCAAAGTAAC
1 GAAAACACGAAGCAAAGCAAC
89520462 GAAA
1 GAAA
89520466 TCCCTCCCCC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.57, C:0.17, G:0.22, T:0.04
Consensus pattern (21 bp):
GAAAACACGAAGCAAAGCAAC
Found at i:89523277 original size:27 final size:28
Alignment explanation
Indices: 89523222--89523278 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 28
89523212 AAAAACTTTT
** *
89523222 AAATTATTTTCATTATTGTAAATATAAA
1 AAATTATTTTCATTATCATAAAAATAAA
*
89523250 AAATTATTTTTA-TATCATAAAAATAAA
1 AAATTATTTTCATTATCATAAAAATAAA
89523277 AA
1 AA
89523279 TAAAAATATA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
27 14 0.56
28 11 0.44
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.42
Consensus pattern (28 bp):
AAATTATTTTCATTATCATAAAAATAAA
Found at i:89528204 original size:13 final size:13
Alignment explanation
Indices: 89528171--89528197 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
89528161 TTTATTAGTA
89528171 CTTCTTTTTTTTT
1 CTTCTTTTTTTTT
89528184 CTTCTTTTTTTTT
1 CTTCTTTTTTTTT
89528197 C
1 C
89528198 CTTTTTTGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (13 bp):
CTTCTTTTTTTTT
Found at i:89528210 original size:8 final size:8
Alignment explanation
Indices: 89528199--89528236 Score: 76
Period size: 8 Copynumber: 4.8 Consensus size: 8
89528189 TTTTTTTTCC
89528199 TTTTTTGA
1 TTTTTTGA
89528207 TTTTTTGA
1 TTTTTTGA
89528215 TTTTTTGA
1 TTTTTTGA
89528223 TTTTTTGA
1 TTTTTTGA
89528231 TTTTTT
1 TTTTTT
89528237 AAATTTATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 30 1.00
ACGTcount: A:0.11, C:0.00, G:0.11, T:0.79
Consensus pattern (8 bp):
TTTTTTGA
Found at i:89528210 original size:16 final size:16
Alignment explanation
Indices: 89528191--89528236 Score: 65
Period size: 16 Copynumber: 2.9 Consensus size: 16
89528181 TTTCTTCTTT
*
89528191 TTTTTTCCTTTTTTGA
1 TTTTTTCATTTTTTGA
*
89528207 TTTTTTGATTTTTTGA
1 TTTTTTCATTTTTTGA
*
89528223 TTTTTTGATTTTTT
1 TTTTTTCATTTTTT
89528237 AAATTTATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.09, C:0.04, G:0.09, T:0.78
Consensus pattern (16 bp):
TTTTTTCATTTTTTGA
Found at i:89528218 original size:24 final size:24
Alignment explanation
Indices: 89528191--89528236 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
89528181 TTTCTTCTTT
*
89528191 TTTTTTCCTTTTTTGATTTTTTGA
1 TTTTTTCATTTTTTGATTTTTTGA
*
89528215 TTTTTTGATTTTTTGATTTTTT
1 TTTTTTCATTTTTTGATTTTTT
89528237 AAATTTATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.09, C:0.04, G:0.09, T:0.78
Consensus pattern (24 bp):
TTTTTTCATTTTTTGATTTTTTGA
Found at i:89528517 original size:118 final size:118
Alignment explanation
Indices: 89528361--89528591 Score: 381
Period size: 118 Copynumber: 2.0 Consensus size: 118
89528351 TATTTCCGGT
89528361 TAGCGGAGTTTTACCCAACACGTCACACAACCTTTTGACGCAAAGTAGAATGACAACCCAAGCAC
1 TAGCGGAGTTTTACCCAACACGTCACACAACCTTTTGACGCAAAGTAGAATGACAACCCAAGCAC
* *
89528426 CCTACCCCGGTTACTCAGTCAGTCACGATTTGAGCCATACTCATAACCTCGGC
66 CCTACCCCGGTTACTCAGTCAGTCACGATCTAAGCCATACTCATAACCTCGGC
**** *
89528479 TAGCGGAGTTTTACTTGTCACGTCACACAACCTTTTGACGCGAAGTAGAATGACAACCCAAGCAC
1 TAGCGGAGTTTTACCCAACACGTCACACAACCTTTTGACGCAAAGTAGAATGACAACCCAAGCAC
**
89528544 CCTACCCCGGTTACTCAGTCAGTCACGATCTAAGCTGTACTCATAACC
66 CCTACCCCGGTTACTCAGTCAGTCACGATCTAAGCCATACTCATAACC
89528592 ATGGAAAACA
Statistics
Matches: 104, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
118 104 1.00
ACGTcount: A:0.29, C:0.31, G:0.17, T:0.23
Consensus pattern (118 bp):
TAGCGGAGTTTTACCCAACACGTCACACAACCTTTTGACGCAAAGTAGAATGACAACCCAAGCAC
CCTACCCCGGTTACTCAGTCAGTCACGATCTAAGCCATACTCATAACCTCGGC
Found at i:89529496 original size:42 final size:42
Alignment explanation
Indices: 89529373--89529499 Score: 182
Period size: 42 Copynumber: 3.0 Consensus size: 42
89529363 GGGATTCTAA
* * * * *
89529373 GGCTGAAATAGGACTGTTTGGCTGCAGAGATATGACATTCTG
1 GGCTGGAATAGAACTGTTTGGCAGCAGAGATATGCCATTTTG
*
89529415 GGCTGGAATAGAACTGTTTGGCAGCAGGGATATGCCATTTTG
1 GGCTGGAATAGAACTGTTTGGCAGCAGAGATATGCCATTTTG
* *
89529457 GGCTGGAATAGAACTGTTTGGCAACAGTGATATGCCATTTTG
1 GGCTGGAATAGAACTGTTTGGCAGCAGAGATATGCCATTTTG
89529499 G
1 G
89529500 TGCACACTTT
Statistics
Matches: 77, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 77 1.00
ACGTcount: A:0.25, C:0.14, G:0.31, T:0.29
Consensus pattern (42 bp):
GGCTGGAATAGAACTGTTTGGCAGCAGAGATATGCCATTTTG
Found at i:89529650 original size:23 final size:22
Alignment explanation
Indices: 89529609--89529651 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
89529599 AATAAATCAT
89529609 AAAAAATAAAAGAAAATAAAGG
1 AAAAAATAAAAGAAAATAAAGG
89529631 AAAATAATAAATA-AAAATAAA
1 AAAA-AATAAA-AGAAAATAAA
89529652 AATAAAGATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 4 0.21
23 14 0.74
24 1 0.05
ACGTcount: A:0.79, C:0.00, G:0.07, T:0.14
Consensus pattern (22 bp):
AAAAAATAAAAGAAAATAAAGG
Found at i:89529654 original size:12 final size:13
Alignment explanation
Indices: 89529585--89529657 Score: 51
Period size: 13 Copynumber: 5.5 Consensus size: 13
89529575 TATTTAACTA
*
89529585 AAAT-AAAATAAA
1 AAATAAAAATAAT
* *
89529597 ATAATAAATCATAAA
1 A-AATAAA-AATAAT
*
89529612 AAATAAAAGAAAAT
1 AAATAAAA-ATAAT
**
89529626 AAAGGAAAATAAT
1 AAATAAAAATAAT
89529639 AAATAAAAATAA-
1 AAATAAAAATAAT
89529651 AAATAAA
1 AAATAAA
89529658 GATTGGGTTG
Statistics
Matches: 48, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
12 8 0.17
13 17 0.35
14 17 0.35
15 6 0.12
ACGTcount: A:0.77, C:0.01, G:0.04, T:0.18
Consensus pattern (13 bp):
AAATAAAAATAAT
Found at i:89562059 original size:17 final size:16
Alignment explanation
Indices: 89562037--89562080 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 16
89562027 TGAAAAGTGT
89562037 ATACATAATAATATTAG
1 ATACATAATAATA-TAG
*
89562054 ATACATACATAATATAT
1 ATACATA-ATAATATAG
89562071 ATACATAATA
1 ATACATAATA
89562081 TTAAAATGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
16 3 0.12
17 16 0.64
18 6 0.24
ACGTcount: A:0.55, C:0.09, G:0.02, T:0.34
Consensus pattern (16 bp):
ATACATAATAATATAG
Found at i:89562107 original size:25 final size:24
Alignment explanation
Indices: 89562067--89562113 Score: 60
Period size: 23 Copynumber: 1.9 Consensus size: 24
89562057 CATACATAAT
89562067 ATATATACATAATATTA-AAATGA
1 ATATATACATAATATTAGAAATGA
*
89562090 ATATATACGATATGTATTAGAAAT
1 ATATATAC-ATA-ATATTAGAAAT
89562114 ACTAATAACA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 8 0.40
24 3 0.15
25 5 0.25
26 4 0.20
ACGTcount: A:0.51, C:0.04, G:0.09, T:0.36
Consensus pattern (24 bp):
ATATATACATAATATTAGAAATGA
Found at i:89562734 original size:22 final size:23
Alignment explanation
Indices: 89562673--89562742 Score: 58
Period size: 22 Copynumber: 3.1 Consensus size: 23
89562663 AGTATTAGAA
89562673 ATATACATACGATAATATAAAAGAT
1 ATATACATA--ATAATATAAAAGAT
* **
89562698 ATATA-ACTAACAATATTCAA-AT
1 ATATACA-TAATAATATAAAAGAT
89562720 ATATACATAATAATA-AAAA-AT
1 ATATACATAATAATATAAAAGAT
89562741 AT
1 AT
89562743 GATATGCGTA
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
21 6 0.16
22 14 0.38
23 9 0.24
24 1 0.03
25 7 0.19
ACGTcount: A:0.59, C:0.09, G:0.03, T:0.30
Consensus pattern (23 bp):
ATATACATAATAATATAAAAGAT
Found at i:89563250 original size:3 final size:3
Alignment explanation
Indices: 89563238--89563311 Score: 132
Period size: 3 Copynumber: 24.7 Consensus size: 3
89563228 CACTACTATG
89563238 TAA TATA TAA TAA TAA TAA TAA TAA TAA TAA T-A TAA TAA TAA TAA
1 TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
89563283 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
89563312 TAGAAATTCA
Statistics
Matches: 69, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.03
3 64 0.93
4 3 0.04
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:89564075 original size:14 final size:15
Alignment explanation
Indices: 89564056--89564092 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
89564046 GGAAAAGGTA
*
89564056 ATTTTTTATT-TTTT
1 ATTTTTTATTGTATT
89564070 ATTTTTT-TTGTATT
1 ATTTTTTATTGTATT
89564084 ATTTTTTAT
1 ATTTTTTAT
89564093 ATATTTATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
13 2 0.10
14 17 0.85
15 1 0.05
ACGTcount: A:0.16, C:0.00, G:0.03, T:0.81
Consensus pattern (15 bp):
ATTTTTTATTGTATT
Found at i:89564642 original size:22 final size:22
Alignment explanation
Indices: 89564614--89564666 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
89564604 GTTTGGGTTT
*
89564614 TTTTGGGTTTAATTGTAATGGG
1 TTTTGGGTTTAATTGTAATAGG
89564636 TTTTGGGTTTAATTGTAATAGG
1 TTTTGGGTTTAATTGTAATAGG
89564658 TTTTGGGTT
1 TTTTGGGTT
89564667 AGTATAACAC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.17, C:0.00, G:0.30, T:0.53
Consensus pattern (22 bp):
TTTTGGGTTTAATTGTAATAGG
Found at i:89566137 original size:40 final size:40
Alignment explanation
Indices: 89566037--89566262 Score: 391
Period size: 40 Copynumber: 5.7 Consensus size: 40
89566027 GCAAACACAT
* *
89566037 TTGCCTTCGGGTCTTAACCCGGACATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
* * *
89566077 TTACC-TCGGGTCTTAGCCCGGATATATCATCCCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
89566116 TTGCCTTCGGGTCATAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
89566156 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
89566196 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
89566236 TTGCCTTCGGGTCTTAGCCCGGATATA
1 TTGCCTTCGGGTCTTAGCCCGGATATA
89566263 ATCCAATGTT
Statistics
Matches: 175, Mismatches: 10, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
39 34 0.19
40 141 0.81
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.29
Consensus pattern (40 bp):
TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
Found at i:89574772 original size:40 final size:40
Alignment explanation
Indices: 89574724--89574948 Score: 339
Period size: 40 Copynumber: 5.7 Consensus size: 40
89574714 GCAAACACAT
* *
89574724 TTGCCTTCGGGTCTTAACCCGGACATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
* * *
89574764 ATGCCTTCGGGTCTTAGCCCGGATATA-CATCCCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
* * *
89574803 TTGCCTTCGCGGTCTTA--CCGGATATGTCATCCCGCATAA
1 TTGCCTTCG-GGTCTTAGCCCGGATATATCAACTCGCATAA
*
89574842 TTGCCTTCGGGTCATAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
89574882 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
89574922 TTGCCTTCGGGTCTTAGCCCGGATATA
1 TTGCCTTCGGGTCTTAGCCCGGATATA
89574949 ATCCAATGTT
Statistics
Matches: 169, Mismatches: 12, Indels: 8
0.89 0.06 0.04
Matches are distributed among these distances:
38 14 0.08
39 39 0.23
40 116 0.69
ACGTcount: A:0.22, C:0.29, G:0.20, T:0.29
Consensus pattern (40 bp):
TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
Found at i:89574897 original size:118 final size:119
Alignment explanation
Indices: 89574724--89574947 Score: 362
Period size: 118 Copynumber: 1.9 Consensus size: 119
89574714 GCAAACACAT
*
89574724 TTGCCTTCGGGTCTTAACCCGGACATATCAACTCGCATAAATGCCTTCGGGTCTTAGCCCGGATA
1 TTGCCTTCGGGTCATAACCCGGACATATCAACTCGCATAAATGCCTTCGGGTCTTAGCCCGGATA
*
89574789 TA-CATCCCGCATAATTGCCTTCGCGGTCTTA-CCGGATATGTCATCCCGCATAA
66 TATCAACCCGCATAATTGCCTTCG-GGTCTTACCCGGATATGTCATCCCGCATAA
* * *
89574842 TTGCCTTCGGGTCATAGCCCGGATATATCAACTCGCATAATTGCCTTCGGGTCTTAGCCCGGATA
1 TTGCCTTCGGGTCATAACCCGGACATATCAACTCGCATAAATGCCTTCGGGTCTTAGCCCGGATA
*
89574907 TATCAACTCGCATAATTGCCTTCGGGTCTTAGCCCGGATAT
66 TATCAACCCGCATAATTGCCTTCGGGTCTTA-CCCGGATAT
89574948 AATCCAATGT
Statistics
Matches: 97, Mismatches: 6, Indels: 4
0.91 0.06 0.04
Matches are distributed among these distances:
118 70 0.72
119 19 0.20
120 8 0.08
ACGTcount: A:0.21, C:0.29, G:0.21, T:0.29
Consensus pattern (119 bp):
TTGCCTTCGGGTCATAACCCGGACATATCAACTCGCATAAATGCCTTCGGGTCTTAGCCCGGATA
TATCAACCCGCATAATTGCCTTCGGGTCTTACCCGGATATGTCATCCCGCATAA
Found at i:89587790 original size:22 final size:22
Alignment explanation
Indices: 89587764--89587813 Score: 91
Period size: 22 Copynumber: 2.3 Consensus size: 22
89587754 GGGTTTTTTG
*
89587764 TGGGTTTAATTGTAATGGGTTT
1 TGGGTTTAATTGTAATAGGTTT
89587786 TGGGTTTAATTGTAATAGGTTT
1 TGGGTTTAATTGTAATAGGTTT
89587808 TGGGTT
1 TGGGTT
89587814 AGTATAACAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.18, C:0.00, G:0.32, T:0.50
Consensus pattern (22 bp):
TGGGTTTAATTGTAATAGGTTT
Found at i:89590304 original size:12 final size:13
Alignment explanation
Indices: 89590286--89590319 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
89590276 GGCATCTTAA
89590286 AAAAAGAGAAAAG
1 AAAAAGAGAAAAG
*
89590299 -AAAAGAAAAAAG
1 AAAAAGAGAAAAG
89590311 AAAAAGAGA
1 AAAAAGAGA
89590320 GAGGGATCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (13 bp):
AAAAAGAGAAAAG
Found at i:89591378 original size:13 final size:13
Alignment explanation
Indices: 89591334--89591378 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
89591324 CGCCGAGGTA
* *
89591334 TTTTTAATTTTTA
1 TTTTTAATTTCTG
89591347 TTTTTCAATTTCTG
1 TTTTT-AATTTCTG
*
89591361 CTTTTAATTTCTG
1 TTTTTAATTTCTG
89591374 TTTTT
1 TTTTT
89591379 CAAAAATCAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
13 17 0.63
14 10 0.37
ACGTcount: A:0.16, C:0.09, G:0.04, T:0.71
Consensus pattern (13 bp):
TTTTTAATTTCTG
Found at i:89591379 original size:100 final size:101
Alignment explanation
Indices: 89591261--89591642 Score: 400
Period size: 100 Copynumber: 3.9 Consensus size: 101
89591251 AATTTTCGTT
* * * *
89591261 TTTTCAATTTATGCTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGCTAAGCCTCGGGGCACG
1 TTTT-AATTTCTGCTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACG
*
89591326 CCGAGGTATTTTTAATTTTTATTTTTCAATTTCTG-C
65 CTGAGGTATTTTTAATTTTTATTTTTCAATTTCTGCC
* **
89591362 TTTTAATTTCTGTTTTTCAAAAATCAACTCATATTGTAAGAGGTGAGTTGAGCCTCAGGGCACGC
1 TTTTAATTTCTGCTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGC
* * *
89591427 TGAGGTATTTTTAATTTCTGTTTTTCAATTTTTGCC
66 TGAGGTATTTTTAATTTTTATTTTTCAATTTCTGCC
** * * *
89591463 TTACAAATTCTGCTTTTC--AAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGACACGC
1 TTTTAATTTCTGCTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGC
* *
89591526 TGAGGTA-TTTTCA-----A-TTTTC--GTT-T---
66 TGAGGTATTTTTAATTTTTATTTTTCAATTTCTGCC
* * ** * *
89591549 TTTTAATTTATGTTTCTAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGACACG
1 TTTTAATTTCTGCTT-TTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACG
* *
89591614 CTGAGGTAATTTTAATTTTTATTTGTCAA
65 CTGAGGTATTTTTAATTTTTATTTTTCAA
89591643 AAATCAACTC
Statistics
Matches: 237, Mismatches: 31, Indels: 29
0.80 0.10 0.10
Matches are distributed among these distances:
86 10 0.04
87 1 0.00
89 53 0.22
90 7 0.03
92 5 0.02
95 1 0.00
96 4 0.02
98 5 0.02
99 48 0.20
100 84 0.35
101 19 0.08
ACGTcount: A:0.27, C:0.16, G:0.18, T:0.40
Consensus pattern (101 bp):
TTTTAATTTCTGCTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGC
TGAGGTATTTTTAATTTTTATTTTTCAATTTCTGCC
Done.