Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr3
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: 100348136
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3062571 characters in sequence are not A, C, G, or T
File 144 of 290
Found at i:49070388 original size:21 final size:21
Alignment explanation
Indices: 49070346--49070401 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 21
49070336 ATTTATTTAA
* * *
49070346 AAACCTTAAGCCTTAAGCCTT
1 AAACCTTAAACCCTAAACCTT
*
49070367 AAACCTTAAACCCTAAATCTT
1 AAACCTTAAACCCTAAACCTT
49070388 -AACCTT-AACCCTAA
1 AAACCTTAAACCCTAA
49070402 CCTAAAAGTA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 8 0.26
20 6 0.19
21 17 0.55
ACGTcount: A:0.39, C:0.30, G:0.04, T:0.27
Consensus pattern (21 bp):
AAACCTTAAACCCTAAACCTT
Found at i:49070744 original size:115 final size:116
Alignment explanation
Indices: 49070410--49070751 Score: 471
Period size: 115 Copynumber: 3.0 Consensus size: 116
49070400 AACCTAAAAG
* *
49070410 TAAAAACCCTAACCCTAACCTAA---AAGTAAAAACCCTAACCCTAACCTAATTTAATAAAAAAA
1 TAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTT-ATTAAAAAA
* *
49070472 CCCTAACCCTAACCTAATTTAATAAAAAAACCGTAACACTAACCTAATTTAAT
65 CCCTAACCCTAACCTAATTTAATTAAAAACCCGT-ACACTAACCTAATTTAAT
* * ***
49070525 TAAAAACCCTAACCCCAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATCCTAAAC
1 TAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTATTAAAAAAC
* * *
49070590 CCTAACCCTAAACTAATTCAATT-AAAACCC-TAACACTAACCTAATTTATT
66 CCTAACCCTAACCTAATTTAATTAAAAACCCGT-ACACTAACCTAATTTAAT
* * *
49070640 TAAAAACCCTAAACCTAATCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTATTTAAAAAC
1 TAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTATTAAAAAAC
*
49070705 CCTAACCCTAACCTAATTTAATTAAAAACCCGT-CCCTAACCTAATTT
66 CCTAACCCTAACCTAATTTAATTAAAAACCCGTACACTAACCTAATTT
49070752 TACATAATTT
Statistics
Matches: 200, Mismatches: 22, Indels: 10
0.86 0.09 0.04
Matches are distributed among these distances:
115 133 0.67
116 13 0.06
117 26 0.13
118 28 0.14
ACGTcount: A:0.45, C:0.27, G:0.01, T:0.26
Consensus pattern (116 bp):
TAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTATTAAAAAAC
CCTAACCCTAACCTAATTTAATTAAAAACCCGTACACTAACCTAATTTAAT
Found at i:49074741 original size:23 final size:23
Alignment explanation
Indices: 49074715--49074776 Score: 79
Period size: 23 Copynumber: 2.6 Consensus size: 23
49074705 AAATAAATAC
* *
49074715 CCTAATTTAATTGAAAACCCTAA
1 CCTAACTTAATTAAAAACCCTAA
49074738 CCTAACTTAATTAAAAACCCTAA
1 CCTAACTTAATTAAAAACCCTAA
*
49074761 CCCTAACCTAAATTAA
1 -CCTAA-CTTAATTAA
49074777 TTAAAAAACC
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
23 21 0.62
24 5 0.15
25 8 0.24
ACGTcount: A:0.45, C:0.26, G:0.02, T:0.27
Consensus pattern (23 bp):
CCTAACTTAATTAAAAACCCTAA
Found at i:49074763 original size:29 final size:29
Alignment explanation
Indices: 49074730--49075328 Score: 721
Period size: 29 Copynumber: 19.7 Consensus size: 29
49074720 TTTAATTGAA
49074730 AACCCTAACCTAACTTAATTAAAAACCCT
1 AACCCTAACCTAACTTAATTAAAAACCCT
* *
49074759 AACCCTAACCTAAATTAATTAAAAAACCT
1 AACCCTAACCTAACTTAATTAAAAACCCT
* *
49074788 AACCCTAACCTAAATTAACTAAAAACCCT
1 AACCCTAACCTAACTTAATTAAAAACCCT
* * *
49074817 AACCCTAACCTAAATTAACTAAAAACCTT
1 AACCCTAACCTAACTTAATTAAAAACCCT
* *
49074846 AACCCTAACCTAAATTAATTAAAAACCTT
1 AACCCTAACCTAACTTAATTAAAAACCCT
* * *
49074875 AACCTTAACCTAACCTAACTAAAAACCCT
1 AACCCTAACCTAACTTAATTAAAAACCCT
49074904 AACCCTAACCTAACTTAATTAAAACTCTAACCCT
1 AACCCTAACCTAACTTAATT-AAA----AACCCT
49074938 AACCCTAACCCTAACTTAATTAAAAACCCT
1 AACCCTAA-CCTAACTTAATTAAAAACCCT
*
49074968 AACCCTAATCTAACTTAATTAAAAACTCTAACCCT
1 AACCCTAACCTAACTTAATT--AAA----AACCCT
*
49075003 AACCCTAACCTAACTTAATTAAAAATCCT
1 AACCCTAACCTAACTTAATTAAAAACCCT
* *
49075032 AACCCTAACCTAAATTAACTAAAAACCCT
1 AACCCTAACCTAACTTAATTAAAAACCCT
*
49075061 AACCCTAACCTAAATTAATTAAAAACCCT
1 AACCCTAACCTAACTTAATTAAAAACCCT
49075090 AACCTAACCTAACCTAACTTAATTAAAAACCCT
1 AA-C---CCTAACCTAACTTAATTAAAAACCCT
49075123 AACCCTAATCCTAACCTAACTTAATTAAAAACCCT
1 AA--C----CCTAACCTAACTTAATTAAAAACCCT
49075158 AACCCTAACCTAACTTAATTAAAAACCCT
1 AACCCTAACCTAACTTAATTAAAAACCCT
*
49075187 AACCCTAACCCTAACCTAAATTAACTAAAAACCCT
1 AACCCTAA-CCTAA-C----TTAATTAAAAACCCT
49075222 AACCCTAACCTAACTTAATTAAAAACCCT
1 AACCCTAACCTAACTTAATTAAAAACCCT
*
49075251 AACCCTAACATAACTTAATTAAAAACCCT
1 AACCCTAACCTAACTTAATTAAAAACCCT
*****
49075280 AACCCTAACCTAACTTAAACCCTAACCCT
1 AACCCTAACCTAACTTAATTAAAAACCCT
*
49075309 AACCCTAACGTAACTTAATT
1 AACCCTAACCTAACTTAATT
49075329 TGATAAATTT
Statistics
Matches: 510, Mismatches: 36, Indels: 48
0.86 0.06 0.08
Matches are distributed among these distances:
29 339 0.66
30 23 0.05
31 4 0.01
33 32 0.06
34 24 0.05
35 88 0.17
ACGTcount: A:0.45, C:0.30, G:0.00, T:0.24
Consensus pattern (29 bp):
AACCCTAACCTAACTTAATTAAAAACCCT
Found at i:49074791 original size:23 final size:23
Alignment explanation
Indices: 49074715--49074791 Score: 64
Period size: 23 Copynumber: 3.1 Consensus size: 23
49074705 AAATAAATAC
* * *
49074715 CCTAATTTAATTGAAAACCCTAA
1 CCTAAATTAATTAAAAAACCTAA
*
49074738 CCTAACTTAATTAAAAACCCTAACCCTAA
1 CCTAAATTAATT-AAAA----AA-CCTAA
49074767 CCTAAATTAATTAAAAAACCTAA
1 CCTAAATTAATTAAAAAACCTAA
49074790 CC
1 CC
49074792 CTAACCTAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
23 18 0.41
24 5 0.11
28 5 0.11
29 16 0.36
ACGTcount: A:0.47, C:0.26, G:0.01, T:0.26
Consensus pattern (23 bp):
CCTAAATTAATTAAAAAACCTAA
Found at i:49075252 original size:23 final size:24
Alignment explanation
Indices: 49075222--49075311 Score: 96
Period size: 23 Copynumber: 3.6 Consensus size: 24
49075212 TAAAAACCCT
49075222 AACCCTAA-CCTAACTTAATTAAA
1 AACCCTAACCCTAACTTAATTAAA
49075245 AACCCTAACCCTAACATAACTTAATTAAA
1 AACCCTAA-CC---C-TAACTTAATTAAA
*
49075274 AACCCTAACCCTAACCTAACTT--A
1 AACCCTAACCCTAACTTAA-TTAAA
49075297 AACCCTAACCCTAAC
1 AACCCTAACCCTAAC
49075312 CCTAACGTAA
Statistics
Matches: 59, Mismatches: 1, Indels: 14
0.80 0.01 0.19
Matches are distributed among these distances:
23 24 0.41
24 7 0.12
25 4 0.07
28 3 0.05
29 21 0.36
ACGTcount: A:0.44, C:0.33, G:0.00, T:0.22
Consensus pattern (24 bp):
AACCCTAACCCTAACTTAATTAAA
Found at i:49075285 original size:6 final size:6
Alignment explanation
Indices: 49075274--49075317 Score: 56
Period size: 6 Copynumber: 7.5 Consensus size: 6
49075264 CTTAATTAAA
*
49075274 AACCCT AACCCT AA-CCT AA-CTT AAACCCT AACCCT AACCCT AAC
1 AACCCT AACCCT AACCCT AACCCT -AACCCT AACCCT AACCCT AAC
49075318 GTAACTTAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
5 7 0.21
6 25 0.74
7 2 0.06
ACGTcount: A:0.39, C:0.43, G:0.00, T:0.18
Consensus pattern (6 bp):
AACCCT
Found at i:49075312 original size:23 final size:24
Alignment explanation
Indices: 49075273--49075317 Score: 83
Period size: 23 Copynumber: 1.9 Consensus size: 24
49075263 ACTTAATTAA
49075273 AAACCCTAACCCTAA-CCTAACTT
1 AAACCCTAACCCTAACCCTAACTT
49075296 AAACCCTAACCCTAACCCTAAC
1 AAACCCTAACCCTAACCCTAAC
49075318 GTAACTTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
23 15 0.71
24 6 0.29
ACGTcount: A:0.40, C:0.42, G:0.00, T:0.18
Consensus pattern (24 bp):
AAACCCTAACCCTAACCCTAACTT
Found at i:49075392 original size:56 final size:54
Alignment explanation
Indices: 49075328--49075654 Score: 410
Period size: 56 Copynumber: 5.9 Consensus size: 54
49075318 GTAACTTAAT
49075328 TTGATAAATTTTACTAACCATTAACACAATTTTTGGACTTAATAATTTTAGTTTA
1 TTGATAAATTTTACTAACCATTAACACAATTTTTGG-CTTAATAATTTTAGTTTA
* * *
49075383 TGTCATAAATTTTACTAACCATTAATACAATTTTTGGCTTAATAATTTTACATATT-
1 T-TGATAAATTTTACTAACCATTAACACAATTTTTGGCTTAATAATTTTA-GT-TTA
* **
49075439 TTGAT-AATTTTACTAACCATTAGCACAATTTCCGGACTTAATAATTTTAGTTTA
1 TTGATAAATTTTACTAACCATTAACACAATTTTTGG-CTTAATAATTTTAGTTTA
* * *
49075493 TTTCATAAATTTTACTAACCATTAATACAATTTTTGGCTTAATAATTTTACATATT-
1 -TTGATAAATTTTACTAACCATTAACACAATTTTTGGCTTAATAATTTTA-GT-TTA
* **
49075549 TTGAT-AATTTTACTAACCATTAGCACAATTTCCGGACTTAATAATTTTAGTTTA
1 TTGATAAATTTTACTAACCATTAACACAATTTTTGG-CTTAATAATTTTAGTTTA
49075603 TTTGATAAATTTTACTAACCATTAACACAATTTTTTTGGCTTAATAATTTTA
1 -TTGATAAATTTTACTAACCATTAACACAA--TTTTTGGCTTAATAATTTTA
49075655 CATAATTTTA
Statistics
Matches: 233, Mismatches: 24, Indels: 28
0.82 0.08 0.10
Matches are distributed among these distances:
53 4 0.02
54 54 0.23
55 69 0.30
56 84 0.36
57 17 0.07
58 5 0.02
ACGTcount: A:0.35, C:0.13, G:0.07, T:0.46
Consensus pattern (54 bp):
TTGATAAATTTTACTAACCATTAACACAATTTTTGGCTTAATAATTTTAGTTTA
Found at i:49075452 original size:110 final size:110
Alignment explanation
Indices: 49075327--49075663 Score: 584
Period size: 110 Copynumber: 3.0 Consensus size: 110
49075317 CGTAACTTAA
* ** *
49075327 TTTGATAAATTTTACTAACCATTAACACAATTTTTGGACTTAATAATTTTAGTTTATGTCATAAA
1 TTTGAT-AATTTTACTAACCATTAGCACAATTTCCGGACTTAATAATTTTAGTTTATTTCATAAA
49075392 TTTTACTAACCATTAATACAATTTTTGGCTTAATAATTTTACATAT
65 TTTTACTAACCATTAATACAATTTTTGGCTTAATAATTTTACATAT
49075438 TTTGATAATTTTACTAACCATTAGCACAATTTCCGGACTTAATAATTTTAGTTTATTTCATAAAT
1 TTTGATAATTTTACTAACCATTAGCACAATTTCCGGACTTAATAATTTTAGTTTATTTCATAAAT
49075503 TTTACTAACCATTAATACAATTTTTGGCTTAATAATTTTACATAT
66 TTTACTAACCATTAATACAATTTTTGGCTTAATAATTTTACATAT
*
49075548 TTTGATAATTTTACTAACCATTAGCACAATTTCCGGACTTAATAATTTTAGTTTATTTGATAAAT
1 TTTGATAATTTTACTAACCATTAGCACAATTTCCGGACTTAATAATTTTAGTTTATTTCATAAAT
*
49075613 TTTACTAACCATTAACACAATTTTTTTGGCTTAATAATTTTACATAAT
66 TTTACTAACCATTAATACAA--TTTTTGGCTTAATAATTTTACAT-AT
49075661 TTT
1 TTT
49075664 ACATAATGTT
Statistics
Matches: 217, Mismatches: 6, Indels: 4
0.96 0.03 0.02
Matches are distributed among these distances:
110 183 0.84
111 6 0.03
112 23 0.11
113 5 0.02
ACGTcount: A:0.35, C:0.13, G:0.07, T:0.46
Consensus pattern (110 bp):
TTTGATAATTTTACTAACCATTAGCACAATTTCCGGACTTAATAATTTTAGTTTATTTCATAAAT
TTTACTAACCATTAATACAATTTTTGGCTTAATAATTTTACATAT
Found at i:49075661 original size:10 final size:10
Alignment explanation
Indices: 49075646--49075670 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
49075636 TTTTGGCTTA
49075646 ATAATTTTAC
1 ATAATTTTAC
49075656 ATAATTTTAC
1 ATAATTTTAC
49075666 ATAAT
1 ATAAT
49075671 GTTAGATTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (10 bp):
ATAATTTTAC
Found at i:49078652 original size:126 final size:126
Alignment explanation
Indices: 49078427--49078864 Score: 727
Period size: 126 Copynumber: 3.5 Consensus size: 126
49078417 TTTGACAAAA
* * **
49078427 ACATGACCTGCTGTAGCAAAATCGTGTCCACGAGGGTGCGATTTCACAATTTCTTCTCAAATAGC
1 ACATGACCTACTGTAGCAAAATCGCGTCCACGAGGGCACGATTTCACAATTTCTTCTCAAATAGC
49078492 ATTCTCGTAGAAACAATTTTATACTATTTGCTCAGAAAGATCAGAAAAAAAATTATTTCTT
66 ATTCTCGTAGAAACAATTTTATACTATTTGCTCAGAAAGATCAGAAAAAAAATTATTTCTT
49078553 ACATGACCTACTGTAGCAAAATCGCGTCCACGAGGGCACGATTTCACAATTTCTTCTCAAATAGC
1 ACATGACCTACTGTAGCAAAATCGCGTCCACGAGGGCACGATTTCACAATTTCTTCTCAAATAGC
* * * * *
49078618 ATCCTGGTAGAAGCGATTTTATACTATTTGCTCAGAAACG-TCA-ACAAAAAAATTATTTCTA
66 ATTCTCGTAGAAACAATTTTATACTATTTGCTCAGAAA-GATCAGA-AAAAAAATTATTTCTT
* * **
49078679 ACATGACCTGCTGTAGCAAAATCGTGTCCACGAGGGTGCGATTTCACAATTTCTTCTCAAATAGC
1 ACATGACCTACTGTAGCAAAATCGCGTCCACGAGGGCACGATTTCACAATTTCTTCTCAAATAGC
49078744 ATTCTCGTAGAAACAATTTTATACTATTTGCTCAGAAAGATCAGAAAAAAAATTATTTCTT
66 ATTCTCGTAGAAACAATTTTATACTATTTGCTCAGAAAGATCAGAAAAAAAATTATTTCTT
49078805 ACATGACCTACTGTAGCAAAATCGCGTCCACGAGGGCACGATTTCACAATTTCTTCTCAA
1 ACATGACCTACTGTAGCAAAATCGCGTCCACGAGGGCACGATTTCACAATTTCTTCTCAA
49078865 GAGCGATTTC
Statistics
Matches: 286, Mismatches: 22, Indels: 8
0.91 0.07 0.03
Matches are distributed among these distances:
125 2 0.01
126 282 0.99
127 2 0.01
ACGTcount: A:0.34, C:0.21, G:0.15, T:0.30
Consensus pattern (126 bp):
ACATGACCTACTGTAGCAAAATCGCGTCCACGAGGGCACGATTTCACAATTTCTTCTCAAATAGC
ATTCTCGTAGAAACAATTTTATACTATTTGCTCAGAAAGATCAGAAAAAAAATTATTTCTT
Found at i:49080909 original size:23 final size:24
Alignment explanation
Indices: 49080856--49080946 Score: 105
Period size: 26 Copynumber: 3.7 Consensus size: 24
49080846 AAATTTGTTA
49080856 TTTAT-TTATTTATTTTAAATTTT
1 TTTATATTATTTATTTTAAATTTT
*
49080879 TTCATATATTATTTATTTTAAA-CTT
1 TT--TATATTATTTATTTTAAATTTT
*
49080904 TTTATATTATTTACTTTAAATTGTTT
1 TTTATATTATTTATTTTAAA-T-TTT
49080930 TTTATATTATTTTATTT
1 TTTATATTA-TTTATTT
49080947 CATTTGTCTT
Statistics
Matches: 57, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
23 19 0.33
25 7 0.12
26 25 0.44
27 6 0.11
ACGTcount: A:0.27, C:0.03, G:0.01, T:0.68
Consensus pattern (24 bp):
TTTATATTATTTATTTTAAATTTT
Found at i:49083875 original size:25 final size:25
Alignment explanation
Indices: 49083844--49083904 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
49083834 TGTACGTTAG
*
49083844 ATTAAAAATTAAATTAGTATTTTA-T
1 ATTAAAAATTAAATTAAT-TTTTACT
* **
49083869 GTTAAAAATTTTATTAATTTTTACT
1 ATTAAAAATTAAATTAATTTTTACT
49083894 ATTAAAAATTA
1 ATTAAAAATTA
49083905 GGATGATTGA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
24 5 0.17
25 24 0.83
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (25 bp):
ATTAAAAATTAAATTAATTTTTACT
Found at i:49093231 original size:42 final size:45
Alignment explanation
Indices: 49093147--49093231 Score: 106
Period size: 46 Copynumber: 1.9 Consensus size: 45
49093137 TTACTAATAC
*
49093147 TATTTATTTATATTATTATTACTGTATCATTATTAGTTTATATTTT
1 TATTTATTTATATTATTATTAC-GTATCATTATTAGTCTATATTTT
*
49093193 TATTTA-TTATATTATATGTTAC-TATCATTA-TA-TCTATAT
1 TATTTATTTATATTAT-TATTACGTATCATTATTAGTCTATAT
49093232 ATGCACATAT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
42 6 0.17
43 2 0.06
44 8 0.22
45 9 0.25
46 11 0.31
ACGTcount: A:0.31, C:0.06, G:0.04, T:0.60
Consensus pattern (45 bp):
TATTTATTTATATTATTATTACGTATCATTATTAGTCTATATTTT
Found at i:49093408 original size:27 final size:28
Alignment explanation
Indices: 49093363--49093427 Score: 71
Period size: 27 Copynumber: 2.4 Consensus size: 28
49093353 ATATACATTT
*
49093363 ATATTTTATAATAGTTACACGTTT-TCC
1 ATATTTTATAATAGTTACACGTTTATAC
* *
49093390 ATATTTTATAAT-TTATACATGTTTATAC
1 ATATTTTATAATAGT-TACACGTTTATAC
*
49093418 ATTTTTTATA
1 ATATTTTATA
49093428 TAATATGTAC
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
26 1 0.03
27 20 0.62
28 11 0.34
ACGTcount: A:0.32, C:0.09, G:0.05, T:0.54
Consensus pattern (28 bp):
ATATTTTATAATAGTTACACGTTTATAC
Found at i:49094126 original size:186 final size:186
Alignment explanation
Indices: 49093812--49094184 Score: 746
Period size: 186 Copynumber: 2.0 Consensus size: 186
49093802 AGCATTAAAA
49093812 TCGTCATATTTTACAAATTTTCAAAATATTTGGTATTCATGATTCTCAAGAAAGATCGTGTCCTA
1 TCGTCATATTTTACAAATTTTCAAAATATTTGGTATTCATGATTCTCAAGAAAGATCGTGTCCTA
49093877 ACTTACTGGATTGCGATTATTTTTCGATGGATTTAGAAAGCCAAGTATTTGTTTTGCAATAAATT
66 ACTTACTGGATTGCGATTATTTTTCGATGGATTTAGAAAGCCAAGTATTTGTTTTGCAATAAATT
49093942 CATAAATTTCAAATAAAAGCTTATTCTCGGGAATTCAAAAATGTTGGGTCCTAACT
131 CATAAATTTCAAATAAAAGCTTATTCTCGGGAATTCAAAAATGTTGGGTCCTAACT
49093998 TCGTCATATTTTACAAATTTTCAAAATATTTGGTATTCATGATTCTCAAGAAAGATCGTGTCCTA
1 TCGTCATATTTTACAAATTTTCAAAATATTTGGTATTCATGATTCTCAAGAAAGATCGTGTCCTA
49094063 ACTTACTGGATTGCGATTATTTTTCGATGGATTTAGAAAGCCAAGTATTTGTTTTGCAATAAATT
66 ACTTACTGGATTGCGATTATTTTTCGATGGATTTAGAAAGCCAAGTATTTGTTTTGCAATAAATT
49094128 CATAAATTTCAAATAAAAGCTTATTCTCGGGAATTCAAAAATGTTGGGTCCTAACT
131 CATAAATTTCAAATAAAAGCTTATTCTCGGGAATTCAAAAATGTTGGGTCCTAACT
49094184 T
1 T
49094185 ACTGGTCATG
Statistics
Matches: 187, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
186 187 1.00
ACGTcount: A:0.33, C:0.14, G:0.15, T:0.38
Consensus pattern (186 bp):
TCGTCATATTTTACAAATTTTCAAAATATTTGGTATTCATGATTCTCAAGAAAGATCGTGTCCTA
ACTTACTGGATTGCGATTATTTTTCGATGGATTTAGAAAGCCAAGTATTTGTTTTGCAATAAATT
CATAAATTTCAAATAAAAGCTTATTCTCGGGAATTCAAAAATGTTGGGTCCTAACT
Found at i:49095191 original size:17 final size:17
Alignment explanation
Indices: 49095165--49095200 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
49095155 GTGTGTTTTG
*
49095165 TTTTGGCTGCATGACAT
1 TTTTGACTGCATGACAT
49095182 TTTTGACTGCATGACAT
1 TTTTGACTGCATGACAT
49095199 TT
1 TT
49095201 CATCATAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.19, C:0.17, G:0.19, T:0.44
Consensus pattern (17 bp):
TTTTGACTGCATGACAT
Found at i:49098290 original size:17 final size:17
Alignment explanation
Indices: 49098255--49098292 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
49098245 TTGAGTCATT
*
49098255 AAAAAAATGATGAAATG
1 AAAAAAATGATAAAATG
49098272 AAAAAAATGA-AAAAGTG
1 AAAAAAATGATAAAA-TG
49098289 AAAA
1 AAAA
49098293 GGAAAAATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 3 0.16
17 16 0.84
ACGTcount: A:0.71, C:0.00, G:0.16, T:0.13
Consensus pattern (17 bp):
AAAAAAATGATAAAATG
Found at i:49098292 original size:14 final size:14
Alignment explanation
Indices: 49098275--49098319 Score: 58
Period size: 14 Copynumber: 3.3 Consensus size: 14
49098265 TGAAATGAAA
*
49098275 AAAATGAAAAAGTG
1 AAAAGGAAAAAGTG
49098289 AAAAGGAAAAA-TG
1 AAAAGGAAAAAGTG
49098302 AAAAAGGAAAAAGT-
1 -AAAAGGAAAAAGTG
49098316 AAAA
1 AAAA
49098320 TAGAGAGGCT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
13 6 0.21
14 21 0.75
15 1 0.04
ACGTcount: A:0.71, C:0.00, G:0.20, T:0.09
Consensus pattern (14 bp):
AAAAGGAAAAAGTG
Found at i:49098319 original size:21 final size:21
Alignment explanation
Indices: 49098274--49098312 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
49098264 ATGAAATGAA
49098274 AAAAATGAAAAAGTGAAAAGG
1 AAAAATGAAAAAGTGAAAAGG
49098295 AAAAATGAAAAAG-GAAAA
1 AAAAATGAAAAAGTGAAAA
49098313 AGTAAAATAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.72, C:0.00, G:0.21, T:0.08
Consensus pattern (21 bp):
AAAAATGAAAAAGTGAAAAGG
Found at i:49099745 original size:44 final size:44
Alignment explanation
Indices: 49099606--49100266 Score: 672
Period size: 44 Copynumber: 15.0 Consensus size: 44
49099596 GAAAAGCAGC
* **
49099606 GGATCTTGTCTTTATGTATTGACATGAAGTAGATC-GAAGATAGC
1 GGATCTTGTCTTCATGTATTGACATGAAGTAGATCAG-AGATAAT
* *** ** *** *
49099650 AGATCTTGTCTTCCCATACCGGTGGTGAAGTAGATC-GAAGATGAT
1 GGATCTTGTCTTCATGTA-TTGACATGAAGTAGATCAG-AGATAAT
*
49099695 GGATCTTGTCTTCATGCATTGACATGAAGTAGATCAGAGATAAT
1 GGATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGATAAT
* **
49099739 GCATCTTGTCTTCATGTATTGACATGAAGTAGATC-GAAGATAGC
1 GGATCTTGTCTTCATGTATTGACATGAAGTAGATCAG-AGATAAT
* *** * *** *
49099783 GGATCTTATCTTCCCATACTGGTGGTGAAGTAGATCAAAGATAAT
1 GGATCTTGTCTTCATGTA-TTGACATGAAGTAGATCAGAGATAAT
*
49099828 AGATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGATAAT
1 GGATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGATAAT
* * * **
49099872 GAATCTTGTCTTTATGTATTGACATGGAGTAGATC-GAAGATAGC
1 GGATCTTGTCTTCATGTATTGACATGAAGTAGATCAG-AGATAAT
*
49099916 GGATCTTGTCTTCATGTATTGACATAAAGTAGATCAGAGATAAT
1 GGATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGATAAT
**
49099960 GGATCTTGTCTTCATGTATTGACATGAAGTAGATCCA-AGATAGC
1 GGATCTTGTCTTCATGTATTGACATGAAGTAGAT-CAGAGATAAT
* * * * **
49100004 AGATCTTGTCTTCACGTATTGATATAAAGTAGATC-GAAGATAGC
1 GGATCTTGTCTTCATGTATTGACATGAAGTAGATCAG-AGATAAT
*
49100048 GGATCTTGTCTACATGTATTGACATGAAGTAGATC-GAAGATAAT
1 GGATCTTGTCTTCATGTATTGACATGAAGTAGATCAG-AGATAAT
*
49100092 GGATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGATAGT
1 GGATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGATAAT
* * *
49100136 GGATCTTGTCTTCATGTATTGACATGAAGTAGATCAAAGATGAC
1 GGATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGATAAT
* *** * ***
49100180 AGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATC-GAAGATAAT
1 GGATCTTGTCTTCATGTA-TTGACATGAAGTAGATCAG-AGATAAT
*
49100225 GGATCTTGTCTTCATGTATTGACATTAAGTAGATCAGAGATA
1 GGATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGATA
49100267 GCAGACCATG
Statistics
Matches: 501, Mismatches: 102, Indels: 28
0.79 0.16 0.04
Matches are distributed among these distances:
43 3 0.01
44 398 0.79
45 100 0.20
ACGTcount: A:0.31, C:0.13, G:0.23, T:0.33
Consensus pattern (44 bp):
GGATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGATAAT
Found at i:49100221 original size:45 final size:43
Alignment explanation
Indices: 49100160--49100318 Score: 130
Period size: 44 Copynumber: 3.6 Consensus size: 43
49100150 TGTATTGACA
* *
49100160 TGAAGTAGATCAAAGATGACAGATCTTGTCTTCCCATACTGGTGG
1 TGAAGTAGATCGAAGAT-ACAGATCTTGTCTTCCCATACTAGT-G
* *
49100205 TGAAGTAGATCGAAGATA-ATGGATCTTGTCTT--CAT-GTATTG
1 TGAAGTAGATCGAAGATACA--GATCTTGTCTTCCCATACTAGTG
* * *
49100246 ACATTAAGTAGATC-AGAGATAGCAGACCATGTCTTCCCATACTAGTG
1 ---TGAAGTAGATCGA-AGATA-CAGATCTTGTCTTCCCATACTAGTG
*
49100293 TGAAGTAGATCGAAGATACAGGTCTT
1 TGAAGTAGATCGAAGATACAGATCTT
49100319 ACCTCCCCAA
Statistics
Matches: 89, Mismatches: 13, Indels: 26
0.70 0.10 0.20
Matches are distributed among these distances:
41 1 0.01
42 2 0.02
43 10 0.11
44 40 0.45
45 28 0.31
46 4 0.04
47 4 0.04
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Consensus pattern (43 bp):
TGAAGTAGATCGAAGATACAGATCTTGTCTTCCCATACTAGTG
Found at i:49100267 original size:133 final size:133
Alignment explanation
Indices: 49099606--49100267 Score: 920
Period size: 133 Copynumber: 5.0 Consensus size: 133
49099596 GAAAAGCAGC
* * *
49099606 GGATCTTGTCTTTATGTATTGACATGAAGTAGATCGAAGATAGCAGATCTTGTCTTCCCATACCG
1 GGATCTTGTCTTCATGTATTGACATGAAGTAGATCGAAGATAGCGGATCTTGTCTTCCCATACTG
* *
49099671 GTGGTGAAGTAGATCGAAGATGATGGATCTTGTCTTCATGCATTGACATGAAGTAGATCAGAGAT
66 GTGGTGAAGTAGATCGAAGATAATGGATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGAT
*
49099736 AAT
131 AGT
* *
49099739 GCATCTTGTCTTCATGTATTGACATGAAGTAGATCGAAGATAGCGGATCTTATCTTCCCATACTG
1 GGATCTTGTCTTCATGTATTGACATGAAGTAGATCGAAGATAGCGGATCTTGTCTTCCCATACTG
* *
49099804 GTGGTGAAGTAGATCAAAGATAATAGATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGAT
66 GTGGTGAAGTAGATCGAAGATAATGGATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGAT
*
49099869 AAT
131 AGT
* * * *** *
49099872 GAATCTTGTCTTTATGTATTGACATGGAGTAGATCGAAGATAGCGGATCTTGTCTTCATGTA-TT
1 GGATCTTGTCTTCATGTATTGACATGAAGTAGATCGAAGATAGCGGATCTTGTCTTCCCATACTG
*** *
49099936 GACATAAAGTAGATC-AGAGATAATGGATCTTGTCTTCATGTATTGACATGAAGTAGATCCA-AG
66 GTGGTGAAGTAGATCGA-AGATAATGGATCTTGTCTTCATGTATTGACATGAAGTAGAT-CAGAG
*
49099999 ATAGC
129 ATAGT
* * * * * *** *
49100004 AGATCTTGTCTTCACGTATTGATATAAAGTAGATCGAAGATAGCGGATCTTGTCTACATGTA-TT
1 GGATCTTGTCTTCATGTATTGACATGAAGTAGATCGAAGATAGCGGATCTTGTCTTCCCATACTG
***
49100068 GACATGAAGTAGATCGAAGATAATGGATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGAT
66 GTGGTGAAGTAGATCGAAGATAATGGATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGAT
49100133 AGT
131 AGT
* *
49100136 GGATCTTGTCTTCATGTATTGACATGAAGTAGATCAAAGAT-GACAGATCTTGTCTTCCCATACT
1 GGATCTTGTCTTCATGTATTGACATGAAGTAGATCGAAGATAG-CGGATCTTGTCTTCCCATACT
*
49100200 GGTGGTGAAGTAGATCGAAGATAATGGATCTTGTCTTCATGTATTGACATTAAGTAGATCAGAGA
65 GGTGGTGAAGTAGATCGAAGATAATGGATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGA
49100265 TAG
130 TAG
49100268 CAGACCATGT
Statistics
Matches: 474, Mismatches: 49, Indels: 12
0.89 0.09 0.02
Matches are distributed among these distances:
131 4 0.01
132 224 0.47
133 246 0.52
ACGTcount: A:0.31, C:0.13, G:0.23, T:0.32
Consensus pattern (133 bp):
GGATCTTGTCTTCATGTATTGACATGAAGTAGATCGAAGATAGCGGATCTTGTCTTCCCATACTG
GTGGTGAAGTAGATCGAAGATAATGGATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGAT
AGT
Found at i:49101216 original size:42 final size:45
Alignment explanation
Indices: 49101132--49101216 Score: 106
Period size: 46 Copynumber: 1.9 Consensus size: 45
49101122 TTACTAATAC
*
49101132 TATTTATTTATATTATTATTACTGTATCATTATTAGTTTATATTTT
1 TATTTATTTATATTATTATTAC-GTATCATTATTAGTCTATATTTT
*
49101178 TATTTA-TTATATTATATGTTAC-TATCATTA-TA-TCTATAT
1 TATTTATTTATATTAT-TATTACGTATCATTATTAGTCTATAT
49101217 ATGCACATAT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
42 6 0.17
43 2 0.06
44 8 0.22
45 9 0.25
46 11 0.31
ACGTcount: A:0.31, C:0.06, G:0.04, T:0.60
Consensus pattern (45 bp):
TATTTATTTATATTATTATTACGTATCATTATTAGTCTATATTTT
Found at i:49101384 original size:27 final size:28
Alignment explanation
Indices: 49101339--49101403 Score: 71
Period size: 27 Copynumber: 2.4 Consensus size: 28
49101329 ATATACATTT
*
49101339 ATATTTTATAATAGTTACACGTTT-TCC
1 ATATTTTATAATAGTTACACGTTTATAC
* *
49101366 ATATTTTATAAT-TTATACATGTTTATAC
1 ATATTTTATAATAGT-TACACGTTTATAC
*
49101394 ATTTTTTATA
1 ATATTTTATA
49101404 TAATATGTAC
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
26 1 0.03
27 20 0.62
28 11 0.34
ACGTcount: A:0.32, C:0.09, G:0.05, T:0.54
Consensus pattern (28 bp):
ATATTTTATAATAGTTACACGTTTATAC
Found at i:49104204 original size:13 final size:13
Alignment explanation
Indices: 49104186--49104218 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
49104176 TTTGGTTACC
49104186 AAACTA-CAGTTAA
1 AAACTATCA-TTAA
49104199 AAACTATCATTAA
1 AAACTATCATTAA
49104212 AAACTAT
1 AAACTAT
49104219 TCACATATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 17 0.89
14 2 0.11
ACGTcount: A:0.55, C:0.15, G:0.03, T:0.27
Consensus pattern (13 bp):
AAACTATCATTAA
Found at i:49104571 original size:48 final size:48
Alignment explanation
Indices: 49104507--49104606 Score: 200
Period size: 48 Copynumber: 2.1 Consensus size: 48
49104497 ATTTAGTGGG
49104507 AAAATATTTACAATTAGTTCTAGAAAATGAATAAAATTAAAGGAAATT
1 AAAATATTTACAATTAGTTCTAGAAAATGAATAAAATTAAAGGAAATT
49104555 AAAATATTTACAATTAGTTCTAGAAAATGAATAAAATTAAAGGAAATT
1 AAAATATTTACAATTAGTTCTAGAAAATGAATAAAATTAAAGGAAATT
49104603 AAAA
1 AAAA
49104607 AGATAATTTT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 52 1.00
ACGTcount: A:0.56, C:0.04, G:0.10, T:0.30
Consensus pattern (48 bp):
AAAATATTTACAATTAGTTCTAGAAAATGAATAAAATTAAAGGAAATT
Found at i:49105872 original size:25 final size:25
Alignment explanation
Indices: 49105834--49105882 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
49105824 ATTTTTAATA
*
49105834 TTTTTAAAAATAAATTATTAATTAC
1 TTTTTAAAAATAAATTACTAATTAC
*
49105859 TTTTTAAAATTAAATTACTAATTA
1 TTTTTAAAAATAAATTACTAATTA
49105883 TTAAATATAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (25 bp):
TTTTTAAAAATAAATTACTAATTAC
Found at i:49122793 original size:22 final size:23
Alignment explanation
Indices: 49122762--49122805 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
49122752 TTTAGGAAGA
49122762 TTCATTAAAA-CATCATGCATTTC
1 TTCATTAAAATCATCAT-CATTTC
49122785 TTCA-TAAAATCATCATCATTT
1 TTCATTAAAATCATCATCATTT
49122806 AATTAGTTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.36, C:0.20, G:0.02, T:0.41
Consensus pattern (23 bp):
TTCATTAAAATCATCATCATTTC
Found at i:49123435 original size:17 final size:17
Alignment explanation
Indices: 49123416--49123487 Score: 92
Period size: 17 Copynumber: 4.2 Consensus size: 17
49123406 TTCATATGAA
*
49123416 ATAACAGTTCATGC-AT
1 ATAACAGTTCATACAAT
*
49123432 AATAACAGTTCATTCAAT
1 -ATAACAGTTCATACAAT
*
49123450 ATAATAGTTCATACAAT
1 ATAACAGTTCATACAAT
*
49123467 ATAACAGTTCATTCAAT
1 ATAACAGTTCATACAAT
49123484 ATAA
1 ATAA
49123488 TAATTCATTC
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
17 47 0.96
18 2 0.04
ACGTcount: A:0.44, C:0.15, G:0.07, T:0.33
Consensus pattern (17 bp):
ATAACAGTTCATACAAT
Found at i:49123488 original size:34 final size:34
Alignment explanation
Indices: 49123398--49123500 Score: 120
Period size: 34 Copynumber: 3.0 Consensus size: 34
49123388 GTTCGCATAA
* * * *
49123398 AATAACAATTCATATGAA-ATAACAGTTCATGCAT
1 AATAACAGTTCAT-TCAATATAATAGTTCATACAT
49123432 AATAACAGTTCATTCAATATAATAGTTCATACA-
1 AATAACAGTTCATTCAATATAATAGTTCATACAT
* *
49123465 ATATAACAGTTCATTCAATATAATAATTCATTCAT
1 A-ATAACAGTTCATTCAATATAATAGTTCATACAT
49123500 A
1 A
49123501 CCACATCGTA
Statistics
Matches: 60, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
33 4 0.07
34 55 0.92
35 1 0.02
ACGTcount: A:0.46, C:0.15, G:0.06, T:0.34
Consensus pattern (34 bp):
AATAACAGTTCATTCAATATAATAGTTCATACAT
Found at i:49123494 original size:17 final size:17
Alignment explanation
Indices: 49123433--49123498 Score: 96
Period size: 17 Copynumber: 3.9 Consensus size: 17
49123423 TTCATGCATA
*
49123433 ATAACAGTTCATTCAAT
1 ATAATAGTTCATTCAAT
*
49123450 ATAATAGTTCATACAAT
1 ATAATAGTTCATTCAAT
*
49123467 ATAACAGTTCATTCAAT
1 ATAATAGTTCATTCAAT
*
49123484 ATAATAATTCATTCA
1 ATAATAGTTCATTCA
49123499 TACCACATCG
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 43 1.00
ACGTcount: A:0.44, C:0.15, G:0.05, T:0.36
Consensus pattern (17 bp):
ATAATAGTTCATTCAAT
Found at i:49124189 original size:18 final size:18
Alignment explanation
Indices: 49124166--49124236 Score: 79
Period size: 18 Copynumber: 3.9 Consensus size: 18
49124156 AGTTTGGCAA
49124166 ATTAATACAATTCGCCAT
1 ATTAATACAATTCGCCAT
* * * *
49124184 ATTAATGCAAATCACCAA
1 ATTAATACAATTCGCCAT
*
49124202 ATTAACACAATTCGCCAT
1 ATTAATACAATTCGCCAT
* *
49124220 AGTAATATAATTCGCCA
1 ATTAATACAATTCGCCA
49124237 AGTTAACATG
Statistics
Matches: 41, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 41 1.00
ACGTcount: A:0.42, C:0.23, G:0.07, T:0.28
Consensus pattern (18 bp):
ATTAATACAATTCGCCAT
Found at i:49124243 original size:36 final size:36
Alignment explanation
Indices: 49124163--49124244 Score: 101
Period size: 36 Copynumber: 2.3 Consensus size: 36
49124153 CACAGTTTGG
* * *
49124163 CAAATTAATACAATTCGCCATATTAATGCAAATCAC
1 CAAATTAACACAATTCGCCATAGTAATACAAATCAC
* * *
49124199 CAAATTAACACAATTCGCCATAGTAATATAATTCGC
1 CAAATTAACACAATTCGCCATAGTAATACAAATCAC
*
49124235 CAAGTTAACA
1 CAAATTAACA
49124245 TGGTTCACAA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.44, C:0.22, G:0.07, T:0.27
Consensus pattern (36 bp):
CAAATTAACACAATTCGCCATAGTAATACAAATCAC
Found at i:49124625 original size:29 final size:29
Alignment explanation
Indices: 49124518--49124617 Score: 137
Period size: 29 Copynumber: 3.3 Consensus size: 29
49124508 ACTCATATAT
*
49124518 GCATATATATTATATATATAATCAAGACCCAC
1 GCATATATA-T-TATATATAA-CAAAACCCAC
*
49124550 GCATATATATTATATATATCAAAACCCAC
1 GCATATATATTATATATAACAAAACCCAC
* *
49124579 TCATATATATTATATATAACAAAACCCGC
1 GCATATATATTATATATAACAAAACCCAC
49124608 GCATATATAT
1 GCATATATAT
49124618 ATTGTATATA
Statistics
Matches: 62, Mismatches: 6, Indels: 3
0.87 0.08 0.04
Matches are distributed among these distances:
29 44 0.71
30 8 0.13
31 1 0.02
32 9 0.15
ACGTcount: A:0.44, C:0.19, G:0.05, T:0.32
Consensus pattern (29 bp):
GCATATATATTATATATAACAAAACCCAC
Found at i:49128180 original size:22 final size:22
Alignment explanation
Indices: 49128131--49128185 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
49128121 TCTGCTCCTA
*
49128131 TGTTGTGACATCACACTCCCTG
1 TGTTGCGACATCACACTCCCTG
**
49128153 CATTGCGACATCACACTCCCTG
1 TGTTGCGACATCACACTCCCTG
*
49128175 TGTTGCAACAT
1 TGTTGCGACAT
49128186 AGCGACTAGA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.22, C:0.33, G:0.16, T:0.29
Consensus pattern (22 bp):
TGTTGCGACATCACACTCCCTG
Found at i:49130587 original size:25 final size:25
Alignment explanation
Indices: 49130559--49130606 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
49130549 CAAGCGAGGC
*
49130559 ATATCAGGAAGCTCATAAAGAGCCT
1 ATATCAGGAAGCTCACAAAGAGCCT
* *
49130584 ATATCGGGACGCTCACAAAGAGC
1 ATATCAGGAAGCTCACAAAGAGC
49130607 TATGGTATGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.17
Consensus pattern (25 bp):
ATATCAGGAAGCTCACAAAGAGCCT
Found at i:49139131 original size:11 final size:11
Alignment explanation
Indices: 49139115--49139139 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
49139105 TGTACTTTGA
49139115 AAACAAGTTCT
1 AAACAAGTTCT
49139126 AAACAAGTTCT
1 AAACAAGTTCT
49139137 AAA
1 AAA
49139140 TAATAAAGAT
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:0.52, C:0.16, G:0.08, T:0.24
Consensus pattern (11 bp):
AAACAAGTTCT
Found at i:49142283 original size:47 final size:47
Alignment explanation
Indices: 49142218--49142331 Score: 142
Period size: 48 Copynumber: 2.4 Consensus size: 47
49142208 GTCATGGTAA
* * *
49142218 TGCAGATAAACTGTCACATAATC-AAA-TTGTGGACAAGCCTCGACTTT
1 TGCAGAT-AACTGCCACATAA-CAAAATTTGTGGACAAGCCACCACTTT
*
49142265 TGTAGATATACTGCCACATAACAAAATTTGTGGACAAGCCACCACTTT
1 TGCAGATA-ACTGCCACATAACAAAATTTGTGGACAAGCCACCACTTT
49142313 TGCAGATAAGCTGCCACAT
1 TGCAGATAA-CTGCCACAT
49142332 TCTTTCACCT
Statistics
Matches: 58, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
46 2 0.03
47 21 0.36
48 35 0.60
ACGTcount: A:0.34, C:0.23, G:0.17, T:0.26
Consensus pattern (47 bp):
TGCAGATAACTGCCACATAACAAAATTTGTGGACAAGCCACCACTTT
Found at i:49144646 original size:24 final size:24
Alignment explanation
Indices: 49144619--49144670 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
49144609 TTAGTAAGTC
*
49144619 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
49144643 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
49144667 AAAT
1 AAAT
49144671 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:49146618 original size:24 final size:24
Alignment explanation
Indices: 49146591--49146642 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
49146581 TTAGTAAGTC
*
49146591 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
49146615 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
49146639 AAAT
1 AAAT
49146643 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:49148666 original size:21 final size:21
Alignment explanation
Indices: 49148642--49148691 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
49148632 ACTTTGAAGG
49148642 AACATATAAGTAAATACTGAA
1 AACATATAAGTAAATACTGAA
*
49148663 AACATATAAGTAAATAGTGAA
1 AACATATAAGTAAATACTGAA
49148684 AACATATA
1 AACATATA
49148692 TGAATAATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.58, C:0.08, G:0.10, T:0.24
Consensus pattern (21 bp):
AACATATAAGTAAATACTGAA
Found at i:49150011 original size:33 final size:32
Alignment explanation
Indices: 49149955--49150050 Score: 88
Period size: 33 Copynumber: 2.9 Consensus size: 32
49149945 GTTCTTTTTG
* *
49149955 TGCCATAGTCCTA-CTATGGTCTTACACATGCAT
1 TGCCATA-ACCTAGCTATGGTCTTACACATG-AA
* *
49149988 TGTCATAACCTAGTTATGGTCTTATCATCA-GAA
1 TGCCATAACCTAGCTATGGTCTTA-CA-CATGAA
* *
49150021 TGCCATAGCCTAGCTATGGTTTTACACATG
1 TGCCATAACCTAGCTATGGTCTTACACATG
49150051 TATCTATACT
Statistics
Matches: 51, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
31 2 0.04
32 7 0.14
33 37 0.73
34 3 0.06
35 2 0.04
ACGTcount: A:0.26, C:0.23, G:0.17, T:0.34
Consensus pattern (32 bp):
TGCCATAACCTAGCTATGGTCTTACACATGAA
Found at i:49154988 original size:17 final size:17
Alignment explanation
Indices: 49154966--49155000 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
49154956 AAAATGGATC
49154966 GTAAAAGTACCTTCATT
1 GTAAAAGTACCTTCATT
*
49154983 GTAAAAGTACCTTTATT
1 GTAAAAGTACCTTCATT
49155000 G
1 G
49155001 ACGCTAGATG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.37
Consensus pattern (17 bp):
GTAAAAGTACCTTCATT
Found at i:49158382 original size:21 final size:21
Alignment explanation
Indices: 49158357--49158396 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
49158347 TTCATACATA
49158357 TTTTATAAACCCACAAACAAT
1 TTTTATAAACCCACAAACAAT
*
49158378 TTTTATAAACCTACAAACA
1 TTTTATAAACCCACAAACA
49158397 TAATAGATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.23, G:0.00, T:0.30
Consensus pattern (21 bp):
TTTTATAAACCCACAAACAAT
Found at i:49163348 original size:2 final size:2
Alignment explanation
Indices: 49163341--49163476 Score: 272
Period size: 2 Copynumber: 68.0 Consensus size: 2
49163331 TTAAGAGCCA
49163341 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
49163383 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
49163425 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
49163467 AG AG AG AG AG
1 AG AG AG AG AG
49163477 GAGGGTGTTT
Statistics
Matches: 134, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 134 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:49165593 original size:25 final size:25
Alignment explanation
Indices: 49165559--49165659 Score: 202
Period size: 25 Copynumber: 4.0 Consensus size: 25
49165549 TATGGTAGAC
49165559 TAAGCTTTGAACCAACTATTCCATT
1 TAAGCTTTGAACCAACTATTCCATT
49165584 TAAGCTTTGAACCAACTATTCCATT
1 TAAGCTTTGAACCAACTATTCCATT
49165609 TAAGCTTTGAACCAACTATTCCATT
1 TAAGCTTTGAACCAACTATTCCATT
49165634 TAAGCTTTGAACCAACTATTCCATT
1 TAAGCTTTGAACCAACTATTCCATT
49165659 T
1 T
49165660 GATTAACTGA
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 76 1.00
ACGTcount: A:0.32, C:0.24, G:0.08, T:0.37
Consensus pattern (25 bp):
TAAGCTTTGAACCAACTATTCCATT
Found at i:49171272 original size:30 final size:30
Alignment explanation
Indices: 49171238--49171305 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 30
49171228 TTAACTAAAA
* *
49171238 AAAAGTTACAATTTGA-TCACTGAACTATTG
1 AAAAGTTAC-ATTTAAGTCACTGAACTATTC
* *
49171268 AAAAGTTTTCATTTAAGTCATTGAACTATTC
1 AAAAG-TTACATTTAAGTCACTGAACTATTC
49171299 AAAAGTT
1 AAAAGTT
49171306 TTTATTTAAG
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
30 12 0.38
31 20 0.62
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.37
Consensus pattern (30 bp):
AAAAGTTACATTTAAGTCACTGAACTATTC
Found at i:49171295 original size:31 final size:31
Alignment explanation
Indices: 49171258--49171321 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
49171248 ATTTGATCAC
*
49171258 TGAACTATTGAAAAGTTTTCATTTAAGTCAT
1 TGAACTATTCAAAAGTTTTCATTTAAGTCAT
*
49171289 TGAACTATTCAAAAGTTTTTATTTAAGTCAT
1 TGAACTATTCAAAAGTTTTCATTTAAGTCAT
49171320 TG
1 TG
49171322 GGTTGTTAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.34, C:0.09, G:0.12, T:0.44
Consensus pattern (31 bp):
TGAACTATTCAAAAGTTTTCATTTAAGTCAT
Found at i:49171942 original size:18 final size:18
Alignment explanation
Indices: 49171916--49171951 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
49171906 AATGCGTGGT
*
49171916 TTATAAAAATTTTAAAAA
1 TTATAAAAAATTTAAAAA
*
49171934 TTATGAAAAATTTAAAAA
1 TTATAAAAAATTTAAAAA
49171952 AGTATATACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (18 bp):
TTATAAAAAATTTAAAAA
Found at i:49184636 original size:18 final size:19
Alignment explanation
Indices: 49184613--49184654 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
49184603 ATATAAACTA
**
49184613 AAAAATTA-AAATTCTTTT
1 AAAAATTATAAATTAATTT
49184631 AAAAA-TATAAATTAATTT
1 AAAAATTATAAATTAATTT
49184649 AAAAAT
1 AAAAAT
49184655 GTACAATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 2 0.10
18 18 0.90
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (19 bp):
AAAAATTATAAATTAATTT
Found at i:49184723 original size:32 final size:30
Alignment explanation
Indices: 49184662--49184741 Score: 92
Period size: 32 Copynumber: 2.6 Consensus size: 30
49184652 AATGTACAAT
*
49184662 TTTTTGAACAAGTTCAAGTACCAATTAGGTAC
1 TTTTTGAACAAGTTC-AG-ACCAACTAGGTAC
49184694 TTTTTGAACAAGTTCAGACATCAACTAGGTAC
1 TTTTTGAACAAGTTCAGAC--CAACTAGGTAC
*
49184726 --TTTGGACAAGTTCAGA
1 TTTTTGAACAAGTTCAGA
49184742 GGACAAATTA
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
30 17 0.39
31 2 0.05
32 25 0.57
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Consensus pattern (30 bp):
TTTTTGAACAAGTTCAGACCAACTAGGTAC
Found at i:49186454 original size:50 final size:50
Alignment explanation
Indices: 49186372--49186473 Score: 143
Period size: 50 Copynumber: 2.0 Consensus size: 50
49186362 TAAATACTTT
* *
49186372 ATATCTAATCTATAAAATTTATACACTTTCATTACTTAAAACAATGATAAA
1 ATATCTAAGCTATAAAATTTATACACTTTCATTACTT-AAACAATGACAAA
* * *
49186423 ATATCTAAGGTAT-AAATTTTTACGCTTTCATTACTTAAACAATGACAAA
1 ATATCTAAGCTATAAAATTTATACACTTTCATTACTTAAACAATGACAAA
49186472 AT
1 AT
49186474 TCAAACCATG
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
49 14 0.30
50 21 0.46
51 11 0.24
ACGTcount: A:0.44, C:0.14, G:0.05, T:0.37
Consensus pattern (50 bp):
ATATCTAAGCTATAAAATTTATACACTTTCATTACTTAAACAATGACAAA
Found at i:49188827 original size:18 final size:18
Alignment explanation
Indices: 49188792--49188827 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
49188782 ACTTGTGTAA
*
49188792 TTTTCTTTTTGAATTTTT
1 TTTTCTTTTTGAACTTTT
*
49188810 TTTTCTTTTTGCACTTTT
1 TTTTCTTTTTGAACTTTT
49188828 AAGCTAACCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.08, C:0.11, G:0.06, T:0.75
Consensus pattern (18 bp):
TTTTCTTTTTGAACTTTT
Found at i:49194505 original size:23 final size:23
Alignment explanation
Indices: 49194472--49194521 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
49194462 GAAGAGCCAT
* *
49194472 ATATCGAGAAGTTCAAGCGAGCC
1 ATATCGAGAAGCTCAAGAGAGCC
* *
49194495 ATATCGGGAAGCTCTAGAGAGCC
1 ATATCGAGAAGCTCAAGAGAGCC
49194518 ATAT
1 ATAT
49194522 TTCAGAAAGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.34, C:0.20, G:0.26, T:0.20
Consensus pattern (23 bp):
ATATCGAGAAGCTCAAGAGAGCC
Found at i:49195590 original size:16 final size:15
Alignment explanation
Indices: 49195531--49195595 Score: 55
Period size: 16 Copynumber: 4.4 Consensus size: 15
49195521 CTTCATCTCC
*
49195531 TTCTTTCTCC-CT-T
1 TTCTTTCTCCTTTGT
* *
49195544 TTCTTT-TTCTTTCT
1 TTCTTTCTCCTTTGT
*
49195558 TTCTTTTTCCTTCTGT
1 TTCTTTCTCCTT-TGT
49195574 TTCGTTTCTCCTTTGT
1 TTC-TTTCTCCTTTGT
49195590 TTCTTT
1 TTCTTT
49195596 TTTTAATTCT
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
12 2 0.05
13 7 0.17
14 7 0.17
15 7 0.17
16 11 0.26
17 8 0.19
ACGTcount: A:0.00, C:0.26, G:0.05, T:0.69
Consensus pattern (15 bp):
TTCTTTCTCCTTTGT
Found at i:49217993 original size:44 final size:44
Alignment explanation
Indices: 49217576--49217982 Score: 566
Period size: 44 Copynumber: 9.2 Consensus size: 44
49217566 CACAAAGCCT
* *
49217576 TATCTCCCTGGCCAGCAGTGGAATAGGTTGAAGATTGTGAGTCC
1 TATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGTAAGTCC
49217620 TATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGTAAGTCC
1 TATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGTAAGTCC
* *
49217664 TATCTCCCTGACCAGCAGTGAAAGAGGTTGAAGATTGTAAGTCC
1 TATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGTAAGTCC
* * * *
49217708 TATCTCCCTGACCAGTAGTGAAATAGGTTGAAGATTGCAACTCC
1 TATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGTAAGTCC
* *
49217752 TATCTCCCTGACCAGCAGTGGAATAGGTGGAAGATTGTAAGTCA
1 TATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGTAAGTCC
* *
49217796 TATCTCCCTGGA-CAGTAGTGGAATAGGTGGAAGATTGTAAGTCC
1 TATCTCCCT-GACCAGCAGTGGAATAGGTTGAAGATTGTAAGTCC
* * * *
49217840 TAGCTCCCTGAACAGCAGTGGAATGGGTGGAAGATTGTAAGTCC
1 TATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGTAAGTCC
* * * * * *
49217884 TAGCTCCCTGAACAACAGTGGAATAGGTGGAAGATTGTATGTCT
1 TATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGTAAGTCC
*
49217928 TATCTCCCTGAACAGCAGTGGAATAGGTTGAAGATTGT-AGATCC
1 TATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGTAAG-TCC
*
49217972 TGTCTCCCTGA
1 TATCTCCCTGA
49217983 GCAATAGTGG
Statistics
Matches: 331, Mismatches: 29, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
43 3 0.01
44 326 0.98
45 2 0.01
ACGTcount: A:0.28, C:0.19, G:0.27, T:0.27
Consensus pattern (44 bp):
TATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGTAAGTCC
Found at i:49230795 original size:19 final size:19
Alignment explanation
Indices: 49230771--49230809 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
49230761 AAACATAATC
49230771 TTATAAATTAATAAAAAAT
1 TTATAAATTAATAAAAAAT
* * *
49230790 TTATAAGTTATTAAATAAT
1 TTATAAATTAATAAAAAAT
49230809 T
1 T
49230810 GTGTCAAATG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (19 bp):
TTATAAATTAATAAAAAAT
Found at i:49233436 original size:3 final size:3
Alignment explanation
Indices: 49233428--49233478 Score: 93
Period size: 3 Copynumber: 17.0 Consensus size: 3
49233418 AGCCAAAATA
*
49233428 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AGT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
49233476 AAT
1 AAT
49233479 GATGATGATA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:49240289 original size:15 final size:15
Alignment explanation
Indices: 49240239--49240291 Score: 58
Period size: 17 Copynumber: 3.5 Consensus size: 15
49240229 CAATTACAAC
49240239 AATTCAATCAATAT-
1 AATTCAATCAATATA
49240253 -ATTCAAT-ATATATA
1 AATTCAATCA-ATATA
49240267 CCAATTCAATCAATATA
1 --AATTCAATCAATATA
49240284 AATTCAAT
1 AATTCAAT
49240292 AAATTCATCA
Statistics
Matches: 33, Mismatches: 0, Indels: 11
0.75 0.00 0.25
Matches are distributed among these distances:
12 1 0.03
13 11 0.33
15 8 0.24
17 12 0.36
18 1 0.03
ACGTcount: A:0.49, C:0.15, G:0.00, T:0.36
Consensus pattern (15 bp):
AATTCAATCAATATA
Found at i:49240314 original size:24 final size:24
Alignment explanation
Indices: 49240269--49240315 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
49240259 TATATATACC
49240269 AATTCAATCAATATAAATTCAATA
1 AATTCAATCAATATAAATTCAATA
49240293 AATTC-ATCACATACTAAA-TCAAT
1 AATTCAATCA-ATA-TAAATTCAAT
49240316 CCATTTCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 4 0.19
24 13 0.62
25 4 0.19
ACGTcount: A:0.51, C:0.17, G:0.00, T:0.32
Consensus pattern (24 bp):
AATTCAATCAATATAAATTCAATA
Found at i:49241114 original size:8 final size:8
Alignment explanation
Indices: 49241101--49241132 Score: 64
Period size: 8 Copynumber: 4.0 Consensus size: 8
49241091 AACATTAAGA
49241101 TATAATAT
1 TATAATAT
49241109 TATAATAT
1 TATAATAT
49241117 TATAATAT
1 TATAATAT
49241125 TATAATAT
1 TATAATAT
49241133 ATATTTTAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (8 bp):
TATAATAT
Found at i:49244081 original size:24 final size:24
Alignment explanation
Indices: 49244052--49244104 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
49244042 ATCAATGCCT
* *
49244052 AATATATTATGCTAATAAATTCTA
1 AATATATTATACTAATAAATACTA
49244076 AATATATTATACTAATAAATACTA
1 AATATATTATACTAATAAATACTA
49244100 AATAT
1 AATAT
49244105 TCTAGAAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.51, C:0.08, G:0.02, T:0.40
Consensus pattern (24 bp):
AATATATTATACTAATAAATACTA
Found at i:49251439 original size:51 final size:51
Alignment explanation
Indices: 49251372--49251863 Score: 458
Period size: 51 Copynumber: 10.1 Consensus size: 51
49251362 CACAATTTGT
* *
49251372 AGCTTTAATCTATTCCACTGCAATGCCAGGGAAAAAAGATTCGCTACCTTC
1 AGCTTTAATCTGTTCCACTGCAACGCCAGGGAAAAAAGATTCGCTACCTTC
* *
49251423 AGCTTTAATCTGTTCCACTGCAACGCCAGGGAAATAATATTCG-----TT-
1 AGCTTTAATCTGTTCCACTGCAACGCCAGGGAAAAAAGATTCGCTACCTTC
* * * * * *
49251468 -GC---ATTCTATTCCACTGCAACACCAGGGAAAAAAGATTCACTGCTTTC
1 AGCTTTAATCTGTTCCACTGCAACGCCAGGGAAAAAAGATTCGCTACCTTC
* * *
49251515 AGCTTTAATCTGTTCCATTCCAACGCCAGGGAAATAAGATTCG-----TT-
1 AGCTTTAATCTGTTCCACTGCAACGCCAGGGAAAAAAGATTCGCTACCTTC
* * * **
49251560 -GC-CT--TCTGTTCTACTGCAACACCAGGGAAAAAAGATTCATTACCTTC
1 AGCTTTAATCTGTTCCACTGCAACGCCAGGGAAAAAAGATTCGCTACCTTC
* * * * *
49251607 AGCTTTAATCTGTTCCACTGCAATGCCAGGGAAATAAGATTCACTGCCTTT
1 AGCTTTAATCTGTTCCACTGCAACGCCAGGGAAAAAAGATTCGCTACCTTC
* * *
49251658 AGCTTTAATC---T--ATTGCAACGCTAGGGAAAAAAGATTCGCTGCCTTC
1 AGCTTTAATCTGTTCCACTGCAACGCCAGGGAAAAAAGATTCGCTACCTTC
* * * * *
49251704 AACTTTAATTTGTTCCACTACAACACCAGGGAAAAAAGATTCACTACCTTC
1 AGCTTTAATCTGTTCCACTGCAACGCCAGGGAAAAAAGATTCGCTACCTTC
* * * *
49251755 AGCTTTAATCTATTCCACTGCAATGCCAGGGAAATAAGATTCGCTGCCTTC
1 AGCTTTAATCTGTTCCACTGCAACGCCAGGGAAAAAAGATTCGCTACCTTC
* * * *
49251806 AGCTTTAATCTGTTCCACTGCAATGCTAGGGAAATAAGATTCGCTACTTTC
1 AGCTTTAATCTGTTCCACTGCAACGCCAGGGAAAAAAGATTCGCTACCTTC
49251857 AGCTTTA
1 AGCTTTA
49251864 GGGTCCGTTT
Statistics
Matches: 357, Mismatches: 59, Indels: 50
0.77 0.13 0.11
Matches are distributed among these distances:
41 60 0.17
43 1 0.00
44 4 0.01
46 45 0.13
48 5 0.01
49 2 0.01
51 240 0.67
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.29
Consensus pattern (51 bp):
AGCTTTAATCTGTTCCACTGCAACGCCAGGGAAAAAAGATTCGCTACCTTC
Found at i:49251539 original size:92 final size:92
Alignment explanation
Indices: 49251380--49251848 Score: 497
Period size: 92 Copynumber: 4.9 Consensus size: 92
49251370 GTAGCTTTAA
* *
49251380 TCTATTCCACTGCAATGCCAGGGAAAAAAGATTCGCTACCTTCAGCTTTAATCTGTTCCACTGCA
1 TCTATTCCACTGCAACGCCAGGGAAAAAAGATTCGCTGCCTTCAGCTTTAATCTGTTCCACTGCA
*
49251445 ACGCCAGGGAAATAATATTCGTTGCAT
66 ACGCCAGGGAAATAAGATTCGTTGCAT
* * * * *
49251472 TCTATTCCACTGCAACACCAGGGAAAAAAGATTCACTGCTTTCAGCTTTAATCTGTTCCATTCCA
1 TCTATTCCACTGCAACGCCAGGGAAAAAAGATTCGCTGCCTTCAGCTTTAATCTGTTCCACTGCA
*
49251537 ACGCCAGGGAAATAAGATTCGTTGCCT
66 ACGCCAGGGAAATAAGATTCGTTGCAT
* * * ** *
49251564 TCTGTTCTACTGCAACACCAGGGAAAAAAGATTCATTACCTTCAGCTTTAATCTGTTCCACTGCA
1 TCTATTCCACTGCAACGCCAGGGAAAAAAGATTCGCTGCCTTCAGCTTTAATCTGTTCCACTGCA
* ** *
49251629 ATGCCAGGGAAATAAGATTCACTGCCTT
66 ACGCCAGGGAAATAAGATTCGTTG-CAT
* * * * * *
49251657 TAGCTTTAATCTATTGCAACGCTAGGGAAAAAAGATTCGCTGCCTTCAACTTTAATTTGTTCCAC
1 T--C--TATTCCACTGCAACGCCAGGGAAAAAAGATTCGCTGCCTTCAGCTTTAATCTGTTCCAC
* * * * *
49251722 TACAACACCAGGGAAAAAAGATTCACTACCTTCAGCTTTAA
62 TGCAACGCCAGGGAAATAAGA-T---T-CGTT--GC---AT
* *
49251763 TCTATTCCACTGCAATGCCAGGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTGTTCCACTGCA
1 TCTATTCCACTGCAACGCCAGGGAAAAAAGATTCGCTGCCTTCAGCTTTAATCTGTTCCACTGCA
* *
49251828 ATGCTAGGGAAATAAGATTCG
66 ACGCCAGGGAAATAAGATTCG
49251849 CTACTTTCAG
Statistics
Matches: 310, Mismatches: 52, Indels: 25
0.80 0.13 0.06
Matches are distributed among these distances:
92 162 0.52
93 3 0.01
95 1 0.00
97 67 0.22
98 2 0.01
101 2 0.01
102 69 0.22
103 1 0.00
104 2 0.01
106 1 0.00
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29
Consensus pattern (92 bp):
TCTATTCCACTGCAACGCCAGGGAAAAAAGATTCGCTGCCTTCAGCTTTAATCTGTTCCACTGCA
ACGCCAGGGAAATAAGATTCGTTGCAT
Found at i:49251901 original size:14 final size:14
Alignment explanation
Indices: 49251882--49251921 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
49251872 TTGTTTGCCA
49251882 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
49251896 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
49251910 GGAAAATGTTTT
1 GTAAAATGTTTT
49251922 ACTTTTCTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:49251930 original size:20 final size:20
Alignment explanation
Indices: 49251905--49251944 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
49251895 CGTAAAATGA
*
49251905 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
49251925 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
49251945 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:49251934 original size:34 final size:35
Alignment explanation
Indices: 49251890--49251956 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
49251880 CAGTAAAATG
*
49251890 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
49251924 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
49251957 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:49251960 original size:14 final size:15
Alignment explanation
Indices: 49251884--49251960 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
49251874 GTTTGCCAGT
* *
49251884 AAAATG-TTTTCCGT
1 AAAATGATTTTCTGG
49251898 AAAATGA-TTTCTGG
1 AAAATGATTTTCTGG
*
49251912 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
49251932 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
49251947 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
49251961 TGTTTGGATG
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 25 0.50
15 11 0.22
16 1 0.02
18 1 0.02
20 12 0.24
ACGTcount: A:0.32, C:0.09, G:0.16, T:0.43
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:49252021 original size:32 final size:32
Alignment explanation
Indices: 49251935--49252021 Score: 88
Period size: 33 Copynumber: 2.7 Consensus size: 32
49251925 TTTCTGTAAA
* *
49251935 ATGATTTACTGGAAAATATTTTCTGGTGTTTGG
1 ATGATTTCCT-GAAAATATTTTCTGCTGTTTGG
* *
49251968 ATGA-ATCTGTGTAAAATATTTTCTGCTGTTTGG
1 ATGATTTC-CTG-AAAATATTTTCTGCTGTTTGG
49252001 CA-GATTTCCTGAAAATATTTT
1 -ATGATTTCCTGAAAATATTTT
49252022 TCGGCAAAGT
Statistics
Matches: 44, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
32 12 0.27
33 29 0.66
34 3 0.07
ACGTcount: A:0.26, C:0.09, G:0.20, T:0.45
Consensus pattern (32 bp):
ATGATTTCCTGAAAATATTTTCTGCTGTTTGG
Found at i:49256445 original size:14 final size:14
Alignment explanation
Indices: 49256426--49256465 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
49256416 TTGTTTGCCA
49256426 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
49256440 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
49256454 GGAAAATGTTTT
1 GTAAAATGTTTT
49256466 ACTTTTCTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:49256474 original size:20 final size:20
Alignment explanation
Indices: 49256449--49256488 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
49256439 CGTAAAATGA
*
49256449 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
49256469 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
49256489 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:49256478 original size:34 final size:35
Alignment explanation
Indices: 49256434--49256500 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
49256424 CAGTAAAATG
*
49256434 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
49256468 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
49256501 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:49256504 original size:14 final size:15
Alignment explanation
Indices: 49256428--49256504 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
49256418 GTTTGCCAGT
* *
49256428 AAAATG-TTTTCCGT
1 AAAATGATTTTCTGG
49256442 AAAATGA-TTTCTGG
1 AAAATGATTTTCTGG
*
49256456 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
49256476 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
49256491 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
49256505 TGTTTGGATG
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 25 0.50
15 11 0.22
16 1 0.02
18 1 0.02
20 12 0.24
ACGTcount: A:0.32, C:0.09, G:0.16, T:0.43
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:49256565 original size:32 final size:32
Alignment explanation
Indices: 49256479--49256565 Score: 88
Period size: 33 Copynumber: 2.7 Consensus size: 32
49256469 TTTCTGTAAA
* *
49256479 ATGATTTACTGGAAAATATTTTCTGGTGTTTGG
1 ATGATTTCCT-GAAAATATTTTCTGCTGTTTGG
* *
49256512 ATGA-ATCTGTGTAAAATATTTTCTGCTGTTTGG
1 ATGATTTC-CTG-AAAATATTTTCTGCTGTTTGG
49256545 CA-GATTTCCTGAAAATATTTT
1 -ATGATTTCCTGAAAATATTTT
49256566 TCGGAAAAGT
Statistics
Matches: 44, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
32 12 0.27
33 29 0.66
34 3 0.07
ACGTcount: A:0.26, C:0.09, G:0.20, T:0.45
Consensus pattern (32 bp):
ATGATTTCCTGAAAATATTTTCTGCTGTTTGG
Found at i:49259154 original size:51 final size:51
Alignment explanation
Indices: 49259068--49259353 Score: 419
Period size: 51 Copynumber: 5.6 Consensus size: 51
49259058 AAACGCACCC
* * *
49259068 TTAATTTGTTCCACTGTAACGCCAGAGAAATAAGATTCGCTGCCTTCAGCT
1 TTAATCTGTTCCACTGCAACGCCAGGGAAATAAGATTCGCTGCCTTCAGCT
* * * *
49259119 TTAATTTGTTCCACTGCAACACCAGGGAAAAAAGATTCGTTGCCTTCAGCT
1 TTAATCTGTTCCACTGCAACGCCAGGGAAATAAGATTCGCTGCCTTCAGCT
* *
49259170 TTAATCTGTTCCACTGCAATGCCAAGGGAAATAAGATTCGCTACCTTCAGCT
1 TTAATCTGTTCCACTGCAACGCC-AGGGAAATAAGATTCGCTGCCTTCAGCT
* ** *
49259222 TTAATCTGTTCCACTACAATTCCATGGAAATAAGATTCGCTGCCTTCAGCT
1 TTAATCTGTTCCACTGCAACGCCAGGGAAATAAGATTCGCTGCCTTCAGCT
* *
49259273 TTAATCTGTTCCACTGTAACGCCAAGGAAATAAGATTCGCTGCCTTCAGCT
1 TTAATCTGTTCCACTGCAACGCCAGGGAAATAAGATTCGCTGCCTTCAGCT
*
49259324 TTAATCTGTTCCACTGCAACACCAGGGAAA
1 TTAATCTGTTCCACTGCAACGCCAGGGAAA
49259354 AAAATTTTCC
Statistics
Matches: 211, Mismatches: 23, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
51 165 0.78
52 46 0.22
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.30
Consensus pattern (51 bp):
TTAATCTGTTCCACTGCAACGCCAGGGAAATAAGATTCGCTGCCTTCAGCT
Found at i:49259251 original size:103 final size:103
Alignment explanation
Indices: 49259068--49259356 Score: 456
Period size: 103 Copynumber: 2.8 Consensus size: 103
49259058 AAACGCACCC
* * *
49259068 TTAATTTGTTCCACTGTAACGCC-AGAGAAATAAGATTCGCTGCCTTCAGCTTTAATTTGTTCCA
1 TTAATCTGTTCCACTGTAACGCCAAGGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTGTTCCA
*
49259132 CTGCAACACCAGGGAAAAAAGATTCGTTGCCTTCAGCT
66 CTGCAACACCAGGGAAAAAAGATTCGCTGCCTTCAGCT
* * *
49259170 TTAATCTGTTCCACTGCAATGCCAAGGGAAATAAGATTCGCTACCTTCAGCTTTAATCTGTTCCA
1 TTAATCTGTTCCACTGTAACGCCAAGGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTGTTCCA
* ** * *
49259235 CTACAATTCCATGGAAATAAGATTCGCTGCCTTCAGCT
66 CTGCAACACCAGGGAAAAAAGATTCGCTGCCTTCAGCT
49259273 TTAATCTGTTCCACTGTAACGCCAA-GGAAATAAGATTCGCTGCCTTCAGCTTTAATCTGTTCCA
1 TTAATCTGTTCCACTGTAACGCCAAGGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTGTTCCA
49259337 CTGCAACACCAGGGAAAAAA
66 CTGCAACACCAGGGAAAAAA
49259357 ATTTTCCATA
Statistics
Matches: 166, Mismatches: 20, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
102 73 0.44
103 93 0.56
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.29
Consensus pattern (103 bp):
TTAATCTGTTCCACTGTAACGCCAAGGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTGTTCCA
CTGCAACACCAGGGAAAAAAGATTCGCTGCCTTCAGCT
Found at i:49260629 original size:53 final size:53
Alignment explanation
Indices: 49260556--49260690 Score: 168
Period size: 53 Copynumber: 2.6 Consensus size: 53
49260546 TCTCAAGGAA
49260556 CCCTTTGCGAGTTTTCACCTTGGCCTCTCCTTTTTT-T-TTTAGAACTCAAAGCG
1 CCCTTTGCGAGTTTTCACCTTGG--TCTCCTTTTTTGTATTTAGAACTCAAAGCG
* * * ** * *
49260609 CCTTTTGCGGGTTTTTACCTTGGTCTTTTTTTTTGTATTTAGGACTCAAATCG
1 CCCTTTGCGAGTTTTCACCTTGGTCTCCTTTTTTGTATTTAGAACTCAAAGCG
49260662 CCCTTTGCGAGTTTTCACCTTGGTC-CCTT
1 CCCTTTGCGAGTTTTCACCTTGGTCTCCTT
49260691 CTCCTTCTTT
Statistics
Matches: 68, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
51 9 0.13
52 3 0.04
53 56 0.82
ACGTcount: A:0.13, C:0.25, G:0.17, T:0.45
Consensus pattern (53 bp):
CCCTTTGCGAGTTTTCACCTTGGTCTCCTTTTTTGTATTTAGAACTCAAAGCG
Found at i:49261137 original size:17 final size:15
Alignment explanation
Indices: 49261115--49261179 Score: 69
Period size: 17 Copynumber: 4.0 Consensus size: 15
49261105 CCGGTAAAAG
49261115 TTTTTGTTTCTTTTTGT
1 TTTTTGTTT-TTTTT-T
49261132 TTTTTGTTTTTTTATT
1 TTTTTGTTTTTTT-TT
49261148 TTTTTGTATTTTTTTCT
1 TTTTTGT-TTTTTTT-T
49261165 TTTTT-TCTTTTTTTT
1 TTTTTGT-TTTTTTTT
49261180 CCTCTACTGC
Statistics
Matches: 44, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
15 1 0.02
16 21 0.48
17 22 0.50
ACGTcount: A:0.03, C:0.05, G:0.06, T:0.86
Consensus pattern (15 bp):
TTTTTGTTTTTTTTT
Found at i:49261142 original size:8 final size:8
Alignment explanation
Indices: 49261115--49261178 Score: 58
Period size: 8 Copynumber: 7.6 Consensus size: 8
49261105 CCGGTAAAAG
49261115 TTTTTGTT
1 TTTTTGTT
49261123 TCTTTT-TGT
1 T-TTTTGT-T
49261132 TTTTTGTT
1 TTTTTGTT
*
49261140 TTTTTATT
1 TTTTTGTT
49261148 TTTTTGTATT
1 TTTTTG--TT
*
49261158 TTTTTCTT
1 TTTTTGTT
*
49261166 TTTTTCTT
1 TTTTTGTT
49261174 TTTTT
1 TTTTT
49261179 TCCTCTACTG
Statistics
Matches: 48, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
8 34 0.71
9 7 0.15
10 7 0.15
ACGTcount: A:0.03, C:0.05, G:0.06, T:0.86
Consensus pattern (8 bp):
TTTTTGTT
Found at i:49261144 original size:10 final size:10
Alignment explanation
Indices: 49261115--49261179 Score: 51
Period size: 10 Copynumber: 6.2 Consensus size: 10
49261105 CCGGTAAAAG
*
49261115 TTTTTGTTTC
1 TTTTTGTTTT
49261125 TTTTTGTTTTT
1 TTTTTG-TTTT
*
49261136 TGTTTTTTTATT
1 T-TTTTGTT-TT
*
49261148 TTTTTGTATT
1 TTTTTGTTTT
*
49261158 TTTTTCTTTT
1 TTTTTGTTTT
49261168 TTTCTT-TTTT
1 TTT-TTGTTTT
49261178 TT
1 TT
49261180 CCTCTACTGC
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
10 25 0.56
11 13 0.29
12 7 0.16
ACGTcount: A:0.03, C:0.05, G:0.06, T:0.86
Consensus pattern (10 bp):
TTTTTGTTTT
Found at i:49270451 original size:18 final size:17
Alignment explanation
Indices: 49270425--49270458 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
49270415 AATTGCACTC
49270425 TAATGAATGCTAAATAAT
1 TAATGAATGC-AAATAAT
*
49270443 TAATTAATGCAAATAA
1 TAATGAATGCAAATAA
49270459 ACAATACCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.53, C:0.06, G:0.09, T:0.32
Consensus pattern (17 bp):
TAATGAATGCAAATAAT
Found at i:49271174 original size:24 final size:22
Alignment explanation
Indices: 49271110--49271175 Score: 69
Period size: 24 Copynumber: 2.8 Consensus size: 22
49271100 TTACAAGTTT
*
49271110 AAATAATATTAATTATGAATTCA
1 AAATAATATTAATT-TAAATTCA
* *
49271133 AAATAATATTAAGCTTAAATATTA
1 AAATAATATTAA-TTTAAAT-TCA
49271157 AAATAATATTAGATTTAAA
1 AAATAATATTA-ATTTAAA
49271176 ATTTAATACG
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
23 16 0.44
24 19 0.53
25 1 0.03
ACGTcount: A:0.55, C:0.03, G:0.05, T:0.38
Consensus pattern (22 bp):
AAATAATATTAATTTAAATTCA
Found at i:49271181 original size:24 final size:23
Alignment explanation
Indices: 49271081--49271181 Score: 75
Period size: 23 Copynumber: 4.3 Consensus size: 23
49271071 TTTTGATGAT
*
49271081 AATTTAAAATAATAGTACATTACA
1 AATTTAAAATAATATTA-ATTACA
* **
49271105 AGTTT-AAATAATATTAATTATG
1 AATTTAAAATAATATTAATTACA
*
49271127 AATTCAAAATAATATTAAGCTT--A
1 AATTTAAAATAATATTAA--TTACA
49271150 AATATTAAAATAATATTAGATTTA-A
1 AAT-TTAAAATAATATTA-A-TTACA
49271175 AATTTAA
1 AATTTAA
49271182 TACGTTTTTA
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
22 7 0.11
23 25 0.40
24 23 0.37
25 7 0.11
ACGTcount: A:0.52, C:0.04, G:0.05, T:0.39
Consensus pattern (23 bp):
AATTTAAAATAATATTAATTACA
Found at i:49274218 original size:28 final size:27
Alignment explanation
Indices: 49274185--49274283 Score: 119
Period size: 28 Copynumber: 3.6 Consensus size: 27
49274175 TAATGAGATT
*
49274185 AGCACTAAGTGTGCGAGTTTAATTGAA
1 AGCACTAAGTGTGCGAGTATAATTGAA
*
49274212 ATGCACTAAGTGTGCGAGTATAATGGTAA
1 A-GCACTAAGTGTGCGAGTATAATTG-AA
* *
49274241 AGCACTAAGTGTGCGAGTGTGATT-ATTA
1 AGCACTAAGTGTGCGAGTATAATTGA--A
49274269 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
49274284 TACTTATTAA
Statistics
Matches: 63, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
26 1 0.02
27 1 0.02
28 58 0.92
29 3 0.05
ACGTcount: A:0.31, C:0.12, G:0.28, T:0.28
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGTATAATTGAA
Found at i:49277243 original size:27 final size:27
Alignment explanation
Indices: 49277203--49277258 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
49277193 CAGTAACAGA
* *
49277203 ACAGAACAATGTGGGCTTTAGCCCAAT
1 ACAGAACAAGGTGGGCCTTAGCCCAAT
*
49277230 ACAGAACAAGGTGGGCCTTAGCCTAAT
1 ACAGAACAAGGTGGGCCTTAGCCCAAT
49277257 AC
1 AC
49277259 CATATCAGTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.34, C:0.23, G:0.23, T:0.20
Consensus pattern (27 bp):
ACAGAACAAGGTGGGCCTTAGCCCAAT
Found at i:49277618 original size:28 final size:27
Alignment explanation
Indices: 49277559--49277702 Score: 91
Period size: 27 Copynumber: 5.3 Consensus size: 27
49277549 TTACCCTATA
*
49277559 AGGGTATTTTGGTAATTTTCCAAACTG
1 AGGGTATTTTGGTAATTTTCCAAACAG
*
49277586 AGGGTATTTTGGTAACTTTTGCAAATCAG
1 AGGGTATTTTGGTAA-TTTTCCAAA-CAG
* * *
49277615 -GGGTACTTTT-GCAA-TTTCAAAAACTG
1 AGGGTA-TTTTGGTAATTTTC-CAAACAG
* ** *
49277641 AGGGTA-TTCGGTAATTTTGTAAACTG
1 AGGGTATTTTGGTAATTTTCCAAACAG
* * * *
49277667 GGGGTACTTTGGTAATTTTACAATTC-G
1 AGGGTATTTTGGTAATTTTCCAA-ACAG
49277694 AGGGTATTT
1 AGGGTATTT
49277703 CAGAAATTTT
Statistics
Matches: 91, Mismatches: 17, Indels: 18
0.72 0.13 0.14
Matches are distributed among these distances:
25 2 0.02
26 19 0.21
27 47 0.52
28 17 0.19
29 6 0.07
ACGTcount: A:0.26, C:0.10, G:0.24, T:0.39
Consensus pattern (27 bp):
AGGGTATTTTGGTAATTTTCCAAACAG
Found at i:49277657 original size:26 final size:27
Alignment explanation
Indices: 49277627--49277684 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 27
49277617 GTACTTTTGC
49277627 AATTTCAAAAACTGAGGGTA-TTCGGT
1 AATTTCAAAAACTGAGGGTACTTCGGT
*** * *
49277653 AATTTTGTAAACTGGGGGTACTTTGGT
1 AATTTCAAAAACTGAGGGTACTTCGGT
49277680 AATTT
1 AATTT
49277685 TACAATTCGA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
26 16 0.62
27 10 0.38
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (27 bp):
AATTTCAAAAACTGAGGGTACTTCGGT
Found at i:49277710 original size:27 final size:27
Alignment explanation
Indices: 49277694--49277771 Score: 122
Period size: 27 Copynumber: 2.9 Consensus size: 27
49277684 TTACAATTCG
*
49277694 AGGGTATTTCAGAAATTTTGTAAACCA
1 AGGGTATTTCAGAAATTTTGTAAATCA
49277721 AGGGTATTTCA-ATAATTTTGTAAATCA
1 AGGGTATTTCAGA-AATTTTGTAAATCA
*
49277748 AGGGTATTTCAGTAATTTTGTAAA
1 AGGGTATTTCAGAAATTTTGTAAA
49277772 CCAAAGTATT
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
26 1 0.02
27 46 0.98
ACGTcount: A:0.36, C:0.08, G:0.18, T:0.38
Consensus pattern (27 bp):
AGGGTATTTCAGAAATTTTGTAAATCA
Found at i:49282802 original size:27 final size:27
Alignment explanation
Indices: 49282671--49283005 Score: 370
Period size: 27 Copynumber: 12.5 Consensus size: 27
49282661 GGGTATAACA
*
49282671 GTTATTTTACCCTAT-GGGGGTATTTTG
1 GTTATTTTACCC-ATCGAGGGTATTTTG
* *
49282698 GTTATTTTACCCTTCGGGGGTATTTTG
1 GTTATTTTACCCATCGAGGGTATTTTG
* *
49282725 GTTATTTTACCCATCGAGGATATTTCG
1 GTTATTTTACCCATCGAGGGTATTTTG
* *
49282752 ATTATTTTACCCATCGAGGGTATTTCG
1 GTTATTTTACCCATCGAGGGTATTTTG
49282779 GTTATTTTACCCATCGAGGGTATTTTG
1 GTTATTTTACCCATCGAGGGTATTTTG
* * * * *
49282806 ATCATTTTACCCTTTGAGGGTATTTTA
1 GTTATTTTACCCATCGAGGGTATTTTG
* *
49282833 ATTATTTTACCCATCGAGGGTATTTCG
1 GTTATTTTACCCATCGAGGGTATTTTG
* * * *
49282860 ATCAATTTACCCATTGAGGGTATTTTG
1 GTTATTTTACCCATCGAGGGTATTTTG
* * **
49282887 GTCATTTTACCTATCGAATGTA-TTTG
1 GTTATTTTACCCATCGAGGGTATTTTG
* * *
49282913 GTCATTTTACCCATCTAGGGTATTTCG
1 GTTATTTTACCCATCGAGGGTATTTTG
* * * *
49282940 GTCATTTTACCTATCGAGCGTATTTCG
1 GTTATTTTACCCATCGAGGGTATTTTG
*
49282967 GTCATTTTACCCATCGAGGGTATTTTG
1 GTTATTTTACCCATCGAGGGTATTTTG
49282994 GTTA-TTTACCCA
1 GTTATTTTACCCA
49283006 CGAATCGCAA
Statistics
Matches: 265, Mismatches: 41, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
26 31 0.12
27 234 0.88
ACGTcount: A:0.20, C:0.17, G:0.19, T:0.43
Consensus pattern (27 bp):
GTTATTTTACCCATCGAGGGTATTTTG
Found at i:49287518 original size:42 final size:43
Alignment explanation
Indices: 49287425--49287523 Score: 119
Period size: 42 Copynumber: 2.3 Consensus size: 43
49287415 TCCTAGACGT
* * * *
49287425 GGTCTTACATGTAGTCATATAACGATGCCACTATCCCAGACAG
1 GGTCTTACACGTAATCATATAACGATGCCAATATCCCAAACAG
* *
49287468 GGTCTTACACGTAATCATAT-ACGATGCCAATGTCCCAAACAT
1 GGTCTTACACGTAATCATATAACGATGCCAATATCCCAAACAG
* *
49287510 GTTTTTACACGTAA
1 GGTCTTACACGTAA
49287524 ATCCCAAATC
Statistics
Matches: 48, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
42 30 0.62
43 18 0.38
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.28
Consensus pattern (43 bp):
GGTCTTACACGTAATCATATAACGATGCCAATATCCCAAACAG
Found at i:49294777 original size:2 final size:2
Alignment explanation
Indices: 49294770--49294796 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
49294760 CAACTGCATG
49294770 CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT C
49294797 ACGTACATTA
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:49312251 original size:16 final size:16
Alignment explanation
Indices: 49312232--49312262 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
49312222 TAATAGAGAA
49312232 TATTTTTAATTATTTT
1 TATTTTTAATTATTTT
*
49312248 TATTTTTATTTATTT
1 TATTTTTAATTATTT
49312263 ATTTTAATAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (16 bp):
TATTTTTAATTATTTT
Found at i:49312280 original size:16 final size:15
Alignment explanation
Indices: 49312235--49312280 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
49312225 TAGAGAATAT
49312235 TTTTAATTATT-TTTA
1 TTTTAA-TATTATTTA
*
49312250 TTTTTAT-TTATTTA
1 TTTTAATATTATTTA
49312264 TTTTAATATTATATTA
1 TTTTAATATTAT-TTA
49312280 T
1 T
49312281 CTTATGAGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
13 2 0.08
14 11 0.42
15 9 0.35
16 4 0.15
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (15 bp):
TTTTAATATTATTTA
Found at i:49317318 original size:22 final size:21
Alignment explanation
Indices: 49317293--49317340 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
49317283 ATTTTACATA
*
49317293 TATATATACATTGGTTTATTTT
1 TATATATACATTAGTTTA-TTT
* *
49317315 TATATATGCATTATTTTATTT
1 TATATATACATTAGTTTATTT
49317336 TATAT
1 TATAT
49317341 GTATTTTTGT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 8 0.35
22 15 0.65
ACGTcount: A:0.29, C:0.04, G:0.06, T:0.60
Consensus pattern (21 bp):
TATATATACATTAGTTTATTT
Found at i:49317649 original size:28 final size:27
Alignment explanation
Indices: 49317608--49317702 Score: 77
Period size: 29 Copynumber: 3.4 Consensus size: 27
49317598 TTATATAGAT
*
49317608 ATTTT-ATTTCTTTCAAATATTTTAAC
1 ATTTTAATTTATTTCAAATATTTTAAC
* *
49317634 ATCTTTAATTTATTTCAACTTATTTCAAC
1 AT-TTTAATTTATTTCAA-ATATTTTAAC
* *
49317663 ATTGTCAATTCA-TTCAAATTTATTTTAAC
1 ATT-TTAATTTATTTCAAA--TATTTTAAC
*
49317692 TTTTTAATTTA
1 ATTTTAATTTA
49317703 CATATATTAT
Statistics
Matches: 53, Mismatches: 10, Indels: 10
0.73 0.14 0.14
Matches are distributed among these distances:
26 2 0.04
27 3 0.06
28 22 0.42
29 26 0.49
ACGTcount: A:0.32, C:0.13, G:0.01, T:0.55
Consensus pattern (27 bp):
ATTTTAATTTATTTCAAATATTTTAAC
Found at i:49322160 original size:34 final size:36
Alignment explanation
Indices: 49322097--49322171 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 36
49322087 CAGATCCAAT
49322097 TCAAAAAAAAAAGAAGGAGCAAAAGAAAAAATC-AAAA
1 TCAAAAAAAAAAGAAGGA-CAAAAG-AAAAATCAAAAA
*
49322134 TCAAAACAAAAAGAA-GA-AAAAGAAAAATCAAAAA
1 TCAAAAAAAAAAGAAGGACAAAAGAAAAATCAAAAA
49322168 TCAA
1 TCAA
49322172 GGTCAAAATG
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
33 7 0.19
34 13 0.36
36 2 0.06
37 14 0.39
ACGTcount: A:0.73, C:0.09, G:0.11, T:0.07
Consensus pattern (36 bp):
TCAAAAAAAAAAGAAGGACAAAAGAAAAATCAAAAA
Found at i:49324493 original size:11 final size:11
Alignment explanation
Indices: 49324477--49324501 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
49324467 AGTTGAAAGT
49324477 GAAAAAAAAAA
1 GAAAAAAAAAA
49324488 GAAAAAAAAAA
1 GAAAAAAAAAA
49324499 GAA
1 GAA
49324502 GAGATAATGT
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:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (11 bp):
GAAAAAAAAAA
Found at i:49330183 original size:10 final size:10
Alignment explanation
Indices: 49330165--49330218 Score: 53
Period size: 9 Copynumber: 5.8 Consensus size: 10
49330155 TTATATGTTT
49330165 TTTTTATATA
1 TTTTTATATA
*
49330175 TTTTCATATA
1 TTTTTATATA
*
49330185 -ATTTA-ATA
1 TTTTTATATA
49330193 TTTTTATATA
1 TTTTTATATA
49330203 -TTTTATA-A
1 TTTTTATATA
*
49330211 TTTATATA
1 TTTTTATA
49330219 CACATACTTA
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
8 4 0.11
9 20 0.56
10 12 0.33
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (10 bp):
TTTTTATATA
Found at i:49330195 original size:18 final size:19
Alignment explanation
Indices: 49330167--49330213 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 19
49330157 ATATGTTTTT
49330167 TTTATATATTTTCATATAA
1 TTTATATATTTTCATATAA
* *
49330186 TTTA-ATATTTTTATATAT
1 TTTATATATTTTCATATAA
49330204 TTTATA-ATTT
1 TTTATATATTT
49330214 ATATACACAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 20 0.80
19 5 0.20
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (19 bp):
TTTATATATTTTCATATAA
Found at i:49330304 original size:24 final size:22
Alignment explanation
Indices: 49330262--49330346 Score: 75
Period size: 24 Copynumber: 3.8 Consensus size: 22
49330252 TTTTTATAAG
*
49330262 TATATATTTATA-TGTACATACT
1 TATATATTTATATTTTACATA-T
49330284 TATATATTTATATTTTCACATAT
1 TATATATTTATATTTT-ACATAT
* * *
49330307 TAAAATATGTATATTTATATATAT
1 T-ATATATTTATATTT-TACATAT
*
49330331 TATATATAT-TATTTTA
1 TATATATTTATATTTTA
49330347 TTATAATTCA
Statistics
Matches: 53, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
21 2 0.04
22 17 0.32
23 10 0.19
24 23 0.43
25 1 0.02
ACGTcount: A:0.39, C:0.05, G:0.02, T:0.54
Consensus pattern (22 bp):
TATATATTTATATTTTACATAT
Found at i:49330413 original size:16 final size:17
Alignment explanation
Indices: 49330392--49330424 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
49330382 GTACATATAC
49330392 ATATTTT-TATATTTTT
1 ATATTTTATATATTTTT
*
49330408 ATATTTTATCTATTTTT
1 ATATTTTATATATTTTT
49330425 TTGTTATTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.73
Consensus pattern (17 bp):
ATATTTTATATATTTTT
Found at i:49335381 original size:12 final size:12
Alignment explanation
Indices: 49335364--49335427 Score: 56
Period size: 12 Copynumber: 5.2 Consensus size: 12
49335354 AAGAATGTTC
49335364 AAAAAAAAAGAA
1 AAAAAAAAAGAA
* *
49335376 AAAAAATAACAA
1 AAAAAAAAAGAA
*
49335388 AAAAGGAAAAGAA
1 AAAA-AAAAAGAA
* *
49335401 AAATAAAAATAA
1 AAAAAAAAAGAA
* *
49335413 AAATAAAAATAA
1 AAAAAAAAAGAA
49335425 AAA
1 AAA
49335428 GGAGAGGCCA
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
12 35 0.81
13 8 0.19
ACGTcount: A:0.84, C:0.02, G:0.06, T:0.08
Consensus pattern (12 bp):
AAAAAAAAAGAA
Found at i:49335408 original size:18 final size:18
Alignment explanation
Indices: 49335387--49335430 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
49335377 AAAAATAACA
49335387 AAAAAGGAAAAGAAAAAT
1 AAAAAGGAAAAGAAAAAT
** *
49335405 AAAAATAAAAATAAAAAT
1 AAAAAGGAAAAGAAAAAT
49335423 AAAAAGGA
1 AAAAAGGA
49335431 GAGGCCAAGG
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.80, C:0.00, G:0.11, T:0.09
Consensus pattern (18 bp):
AAAAAGGAAAAGAAAAAT
Found at i:49335909 original size:108 final size:107
Alignment explanation
Indices: 49335691--49335910 Score: 273
Period size: 108 Copynumber: 2.0 Consensus size: 107
49335681 GGGCACCTGC
* * *** *
49335691 TTTCATTTTATTCATTTCGTATCTTAGCAAAATTTGTTATCTTGATCATTTATTTATTTCAAGCT
1 TTTCATCTTATTCATTTCGAATCTTAGCAAAATTCACTATCTTGATAATTTATTTATTTCAAGCT
* ** * *
49335756 TTGTTCTTAATAAAATTTCATCTTGTCCATTGTGATAATCCT
66 CTACTCTCAATAAAATTTCATCTTGTCCATTGTGATAATACT
* *
49335798 TTTCATCTTATTCATTTTGAATCTTAGCAAAATTCACTATCTTGATTAATTTATTTGTTT-AGAG
1 TTTCATCTTATTCATTTCGAATCTTAGCAAAATTCACTATCTTGA-TAATTTATTTATTTCA-AG
*
49335862 CTCTACTCTCAATAAAATTTCATCTT-TCCCATTGTGATAATATT
64 CTCTACTCTCAATAAAATTTCATCTTGT-CCATTGTGATAATACT
49335906 TTTCA
1 TTTCA
49335911 AGCATTTTTC
Statistics
Matches: 96, Mismatches: 14, Indels: 5
0.83 0.12 0.04
Matches are distributed among these distances:
107 41 0.43
108 55 0.57
ACGTcount: A:0.27, C:0.16, G:0.08, T:0.50
Consensus pattern (107 bp):
TTTCATCTTATTCATTTCGAATCTTAGCAAAATTCACTATCTTGATAATTTATTTATTTCAAGCT
CTACTCTCAATAAAATTTCATCTTGTCCATTGTGATAATACT
Found at i:49337368 original size:44 final size:44
Alignment explanation
Indices: 49337290--49337502 Score: 161
Period size: 44 Copynumber: 4.8 Consensus size: 44
49337280 AATAGAAAAC
* **
49337290 CTTATC-CCCATGAAGTTGCAATGGGGCA-AGTTGAAGATA-CAAGT
1 CTTATCTCCC-TGAAGTTGCAGTGGATCAGA-TTGAAGATAGCAA-T
*
49337334 CTTATCTCCCTGAAGTTGCAGTGGATCAGATTGAAGTTA-CTAAT
1 CTTATCTCCCTGAAGTTGCAGTGGATCAGATTGAAGATAGC-AAT
* * * * *
49337378 CCTACCTCCCTGAAGTTGCAGTGGAAT-AGATT-AAAATGATGGATT
1 CTTATCTCCCTGAAGTTGCAGTGG-ATCAGATTGAAGAT-A-GCAAT
* * *
49337423 C-TATCTCCCTGAAGTTGCAGTGGACCATATTAAAGATAGCAAAT
1 CTTATCTCCCTGAAGTTGCAGTGGATCAGATTGAAGATAGC-AAT
* * * *
49337467 CTTATTTTCCTGAAGTTGCAATGGAACAGATTGAAG
1 CTTATCTCCCTGAAGTTGCAGTGGATCAGATTGAAG
49337503 CTATAGGCTA
Statistics
Matches: 136, Mismatches: 22, Indels: 21
0.76 0.12 0.12
Matches are distributed among these distances:
43 5 0.04
44 88 0.65
45 43 0.32
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.30
Consensus pattern (44 bp):
CTTATCTCCCTGAAGTTGCAGTGGATCAGATTGAAGATAGCAAT
Found at i:49337853 original size:41 final size:44
Alignment explanation
Indices: 49337749--49337859 Score: 113
Period size: 45 Copynumber: 2.6 Consensus size: 44
49337739 TGAAGCTACA
* *
49337749 AGTCTTATCTCACTGATGTTGCAGTAGAATAGACTGAAGATAGC
1 AGTCTTATCTCACTGAAGTTGCAGTAGAATAGACTCAAGATAGC
* * *
49337793 AGATATTATCTCTCTGAAGTTGCAGTA-AAGTAGAC-CACGAT-G-
1 AG-TCTTATCTCACTGAAGTTGCAGTAGAA-TAGACTCAAGATAGC
* *
49337835 AGTCTTATCTCCCTGAAGTTACAGT
1 AGTCTTATCTCACTGAAGTTGCAGT
49337860 GGAGCGGACC
Statistics
Matches: 57, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
41 20 0.35
42 2 0.04
43 1 0.02
44 8 0.14
45 26 0.46
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.31
Consensus pattern (44 bp):
AGTCTTATCTCACTGAAGTTGCAGTAGAATAGACTCAAGATAGC
Found at i:49339907 original size:24 final size:22
Alignment explanation
Indices: 49339865--49339949 Score: 75
Period size: 24 Copynumber: 3.8 Consensus size: 22
49339855 TTTTTATAAG
*
49339865 TATATATTTATA-TGTACATACT
1 TATATATTTATATTTTACATA-T
49339887 TATATATTTATATTTTCACATAT
1 TATATATTTATATTTT-ACATAT
* * *
49339910 TAAAATATGTATATTTATATATAT
1 T-ATATATTTATATTT-TACATAT
*
49339934 TATATATAT-TATTTTA
1 TATATATTTATATTTTA
49339950 TTATAATTCA
Statistics
Matches: 53, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
21 2 0.04
22 17 0.32
23 10 0.19
24 23 0.43
25 1 0.02
ACGTcount: A:0.39, C:0.05, G:0.02, T:0.54
Consensus pattern (22 bp):
TATATATTTATATTTTACATAT
Found at i:49341402 original size:5 final size:5
Alignment explanation
Indices: 49341389--49341465 Score: 54
Period size: 5 Copynumber: 15.4 Consensus size: 5
49341379 TTAATTTAAA
* * *
49341389 ATATAT ATATT ATATT AAATT -TACTT A-ATT A-ATA AGTATT -TTTT
1 ATAT-T ATATT ATATT ATATT ATA-TT ATATT ATATT A-TATT ATATT
*
49341433 ATATT ATATT ATTAAT ATATT ATATT ATATT AT
1 ATATT ATATT A-TATT ATATT ATATT ATATT AT
49341466 TATATATTTA
Statistics
Matches: 57, Mismatches: 8, Indels: 13
0.73 0.10 0.17
Matches are distributed among these distances:
4 10 0.18
5 37 0.65
6 10 0.18
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.56
Consensus pattern (5 bp):
ATATT
Found at i:49341476 original size:21 final size:20
Alignment explanation
Indices: 49341430--49341477 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 20
49341420 ATAAGTATTT
49341430 TTTATATTATATTATTAATA
1 TTTATATTATATTATTAATA
49341450 TATTATATTATATTATTATATA
1 T-TTATATTATATTATTA-ATA
49341472 TTTATA
1 TTTATA
49341478 AAACAAAAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.04
21 21 0.81
22 4 0.15
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
TTTATATTATATTATTAATA
Found at i:49346433 original size:12 final size:12
Alignment explanation
Indices: 49346410--49346445 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 12
49346400 TTGGACTTGC
49346410 CTTTTTTCTTTTT
1 CTTTTTT-TTTTT
49346423 CTTTTTTTTTTT
1 CTTTTTTTTTTT
49346435 CTTTTGTTTTT
1 CTTTT-TTTTT
49346446 AATATTAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 10 0.45
13 12 0.55
ACGTcount: A:0.00, C:0.11, G:0.03, T:0.86
Consensus pattern (12 bp):
CTTTTTTTTTTT
Found at i:49354504 original size:21 final size:21
Alignment explanation
Indices: 49354478--49354521 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
49354468 TCCTGGGACA
*
49354478 TAATTTTTCAAAAAAATTGAC
1 TAATTTTTCAAAAAAATCGAC
*
49354499 TAATTTTTCACAAAAATCGAC
1 TAATTTTTCAAAAAAATCGAC
49354520 TA
1 TA
49354522 TTACACGGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.45, C:0.14, G:0.05, T:0.36
Consensus pattern (21 bp):
TAATTTTTCAAAAAAATCGAC
Found at i:49360687 original size:22 final size:23
Alignment explanation
Indices: 49360662--49360707 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
49360652 ATACGCTAAT
*
49360662 AAAATATTA-CAAAACTTGCCAC
1 AAAATATTAGCAAAACATGCCAC
* *
49360684 AAAATCTTAGCAAATCATGCCAC
1 AAAATATTAGCAAAACATGCCAC
49360707 A
1 A
49360708 CAAGCAAACA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.48, C:0.24, G:0.07, T:0.22
Consensus pattern (23 bp):
AAAATATTAGCAAAACATGCCAC
Found at i:49360979 original size:108 final size:108
Alignment explanation
Indices: 49360824--49361029 Score: 315
Period size: 108 Copynumber: 1.9 Consensus size: 108
49360814 CTAGTTTGAC
* *
49360824 CTACACATTATCGAAGGCTTCACCATGAATATTCATACAGTCATATATTGCCATGGGT-TTCAAC
1 CTACACATTATCGAAGGCTTCACCATGAACATTCATACAATCATATATTGCCATGGGTCTT-AAC
* *
49360888 CACATGGACTTACATATTCTCATGTCGTGATCTGCCAAGTCAAT
65 CACATGAACTTACACATTCTCATGTCGTGATCTGCCAAGTCAAT
** * *
49360932 CTACACATTATCGCCGGCTTCACCATGAACATTCATACAATCATATATTGTCATGGGTCTTAGCC
1 CTACACATTATCGAAGGCTTCACCATGAACATTCATACAATCATATATTGCCATGGGTCTTAACC
*
49360997 ACATGAACTTACACATTCTTATGTCGTGATCTG
66 ACATGAACTTACACATTCTCATGTCGTGATCTG
49361030 TCAGTCCAAG
Statistics
Matches: 88, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
108 86 0.98
109 2 0.02
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.32
Consensus pattern (108 bp):
CTACACATTATCGAAGGCTTCACCATGAACATTCATACAATCATATATTGCCATGGGTCTTAACC
ACATGAACTTACACATTCTCATGTCGTGATCTGCCAAGTCAAT
Found at i:49370319 original size:7 final size:7
Alignment explanation
Indices: 49370307--49370339 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
49370297 TTTTATTTAT
49370307 ATAAAGA
1 ATAAAGA
49370314 ATAAAGA
1 ATAAAGA
49370321 ATAAAGA
1 ATAAAGA
*
49370328 ACAAAGA
1 ATAAAGA
49370335 ATAAA
1 ATAAA
49370340 ACTTTATAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.73, C:0.03, G:0.12, T:0.12
Consensus pattern (7 bp):
ATAAAGA
Found at i:49373159 original size:6 final size:6
Alignment explanation
Indices: 49373148--49373180 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
49373138 TTATATATTC
49373148 TAGTGT TAGTGT TAGTGT TAGTGT TAGTGT TAG
1 TAGTGT TAGTGT TAGTGT TAGTGT TAGTGT TAG
49373181 CTTTGACATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.18, C:0.00, G:0.33, T:0.48
Consensus pattern (6 bp):
TAGTGT
Found at i:49382651 original size:6 final size:6
Alignment explanation
Indices: 49382640--49382737 Score: 196
Period size: 6 Copynumber: 16.3 Consensus size: 6
49382630 TTGTTCTGCA
49382640 TATCTG TATCTG TATCTG TATCTG TATCTG TATCTG TATCTG TATCTG
1 TATCTG TATCTG TATCTG TATCTG TATCTG TATCTG TATCTG TATCTG
49382688 TATCTG TATCTG TATCTG TATCTG TATCTG TATCTG TATCTG TATCTG
1 TATCTG TATCTG TATCTG TATCTG TATCTG TATCTG TATCTG TATCTG
49382736 TA
1 TA
49382738 AAGGACTTAA
Statistics
Matches: 92, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 92 1.00
ACGTcount: A:0.17, C:0.16, G:0.16, T:0.50
Consensus pattern (6 bp):
TATCTG
Found at i:49385534 original size:20 final size:20
Alignment explanation
Indices: 49385490--49385537 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
49385480 AAGTAAGAGA
* *
49385490 CTTTCTTCCTTTTTTATTTT
1 CTTTCTTTCTTTATTATTTT
49385510 CTTTCTTTCTTTATTATTTGT
1 CTTTCTTTCTTTATTATTT-T
49385531 -TTTCTTT
1 CTTTCTTT
49385538 GATTGTAGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 24 0.96
21 1 0.04
ACGTcount: A:0.06, C:0.17, G:0.02, T:0.75
Consensus pattern (20 bp):
CTTTCTTTCTTTATTATTTT
Found at i:49386522 original size:14 final size:14
Alignment explanation
Indices: 49386503--49386533 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
49386493 TTTGATTGGT
*
49386503 GGAAAATATTTTCC
1 GGAAAATATTTTAC
49386517 GGAAAATATTTTAC
1 GGAAAATATTTTAC
49386531 GGA
1 GGA
49386534 TTTTCCAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.39, C:0.10, G:0.19, T:0.32
Consensus pattern (14 bp):
GGAAAATATTTTAC
Done.