Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr4
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: 30015117
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1306243 characters in sequence are not A, C, G, or T
File 6 of 85
Found at i:2110891 original size:216 final size:215
Alignment explanation
Indices: 2110436--2110959 Score: 683
Period size: 216 Copynumber: 2.4 Consensus size: 215
2110426 ATAAGCAGAT
* *
2110436 TTTTCAGTTTTTGAGCACTAAAAATCAACAATGATGGTAAATAATAATTACCCAGAAAGCGAAAA
1 TTTTCAG-TTTTGA-CACTAAAAATCAATAATTATGGTAAATAATAATTACCCAGAAAGCGAAAA
** * *
2110501 CGGATGGTTATCAAGTGCTTCAAGCCTTAAAGTATTTAGACACAATTCGATGAAAAACAAAAAAA
64 TTGATGATTATCAAGTGCTTCAAGCCTTAAACTATTTAGACACAATTCGATGAAAAAC---AAAA
* * * ** *
2110566 AATTAACTTTTGAGACAGCACAATGTATCGTTTTACTAATTCAATTATTCAGTAAGTAATTGACT
126 AATTAACTTTAGAGACAGCAAAATATATAATTTTACTAATTCAATTATTCAGTAAATAATTGACT
* * *
2110631 TCGAACAATAACTAGATAAACAGAA
191 TCAAACAATAACTACATAAACAAAA
* *
2110656 TTCTCAGTTTTGAACACTAAAAATCAATAATTATGAGTAAATAATAACTACCCAGAAAGCGAAAA
1 TTTTCAGTTTTG-ACACTAAAAATCAATAATTATG-GTAAATAATAATTACCCAGAAAGCGAAAA
* * * *
2110721 TTGATGATTATCAAGTGGTTCAAGCC-TAAACTATTTATACATAATTCGATGAAGAAC-AAAAAT
64 TTGATGATTATCAAGTGCTTCAAGCCTTAAACTATTTAGACACAATTCGATGAAAAACAAAAAAT
* *
2110784 TCAACTTTAGAGATAGCAAAATATATAATTTTACTCATTCAATTATTCAGTAAATAATTGACTTC
129 T-AACTTTAGAGACAGCAAAATATATAATTTTACTAATTCAATTATTCAGTAAATAATTGACTTC
* *
2110849 AAACAATAAGTACATGAACAAAA
193 AAACAATAACTACATAAACAAAA
* *
2110872 TTTTCAGTTTTGCACACTAAAAATCAATGATTATGGGTGAATAATAATTACCCAGAAAGCGAAAA
1 TTTTCAGTTTTG-ACACTAAAAATCAATAATTAT-GGTAAATAATAATTACCCAGAAAGCGAAAA
* *
2110937 TTGATGATTATCGACTGCTTCAA
64 TTGATGATTATCAAGTGCTTCAA
2110960 CGAATTTATG
Statistics
Matches: 267, Mismatches: 33, Indels: 12
0.86 0.11 0.04
Matches are distributed among these distances:
215 7 0.03
216 151 0.57
217 1 0.00
219 51 0.19
220 57 0.21
ACGTcount: A:0.43, C:0.14, G:0.13, T:0.30
Consensus pattern (215 bp):
TTTTCAGTTTTGACACTAAAAATCAATAATTATGGTAAATAATAATTACCCAGAAAGCGAAAATT
GATGATTATCAAGTGCTTCAAGCCTTAAACTATTTAGACACAATTCGATGAAAAACAAAAAATTA
ACTTTAGAGACAGCAAAATATATAATTTTACTAATTCAATTATTCAGTAAATAATTGACTTCAAA
CAATAACTACATAAACAAAA
Found at i:2112008 original size:16 final size:17
Alignment explanation
Indices: 2111989--2112034 Score: 85
Period size: 16 Copynumber: 2.8 Consensus size: 17
2111979 GTTTAAAGTT
2111989 ATTTTCTACTACAAT-A
1 ATTTTCTACTACAATCA
2112005 ATTTTCTACTACAATCA
1 ATTTTCTACTACAATCA
2112022 ATTTTCTACTACA
1 ATTTTCTACTACA
2112035 TATGATGAGG
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
16 15 0.52
17 14 0.48
ACGTcount: A:0.35, C:0.22, G:0.00, T:0.43
Consensus pattern (17 bp):
ATTTTCTACTACAATCA
Found at i:2117341 original size:120 final size:117
Alignment explanation
Indices: 2117099--2117467 Score: 291
Period size: 124 Copynumber: 3.0 Consensus size: 117
2117089 GTATGCGAGT
* * *
2117099 TTTTTTAGATTGATAGCTGATTCTTGCTTCATAAGTAAATAGT-TTACGTTAATATGATTGAAAA
1 TTTTTTAGATTGAT-GCTGATTCTTGCTTCCTAAGTAAATAGTATT-TGTTAATATGATCG-AAA
* **
2117163 TGTTCATTCGATATTTGGAGATTTAACTGA-T---GGCATCGAAGCTA-ATAAACTGTCAG
63 TGTTCA----ATATTTTGAGATTTAACTGACTGCAGGCATCGAAGCTAGATGTA-T-TCAG
* *
2117219 TTTTTTAGATTTAATGCTGATTCTTGCTTCCTAAGTAAATAGTATTTGTTGATATGATCGAAATG
1 TTTTTTAGA-TTGATGCTGATTCTTGCTTCCTAAGTAAATAGTATTTGTTAATATGATCGAAATG
* *
2117284 TTCAAAATTTTGAGATTTAACTGACTGCAGGCATCGAAGCTAGGTTGTATTCTAG
65 TTCAATATTTTGAGATTTAACTGACTGCAGGCATCGAAGCTA-GATGTATTC-AG
* * * * * ** * *
2117339 TTTCTTAGATCGATGTCTGATTGTTTCTTGTTTCCCAAGTAAATAGCAGATGCTAATATGATCAA
1 TTTTTTAGATTGATG-CTGA----TTCTTGCTTCCTAAGTAAATAGTATTTGTTAATATGATCGA
** * * * * *
2117404 AATGTTTGATATTTTAAGATTCAACTGACTGCATGCATCGAAGCTAAGCTGTATGCGAG
61 AATGTTCAATATTTTGAGATTTAACTGACTGCAGGCATCGAAGCT-AGATGTATTC-AG
2117463 TTTTT
1 TTTTT
2117468 CTGATTCATG
Statistics
Matches: 203, Mismatches: 31, Indels: 26
0.78 0.12 0.10
Matches are distributed among these distances:
115 18 0.09
116 1 0.00
119 28 0.14
120 62 0.31
121 8 0.04
124 85 0.42
125 1 0.00
ACGTcount: A:0.29, C:0.12, G:0.19, T:0.40
Consensus pattern (117 bp):
TTTTTTAGATTGATGCTGATTCTTGCTTCCTAAGTAAATAGTATTTGTTAATATGATCGAAATGT
TCAATATTTTGAGATTTAACTGACTGCAGGCATCGAAGCTAGATGTATTCAG
Found at i:2117399 original size:124 final size:123
Alignment explanation
Indices: 2117270--2117706 Score: 418
Period size: 124 Copynumber: 3.5 Consensus size: 123
2117260 GTATTTGTTG
* * * * *
2117270 ATATGATCGAAATGTTCAAAATTTTGAGATTTAACTGACTGCAGGCATCGAAGCTAGGTTGTATT
1 ATATGATCGAAATGTTCGATATTTTGAGATTCAACTGACTGCAGGCATCGAAGCTAAGTTGTATG
2117335 CTAGTTTCTTAGATCGATGTCTGATTGTTTCTTGTTTCCCAAGTAAATAGCAGATGCTA
66 CTAGTTTCTTAGATCGATGTCTGATTGTTTCTTGTTTCCCAAGTAAATAG-AGATGCTA
* * * * *
2117394 ATATGATCAAAATGTTTGATATTTTAAGATTCAACTGACTGCATGCATCGAAGCTAAGCTGTATG
1 ATATGATCGAAATGTTCGATATTTTGAGATTCAACTGACTGCAGGCATCGAAGCTAAGTTGTATG
* * ** * *
2117459 CGAGTTT-TTCTGATTC-ATGGT-TGATTGATGCTTGCTTGTTTAGCAAGT--A-AGAGATGTTG
66 CTAGTTTCTT-AGA-TCGAT-GTCTGATTG-T--TT-CTTGTTTCCCAAGTAAATAGAGATGCTA
* * * * * *
2117518 ATGTGATCGAAATGTTCGATATTTCGAGAATCAACTGATTGCAGGCATTGAAGCCAAGTTGTATG
1 ATATGATCGAAATGTTCGATATTTTGAGATTCAACTGACTGCAGGCATCGAAGCTAAGTTGTATG
* * * ** *
2117583 CTGGTTTCTTAGATTGATGTCTGATTGTTTCTTGCTTCCCAAGTAAATAGTAGATTTTT
66 CTAGTTTCTTAGATCGATGTCTGATTGTTTCTTGTTTCCCAAGTAAATAG-AGATGCTA
* ** * ** * * *
2117642 ATATGATCGTAACATTCGATATTTCGAGATTCAAAGGACTGCATGCATTGAAGCTAAGTTTTATG
1 ATATGATCGAAATGTTCGATATTTTGAGATTCAACTGACTGCAGGCATCGAAGCTAAGTTGTATG
2117707 TTCCTTTTTA
Statistics
Matches: 252, Mismatches: 47, Indels: 28
0.77 0.14 0.09
Matches are distributed among these distances:
120 11 0.04
121 2 0.01
122 1 0.00
123 8 0.03
124 206 0.82
125 9 0.04
126 1 0.00
127 2 0.01
128 12 0.05
ACGTcount: A:0.28, C:0.14, G:0.21, T:0.37
Consensus pattern (123 bp):
ATATGATCGAAATGTTCGATATTTTGAGATTCAACTGACTGCAGGCATCGAAGCTAAGTTGTATG
CTAGTTTCTTAGATCGATGTCTGATTGTTTCTTGTTTCCCAAGTAAATAGAGATGCTA
Found at i:2127812 original size:16 final size:17
Alignment explanation
Indices: 2127775--2127820 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 17
2127765 GATGTCAGTG
*
2127775 AAAAAATTATATATAGA
1 AAAAAATTATTTATAGA
2127792 AAAAAATTATTTATA-A
1 AAAAAATTATTTATAGA
* *
2127808 TAAAATTTATTTA
1 AAAAAATTATTTA
2127821 ATTTTGAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
16 12 0.46
17 14 0.54
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (17 bp):
AAAAAATTATTTATAGA
Found at i:2134594 original size:41 final size:41
Alignment explanation
Indices: 2134408--2134593 Score: 284
Period size: 41 Copynumber: 4.5 Consensus size: 41
2134398 TTTAACATAT
* * * *
2134408 TCACCAGCACTTAGCCTGCTAGGCTTATAGCCTAATTCCA-A
1 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATT-CAGA
*
2134449 TCACTGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
*
2134490 TCACCGGCACTTAGCCTGCTAGGTTTATAACTTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
* *
2134531 TCACCGGCACTTAGCCTACTAGATTTATAACCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
2134572 TCACCGGCACTTAGCCTGCTAG
1 TCACCGGCACTTAGCCTGCTAG
2134594 ACTTAAAGTT
Statistics
Matches: 133, Mismatches: 11, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
40 2 0.02
41 131 0.98
ACGTcount: A:0.25, C:0.28, G:0.18, T:0.29
Consensus pattern (41 bp):
TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
Found at i:2134617 original size:82 final size:82
Alignment explanation
Indices: 2134408--2134647 Score: 283
Period size: 82 Copynumber: 2.9 Consensus size: 82
2134398 TTTAACATAT
* * * * * *
2134408 TCACCAGCACTTAGCCTGCTAGGCTTATAGCCTAATTCCA-ATCACTGGCACTTAGCCTGCTAGG
1 TCACCGGCACTTAGCCTGCTAGACTTATAACTTGATT-CAGATCACCGGCACTTAGCCTGCTAGG
2134472 TTTATAACCTGATTCAGA
65 TTTATAACCTGATTCAGA
** * *
2134490 TCACCGGCACTTAGCCTGCTAGGTTTATAACTTGATTCAGATCACCGGCACTTAGCCTACTAGAT
1 TCACCGGCACTTAGCCTGCTAGACTTATAACTTGATTCAGATCACCGGCACTTAGCCTGCTAGGT
2134555 TTATAACCTGATTCAGA
66 TTATAACCTGATTCAGA
* **
2134572 TCACCGGCACTTAGCCTGCTAGACTTA-AAGTTCGAATT-ATTTCACCGGC-CTTAAGCCTGCTA
1 TCACCGGCACTTAGCCTGCTAGACTTATAACTT-G-ATTCAGATCACCGGCACTT-AGCCTGCTA
2134634 GGTTT-TAAACCTGA
63 GGTTTAT-AACCTGA
2134648 AAATTTCAAT
Statistics
Matches: 138, Mismatches: 15, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
81 10 0.07
82 125 0.91
83 3 0.02
ACGTcount: A:0.26, C:0.27, G:0.17, T:0.30
Consensus pattern (82 bp):
TCACCGGCACTTAGCCTGCTAGACTTATAACTTGATTCAGATCACCGGCACTTAGCCTGCTAGGT
TTATAACCTGATTCAGA
Found at i:2144596 original size:26 final size:26
Alignment explanation
Indices: 2144522--2144597 Score: 66
Period size: 29 Copynumber: 2.8 Consensus size: 26
2144512 ACGTGGTAAG
*
2144522 AAAA-TAAAATAAATAAAACTTGTTTT
1 AAAATTAAAA-AAATAAAAATTGTTTT
**
2144548 AAAATATAGAAAAATATTTAAATT-TTGTT
1 AAAAT-TA-AAAAA-ATAAAAATTGTT-TT
2144577 AAAATTAAAAAAATAAAAATT
1 AAAATTAAAAAAATAAAAATT
2144598 ATAGAAAGTT
Statistics
Matches: 40, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
26 11 0.28
27 5 0.12
28 8 0.20
29 16 0.40
ACGTcount: A:0.61, C:0.01, G:0.04, T:0.34
Consensus pattern (26 bp):
AAAATTAAAAAAATAAAAATTGTTTT
Found at i:2144621 original size:21 final size:22
Alignment explanation
Indices: 2144592--2144701 Score: 62
Period size: 21 Copynumber: 5.4 Consensus size: 22
2144582 TAAAAAAATA
*
2144592 AAAAT-TATAGAAAGTTATTA-
1 AAAATATATAGAAAATTATTAT
*
2144612 AGAATATATA-AAAATTATTAT
1 AAAATATATAGAAAATTATTAT
*
2144633 AAAATATA-AG-AAA-TA-TAGG
1 AAAATATATAGAAAATTATTA-T
* *
2144652 AAAAT-TATATAAAAGTA-TAT
1 AAAATATATAGAAAATTATTAT
* *
2144672 GTAAAT-TATAGAAATTTATTA-
1 -AAAATATATAGAAAATTATTAT
2144693 AAAATATAT
1 AAAATATAT
2144702 TAAACGATGT
Statistics
Matches: 69, Mismatches: 11, Indels: 19
0.70 0.11 0.19
Matches are distributed among these distances:
18 4 0.06
19 8 0.12
20 24 0.35
21 31 0.45
22 2 0.03
ACGTcount: A:0.57, C:0.00, G:0.08, T:0.35
Consensus pattern (22 bp):
AAAATATATAGAAAATTATTAT
Found at i:2144701 original size:30 final size:29
Alignment explanation
Indices: 2144617--2144705 Score: 94
Period size: 30 Copynumber: 3.0 Consensus size: 29
2144607 TATTAAGAAT
*
2144617 ATATA-AAAATTATTATAAAATATAAG-AA
1 ATATAGAAAATTATTA-AAAATATATGTAA
*
2144645 ATATAGGAAAATTATATAAAAGTATATGTAA
1 ATATA-GAAAATTAT-TAAAAATATATGTAA
*
2144676 ATTATAGAAATTTATTAAAAATATAT-TAA
1 A-TATAGAAAATTATTAAAAATATATGTAA
2144705 A
1 A
2144706 CGATGTTTAG
Statistics
Matches: 52, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
28 5 0.10
29 4 0.08
30 26 0.50
31 13 0.25
32 4 0.08
ACGTcount: A:0.58, C:0.00, G:0.07, T:0.35
Consensus pattern (29 bp):
ATATAGAAAATTATTAAAAATATATGTAA
Found at i:2146012 original size:19 final size:21
Alignment explanation
Indices: 2145990--2146034 Score: 67
Period size: 19 Copynumber: 2.2 Consensus size: 21
2145980 TTTATATACA
2145990 TTTATAAATTTTT-AAT-AAT
1 TTTATAAATTTTTAAATAAAT
*
2146009 TTTATATATTTTTAAATAAAT
1 TTTATAAATTTTTAAATAAAT
2146030 TTTAT
1 TTTAT
2146035 TGATTTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 12 0.52
20 3 0.13
21 8 0.35
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TTTATAAATTTTTAAATAAAT
Found at i:2146014 original size:27 final size:28
Alignment explanation
Indices: 2145970--2146025 Score: 71
Period size: 27 Copynumber: 2.0 Consensus size: 28
2145960 TTTGATAATT
2145970 TTTTATAATATTTATATACATTTATAAA
1 TTTTATAATATTTATATACATTTATAAA
* *
2145998 TTTT-TAATAATTT-TATATATTTTTAAA
1 TTTTATAAT-ATTTATATACATTTATAAA
2146025 T
1 T
2146026 AAATTTTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 17 0.68
28 8 0.32
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (28 bp):
TTTTATAATATTTATATACATTTATAAA
Found at i:2146021 original size:20 final size:21
Alignment explanation
Indices: 2145998--2146043 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
2145988 CATTTATAAA
2145998 TTTTTAAT-AATTTTATAT-AT
1 TTTTTAATAAATTTTAT-TGAT
*
2146018 TTTTAAATAAATTTTATTGAT
1 TTTTTAATAAATTTTATTGAT
2146039 TTTTT
1 TTTTT
2146044 TTTATTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 8 0.36
21 14 0.64
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (21 bp):
TTTTTAATAAATTTTATTGAT
Found at i:2146022 original size:29 final size:31
Alignment explanation
Indices: 2145966--2146032 Score: 84
Period size: 30 Copynumber: 2.2 Consensus size: 31
2145956 NNAATTTGAT
*
2145966 AATTTTTTATAATATTTATATACATTT-ATA
1 AATTTTTAATAATATTTATATACATTTAATA
**
2145996 AATTTTTAATAAT-TTTATATATTTTTAAATA
1 AATTTTTAATAATATTTATATACATTT-AATA
2146027 AATTTT
1 AATTTT
2146033 ATTGATTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 11 0.34
30 12 0.38
31 9 0.28
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.58
Consensus pattern (31 bp):
AATTTTTAATAATATTTATATACATTTAATA
Found at i:2150883 original size:43 final size:43
Alignment explanation
Indices: 2150822--2151000 Score: 322
Period size: 43 Copynumber: 4.2 Consensus size: 43
2150812 AAAAATTCCG
2150822 CTATAGACCATGACCTTTAGCGGCGCTTTTCCCACAAACGCCA
1 CTATAGACCATGACCTTTAGCGGCGCTTTTCCCACAAACGCCA
2150865 CTATAGACCATGACCTTTAGCGGCGCTTTTCCCACAAACGCCA
1 CTATAGACCATGACCTTTAGCGGCGCTTTTCCCACAAACGCCA
* *
2150908 CTATAGACCATGACCTTTAGCGGCGCTTTTTCCACAAACGCCG
1 CTATAGACCATGACCTTTAGCGGCGCTTTTCCCACAAACGCCA
* *
2150951 CTATAGACCATGACCTTTAGCGGCGCTTTTTCCACAAACGCCG
1 CTATAGACCATGACCTTTAGCGGCGCTTTTCCCACAAACGCCA
2150994 CTATAGA
1 CTATAGA
2151001 GCGACGCTTT
Statistics
Matches: 134, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
43 134 1.00
ACGTcount: A:0.25, C:0.33, G:0.17, T:0.25
Consensus pattern (43 bp):
CTATAGACCATGACCTTTAGCGGCGCTTTTCCCACAAACGCCA
Found at i:2150967 original size:86 final size:86
Alignment explanation
Indices: 2150822--2151070 Score: 333
Period size: 86 Copynumber: 3.0 Consensus size: 86
2150812 AAAAATTCCG
* *
2150822 CTATAGACCATGACCTTTAGCGGCGCTTTTCCCACAAACGCCACTATAGACCATGACCTTTAGCG
1 CTATAGACCATGACCTTTAGCGGCGCTTTTTCCACAAACGCCGCTATAGACCATGACCTTTAGCG
2150887 GCGCTTTTCCCACAAACGCCA
66 GCGCTTTTCCCACAAACGCCA
2150908 CTATAGACCATGACCTTTAGCGGCGCTTTTTCCACAAACGCCGCTATAGACCATGACCTTTAGCG
1 CTATAGACCATGACCTTTAGCGGCGCTTTTTCCACAAACGCCGCTATAGACCATGACCTTTAGCG
* *
2150973 GCGCTTTTTCCACAAACGCCG
66 GCGCTTTTCCCACAAACGCCA
* * *
2150994 CTAT-----A-G------AGCGACGCTTTTTCCACAAACGCCGCTATAGATCATGACTTTTAGCG
1 CTATAGACCATGACCTTTAGCGGCGCTTTTTCCACAAACGCCGCTATAGACCATGACCTTTAGCG
* *
2151047 GCACTTTTGCCACAAACGCCA
66 GCGCTTTTCCCACAAACGCCA
2151068 CTA
1 CTA
2151071 ATTTTGGCAG
Statistics
Matches: 153, Mismatches: 10, Indels: 12
0.87 0.06 0.07
Matches are distributed among these distances:
74 65 0.42
80 1 0.01
81 1 0.01
86 86 0.56
ACGTcount: A:0.25, C:0.33, G:0.17, T:0.25
Consensus pattern (86 bp):
CTATAGACCATGACCTTTAGCGGCGCTTTTTCCACAAACGCCGCTATAGACCATGACCTTTAGCG
GCGCTTTTCCCACAAACGCCA
Found at i:2151042 original size:31 final size:31
Alignment explanation
Indices: 2150969--2151031 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
2150959 CATGACCTTT
*
2150969 AGCGGCGCTTTTTCCACAAACGCCGCTATAG
1 AGCGACGCTTTTTCCACAAACGCCGCTATAG
2151000 AGCGACGCTTTTTCCACAAACGCCGCTATAG
1 AGCGACGCTTTTTCCACAAACGCCGCTATAG
2151031 A
1 A
2151032 TCATGACTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.25, C:0.32, G:0.21, T:0.22
Consensus pattern (31 bp):
AGCGACGCTTTTTCCACAAACGCCGCTATAG
Found at i:2151054 original size:74 final size:74
Alignment explanation
Indices: 2150926--2151066 Score: 237
Period size: 74 Copynumber: 1.9 Consensus size: 74
2150916 CATGACCTTT
* * *
2150926 AGCGGCGCTTTTTCCACAAACGCCGCTATAGACCATGACCTTTAGCGGCGCTTTTTCCACAAACG
1 AGCGACGCTTTTTCCACAAACGCCGCTATAGACCATGACCTTTAGCGGCACTTTTGCCACAAACG
2150991 CCGCTATAG
66 CCGCTATAG
* *
2151000 AGCGACGCTTTTTCCACAAACGCCGCTATAGATCATGACTTTTAGCGGCACTTTTGCCACAAACG
1 AGCGACGCTTTTTCCACAAACGCCGCTATAGACCATGACCTTTAGCGGCACTTTTGCCACAAACG
2151065 CC
66 CC
2151067 ACTAATTTTG
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
74 62 1.00
ACGTcount: A:0.24, C:0.32, G:0.19, T:0.25
Consensus pattern (74 bp):
AGCGACGCTTTTTCCACAAACGCCGCTATAGACCATGACCTTTAGCGGCACTTTTGCCACAAACG
CCGCTATAG
Found at i:2151410 original size:21 final size:21
Alignment explanation
Indices: 2151376--2151446 Score: 79
Period size: 21 Copynumber: 3.4 Consensus size: 21
2151366 TTCTACTCTG
*
2151376 CTCTACTTCCCTCGCTGCAGC
1 CTCTGCTTCCCTCGCTGCAGC
* * * *
2151397 CTTTGCTTCTCTCGTTGCTGC
1 CTCTGCTTCCCTCGCTGCAGC
*
2151418 CTCTGCTTCCCTCGCTGCCGC
1 CTCTGCTTCCCTCGCTGCAGC
*
2151439 ATCTGCTT
1 CTCTGCTT
2151447 TAAGCTTCTC
Statistics
Matches: 40, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.04, C:0.42, G:0.17, T:0.37
Consensus pattern (21 bp):
CTCTGCTTCCCTCGCTGCAGC
Found at i:2151454 original size:28 final size:28
Alignment explanation
Indices: 2151422--2151478 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
2151412 TGCTGCCTCT
2151422 GCTTCCCTCGCTGCCGCATCTGCTTTAA
1 GCTTCCCTCGCTGCCGCATCTGCTTTAA
* **
2151450 GCTTCTCTCGCTGTTGCATCTGCTTTAA
1 GCTTCCCTCGCTGCCGCATCTGCTTTAA
2151478 G
1 G
2151479 TTGTAGTTGG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.11, C:0.33, G:0.19, T:0.37
Consensus pattern (28 bp):
GCTTCCCTCGCTGCCGCATCTGCTTTAA
Found at i:2156094 original size:13 final size:14
Alignment explanation
Indices: 2156074--2156131 Score: 59
Period size: 15 Copynumber: 4.1 Consensus size: 14
2156064 TTTAAACACT
*
2156074 TAAACCCTAAACCC
1 TAAACCCTAATCCC
2156088 T-AACCCTAA-CCC
1 TAAACCCTAATCCC
2156100 TTAAACACC-AATCCC
1 -TAAAC-CCTAATCCC
2156115 TAAACCCATAATCCC
1 TAAACCC-TAATCCC
2156130 TA
1 TA
2156132 GTCCACAAAC
Statistics
Matches: 38, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
12 3 0.08
13 11 0.29
14 11 0.29
15 13 0.34
ACGTcount: A:0.40, C:0.41, G:0.00, T:0.19
Consensus pattern (14 bp):
TAAACCCTAATCCC
Found at i:2156217 original size:14 final size:14
Alignment explanation
Indices: 2156198--2156248 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
2156188 AATCCCTAAC
2156198 CTCTAAACCTTAAA
1 CTCTAAACCTTAAA
2156212 CTCT-AACCATTAAA
1 CTCTAAACC-TTAAA
* *
2156226 CACTAAACACTTAAC
1 CTCTAAAC-CTTAAA
2156241 CT-TAAACC
1 CTCTAAACC
2156249 CCAACCCTTG
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
13 5 0.16
14 17 0.55
15 8 0.26
16 1 0.03
ACGTcount: A:0.43, C:0.31, G:0.00, T:0.25
Consensus pattern (14 bp):
CTCTAAACCTTAAA
Found at i:2156225 original size:21 final size:20
Alignment explanation
Indices: 2156193--2156248 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 20
2156183 CCCTTAATCC
*
2156193 CTAACCTCTAAACCTTAAACT
1 CTAACCT-TAAACCTTAAACA
2156214 CTAACCATTAAACAC-TAAACA
1 CTAACC-TTAAAC-CTTAAACA
2156235 CTTAACCTTAAACC
1 C-TAACCTTAAACC
2156249 CCAACCCTTG
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
20 1 0.03
21 23 0.74
22 7 0.23
ACGTcount: A:0.43, C:0.32, G:0.00, T:0.25
Consensus pattern (20 bp):
CTAACCTTAAACCTTAAACA
Found at i:2157299 original size:230 final size:228
Alignment explanation
Indices: 2156706--2157321 Score: 908
Period size: 229 Copynumber: 2.7 Consensus size: 228
2156696 TTAACTTATT
* * * * *
2156706 AGCAAAGCGAAGAAATAAAACGCTGCCATTTTGATCAACATATTTGCAACGTTTGTTTATATGCA
1 AGCAAAGCGAAGAAATAAAACGCTGCCGTTTTGATCAAC-TTTTTGCAGCGTTTGTTTACATGCG
* *
2156771 CCGCTAACACCTAACCTTTAGCGACGTTTTACAAAAAGCGCCGCTAATGTCCCTATACCTCAACA
65 CCGCTATCACCTAACCTTTAGCGGCGTTTTACAAAAAGCGCCGCTAATGTCCCTATACCTCAACA
* *
2156836 GAAAACAACGTCGTTTTGCTTAACTTATTAACGGCGCTTATGGAAAAGCGCCGGTAAAGACCGAA
130 GAAAACAACGTTGTTTTGCTTAACTTACTAACGGCGCTTATGGAAAAGCGCCGGTAAAGACCGAA
* * *
2156901 AGTTGCGGCGTTTTTAAAAATCGCCATTAAATCA
195 AGTTGAGGCGTTTTTAAAAAACGCCACTAAATCA
* * * **
2156935 AGCAAAGCGAAGAAATAGAACGCTGCCGTTTTTGATCAACTTTATACAGCGTTTGTTTACATTTG
1 AGCAAAGCGAAGAAATAAAACGCTGCCG-TTTTGATCAACTTTTTGCAGCGTTTGTTTACATGCG
* * *
2157000 CCGCTATCACCTAACCGTTAGCGGTGTTTTACAAAAAGCGCCGCTAATGTCCCTATACATCAACA
65 CCGCTATCACCTAACCTTTAGCGGCGTTTTACAAAAAGCGCCGCTAATGTCCCTATACCTCAACA
* * *
2157065 GAAAACAACGTTGTTTTGCTTAACTTACTAGCGGCGCTTTTGGAAAAGCGCCGGTAAAGACTGAA
130 GAAAACAACGTTGTTTTGCTTAACTTACTAACGGCGCTTATGGAAAAGCGCCGGTAAAGACCGAA
2157130 AGTTGAGGCGTTTTTAAAAAAACGCCACTAAATCA
195 AGTTGAGGCGTTTTT-AAAAAACGCCACTAAATCA
* * * *
2157165 AGTAAAGCGAAGAAACAAAACGCTGCCGTTTTGATCAACTTTTTTGCGGCGTTTGTTTACGTGCG
1 AGCAAAGCGAAGAAATAAAACGCTGCCGTTTTGATCAAC-TTTTTGCAGCGTTTGTTTACATGCG
* * * * *
2157230 CCGCTATTACCTAACATTTAGTGGCGTTTTATAGAAAGCGCCGCTAATGTCCCTATACCTCAACA
65 CCGCTATCACCTAACCTTTAGCGGCGTTTTACAAAAAGCGCCGCTAATGTCCCTATACCTCAACA
2157295 GAAAACAACGTTGTTTTGCTTAACTTA
130 GAAAACAACGTTGTTTTGCTTAACTTA
2157322 TTTGCGGCAT
Statistics
Matches: 344, Mismatches: 40, Indels: 5
0.88 0.10 0.01
Matches are distributed among these distances:
229 188 0.55
230 156 0.45
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.28
Consensus pattern (228 bp):
AGCAAAGCGAAGAAATAAAACGCTGCCGTTTTGATCAACTTTTTGCAGCGTTTGTTTACATGCGC
CGCTATCACCTAACCTTTAGCGGCGTTTTACAAAAAGCGCCGCTAATGTCCCTATACCTCAACAG
AAAACAACGTTGTTTTGCTTAACTTACTAACGGCGCTTATGGAAAAGCGCCGGTAAAGACCGAAA
GTTGAGGCGTTTTTAAAAAACGCCACTAAATCA
Found at i:2159747 original size:23 final size:23
Alignment explanation
Indices: 2159711--2159774 Score: 76
Period size: 23 Copynumber: 2.8 Consensus size: 23
2159701 TAGTCCTTTC
* * *
2159711 ATAAATAATGAAATTATAAGTTA
1 ATAAATGATAAAATTATAAATTA
*
2159734 A-AAACTGATAAAATCATAAATTA
1 ATAAA-TGATAAAATTATAAATTA
2159757 ATAAATGATAAAATTATA
1 ATAAATGATAAAATTATA
2159775 TTTTGACCTT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
22 3 0.09
23 28 0.82
24 3 0.09
ACGTcount: A:0.59, C:0.03, G:0.06, T:0.31
Consensus pattern (23 bp):
ATAAATGATAAAATTATAAATTA
Found at i:2166854 original size:24 final size:25
Alignment explanation
Indices: 2166822--2166875 Score: 101
Period size: 25 Copynumber: 2.2 Consensus size: 25
2166812 CACACTTTTT
2166822 CCTTTTTTAA-GAATATAATTATTC
1 CCTTTTTTAATGAATATAATTATTC
2166846 CCTTTTTTAATGAATATAATTATTC
1 CCTTTTTTAATGAATATAATTATTC
2166871 CCTTT
1 CCTTT
2166876 GACGAATTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
24 10 0.34
25 19 0.66
ACGTcount: A:0.30, C:0.15, G:0.04, T:0.52
Consensus pattern (25 bp):
CCTTTTTTAATGAATATAATTATTC
Found at i:2174516 original size:133 final size:131
Alignment explanation
Indices: 2174269--2174522 Score: 386
Period size: 133 Copynumber: 1.9 Consensus size: 131
2174259 AGGTAGCATA
2174269 CACATGGATTACCACATGGATGACATGTTAGCATTTAATTAATTTTTTAAAATTTTAAAAATATT
1 CACATGGATTACCACATGGATGACATGTTAGCATTTAATTAATTTTTTAAAATTTTAAAAATATT
* * * *
2174334 AAAAAATATATTTTATATTCTTTTTATACTTTTTAAATAATTTTTAATTTTTAAAAATACATTTT
66 AAAAAATATATTTTATATTCTTTTAATAC-ATTTAAATAA-TTTAAAATTTTAAAAATACATTTT
2174399 TAT
129 TAT
2174402 CACATGGATTACCACATGGATGACATGTTAGCATTTAATTAATTTTTTAAAATTTTAAAAATATT
1 CACATGGATTACCACATGGATGACATGTTAGCATTTAATTAATTTTTTAAAATTTTAAAAATATT
* * *
2174467 AAAAAGTATTTTTTAAATATT-TTTTAATA-ATTTAAATTATTTAAAAATTTTAAAAA
66 AAAAAATATATTTT--ATATTCTTTTAATACATTTAAATAATTT-AAAATTTTAAAAA
2174523 CAAATTTTAT
Statistics
Matches: 111, Mismatches: 7, Indels: 7
0.89 0.06 0.06
Matches are distributed among these distances:
131 3 0.03
132 19 0.17
133 77 0.69
134 7 0.06
135 5 0.05
ACGTcount: A:0.41, C:0.07, G:0.06, T:0.46
Consensus pattern (131 bp):
CACATGGATTACCACATGGATGACATGTTAGCATTTAATTAATTTTTTAAAATTTTAAAAATATT
AAAAAATATATTTTATATTCTTTTAATACATTTAAATAATTTAAAATTTTAAAAATACATTTTTA
T
Found at i:2174555 original size:51 final size:50
Alignment explanation
Indices: 2174440--2174557 Score: 118
Period size: 51 Copynumber: 2.3 Consensus size: 50
2174430 TAGCATTTAA
** *
2174440 TTAATTTTTTAAAA-TTTTAAAAATATTAAAAAGTATTTTTTAAATATTTT
1 TTAA-TTTTTAAAATTTTTAAAAATATTAAAAAAAATTTTATAAATATTTT
* *
2174490 TTAATAATTT-AAATTATTTAAAAATTTTAAAAACAAATTTTAT-AAT-TTTT
1 TTAAT-TTTTAAAATT-TTTAAAAATATTAAAAA-AAATTTTATAAATATTTT
2174540 TTGAATTTTTAAAATTTT
1 TT-AATTTTTAAAATTTT
2174558 AATAAGGCTG
Statistics
Matches: 56, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
49 4 0.07
50 19 0.34
51 27 0.48
52 6 0.11
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.53
Consensus pattern (50 bp):
TTAATTTTTAAAATTTTTAAAAATATTAAAAAAAATTTTATAAATATTTT
Found at i:2180112 original size:42 final size:42
Alignment explanation
Indices: 2180064--2180233 Score: 234
Period size: 42 Copynumber: 4.0 Consensus size: 42
2180054 GCCGAATGAG
*
2180064 GAATTGGTAGCTGATGAGACCAATGATGCTGCTGTATCTGAA
1 GAATTGGTAGCTGATGAGACCAATGATGCTGCTGTTTCTGAA
* * * *
2180106 GAATTGGTGGCTGATGAGACCAACGATGCTGTTGTTACTGAA
1 GAATTGGTAGCTGATGAGACCAATGATGCTGCTGTTTCTGAA
* * *
2180148 GAATTGGTGGCTGATGAGACCTATGATGCTGCTGTTTCTCAA
1 GAATTGGTAGCTGATGAGACCAATGATGCTGCTGTTTCTGAA
* *
2180190 GAATTGGCAGCTGATG-GAACCAATGATGCTGCTGTTTCCGAA
1 GAATTGGTAGCTGATGAG-ACCAATGATGCTGCTGTTTCTGAA
2180232 GA
1 GA
2180234 TGCACCTGAA
Statistics
Matches: 112, Mismatches: 15, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
41 1 0.01
42 111 0.99
ACGTcount: A:0.26, C:0.16, G:0.29, T:0.29
Consensus pattern (42 bp):
GAATTGGTAGCTGATGAGACCAATGATGCTGCTGTTTCTGAA
Found at i:2182769 original size:16 final size:16
Alignment explanation
Indices: 2182748--2182781 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2182738 GGCAACTGAT
*
2182748 AAGGATCATAACCTTC
1 AAGGATCATAACATTC
*
2182764 AAGGATCGTAACATTC
1 AAGGATCATAACATTC
2182780 AA
1 AA
2182782 ATTTTCTAGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.41, C:0.21, G:0.15, T:0.24
Consensus pattern (16 bp):
AAGGATCATAACATTC
Found at i:2197041 original size:18 final size:19
Alignment explanation
Indices: 2197018--2197053 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
2197008 TTTTCTTTAA
2197018 TTTTTTAGATTTT-AATAT
1 TTTTTTAGATTTTCAATAT
*
2197036 TTTTTTATATTTTCAATA
1 TTTTTTAGATTTTCAATA
2197054 AATTTTTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.67
Consensus pattern (19 bp):
TTTTTTAGATTTTCAATAT
Found at i:2197059 original size:19 final size:18
Alignment explanation
Indices: 2196978--2197061 Score: 51
Period size: 19 Copynumber: 4.3 Consensus size: 18
2196968 TTTTAAATGT
*
2196978 TTTTTATATTTTTATGAACA
1 TTTTTATATTTTAAT-AA-A
** *
2196998 TTTTTAATAATTTTCTTTAAT
1 TTTTT-AT-ATTTT-AATAAA
* **
2197019 TTTTTAGATTTTAATATT
1 TTTTTATATTTTAATAAA
2197037 TTTTTATATTTTCAATAAA
1 TTTTTATATTTT-AATAAA
2197056 TTTTTA
1 TTTTTA
2197062 AAAGTTTTCT
Statistics
Matches: 51, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
18 14 0.27
19 15 0.29
20 6 0.12
21 7 0.14
22 7 0.14
23 2 0.04
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.64
Consensus pattern (18 bp):
TTTTTATATTTTAATAAA
Found at i:2207028 original size:3 final size:3
Alignment explanation
Indices: 2207020--2207135 Score: 106
Period size: 3 Copynumber: 38.7 Consensus size: 3
2207010 GCAGATAGTG
* * *
2207020 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA AAA GAA AAA GAA GGA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
* * * * * * * * * *
2207068 GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
*
2207116 GAA GAA GAA GAA GCA GAA GA
1 GAA GAA GAA GAA GAA GAA GA
2207136 CTGGTGTTTT
Statistics
Matches: 105, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 105 1.00
ACGTcount: A:0.58, C:0.01, G:0.41, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:2207459 original size:14 final size:14
Alignment explanation
Indices: 2207436--2207465 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2207426 AAAGAAGATT
*
2207436 AAAGGTAAAGGAAA
1 AAAGGAAAAGGAAA
2207450 AAAGGAAAAGGAAA
1 AAAGGAAAAGGAAA
2207464 AA
1 AA
2207466 GAAAAACAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.70, C:0.00, G:0.27, T:0.03
Consensus pattern (14 bp):
AAAGGAAAAGGAAA
Found at i:2212537 original size:12 final size:12
Alignment explanation
Indices: 2212520--2212545 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2212510 TGGTGACTTG
2212520 ACCGGTTTAATC
1 ACCGGTTTAATC
2212532 ACCGGTTTAATC
1 ACCGGTTTAATC
2212544 AC
1 AC
2212546 TTGTATGGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.31
Consensus pattern (12 bp):
ACCGGTTTAATC
Found at i:2218404 original size:18 final size:18
Alignment explanation
Indices: 2218378--2218430 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
2218368 GTAAGGGTTA
*
2218378 ATTTTATTTTTTAATATT
1 ATTTAATTTTTTAATATT
2218396 ATTTAATTTTTATAAT-TT
1 ATTTAATTTTT-TAATATT
*
2218414 AATTAATATTTTTAATA
1 ATTTAAT-TTTTTAATA
2218431 ATTTTTTTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
18 22 0.73
19 8 0.27
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
ATTTAATTTTTTAATATT
Found at i:2220411 original size:55 final size:55
Alignment explanation
Indices: 2220327--2220516 Score: 371
Period size: 55 Copynumber: 3.5 Consensus size: 55
2220317 ACATGCATTG
2220327 ATTATTTTTATATTGTTTCATTTAATAAATAGTTCTTTTGAATATTTTTATACAA
1 ATTATTTTTATATTGTTTCATTTAATAAATAGTTCTTTTGAATATTTTTATACAA
2220382 ATTATTTTTATATTGTTTCATTTAATAAATAGTTCTTTTGAATATTTTTATACAA
1 ATTATTTTTATATTGTTTCATTTAATAAATAGTTCTTTTGAATATTTTTATACAA
2220437 ATTATTTTTATATTGTTTCATTTAATAAATAGTTCTTTTGAATATTTTTATACAA
1 ATTATTTTTATATTGTTTCATTTAATAAATAGTTCTTTTGAATATTTTTATACAA
*
2220492 ATTACTTTTATATTGTTTCATTTAA
1 ATTATTTTTATATTGTTTCATTTAA
2220517 CAAAATAGAA
Statistics
Matches: 134, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
55 134 1.00
ACGTcount: A:0.32, C:0.06, G:0.05, T:0.57
Consensus pattern (55 bp):
ATTATTTTTATATTGTTTCATTTAATAAATAGTTCTTTTGAATATTTTTATACAA
Found at i:2224004 original size:63 final size:63
Alignment explanation
Indices: 2223936--2224135 Score: 346
Period size: 63 Copynumber: 3.2 Consensus size: 63
2223926 ATTTGGGATT
2223936 ATCTTCCTTTCTATCAACAACATTATAAATGTAAATACTTGCAGAATTCAACTAAAATTTATG
1 ATCTTCCTTTCTATCAACAACATTATAAATGTAAATACTTGCAGAATTCAACTAAAATTTATG
* * *
2223999 ATCTTCCTTTCTATCAGCAACACTATAAATGTAAATACTGGCAGAATTCAACTAAAATTTATG
1 ATCTTCCTTTCTATCAACAACATTATAAATGTAAATACTTGCAGAATTCAACTAAAATTTATG
* * *
2224062 ATCTTCCTTTCTATCAAGATCATTATAAATGTAAATACTTGCAGAATTCAAATAAAATTTATG
1 ATCTTCCTTTCTATCAACAACATTATAAATGTAAATACTTGCAGAATTCAACTAAAATTTATG
2224125 ATCTTCCTTTC
1 ATCTTCCTTTC
2224136 AAACTACAAT
Statistics
Matches: 128, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
63 128 1.00
ACGTcount: A:0.38, C:0.18, G:0.07, T:0.37
Consensus pattern (63 bp):
ATCTTCCTTTCTATCAACAACATTATAAATGTAAATACTTGCAGAATTCAACTAAAATTTATG
Found at i:2232914 original size:84 final size:83
Alignment explanation
Indices: 2232773--2232940 Score: 318
Period size: 84 Copynumber: 2.0 Consensus size: 83
2232763 AGGCATCTTT
*
2232773 ATACAAGATAAAAGCACCTAGTAGATATCTTTACAGGTGAAGTATACAAATCATTGCAAGAAGAA
1 ATACAAGATAAAAGCACCTAGTACATATCTTTACAGGTGAAGTATACAAATCATTGCAAGAAG-A
2232838 AAAAAAAACCTTTCTTAAG
65 AAAAAAAACCTTTCTTAAG
2232857 ATACAAGATAAAAGCACCTAGTACATATCTTTACAGGTGAAGTATACAAATCATTGCAAGAAGAA
1 ATACAAGATAAAAGCACCTAGTACATATCTTTACAGGTGAAGTATACAAATCATTGCAAGAAGAA
2232922 AAAAAAACCTTTCTTAAG
66 AAAAAAACCTTTCTTAAG
2232940 A
1 A
2232941 AGAAAGCCAC
Statistics
Matches: 83, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
83 21 0.25
84 62 0.75
ACGTcount: A:0.48, C:0.15, G:0.14, T:0.24
Consensus pattern (83 bp):
ATACAAGATAAAAGCACCTAGTACATATCTTTACAGGTGAAGTATACAAATCATTGCAAGAAGAA
AAAAAAACCTTTCTTAAG
Found at i:2238947 original size:22 final size:22
Alignment explanation
Indices: 2238912--2238956 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 22
2238902 TTTGTGAGAA
2238912 AAAAGGAGGGGGGGGGGGGGGG
1 AAAAGGAGGGGGGGGGGGGGGG
*
2238934 NAAAAGGGGGGGGGGGGGGGGGG
1 -AAAAGGAGGGGGGGGGGGGGGG
2238957 CAGCTTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.20, C:0.00, G:0.78, T:0.00
Consensus pattern (22 bp):
AAAAGGAGGGGGGGGGGGGGGG
Found at i:2241716 original size:59 final size:57
Alignment explanation
Indices: 2241613--2241732 Score: 179
Period size: 59 Copynumber: 2.1 Consensus size: 57
2241603 TTTTTAGAAC
2241613 AATAAAATTTAATTATACCATTTAATAAAAAATCATTTAATTTTTA-ATAAAATTTT
1 AATAAAATTTAATTATACCATTTAATAAAAAATCATTTAATTTTTATATAAAATTTT
* * *
2241669 AATAAACATTTAATTCTATCATTTTAATAAAAAATTCATTTAATTTTTATATAAACTTTT
1 AATAAA-ATTTAATTATACCA-TTTAATAAAAAA-TCATTTAATTTTTATATAAAATTTT
2241729 AATA
1 AATA
2241733 TGGAAAAGGT
Statistics
Matches: 57, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
56 6 0.11
57 12 0.21
58 12 0.21
59 14 0.25
60 13 0.23
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.46
Consensus pattern (57 bp):
AATAAAATTTAATTATACCATTTAATAAAAAATCATTTAATTTTTATATAAAATTTT
Found at i:2242197 original size:5 final size:6
Alignment explanation
Indices: 2242181--2242205 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
2242171 GCCGTCTCTT
2242181 TAAAAA TAAAAA TAAAAA TAAAAA T
1 TAAAAA TAAAAA TAAAAA TAAAAA T
2242206 CATTCTCTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (6 bp):
TAAAAA
Found at i:2242860 original size:1 final size:1
Alignment explanation
Indices: 2242854--2242888 Score: 70
Period size: 1 Copynumber: 35.0 Consensus size: 1
2242844 AGTAATGCTG
2242854 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
2242889 ACTTTTATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:2244814 original size:23 final size:24
Alignment explanation
Indices: 2244786--2244832 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
2244776 TTTAGGCTTG
2244786 GTTCATTTA-ATGTTTGTGAACAT
1 GTTCATTTATATGTTTGTGAACAT
2244809 GTTCATTTATATGTTTGTGAACAT
1 GTTCATTTATATGTTTGTGAACAT
2244833 TAAGCGAACC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 9 0.39
24 14 0.61
ACGTcount: A:0.26, C:0.09, G:0.17, T:0.49
Consensus pattern (24 bp):
GTTCATTTATATGTTTGTGAACAT
Found at i:2247077 original size:11 final size:11
Alignment explanation
Indices: 2247061--2247088 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
2247051 TGTGTGGGTA
2247061 TGTTTTTGATC
1 TGTTTTTGATC
2247072 TGTTTTTGATC
1 TGTTTTTGATC
2247083 TGTTTT
1 TGTTTT
2247089 AGAGTATTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.07, C:0.07, G:0.18, T:0.68
Consensus pattern (11 bp):
TGTTTTTGATC
Found at i:2261383 original size:31 final size:32
Alignment explanation
Indices: 2261348--2261407 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 32
2261338 AAAATTTAGG
*
2261348 ATTAAT-ATATAATTTGGTATTT-AATTTTATT
1 ATTAATAAT-TAATTAGGTATTTGAATTTTATT
2261379 ATTAATAATTAATTAGGTATTTGAATTTT
1 ATTAATAATTAATTAGGTATTTGAATTTT
2261408 TTTTCTTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
31 18 0.69
32 8 0.31
ACGTcount: A:0.37, C:0.00, G:0.08, T:0.55
Consensus pattern (32 bp):
ATTAATAATTAATTAGGTATTTGAATTTTATT
Found at i:2263606 original size:18 final size:18
Alignment explanation
Indices: 2263566--2263600 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2263556 CCAGGTGCGT
*
2263566 ATCCTAGCCCTTATATGC
1 ATCCTAACCCTTATATGC
2263584 ATCCTAACCCTTATATG
1 ATCCTAACCCTTATATG
2263601 TTTCCTTTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.31, G:0.09, T:0.34
Consensus pattern (18 bp):
ATCCTAACCCTTATATGC
Found at i:2266525 original size:125 final size:125
Alignment explanation
Indices: 2266099--2266993 Score: 1128
Period size: 125 Copynumber: 7.1 Consensus size: 125
2266089 AGGCCAAACA
* * * * * *
2266099 AGAACTACTGTAGAAAAAGAGCGTTCATGTGGGAGCTTTTTTTAGTAATTTTGTTGACAGCGTAT
1 AGAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGCAT
* * * *
2266164 CTTGCTTGAAGCGTTTTTGACACTATTTTTTTAGAA-CTTTCTTCTCAAAATTATTTTTTC
66 CCTGCTTGAAGCGTTTTTGACATTATTTTTTCAGAATC-GTCTTCTCAAAATTATTTTTTC
* * * *
2266224 AAGAACTACTGTAGAGAAAGAGCATCCACGTGGGAGCTTTTTTCAGTAATTTTACTGACAATGCA
1 -AGAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGCA
* * * * * *
2266289 TTCTGCTTGAAGAGTTTTTGACACTATTTTTTCAGAACCGTCTTCTC--AAGTGTTTTTTC
65 TCCTGCTTGAAGCGTTTTTGACATTATTTTTTCAGAATCGTCTTCTCAAAATTATTTTTTC
* * *
2266348 AGAAACTACTTTAGAAAAAGAGCGTCGACGTGAGAG-TTTTTTCAGTAATTTTGCTGACAGTGCA
1 AG-AACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGCA
*
2266412 TCCTGCTTGAAGCGTTTTTGACATTATTTTTTCAGAATGGTCTTCTCAAAATTATTTTTTC
65 TCCTGCTTGAAGCGTTTTTGACATTATTTTTTCAGAATCGTCTTCTCAAAATTATTTTTTC
*
2266473 GAGAACTACTATAGAAAAAGAGCGTCCACGTGGGAG-TTTTTTCAGTAATTTTGCTGACAGTGCA
1 -AGAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGCA
* * *
2266537 TCCTGCTTGAAGCATTTTTTACATT-TTTTTT-AGAATCTTCTTCTCAAAATTATTTTTTC
65 TCCTGCTTGAAGCGTTTTTGACATTATTTTTTCAGAATCGTCTTCTCAAAATTATTTTTTC
* * *
2266596 AGGAATTACTGTAGAAAAAGAGCATCCACGTGGGAGCTTTTTTCAGTAATTTTGCTGACAGTTCA
1 A-GAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGCA
* * * * *
2266661 TCATGCTTGAAACATTTTTGAAACGATT-TTTTTTCA-AAACTTTCTTCTCAAAATTATTTTTTC
65 TCCTGCTTGAAGCGTTTTTG--AC-ATTATTTTTTCAGAATC-GTCTTCTCAAAATTATTTTTTC
*
2266724 AGGAACTACTGTAGAAAAAGAGCGTCCAAGTGGGAGCTTTTTTCAGTAATTTTGCTGACA-TGCA
1 A-GAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGCA
* * * * * *
2266788 TCCTGGTTGAAGTGTTTTTAAAACTATTTTTAT-AGAATCGTCTTTTCAAAATTATTTTTTC
65 TCCTGCTTGAAGCGTTTTTGACATTATTTTT-TCAGAATCGTCTTCTCAAAATTATTTTTTC
* * * *
2266849 AAGAACTACTGTAAAAAAAGAGCATCCACGTGAGAGCTTTTTTCAGTAATTTTGCTGACAGTTCA
1 -AGAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGCA
* * * *
2266914 TCCTGCTTGAAGCATTTTTGACATTATCTTTTCAGAATCGTTTTCTCAAAATTAATTTTTC
65 TCCTGCTTGAAGCGTTTTTGACATTATTTTTTCAGAATCGTCTTCTCAAAATTATTTTTTC
*
2266975 TGAAACTACTGTAGAAAAA
1 AG-AACTACTGTAGAAAAA
2266994 AAATAAAATC
Statistics
Matches: 672, Mismatches: 78, Indels: 38
0.85 0.10 0.05
Matches are distributed among these distances:
122 1 0.00
123 127 0.19
124 90 0.13
125 174 0.26
126 170 0.25
127 30 0.04
128 80 0.12
ACGTcount: A:0.28, C:0.16, G:0.17, T:0.39
Consensus pattern (125 bp):
AGAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGCAT
CCTGCTTGAAGCGTTTTTGACATTATTTTTTCAGAATCGTCTTCTCAAAATTATTTTTTC
Found at i:2266639 original size:249 final size:250
Alignment explanation
Indices: 2266100--2266993 Score: 1153
Period size: 249 Copynumber: 3.6 Consensus size: 250
2266090 GGCCAAACAA
* * * * * * * *
2266100 GAACTACTGTAGAAAAAGAGCGTTCATGTGGGAGCTTTTTTTAGTAATTTTGTTGACAGCGTATC
1 GAACTACTGTAGAAAAAGAGCATCCACGTGAGAGCTTTTTTCAGTAATTTTGCTGACAGTGCATC
* * * * * *
2266165 TTGCTTGAAGCGTTTTTGACACTATTTTTTTAGAACTTTCTTCTCAAAATTATTTTTTCAAGAAC
66 CTGCTTGAAGCATTTTTGACATTATTTTTTCAGAACTGTCTTCTCAAAATTATTTTTTCGAGAAC
* * * *
2266230 TACTGTAGAGAAAGAGCATCCACGTGGGAGCTTTTTTCAGTAATTTTACTGACAATGCATTCTGC
131 TACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGTAATTTTGCTGAC-ATGCATCCTGC
* * * * *
2266295 TTGAAGAGTTTTTGACACTATTTTTTCAGAACCGTCTTCTC--AAGTGTTTTTTCAG
195 TTGAAGA-TTTTTAACACTATTTTTTTAGAATCGTCTTCTCAAAATTATTTTTTCAG
* * * *
2266350 AAACTACTTTAGAAAAAGAGCGTCGACGTGAGAG-TTTTTTCAGTAATTTTGCTGACAGTGCATC
1 GAACTACTGTAGAAAAAGAGCATCCACGTGAGAGCTTTTTTCAGTAATTTTGCTGACAGTGCATC
*
2266414 CTGCTTGAAGCGTTTTTGACATTATTTTTTCAGAA-TGGTCTTCTCAAAATTATTTTTTCGAGAA
66 CTGCTTGAAGCATTTTTGACATTATTTTTTCAGAACT-GTCTTCTCAAAATTATTTTTTCGAGAA
*
2266478 CTACTATAGAAAAAGAGCGTCCACGTGGGAG-TTTTTTCAGTAATTTTGCTGACAGTGCATCCTG
130 CTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGTAATTTTGCTGACA-TGCATCCTG
* *
2266542 CTTGAAGCATTTTTTACA-T-TTTTTTTAGAATCTTCTTCTCAAAATTATTTTTTCAG
194 CTTGAAG-ATTTTTAACACTATTTTTTTAGAATCGTCTTCTCAAAATTATTTTTTCAG
* * *
2266598 GAATTACTGTAGAAAAAGAGCATCCACGTGGGAGCTTTTTTCAGTAATTTTGCTGACAGTTCATC
1 GAACTACTGTAGAAAAAGAGCATCCACGTGAGAGCTTTTTTCAGTAATTTTGCTGACAGTGCATC
* * * *
2266663 ATGCTTGAAACATTTTTGAAACGATT-TTTTTTCAAAACTTTCTTCTCAAAATTATTTTTTC-AG
66 CTGCTTGAAGCATTTTTG--AC-ATTATTTTTTCAGAACTGTCTTCTCAAAATTATTTTTTCGA-
*
2266726 GAACTACTGTAGAAAAAGAGCGTCCAAGTGGGAGCTTTTTTCAGTAATTTTGCTGACATGCATCC
127 GAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGTAATTTTGCTGACATGCATCC
* * * * * *
2266791 TGGTTGAAGTGTTTTTAAAACTATTTTTATAGAATCGTCTTTTCAAAATTATTTTTTCAA
192 TGCTTGAAG-ATTTTTAACACTATTTTTTTAGAATCGTCTTCTCAAAATTATTTTTTCAG
* *
2266851 GAACTACTGTAAAAAAAGAGCATCCACGTGAGAGCTTTTTTCAGTAATTTTGCTGACAGTTCATC
1 GAACTACTGTAGAAAAAGAGCATCCACGTGAGAGCTTTTTTCAGTAATTTTGCTGACAGTGCATC
* * *
2266916 CTGCTTGAAGCATTTTTGACATTATCTTTTCAGAA-TCGTTTTCTCAAAATTAATTTTTCTGA-A
66 CTGCTTGAAGCATTTTTGACATTATTTTTTCAGAACT-GTCTTCTCAAAATTATTTTTTC-GAGA
2266979 ACTACTGTAGAAAAA
129 ACTACTGTAGAAAAA
2266994 AAATAAAATC
Statistics
Matches: 567, Mismatches: 59, Indels: 35
0.86 0.09 0.05
Matches are distributed among these distances:
246 18 0.03
247 2 0.00
248 85 0.15
249 156 0.28
250 33 0.06
251 133 0.23
252 28 0.05
253 112 0.20
ACGTcount: A:0.28, C:0.16, G:0.17, T:0.39
Consensus pattern (250 bp):
GAACTACTGTAGAAAAAGAGCATCCACGTGAGAGCTTTTTTCAGTAATTTTGCTGACAGTGCATC
CTGCTTGAAGCATTTTTGACATTATTTTTTCAGAACTGTCTTCTCAAAATTATTTTTTCGAGAAC
TACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGTAATTTTGCTGACATGCATCCTGCT
TGAAGATTTTTAACACTATTTTTTTAGAATCGTCTTCTCAAAATTATTTTTTCAG
Found at i:2267095 original size:34 final size:33
Alignment explanation
Indices: 2267054--2267173 Score: 132
Period size: 34 Copynumber: 3.6 Consensus size: 33
2267044 CACAAAATTA
* *
2267054 TTTTTAAAAAAACTAAACCCTAATTTAACTAAT
1 TTTTTAAAAACACTAAACCCTAATTTAATTAAT
**
2267087 TTTCTTAAAAACTTTAAACCCTAATTTAATTAAT
1 TTT-TTAAAAACACTAAACCCTAATTTAATTAAT
* * *
2267121 TTATTTAAAACCCCTAAAACCTAATTTAATTAAT
1 TT-TTTAAAAACACTAAACCCTAATTTAATTAAT
* * *
2267155 TTTTTTAAAGCTCTAAACC
1 TTTTTAAAAACACTAAACC
2267174 TTTATTTGTT
Statistics
Matches: 73, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
33 16 0.22
34 56 0.77
35 1 0.01
ACGTcount: A:0.42, C:0.17, G:0.01, T:0.40
Consensus pattern (33 bp):
TTTTTAAAAACACTAAACCCTAATTTAATTAAT
Found at i:2272613 original size:99 final size:100
Alignment explanation
Indices: 2272441--2272652 Score: 392
Period size: 99 Copynumber: 2.1 Consensus size: 100
2272431 ATTGTAAATA
*
2272441 ATATAAATACTT-TTAAAAATAAATAATAATATTAATTATGTTTAACTTTTAAATTGACCTATAG
1 ATATAAATA-TTAATAAAAATAAATAATAATATTAATTATGTTTAACTTTTAAATTGACCTATAG
2272505 TGTAATTTACCTTATAATCAATGAGAGAATTAGGAG
65 TGTAATTTACCTTATAATCAATGAGAGAATTAGGAG
2272541 ATATAAATATTAATAAAAATAAA-AATAATATTAATTATGTTTAACTTTTAAATTGACCTATAGT
1 ATATAAATATTAATAAAAATAAATAATAATATTAATTATGTTTAACTTTTAAATTGACCTATAGT
2272605 GTAATTTACCTTATAATCAATGAGAGAATTAGGAG
66 GTAATTTACCTTATAATCAATGAGAGAATTAGGAG
2272640 ATATAAATATTAA
1 ATATAAATATTAA
2272653 ATATATATTT
Statistics
Matches: 110, Mismatches: 1, Indels: 3
0.96 0.01 0.03
Matches are distributed among these distances:
99 91 0.83
100 19 0.17
ACGTcount: A:0.46, C:0.06, G:0.09, T:0.38
Consensus pattern (100 bp):
ATATAAATATTAATAAAAATAAATAATAATATTAATTATGTTTAACTTTTAAATTGACCTATAGT
GTAATTTACCTTATAATCAATGAGAGAATTAGGAG
Found at i:2273440 original size:20 final size:20
Alignment explanation
Indices: 2273415--2273452 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2273405 CTTGAGTCAA
2273415 GACTAAAATTGACCAAATGG
1 GACTAAAATTGACCAAATGG
*
2273435 GACTAAAATTGATCAAAT
1 GACTAAAATTGACCAAAT
2273453 TAAAGTACAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.47, C:0.13, G:0.16, T:0.24
Consensus pattern (20 bp):
GACTAAAATTGACCAAATGG
Found at i:2274061 original size:21 final size:22
Alignment explanation
Indices: 2274026--2274066 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
2274016 CCAAACTAGT
2274026 AACATGTGACCCCGAACCCTTG
1 AACATGTGACCCCGAACCCTTG
*
2274048 AACAT-TGAGCCCGAACCCT
1 AACATGTGACCCCGAACCCT
2274067 AAATCCCGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.29, C:0.37, G:0.17, T:0.17
Consensus pattern (22 bp):
AACATGTGACCCCGAACCCTTG
Found at i:2274172 original size:20 final size:19
Alignment explanation
Indices: 2274110--2274173 Score: 56
Period size: 20 Copynumber: 3.2 Consensus size: 19
2274100 CCTAAACATG
*
2274110 AACCTTGAATCTCGAACCCA
1 AACCTTAAATCT-GAACCCA
** * *
2274130 AACCCCAAATCAGAACCTTA
1 AACCTTAAATCTGAACC-CA
2274150 AACCTTAAATTCTGAACCCA
1 AACCTTAAA-TCTGAACCCA
2274170 AACC
1 AACC
2274174 CTGAACCTCG
Statistics
Matches: 33, Mismatches: 9, Indels: 4
0.72 0.20 0.09
Matches are distributed among these distances:
19 5 0.15
20 21 0.64
21 7 0.21
ACGTcount: A:0.41, C:0.34, G:0.06, T:0.19
Consensus pattern (19 bp):
AACCTTAAATCTGAACCCA
Found at i:2276654 original size:22 final size:21
Alignment explanation
Indices: 2276598--2276654 Score: 60
Period size: 22 Copynumber: 2.7 Consensus size: 21
2276588 TAGAATTTCG
2276598 ATAAATATTATATTAAGATTT
1 ATAAATATTATATTAAGATTT
* * * *
2276619 TTAAATTTTTTATTATGAATTT
1 ATAAATATTATATTAAG-ATTT
*
2276641 ATAAATATAATATT
1 ATAAATATTATATT
2276655 TACCACACCT
Statistics
Matches: 27, Mismatches: 8, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
21 13 0.48
22 14 0.52
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.53
Consensus pattern (21 bp):
ATAAATATTATATTAAGATTT
Found at i:2282223 original size:22 final size:22
Alignment explanation
Indices: 2282180--2282223 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
2282170 GTGAAACATT
*
2282180 TAAAATAAATAATATATGTAAA
1 TAAAATAAATAATATATATAAA
*
2282202 TAAAATACATAATA-ATAATAAA
1 TAAAATAAATAATATAT-ATAAA
2282224 AGAAGAGCCC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 2 0.11
22 17 0.89
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (22 bp):
TAAAATAAATAATATATATAAA
Found at i:2282317 original size:16 final size:18
Alignment explanation
Indices: 2282296--2282330 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2282286 ACTAATTAAA
2282296 TGAAAT-AGG-ACAAAAT
1 TGAAATCAGGCACAAAAT
2282312 TGAAATCAGGCACAAAAT
1 TGAAATCAGGCACAAAAT
2282330 T
1 T
2282331 CGGGGTTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.35
17 3 0.18
18 8 0.47
ACGTcount: A:0.51, C:0.11, G:0.17, T:0.20
Consensus pattern (18 bp):
TGAAATCAGGCACAAAAT
Found at i:2290960 original size:50 final size:49
Alignment explanation
Indices: 2290886--2290980 Score: 163
Period size: 50 Copynumber: 1.9 Consensus size: 49
2290876 GTGATCTCTA
* *
2290886 ATCATGTTTTTTTTTTCATCTCATAAATCTGAACCACTATTTTCCCCTG
1 ATCATGTTTTTTTTTCCATCTCATAAATCTGAACCAATATTTTCCCCTG
2290935 ATCATGTTATTTTTTTCCATCTCATAAATCTGAACCAATATTTTCC
1 ATCATGTT-TTTTTTTCCATCTCATAAATCTGAACCAATATTTTCC
2290981 TATTTTTCTC
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
49 8 0.19
50 35 0.81
ACGTcount: A:0.25, C:0.23, G:0.05, T:0.46
Consensus pattern (49 bp):
ATCATGTTTTTTTTTCCATCTCATAAATCTGAACCAATATTTTCCCCTG
Found at i:2313093 original size:14 final size:15
Alignment explanation
Indices: 2313074--2313104 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
2313064 GTTGAATCTG
2313074 AAAACAAATCA-AAA
1 AAAACAAATCAGAAA
2313088 AAAACAAATCAGAAA
1 AAAACAAATCAGAAA
2313103 AA
1 AA
2313105 TAATAAATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.69
15 5 0.31
ACGTcount: A:0.77, C:0.13, G:0.03, T:0.06
Consensus pattern (15 bp):
AAAACAAATCAGAAA
Found at i:2313832 original size:18 final size:18
Alignment explanation
Indices: 2313809--2313843 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2313799 TATTTTTATG
*
2313809 TATTACAAATTATATATT
1 TATTACAAATTAAATATT
2313827 TATTACAAATTAAATAT
1 TATTACAAATTAAATAT
2313844 ATAAACATAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.46
Consensus pattern (18 bp):
TATTACAAATTAAATATT
Found at i:2320706 original size:15 final size:16
Alignment explanation
Indices: 2320681--2320710 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2320671 TAAATAAGAA
2320681 AAAAAATATTTAAATG
1 AAAAAATATTTAAATG
2320697 AAAAAA-ATTTAAAT
1 AAAAAATATTTAAAT
2320711 TCCTAATATA
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:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (16 bp):
AAAAAATATTTAAATG
Found at i:2321477 original size:24 final size:24
Alignment explanation
Indices: 2321434--2321482 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
2321424 CTATGAAATT
* *
2321434 AAATAATTTATTATAGATTTTAAA
1 AAATAATTTATTATAAATTTGAAA
* *
2321458 AAATCATTTATTTTAAATTTGAAA
1 AAATAATTTATTATAAATTTGAAA
2321482 A
1 A
2321483 GTAAATATTG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.45
Consensus pattern (24 bp):
AAATAATTTATTATAAATTTGAAA
Found at i:2324003 original size:18 final size:18
Alignment explanation
Indices: 2323980--2324015 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
2323970 TTCTTATTTA
2323980 TTTTATA-ATTTTCAATAT
1 TTTTATAGATTTT-AATAT
2323998 TTTTATAGATTTTAATAT
1 TTTTATAGATTTTAATAT
2324016 ATGTAAGAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.61
Consensus pattern (18 bp):
TTTTATAGATTTTAATAT
Found at i:2324295 original size:21 final size:20
Alignment explanation
Indices: 2324264--2324350 Score: 60
Period size: 17 Copynumber: 4.5 Consensus size: 20
2324254 TGTCTTTACC
2324264 TATTAAAAATTTATATTAAGTA
1 TATT-AAAATTTATATTAA-TA
2324286 TATTAAAATTT-TA--AATA
1 TATTAAAATTTATATTAATA
* **
2324303 TGTTAAAAAATATATTAAATA
1 TATTAAAATTTATATT-AATA
*
2324324 TATT-AAA--TATATTAAAA
1 TATTAAAATTTATATTAATA
*
2324341 TTTTAAAATT
1 TATTAAAATT
2324351 AATTATACTT
Statistics
Matches: 52, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
17 16 0.31
18 13 0.25
20 5 0.10
21 14 0.27
22 4 0.08
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (20 bp):
TATTAAAATTTATATTAATA
Found at i:2324308 original size:9 final size:9
Alignment explanation
Indices: 2324275--2324339 Score: 69
Period size: 9 Copynumber: 7.0 Consensus size: 9
2324265 ATTAAAAATT
*
2324275 TATATTAAG
1 TATATTAAA
2324284 TATATTAAA
1 TATATTAAA
*
2324293 -ATTTTAAA
1 TATATTAAA
*
2324301 TATGTTAAAAAA
1 TATATT---AAA
2324313 TATATTAAA
1 TATATTAAA
2324322 TATATTAAA
1 TATATTAAA
2324331 TATATTAAA
1 TATATTAAA
2324340 ATTTTAAAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
8 7 0.15
9 33 0.69
12 8 0.17
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (9 bp):
TATATTAAA
Found at i:2324326 original size:38 final size:39
Alignment explanation
Indices: 2324266--2324348 Score: 107
Period size: 38 Copynumber: 2.2 Consensus size: 39
2324256 TCTTTACCTA
* * *
2324266 TTAAAAATTTATATTAAGTATATTAAA-ATTTTAAATATG
1 TTAAAAATATATATTAAATATATTAAATATATTAAA-ATG
*
2324305 TTAAAAA-ATATATTAAATATATTAAATATATTAAAATT
1 TTAAAAATATATATTAAATATATTAAATATATTAAAATG
2324343 TTAAAA
1 TTAAAA
2324349 TTAATTATAC
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
38 25 0.64
39 14 0.36
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.43
Consensus pattern (39 bp):
TTAAAAATATATATTAAATATATTAAATATATTAAAATG
Found at i:2324332 original size:30 final size:29
Alignment explanation
Indices: 2324284--2324340 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 29
2324274 TTATATTAAG
* *
2324284 TATATTAAAATTTTAAATATGTTAAAAAA
1 TATATTAAAATATTAAATATATTAAAAAA
2324313 TATATTAAATATATTAAATATATTAAAA
1 TATATTAAA-ATATTAAATATATTAAAA
2324341 TTTTAAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 9 0.36
30 16 0.64
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (29 bp):
TATATTAAAATATTAAATATATTAAAAAA
Found at i:2324349 original size:18 final size:19
Alignment explanation
Indices: 2324275--2324349 Score: 77
Period size: 18 Copynumber: 4.1 Consensus size: 19
2324265 ATTAAAAATT
*
2324275 TATATTAAGTATATTAAAA
1 TATATTAAATATATTAAAA
*
2324294 T-T-TTAAATATGTTAAAAAA
1 TATATTAAATATATT--AAAA
2324313 TATATTAAATATATT-AAA
1 TATATTAAATATATTAAAA
*
2324331 TATATTAAA-ATTTTAAAA
1 TATATTAAATATATTAAAA
2324349 T
1 T
2324350 TAATTATACT
Statistics
Matches: 47, Mismatches: 4, Indels: 11
0.76 0.06 0.18
Matches are distributed among these distances:
17 13 0.28
18 17 0.36
19 6 0.13
20 1 0.02
21 10 0.21
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (19 bp):
TATATTAAATATATTAAAA
Found at i:2324620 original size:99 final size:97
Alignment explanation
Indices: 2324438--2324628 Score: 301
Period size: 99 Copynumber: 1.9 Consensus size: 97
2324428 GGTGGCGCCG
2324438 ATTTATTTAGCTCCAACAGAAAATGGAAATTTTTTGTAAAGTCTCCCCTTTTTTCAAAAATTATA
1 ATTTATTTAGCTCCAACAGAAAATGGAAATTTTTTGTAAAGTCTCCCCTTTTTTCAAAAATTATA
*
2324503 GTATTTCCTTGATATTTATACAGGTGGTGTCA
66 GTATTTCCTTAATATTTATACAGGTGGTGTCA
* * * * *
2324535 ATTTATTTCGCTCCACCAGAAAATGGAAAATTTTTTTTTAAGTCTCCCCATTTTTTCAGAAATTA
1 ATTTATTTAGCTCCAACAGAAAATGG-AAATTTTTTGTAAAGTCTCCCC-TTTTTTCAAAAATTA
*
2324600 TAGTATTTCTTTAATATTTATACAGGTGG
64 TAGTATTTCCTTAATATTTATACAGGTGG
2324629 CGCCATTCTA
Statistics
Matches: 85, Mismatches: 7, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
97 24 0.28
98 20 0.24
99 41 0.48
ACGTcount: A:0.30, C:0.15, G:0.13, T:0.42
Consensus pattern (97 bp):
ATTTATTTAGCTCCAACAGAAAATGGAAATTTTTTGTAAAGTCTCCCCTTTTTTCAAAAATTATA
GTATTTCCTTAATATTTATACAGGTGGTGTCA
Found at i:2324648 original size:99 final size:97
Alignment explanation
Indices: 2324428--2324657 Score: 293
Period size: 99 Copynumber: 2.4 Consensus size: 97
2324418 GTTGGAAACT
* * * * *
2324428 GGTGGCGCCGATTTATTTAGCTCCAACAGAAAATGGAAATTTTTTGTAAAGTCTCCCCTTTTTTC
1 GGTGGCGTCAATTTATATCGCTCCACCAGAAAATGGAAATTTTTTGTAAAGTCTCCCCTTTTTTC
*
2324493 AAAAATTATAGTATTTCCTTGATATTTATACA
66 AAAAATTATAGTATTTCCTTAATATTTATACA
* * * *
2324525 GGTGGTGTCAATTTATTTCGCTCCACCAGAAAATGGAAAATTTTTTTTTAAGTCTCCCCATTTTT
1 GGTGGCGTCAATTTATATCGCTCCACCAGAAAATGG-AAATTTTTTGTAAAGTCTCCCC-TTTTT
* *
2324590 TCAGAAATTATAGTATTTCTTTAATATTTATACA
64 TCAAAAATTATAGTATTTCCTTAATATTTATACA
*
2324624 GGTGGCG-CCATTCTATAT-GACTCCACCAGAAAAT
1 GGTGGCGTCAATT-TATATCG-CTCCACCAGAAAAT
2324658 CGATTTTTTT
Statistics
Matches: 116, Mismatches: 13, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
97 31 0.27
98 25 0.22
99 60 0.52
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.39
Consensus pattern (97 bp):
GGTGGCGTCAATTTATATCGCTCCACCAGAAAATGGAAATTTTTTGTAAAGTCTCCCCTTTTTTC
AAAAATTATAGTATTTCCTTAATATTTATACA
Found at i:2328467 original size:4 final size:4
Alignment explanation
Indices: 2328458--2328498 Score: 82
Period size: 4 Copynumber: 10.2 Consensus size: 4
2328448 ACATATTAAA
2328458 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC A
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC A
2328499 ATAGGACTAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 37 1.00
ACGTcount: A:0.51, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAC
Found at i:2334348 original size:7 final size:7
Alignment explanation
Indices: 2334330--2334359 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
2334320 TAAATAAGAG
2334330 TATTTT-
1 TATTTTA
2334336 TATTTTA
1 TATTTTA
2334343 TATTTTA
1 TATTTTA
2334350 TATTTTA
1 TATTTTA
2334357 TAT
1 TAT
2334360 AAAAGTAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 6 0.26
7 17 0.74
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (7 bp):
TATTTTA
Found at i:2337100 original size:10 final size:10
Alignment explanation
Indices: 2337087--2337120 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
2337077 TATTTAAGTA
2337087 TAATTTTTTT
1 TAATTTTTTT
2337097 TAA--TTTTT
1 TAATTTTTTT
2337105 TAATTTTTTT
1 TAATTTTTTT
2337115 TAATTT
1 TAATTT
2337121 GTTTATAAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
8 8 0.36
10 14 0.64
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (10 bp):
TAATTTTTTT
Found at i:2337110 original size:18 final size:19
Alignment explanation
Indices: 2337087--2337125 Score: 71
Period size: 18 Copynumber: 2.1 Consensus size: 19
2337077 TATTTAAGTA
2337087 TAATTTTTTTTAATTT-TT
1 TAATTTTTTTTAATTTGTT
2337105 TAATTTTTTTTAATTTGTT
1 TAATTTTTTTTAATTTGTT
2337124 TA
1 TA
2337126 TAAACATTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (19 bp):
TAATTTTTTTTAATTTGTT
Found at i:2337547 original size:31 final size:31
Alignment explanation
Indices: 2337496--2337554 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
2337486 TAAAATGGTT
2337496 AAATTTTAATTTAATATTTATA-TTTCACTC
1 AAATTTTAATTTAATATTTATACTTTCACTC
*
2337526 AAATTTTAATTTTAATCTTTATACTTTCA
1 AAATTTTAA-TTTAATATTTATACTTTCA
2337555 TTTTAACATA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 9 0.35
31 12 0.46
32 5 0.19
ACGTcount: A:0.36, C:0.10, G:0.00, T:0.54
Consensus pattern (31 bp):
AAATTTTAATTTAATATTTATACTTTCACTC
Found at i:2343072 original size:34 final size:35
Alignment explanation
Indices: 2343012--2343078 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
2343002 CAAACACCAG
* *
2343012 AAAATATTTTCCAGTAAATTATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
2343047 AAAACATTTTCCCG-AAATCATTTTACAGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
2343079 TATTTTACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.46, C:0.13, G:0.07, T:0.33
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:2344642 original size:25 final size:24
Alignment explanation
Indices: 2344596--2344642 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 24
2344586 CAGGGTAACA
*
2344596 ATTTCTCACATTTCATTTATAAAC
1 ATTTCTCACATTTCATTCATAAAC
2344620 ATTTCTC-CATTTCAAATTCATAA
1 ATTTCTCACATTTC--ATTCATAA
2344643 TCACAATCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.34, C:0.21, G:0.00, T:0.45
Consensus pattern (24 bp):
ATTTCTCACATTTCATTCATAAAC
Found at i:2347025 original size:25 final size:25
Alignment explanation
Indices: 2346991--2347044 Score: 99
Period size: 25 Copynumber: 2.2 Consensus size: 25
2346981 CTACTCGATC
2346991 AAAGCGTTCATCTTAGACGAATAAA
1 AAAGCGTTCATCTTAGACGAATAAA
*
2347016 AAAGTGTTCATCTTAGACGAATAAA
1 AAAGCGTTCATCTTAGACGAATAAA
2347041 AAAG
1 AAAG
2347045 GTACAATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.46, C:0.13, G:0.17, T:0.24
Consensus pattern (25 bp):
AAAGCGTTCATCTTAGACGAATAAA
Found at i:2347370 original size:17 final size:17
Alignment explanation
Indices: 2347331--2347364 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
2347321 ACTTTTTTTA
*
2347331 AAAAAATATATAAAAAT
1 AAAAAATACATAAAAAT
2347348 AAAAAATACATAAAAAT
1 AAAAAATACATAAAAAT
2347365 TCAAAAAAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (17 bp):
AAAAAATACATAAAAAT
Found at i:2354625 original size:21 final size:19
Alignment explanation
Indices: 2354601--2354645 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
2354591 ATGTGATTAG
2354601 TAAAACAACATATAAATATCT
1 TAAAACAA-A-ATAAATATCT
* *
2354622 TAAAATAAAATATATATCT
1 TAAAACAAAATAAATATCT
2354641 TAAAA
1 TAAAA
2354646 TTAAAATACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 14 0.64
20 1 0.05
21 7 0.32
ACGTcount: A:0.60, C:0.09, G:0.00, T:0.31
Consensus pattern (19 bp):
TAAAACAAAATAAATATCT
Found at i:2354640 original size:19 final size:20
Alignment explanation
Indices: 2354616--2354653 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
2354606 CAACATATAA
2354616 ATATCTTAAAA-TAAAATAT
1 ATATCTTAAAATTAAAATAT
2354635 ATATCTTAAAATTAAAATA
1 ATATCTTAAAATTAAAATA
2354654 CAATTATTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (20 bp):
ATATCTTAAAATTAAAATAT
Found at i:2357030 original size:116 final size:119
Alignment explanation
Indices: 2356830--2357058 Score: 333
Period size: 116 Copynumber: 1.9 Consensus size: 119
2356820 GGCAACTTTT
2356830 CTTGGTGGCCATATATTTTTCTTTTTCATACACCATTTGTATATGACGTAAGATCCCAAATTCCC
1 CTTGGTGGCCATATATTTTTCTTTTTCATACACCATTTGTATATGACGTAAGATCCCAAATTCCC
* *
2356895 AAAAGAATGAAAGGGATTT-CC-TAA-TTCTAATCTTTAGATTAATTATAACCTC
66 AAAAGAATAAAAGCGATTTCCCATAAGTT-TAATCTTTAGATTAATTATAACCTC
** *
2356947 CTTGGTGGCCATAT-TCTTTTCTTTTTCATACACCATTT-TATATGATTTAAGATCCCACATTCC
1 CTTGGTGGCCATATAT-TTTTCTTTTTCATACACCATTTGTATATGACGTAAGATCCCAAATTCC
* *
2357010 TAAAAGAATAAAAGCGATTTCCCAATAAGTTTAATCTTTATATTAATTA
65 CAAAAGAATAAAAGCGATTTCCC-ATAAGTTTAATCTTTAGATTAATTA
2357059 GAGTTTCCTT
Statistics
Matches: 100, Mismatches: 7, Indels: 8
0.87 0.06 0.07
Matches are distributed among these distances:
116 40 0.40
117 38 0.38
119 20 0.20
120 2 0.02
ACGTcount: A:0.32, C:0.18, G:0.10, T:0.39
Consensus pattern (119 bp):
CTTGGTGGCCATATATTTTTCTTTTTCATACACCATTTGTATATGACGTAAGATCCCAAATTCCC
AAAAGAATAAAAGCGATTTCCCATAAGTTTAATCTTTAGATTAATTATAACCTC
Found at i:2364033 original size:22 final size:19
Alignment explanation
Indices: 2363974--2364024 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 19
2363964 TTAAAAAAAC
* * *
2363974 AATATTTTTTTATTTTT-T
1 AATAATTTTTAATTTTTAA
2363992 AATAATTTTTAATTTTTAA
1 AATAATTTTTAATTTTTAA
2364011 AATAATTTTATAAT
1 AATAATTTT-TAAT
2364025 GCTTTTAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
18 15 0.54
19 9 0.32
20 4 0.14
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (19 bp):
AATAATTTTTAATTTTTAA
Found at i:2369991 original size:20 final size:22
Alignment explanation
Indices: 2369961--2370005 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
2369951 TTGAATCAAT
2369961 ATAATATATATAATACTAAAAA
1 ATAATATATATAATACTAAAAA
2369983 ATAATATATATAATACTAAAAA
1 ATAATATATATAATACTAAAAA
2370005 A
1 A
2370006 GAACACATGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.31
Consensus pattern (22 bp):
ATAATATATATAATACTAAAAA
Found at i:2384230 original size:32 final size:32
Alignment explanation
Indices: 2384194--2384255 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
2384184 ATATTTTGGT
2384194 TTATACAATTTTT-GATAATTTAATAATTTCTA
1 TTATACAATTTTTAGATAATTT-ATAATTTCTA
* * *
2384226 TTATATAATTTTTAGATTATTTGTAATTTC
1 TTATACAATTTTTAGATAATTTATAATTTC
2384256 AGATCTTATG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
32 19 0.73
33 7 0.27
ACGTcount: A:0.34, C:0.05, G:0.05, T:0.56
Consensus pattern (32 bp):
TTATACAATTTTTAGATAATTTATAATTTCTA
Found at i:2387926 original size:32 final size:32
Alignment explanation
Indices: 2387890--2387951 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
2387880 ATATTTTGAT
2387890 TTATACAATTTTT-GATAATTTAATAATTTCTA
1 TTATACAATTTTTAGATAATTT-ATAATTTCTA
* * *
2387922 TTATATAATTTTTAGATTATTTGTAATTTC
1 TTATACAATTTTTAGATAATTTATAATTTC
2387952 AGATCTTATG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
32 19 0.73
33 7 0.27
ACGTcount: A:0.34, C:0.05, G:0.05, T:0.56
Consensus pattern (32 bp):
TTATACAATTTTTAGATAATTTATAATTTCTA
Found at i:2392775 original size:21 final size:21
Alignment explanation
Indices: 2392751--2392801 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
2392741 CCATATTGTA
2392751 ACCCATCTGACCACCCATTTG
1 ACCCATCTGACCACCCATTTG
2392772 ACCCATCTGACCACCCATTTG
1 ACCCATCTGACCACCCATTTG
*
2392793 GCCCATCTG
1 ACCCATCTG
2392802 CCCCATATTC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.22, C:0.43, G:0.12, T:0.24
Consensus pattern (21 bp):
ACCCATCTGACCACCCATTTG
Found at i:2393435 original size:12 final size:11
Alignment explanation
Indices: 2393418--2393483 Score: 60
Period size: 12 Copynumber: 5.5 Consensus size: 11
2393408 AAATTCCCCT
*
2393418 TCATCATCATC
1 TCATCATCAAC
2393429 ATCATCATCGAAC
1 -TCATCATC-AAC
*
2393442 TCATCATCAAAT
1 TCATCATC-AAC
2393454 TCATCATCGAAC
1 TCATCATC-AAC
*
2393466 TCATCACCAAAC
1 TCATCATC-AAC
2393478 TCATCA
1 TCATCA
2393484 AAATCACAAT
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
12 44 0.96
13 2 0.04
ACGTcount: A:0.36, C:0.33, G:0.03, T:0.27
Consensus pattern (11 bp):
TCATCATCAAC
Found at i:2393450 original size:24 final size:24
Alignment explanation
Indices: 2393430--2393483 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
2393420 ATCATCATCA
2393430 TCATCATCGAACTCATCATCAAAT
1 TCATCATCGAACTCATCATCAAAT
* *
2393454 TCATCATCGAACTCATCACCAAAC
1 TCATCATCGAACTCATCATCAAAT
2393478 TCATCA
1 TCATCA
2393484 AAATCACAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.37, C:0.33, G:0.04, T:0.26
Consensus pattern (24 bp):
TCATCATCGAACTCATCATCAAAT
Found at i:2394281 original size:16 final size:16
Alignment explanation
Indices: 2394260--2394302 Score: 61
Period size: 16 Copynumber: 2.7 Consensus size: 16
2394250 GAAAGACAAC
2394260 ACAGAGAAAGAGACAG
1 ACAGAGAAAGAGACAG
*
2394276 ACAGAGAGAGAGACAG
1 ACAGAGAAAGAGACAG
2394292 A-AGATGAAAGA
1 ACAGA-GAAAGA
2394303 TTTGTTTTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 3 0.12
16 21 0.88
ACGTcount: A:0.56, C:0.09, G:0.33, T:0.02
Consensus pattern (16 bp):
ACAGAGAAAGAGACAG
Found at i:2394995 original size:2 final size:2
Alignment explanation
Indices: 2394988--2395012 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2394978 TTGCAAGGAA
2394988 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
2395013 AAAGAATCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2397786 original size:31 final size:30
Alignment explanation
Indices: 2397730--2397787 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 30
2397720 TAGCAAAGTT
**
2397730 AACAATAAAACAAAAGTTATACAATATCCA
1 AACAATAAAACAAAAGGAATACAATATCCA
2397760 AACAATAATAACAAAAGAGAAT-CAATAT
1 AACAATAA-AACAAAAG-GAATACAATAT
2397788 AATAACGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 8 0.33
31 14 0.58
32 2 0.08
ACGTcount: A:0.62, C:0.14, G:0.05, T:0.19
Consensus pattern (30 bp):
AACAATAAAACAAAAGGAATACAATATCCA
Found at i:2416561 original size:11 final size:11
Alignment explanation
Indices: 2416545--2416570 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
2416535 TATTTTTTAA
2416545 AAAAAAATTAT
1 AAAAAAATTAT
2416556 AAAAAAATTAT
1 AAAAAAATTAT
2416567 AAAA
1 AAAA
2416571 TTTTATTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (11 bp):
AAAAAAATTAT
Found at i:2421851 original size:20 final size:21
Alignment explanation
Indices: 2421812--2421852 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
2421802 AAATTTCAAG
*
2421812 TTTTTTATTTTTAATTAATAAC
1 TTTTTTATTTATAA-TAATAAC
2421834 TTTTTTATTTATAA-AATAA
1 TTTTTTATTTATAATAATAA
2421853 AATAATAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
22 13 0.72
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (21 bp):
TTTTTTATTTATAATAATAAC
Found at i:2424833 original size:21 final size:21
Alignment explanation
Indices: 2424809--2424849 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
2424799 ACGAGCGTTT
2424809 TTTTAAAAAAAAAATTTATAA
1 TTTTAAAAAAAAAATTTATAA
***
2424830 TTTTTTTAAAAAAATTTATA
1 TTTTAAAAAAAAAATTTATA
2424850 TAAAAAAGAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
TTTTAAAAAAAAAATTTATAA
Found at i:2425313 original size:3 final size:3
Alignment explanation
Indices: 2425305--2425333 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
2425295 ACTAATTAGC
2425305 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2425334 CTTTTCCTCT
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:2427770 original size:11 final size:11
Alignment explanation
Indices: 2427754--2427787 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
2427744 CTCAACTTGC
2427754 AAAAAAAAAGA
1 AAAAAAAAAGA
2427765 AAAAAAAAAGA
1 AAAAAAAAAGA
* *
2427776 AAGAAAGAAGA
1 AAAAAAAAAGA
2427787 A
1 A
2427788 GATAGTTTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAGA
Found at i:2428645 original size:21 final size:21
Alignment explanation
Indices: 2428620--2428661 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
2428610 TGCTTCATAT
2428620 AAGTTTAATTCTTGCTCTTTC
1 AAGTTTAATTCTTGCTCTTTC
2428641 AAGTTTAATTCTTGCTCTTTC
1 AAGTTTAATTCTTGCTCTTTC
2428662 CTTTAATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.10, T:0.52
Consensus pattern (21 bp):
AAGTTTAATTCTTGCTCTTTC
Found at i:2429693 original size:24 final size:24
Alignment explanation
Indices: 2429627--2429693 Score: 91
Period size: 24 Copynumber: 2.8 Consensus size: 24
2429617 TATCCGGTGT
*
2429627 TACCCGTTAATTGCTCTTAAGAGC
1 TACCCGTTAATTGCTCTTTAGAGC
* *
2429651 TACCTGTTAATTACTCTTTAGAGC
1 TACCCGTTAATTGCTCTTTAGAGC
2429675 TACCCGTT-ATATGCTCTTT
1 TACCCGTTAAT-TGCTCTTT
2429694 GTGAGCTTCT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
23 2 0.05
24 35 0.95
ACGTcount: A:0.22, C:0.24, G:0.13, T:0.40
Consensus pattern (24 bp):
TACCCGTTAATTGCTCTTTAGAGC
Found at i:2445704 original size:25 final size:26
Alignment explanation
Indices: 2445658--2445719 Score: 72
Period size: 25 Copynumber: 2.3 Consensus size: 26
2445648 TAAACATATG
2445658 AATTATAAAACATGAAAATATA-AAT
1 AATTATAAAACATGAAAATATATAAT
* **
2445683 AATTATAAAATATGAATGTATATAAT
1 AATTATAAAACATGAAAATATATAAT
2445709 ATATATATAAA
1 A-AT-TATAAA
2445720 CTATATACAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
25 19 0.61
26 4 0.13
27 2 0.06
28 6 0.19
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.34
Consensus pattern (26 bp):
AATTATAAAACATGAAAATATATAAT
Found at i:2446355 original size:16 final size:16
Alignment explanation
Indices: 2446330--2446364 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
2446320 ATTATTTTTT
2446330 CAAAAACAAAGGAAAA
1 CAAAAACAAAGGAAAA
* *
2446346 CAAAATCAAATGAAAA
1 CAAAAACAAAGGAAAA
2446362 CAA
1 CAA
2446365 TAAAAGAACA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.71, C:0.14, G:0.09, T:0.06
Consensus pattern (16 bp):
CAAAAACAAAGGAAAA
Found at i:2454212 original size:23 final size:24
Alignment explanation
Indices: 2454186--2454232 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
2454176 ATTTGAGCCG
2454186 CCCTTTTCGGG-TTTCAACTCAAA
1 CCCTTTTCGGGTTTTCAACTCAAA
2454209 CCCTTTTCGGGTTTTCAACTCAAA
1 CCCTTTTCGGGTTTTCAACTCAAA
2454233 TCCACTTTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 11 0.48
24 12 0.52
ACGTcount: A:0.21, C:0.30, G:0.13, T:0.36
Consensus pattern (24 bp):
CCCTTTTCGGGTTTTCAACTCAAA
Found at i:2454320 original size:23 final size:23
Alignment explanation
Indices: 2454283--2454332 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
2454273 AGCCTTTCCA
*
2454283 TTTTACTTTTCCATTTTTCAT-T
1 TTTTACTTTTCCATTTCTCATCT
*
2454305 TTTTCACTTTTTCATTTCTCATCT
1 TTTT-ACTTTTCCATTTCTCATCT
2454329 TTTT
1 TTTT
2454333 TTTTTACGAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 4 0.17
23 15 0.62
24 5 0.21
ACGTcount: A:0.12, C:0.20, G:0.00, T:0.68
Consensus pattern (23 bp):
TTTTACTTTTCCATTTCTCATCT
Found at i:2454767 original size:1 final size:1
Alignment explanation
Indices: 2454761--2454866 Score: 77
Period size: 1 Copynumber: 106.0 Consensus size: 1
2454751 CCGGTAGAGG
* * * * * * * * * * * *
2454761 TTTTTTTTGTTTCTTTTTGTTTTTTATTTTTTGTTCTTTTTTGTTCTTTTTTTTATTTTTGTCTA
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * *
2454826 TTTTTTTTGTTTTTTTTTTGTTTTTTTTTCTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
2454867 GAACTGAATC
Statistics
Matches: 75, Mismatches: 30, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
1 75 1.00
ACGTcount: A:0.03, C:0.05, G:0.07, T:0.86
Consensus pattern (1 bp):
T
Found at i:2454843 original size:52 final size:52
Alignment explanation
Indices: 2454764--2454866 Score: 136
Period size: 52 Copynumber: 2.0 Consensus size: 52
2454754 GTAGAGGTTT
* * *
2454764 TTTTTGTTTCTTTTTGTTTTTTATTTTTTGTTCTTTTTTGTTCTTTTTTTTA
1 TTTTTGTCTATTTTTGTTTTTTATTTTTTGTTCTTTTTTCTTCTTTTTTTTA
* * *
2454816 TTTTTGTCTATTTTT-TTTGTTTTTTTTTTGTTTTTTTTTCTTTTTTTTTTT
1 TTTTTGTCTATTTTTGTTT-TTTATTTTTTGTTCTTTTTTCTTCTTTTTTTT
2454867 GAACTGAATC
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
51 3 0.07
52 41 0.93
ACGTcount: A:0.03, C:0.05, G:0.07, T:0.85
Consensus pattern (52 bp):
TTTTTGTCTATTTTTGTTTTTTATTTTTTGTTCTTTTTTCTTCTTTTTTTTA
Found at i:2464902 original size:16 final size:16
Alignment explanation
Indices: 2464877--2464911 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
2464867 ATTATTTTTT
2464877 CAAAAACAAAGGAAAA
1 CAAAAACAAAGGAAAA
* *
2464893 CAAAATCAAATGAAAA
1 CAAAAACAAAGGAAAA
2464909 CAA
1 CAA
2464912 TAAAAGAACA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.71, C:0.14, G:0.09, T:0.06
Consensus pattern (16 bp):
CAAAAACAAAGGAAAA
Found at i:2469512 original size:19 final size:21
Alignment explanation
Indices: 2469466--2469513 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
2469456 ATGTGTATCA
*
2469466 GTCACACGGTCGTGTACCCTT
1 GTCACACGGTCGTGGACCCTT
2469487 GTCACACGGTC-TGGACCCTT
1 GTCACACGGTCGTGGACCCTT
2469507 -TCACACG
1 GTCACACG
2469514 ACTTGGGCAC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 7 0.27
20 8 0.31
21 11 0.42
ACGTcount: A:0.17, C:0.35, G:0.23, T:0.25
Consensus pattern (21 bp):
GTCACACGGTCGTGGACCCTT
Found at i:2469844 original size:41 final size:41
Alignment explanation
Indices: 2469787--2469881 Score: 156
Period size: 41 Copynumber: 2.3 Consensus size: 41
2469777 TTTTTGGGGA
2469787 TTTAGCGGCGTTTTTGAATAAGCGCCGCTAATGCTCT-TATC
1 TTTAGCGGCGTTTTTGAATAAGCGCCGCTAATGCTCTGT-TC
* *
2469828 TTTAGTGGCGTTTTTGAATAGGCGCCGCTAATGCTCTGTTC
1 TTTAGCGGCGTTTTTGAATAAGCGCCGCTAATGCTCTGTTC
2469869 TTTAGCGGCGTTT
1 TTTAGCGGCGTTT
2469882 GTGCGAAAAA
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
41 49 0.98
42 1 0.02
ACGTcount: A:0.16, C:0.20, G:0.25, T:0.39
Consensus pattern (41 bp):
TTTAGCGGCGTTTTTGAATAAGCGCCGCTAATGCTCTGTTC
Found at i:2469935 original size:43 final size:43
Alignment explanation
Indices: 2469849--2470123 Score: 329
Period size: 43 Copynumber: 6.4 Consensus size: 43
2469839 TTTTGAATAG
* * * *
2469849 GCGCCGCTAATGCTC-TGTTCTTTAGCGGCGTTTGTGCGAAAAA
1 GCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTG-GGAAAA
* *
2469892 GTGCCGCTAAAGGTCATGGTCTTTGGCGGCGTTTGTGGGAAAA
1 GCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGGGAAAA
* * ** *
2469935 GCGCCACCAAAACTCATGGTCTTTAGCGGCATTTGTGGGAAAA
1 GCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGGGAAAA
* ** *
2469978 GCGCCGCTAACGGTCAT-AACTTTTAGCGGCGTTTGTGGAAAAA
1 GCGCCGCTAAAGGTCATGGTC-TTTAGCGGCGTTTGTGGGAAAA
* *
2470021 ACGCCACTAAAGGTCATGGTCTTTAGCGGCGTTTGTGGGAAAA
1 GCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGGGAAAA
* * *
2470064 GCGCCGCTAAAGGTCATGGTCTATAGCGGAGTTTGTGGGGAAA
1 GCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGGGAAAA
*
2470107 GCGTCGCTAAAGGTCAT
1 GCGCCGCTAAAGGTCAT
2470124 TACTTTTAGC
Statistics
Matches: 195, Mismatches: 34, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
42 1 0.01
43 174 0.89
44 20 0.10
ACGTcount: A:0.23, C:0.20, G:0.31, T:0.26
Consensus pattern (43 bp):
GCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGGGAAAA
Found at i:2470020 original size:129 final size:130
Alignment explanation
Indices: 2469869--2470136 Score: 396
Period size: 129 Copynumber: 2.1 Consensus size: 130
2469859 TGCTCTGTTC
** * *
2469869 TTTAGCGGCGTTTGTGCGAAAAAGTGCCGCTAAAGGTCATGGTCTTTGGCGGCGTTTGTGGGAAA
1 TTTAGCGGCGTTTGTGCGAAAAAACGCCACTAAAGGTCATGGTCTTTAGCGGCGTTTGTGGGAAA
* *
2469934 AGCGCCACCAAAACTCATGGTCTTTAGCGGCA-TTTGTGGGAAAAGCGCCGCTAACGGTCATAAC
66 AGCGCCACCAAAACTCATGGTCTATAGCGG-AGTTTGTGGGAAAAGCGCCGCTAAAGGTCATAAC
2469998 T
130 T
2469999 TTTAGCGGCGTTTGTG-GAAAAAACGCCACTAAAGGTCATGGTCTTTAGCGGCGTTTGTGGGAAA
1 TTTAGCGGCGTTTGTGCGAAAAAACGCCACTAAAGGTCATGGTCTTTAGCGGCGTTTGTGGGAAA
* * ** * * *
2470063 AGCGCCGCTAAAGGTCATGGTCTATAGCGGAGTTTGTGGGGAAAGCGTCGCTAAAGGTCATTACT
66 AGCGCCACCAAAACTCATGGTCTATAGCGGAGTTTGTGGGAAAAGCGCCGCTAAAGGTCATAACT
2470128 TTTAGCGGC
1 TTTAGCGGC
2470137 ATTTATTTCC
Statistics
Matches: 124, Mismatches: 13, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
128 1 0.01
129 107 0.86
130 16 0.13
ACGTcount: A:0.24, C:0.19, G:0.31, T:0.26
Consensus pattern (130 bp):
TTTAGCGGCGTTTGTGCGAAAAAACGCCACTAAAGGTCATGGTCTTTAGCGGCGTTTGTGGGAAA
AGCGCCACCAAAACTCATGGTCTATAGCGGAGTTTGTGGGAAAAGCGCCGCTAAAGGTCATAACT
Found at i:2470248 original size:22 final size:22
Alignment explanation
Indices: 2470220--2470262 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
2470210 TAGCGACGCT
*
2470220 AAAAAGCACCGCTAAAGGCCTA
1 AAAAAGCACCGCTAAAAGCCTA
*
2470242 AAAAAGCGCCGCTAAAAGCCT
1 AAAAAGCACCGCTAAAAGCCT
2470263 GTTTTGGTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.44, C:0.28, G:0.19, T:0.09
Consensus pattern (22 bp):
AAAAAGCACCGCTAAAAGCCTA
Found at i:2470781 original size:41 final size:41
Alignment explanation
Indices: 2470719--2470954 Score: 339
Period size: 41 Copynumber: 5.8 Consensus size: 41
2470709 CCTTTCGAGT
* ** * *
2470719 CTTTAGCGGCATTTTCAAAAAAGCACCGCTAATGCTCGGGG
1 CTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTGGGGG
* *
2470760 TTTTAGCAGCGTTTTTGAAAAAGCGCCGCTAATGCTGGGGG
1 CTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTGGGGG
2470801 CTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTGGGGG
1 CTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTGGGGG
2470842 CTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTGGGGG
1 CTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTGGGGG
* * * *
2470883 C-TTAGCGGCGTTTTTGAGAAAGTGCCGCTAATGTTGGTGG
1 CTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTGGGGG
* * *
2470923 CTTTAGCGCCGTTTTTGAGAAAGCGCCACTAA
1 CTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAA
2470955 AAACATTTTA
Statistics
Matches: 178, Mismatches: 16, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
40 36 0.20
41 142 0.80
ACGTcount: A:0.22, C:0.20, G:0.31, T:0.28
Consensus pattern (41 bp):
CTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTGGGGG
Found at i:2471332 original size:14 final size:14
Alignment explanation
Indices: 2471315--2471374 Score: 68
Period size: 14 Copynumber: 4.2 Consensus size: 14
2471305 GGGCTGAGAT
2471315 TTAAGGTTTAGGGG
1 TTAAGGTTTAGGGG
* *
2471329 TTAAGGGTTAAGGG
1 TTAAGGTTTAGGGG
2471343 TTAAGGGTTTAGGGG
1 TTAA-GGTTTAGGGG
*
2471358 TTAGACG-TTAGGGG
1 TTA-AGGTTTAGGGG
2471372 TTA
1 TTA
2471375 GAGTTAGGAA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
14 26 0.67
15 12 0.31
16 1 0.03
ACGTcount: A:0.23, C:0.02, G:0.42, T:0.33
Consensus pattern (14 bp):
TTAAGGTTTAGGGG
Found at i:2471336 original size:7 final size:7
Alignment explanation
Indices: 2471315--2471356 Score: 57
Period size: 7 Copynumber: 6.0 Consensus size: 7
2471305 GGGCTGAGAT
*
2471315 TTAAGGT
1 TTAAGGG
*
2471322 TTAGGGG
1 TTAAGGG
2471329 TTAAGGG
1 TTAAGGG
2471336 TTAAGGG
1 TTAAGGG
2471343 TTAAGGG
1 TTAAGGG
*
2471350 TTTAGGG
1 TTAAGGG
2471357 GTTAGACGTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.24, C:0.00, G:0.43, T:0.33
Consensus pattern (7 bp):
TTAAGGG
Found at i:2471361 original size:7 final size:7
Alignment explanation
Indices: 2471322--2471375 Score: 54
Period size: 7 Copynumber: 7.6 Consensus size: 7
2471312 GATTTAAGGT
2471322 TTAGGGG
1 TTAGGGG
*
2471329 TTAAGGG
1 TTAGGGG
*
2471336 TTAAGGG
1 TTAGGGG
*
2471343 TTAAGGGT
1 TT-AGGGG
2471351 TTAGGGG
1 TTAGGGG
**
2471358 TTAGACG
1 TTAGGGG
2471365 TTAGGGG
1 TTAGGGG
2471372 TTAG
1 TTAG
2471376 AGTTAGGAAT
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
7 33 0.87
8 5 0.13
ACGTcount: A:0.22, C:0.02, G:0.44, T:0.31
Consensus pattern (7 bp):
TTAGGGG
Found at i:2471367 original size:29 final size:28
Alignment explanation
Indices: 2471315--2471374 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 28
2471305 GGGCTGAGAT
*
2471315 TTAAGGTTTAGGGGTTAAGGGTTAAGGG
1 TTAAGGTTTAGGGGTTAAGCGTTAAGGG
*
2471343 TTAAGGGTTTAGGGGTT-AGACGTTAGGGG
1 TTAA-GGTTTAGGGGTTAAG-CGTTAAGGG
2471372 TTA
1 TTA
2471375 GAGTTAGGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 6 0.21
29 22 0.79
ACGTcount: A:0.23, C:0.02, G:0.42, T:0.33
Consensus pattern (28 bp):
TTAAGGTTTAGGGGTTAAGCGTTAAGGG
Found at i:2471375 original size:14 final size:13
Alignment explanation
Indices: 2471322--2471382 Score: 59
Period size: 14 Copynumber: 4.4 Consensus size: 13
2471312 GATTTAAGGT
*
2471322 TTAGGGGTTAAGGG
1 TTAGGGGTT-AGAG
* *
2471336 TTAAGGGTTAAGGG
1 TTAGGGGTT-AGAG
2471350 TTTAGGGGTTAGACG
1 -TTAGGGGTTAGA-G
2471365 TTAGGGGTTAGAG
1 TTAGGGGTTAGAG
2471378 TTAGG
1 TTAGG
2471383 AATTTAGGGT
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
13 6 0.14
14 27 0.64
15 9 0.21
ACGTcount: A:0.23, C:0.02, G:0.44, T:0.31
Consensus pattern (13 bp):
TTAGGGGTTAGAG
Found at i:2481287 original size:31 final size:31
Alignment explanation
Indices: 2481245--2481311 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
2481235 AACAGGTTGG
*
2481245 AGCGGAGAAGGCGACAGAGGAGATCACTAGA
1 AGCGGAAAAGGCGACAGAGGAGATCACTAGA
* * *
2481276 AGCGGAAAAGGCGATAGTGGAGATCACTGGA
1 AGCGGAAAAGGCGACAGAGGAGATCACTAGA
2481307 A-CGGA
1 AGCGGA
2481312 CGCTGATGGG
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 4 0.12
31 28 0.88
ACGTcount: A:0.37, C:0.15, G:0.39, T:0.09
Consensus pattern (31 bp):
AGCGGAAAAGGCGACAGAGGAGATCACTAGA
Found at i:2491347 original size:22 final size:22
Alignment explanation
Indices: 2491321--2491362 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
2491311 AAAGAATAGT
2491321 AACCATTACATGCATAATTGAA
1 AACCATTACATGCATAATTGAA
**
2491343 AACCATTTTATGCATAATTG
1 AACCATTACATGCATAATTG
2491363 TGAAGTTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.40, C:0.17, G:0.10, T:0.33
Consensus pattern (22 bp):
AACCATTACATGCATAATTGAA
Found at i:2492638 original size:16 final size:17
Alignment explanation
Indices: 2492614--2492647 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
2492604 TTTCATTTTT
2492614 TAATATATATT-TTAAA
1 TAATATATATTATTAAA
*
2492630 TAATTTATATTATTAAA
1 TAATATATATTATTAAA
2492647 T
1 T
2492648 TACATTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TAATATATATTATTAAA
Done.