Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr1
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: 106989029
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3754247 characters in sequence are not A, C, G, or T
File 170 of 322
Found at i:55496707 original size:16 final size:16
Alignment explanation
Indices: 55496656--55496707 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
55496646 TATGTGTATT
55496656 TAAAATATTTCACATA
1 TAAAATATTTCACATA
* * * *
55496672 TAAAA-ATAATGATATT
1 TAAAATAT-TTCACATA
55496688 TAAAATATTTCACATA
1 TAAAATATTTCACATA
55496704 TAAA
1 TAAA
55496708 TATAAAAATA
Statistics
Matches: 26, Mismatches: 8, Indels: 4
0.68 0.21 0.11
Matches are distributed among these distances:
15 2 0.08
16 22 0.85
17 2 0.08
ACGTcount: A:0.54, C:0.08, G:0.02, T:0.37
Consensus pattern (16 bp):
TAAAATATTTCACATA
Found at i:55496729 original size:32 final size:32
Alignment explanation
Indices: 55496656--55496721 Score: 89
Period size: 32 Copynumber: 2.1 Consensus size: 32
55496646 TATGTGTATT
** *
55496656 TAAAATATTTCACATATAAAAATAATGATATT
1 TAAAATATTTCACATATAAAAATAAAAATATA
*
55496688 TAAAATATTTCACATATAAATATAAAAATA-A
1 TAAAATATTTCACATATAAAAATAAAAATATA
55496719 TAA
1 TAA
55496722 TTATATTTGA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
31 3 0.10
32 27 0.90
ACGTcount: A:0.58, C:0.06, G:0.02, T:0.35
Consensus pattern (32 bp):
TAAAATATTTCACATATAAAAATAAAAATATA
Found at i:55497428 original size:24 final size:24
Alignment explanation
Indices: 55497377--55497428 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
55497367 ATTCTTTCCT
**
55497377 TTTCTTTCTTCTTTTTTTTTCTTC
1 TTTCTTTCTTCTTTTTTTTTCTGA
55497401 TTTCTTTCTTCTTTTTTTGTT-TGA
1 TTTCTTTCTTCTTTTTTT-TTCTGA
55497425 TTTC
1 TTTC
55497429 ATCTTTTCCT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 23 0.92
25 2 0.08
ACGTcount: A:0.02, C:0.17, G:0.04, T:0.77
Consensus pattern (24 bp):
TTTCTTTCTTCTTTTTTTTTCTGA
Found at i:55507898 original size:69 final size:69
Alignment explanation
Indices: 55507782--55507918 Score: 211
Period size: 69 Copynumber: 2.0 Consensus size: 69
55507772 TGGCTTTTAT
* * *
55507782 TTTCCCAGTTAAACTCTATTTTTAGTTTTCGAATTACACTCTAATTAGTGTAGGTTATTTGAATA
1 TTTCCCAGTTAAACTCTATTTTTAGTTTCCCAATTAAACTCTAATTAGTGTAGGTTATTTGAATA
55507847 TTAG
66 TTAG
* * * *
55507851 TTTCCCAGTTAAGCTCTATTTTTAGTTTCCCACTTAAACTCTGATTAGTGTAGGTTATTTTAATA
1 TTTCCCAGTTAAACTCTATTTTTAGTTTCCCAATTAAACTCTAATTAGTGTAGGTTATTTGAATA
55507916 TTA
66 TTA
55507919 TTTGACCTAC
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
69 61 1.00
ACGTcount: A:0.26, C:0.15, G:0.12, T:0.47
Consensus pattern (69 bp):
TTTCCCAGTTAAACTCTATTTTTAGTTTCCCAATTAAACTCTAATTAGTGTAGGTTATTTGAATA
TTAG
Found at i:55510908 original size:19 final size:19
Alignment explanation
Indices: 55510872--55510908 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
55510862 TAATTAGGCT
* *
55510872 TTAATTAAGTGAATTTAGC
1 TTAATTAAGAGAAATTAGC
55510891 TTAATTAAGAGAAATTAG
1 TTAATTAAGAGAAATTAG
55510909 GAAAAAGGGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.43, C:0.03, G:0.16, T:0.38
Consensus pattern (19 bp):
TTAATTAAGAGAAATTAGC
Found at i:55511538 original size:2 final size:2
Alignment explanation
Indices: 55511531--55511577 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
55511521 TTATTAACTA
*
55511531 AT AT AT AT AG AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
55511573 AT AT A
1 AT AT A
55511578 AGAAAGCAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:55512028 original size:17 final size:18
Alignment explanation
Indices: 55512006--55512039 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
55511996 TAAATGAGTT
55512006 AATTAGGAT-TAAATTGG
1 AATTAGGATATAAATTGG
*
55512023 AATTAGGGTATAAATTG
1 AATTAGGATATAAATTG
55512040 AATAGAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.41, C:0.00, G:0.24, T:0.35
Consensus pattern (18 bp):
AATTAGGATATAAATTGG
Found at i:55512199 original size:21 final size:21
Alignment explanation
Indices: 55512175--55512216 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
55512165 GGAGTAATCG
55512175 AACAAATCTGGGTTTGTATTA
1 AACAAATCTGGGTTTGTATTA
55512196 AACAAATCTGGGTTTGTATTA
1 AACAAATCTGGGTTTGTATTA
55512217 CTATAATTCA
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:0.33, C:0.10, G:0.19, T:0.38
Consensus pattern (21 bp):
AACAAATCTGGGTTTGTATTA
Found at i:55514247 original size:36 final size:35
Alignment explanation
Indices: 55514207--55514299 Score: 100
Period size: 36 Copynumber: 2.5 Consensus size: 35
55514197 TATATGTGTG
*
55514207 GAATTGAATTGAATAT-TGACTTGAAAA-TGGAAAAGT
1 GAATTGAATTGAAT-TGTGA-TT-AAAAGTGAAAAAGT
55514243 GAATTTTGAATTGAATTGTGATTAAAAGTGAAAAAGT
1 GAA--TTGAATTGAATTGTGATTAAAAGTGAAAAAGT
*
55514280 GAAATTGAATTGAAATGTGA
1 G-AATTGAATTGAATTGTGA
55514300 ATTTGGAGAC
Statistics
Matches: 50, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
36 22 0.44
37 12 0.24
38 16 0.32
ACGTcount: A:0.44, C:0.01, G:0.23, T:0.32
Consensus pattern (35 bp):
GAATTGAATTGAATTGTGATTAAAAGTGAAAAAGT
Found at i:55515189 original size:12 final size:12
Alignment explanation
Indices: 55515148--55515189 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
55515138 TTAAATAGAA
55515148 ATGAATGAAATT
1 ATGAATGAAATT
*
55515160 ATCAAT-AAATT
1 ATGAATGAAATT
* *
55515171 TTGAATGATATT
1 ATGAATGAAATT
55515183 ATGAATG
1 ATGAATG
55515190 TTTATTTAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
11 9 0.38
12 15 0.62
ACGTcount: A:0.45, C:0.02, G:0.14, T:0.38
Consensus pattern (12 bp):
ATGAATGAAATT
Found at i:55515298 original size:22 final size:22
Alignment explanation
Indices: 55515248--55515298 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 22
55515238 TATTCAAATG
55515248 TGAA-TTGGATTGGTTGTGATT
1 TGAATTTGGATTGGTTGTGATT
***
55515269 TTTGTTTGGATTGGTCT-TGATT
1 TGAATTTGGATTGGT-TGTGATT
55515291 TGAATTTG
1 TGAATTTG
55515299 TAGGGAATGT
Statistics
Matches: 22, Mismatches: 6, Indels: 3
0.71 0.19 0.10
Matches are distributed among these distances:
21 1 0.05
22 20 0.91
23 1 0.05
ACGTcount: A:0.16, C:0.02, G:0.29, T:0.53
Consensus pattern (22 bp):
TGAATTTGGATTGGTTGTGATT
Found at i:55515644 original size:16 final size:16
Alignment explanation
Indices: 55515623--55515653 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
55515613 TTCCATCCCG
55515623 ATTTTGATTAAATTTT
1 ATTTTGATTAAATTTT
55515639 ATTTTGATTAAATTT
1 ATTTTGATTAAATTT
55515654 ATAATTATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.61
Consensus pattern (16 bp):
ATTTTGATTAAATTTT
Found at i:55515839 original size:19 final size:21
Alignment explanation
Indices: 55515798--55515839 Score: 52
Period size: 19 Copynumber: 2.1 Consensus size: 21
55515788 AAAATTATTG
**
55515798 ATTTTTAAAAATATTTATGAA
1 ATTTTTAAAAATATTTACCAA
55515819 ATTTTT-AAAAT-TTTACCAA
1 ATTTTTAAAAATATTTACCAA
55515838 AT
1 AT
55515840 AATATCCAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 8 0.42
20 5 0.26
21 6 0.32
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (21 bp):
ATTTTTAAAAATATTTACCAA
Found at i:55518910 original size:56 final size:57
Alignment explanation
Indices: 55518762--55518918 Score: 183
Period size: 56 Copynumber: 2.8 Consensus size: 57
55518752 CTAATTGAGC
* * * * ***
55518762 CTTT-GAGCATATGTTAAAGTCTGGATTTAGCCTAGACTGGTAATCCAGATTGAGCT
1 CTTTAGAGCATATGTTACAGACAGGATTTAGCCTGGACTGGTAATCCAGACAAAGCT
* * * * *
55518818 CTTTAGAGTATTTGTCACAGAAAGGATTTAGCCTGGACTGGTAATCCTGACAAAGCT
1 CTTTAGAGCATATGTTACAGACAGGATTTAGCCTGGACTGGTAATCCAGACAAAGCT
*
55518875 C-TTAGAGCATATGTTACAGACAGGATTTAGACTGGACTGGTAAT
1 CTTTAGAGCATATGTTACAGACAGGATTTAGCCTGGACTGGTAAT
55518919 GCTGCTGTAT
Statistics
Matches: 83, Mismatches: 17, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
56 42 0.51
57 41 0.49
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.31
Consensus pattern (57 bp):
CTTTAGAGCATATGTTACAGACAGGATTTAGCCTGGACTGGTAATCCAGACAAAGCT
Found at i:55525168 original size:57 final size:57
Alignment explanation
Indices: 55525080--55525193 Score: 201
Period size: 57 Copynumber: 2.0 Consensus size: 57
55525070 CAACAATACA
*
55525080 CGGGTGTGCTACCATAACACACAGGCGTGGGACAGTAGTCGGGCACGACCTAAATTG
1 CGGGTGTGATACCATAACACACAGGCGTGGGACAGTAGTCGGGCACGACCTAAATTG
* *
55525137 CGGGTGTGATCCCATAACCCACAGGCGTGGGACAGTAGTCGGGCACGACCTAAATTG
1 CGGGTGTGATACCATAACACACAGGCGTGGGACAGTAGTCGGGCACGACCTAAATTG
55525194 AAAAATTCGA
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
57 54 1.00
ACGTcount: A:0.25, C:0.25, G:0.32, T:0.18
Consensus pattern (57 bp):
CGGGTGTGATACCATAACACACAGGCGTGGGACAGTAGTCGGGCACGACCTAAATTG
Found at i:55531322 original size:15 final size:15
Alignment explanation
Indices: 55531302--55531331 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
55531292 GTAAGTTTTC
55531302 TTTCTATTACACGAA
1 TTTCTATTACACGAA
*
55531317 TTTCTATTACGCGAA
1 TTTCTATTACACGAA
55531332 CTTACTAAGC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.20, G:0.10, T:0.40
Consensus pattern (15 bp):
TTTCTATTACACGAA
Found at i:55535952 original size:21 final size:21
Alignment explanation
Indices: 55535926--55535967 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
55535916 TCACGCCAAG
55535926 TAGTAAATGCATTTGTATAGT
1 TAGTAAATGCATTTGTATAGT
55535947 TAGTAAATGCATTTGTATAGT
1 TAGTAAATGCATTTGTATAGT
55535968 AAACTTTTAA
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:0.33, C:0.05, G:0.19, T:0.43
Consensus pattern (21 bp):
TAGTAAATGCATTTGTATAGT
Found at i:55539491 original size:33 final size:32
Alignment explanation
Indices: 55539369--55539681 Score: 158
Period size: 33 Copynumber: 9.3 Consensus size: 32
55539359 AATTGACGGA
* * * * *
55539369 TAAGACCATAACTGGGTTATGGCACTATGAACG
1 TAAGACCATAGCTGGGCTATGGCATTTTG-ATG
* * * * *
55539402 TAAGACCATGGTTGGACCATGGCAGTGTTTATATG
1 TAAGACCATAGCTGGGCTATGGCA-T-TTT-GATG
*
55539437 TAAGATCATAGCTGGGCTATGGCATTTTGATG
1 TAAGACCATAGCTGGGCTATGGCATTTTGATG
* * * * *
55539469 ATATGACCATAACTGGGTTATGGCACTATGAATG
1 -TAAGACCATAGCTGGGCTATGGCATTTTG-ATG
* * * * *
55539503 TAAGACCATGGTTGGACCATGGCAGTGTTTATATG
1 TAAGACCATAGCTGGGCTATGGCA-T-TTT-GATG
*
55539538 TAAGATCATAGCTGGGCTATGGCATTTTGATG
1 TAAGACCATAGCTGGGCTATGGCATTTTGATG
* * * * *
55539570 ATATGACCATAACTGGGTTATGGCACTATGAATG
1 -TAAGACCATAGCTGGGCTATGGCATTTTG-ATG
* * * * *
55539604 TAAGACCATGGTTGGACCATGGCAGTGTTTATATG
1 TAAGACCATAGCTGGGCTATGGCA-T-TTT-GATG
* * * *
55539639 TAAGACCAGAGTTGGGCTATTGCATTCTGATG
1 TAAGACCATAGCTGGGCTATGGCATTTTGATG
*
55539671 ATAAAACCATA
1 -TAAGACCATA
55539682 ACTAGGTTAT
Statistics
Matches: 203, Mismatches: 63, Indels: 28
0.69 0.21 0.10
Matches are distributed among these distances:
32 9 0.04
33 114 0.56
34 9 0.04
35 71 0.35
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.30
Consensus pattern (32 bp):
TAAGACCATAGCTGGGCTATGGCATTTTGATG
Found at i:55539547 original size:101 final size:101
Alignment explanation
Indices: 55539367--55539707 Score: 574
Period size: 101 Copynumber: 3.4 Consensus size: 101
55539357 TGAATTGACG
*
55539367 GATAAGACCATAACTGGGTTATGGCACTATGAACGTAAGACCATGGTTGGACCATGGCAGTGTTT
1 GATAAGACCATAACTGGGTTATGGCACTATGAATGTAAGACCATGGTTGGACCATGGCAGTGTTT
55539432 ATATGTAAGATCATAGCTGGGCTATGGCATTTTGAT
66 ATATGTAAGATCATAGCTGGGCTATGGCATTTTGAT
*
55539468 GATATGACCATAACTGGGTTATGGCACTATGAATGTAAGACCATGGTTGGACCATGGCAGTGTTT
1 GATAAGACCATAACTGGGTTATGGCACTATGAATGTAAGACCATGGTTGGACCATGGCAGTGTTT
55539533 ATATGTAAGATCATAGCTGGGCTATGGCATTTTGAT
66 ATATGTAAGATCATAGCTGGGCTATGGCATTTTGAT
*
55539569 GATATGACCATAACTGGGTTATGGCACTATGAATGTAAGACCATGGTTGGACCATGGCAGTGTTT
1 GATAAGACCATAACTGGGTTATGGCACTATGAATGTAAGACCATGGTTGGACCATGGCAGTGTTT
* * * * *
55539634 ATATGTAAGACCAGAGTTGGGCTATTGCATTCTGAT
66 ATATGTAAGATCATAGCTGGGCTATGGCATTTTGAT
* * * *
55539670 GATAAAACCATAACTAGGTTATAGCACTACGAATGTAA
1 GATAAGACCATAACTGGGTTATGGCACTATGAATGTAA
55539708 AGGATGAATT
Statistics
Matches: 228, Mismatches: 12, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
101 228 1.00
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.30
Consensus pattern (101 bp):
GATAAGACCATAACTGGGTTATGGCACTATGAATGTAAGACCATGGTTGGACCATGGCAGTGTTT
ATATGTAAGATCATAGCTGGGCTATGGCATTTTGAT
Found at i:55543570 original size:23 final size:23
Alignment explanation
Indices: 55543526--55543570 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 23
55543516 CCACTTATTT
*
55543526 TGGCTTGTTTTGAATGTTTAATTA
1 TGGCTTG-TTTGAATGTGTAATTA
55543550 TGGCTTG-TTGATATGTGTAAT
1 TGGCTTGTTTGA-ATGTGTAAT
55543571 GTTGATTCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 4 0.21
23 8 0.42
24 7 0.37
ACGTcount: A:0.20, C:0.04, G:0.24, T:0.51
Consensus pattern (23 bp):
TGGCTTGTTTGAATGTGTAATTA
Found at i:55546922 original size:21 final size:21
Alignment explanation
Indices: 55546879--55546924 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
55546869 CTCTTTAATC
**
55546879 TCTTCACTTTCTCTTCAACTT
1 TCTTCACTTTCAATTCAACTT
55546900 TCTTCACTTTCAATTCCAA-TT
1 TCTTCACTTTCAATT-CAACTT
55546921 TCTT
1 TCTT
55546925 GTTTCCAAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 19 0.86
22 3 0.14
ACGTcount: A:0.17, C:0.30, G:0.00, T:0.52
Consensus pattern (21 bp):
TCTTCACTTTCAATTCAACTT
Found at i:55547150 original size:13 final size:11
Alignment explanation
Indices: 55547123--55547169 Score: 58
Period size: 11 Copynumber: 4.1 Consensus size: 11
55547113 TTTTCATAGT
55547123 TAAAATATTAA
1 TAAAATATTAA
55547134 TAAAATATCTAAA
1 TAAAATAT-T-AA
*
55547147 TAAAATATTAT
1 TAAAATATTAA
*
55547158 TAAAATAATAA
1 TAAAATATTAA
55547169 T
1 T
55547170 TAACTAATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
11 19 0.61
12 2 0.06
13 10 0.32
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (11 bp):
TAAAATATTAA
Found at i:55550579 original size:28 final size:28
Alignment explanation
Indices: 55550537--55550592 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
55550527 ACCAAGGCTG
*
55550537 GCTAAAAAAATTAAAATTTAACTGTCAA
1 GCTAAAAAAAGTAAAATTTAACTGTCAA
*
55550565 GCTAAACAAAGTAAAATTTAACTGTCAA
1 GCTAAAAAAAGTAAAATTTAACTGTCAA
55550593 AGCCTTAAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.52, C:0.12, G:0.09, T:0.27
Consensus pattern (28 bp):
GCTAAAAAAAGTAAAATTTAACTGTCAA
Found at i:55553206 original size:21 final size:21
Alignment explanation
Indices: 55553181--55553239 Score: 109
Period size: 21 Copynumber: 2.8 Consensus size: 21
55553171 TGGGTTTGAG
55553181 TTTGGGTGCGAATTTGGAAGA
1 TTTGGGTGCGAATTTGGAAGA
55553202 TTTGGGTGCGAATTTGGAAGA
1 TTTGGGTGCGAATTTGGAAGA
*
55553223 TTTGGGCGCGAATTTGG
1 TTTGGGTGCGAATTTGG
55553240 TGGTTCGAGT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.20, C:0.07, G:0.39, T:0.34
Consensus pattern (21 bp):
TTTGGGTGCGAATTTGGAAGA
Found at i:55554020 original size:3 final size:3
Alignment explanation
Indices: 55554012--55554132 Score: 242
Period size: 3 Copynumber: 40.3 Consensus size: 3
55554002 TCATTAGTGT
55554012 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
55554060 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
55554108 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
55554133 ACATATATGT
Statistics
Matches: 118, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 118 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:55557042 original size:12 final size:11
Alignment explanation
Indices: 55557005--55557052 Score: 51
Period size: 12 Copynumber: 4.1 Consensus size: 11
55556995 AAGTCTAAGG
*
55557005 AAATAAAAAAA
1 AAATAAAAGAA
*
55557016 ACAACTAAAACAA
1 A-AA-TAAAAGAA
55557029 AAATAAAATGAA
1 AAATAAAA-GAA
55557041 AAATAAAAGAA
1 AAATAAAAGAA
55557052 A
1 A
55557053 TAAACTAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
11 10 0.31
12 14 0.44
13 8 0.25
ACGTcount: A:0.79, C:0.06, G:0.04, T:0.10
Consensus pattern (11 bp):
AAATAAAAGAA
Found at i:55557098 original size:12 final size:12
Alignment explanation
Indices: 55557083--55557123 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
55557073 AAATTAAAGG
55557083 TAATAGTAAAAA
1 TAATAGTAAAAA
55557095 TAATAGTAAAAA
1 TAATAGTAAAAA
* *
55557107 -ATTACTAAAAA
1 TAATAGTAAAAA
55557118 TAATAG
1 TAATAG
55557124 AAATAGCATA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
11 9 0.38
12 15 0.62
ACGTcount: A:0.63, C:0.02, G:0.07, T:0.27
Consensus pattern (12 bp):
TAATAGTAAAAA
Found at i:55557208 original size:23 final size:24
Alignment explanation
Indices: 55557169--55557223 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 24
55557159 TAAGCATAAG
*
55557169 AAAAATAAAACAAATAAGAAAA-A
1 AAAAATAAAACAAATAAAAAAATA
* * *
55557192 AATAATAAAGCAGATAAAAAAATA
1 AAAAATAAAACAAATAAAAAAATA
55557216 AAAAATAA
1 AAAAATAA
55557224 TATAACAAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
23 18 0.69
24 8 0.31
ACGTcount: A:0.78, C:0.04, G:0.05, T:0.13
Consensus pattern (24 bp):
AAAAATAAAACAAATAAAAAAATA
Found at i:55557263 original size:11 final size:11
Alignment explanation
Indices: 55557243--55557280 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
55557233 TAATAATGAG
55557243 AAAA-AAAATC
1 AAAATAAAATC
55557253 AAAATAAAATC
1 AAAATAAAATC
55557264 AAAATAAAA--
1 AAAATAAAATC
55557273 AAAATAAA
1 AAAATAAA
55557281 GTAAAAGTGG
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
9 8 0.30
10 4 0.15
11 15 0.56
ACGTcount: A:0.82, C:0.05, G:0.00, T:0.13
Consensus pattern (11 bp):
AAAATAAAATC
Found at i:55558135 original size:19 final size:19
Alignment explanation
Indices: 55558108--55558144 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
55558098 ATTTTCAGAA
*
55558108 TCCATACGGCCTGGGCATT
1 TCCACACGGCCTGGGCATT
*
55558127 TCCACACGGGCTGGGCAT
1 TCCACACGGCCTGGGCAT
55558145 ACACCTGTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.16, C:0.32, G:0.30, T:0.22
Consensus pattern (19 bp):
TCCACACGGCCTGGGCATT
Found at i:55564218 original size:42 final size:42
Alignment explanation
Indices: 55564096--55564263 Score: 156
Period size: 42 Copynumber: 3.9 Consensus size: 42
55564086 AGAAGCACAT
* * * *
55564096 AAGAGCTAAACAGAAACCCGTAAGGGTTGAACGGAAGCTCGT
1 AAGAGCTAAACAGAAACCCATAAGGGTTAAACTGAAGCTCGG
* * * *
55564138 AAGAGTTGAATAGAAACCCATAAGGGTTAATCTGAAGCTCGG
1 AAGAGCTAAACAGAAACCCATAAGGGTTAAACTGAAGCTCGG
* * * *
55564180 AAGAGCTAAACGGAAACCCATTAGAGTTAAACTAAAGCTCAAAAGAGG
1 AAGAGCTAAACAGAAACCCATAAGGGTTAAACTGAAGCTC------GG
* *
55564228 AAGAGCTAAACTGAAACCCAGAAGGGTTAAACTGAA
1 AAGAGCTAAACAGAAACCCATAAGGGTTAAACTGAA
55564264 ACTCATATGA
Statistics
Matches: 99, Mismatches: 21, Indels: 6
0.79 0.17 0.05
Matches are distributed among these distances:
42 66 0.67
48 33 0.33
ACGTcount: A:0.43, C:0.17, G:0.24, T:0.16
Consensus pattern (42 bp):
AAGAGCTAAACAGAAACCCATAAGGGTTAAACTGAAGCTCGG
Found at i:55570500 original size:44 final size:45
Alignment explanation
Indices: 55570445--55570549 Score: 124
Period size: 44 Copynumber: 2.4 Consensus size: 45
55570435 TGGTATAGTG
55570445 CCATAGTATCTTTCAACTAGGGT-ATTTCCTGTTCCGATT-TAATA
1 CCATAGTATCTTTCAACTAGGGTCATTTCCT-TTCCGATTATAATA
* * * * *
55570489 CCATAGTATCTTTCAATTATGGTCTTTTCCTTTTCGATTATAATG
1 CCATAGTATCTTTCAACTAGGGTCATTTCCTTTCCGATTATAATA
* *
55570534 TCATAATATCTTTCAA
1 CCATAGTATCTTTCAA
55570550 TCATGGTGTT
Statistics
Matches: 52, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
44 28 0.54
45 24 0.46
ACGTcount: A:0.26, C:0.19, G:0.10, T:0.45
Consensus pattern (45 bp):
CCATAGTATCTTTCAACTAGGGTCATTTCCTTTCCGATTATAATA
Found at i:55570545 original size:45 final size:45
Alignment explanation
Indices: 55570396--55570568 Score: 156
Period size: 45 Copynumber: 3.8 Consensus size: 45
55570386 TCCCGACATG
* * * *
55570396 ATGCCATAATATCTTTTAACTATGGTCTTGATCATTTTCTG-GTATA
1 ATGCCATAATATCTTTCAACTATGGTCTT-TTCCTTTTC-GATTATA
* * * * *
55570442 GTGCCATAGTATCTTTCAACTAGGGT-ATTTCCTGTTCCGATT-TA
1 ATGCCATAATATCTTTCAACTATGGTCTTTTCCT-TTTCGATTATA
* * *
55570486 ATACCATAGTATCTTTCAATTATGGTCTTTTCCTTTTCGATTATA
1 ATGCCATAATATCTTTCAACTATGGTCTTTTCCTTTTCGATTATA
* *
55570531 ATGTCATAATATCTTTCAA-TCATGGTGTTTTCCTTTTC
1 ATGCCATAATATCTTTCAACT-ATGGTCTTTTCCTTTTC
55570569 TAAAATCAAT
Statistics
Matches: 103, Mismatches: 19, Indels: 11
0.77 0.14 0.08
Matches are distributed among these distances:
44 36 0.35
45 45 0.44
46 22 0.21
ACGTcount: A:0.23, C:0.18, G:0.13, T:0.46
Consensus pattern (45 bp):
ATGCCATAATATCTTTCAACTATGGTCTTTTCCTTTTCGATTATA
Found at i:55576702 original size:28 final size:28
Alignment explanation
Indices: 55576671--55576788 Score: 148
Period size: 28 Copynumber: 4.2 Consensus size: 28
55576661 TTAGTGTGGG
**
55576671 AGACATTGATTATGTAACTTAGTGTATA
1 AGACATTGATTATGGCACTTAGTGTATA
* * *
55576699 AGACATCGATTATGGCACTTAGTGTGTG
1 AGACATTGATTATGGCACTTAGTGTATA
*
55576727 AGACATTGATTATGGCACTTAGTGT-TCG
1 AGACATTGATTATGGCACTTAGTGTAT-A
* *
55576755 AGACATTGATTGTGGCACTTAGTGTACA
1 AGACATTGATTATGGCACTTAGTGTATA
55576783 AGACAT
1 AGACAT
55576789 CGAGTATGCG
Statistics
Matches: 79, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
27 1 0.01
28 78 0.99
ACGTcount: A:0.30, C:0.13, G:0.24, T:0.34
Consensus pattern (28 bp):
AGACATTGATTATGGCACTTAGTGTATA
Found at i:55576747 original size:56 final size:56
Alignment explanation
Indices: 55576658--55576779 Score: 174
Period size: 56 Copynumber: 2.2 Consensus size: 56
55576648 CTATGTACGA
*
55576658 CACTTAGTGTGGGAGACATTGATTATGTAACTTAGTGTAT-AAGACATCGATTATGG
1 CACTTAGTGTGGGAGACATTGATTATGGAACTTAGTGT-TCAAGACATCGATTATGG
* * * * *
55576714 CACTTAGTGTGTGAGACATTGATTATGGCACTTAGTGTTCGAGACATTGATTGTGG
1 CACTTAGTGTGGGAGACATTGATTATGGAACTTAGTGTTCAAGACATCGATTATGG
55576770 CACTTAGTGT
1 CACTTAGTGT
55576780 ACAAGACATC
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
55 1 0.02
56 58 0.98
ACGTcount: A:0.26, C:0.12, G:0.26, T:0.35
Consensus pattern (56 bp):
CACTTAGTGTGGGAGACATTGATTATGGAACTTAGTGTTCAAGACATCGATTATGG
Found at i:55581421 original size:213 final size:213
Alignment explanation
Indices: 55581047--55581687 Score: 1246
Period size: 213 Copynumber: 3.0 Consensus size: 213
55581037 ATTTAGTATC
* *
55581047 TAGTAAGACTTTGCCTATAGAGTCTACTAAATTTGTGATTTGAGTATCGAACCCCTTAGGCAAGT
1 TAGTAAAACTTTGCCTATAGAGTCTACTAAATTTGTGATTTGAGTATCGAACCCCTTAGGAAAGT
55581112 GTGTTTTGATTGATAAAGTGTGCAAGAACTATCCGTTGATGATTCAGGATTTTTGTTTTCCTGTT
66 GTGTTTTGATTGATAAAGTGTGCAAGAACTATCCGTTGATGATTCAGGATTTTTGTTTTCCTGTT
55581177 GATCTCATGTTGTTGCCATTTGATGAATTTGATATAATTCTGGGTATGGATTGGCTAACGCTACA
131 GATCTCATGTTGTTGCCATTTGATGAATTTGATATAATTCTGGGTATGGATTGGCTAACGCTACA
55581242 TGACGCTATAGTAAGCTA
196 TGACGCTATAGTAAGCTA
55581260 TAGTAAAACTTTGCCTATAGAGTCTACTAAATTTGTGATTTGAGTATCGAACCCCTTAGGAAAGT
1 TAGTAAAACTTTGCCTATAGAGTCTACTAAATTTGTGATTTGAGTATCGAACCCCTTAGGAAAGT
55581325 GTGTTTTGATTGATAAAGTGTGCAAGAACTATCCGTTGATGATTCAGGATTTTTGTTTTCCTGTT
66 GTGTTTTGATTGATAAAGTGTGCAAGAACTATCCGTTGATGATTCAGGATTTTTGTTTTCCTGTT
*
55581390 GATCTGATGTTGTTGCCATTTGATGAATTTGATATAATTCTGGGTATGGATTGGCTAACGCTACA
131 GATCTCATGTTGTTGCCATTTGATGAATTTGATATAATTCTGGGTATGGATTGGCTAACGCTACA
55581455 TGACGCTATAGTAAGCTA
196 TGACGCTATAGTAAGCTA
*
55581473 TAGTAAAACTTTGCCTATAGAGTCTACTAAATTTGTGGTTTGAGTATCGAACCCCTTAGGAAAGT
1 TAGTAAAACTTTGCCTATAGAGTCTACTAAATTTGTGATTTGAGTATCGAACCCCTTAGGAAAGT
55581538 GTGTTTTGATTGATAAAGTGTGCAAGAACTATCCGTTGATGATTCAGGATTTTTGTTTTCCTGTT
66 GTGTTTTGATTGATAAAGTGTGCAAGAACTATCCGTTGATGATTCAGGATTTTTGTTTTCCTGTT
55581603 GATCTCATGTTGTTGCCATTTGATGAATTTGATATAATTCTGGGTATGGATTGGCTAACGCTACA
131 GATCTCATGTTGTTGCCATTTGATGAATTTGATATAATTCTGGGTATGGATTGGCTAACGCTACA
55581668 TGACGCTATAGTAAGCTA
196 TGACGCTATAGTAAGCTA
55581686 TA
1 TA
55581688 AATGAAAGAT
Statistics
Matches: 423, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
213 423 1.00
ACGTcount: A:0.26, C:0.14, G:0.22, T:0.38
Consensus pattern (213 bp):
TAGTAAAACTTTGCCTATAGAGTCTACTAAATTTGTGATTTGAGTATCGAACCCCTTAGGAAAGT
GTGTTTTGATTGATAAAGTGTGCAAGAACTATCCGTTGATGATTCAGGATTTTTGTTTTCCTGTT
GATCTCATGTTGTTGCCATTTGATGAATTTGATATAATTCTGGGTATGGATTGGCTAACGCTACA
TGACGCTATAGTAAGCTA
Found at i:55589254 original size:40 final size:40
Alignment explanation
Indices: 55589180--55589262 Score: 112
Period size: 40 Copynumber: 2.1 Consensus size: 40
55589170 GACATATCGA
* *
55589180 CTAAATGTGGCACTTAGTGTGCGGTTCAATATAGCTTCGG
1 CTAAATGTGGCACTTAGTGTGCGATTCAAGATAGCTTCGG
* ** *
55589220 CTAAATTTGGCACTTAGTGTGCGATTTGAGATAGCTTTGG
1 CTAAATGTGGCACTTAGTGTGCGATTCAAGATAGCTTCGG
55589260 CTA
1 CTA
55589263 TGTACGACAC
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.23, C:0.16, G:0.27, T:0.35
Consensus pattern (40 bp):
CTAAATGTGGCACTTAGTGTGCGATTCAAGATAGCTTCGG
Found at i:55589314 original size:28 final size:28
Alignment explanation
Indices: 55589270--55589372 Score: 161
Period size: 28 Copynumber: 3.7 Consensus size: 28
55589260 CTATGTACGA
* *
55589270 CACTTAGGGTGTGAGACATTGATTATGG
1 CACTTAGTGTGCGAGACATTGATTATGG
*
55589298 CACTTAGTGTGCTAGACATTGATTATGG
1 CACTTAGTGTGCGAGACATTGATTATGG
*
55589326 CACTTAGTGTGCGAGACATTGATTGTGG
1 CACTTAGTGTGCGAGACATTGATTATGG
*
55589354 CACTTAGTTTGCGAGACAT
1 CACTTAGTGTGCGAGACAT
55589373 CAAGTATGCG
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 69 1.00
ACGTcount: A:0.24, C:0.15, G:0.28, T:0.33
Consensus pattern (28 bp):
CACTTAGTGTGCGAGACATTGATTATGG
Found at i:55596931 original size:5 final size:5
Alignment explanation
Indices: 55596921--55596947 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
55596911 TCTAACATTA
55596921 TTCTT TTCTT TTCTT TTCTT TTCTT TT
1 TTCTT TTCTT TTCTT TTCTT TTCTT TT
55596948 TTGTGAATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TTCTT
Found at i:55602129 original size:16 final size:17
Alignment explanation
Indices: 55602084--55602135 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 17
55602074 GTATTAATAA
*
55602084 TTATGTTATTATATAAGAT
1 TTAT-TTATTATATAA-AC
*
55602103 TTATTTTTTATATAAAC
1 TTATTTATTATATAAAC
55602120 TT-TTTATTATGATAAA
1 TTATTTATTAT-ATAAA
55602136 TATATTTTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
16 7 0.24
17 8 0.28
18 10 0.34
19 4 0.14
ACGTcount: A:0.37, C:0.02, G:0.06, T:0.56
Consensus pattern (17 bp):
TTATTTATTATATAAAC
Found at i:55602246 original size:16 final size:17
Alignment explanation
Indices: 55602217--55602250 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
55602207 AATATGATTT
*
55602217 TATTTTTTTAAAATGAA
1 TATTTTATTAAAATGAA
55602234 TATTTTATT-AAATGAA
1 TATTTTATTAAAATGAA
55602250 T
1 T
55602251 TTATAAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (17 bp):
TATTTTATTAAAATGAA
Found at i:55614417 original size:30 final size:30
Alignment explanation
Indices: 55614352--55614420 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
55614342 ACCCCAGGGG
* *
55614352 ACACACGGCCATGTAACATAGCCGTGTGTC
1 ACACACGGCCAAGTAACATAGCCGTATGTC
*
55614382 ACACACGGCCAAGTAACATAG-TGCTATGTC
1 ACACACGGCCAAGTAACATAGCCG-TATGTC
*
55614412 GCACACGGC
1 ACACACGGC
55614421 TGAGACACAC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 1 0.03
30 33 0.97
ACGTcount: A:0.29, C:0.30, G:0.23, T:0.17
Consensus pattern (30 bp):
ACACACGGCCAAGTAACATAGCCGTATGTC
Found at i:55615505 original size:40 final size:40
Alignment explanation
Indices: 55615404--55615506 Score: 100
Period size: 40 Copynumber: 2.6 Consensus size: 40
55615394 ATCTCAGTAT
* * * *
55615404 CGCACACTTAGTGCCACATAAAGCTCAAGCTATTCCAATT
1 CGCACACTAAGTGCCAAATATAGCTCAAGCTATTCCAATA
*** * *
55615444 CGCACACTAAGTGCTGTATATAGCTGAAGCTATCTCGAA-A
1 CGCACACTAAGTGCCAAATATAGCTCAAGCTAT-TCCAATA
*
55615484 CGTACACTAAGTGCCAAATATAG
1 CGCACACTAAGTGCCAAATATAG
55615507 TAGATTTGTC
Statistics
Matches: 50, Mismatches: 12, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
40 46 0.92
41 4 0.08
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.24
Consensus pattern (40 bp):
CGCACACTAAGTGCCAAATATAGCTCAAGCTATTCCAATA
Found at i:55615943 original size:29 final size:29
Alignment explanation
Indices: 55615910--55615968 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
55615900 TATTTCACAC
*
55615910 ATTTAACCCCTCAATTTACACTTTT-CTCA
1 ATTTAACCCCT-AATATACACTTTTACTCA
* *
55615939 ATTTAATCCCTAATATACATTTTTACTCA
1 ATTTAACCCCTAATATACACTTTTACTCA
55615968 A
1 A
55615969 AATCACTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
28 11 0.42
29 15 0.58
ACGTcount: A:0.32, C:0.25, G:0.00, T:0.42
Consensus pattern (29 bp):
ATTTAACCCCTAATATACACTTTTACTCA
Found at i:55617484 original size:20 final size:20
Alignment explanation
Indices: 55617459--55617499 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
55617449 CCGAGTTTAT
55617459 GAGAGCAATTGTCATTAAAA
1 GAGAGCAATTGTCATTAAAA
55617479 GAGAGCAATTGTCATTAAAA
1 GAGAGCAATTGTCATTAAAA
55617499 G
1 G
55617500 GGATTTAGCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.44, C:0.10, G:0.22, T:0.24
Consensus pattern (20 bp):
GAGAGCAATTGTCATTAAAA
Found at i:55619994 original size:13 final size:13
Alignment explanation
Indices: 55619976--55620000 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
55619966 AAGTAATCGC
55619976 ACACGGGCGTGTT
1 ACACGGGCGTGTT
55619989 ACACGGGCGTGT
1 ACACGGGCGTGT
55620001 CCCTGCCGAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.24, G:0.40, T:0.20
Consensus pattern (13 bp):
ACACGGGCGTGTT
Found at i:55620059 original size:13 final size:13
Alignment explanation
Indices: 55620041--55620066 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
55620031 GAAAAGGTTA
55620041 ATTTTGAGGGCTC
1 ATTTTGAGGGCTC
55620054 ATTTTGAGGGCTC
1 ATTTTGAGGGCTC
55620067 TTAGGCATTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.15, G:0.31, T:0.38
Consensus pattern (13 bp):
ATTTTGAGGGCTC
Found at i:55637850 original size:16 final size:17
Alignment explanation
Indices: 55637818--55637850 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
55637808 GTTACACGAA
55637818 CTTACTTAGCATTTTATG
1 CTTACTTAG-ATTTTATG
55637836 CTTACTTAG-TTTTAT
1 CTTACTTAGATTTTAT
55637851 TTCCCTGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
18 9 0.60
ACGTcount: A:0.21, C:0.15, G:0.09, T:0.55
Consensus pattern (17 bp):
CTTACTTAGATTTTATG
Found at i:55644064 original size:40 final size:40
Alignment explanation
Indices: 55643994--55644170 Score: 187
Period size: 40 Copynumber: 4.5 Consensus size: 40
55643984 ACCCAAGTAT
* *
55643994 CTTCGGGAT-TTAG-CCGGATATAACAGCTCGCACCAATGC
1 CTTCGGG-TCTTAGCCCGGATATAACAACTCGCACAAATGC
*
55644033 CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAACAACTCGCACAAATGC
* * * *
55644073 CTTCGGGTCTTAGCCCGAATATAACCACTAGCATAAATGC
1 CTTCGGGTCTTAGCCCGGATATAACAACTCGCACAAATGC
* * * * * * *
55644113 CTTCGGGACATAGCTCGGATATAGCAACTTGCACGAATTC
1 CTTCGGGTCTTAGCCCGGATATAACAACTCGCACAAATGC
* *
55644153 CTTCGGATCTTAGTCCGG
1 CTTCGGGTCTTAGCCCGG
55644171 TTATCATACG
Statistics
Matches: 113, Mismatches: 23, Indels: 3
0.81 0.17 0.02
Matches are distributed among these distances:
38 1 0.01
39 11 0.10
40 101 0.89
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CTTCGGGTCTTAGCCCGGATATAACAACTCGCACAAATGC
Found at i:55648697 original size:43 final size:43
Alignment explanation
Indices: 55648650--55648757 Score: 123
Period size: 43 Copynumber: 2.5 Consensus size: 43
55648640 TAGCCCAGCT
*
55648650 ATGGTCTTACACGA-AATTA-ATTAACGATGCCAATGT-CTCAAAC
1 ATGGTCTTACAC-ATAATCACA-TAACGATGCCAATGTCCT-AAAC
* * *
55648693 ATGGTCTTACACATAATCACATAATGATGCCAATGTCCTAGAT
1 ATGGTCTTACACATAATCACATAACGATGCCAATGTCCTAAAC
*
55648736 ATGGTCTTACACATAATTACAT
1 ATGGTCTTACACATAATCACAT
55648758 CTCGATAATC
Statistics
Matches: 57, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
42 1 0.02
43 53 0.93
44 3 0.05
ACGTcount: A:0.36, C:0.20, G:0.13, T:0.31
Consensus pattern (43 bp):
ATGGTCTTACACATAATCACATAACGATGCCAATGTCCTAAAC
Found at i:55649286 original size:29 final size:28
Alignment explanation
Indices: 55649240--55649299 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 28
55649230 CTTTCATTTA
* *
55649240 TTTCACATTTCAACCCCTCAATTT-ACATT
1 TTTCACAATTAAACCCCT--ATTTGACATT
*
55649269 TTTCACAATTAAATCCCTATTTGACATT
1 TTTCACAATTAAACCCCTATTTGACATT
55649297 TTT
1 TTT
55649300 GTCAAAAATC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 4 0.15
28 8 0.30
29 15 0.56
ACGTcount: A:0.28, C:0.25, G:0.02, T:0.45
Consensus pattern (28 bp):
TTTCACAATTAAACCCCTATTTGACATT
Found at i:55650627 original size:6 final size:6
Alignment explanation
Indices: 55650597--55650727 Score: 74
Period size: 6 Copynumber: 21.3 Consensus size: 6
55650587 AAGAAACATT
* * *
55650597 ATCAGA A-CTAGA ATCAAA ATGAGA ATCAGA ATCAGA ATCAG- GTGACAGA
1 ATCAGA ATC-AGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA AT--CAGA
* * *
55650646 ATCAAA ATCAGA ATCAGA ATCAGA ATTAGGTGA A--AGA ATTAGA ATCAGA
1 ATCAGA ATCAGA ATCAGA ATCAGA ATCA---GA ATCAGA ATCAGA ATCAGA
* * *
55650695 ATCAGT ATCAGGTA A-CAGA ATCAAA ATAAGA AT
1 ATCAGA ATCA-G-A ATCAGA ATCAGA ATCAGA AT
55650728 GTGAATGCAA
Statistics
Matches: 97, Mismatches: 15, Indels: 26
0.70 0.11 0.19
Matches are distributed among these distances:
4 3 0.03
5 4 0.04
6 77 0.79
7 8 0.08
8 2 0.02
9 3 0.03
ACGTcount: A:0.50, C:0.12, G:0.18, T:0.19
Consensus pattern (6 bp):
ATCAGA
Found at i:55650652 original size:37 final size:36
Alignment explanation
Indices: 55650606--55650727 Score: 146
Period size: 37 Copynumber: 3.4 Consensus size: 36
55650596 TATCAGAACT
55650606 AGAATCAAAATGAGAATCAGAATCAGAATCAGGTGAC
1 AGAATCAAAAT-AGAATCAGAATCAGAATCAGGTGAC
* *
55650643 AGAATCAAAATCAGAATCAGAATCAGAATTAGGTGAA
1 AGAATCAAAAT-AGAATCAGAATCAGAATCAGGTGAC
* *
55650680 AGAAT-----TAGAATCAGAATCAGTATCAGGTAAC
1 AGAATCAAAATAGAATCAGAATCAGAATCAGGTGAC
55650711 AGAATCAAAATAAGAAT
1 AGAATCAAAAT-AGAAT
55650728 GTGAATGCAA
Statistics
Matches: 72, Mismatches: 7, Indels: 12
0.79 0.08 0.13
Matches are distributed among these distances:
31 26 0.36
32 1 0.01
36 1 0.01
37 44 0.61
ACGTcount: A:0.51, C:0.11, G:0.19, T:0.19
Consensus pattern (36 bp):
AGAATCAAAATAGAATCAGAATCAGAATCAGGTGAC
Found at i:55650657 original size:31 final size:31
Alignment explanation
Indices: 55650620--55650727 Score: 108
Period size: 31 Copynumber: 3.3 Consensus size: 31
55650610 TCAAAATGAG
55650620 AATCAGAATCAGAATCAGGTGACAGAATCAA
1 AATCAGAATCAGAATCAGGTGACAGAATCAA
* * *
55650651 AATCAGAATCAGAATCAGAATTAGGTGAAAGAATTAG
1 AATCAGAATCAGAATC------AGGTGACAGAATCAA
* *
55650688 AATCAGAATCAGTATCAGGTAACAGAATCAA
1 AATCAGAATCAGAATCAGGTGACAGAATCAA
*
55650719 AATAAGAAT
1 AATCAGAAT
55650728 GTGAATGCAA
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
31 35 0.56
37 27 0.44
ACGTcount: A:0.50, C:0.12, G:0.19, T:0.19
Consensus pattern (31 bp):
AATCAGAATCAGAATCAGGTGACAGAATCAA
Found at i:55650894 original size:27 final size:26
Alignment explanation
Indices: 55650846--55650905 Score: 66
Period size: 27 Copynumber: 2.3 Consensus size: 26
55650836 GCGAGGCTGC
*
55650846 CAGATATTGTGACGAAGTCACCAGATA
1 CAGATATTGTGACGAAGCCACCAGA-A
* * *
55650873 CAGATATTGTGGCTAGGCCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
*
55650899 CAAATAT
1 CAGATAT
55650906 ATATATGTGG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 7 0.25
27 21 0.75
ACGTcount: A:0.37, C:0.20, G:0.22, T:0.22
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:55650992 original size:27 final size:26
Alignment explanation
Indices: 55650944--55650995 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
55650934 GCGAGGCTGC
*
55650944 CAGATATTGTGACGAAGTCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
* *
55650970 CAGATATATGTGGCGAGGCCACCAGA
1 CAGATAT-TGTGACGAAGCCACCAGA
55650996 TTGCAGCGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.35, C:0.21, G:0.27, T:0.17
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:55651280 original size:27 final size:27
Alignment explanation
Indices: 55651231--55651478 Score: 316
Period size: 27 Copynumber: 9.2 Consensus size: 27
55651221 AACACCTTAG
* * * *
55651231 GGGTAAAACAGTAATTTTATAAATTGA
1 GGGTAAAACGGTAATTCTGTAAATCGA
*
55651258 GGGTAAAACAGTAATTCTGTAAATCGA
1 GGGTAAAACGGTAATTCTGTAAATCGA
* *
55651285 GGATAAAACGGTAATTCTGTAAATCAA
1 GGGTAAAACGGTAATTCTGTAAATCGA
* * ** *
55651312 TGATAAAATAGTAATTTTGTAAATCGA
1 GGGTAAAACGGTAATTCTGTAAATCGA
*
55651339 GGGTAAAACGGTAATTCTGTAAATCAA
1 GGGTAAAACGGTAATTCTGTAAATCGA
*
55651366 GGGTAAAACAGTAATTCTGTAAATCGA
1 GGGTAAAACGGTAATTCTGTAAATCGA
* * *
55651393 GGGTAAAATGGTAATTTTATAAATCGA
1 GGGTAAAACGGTAATTCTGTAAATCGA
*
55651420 GGGTAAAATGGTAATTCTGTAAATCGA
1 GGGTAAAACGGTAATTCTGTAAATCGA
* *
55651447 GGGTAAAACGGTAATTTTGTAAATTGA
1 GGGTAAAACGGTAATTCTGTAAATCGA
55651474 GGGTA
1 GGGTA
55651479 CTTTGATAAT
Statistics
Matches: 193, Mismatches: 28, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 193 1.00
ACGTcount: A:0.41, C:0.07, G:0.22, T:0.30
Consensus pattern (27 bp):
GGGTAAAACGGTAATTCTGTAAATCGA
Found at i:55651476 original size:81 final size:81
Alignment explanation
Indices: 55651231--55651478 Score: 370
Period size: 81 Copynumber: 3.1 Consensus size: 81
55651221 AACACCTTAG
* * * *
55651231 GGGTAAAACAGTAATTTTATAAATTGAGGGTAAAACAGTAATTCTGTAAATCGAGGATAAAACGG
1 GGGTAAAATAGTAATTTTATAAATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACGG
*
55651296 TAATTCTGTAAATCAA
66 TAATTCTGTAAATCGA
* * * * *
55651312 TGATAAAATAGTAATTTTGTAAATCGAGGGTAAAACGGTAATTCTGTAAATCAAGGGTAAAACAG
1 GGGTAAAATAGTAATTTTATAAATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACGG
55651377 TAATTCTGTAAATCGA
66 TAATTCTGTAAATCGA
* *
55651393 GGGTAAAATGGTAATTTTATAAATCGAGGGTAAAATGGTAATTCTGTAAATCGAGGGTAAAACGG
1 GGGTAAAATAGTAATTTTATAAATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACGG
* *
55651458 TAATTTTGTAAATTGA
66 TAATTCTGTAAATCGA
55651474 GGGTA
1 GGGTA
55651479 CTTTGATAAT
Statistics
Matches: 148, Mismatches: 19, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
81 148 1.00
ACGTcount: A:0.41, C:0.07, G:0.22, T:0.30
Consensus pattern (81 bp):
GGGTAAAATAGTAATTTTATAAATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACGG
TAATTCTGTAAATCGA
Found at i:55651529 original size:27 final size:27
Alignment explanation
Indices: 55651457--55651623 Score: 130
Period size: 27 Copynumber: 6.3 Consensus size: 27
55651447 GGGTAAAACG
** * *
55651457 GTAATTTTGTAAATTGAGGGTACTTTGA
1 GTAATTTTACAAACTGAGGGTA-TTTCA
*
55651485 -TAA-TTTACAAGTCT-AGGGTATTTCA
1 GTAATTTTACAA-ACTGAGGGTATTTCA
*
55651510 GTAATTTTACAAACTGAGGGTATTTCG
1 GTAATTTTACAAACTGAGGGTATTTCA
* * **
55651537 GTAATTCTACAAA-TCGAGGATATTTGG
1 GTAATTTTACAAACT-GAGGGTATTTCA
* * *
55651564 GTAATTTTATAAACTGGGGGTACTTT-G
1 GTAATTTTACAAACTGAGGGTA-TTTCA
*
55651591 GTAATTTTAC-AACTGGGGGTATTTCA
1 GTAATTTTACAAACTGAGGGTATTTCA
55651617 GTAATTT
1 GTAATTT
55651624 GGTAAACTAA
Statistics
Matches: 115, Mismatches: 16, Indels: 18
0.77 0.11 0.12
Matches are distributed among these distances:
25 7 0.06
26 35 0.30
27 69 0.60
28 4 0.03
ACGTcount: A:0.29, C:0.09, G:0.22, T:0.40
Consensus pattern (27 bp):
GTAATTTTACAAACTGAGGGTATTTCA
Found at i:55651570 original size:54 final size:53
Alignment explanation
Indices: 55651402--55651602 Score: 172
Period size: 54 Copynumber: 3.7 Consensus size: 53
55651392 AGGGTAAAAT
*** ** * ***
55651402 GGTAATTTTATAAA-TCGAGGGTAAAATGGTAATTCTGTAAATCGAGGGTAAAAC
1 GGTAATTTTATAAACT-GAGGGTACTTTGGTAATT-TACAAATCGAGGATATTTC
* * * * * *
55651456 GGTAATTTTGTAAATTGAGGGTACTTTGATAATTTACAAGTCTAGGGTATTTC
1 GGTAATTTTATAAACTGAGGGTACTTTGGTAATTTACAAATCGAGGATATTTC
* * *
55651509 AGTAATTTTACAAACTGAGGGTA-TTTCGGTAATTCTACAAATCGAGGATATTTG
1 GGTAATTTTATAAACTGAGGGTACTTT-GGTAATT-TACAAATCGAGGATATTTC
*
55651563 GGTAATTTTATAAACTGGGGGTACTTTGGTAATTTTACAA
1 GGTAATTTTATAAACTGAGGGTACTTTGGTAA-TTTACAA
55651603 CTGGGGGTAT
Statistics
Matches: 118, Mismatches: 24, Indels: 10
0.78 0.16 0.07
Matches are distributed among these distances:
52 3 0.03
53 37 0.31
54 72 0.61
55 6 0.05
ACGTcount: A:0.33, C:0.08, G:0.22, T:0.36
Consensus pattern (53 bp):
GGTAATTTTATAAACTGAGGGTACTTTGGTAATTTACAAATCGAGGATATTTC
Found at i:55651631 original size:27 final size:25
Alignment explanation
Indices: 55651564--55651623 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 25
55651554 GGATATTTGG
*
55651564 GTAATTTTATAAACTGGGGGTACTTTG
1 GTAA-TTT-TAAACTGGGGGTACTTTA
55651591 GTAATTTTACAACTGGGGGTA-TTTCA
1 GTAATTTTA-AACTGGGGGTACTTT-A
55651617 GTAATTT
1 GTAATTT
55651624 GGTAAACTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
25 5 0.17
26 21 0.70
27 4 0.13
ACGTcount: A:0.27, C:0.08, G:0.23, T:0.42
Consensus pattern (25 bp):
GTAATTTTAAACTGGGGGTACTTTA
Found at i:55657272 original size:20 final size:20
Alignment explanation
Indices: 55657241--55657292 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
55657231 TAAAAATCAT
*
55657241 TTAAAATGATTTTAACTTCA
1 TTAAAATCATTTTAACTTCA
* * **
55657261 TTGAAATCATTTTGACTTGG
1 TTAAAATCATTTTAACTTCA
55657281 TTAAAATCATTT
1 TTAAAATCATTT
55657293 GCACTTGATT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.35, C:0.10, G:0.10, T:0.46
Consensus pattern (20 bp):
TTAAAATCATTTTAACTTCA
Found at i:55666459 original size:14 final size:14
Alignment explanation
Indices: 55666440--55666467 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
55666430 GCACAGCCGA
55666440 AGGGAGAGGGAGAG
1 AGGGAGAGGGAGAG
55666454 AGGGAGAGGGAGAG
1 AGGGAGAGGGAGAG
55666468 GCAGCGAAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.64, T:0.00
Consensus pattern (14 bp):
AGGGAGAGGGAGAG
Found at i:55670680 original size:24 final size:24
Alignment explanation
Indices: 55670648--55670934 Score: 87
Period size: 27 Copynumber: 11.0 Consensus size: 24
55670638 CTCTTCCTCT
55670648 TCTCTCCTTC-GAGCATCCTCTTCC
1 TCTCTCCTTCTG-GCATCCTCTTCC
*
55670672 TCTCTCCTTCTGGCCTCCTCTTCC
1 TCTCTCCTTCTGGCATCCTCTTCC
* * * *
55670696 TCT-TCCGTACTAGCTTCTTCTTCCTCC
1 TCTCTCC-TTCTGGCATC--C-TCTTCC
* *
55670723 TCTCTCCTCCTGGCCTCTTCTTCCTCCTCC
1 TCTCTCCTTCTGGCATC--C-T-CT--TCC
* * *
55670753 TCTCTCCTTCTGGCCTCCTTTTCT
1 TCTCTCCTTCTGGCATCCTCTTCC
* *
55670777 TCTCTTCTCTTAGCT-TCTTCCTCTTCC
1 TCTC-TC-CTT--CTGGCATCCTCTTCC
* *
55670804 TCTCTCCTCCTCTTAGCTTCCTCTTCC
1 TCTCTCCT--TC-TGGCATCCTCTTCC
* *
55670831 TCTCTCCTTCTCTTAGCTTCTTCCTCTTCC
1 TCTCTCC-T-TC-T-G--GCATCCTCTTCC
* * **
55670861 TCTCTCCTTCTGGCCTCCTTTTTT
1 TCTCTCCTTCTGGCATCCTCTTCC
* *
55670885 TCTCTTCTCTTAGCT-TCTTCCTCTTCC
1 TCTC-TC-CTT--CTGGCATCCTCTTCC
*
55670912 TCTCTCCTTCTGGCTTCCTCTTC
1 TCTCTCCTTCTGGCATCCTCTTC
55670935 TTCTTCCCTT
Statistics
Matches: 207, Mismatches: 30, Indels: 52
0.72 0.10 0.18
Matches are distributed among these distances:
23 5 0.02
24 58 0.28
25 11 0.05
26 14 0.07
27 69 0.33
28 12 0.06
29 1 0.00
30 37 0.18
ACGTcount: A:0.03, C:0.44, G:0.06, T:0.47
Consensus pattern (24 bp):
TCTCTCCTTCTGGCATCCTCTTCC
Found at i:55670741 original size:27 final size:27
Alignment explanation
Indices: 55670669--55670760 Score: 93
Period size: 27 Copynumber: 3.5 Consensus size: 27
55670659 AGCATCCTCT
* *
55670669 TCCTCTCTCCTTCTGGCCTCCTCTTCC
1 TCCTCTCTCCTCCTGGCCTCTTCTTCC
* * * *
55670696 T-CT-TC-CGTACTAGCTTCTTCTTCC
1 TCCTCTCTCCTCCTGGCCTCTTCTTCC
55670720 TCCTCTCTCCTCCTGGCCTCTTCTTCC
1 TCCTCTCTCCTCCTGGCCTCTTCTTCC
55670747 TCCTC-CTCTCTCCT
1 TCCTCTCTC-CTCCT
55670761 TCTGGCCTCC
Statistics
Matches: 52, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
24 15 0.29
25 4 0.08
26 7 0.13
27 26 0.50
ACGTcount: A:0.02, C:0.49, G:0.07, T:0.42
Consensus pattern (27 bp):
TCCTCTCTCCTCCTGGCCTCTTCTTCC
Found at i:55670749 original size:17 final size:15
Alignment explanation
Indices: 55670721--55670769 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
55670711 TCTTCTTCCT
55670721 CCTCTCTCCTCCTGG
1 CCTCTCTCCTCCTGG
55670736 CCTCTTCTTCCTCCT--
1 CCTC-TC-TCCTCCTGG
*
55670751 CCTCTCTCCTTCTGG
1 CCTCTCTCCTCCTGG
55670766 CCTC
1 CCTC
55670770 CTTTTCTTCT
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
13 6 0.21
14 2 0.07
15 12 0.41
16 2 0.07
17 7 0.24
ACGTcount: A:0.00, C:0.53, G:0.08, T:0.39
Consensus pattern (15 bp):
CCTCTCTCCTCCTGG
Found at i:55670778 original size:108 final size:105
Alignment explanation
Indices: 55670642--55670919 Score: 273
Period size: 108 Copynumber: 2.6 Consensus size: 105
55670632 AGCTCCCTCT
* * * *
55670642 TCCTCTTCTCTCCTTC-GAGCATCCTCTTCCTCTC-TC-CTT-CTGGCCTCCTCTTCCTCT-TCC
1 TCCTCCTCTCTCCTTCTG-GCCTCCTTTTCTTCTCTTCTCTTACT-GCCTCCTCTTCCTCTCTCC
*
55670702 GTACTAGCTT-CTTCTTCCTCCTCTCTCCTCCTGGCCT-CTTCTTCC
64 -TACT--CTTACTTCCTCCTCCTCTCTCCTCCT--CCTACTTCTTCC
* *
55670747 TCCTCCTCTCTCCTTCTGGCCTCCTTTTCTTCTCTTCTCTTAGCTTCTTCCTCTTCCTCTCTCCT
1 TCCTCCTCTCTCCTTCTGGCCTCCTTTTCTTCTCTTCTCTTA-CTGCCTCCTCTTCCTCTCTCCT
* * * *
55670812 CCTCTTAGCTTCCTCTTCCTCTCTCCTTCTCTTAGCTTCTTCC
65 ACTCTTA-CTTCCTCCTCCTCTCTCCTCCTCCTA-CTTCTTCC
* * * *
55670855 TCTTCCTCTCTCCTTCTGGCCTCCTTTTTTTCTCTTCTCTTAGCTTCTTCCTCTTCCTCTCTCCT
1 TCCTCCTCTCTCCTTCTGGCCTCCTTTTCTTCTCTTCTCTTA-CTGCCTCCTCTTCCTCTCTCCT
55670920 TCTGGCTTCC
Statistics
Matches: 150, Mismatches: 13, Indels: 17
0.83 0.07 0.09
Matches are distributed among these distances:
105 28 0.19
106 8 0.05
107 3 0.02
108 106 0.71
109 5 0.03
ACGTcount: A:0.03, C:0.45, G:0.06, T:0.47
Consensus pattern (105 bp):
TCCTCCTCTCTCCTTCTGGCCTCCTTTTCTTCTCTTCTCTTACTGCCTCCTCTTCCTCTCTCCTA
CTCTTACTTCCTCCTCCTCTCTCCTCCTCCTACTTCTTCC
Found at i:55670791 original size:81 final size:80
Alignment explanation
Indices: 55670663--55670814 Score: 218
Period size: 81 Copynumber: 1.9 Consensus size: 80
55670653 CCTTCGAGCA
* *
55670663 TCCTCTTCCTCTCTCCTTCTGGCCTCCTCTTCCTCTTCCGTACTAGCTTCTTCTTCCTCCTCTCT
1 TCCTCCTCCTCTCTCCTTCTGGCCTCCTCTTCCTCTTCCGTA-TAGCTTCTTCCTCCTCCTCTCT
55670728 CCTCCTGGCCTCTTCT
65 CCTCCTGGCCTCTTCT
* *
55670744 TCCTCCTCCTCTCTCCTTCTGGCCTCCTTTTCTTCTCTTCTC-T-TAGCTTCTTCCTCTTCCTCT
1 TCCTCCTCCTCTCTCCTTCTGGCCTCCTCTTC--CTCTTC-CGTATAGCTTCTTCCTCCTCCTCT
55670807 CTCCTCCT
63 CTCCTCCT
55670815 CTTAGCTTCC
Statistics
Matches: 64, Mismatches: 4, Indels: 6
0.86 0.05 0.08
Matches are distributed among these distances:
81 56 0.88
83 7 0.11
84 1 0.02
ACGTcount: A:0.02, C:0.47, G:0.06, T:0.45
Consensus pattern (80 bp):
TCCTCCTCCTCTCTCCTTCTGGCCTCCTCTTCCTCTTCCGTATAGCTTCTTCCTCCTCCTCTCTC
CTCCTGGCCTCTTCT
Found at i:55670794 original size:51 final size:51
Alignment explanation
Indices: 55670739--55670938 Score: 283
Period size: 51 Copynumber: 3.8 Consensus size: 51
55670729 CTCCTGGCCT
*
55670739 CTTCTTCCTCCTCCTCTCTCCTTCTGGCCTCCTTTTCTTCTCTTCTCTTAG
1 CTTCTTCCTCTTCCTCTCTCCTTCTGGCCTCCTTTTCTTCTCTTCTCTTAG
* * *
55670790 CTTCTTCCTCTTCCTCTCTCCTCCTCTTAGCTTCCTCTTCCTCTCTCCTTCTCTTAG
1 CTTCTTCCTCTTCCTCTCTCCT--TC-TGGCCTCCT-TTTCT-TCT-CTTCTCTTAG
*
55670847 CTTCTTCCTCTTCCTCTCTCCTTCTGGCCTCCTTTTTTTCTCTTCTCTTAG
1 CTTCTTCCTCTTCCTCTCTCCTTCTGGCCTCCTTTTCTTCTCTTCTCTTAG
* *
55670898 CTTCTTCCTCTTCCTCTCTCCTTCTGGCTTCCTCTTCTTCT
1 CTTCTTCCTCTTCCTCTCTCCTTCTGGCCTCCTTTTCTTCT
55670939 TCCCTTCTCT
Statistics
Matches: 132, Mismatches: 11, Indels: 12
0.85 0.07 0.08
Matches are distributed among these distances:
51 69 0.52
52 3 0.02
53 5 0.04
54 14 0.11
55 6 0.05
56 3 0.02
57 32 0.24
ACGTcount: A:0.02, C:0.43, G:0.05, T:0.50
Consensus pattern (51 bp):
CTTCTTCCTCTTCCTCTCTCCTTCTGGCCTCCTTTTCTTCTCTTCTCTTAG
Found at i:55670798 original size:27 final size:27
Alignment explanation
Indices: 55670768--55670916 Score: 103
Period size: 27 Copynumber: 5.5 Consensus size: 27
55670758 CCTTCTGGCC
55670768 TCCTTTTCTTCTCTTCTCTTAGCTTCT
1 TCCTTTTCTTCTCTTCTCTTAGCTTCT
* * *
55670795 TCCTCTTCCTCTCTCCTCCTCTTAGCTTCC
1 TCCT-TTTCT-TCT-CTTCTCTTAGCTTCT
*
55670825 T-C-TTCCTCTCTCCTTCTCTTAGCTTCT
1 TCCTTTTCT-TCT-CTTCTCTTAGCTTCT
* * * *
55670852 TCCTCTTCCTCTC-TC-CTT--CTGGCC
1 TCCTTTTCTTCTCTTCTCTTAGCT-TCT
*
55670876 TCCTTTTTTTCTCTTCTCTTAGCTTCT
1 TCCTTTTCTTCTCTTCTCTTAGCTTCT
* *
55670903 TCCTCTTCCTCTCT
1 TCCTTTTCTTCTCT
55670917 CCTTCTGGCT
Statistics
Matches: 94, Mismatches: 18, Indels: 20
0.71 0.14 0.15
Matches are distributed among these distances:
23 2 0.02
24 11 0.12
25 5 0.05
26 5 0.05
27 41 0.44
28 10 0.11
29 6 0.06
30 14 0.15
ACGTcount: A:0.03, C:0.42, G:0.04, T:0.52
Consensus pattern (27 bp):
TCCTTTTCTTCTCTTCTCTTAGCTTCT
Found at i:55670934 original size:81 final size:81
Alignment explanation
Indices: 55670663--55671018 Score: 208
Period size: 81 Copynumber: 4.4 Consensus size: 81
55670653 CCTTCGAGCA
* * * *
55670663 TCCTCTTCCTCTCTCCTTCTGGCCTCCTCTTCCTCTTCCGTACTAGCTTCT-----TCTTCCTCC
1 TCCTCTTCCTCTCTCCTTCTGGCTTCCTCTTCCTCTTCCCTTCT--CTTCTGGGCCTCTTCTTCC
* * * *
55670723 TCTCTCCTCCTGGCCTCTTCT
64 GCTTTCCTCTTAG---CTTCT
* * * * ** * *
55670744 TCCTCCTCCTCTCTCCTTCTGGCCTCCTTTTCTTCTCTTCTCTTAGCTTCT--TCCTCTTCCT-C
1 TCCTCTTCCTCTCTCCTTCTGGCTTCCTCTTC--CTCTTCCCTTCTCTTCTGGGCCTCTTCTTCC
* *
55670806 TCTCCTCCTCTTAG---CT
64 GCT-TTCCTCTTAGCTTCT
*
55670822 TCCTCTTCCTCTCTCCTTCT--CTTAGCTTCTTCCTCTT-CCTCTCTCCTTCT-GGCCTCCTT-T
1 TCCTCTTCCTCTCTCCTTCTGGCTT--CCTCTTCCTCTTCCCT-TCT-CTTCTGGGCCT-CTTCT
***
55670882 TTTTCTCTT-CTCTTAGCTTCT
61 TCCGCT-TTCCTCTTAGCTTCT
* *
55670903 TCCTCTTCCTCTCTCCTTCTGGCTTCCTCTTCTTCTTCCCTTCTCTTTTGGGCCTCTTCTTCCGC
1 TCCTCTTCCTCTCTCCTTCTGGCTTCCTCTTCCTCTTCCCTTCTCTTCTGGGCCTCTTCTTCCGC
55670968 TTTCCTCTTAGCTTCT
66 TTTCCTCTTAGCTTCT
* * *
55670984 TCCTCCT-CTCTTCTCTTTCTGGCCTCCTCTTCCTC
1 TCCTCTTCCTC-TCTCCTTCTGGCTTCCTCTTCCTC
55671019 CTCTTTCCTC
Statistics
Matches: 222, Mismatches: 30, Indels: 46
0.74 0.10 0.15
Matches are distributed among these distances:
75 2 0.01
76 8 0.04
77 5 0.02
78 37 0.17
79 8 0.04
80 12 0.05
81 118 0.53
82 3 0.01
83 14 0.06
84 15 0.07
ACGTcount: A:0.02, C:0.44, G:0.06, T:0.48
Consensus pattern (81 bp):
TCCTCTTCCTCTCTCCTTCTGGCTTCCTCTTCCTCTTCCCTTCTCTTCTGGGCCTCTTCTTCCGC
TTTCCTCTTAGCTTCT
Found at i:55670937 original size:108 final size:106
Alignment explanation
Indices: 55670687--55670949 Score: 333
Period size: 108 Copynumber: 2.5 Consensus size: 106
55670677 CCTTCTGGCC
* * * * *
55670687 TCCTCTTCCTCT-TCCGTACTAGCTTCTTCTTCCTCCTCTCTCCTCCTGGCCTCTTCTTCCTCCT
1 TCCTCTTCCTCTCTCC-TTCTAGCTTCCTCTTCTTCCTCTCTCCTTCT--CTTCTTCTTCCTCCT
55670751 CCTCTCTCCTTCTGGCCTCCTTTTCTTCTCTTCTCTTAGCTTCT
63 CCTCTCTCCTTCTGGCCTCCTTTTCTTCTCTTCTCTTAGCTTCT
55670795 TCCTCTTCCTCTCTCCTCCTCTTAGCTT-C-C-TCTTCCTCTCTCCTTCTCTTAGCTTCTTCCTC
1 TCCTCTTCCTCTCTCCT--TC-TAGCTTCCTCTTCTTCCTCTCTCCTTCTCTT--CTTCTTCCTC
* *
55670857 TTCCTCTCTCCTTCTGGCCTCCTTTTTTTCTCTTCTCTTAGCTTCT
61 CTCCTCTCTCCTTCTGGCCTCCTTTTCTTCTCTTCTCTTAGCTTCT
*
55670903 TCCTCTTCCTCTCTCCTTCTGGCTTCCTCTTCTT-CT-TC-CCTTCTCTT
1 TCCTCTTCCTCTCTCCTTCTAGCTTCCTCTTCTTCCTCTCTCCTTCTCTT
55670950 TTGGGCCTCT
Statistics
Matches: 138, Mismatches: 8, Indels: 21
0.83 0.05 0.13
Matches are distributed among these distances:
105 14 0.10
106 7 0.05
107 3 0.02
108 103 0.75
109 4 0.03
110 1 0.01
111 6 0.04
ACGTcount: A:0.02, C:0.44, G:0.05, T:0.49
Consensus pattern (106 bp):
TCCTCTTCCTCTCTCCTTCTAGCTTCCTCTTCTTCCTCTCTCCTTCTCTTCTTCTTCCTCCTCCT
CTCTCCTTCTGGCCTCCTTTTCTTCTCTTCTCTTAGCTTCT
Found at i:55670946 original size:24 final size:24
Alignment explanation
Indices: 55670850--55670934 Score: 82
Period size: 24 Copynumber: 3.4 Consensus size: 24
55670840 CTCTTAGCTT
55670850 CTTCCTCTTCCTCTCTCCTTCTGG
1 CTTCCTCTTCCTCTCTCCTTCTGG
* * ** *
55670874 CCTCCTTTTTTTCTCTTCTCTTAGCT-T
1 CTTCCTCTTCCTCTC-TC-CTT--CTGG
55670901 CTTCCTCTTCCTCTCTCCTTCTGG
1 CTTCCTCTTCCTCTCTCCTTCTGG
55670925 CTTCCTCTTC
1 CTTCCTCTTC
55670935 TTCTTCCCTT
Statistics
Matches: 46, Mismatches: 10, Indels: 10
0.70 0.15 0.15
Matches are distributed among these distances:
23 2 0.04
24 21 0.46
25 5 0.11
26 5 0.11
27 11 0.24
28 2 0.04
ACGTcount: A:0.01, C:0.42, G:0.06, T:0.51
Consensus pattern (24 bp):
CTTCCTCTTCCTCTCTCCTTCTGG
Found at i:55670959 original size:51 final size:49
Alignment explanation
Indices: 55670745--55670961 Score: 148
Period size: 51 Copynumber: 4.1 Consensus size: 49
55670735 GCCTCTTCTT
* * * **
55670745 CCTCCTCCTCTCTCCTTCTGGCCTCCTTTTCTTCTCTTCTCTTAGCTTCTT
1 CCTCTTCCTCTCTCCTTCTGGCCTCCTTTTTTTCCCTTCTCTTA--TTCGG
* * * * **
55670796 CCTCTTCCTCTCTCCTCCTCTTAGCTTCCTCTTCCTCTCTCCTTCTCTTAGCTTCTT
1 CCTCTTCCTCTCTCCT--TC-TGGCCTCCT-TT-TTTTC-CCTTCTCTTA--TTCGG
* **
55670853 CCTCTTCCTCTCTCCTTCTGGCCTCCTTTTTTTCTCTTCTCTTAGCTTCTT
1 CCTCTTCCTCTCTCCTTCTGGCCTCCTTTTTTTCCCTTCTCTTA--TTCGG
* *
55670904 CCTCTTCCTCTCTCCTTCTGGCTTCCTCTTCTTCTTCCCTTCTCTT-TTGGG
1 CCTCTTCCTCTCTCCTTCTGGCCTCCT-TT-TT-TTCCCTTCTCTTATTCGG
55670955 CCTCTTC
1 CCTCTTC
55670962 TTCCGCTTTC
Statistics
Matches: 140, Mismatches: 17, Indels: 18
0.80 0.10 0.10
Matches are distributed among these distances:
51 66 0.47
52 5 0.04
53 6 0.04
54 25 0.18
55 4 0.03
56 2 0.01
57 32 0.23
ACGTcount: A:0.02, C:0.43, G:0.06, T:0.49
Consensus pattern (49 bp):
CCTCTTCCTCTCTCCTTCTGGCCTCCTTTTTTTCCCTTCTCTTATTCGG
Found at i:55670961 original size:108 final size:107
Alignment explanation
Indices: 55670741--55670949 Score: 334
Period size: 108 Copynumber: 2.0 Consensus size: 107
55670731 CCTGGCCTCT
55670741 TCTTCCTCCTCCTCTCTCCTTCTGGCCTCCTTTTCTTCTCTTCTCTTAGCTTCTTCCTCTTCCTC
1 TCTTCCTCCTCCTCTCTCCTTCTGGCCTCCTTTTCTTCTCTTCTCTTAGCTTCTTCCTCTTCCTC
*
55670806 TCTCCTCCTCTTAGCTTCCTCTTCCTCTCTCCTTCTCTTAGCT
66 TCTCCT-CTCTTAGCTTCCTCTTCCTCTCTCCTTCTCTTAGCC
* *
55670849 TCTTCCTCTTCCTCTCTCCTTCTGGCCTCCTTTTTTTCTCTTCTCTTAGCTTCTTCCTCTTCCTC
1 TCTTCCTCCTCCTCTCTCCTTCTGGCCTCCTTTTCTTCTCTTCTCTTAGCTTCTTCCTCTTCCTC
* *
55670914 TCTCCT-TC-TGGCTTCCTCTTCTTCT-TCCCTTCTCTT
66 TCTCCTCTCTTAGCTTCCTCTTCCTCTCT-CCTTCTCTT
55670950 TTGGGCCTCT
Statistics
Matches: 96, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
104 1 0.01
105 24 0.25
106 2 0.02
108 69 0.72
ACGTcount: A:0.02, C:0.43, G:0.05, T:0.50
Consensus pattern (107 bp):
TCTTCCTCCTCCTCTCTCCTTCTGGCCTCCTTTTCTTCTCTTCTCTTAGCTTCTTCCTCTTCCTC
TCTCCTCTCTTAGCTTCCTCTTCCTCTCTCCTTCTCTTAGCC
Found at i:55670997 original size:51 final size:53
Alignment explanation
Indices: 55670942--55671054 Score: 135
Period size: 54 Copynumber: 2.2 Consensus size: 53
55670932 TTCTTCTTCC
* *
55670942 CTTCTCTTT-TGG-GCCTCTTCTTCCGCTTTCCTCTTAGCTTCTTCCTCCTCT
1 CTTCTCTTTCTGGCGCCTCTTCCTCCGCTTTCCTCCTAGCTTCTTCCTCCTCT
* * * *
55670993 CTTCTCTTTCTGGCCTCCTCTTCCTCCTCTTTCCTCCTGGCTTCTTCCTCTTC-
1 CTTCTCTTTCTGG-CGCCTCTTCCTCCGCTTTCCTCCTAGCTTCTTCCTCCTCT
55671046 CTTC-CTTTC
1 CTTCTCTTTC
55671055 CCTTTCAATT
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
51 9 0.17
52 8 0.15
53 4 0.08
54 32 0.60
ACGTcount: A:0.01, C:0.42, G:0.08, T:0.49
Consensus pattern (53 bp):
CTTCTCTTTCTGGCGCCTCTTCCTCCGCTTTCCTCCTAGCTTCTTCCTCCTCT
Found at i:55680748 original size:114 final size:114
Alignment explanation
Indices: 55680545--55680951 Score: 627
Period size: 114 Copynumber: 3.6 Consensus size: 114
55680535 AACTATGCAA
* * *
55680545 TTCCACTGCAGTTCACATACACGTGGCACTAATAACATCTAAATGTAATTAGAATCGATCGCAAA
1 TTCCACTGCAGTCCACATACACGTGGCGCTAACAACATCTAAATGTAATTAGAATCGATCGCAAA
*
55680610 GTGATTTGG-TGATGAGTCCTTTAACCGTCAACTATGCTATTAACAAAGG
66 TTGA-TTGGATGATGAGTCCTTTAACCGTCAACTATGCTATTAACAAAGG
*
55680659 TTCCACTGCAGTCCACATACACGTGGCGCTAACAACATCCAAATGTAATTAGAATCGATCGCAAA
1 TTCCACTGCAGTCCACATACACGTGGCGCTAACAACATCTAAATGTAATTAGAATCGATCGCAAA
* *
55680724 TTGATTGGATGATGAGTCCCTTAACCGTCAACTATGCTATTACCAAAGG
66 TTGATTGGATGATGAGTCCTTTAACCGTCAACTATGCTATTAACAAAGG
* *
55680773 TTCCACTGCAGTCCACATACACGTGGCGCTAACATCATCTAAATGTAATTAGAATCTATCGCAAA
1 TTCCACTGCAGTCCACATACACGTGGCGCTAACAACATCTAAATGTAATTAGAATCGATCGCAAA
* * * *
55680838 TCGATTGGATGATGAGTCCTTTAACCGTCAATTATGCTATGAACAAAGA
66 TTGATTGGATGATGAGTCCTTTAACCGTCAACTATGCTATTAACAAAGG
* * * * * *
55680887 TTCAACTGCAGTCCACATACATGCGGCGCTAACAACATCTAAATGTAGTTACAATCGATCTCAAA
1 TTCCACTGCAGTCCACATACACGTGGCGCTAACAACATCTAAATGTAATTAGAATCGATCGCAAA
55680952 ATCTTTTAAT
Statistics
Matches: 268, Mismatches: 24, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
113 4 0.01
114 264 0.99
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.27
Consensus pattern (114 bp):
TTCCACTGCAGTCCACATACACGTGGCGCTAACAACATCTAAATGTAATTAGAATCGATCGCAAA
TTGATTGGATGATGAGTCCTTTAACCGTCAACTATGCTATTAACAAAGG
Found at i:55685174 original size:16 final size:17
Alignment explanation
Indices: 55685141--55685174 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
55685131 TGAGGGTGAT
55685141 AGGAATAATGGTGAAGA
1 AGGAATAATGGTGAAGA
*
55685158 AGGAATAGTGG-GAAGA
1 AGGAATAATGGTGAAGA
55685174 A
1 A
55685175 AAGGAAAGGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.47, C:0.00, G:0.38, T:0.15
Consensus pattern (17 bp):
AGGAATAATGGTGAAGA
Found at i:55685614 original size:7 final size:7
Alignment explanation
Indices: 55685602--55685626 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
55685592 TATTTCAATT
55685602 AATAATA
1 AATAATA
55685609 AATAATA
1 AATAATA
55685616 AATAATA
1 AATAATA
55685623 AATA
1 AATA
55685627 TAATAAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (7 bp):
AATAATA
Found at i:55691403 original size:3 final size:3
Alignment explanation
Indices: 55691395--55691423 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
55691385 TCTATTTTTG
55691395 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
55691424 CCATACTTAG
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:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:55694765 original size:10 final size:10
Alignment explanation
Indices: 55694733--55694782 Score: 50
Period size: 10 Copynumber: 4.9 Consensus size: 10
55694723 CCTAAACTAA
55694733 AAATGAAAAG
1 AAATGAAAAG
*
55694743 AAAAAGAAAAAG
1 -AAATG-AAAAG
55694755 AGAA-GAAAAG
1 A-AATGAAAAG
55694765 AAATGAAAAG
1 AAATGAAAAG
55694775 AAAT-AAAA
1 AAATGAAAA
55694783 CCCTAACCCT
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
9 6 0.17
10 16 0.46
11 6 0.17
12 7 0.20
ACGTcount: A:0.76, C:0.00, G:0.18, T:0.06
Consensus pattern (10 bp):
AAATGAAAAG
Found at i:55702918 original size:13 final size:13
Alignment explanation
Indices: 55702900--55702926 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
55702890 GCTCGGCAGG
55702900 GACACGCCCGTGT
1 GACACGCCCGTGT
55702913 GACACGCCCGTGT
1 GACACGCCCGTGT
55702926 G
1 G
55702927 CGATTACTCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.37, G:0.33, T:0.15
Consensus pattern (13 bp):
GACACGCCCGTGT
Found at i:55717301 original size:48 final size:48
Alignment explanation
Indices: 55717177--55717535 Score: 454
Period size: 48 Copynumber: 7.5 Consensus size: 48
55717167 AATACCAATA
* * * *
55717177 CCATGTCCGAAACATGGTCTTACA-TGAGTC-CACATATCATCGCCAATG
1 CCATGTCCCAGACATGGTCTTACACTG-G-CACATATATCATCGCCGATG
* * * *
55717225 CCA-CTCCCTGACATGGTCTTACAATGGCACATATATCATCGCCAATG
1 CCATGTCCCAGACATGGTCTTACACTGGCACATATATCATCGCCGATG
* * *
55717272 CCATGTCCCAGACATAGTCTTACACTGGCACATATATCATTGTCGATG
1 CCATGTCCCAGACATGGTCTTACACTGGCACATATATCATCGCCGATG
* * * * *
55717320 CCATATCCCAGACATGGTCTTAAACTGGCACATACATTATCGTCGATG
1 CCATGTCCCAGACATGGTCTTACACTGGCACATATATCATCGCCGATG
* * *
55717368 CCATGTCCCAAACATGGTCTTACACTGGCACATACATTATCGCCGATG
1 CCATGTCCCAGACATGGTCTTACACTGGCACATATATCATCGCCGATG
* * * *
55717416 CCATGTCCCAGATATGGTTTTACACAGGCACATATATCATTGCCGATG
1 CCATGTCCCAGACATGGTCTTACACTGGCACATATATCATCGCCGATG
*
55717464 CCATGTCCCAGACATGGTCTTACACAGGCACATATATCATCGCCGATG
1 CCATGTCCCAGACATGGTCTTACACTGGCACATATATCATCGCCGATG
*
55717512 CCATGTCCCATACATGGTCTTACA
1 CCATGTCCCAGACATGGTCTTACA
55717536 TTGAATCTCA
Statistics
Matches: 275, Mismatches: 33, Indels: 6
0.88 0.11 0.02
Matches are distributed among these distances:
46 1 0.00
47 37 0.13
48 237 0.86
ACGTcount: A:0.28, C:0.29, G:0.17, T:0.26
Consensus pattern (48 bp):
CCATGTCCCAGACATGGTCTTACACTGGCACATATATCATCGCCGATG
Found at i:55727918 original size:113 final size:114
Alignment explanation
Indices: 55727784--55727999 Score: 310
Period size: 114 Copynumber: 1.9 Consensus size: 114
55727774 TGAATATTAA
* * * * *
55727784 TTTTTTGTTTTTTATTTACTTAACGAATGGTCCTATTGT-CAT-TTTTTTTGAGATTTTGGTATT
1 TTTTTTGTTTTTTATTTACTTAACAAATAGTCCCATTGTGCATATTTTTTTGAGAATTT-ATATT
*
55727847 GTAGAAAGGGTGTTAGGAAGAAAGGAAGCAAGTATGTTTTCTTTTATTTT
65 GTAGAAAGAGTGTTAGGAAGAAAGGAAGCAAGTATGTTTTCTTTTATTTT
** *
55727897 TTTTTTGTTTTTTATTTACTTAACAAATAGTCCCATTGTGTTTATTTTTTTGAGAATTTATTTTG
1 TTTTTTGTTTTTTATTTACTTAACAAATAGTCCCATTGTGCATATTTTTTTGAGAATTTATATTG
* *
55727962 TAGGAAGAGTGTTTGGAAGAAAGGAAGCAAGTATGTTT
66 TAGAAAGAGTGTTAGGAAGAAAGGAAGCAAGTATGTTT
55728000 GTGTTTTTTT
Statistics
Matches: 90, Mismatches: 11, Indels: 3
0.87 0.11 0.03
Matches are distributed among these distances:
113 36 0.40
114 40 0.44
115 14 0.16
ACGTcount: A:0.25, C:0.06, G:0.20, T:0.49
Consensus pattern (114 bp):
TTTTTTGTTTTTTATTTACTTAACAAATAGTCCCATTGTGCATATTTTTTTGAGAATTTATATTG
TAGAAAGAGTGTTAGGAAGAAAGGAAGCAAGTATGTTTTCTTTTATTTT
Found at i:55728022 original size:114 final size:113
Alignment explanation
Indices: 55727791--55728023 Score: 272
Period size: 114 Copynumber: 2.1 Consensus size: 113
55727781 TAATTTTTTG
* * * * * *
55727791 TTTTTTATTTACTTAACGAATGGTCCTATTGTCATTTTTTTTGAGATTTTGGTATTGTAGAAAGG
1 TTTTTTATTTACTTAACAAATAGTCCCATTGTCATTTTTTTTGAGAATTTGATATTGTAGAAAGA
**** *
55727856 GTGTTAGGAAGAAAGGAAGCAAGTATGTTTTCTTTTATTTTTTTTTTG
66 GTGTTAGGAAGAAAGGAAGCAAGTATGTTTTCTTTTATTTTAACATTA
** * *
55727904 TTTTTTATTTACTTAACAAATAGTCCCATTGTGTTTATTTTTTTGAGAATTT-ATTTTGTAGGAA
1 TTTTTTATTTACTTAACAAATAGTCCCATTGT-CAT-TTTTTTTGAGAATTTGATATTGTAGAAA
* *
55727968 GAGTGTTTGGAAGAAAGGAAGCAAGTATGTTTGTGTTTT-TTTTAACATTA
64 GAGTGTTAGGAAGAAAGGAAGCAAGTATGTTT-TCTTTTATTTTAACATTA
55728018 TTTTTT
1 TTTTTT
55728024 TGTTTTTTTA
Statistics
Matches: 100, Mismatches: 17, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
113 29 0.29
114 52 0.52
115 19 0.19
ACGTcount: A:0.25, C:0.06, G:0.19, T:0.50
Consensus pattern (113 bp):
TTTTTTATTTACTTAACAAATAGTCCCATTGTCATTTTTTTTGAGAATTTGATATTGTAGAAAGA
GTGTTAGGAAGAAAGGAAGCAAGTATGTTTTCTTTTATTTTAACATTA
Found at i:55728039 original size:123 final size:114
Alignment explanation
Indices: 55727778--55728084 Score: 330
Period size: 123 Copynumber: 2.6 Consensus size: 114
55727768 GGGTTTTGAA
* * * **
55727778 TATTAATTTTTTGTTTTTTATTTACTTAACGAATGGTCCTATTGT-CAT-TTTTTTTGAGATTTT
1 TATTATTTTTTTGTTTTTTATTTACTTAACAAATGGTCCCATTGTGTTTATTTTTTTGAGATTTT
* * *
55727841 GGTATTGTAGAAAGGGTGTTAGGAAGAAAGGAAGCAAGTATGTTTTCTTT
66 -ATTTTGTAGAAAGAGTGTTAGGAAGAAAGGAAGCAAGTATGTTTTCTTT
* * *
55727891 TATTTTTTTTTTGTTTTTTATTTACTTAACAAATAGTCCCATTGTGTTTATTTTTTTGAGAATTT
1 TATTATTTTTTTGTTTTTTATTTACTTAACAAATGGTCCCATTGTGTTTATTTTTTTGAGATTTT
* * *
55727956 ATTTTGTAGGAAGAGTGTTTGGAAGAAAGGAAGCAAGTATGTTTGTGTTTTTTT
66 ATTTTGTAGAAAGAGTGTTAGGAAGAAAGGAAGCAAGTA----TGT-TTTCTTT
* * * * *
55728010 TAACATTATTTTTTTGTTTTTTTATTTACTTAATAGATGGTCCCATTGTGTTGAATTTGTTGAGA
1 T---ATTATTTTTTTG-TTTTTTATTTACTTAACAAATGGTCCCATTGTGTTTATTTTTTTGAGA
55728075 GTTTTATTTT
62 -TTTTATTTT
55728085 CTATTTTCGT
Statistics
Matches: 160, Mismatches: 22, Indels: 13
0.82 0.11 0.07
Matches are distributed among these distances:
113 40 0.25
114 35 0.22
115 14 0.09
118 3 0.02
119 7 0.04
122 11 0.07
123 42 0.26
124 8 0.05
ACGTcount: A:0.24, C:0.06, G:0.18, T:0.52
Consensus pattern (114 bp):
TATTATTTTTTTGTTTTTTATTTACTTAACAAATGGTCCCATTGTGTTTATTTTTTTGAGATTTT
ATTTTGTAGAAAGAGTGTTAGGAAGAAAGGAAGCAAGTATGTTTTCTTT
Found at i:55740273 original size:20 final size:20
Alignment explanation
Indices: 55740248--55740285 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
55740238 AGTAATTTAA
*
55740248 AAAATAAAATTAAAAGAAAT
1 AAAATAAAATAAAAAGAAAT
55740268 AAAATAAAATAAAAAGAA
1 AAAATAAAATAAAAAGAA
55740286 CTGAAAAAAA
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:0.79, C:0.00, G:0.05, T:0.16
Consensus pattern (20 bp):
AAAATAAAATAAAAAGAAAT
Found at i:55748182 original size:24 final size:24
Alignment explanation
Indices: 55748154--55748200 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
55748144 CAATTAAAAC
55748154 GTGATTGATAATTAATCATTAATG
1 GTGATTGATAATTAATCATTAATG
* *
55748178 GTGATTGGTTATTAATCATTAAT
1 GTGATTGATAATTAATCATTAAT
55748201 TTTTTTATGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.34, C:0.04, G:0.17, T:0.45
Consensus pattern (24 bp):
GTGATTGATAATTAATCATTAATG
Found at i:55748578 original size:13 final size:13
Alignment explanation
Indices: 55748554--55748587 Score: 59
Period size: 13 Copynumber: 2.5 Consensus size: 13
55748544 TTTTAGTTAT
55748554 TATATAATTGTGTG
1 TATAT-ATTGTGTG
55748568 TATATATTGTGTG
1 TATATATTGTGTG
55748581 TATATAT
1 TATATAT
55748588 ATTATATGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 15 0.75
14 5 0.25
ACGTcount: A:0.29, C:0.00, G:0.18, T:0.53
Consensus pattern (13 bp):
TATATATTGTGTG
Found at i:55750539 original size:26 final size:26
Alignment explanation
Indices: 55750510--55750565 Score: 112
Period size: 26 Copynumber: 2.2 Consensus size: 26
55750500 TGGTACAAAT
55750510 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
55750536 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
55750562 TGAT
1 TGAT
55750566 GGGAATTTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.30, C:0.07, G:0.27, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:55751665 original size:51 final size:51
Alignment explanation
Indices: 55751589--55751690 Score: 204
Period size: 51 Copynumber: 2.0 Consensus size: 51
55751579 GGTGTGGTTG
55751589 GCCGAATATTGTAAGGGGTTAATACGTAGTTTGTATTTGAATAGTTAGATT
1 GCCGAATATTGTAAGGGGTTAATACGTAGTTTGTATTTGAATAGTTAGATT
55751640 GCCGAATATTGTAAGGGGTTAATACGTAGTTTGTATTTGAATAGTTAGATT
1 GCCGAATATTGTAAGGGGTTAATACGTAGTTTGTATTTGAATAGTTAGATT
55751691 AACGTGTTAG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.29, C:0.06, G:0.25, T:0.39
Consensus pattern (51 bp):
GCCGAATATTGTAAGGGGTTAATACGTAGTTTGTATTTGAATAGTTAGATT
Found at i:55752275 original size:54 final size:54
Alignment explanation
Indices: 55752176--55752320 Score: 238
Period size: 54 Copynumber: 2.7 Consensus size: 54
55752166 TGGAGGAAGC
*
55752176 GTCCTGGTGGCTATGCCACAATTTATCTAATCTGGTGGCTCTGCCACATATATCT
1 GTCCTGGTGGCTATGCCACAA-TTATCTGATCTGGTGGCTCTGCCACATATATCT
55752231 GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCT
1 GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCT
* *
55752285 GTTCTGGTGGCTCTGCCACAA-TATCTGTATCTGGTG
1 GTCCTGGTGGCTATGCCACAATTATCTG-ATCTGGTG
55752321 ACTTCGTCAC
Statistics
Matches: 86, Mismatches: 3, Indels: 3
0.93 0.03 0.03
Matches are distributed among these distances:
53 6 0.07
54 59 0.69
55 21 0.24
ACGTcount: A:0.18, C:0.25, G:0.23, T:0.34
Consensus pattern (54 bp):
GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCT
Found at i:55752317 original size:27 final size:27
Alignment explanation
Indices: 55752179--55752338 Score: 177
Period size: 27 Copynumber: 5.9 Consensus size: 27
55752169 AGGAAGCGTC
* *
55752179 CTGGTGGCTATGCCACAATTTATCT-AAT
1 CTGGTGGCTCTGCCACAA--TATCTGTAT
*
55752207 CTGGTGGCTCTGCCACATATATCTGT-C
1 CTGGTGGCTCTGCCACA-ATATCTGTAT
*
55752234 CTGGTGGCTATGCCACAATTATCTG-AT
1 CTGGTGGCTCTGCCACAA-TATCTGTAT
55752261 CTGGTGGCTCTGCCACATATATCTGT-T
1 CTGGTGGCTCTGCCACA-ATATCTGTAT
55752288 CTGGTGGCTCTGCCACAATATCTGTAT
1 CTGGTGGCTCTGCCACAATATCTGTAT
* *
55752315 CTGGTGACT-TCGTCACAATATCTG
1 CTGGTGGCTCT-GCCACAATATCTG
55752339 GCAGCCTCGC
Statistics
Matches: 116, Mismatches: 8, Indels: 17
0.82 0.06 0.12
Matches are distributed among these distances:
26 10 0.09
27 88 0.76
28 17 0.15
29 1 0.01
ACGTcount: A:0.19, C:0.25, G:0.21, T:0.34
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACAATATCTGTAT
Found at i:55752332 original size:81 final size:81
Alignment explanation
Indices: 55752179--55752338 Score: 209
Period size: 81 Copynumber: 2.0 Consensus size: 81
55752169 AGGAAGCGTC
* *
55752179 CTGGTGGCTATGCCACAATTTATCTAATCTGGTGGCTCTGCCACATATATCTGTCCTGGTGGCTA
1 CTGGTGGCTATGCCACAATATATCTAATCTGGTGGCTCTGCCACATATATCTGTCCTGGTGACTA
55752244 TGCCACAATTATCTGAT
66 TGCCACAA-TATCTGAT
* ** *
55752261 CTGGTGGCTCTGCCAC-ATATATCTGTTCTGGTGGCTCTGCCACA-ATATCTGTATCTGGTGACT
1 CTGGTGGCTATGCCACAATATATCTAATCTGGTGGCTCTGCCACATATATCTGT-CCTGGTGACT
*
55752324 -TCGTCACAATATCTG
65 AT-GCCACAATATCTG
55752339 GCAGCCTCGC
Statistics
Matches: 69, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
80 15 0.22
81 39 0.57
82 15 0.22
ACGTcount: A:0.19, C:0.25, G:0.21, T:0.34
Consensus pattern (81 bp):
CTGGTGGCTATGCCACAATATATCTAATCTGGTGGCTCTGCCACATATATCTGTCCTGGTGACTA
TGCCACAATATCTGAT
Found at i:55755957 original size:11 final size:11
Alignment explanation
Indices: 55755941--55755974 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
55755931 CGCATCTAGT
55755941 TTTGTTCTTGA
1 TTTGTTCTTGA
*
55755952 TTTGTTCTTGC
1 TTTGTTCTTGA
*
55755963 TTTATTCTTGA
1 TTTGTTCTTGA
55755974 T
1 T
55755975 GATTTGACAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.09, C:0.12, G:0.15, T:0.65
Consensus pattern (11 bp):
TTTGTTCTTGA
Found at i:55764365 original size:37 final size:37
Alignment explanation
Indices: 55764304--55764382 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 37
55764294 TTATTACGAA
* * *
55764304 GTCTTACCCAGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCAGACAAAATCCCCACACGAAGTCATCGG
* *
55764341 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCAGACAAAATCCCCACACGAAGTCATCGG
55764378 GTCTT
1 GTCTT
55764383 TAGAGCTCGG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.27, C:0.32, G:0.18, T:0.24
Consensus pattern (37 bp):
GTCTTACCCAGACAAAATCCCCACACGAAGTCATCGG
Found at i:55764579 original size:47 final size:47
Alignment explanation
Indices: 55764503--55764629 Score: 157
Period size: 47 Copynumber: 2.7 Consensus size: 47
55764493 CTTTGGGACT
* * * *
55764503 TATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCC
1 TATCACATATATACACTTTCACATCCATCACATCGGCCACTAGGCCC
* * * *
55764550 TGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCT
1 TATCACATATATACACTTTCACATCCATCACATCGGCCACTAGGCCC
*
55764597 TATCACATATATGCA-TGTTCACATCCATCACAT
1 TATCACATATATACACT-TTCACATCCATCACAT
55764630 AGAATCCTAT
Statistics
Matches: 68, Mismatches: 11, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
46 1 0.01
47 67 0.99
ACGTcount: A:0.28, C:0.31, G:0.09, T:0.31
Consensus pattern (47 bp):
TATCACATATATACACTTTCACATCCATCACATCGGCCACTAGGCCC
Found at i:55764691 original size:47 final size:47
Alignment explanation
Indices: 55764633--55764738 Score: 160
Period size: 47 Copynumber: 2.2 Consensus size: 47
55764623 ATCACATAGA
55764633 ATCCTATCACATCGGCCATTAGGCCTTATCACATATATACACT-TTCAC
1 ATCC-ATCACATCGGCCATTAGGCCTTATCACATATATACA-TGTTCAC
* * *
55764681 ATTCATCACATCGGCCATTAGGCCTTATCTCATATATGCATGTTCAC
1 ATCCATCACATCGGCCATTAGGCCTTATCACATATATACATGTTCAC
55764728 ATCCATCACAT
1 ATCCATCACAT
55764739 AGAATCCTAA
Statistics
Matches: 53, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
46 1 0.02
47 49 0.92
48 3 0.06
ACGTcount: A:0.28, C:0.30, G:0.09, T:0.32
Consensus pattern (47 bp):
ATCCATCACATCGGCCATTAGGCCTTATCACATATATACATGTTCAC
Found at i:55769240 original size:18 final size:18
Alignment explanation
Indices: 55769203--55769244 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
55769193 AAAATCCCAA
*
55769203 AAGGATTTAAAACCCTTG
1 AAGGATTTAAAAACCTTG
55769221 AAGGATTTAAAATACC-TG
1 AAGGATTTAAAA-ACCTTG
55769239 AAGGAT
1 AAGGAT
55769245 ATAGAGTTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 20 0.91
19 2 0.09
ACGTcount: A:0.43, C:0.12, G:0.19, T:0.26
Consensus pattern (18 bp):
AAGGATTTAAAAACCTTG
Found at i:55771867 original size:108 final size:100
Alignment explanation
Indices: 55771860--55772037 Score: 215
Period size: 98 Copynumber: 1.8 Consensus size: 100
55771850 GATTAGGTTA
* * *
55771860 TATAAATTGTTAGTGTTTAATGGTTTAGTGTATTATGATTTTTTAGAAATGTATTTTTTTTAAAA
1 TATAAATTGTTAGTGTTT-ATGGTTTAGTGTATTGTGATTTTTTAGTAATGTAATTTTTTTAAAA
55771925 A-AA--TTATAGTTATTTTGTGTTAGTAATTTATAAT
65 ATAATTTTATAGTTA-TTTGTGTTAGTAATTTATAAT
* * * *
55771959 TATAAATTGTTAGTGTTTATAGTTTAGTGTTTTGTGATTTTTT--TAATGTAATTTTTATATAAT
1 TATAAATTGTTAGTGTTTATGGTTTAGTGTATTGTGATTTTTTAGTAATGTAATTTTTTTA-AAA
*
55772022 GTAATTTTATA-TTATT
65 ATAATTTTATAGTTATT
55772038 ATTTATTTAT
Statistics
Matches: 67, Mismatches: 8, Indels: 9
0.80 0.10 0.11
Matches are distributed among these distances:
96 13 0.19
97 2 0.03
98 26 0.39
99 21 0.31
100 5 0.07
ACGTcount: A:0.30, C:0.00, G:0.13, T:0.56
Consensus pattern (100 bp):
TATAAATTGTTAGTGTTTATGGTTTAGTGTATTGTGATTTTTTAGTAATGTAATTTTTTTAAAAA
TAATTTTATAGTTATTTGTGTTAGTAATTTATAAT
Found at i:55772029 original size:15 final size:16
Alignment explanation
Indices: 55772002--55772033 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
55771992 GTGATTTTTT
55772002 TAATGTAATTTTTATA
1 TAATGTAATTTTTATA
55772018 TAATGTAA-TTTTATA
1 TAATGTAATTTTTATA
55772033 T
1 T
55772034 TATTATTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (16 bp):
TAATGTAATTTTTATA
Found at i:55774092 original size:33 final size:33
Alignment explanation
Indices: 55774055--55774142 Score: 83
Period size: 33 Copynumber: 2.6 Consensus size: 33
55774045 CAATACTCTG
55774055 CTCCTTCCGGCCAGTATCCACCT-CTGTACTCCA
1 CTCCTTCCGGCCA-TATCCACCTGCTGTACTCCA
* **
55774088 CTCC-TCTAGAGCCATATCCA-CTGCTGTACTTTA
1 CTCCTTC-CG-GCCATATCCACCTGCTGTACTCCA
*
55774121 CTCCTCCCGGCCTATATCCACC
1 CTCCTTCCGGCC-ATATCCACC
55774143 GCCATTTTCT
Statistics
Matches: 44, Mismatches: 5, Indels: 11
0.73 0.08 0.18
Matches are distributed among these distances:
32 7 0.16
33 31 0.70
34 6 0.14
ACGTcount: A:0.17, C:0.43, G:0.11, T:0.28
Consensus pattern (33 bp):
CTCCTTCCGGCCATATCCACCTGCTGTACTCCA
Found at i:55774156 original size:33 final size:33
Alignment explanation
Indices: 55774119--55774197 Score: 86
Period size: 33 Copynumber: 2.4 Consensus size: 33
55774109 TGCTGTACTT
* *
55774119 TACTCCTCCCGGCCTATATCCACCGCCATTTTC
1 TACTCCTCCCGGCCTATATCCACCACCATATTC
*** * * *
55774152 TACTCCTCCTATCCTGTATCTACCACCGTATTC
1 TACTCCTCCCGGCCTATATCCACCACCATATTC
55774185 TACTCCTCCCGGC
1 TACTCCTCCCGGC
55774198 TCAAGTTCAT
Statistics
Matches: 35, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.15, C:0.44, G:0.09, T:0.32
Consensus pattern (33 bp):
TACTCCTCCCGGCCTATATCCACCACCATATTC
Found at i:55778386 original size:17 final size:19
Alignment explanation
Indices: 55778357--55778392 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
55778347 GCCTTGCTCG
55778357 TGTGGGCTCACAC-GCCCA
1 TGTGGGCTCACACGGCCCA
55778375 TGTGGG-TCACACGGCCCA
1 TGTGGGCTCACACGGCCCA
55778393 AATTGGCATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.17, C:0.36, G:0.31, T:0.17
Consensus pattern (19 bp):
TGTGGGCTCACACGGCCCA
Found at i:55780056 original size:26 final size:27
Alignment explanation
Indices: 55779995--55780050 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
55779985 CCTACCAAGA
* * *
55779995 AGGCTCAACTAGTTGCACCTGTCAGGT
1 AGGCTCAACTAGTCGCACCTATCAGAT
55780022 AGGCTCAACTAGTCGC-CCTATCAGAT
1 AGGCTCAACTAGTCGCACCTATCAGAT
55780048 AGG
1 AGG
55780051 TGCAACCTGT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 11 0.42
27 15 0.58
ACGTcount: A:0.25, C:0.27, G:0.25, T:0.23
Consensus pattern (27 bp):
AGGCTCAACTAGTCGCACCTATCAGAT
Found at i:55793030 original size:17 final size:16
Alignment explanation
Indices: 55793009--55793043 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
55792999 TGTTTTTTTT
55793009 ATTTTT-TTTAAGACCA
1 ATTTTTGTTT-AGACCA
55793025 ATTTTTGTTTAGACCA
1 ATTTTTGTTTAGACCA
55793041 ATT
1 ATT
55793044 ACAAATAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 15 0.83
17 3 0.17
ACGTcount: A:0.29, C:0.11, G:0.09, T:0.51
Consensus pattern (16 bp):
ATTTTTGTTTAGACCA
Found at i:55793600 original size:15 final size:15
Alignment explanation
Indices: 55793580--55793618 Score: 69
Period size: 15 Copynumber: 2.5 Consensus size: 15
55793570 TTTTTTTGGT
55793580 TTTTTTTTGCTGGAA
1 TTTTTTTTGCTGGAA
55793595 TTTTTTTTGCTGGAA
1 TTTTTTTTGCTGGAA
55793610 TTTTGTTTT
1 TTTT-TTTT
55793619 TTGTTCTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 19 0.83
16 4 0.17
ACGTcount: A:0.10, C:0.05, G:0.18, T:0.67
Consensus pattern (15 bp):
TTTTTTTTGCTGGAA
Found at i:55793933 original size:31 final size:30
Alignment explanation
Indices: 55793833--55793933 Score: 107
Period size: 31 Copynumber: 3.4 Consensus size: 30
55793823 CTTTTGGGCT
* * *
55793833 AAATGTAATTTTTAGAAAA-TTT-TGGGTTA
1 AAATGTAA-TTTAAGAAAAGTTTAAGGGTCA
*
55793862 AAATGTAATTTAAGAAAAGTTTAAGGGTCT
1 AAATGTAATTTAAGAAAAGTTTAAGGGTCA
* * *
55793892 AAGTGAAATTTAAAGAAAAGTTTAGGGGTCA
1 AAATGTAATTT-AAGAAAAGTTTAAGGGTCA
55793923 AAATGTAATTT
1 AAATGTAATTT
55793934 TTTTATTTTT
Statistics
Matches: 59, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
28 9 0.15
29 11 0.19
30 13 0.22
31 26 0.44
ACGTcount: A:0.43, C:0.02, G:0.20, T:0.36
Consensus pattern (30 bp):
AAATGTAATTTAAGAAAAGTTTAAGGGTCA
Found at i:55795052 original size:41 final size:40
Alignment explanation
Indices: 55794991--55795076 Score: 109
Period size: 41 Copynumber: 2.1 Consensus size: 40
55794981 TATAATCACT
55794991 TTTTATTATATTTTCAATTTGTGTATTGTTTTAAGAATTG
1 TTTTATTATATTTTCAATTTGTGTATTGTTTTAAGAATTG
** * * * *
55795031 TTTTATTATCATTTTTTATTTGTTTCTTGTTTTAATATTTG
1 TTTTATTAT-ATTTTCAATTTGTGTATTGTTTTAAGAATTG
55795072 TTTTA
1 TTTTA
55795077 AATGTATTTG
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
40 9 0.23
41 30 0.77
ACGTcount: A:0.21, C:0.03, G:0.09, T:0.66
Consensus pattern (40 bp):
TTTTATTATATTTTCAATTTGTGTATTGTTTTAAGAATTG
Found at i:55819126 original size:2 final size:2
Alignment explanation
Indices: 55819119--55819143 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
55819109 TATAGAATTT
55819119 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
55819144 TATTGTTTGA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:55819456 original size:13 final size:12
Alignment explanation
Indices: 55819431--55819489 Score: 57
Period size: 13 Copynumber: 4.7 Consensus size: 12
55819421 GTTTATAATG
55819431 TTATTTTAAATT
1 TTATTTTAAATT
*
55819443 TTATTATTACATT
1 TTATT-TTAAATT
55819456 TTA-TTTAAATTAT
1 TTATTTTAAA-T-T
*
55819469 TTATTTTTAAATA
1 TTA-TTTTAAATT
55819482 TTATTTTA
1 TTATTTTA
55819490 TTATTTATCA
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
11 4 0.10
12 12 0.31
13 16 0.41
14 1 0.03
15 6 0.15
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (12 bp):
TTATTTTAAATT
Found at i:55820184 original size:64 final size:66
Alignment explanation
Indices: 55820109--55820276 Score: 180
Period size: 64 Copynumber: 2.5 Consensus size: 66
55820099 AAACATACTT
*
55820109 TAACATTTCATGCAAATATAATATAGAAAACAACAAATA-ACG-ACATAAATTACATAATATAT-
1 TAACATTTCATGCAAATATAATATAAAAAACAACAAATATA-GAACATAAATTACATAATATATC
*
55820171 AT
65 AA
* * * * * *
55820173 TGACATTTCATGCAAATATAATCATATAAAATAATAAATATAGAAATATAAATTGCATAATATAT
1 TAACATTTCATGCAAATATAAT-ATAAAAAACAACAAATATAG-AACATAAATTACATAATATAT
55820238 GCAA
64 -CAA
* **
55820242 TAATATTTCATGCAAATATAACCTAAAAAACAACA
1 TAACATTTCATGCAAATATAATATAAAAAACAACA
55820277 TAAATTACAT
Statistics
Matches: 84, Mismatches: 14, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
64 21 0.25
65 15 0.18
66 1 0.01
67 18 0.21
68 9 0.11
69 20 0.24
ACGTcount: A:0.54, C:0.12, G:0.05, T:0.29
Consensus pattern (66 bp):
TAACATTTCATGCAAATATAATATAAAAAACAACAAATATAGAACATAAATTACATAATATATCA
A
Found at i:55820643 original size:14 final size:14
Alignment explanation
Indices: 55820626--55820667 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
55820616 AAAAAAATTT
55820626 TATATGATAAATAA
1 TATATGATAAATAA
55820640 TATATGA-AAATAA
1 TATATGATAAATAA
55820653 TTATAT-ATAAA-AA
1 -TATATGATAAATAA
55820666 TA
1 TA
55820668 GCGTGTAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 2 0.08
13 9 0.35
14 15 0.58
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.36
Consensus pattern (14 bp):
TATATGATAAATAA
Found at i:55822328 original size:45 final size:45
Alignment explanation
Indices: 55822278--55823334 Score: 400
Period size: 45 Copynumber: 23.5 Consensus size: 45
55822268 AGAGACACCG
* * *
55822278 AATCTG-TCATCTTCAATCTGCTTTGATGTAAACACAAAAATGTCA
1 AATCTGCT-ATCTTCGATCTGCTTCGATGTAAACACAGAAATGTCA
* * * * * * * *
55822323 GATCTGCTATCTTTGATCTGCTCCCCG-TCT-AATACAGAGACGCCA
1 AATCTGCTATCTTCGATCTGCT--TCGATGTAAACACAGAAATGTCA
* *
55822368 AATTTG-TCATCTTCGATCTGCTTCGATGTAAACACACAAATGTCA
1 AATCTGCT-ATCTTCGATCTGCTTCGATGTAAACACAGAAATGTCA
* * * * * * *
55822413 GATCTGCTATCTTCGATCTACTCCCCGCT-T-AATACAGAGATGCCA
1 AATCTGCTATCTTCGATCTGCT--TCGATGTAAACACAGAAATGTCA
*
55822458 AATCTG-TCATCTTCGATCTGCTTCGATGTAAACACACAAATGTCA
1 AATCTGCT-ATCTTCGATCTGCTTCGATGTAAACACAGAAATGTCA
*** * * * * *
55822503 AATCTGCTATCTTCGATCTG-TTCCCCGTCTAATACAGATACGCCA
1 AATCTGCTATCTTCGATCTGCTTCGATGT-AAACACAGAAATGTCA
* * *
55822548 AATCTG-TCATCTTCGATCTGCTTCGATGTAAACAAACAAATGTTA
1 AATCTGCT-ATCTTCGATCTGCTTCGATGTAAACACAGAAATGTCA
* * * * * *
55822593 GATCTGCTATCTTCGATCTGCTCCCCG-TCTAATACAGAGACA--CCA
1 AATCTGCTATCTTCGATCTGCT--TCGATGTAA-ACACAGAAATGTCA
*
55822638 AATCTG-TCATCTTCGATCTGCTTCGATGTAAACACACG-GATGTCA
1 AATCTGCT-ATCTTCGATCTGCTTCGATGTAAACACA-GAAATGTCA
* * * * * * *
55822683 GATCTGCTATCTTCGATCTGCTCCCCG-TCT-AATACAGAGACGCCA
1 AATCTGCTATCTTCGATCTGCT--TCGATGTAAACACAGAAATGTCA
* * *
55822728 AATTTG-TCATCTTCGATCTGCTTTGATGTAAACACACG-AATGTTA
1 AATCTGCT-ATCTTCGATCTGCTTCGATGTAAACACA-GAAATGTCA
* * * * * * *
55822773 GATCTACTATCTTCGATCTGCTCCTCG-TCT-AATACAGAGACGCCA
1 AATCTGCTATCTTCGATCTGCT--TCGATGTAAACACAGAAATGTCA
* *
55822818 AATCTG-TCATCTTCGATCTGCTTCGATGTAAATACACG-AATGTTA
1 AATCTGCT-ATCTTCGATCTGCTTCGATGTAAACACA-GAAATGTCA
* ** * * * * * *
55822863 GATCTGCTATCTTTAATCTGCTCCCCG-TCT-AATACAGAGACGCCA
1 AATCTGCTATCTTCGATCTGCT--TCGATGTAAACACAGAAATGTCA
* *
55822908 AATCTG-TCATCTTCGATCTGCTTCGATGTAAATACACG-AATGTTA
1 AATCTGCT-ATCTTCGATCTGCTTCGATGTAAACACA-GAAATGTCA
* ** * * * * * *
55822953 GATCTGCTATCTTTAATCTGCTCCCCG-TCT-AATACAGAGACGCCA
1 AATCTGCTATCTTCGATCTGCT--TCGATGTAAACACAGAAATGTCA
* *
55822998 AATCTG-TCATCTTCGATCTGCTTCGATGTAAATACACG-AATGTTA
1 AATCTGCT-ATCTTCGATCTGCTTCGATGTAAACACA-GAAATGTCA
* ** * * * * * *
55823043 GATCTGCTATCTTTAATCTGCTCCCCG-TCT-AATACAGAGACGCCA
1 AATCTGCTATCTTCGATCTGCT--TCGATGTAAACACAGAAATGTCA
* *
55823088 AATCTG-TCATCTTCGATCTGCTTCGATGTAAATACACG-AATGTTA
1 AATCTGCT-ATCTTCGATCTGCTTCGATGTAAACACA-GAAATGTCA
* ** * * * * * *
55823133 GATCTGCTATCTTTAATCTGCTCCCCG-TCT-AATACAGAGACGCCA
1 AATCTGCTATCTTCGATCTGCT--TCGATGTAAACACAGAAATGTCA
* *
55823178 AATCTG-TCATCTTCGATCTGCTTCGATGTAAATACACG-AATGTTA
1 AATCTGCT-ATCTTCGATCTGCTTCGATGTAAACACA-GAAATGTCA
* ** * * * * * *
55823223 GATCTGCTATCTTTAATCTGCTCCCCG-TCT-AATACAGAGACGCCA
1 AATCTGCTATCTTCGATCTGCT--TCGATGTAAACACAGAAATGTCA
* *
55823268 AATCTG-TCATCTTCAATATGCTTCGATGTAAACACACG-AAT-TCCA
1 AATCTGCT-ATCTTCGATCTGCTTCGATGTAAACACA-GAAATGT-CA
*
55823313 GATCTGCTATCTTCGATCTGCT
1 AATCTGCTATCTTCGATCTGCT
55823335 CCCCGTCTAA
Statistics
Matches: 731, Mismatches: 198, Indels: 166
0.67 0.18 0.15
Matches are distributed among these distances:
43 26 0.04
44 45 0.06
45 589 0.81
46 45 0.06
47 26 0.04
ACGTcount: A:0.27, C:0.26, G:0.15, T:0.32
Consensus pattern (45 bp):
AATCTGCTATCTTCGATCTGCTTCGATGTAAACACAGAAATGTCA
Found at i:55822353 original size:90 final size:90
Alignment explanation
Indices: 55822240--55823363 Score: 1784
Period size: 90 Copynumber: 12.5 Consensus size: 90
55822230 ACCATGCTGA
* * * * * *
55822240 TATCTTTGACCTGCTCTCCGTCTAATACAGAGACACCGAATCTGTCATCTTCAATCTGCTTTGAT
1 TATCTTTGATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGTCATCTTCGATCTGCTTCGAT
** *
55822305 GTAAACACAAAAATGTCAGATCTGC
66 GTAAACACACGAATGTTAGATCTGC
*
55822330 TATCTTTGATCTGCTCCCCGTCTAATACAGAGACGCCAAATTTGTCATCTTCGATCTGCTTCGAT
1 TATCTTTGATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGTCATCTTCGATCTGCTTCGAT
* *
55822395 GTAAACACACAAATGTCAGATCTGC
66 GTAAACACACGAATGTTAGATCTGC
* * *
55822420 TATCTTCGATCTACTCCCCG-CTTAATACAGAGATGCCAAATCTGTCATCTTCGATCTGCTTCGA
1 TATCTTTGATCTGCTCCCCGTC-TAATACAGAGACGCCAAATCTGTCATCTTCGATCTGCTTCGA
* * *
55822484 TGTAAACACACAAATGTCAAATCTGC
65 TGTAAACACACGAATGTTAGATCTGC
* * *
55822510 TATCTTCGATCTGTTCCCCGTCTAATACAGATACGCCAAATCTGTCATCTTCGATCTGCTTCGAT
1 TATCTTTGATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGTCATCTTCGATCTGCTTCGAT
* *
55822575 GTAAACAAACAAATGTTAGATCTGC
66 GTAAACACACGAATGTTAGATCTGC
* *
55822600 TATCTTCGATCTGCTCCCCGTCTAATACAGAGACACCAAATCTGTCATCTTCGATCTGCTTCGAT
1 TATCTTTGATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGTCATCTTCGATCTGCTTCGAT
* *
55822665 GTAAACACACGGATGTCAGATCTGC
66 GTAAACACACGAATGTTAGATCTGC
* * *
55822690 TATCTTCGATCTGCTCCCCGTCTAATACAGAGACGCCAAATTTGTCATCTTCGATCTGCTTTGAT
1 TATCTTTGATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGTCATCTTCGATCTGCTTCGAT
*
55822755 GTAAACACACGAATGTTAGATCTAC
66 GTAAACACACGAATGTTAGATCTGC
* *
55822780 TATCTTCGATCTGCTCCTCGTCTAATACAGAGACGCCAAATCTGTCATCTTCGATCTGCTTCGAT
1 TATCTTTGATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGTCATCTTCGATCTGCTTCGAT
*
55822845 GTAAATACACGAATGTTAGATCTGC
66 GTAAACACACGAATGTTAGATCTGC
*
55822870 TATCTTTAATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGTCATCTTCGATCTGCTTCGAT
1 TATCTTTGATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGTCATCTTCGATCTGCTTCGAT
*
55822935 GTAAATACACGAATGTTAGATCTGC
66 GTAAACACACGAATGTTAGATCTGC
*
55822960 TATCTTTAATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGTCATCTTCGATCTGCTTCGAT
1 TATCTTTGATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGTCATCTTCGATCTGCTTCGAT
*
55823025 GTAAATACACGAATGTTAGATCTGC
66 GTAAACACACGAATGTTAGATCTGC
*
55823050 TATCTTTAATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGTCATCTTCGATCTGCTTCGAT
1 TATCTTTGATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGTCATCTTCGATCTGCTTCGAT
*
55823115 GTAAATACACGAATGTTAGATCTGC
66 GTAAACACACGAATGTTAGATCTGC
*
55823140 TATCTTTAATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGTCATCTTCGATCTGCTTCGAT
1 TATCTTTGATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGTCATCTTCGATCTGCTTCGAT
*
55823205 GTAAATACACGAATGTTAGATCTGC
66 GTAAACACACGAATGTTAGATCTGC
* * *
55823230 TATCTTTAATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGTCATCTTCAATATGCTTCGAT
1 TATCTTTGATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGTCATCTTCGATCTGCTTCGAT
*
55823295 GTAAACACACGAAT-TCCAGATCTGC
66 GTAAACACACGAATGT-TAGATCTGC
* *
55823320 TATCTTCGATCTGCTCCCCGTCTAATACAGAAACGCCAAATCTG
1 TATCTTTGATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTG
55823364 CTTCTTTGAT
Statistics
Matches: 983, Mismatches: 48, Indels: 6
0.95 0.05 0.01
Matches are distributed among these distances:
89 2 0.00
90 980 1.00
91 1 0.00
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.31
Consensus pattern (90 bp):
TATCTTTGATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGTCATCTTCGATCTGCTTCGAT
GTAAACACACGAATGTTAGATCTGC
Found at i:55831500 original size:14 final size:16
Alignment explanation
Indices: 55831470--55831501 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
55831460 GAATGCATAT
55831470 AATGCGATGAGATGCA
1 AATGCGATGAGATGCA
55831486 AATGC-ATGA-ATGCA
1 AATGCGATGAGATGCA
55831500 AA
1 AA
55831502 AAGATATCGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.44
15 4 0.25
16 5 0.31
ACGTcount: A:0.44, C:0.12, G:0.25, T:0.19
Consensus pattern (16 bp):
AATGCGATGAGATGCA
Found at i:55834860 original size:14 final size:16
Alignment explanation
Indices: 55834821--55834860 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
55834811 CATTTCATGC
55834821 AAATAT-AATCATAGA
1 AAATATAAATCATAGA
55834836 AAATAATAAAT-ATAG-
1 AAAT-ATAAATCATAGA
55834851 AAATATAAAT
1 AAATATAAAT
55834861 TACATAATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
14 6 0.26
15 8 0.35
16 6 0.26
17 3 0.13
ACGTcount: A:0.65, C:0.03, G:0.05, T:0.28
Consensus pattern (16 bp):
AAATATAAATCATAGA
Found at i:55834885 original size:69 final size:66
Alignment explanation
Indices: 55834742--55834911 Score: 198
Period size: 69 Copynumber: 2.5 Consensus size: 66
55834732 ATACATACTT
**
55834742 TAACATTTCATGCAAATATAATATAGAAAACAACAAATAACGACATAAATTACATAATATATGTA
1 TAACATTTCATGCAAATATAATATAGAAAACAACAAATAACGACATAAATTACATAATATATACA
*
55834807 T
66 A
* * * *
55834808 TGACATTTCATGCAAATATAATCATAGAAAATAATAAATATA-GAAATATAAATTACATAATATA
1 TAACATTTCATGCAAATATAAT-ATAGAAAACAACAAATA-ACG--ACATAAATTACATAATATA
55834872 TACAA
62 TACAA
* ** *
55834877 TAATATTTCATGCAAATATAACCTAAAAAACAACA
1 TAACATTTCATGCAAATATAATATAGAAAACAACA
55834912 TAAATTACAT
Statistics
Matches: 86, Mismatches: 14, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
66 21 0.24
67 16 0.19
68 10 0.12
69 39 0.45
ACGTcount: A:0.54, C:0.12, G:0.05, T:0.29
Consensus pattern (66 bp):
TAACATTTCATGCAAATATAATATAGAAAACAACAAATAACGACATAAATTACATAATATATACA
A
Found at i:55838196 original size:258 final size:258
Alignment explanation
Indices: 55837739--55838215 Score: 918
Period size: 258 Copynumber: 1.8 Consensus size: 258
55837729 NNNNAAAAGG
55837739 CAATGCTTGATGTTTGGAAACTTCGAGAAAGGTAGTGCCCTAACTTACTGGGTTGCGACTTTTCT
1 CAATGCTTGATGTTTGGAAACTTCGAGAAAGGTAGTGCCCTAACTTACTGGGTTGCGACTTTTCT
55837804 CGTTGAATTCGAATAGTCAAGCACCCTTCTAAGTGATTTTGAGTTTTCAAAACTTAAACAATTAT
66 CGTTGAATTCGAATAGTCAAGCACCCTTCTAAGTGATTTTGAGTTTTCAAAACTTAAACAATTAT
* *
55837869 TTTGAGATTTCAAAACATAGTGTCCTAACTTACTGGATATGGCGTTTTGTTGTTTCGAGATAGAA
131 TTCGAGATTTCAAAACATAGTGTCCTAACTTACTGGATATGGCGTTTTATTGTTTCGAGATAGAA
55837934 ATTTTCGAAAGACGAGCTTAGTTTCGAAGGTTTTAAAATGTTGCGTCCTAACTTACTGGATGT
196 ATTTTCGAAAGACGAGCTTAGTTTCGAAGGTTTTAAAATGTTGCGTCCTAACTTACTGGATGT
55837997 CAATGCTTGATGTTTGGAAACTTCGAGAAAGGTAGTGCCCTAACTTACTGGGTTGCGACTTTTCT
1 CAATGCTTGATGTTTGGAAACTTCGAGAAAGGTAGTGCCCTAACTTACTGGGTTGCGACTTTTCT
*
55838062 CGTTGAATTCGAATAGTCAAGCACCCTTCTAAGTGATTTTGAGTTTTTAAAACTTAAACAATTAT
66 CGTTGAATTCGAATAGTCAAGCACCCTTCTAAGTGATTTTGAGTTTTCAAAACTTAAACAATTAT
*
55838127 TTCGAGATTTCAAAACATAGTGTCCTAATTTACTGGATATGGCGTTTTATTGTTTCGAGATAGAA
131 TTCGAGATTTCAAAACATAGTGTCCTAACTTACTGGATATGGCGTTTTATTGTTTCGAGATAGAA
55838192 ATTTTCGAAAGACGAGCTTAGTTT
196 ATTTTCGAAAGACGAGCTTAGTTT
55838216 TAAACAATTA
Statistics
Matches: 215, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
258 215 1.00
ACGTcount: A:0.28, C:0.15, G:0.20, T:0.36
Consensus pattern (258 bp):
CAATGCTTGATGTTTGGAAACTTCGAGAAAGGTAGTGCCCTAACTTACTGGGTTGCGACTTTTCT
CGTTGAATTCGAATAGTCAAGCACCCTTCTAAGTGATTTTGAGTTTTCAAAACTTAAACAATTAT
TTCGAGATTTCAAAACATAGTGTCCTAACTTACTGGATATGGCGTTTTATTGTTTCGAGATAGAA
ATTTTCGAAAGACGAGCTTAGTTTCGAAGGTTTTAAAATGTTGCGTCCTAACTTACTGGATGT
Found at i:55838288 original size:100 final size:100
Alignment explanation
Indices: 55838115--55838315 Score: 375
Period size: 100 Copynumber: 2.0 Consensus size: 100
55838105 TTTTTAAAAC
*
55838115 TTAAACAATTATTTCGAGATTTCAAAACATAGTGTCCTAATTTACTGGATATGGCGTTTTATTGT
1 TTAAACAATTATTTCGAGATTTCAAAACATAGTGTCCTAACTTACTGGATATGGCGTTTTATTGT
55838180 TTCGAGATAGAAATTTTCGAAAGACGAGCTTAGTT
66 TTCGAGATAGAAATTTTCGAAAGACGAGCTTAGTT
* *
55838215 TTAAACAATTATTTTGAGATTTCAAAACATAGTGTCCTAACTTACTGGATATGGCGTTTTGTTGT
1 TTAAACAATTATTTCGAGATTTCAAAACATAGTGTCCTAACTTACTGGATATGGCGTTTTATTGT
55838280 TTCGAGATAGAAATTTTCGAAAGACGAGCTTAGTT
66 TTCGAGATAGAAATTTTCGAAAGACGAGCTTAGTT
55838315 T
1 T
55838316 CAAAGGTTTT
Statistics
Matches: 98, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
100 98 1.00
ACGTcount: A:0.31, C:0.12, G:0.18, T:0.38
Consensus pattern (100 bp):
TTAAACAATTATTTCGAGATTTCAAAACATAGTGTCCTAACTTACTGGATATGGCGTTTTATTGT
TTCGAGATAGAAATTTTCGAAAGACGAGCTTAGTT
Done.