Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032251.1 Gossypioides kirkii chromosome KI_09
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: 38743931
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2800 characters in sequence are not A, C, G, or T
File 93 of 144
Found at i:21652760 original size:172 final size:172
Alignment explanation
Indices: 21652467--21652779 Score: 495
Period size: 172 Copynumber: 1.8 Consensus size: 172
21652457 TAATAAGTGT
* *
21652467 TTGAGATGTACCTCACTTATCGCATTTCTCGTTTTGACTGCCCAATTTGCATCACCACTTTTCCC
1 TTGAGATGTACCTCACCTACCGCATTTCTCGTTTTGACTGCCCAATTTGCATCACCACTTTTCCC
*
21652532 ACAAAGCCCGATGCACAATCACCTCTCTTATAGGTGGTAGCCCCACTGTAAACTCAATAGGTTTC
66 ACAAAGCCCGATGCACAATCACCTCTCTTATAGGTGGTAGCCCCACTGTAAACTCAACAGGTTTC
21652597 ATATCAGTTTGATTGCCCAGTTTACATCATAATGTACCTTAC
131 ATATCAGTTTGATTGCCCAGTTTACATCATAATGTACCTTAC
* * * * * *
21652639 TTGAGATGTACCTCACCTGCCGCATTTCTCGTTTTTATTGCTC-GTTTGCATCACCACTTTTCCT
1 TTGAGATGTACCTCACCTACCGCATTTCTCGTTTTGACTGCCCAATTTGCATCACCACTTTTCCC
*
21652703 ACAAAGCCCGATGCACAACTCACCTCTCTTATAGGTGGTAGCCCCACTG-ATAACTCAACATGTT
66 ACAAAGCCCGATGCACAA-TCACCTCTCTTATAGGTGGTAGCCCCACTGTA-AACTCAACAGGTT
*
21652767 TCATATCGGTTTG
129 TCATATCAGTTTG
21652780 TCGTACCTCT
Statistics
Matches: 128, Mismatches: 11, Indels: 4
0.90 0.08 0.03
Matches are distributed among these distances:
171 38 0.30
172 90 0.70
ACGTcount: A:0.23, C:0.28, G:0.15, T:0.34
Consensus pattern (172 bp):
TTGAGATGTACCTCACCTACCGCATTTCTCGTTTTGACTGCCCAATTTGCATCACCACTTTTCCC
ACAAAGCCCGATGCACAATCACCTCTCTTATAGGTGGTAGCCCCACTGTAAACTCAACAGGTTTC
ATATCAGTTTGATTGCCCAGTTTACATCATAATGTACCTTAC
Found at i:21655937 original size:33 final size:33
Alignment explanation
Indices: 21655900--21656032 Score: 185
Period size: 33 Copynumber: 4.0 Consensus size: 33
21655890 CAAACCTTCC
* *
21655900 ACGGAAACCGCTGATTCCAAACCACCAGCGACG
1 ACGGAAACCGCTGACTCCAAACCACCGGCGACG
** *
21655933 ACGGAAACCGCTGGTTCCAAACCACCGGAGACG
1 ACGGAAACCGCTGACTCCAAACCACCGGCGACG
*
21655966 ACGGAAACCGCTGACTCCAAACCACCGGCAACG
1 ACGGAAACCGCTGACTCCAAACCACCGGCGACG
* * *
21655999 ACGGAAACCGCTGACTCCAATCAATCGGCGACG
1 ACGGAAACCGCTGACTCCAAACCACCGGCGACG
21656032 A
1 A
21656033 AACCTTCGAC
Statistics
Matches: 89, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 89 1.00
ACGTcount: A:0.32, C:0.35, G:0.23, T:0.09
Consensus pattern (33 bp):
ACGGAAACCGCTGACTCCAAACCACCGGCGACG
Found at i:21656070 original size:42 final size:41
Alignment explanation
Indices: 21655997--21656132 Score: 137
Period size: 42 Copynumber: 3.2 Consensus size: 41
21655987 CCACCGGCAA
* * * *
21655997 CGACGGAAACCGCTGACTCCAATCAATCGGCGACGAAACCTT
1 CGACGGAAACCCCGGAATCCAA-CAATCGGCGACGAAACCAT
*
21656039 CGACGGAAACCCCGGAATCCGAACAACCGGCGACGAAACCAT
1 CGACGGAAACCCCGGAATCC-AACAATCGGCGACGAAACCAT
* ** * * * *
21656081 CGACAGAAACTTCGGAATCTAAACAATCAGCAACGAAACCGT
1 CGACGGAAACCCCGGAATC-CAACAATCGGCGACGAAACCAT
21656123 CGACGGAAAC
1 CGACGGAAAC
21656133 AGCAGAACCG
Statistics
Matches: 78, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
42 76 0.97
43 2 0.03
ACGTcount: A:0.37, C:0.32, G:0.21, T:0.10
Consensus pattern (41 bp):
CGACGGAAACCCCGGAATCCAACAATCGGCGACGAAACCAT
Found at i:21656930 original size:26 final size:26
Alignment explanation
Indices: 21656901--21656962 Score: 63
Period size: 26 Copynumber: 2.4 Consensus size: 26
21656891 TATTTATATA
21656901 TAAATAAATTAA-TAAAAAAATCTAAG
1 TAAATAAATTAATTAAAAAAAT-TAAG
* * * *
21656927 TAAAAAAATAAATTAACAAAATTGAG
1 TAAATAAATTAATTAAAAAAATTAAG
*
21656953 TAATTAAATT
1 TAAATAAATT
21656963 CGAGCACTAA
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
26 20 0.71
27 8 0.29
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (26 bp):
TAAATAAATTAATTAAAAAAATTAAG
Found at i:21660440 original size:18 final size:18
Alignment explanation
Indices: 21660417--21660454 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
21660407 CTTCATCAAA
21660417 GTCTTCATCCTTATCCAT
1 GTCTTCATCCTTATCCAT
21660435 GTCTTCATCCTTATCCAT
1 GTCTTCATCCTTATCCAT
21660453 GT
1 GT
21660455 AATCCTCCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.16, C:0.32, G:0.08, T:0.45
Consensus pattern (18 bp):
GTCTTCATCCTTATCCAT
Found at i:21660463 original size:18 final size:18
Alignment explanation
Indices: 21660421--21660467 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
21660411 ATCAAAGTCT
**
21660421 TCATCCTTATCCATGTCT
1 TCATCCTTATCCATGTAA
21660439 TCATCCTTATCCATGTAA
1 TCATCCTTATCCATGTAA
*
21660457 TCCTCCTTATC
1 TCATCCTTATC
21660468 TAGATACTGT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.19, C:0.34, G:0.04, T:0.43
Consensus pattern (18 bp):
TCATCCTTATCCATGTAA
Found at i:21664428 original size:15 final size:15
Alignment explanation
Indices: 21664408--21664437 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
21664398 TTTTGAACAG
*
21664408 GATTCAGTTTCTGAA
1 GATTCAGATTCTGAA
21664423 GATTCAGATTCTGAA
1 GATTCAGATTCTGAA
21664438 TGTTGATCTG
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:0.13, G:0.20, T:0.37
Consensus pattern (15 bp):
GATTCAGATTCTGAA
Found at i:21664636 original size:13 final size:13
Alignment explanation
Indices: 21664620--21664651 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
21664610 TTTTACCAAG
21664620 GCTTTTTTCTCTT
1 GCTTTTTTCTCTT
21664633 GCTTTTTTCTCTT
1 GCTTTTTTCTCTT
21664646 GCTTTT
1 GCTTTT
21664652 CTTGCTTCCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.00, C:0.22, G:0.09, T:0.69
Consensus pattern (13 bp):
GCTTTTTTCTCTT
Found at i:21664664 original size:22 final size:21
Alignment explanation
Indices: 21664629--21664669 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
21664619 GGCTTTTTTC
**
21664629 TCTTGCTTTTTTCTCTTGCTTT
1 TCTTGCTTCCTTCT-TTGCTTT
21664651 TCTTGCTTCCTTCTTTGCT
1 TCTTGCTTCCTTCTTTGCT
21664670 CAGCTTCCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.00, C:0.27, G:0.10, T:0.63
Consensus pattern (21 bp):
TCTTGCTTCCTTCTTTGCTTT
Found at i:21674324 original size:27 final size:28
Alignment explanation
Indices: 21674258--21674324 Score: 82
Period size: 28 Copynumber: 2.4 Consensus size: 28
21674248 GTAAAAAATT
* *
21674258 TGTATCTGGCTCAAATGAGCAATTTTTA
1 TGTAACTGGCTCAAATGAGCAATTATTA
* * *
21674286 TGTAATTGGCTCAAATGAGCGA-TATTC
1 TGTAACTGGCTCAAATGAGCAATTATTA
21674313 TGTAACTGGCTC
1 TGTAACTGGCTC
21674325 GGACAAGCGA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
27 14 0.42
28 19 0.58
ACGTcount: A:0.27, C:0.16, G:0.21, T:0.36
Consensus pattern (28 bp):
TGTAACTGGCTCAAATGAGCAATTATTA
Found at i:21680424 original size:82 final size:82
Alignment explanation
Indices: 21680285--21680445 Score: 259
Period size: 82 Copynumber: 2.0 Consensus size: 82
21680275 TTAGAAATTT
* * * *
21680285 ATAGATTGCAAATTCATAATTATTCATTTATTAGAAAGTGATGATTTATTCAATGGTTATATTTG
1 ATAGATTGCAAATTCATAATTATTCATTTACTAAAAAGTGATAATTTATTCAATGGTTACATTTG
21680350 ATTTCCATGAGACATAA
66 ATTTCCATGAGACATAA
* *
21680367 ATAGATTGCAAATTCATAATTATTCATTTACTAAAAAGTGATAATTTTTTCATTGGTTACATTTG
1 ATAGATTGCAAATTCATAATTATTCATTTACTAAAAAGTGATAATTTATTCAATGGTTACATTTG
*
21680432 ATTTCCATGGGACA
66 ATTTCCATGAGACA
21680446 AGTTTTTCTA
Statistics
Matches: 72, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
82 72 1.00
ACGTcount: A:0.35, C:0.10, G:0.13, T:0.42
Consensus pattern (82 bp):
ATAGATTGCAAATTCATAATTATTCATTTACTAAAAAGTGATAATTTATTCAATGGTTACATTTG
ATTTCCATGAGACATAA
Found at i:21682674 original size:15 final size:17
Alignment explanation
Indices: 21682644--21682675 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
21682634 GAAATTCGGC
21682644 AAAGAGGAGAAGGAAAA
1 AAAGAGGAGAAGGAAAA
21682661 AAAG-GGAG-AGGAAAA
1 AAAGAGGAGAAGGAAAA
21682676 GTCGAAAGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 4 0.27
17 4 0.27
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (17 bp):
AAAGAGGAGAAGGAAAA
Found at i:21689352 original size:3 final size:3
Alignment explanation
Indices: 21689344--21689372 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
21689334 AAGTGAGTCC
21689344 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
21689373 TCAAAATGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:21695372 original size:3 final size:3
Alignment explanation
Indices: 21695364--21695413 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
21695354 ACTTTGGTTC
21695364 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
21695412 TA
1 TA
21695414 AAAAATATAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:21698108 original size:16 final size:15
Alignment explanation
Indices: 21698087--21698116 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
21698077 AAAAGCAAAA
21698087 AAAATTTGTGTGAAAT
1 AAAATTTGT-TGAAAT
21698103 AAAATTTGTTGAAA
1 AAAATTTGTTGAAA
21698117 ACACAACAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.47, C:0.00, G:0.17, T:0.37
Consensus pattern (15 bp):
AAAATTTGTTGAAAT
Found at i:21699384 original size:32 final size:32
Alignment explanation
Indices: 21699334--21699402 Score: 111
Period size: 32 Copynumber: 2.2 Consensus size: 32
21699324 CATCCATGAC
*
21699334 GCATTAATTTCAAAGAAGATATTAGGCAAAAA
1 GCATTAATGTCAAAGAAGATATTAGGCAAAAA
* *
21699366 GCATTAATGTCAAGGAAGATATTATGCAAAAA
1 GCATTAATGTCAAAGAAGATATTAGGCAAAAA
21699398 GCATT
1 GCATT
21699403 TATGAAGATG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.46, C:0.10, G:0.17, T:0.26
Consensus pattern (32 bp):
GCATTAATGTCAAAGAAGATATTAGGCAAAAA
Found at i:21700060 original size:32 final size:32
Alignment explanation
Indices: 21700011--21700077 Score: 98
Period size: 32 Copynumber: 2.1 Consensus size: 32
21700001 CATCTTCGTA
* *
21700011 AATGTTTTTTGCATAATATCTTCCTTGACATT
1 AATGCTTTTTGCATAATATCTTCCTTGAAATT
* *
21700043 AATGCTTTTTGCCTAATATCTTCTTTGAAATT
1 AATGCTTTTTGCATAATATCTTCCTTGAAATT
21700075 AAT
1 AAT
21700078 ACCTCTATGG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.27, C:0.15, G:0.09, T:0.49
Consensus pattern (32 bp):
AATGCTTTTTGCATAATATCTTCCTTGAAATT
Found at i:21713113 original size:9 final size:9
Alignment explanation
Indices: 21713099--21713149 Score: 51
Period size: 9 Copynumber: 6.3 Consensus size: 9
21713089 ACAAATGATT
21713099 TTAAAATTA
1 TTAAAATTA
21713108 TTAAAATTA
1 TTAAAATTA
*
21713117 TT----TTT
1 TTAAAATTA
21713122 TTAAAA-TA
1 TTAAAATTA
21713130 -TAAAATTA
1 TTAAAATTA
21713138 TTAAAATTA
1 TTAAAATTA
21713147 TTA
1 TTA
21713150 TATGATTTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 12
0.71 0.04 0.25
Matches are distributed among these distances:
5 4 0.12
7 5 0.15
8 3 0.09
9 22 0.65
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (9 bp):
TTAAAATTA
Found at i:21726270 original size:16 final size:18
Alignment explanation
Indices: 21726249--21726283 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
21726239 AGTTCCTTCA
21726249 TGCTTA-TGTTTT-GTTG
1 TGCTTATTGTTTTAGTTG
21726265 TGCTTATTGTTTTAGTTG
1 TGCTTATTGTTTTAGTTG
21726283 T
1 T
21726284 TATTTGGGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.35
17 6 0.35
18 5 0.29
ACGTcount: A:0.09, C:0.06, G:0.23, T:0.63
Consensus pattern (18 bp):
TGCTTATTGTTTTAGTTG
Found at i:21730829 original size:31 final size:29
Alignment explanation
Indices: 21730772--21730829 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 29
21730762 AATTGGTCTC
*
21730772 TTCTTTTTGAGAAACTCTGTATTTATTCT
1 TTCTTTTTGAGAAACTCTGTAATTATTCT
*
21730801 TTCTTTTTGAGAAGGTCTCTGTAATTATT
1 TTCTTTTTGAGAA--ACTCTGTAATTATT
21730830 ATAGTGAAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 13 0.52
31 12 0.48
ACGTcount: A:0.21, C:0.12, G:0.14, T:0.53
Consensus pattern (29 bp):
TTCTTTTTGAGAAACTCTGTAATTATTCT
Found at i:21730950 original size:2 final size:2
Alignment explanation
Indices: 21730945--21730971 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
21730935 TTGTTTTTGT
21730945 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
21730972 TTGTCTTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:21739358 original size:21 final size:20
Alignment explanation
Indices: 21739312--21739386 Score: 69
Period size: 20 Copynumber: 3.6 Consensus size: 20
21739302 TTTTATTTTG
*
21739312 AATTTTTAAATTTATTTTAT
1 AATTTTTAAATTTATTTGAT
**
21739332 GGTTTTTAAATATTATTTGAT
1 AATTTTTAAAT-TTATTTGAT
* *
21739353 AATTTTTTAAATTTTTTTCAT
1 AA-TTTTTAAATTTATTTGAT
* *
21739374 AAATATTAAATTT
1 AATTTTTAAATTT
21739387 TTTTTAAGAA
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
20 18 0.41
21 17 0.39
22 9 0.20
ACGTcount: A:0.35, C:0.01, G:0.04, T:0.60
Consensus pattern (20 bp):
AATTTTTAAATTTATTTGAT
Found at i:21740111 original size:2 final size:2
Alignment explanation
Indices: 21740094--21740140 Score: 80
Period size: 2 Copynumber: 24.5 Consensus size: 2
21740084 TTAATGTAAA
21740094 AT AT A- AT AT AT A- 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
21740134 AT AT AT A
1 AT AT AT A
21740141 CATTGGATAA
Statistics
Matches: 43, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.05
2 41 0.95
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:21748166 original size:15 final size:16
Alignment explanation
Indices: 21748135--21748167 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
21748125 AATTTTATAC
*
21748135 TTTATTTATTAATTAA
1 TTTATTTATTAAATAA
21748151 TTTATTT-TTAAATAA
1 TTTATTTATTAAATAA
21748166 TT
1 TT
21748168 GTTTGATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
TTTATTTATTAAATAA
Found at i:21749655 original size:12 final size:14
Alignment explanation
Indices: 21749627--21749658 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
21749617 ATATTAAAAT
21749627 TAATTTTATATTAA
1 TAATTTTATATTAA
21749641 TAATTTTAT-TT-A
1 TAATTTTATATTAA
21749653 TAATTT
1 TAATTT
21749659 CAAAAAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.39
13 2 0.11
14 9 0.50
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
TAATTTTATATTAA
Found at i:21753512 original size:68 final size:67
Alignment explanation
Indices: 21753432--21753747 Score: 230
Period size: 65 Copynumber: 4.8 Consensus size: 67
21753422 ATAGAGCAAG
* * **
21753432 TGAGACGGGATCATCATTTACACCGATCTTAGAACACCTATCTCATTTTAT-AGGAATTCTTGAA
1 TGAGATGGGATCATCATTTACA-CGATCTTAGGACTTCTATCTCATTTTATCA-GAATTCTTGAA
21753496 CAAA
64 CAAA
* *
21753500 TGAGATGGG---ATCATTTACA-G--CCTAGGACTTTCT-TCCTCATTTTATCAGAATTC-TAAA
1 TGAGATGGGATCATCATTTACACGATCTTAGGAC-TTCTAT-CTCATTTTATCAGAATTCTTGAA
21753557 CAAA
64 CAAA
* ** *
21753561 GGAGATGAAATCATCATTTACACTGATCTTAGGACTTTTATCTCATTTTATCAGAATTCTTGAAC
1 TGAGATGGGATCATCATTTACAC-GATCTTAGGACTTCTATCTCATTTTATCAGAATTCTTGAAC
21753626 AAA
65 AAA
** * * * * *
21753629 CAAGATGGG---GTCATTTACACTGATTTTAGGGCTTCTATCTCATTTTTTCGGAATTCTATTCT
1 TGAGATGGGATCATCATTTACAC-GATCTTAGGACTTCTATCTCATTTTATCAGAATTC---T-T
*
21753691 AGATCAAA
61 -GAACAAA
* * *
21753699 TGAAATGGGA--A-CATTTACATCGATCTTAGGACTTCTATCTAATCTTATC
1 TGAGATGGGATCATCATTTACA-CGATCTTAGGACTTCTATCTCATTTTATC
21753748 GGCTGTATGG
Statistics
Matches: 197, Mismatches: 32, Indels: 36
0.74 0.12 0.14
Matches are distributed among these distances:
61 20 0.10
62 18 0.09
63 2 0.01
64 10 0.05
65 51 0.26
66 1 0.01
67 21 0.11
68 29 0.15
69 1 0.01
70 43 0.22
71 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (67 bp):
TGAGATGGGATCATCATTTACACGATCTTAGGACTTCTATCTCATTTTATCAGAATTCTTGAACA
AA
Found at i:21756391 original size:27 final size:27
Alignment explanation
Indices: 21756361--21756437 Score: 100
Period size: 27 Copynumber: 2.9 Consensus size: 27
21756351 AACTACTCCA
* *
21756361 TGTTTAATGTCCCATCGGATTATCCCG
1 TGTTTATTGTCCCATCGGACTATCCCG
* * **
21756388 TGTTTATTGTCTCGTTAGACTATCCCG
1 TGTTTATTGTCCCATCGGACTATCCCG
21756415 TGTTTATTGTCCCATCGGACTAT
1 TGTTTATTGTCCCATCGGACTAT
21756438 TCATGATGTC
Statistics
Matches: 40, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.17, C:0.23, G:0.18, T:0.42
Consensus pattern (27 bp):
TGTTTATTGTCCCATCGGACTATCCCG
Found at i:21765669 original size:11 final size:12
Alignment explanation
Indices: 21765651--21765679 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
21765641 CCGCTCATAT
21765651 TATTTTTTAAAA
1 TATTTTTTAAAA
21765663 T-TTTTTTAAAA
1 TATTTTTTAAAA
21765674 TATTTT
1 TATTTT
21765680 ATAATTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (12 bp):
TATTTTTTAAAA
Found at i:21766512 original size:29 final size:31
Alignment explanation
Indices: 21766479--21766541 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
21766469 AAAAATTTGC
21766479 AATTTAA-C-TTTTATATTTTA-AAT-TAATAT
1 AATTTAATCTTTTTA-ATTTTATAATAT-ATAT
21766508 AATTTAATCTTTTTAATTTTATAATATATAT
1 AATTTAATCTTTTTAATTTTATAATATATAT
21766539 AAT
1 AAT
21766542 GTTATTATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
29 7 0.23
30 7 0.23
31 15 0.50
32 1 0.03
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (31 bp):
AATTTAATCTTTTTAATTTTATAATATATAT
Found at i:21766539 original size:31 final size:29
Alignment explanation
Indices: 21766479--21766541 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 29
21766469 AAAAATTTGC
21766479 AATTTAACTTTTATATTTTAAATTAATAT
1 AATTTAACTTTTATATTTTAAATTAATAT
21766508 AATTTAATCTTTT-TAATTTTATAA-TATATAT
1 AATTTAA-CTTTTAT-ATTTTA-AATTA-ATAT
21766539 AAT
1 AAT
21766542 GTTATTATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
29 8 0.27
30 13 0.43
31 9 0.30
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (29 bp):
AATTTAACTTTTATATTTTAAATTAATAT
Found at i:21766720 original size:36 final size:37
Alignment explanation
Indices: 21766657--21766728 Score: 92
Period size: 36 Copynumber: 2.0 Consensus size: 37
21766647 ATTGTCAAGT
21766657 TCAAATCTCAATATGAAAACAAATATCAAATTTAAGG
1 TCAAATCTCAATATGAAAACAAATATCAAATTTAAGG
* * * * *
21766694 TCAAA-CTCAATGTGAGAATAATTATCAAGTTTAAG
1 TCAAATCTCAATATGAAAACAAATATCAAATTTAAG
21766729 CTTCAAATAG
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
36 25 0.83
37 5 0.17
ACGTcount: A:0.47, C:0.12, G:0.11, T:0.29
Consensus pattern (37 bp):
TCAAATCTCAATATGAAAACAAATATCAAATTTAAGG
Found at i:21767413 original size:51 final size:51
Alignment explanation
Indices: 21767346--21767523 Score: 144
Period size: 51 Copynumber: 3.4 Consensus size: 51
21767336 TTCAAGATGT
*
21767346 TTCATTTTTTTAATTAATTAATAAATTATTTTCAATTTTTCTTATTTTTAA
1 TTCATATTTTTAATTAATTAATAAATTATTTTCAATTTTTCTTATTTTTAA
*** * ** ** **
21767397 TTCATATTTTTAATTAA-TAACTCTTTTATTTATAAAATAAAATAATTATTGTCAAA
1 TTCATATTTTTAATTAATTAA-TAAATTATTT-T-CAAT--TTTTCTTATT-TTTAA
* *
21767453 TATCATTATTTTT-AGTAAATATATAAATTATTTTCAATTTTTCTTATTTTTAA
1 T-TCA-TATTTTTAATTAATTA-ATAAATTATTTTCAATTTTTCTTATTTTTAA
21767506 TTCATATTTTTAATTAAT
1 TTCATATTTTTAATTAAT
21767524 AACTCTTTTA
Statistics
Matches: 92, Mismatches: 24, Indels: 21
0.67 0.18 0.15
Matches are distributed among these distances:
50 3 0.03
51 30 0.33
52 8 0.09
53 7 0.08
54 6 0.07
55 6 0.07
56 7 0.08
57 8 0.09
58 16 0.17
59 1 0.01
ACGTcount: A:0.36, C:0.06, G:0.01, T:0.57
Consensus pattern (51 bp):
TTCATATTTTTAATTAATTAATAAATTATTTTCAATTTTTCTTATTTTTAA
Found at i:21767465 original size:109 final size:110
Alignment explanation
Indices: 21767347--21767584 Score: 430
Period size: 109 Copynumber: 2.2 Consensus size: 110
21767337 TCAAGATGTT
* *
21767347 TCATT-TTTTTAATTAATTA-ATAAATTATTTTCAATTTTTCTTATTTTTAATTCATATTTTTAA
1 TCATTATTTTTAAGTAAATATATAAATTATTTTCAATTTTTCTTATTTTTAATTCATATTTTTAA
21767410 TTAATAACTCTTTTATTTATAAAATAAAATAATTATTGTCAAATA
66 TTAATAACTCTTTTATTTATAAAATAAAATAATTATTGTCAAATA
21767455 TCATTATTTTT-AGTAAATATATAAATTATTTTCAATTTTTCTTATTTTTAATTCATATTTTTAA
1 TCATTATTTTTAAGTAAATATATAAATTATTTTCAATTTTTCTTATTTTTAATTCATATTTTTAA
21767519 TTAATAACTCTTTTATTTATAAAATAAAATAATTATTGTCAAATA
66 TTAATAACTCTTTTATTTATAAAATAAAATAATTATTGTCAAATA
21767564 TCATTATTTTT-AGTAAATATA
1 TCATTATTTTTAAGTAAATATA
21767585 ATTTTTATAT
Statistics
Matches: 126, Mismatches: 2, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
108 11 0.09
109 115 0.91
ACGTcount: A:0.38, C:0.06, G:0.02, T:0.54
Consensus pattern (110 bp):
TCATTATTTTTAAGTAAATATATAAATTATTTTCAATTTTTCTTATTTTTAATTCATATTTTTAA
TTAATAACTCTTTTATTTATAAAATAAAATAATTATTGTCAAATA
Found at i:21767752 original size:39 final size:43
Alignment explanation
Indices: 21767663--21767758 Score: 137
Period size: 45 Copynumber: 2.3 Consensus size: 43
21767653 TTTTATATGT
*
21767663 ATATTTGAAATAATTATTTGAAATATTTCACATATAAACATAATG
1 ATATTTGAAATAATTAATTGAAATATTTCACATAT-AACATAA-G
21767708 ATATTTGAAATAATTAATTGAAATATTTCACATAT-A-A-AA-
1 ATATTTGAAATAATTAATTGAAATATTTCACATATAACATAAG
21767747 ATATTTGAAATA
1 ATATTTGAAATA
21767759 TCATACCCAT
Statistics
Matches: 50, Mismatches: 1, Indels: 6
0.88 0.02 0.11
Matches are distributed among these distances:
39 12 0.24
41 2 0.04
42 1 0.02
43 1 0.02
45 34 0.68
ACGTcount: A:0.49, C:0.05, G:0.06, T:0.40
Consensus pattern (43 bp):
ATATTTGAAATAATTAATTGAAATATTTCACATATAACATAAG
Found at i:21779085 original size:29 final size:29
Alignment explanation
Indices: 21779043--21779102 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
21779033 AAAAAAATAC
*
21779043 TTGATACAAAACACTTATAACCATTGTTG
1 TTGAAACAAAACACTTATAACCATTGTTG
21779072 TTGAAACAAAACACTTATAACCATTGTTG
1 TTGAAACAAAACACTTATAACCATTGTTG
21779101 TT
1 TT
21779103 CTGACTCTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.38, C:0.17, G:0.10, T:0.35
Consensus pattern (29 bp):
TTGAAACAAAACACTTATAACCATTGTTG
Found at i:21781609 original size:20 final size:20
Alignment explanation
Indices: 21781554--21781609 Score: 58
Period size: 20 Copynumber: 2.7 Consensus size: 20
21781544 GTTTTGGTGC
*
21781554 TTTTTTACTGTTTGGTTGATTT
1 TTTTTTACTGTTT--TTGAGTT
* *
21781576 TTTTTTGCTATTTTTGAGTT
1 TTTTTTACTGTTTTTGAGTT
*
21781596 TTTTTTATTGTTTT
1 TTTTTTACTGTTTT
21781610 GATTGCTATT
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
20 17 0.61
22 11 0.39
ACGTcount: A:0.09, C:0.04, G:0.14, T:0.73
Consensus pattern (20 bp):
TTTTTTACTGTTTTTGAGTT
Found at i:21781621 original size:24 final size:23
Alignment explanation
Indices: 21781594--21781669 Score: 57
Period size: 24 Copynumber: 3.2 Consensus size: 23
21781584 TATTTTTGAG
21781594 TTTTTTTTATTGTTTTGATTGCTA
1 TTTTTTTTA-TGTTTTGATTGCTA
* *
21781618 TTTTTGTGTTAT-TTTTG-CTGTTA
1 TTTTT-T-TTATGTTTTGATTGCTA
** *
21781641 TTTTTGTTGCTGTTTTTATTGCTA
1 TTTTT-TTTATGTTTTGATTGCTA
21781665 TTTTT
1 TTTTT
21781670 GTTGTTTTTA
Statistics
Matches: 41, Mismatches: 7, Indels: 8
0.73 0.12 0.14
Matches are distributed among these distances:
22 2 0.05
23 15 0.37
24 19 0.46
25 2 0.05
26 3 0.07
ACGTcount: A:0.09, C:0.05, G:0.14, T:0.71
Consensus pattern (23 bp):
TTTTTTTTATGTTTTGATTGCTA
Found at i:21781656 original size:12 final size:12
Alignment explanation
Indices: 21781606--21781673 Score: 75
Period size: 12 Copynumber: 5.7 Consensus size: 12
21781596 TTTTTTATTG
21781606 TTTTGATTGCTAT
1 TTTTG-TTGCTAT
*
21781619 TTTTG-TGTTAT
1 TTTTGTTGCTAT
* *
21781630 TTTTGCTGTTAT
1 TTTTGTTGCTAT
*
21781642 TTTTGTTGCTGT
1 TTTTGTTGCTAT
*
21781654 TTTTATTGCTAT
1 TTTTGTTGCTAT
21781666 TTTTGTTG
1 TTTTGTTG
21781674 TTTTTAATGT
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
11 10 0.21
12 32 0.68
13 5 0.11
ACGTcount: A:0.09, C:0.06, G:0.18, T:0.68
Consensus pattern (12 bp):
TTTTGTTGCTAT
Found at i:21781675 original size:68 final size:68
Alignment explanation
Indices: 21781597--21781729 Score: 160
Period size: 68 Copynumber: 2.0 Consensus size: 68
21781587 TTTTGAGTTT
* ** * *
21781597 TTTTTATTGTTTTGATTGCTATTTT-TGTGTTATTTTTGCTGTTATTTTTGTTGCTGTTTTTATT
1 TTTTTATTGTTTTGAATGCTATTTTAT-TGTTATTTTTGCTACTATTTTGGTTGCTATTTTTATT
21781661 GCTA
65 GCTA
* * * * *
21781665 TTTTTGTTGTTTTTAATGTTGTTTTATTGTTATTTTTGCTACTATTTTGGTTGTTATTTTTATTG
1 TTTTTATTGTTTTGAATGCTATTTTATTGTTATTTTTGCTACTATTTTGGTTGCTATTTTTATTG
21781730 TTTGAATGTT
Statistics
Matches: 54, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
68 53 0.98
69 1 0.02
ACGTcount: A:0.11, C:0.05, G:0.16, T:0.68
Consensus pattern (68 bp):
TTTTTATTGTTTTGAATGCTATTTTATTGTTATTTTTGCTACTATTTTGGTTGCTATTTTTATTG
CTA
Found at i:21781695 original size:47 final size:47
Alignment explanation
Indices: 21781604--21781695 Score: 116
Period size: 47 Copynumber: 2.0 Consensus size: 47
21781594 TTTTTTTTAT
* *
21781604 TGTTTTGATTGCTATTTTTGTGTTATTTTTGCTGTTATTTTTGTTGC
1 TGTTTTGATTGCTATTTTTGTGTTATTTATGCTGTTATTATTGTTGC
* *
21781651 TGTTTTTATTGCTATTTTTGTTGTT-TTTAATGTTGTT-TTATTGTT
1 TGTTTTGATTGCTATTTTTG-TGTTATTT-ATGCTGTTATTATTGTT
21781696 ATTTTTGCTA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
47 29 0.74
48 10 0.26
ACGTcount: A:0.10, C:0.04, G:0.17, T:0.68
Consensus pattern (47 bp):
TGTTTTGATTGCTATTTTTGTGTTATTTATGCTGTTATTATTGTTGC
Found at i:21781701 original size:12 final size:12
Alignment explanation
Indices: 21781606--21781731 Score: 55
Period size: 12 Copynumber: 10.9 Consensus size: 12
21781596 TTTTTTATTG
* *
21781606 TTTTGATTGCTA
1 TTTTTATTGTTA
*
21781618 TTTTT-GTGTTA
1 TTTTTATTGTTA
**
21781629 TTTTTGCTGTTA
1 TTTTTATTGTTA
* * *
21781641 TTTTTGTTGCTG
1 TTTTTATTGTTA
*
21781653 TTTTTATTGCTA
1 TTTTTATTGTTA
*
21781665 --TTT-TTGTTG
1 TTTTTATTGTTA
*
21781674 TTTTTAATGTT-
1 TTTTTATTGTTA
*
21781685 GTTTTATTGTTA
1 TTTTTATTGTTA
** **
21781697 TTTTTGCTACTA
1 TTTTTATTGTTA
**
21781709 TTTTGGTTGTTA
1 TTTTTATTGTTA
21781721 TTTTTATTGTT
1 TTTTTATTGTT
21781732 TGAATGTTAT
Statistics
Matches: 84, Mismatches: 25, Indels: 10
0.71 0.21 0.08
Matches are distributed among these distances:
9 4 0.05
10 3 0.04
11 21 0.25
12 56 0.67
ACGTcount: A:0.11, C:0.05, G:0.16, T:0.68
Consensus pattern (12 bp):
TTTTTATTGTTA
Found at i:21781718 original size:44 final size:44
Alignment explanation
Indices: 21781662--21781745 Score: 107
Period size: 44 Copynumber: 1.9 Consensus size: 44
21781652 GTTTTTATTG
* * * *
21781662 CTATTTTTGTTGTT-TTTAATGTTGTTTTATTGTTATTTTTGCTA
1 CTATTTTGGTTGTTATTT-ATATTGTTTGAATGTTATTTTTGCTA
*
21781706 CTATTTTGGTTGTTATTTTTATTGTTTGAATGTTATTTTT
1 CTATTTTGGTTGTTATTTATATTGTTTGAATGTTATTTTT
21781746 TATGCGTTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
44 31 0.91
45 3 0.09
ACGTcount: A:0.14, C:0.04, G:0.14, T:0.68
Consensus pattern (44 bp):
CTATTTTGGTTGTTATTTATATTGTTTGAATGTTATTTTTGCTA
Found at i:21781942 original size:38 final size:38
Alignment explanation
Indices: 21781857--21781950 Score: 100
Period size: 39 Copynumber: 2.4 Consensus size: 38
21781847 TCTTAATATA
** * *
21781857 ATTTTTTTAATGTATTTTAAATTTATTTATTTTTTAAT
1 ATTTTTTTAATGTATTTTAAATGCATTTATATATTAAT
21781895 ATTTGTTTTAATGT-TTTTAAATGCATTTGATATATTATAT
1 ATTT-TTTTAATGTATTTTAAATGCATTT-ATATATTA-AT
* *
21781935 ATTTTTTAAATTTATT
1 ATTTTTTTAATGTATT
21781951 GTATATAATA
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
38 16 0.35
39 22 0.48
40 8 0.17
ACGTcount: A:0.30, C:0.01, G:0.05, T:0.64
Consensus pattern (38 bp):
ATTTTTTTAATGTATTTTAAATGCATTTATATATTAAT
Found at i:21781969 original size:13 final size:13
Alignment explanation
Indices: 21781953--21781982 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
21781943 AATTTATTGT
*
21781953 ATATAATAAAATA
1 ATATAAAAAAATA
21781966 ATATAAAAAAATA
1 ATATAAAAAAATA
21781979 ATAT
1 ATAT
21781983 GGGTTGGATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (13 bp):
ATATAAAAAAATA
Found at i:21792294 original size:20 final size:20
Alignment explanation
Indices: 21792269--21792310 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
21792259 AAAAAGTGTC
*
21792269 AAGTTTGAGTACCAAATTAA
1 AAGTTTAAGTACCAAATTAA
*
21792289 AAGTTTAAGTACCAACTTAA
1 AAGTTTAAGTACCAAATTAA
21792309 AA
1 AA
21792311 AAAGTGTCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.48, C:0.12, G:0.12, T:0.29
Consensus pattern (20 bp):
AAGTTTAAGTACCAAATTAA
Found at i:21792376 original size:32 final size:32
Alignment explanation
Indices: 21792289--21792423 Score: 121
Period size: 30 Copynumber: 4.5 Consensus size: 32
21792279 ACCAAATTAA
*
21792289 AAGTTTAAGTACCAACTTA--AAAAAAGTGTC
1 AAGTTTAAGTACCAAATTAGGAAAAAAGTGTC
21792319 AAGTTTAAGTACCAAATTAGGAAAAAA-TGTC
1 AAGTTTAAGTACCAAATTAGGAAAAAAGTGTC
*
21792350 AAGTTTGAGTACCAAATT-GGACAAAAA-----
1 AAGTTTAAGTACCAAATTAGGA-AAAAAGTGTC
* * *
21792377 AAATTTAAGTACCAAATT--GAAAAAGGTATC
1 AAGTTTAAGTACCAAATTAGGAAAAAAGTGTC
* *
21792407 AAGTTCAAGTATCAAAT
1 AAGTTTAAGTACCAAAT
21792424 ATTATATTAA
Statistics
Matches: 89, Mismatches: 8, Indels: 16
0.79 0.07 0.14
Matches are distributed among these distances:
25 4 0.04
26 2 0.02
27 16 0.18
30 35 0.39
31 26 0.29
32 6 0.07
ACGTcount: A:0.48, C:0.11, G:0.15, T:0.26
Consensus pattern (32 bp):
AAGTTTAAGTACCAAATTAGGAAAAAAGTGTC
Found at i:21792395 original size:27 final size:27
Alignment explanation
Indices: 21792322--21792400 Score: 81
Period size: 31 Copynumber: 2.8 Consensus size: 27
21792312 AAGTGTCAAG
*
21792322 TTTAAGTACCAAATTAGGAAAAAATGTCAAG
1 TTTAAGTACCAAATT-GGAAAAAA--T-AAA
*
21792353 TTTGAGTACCAAATTGGACAAAAA-AAA
1 TTTAAGTACCAAATTGGA-AAAAATAAA
21792380 TTTAAGTACCAAATT-GAAAAA
1 TTTAAGTACCAAATTGGAAAAA
21792401 GGTATCAAGT
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
25 4 0.09
26 2 0.05
27 16 0.36
30 3 0.07
31 19 0.43
ACGTcount: A:0.51, C:0.10, G:0.14, T:0.25
Consensus pattern (27 bp):
TTTAAGTACCAAATTGGAAAAAATAAA
Found at i:21795297 original size:26 final size:26
Alignment explanation
Indices: 21795218--21795297 Score: 72
Period size: 26 Copynumber: 3.0 Consensus size: 26
21795208 TAATTTAATT
* *
21795218 TTTAAAAAA-AGAGTAAAATGATTGAA
1 TTTAAAAAATAGAATAAAATAATT-AA
* * *
21795244 TTTAAAAAAATAAAAATAAAAGATTTAA
1 TTT-AAAAAAT-AGAATAAAATAATTAA
*
21795272 TTTAAAAAATAGAATAAATTAATTAA
1 TTTAAAAAATAGAATAAAATAATTAA
21795298 GAATTAAATT
Statistics
Matches: 42, Mismatches: 9, Indels: 6
0.74 0.16 0.11
Matches are distributed among these distances:
26 15 0.36
27 13 0.31
28 5 0.12
29 9 0.21
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.30
Consensus pattern (26 bp):
TTTAAAAAATAGAATAAAATAATTAA
Found at i:21797114 original size:40 final size:40
Alignment explanation
Indices: 21796975--21797133 Score: 178
Period size: 40 Copynumber: 4.0 Consensus size: 40
21796965 GAGATGGTTA
* * * * *
21796975 CTTCAATCTGCCCTCTGATTAGGGTAAAAGATTGGGTTG-
1 CTTCAATTTGCCCTATGGTTAGGGTAAAAGATTGGATGGT
** *
21797014 CTTCAATCTT-CCCTATGGTCGGGGTAAGAGATTGGATGGTGT
1 CTTCAAT-TTGCCCTATGGTTAGGGTAAAAGATTGGAT-G-GT
* *
21797056 CTTCAATTTACCCTATGGTTAGGGTAAAAGATTGAATGGT
1 CTTCAATTTGCCCTATGGTTAGGGTAAAAGATTGGATGGT
*
21797096 CTTCAATTTGCCCAATGGTTAGGGTAAAAGATTGGATG
1 CTTCAATTTGCCCTATGGTTAGGGTAAAAGATTGGATG
21797134 TGGTGACGTA
Statistics
Matches: 100, Mismatches: 15, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
39 28 0.28
40 38 0.38
41 4 0.04
42 30 0.30
ACGTcount: A:0.25, C:0.15, G:0.26, T:0.33
Consensus pattern (40 bp):
CTTCAATTTGCCCTATGGTTAGGGTAAAAGATTGGATGGT
Found at i:21797469 original size:92 final size:92
Alignment explanation
Indices: 21797145--21797469 Score: 343
Period size: 92 Copynumber: 3.5 Consensus size: 92
21797135 GGTGACGTAA
* * * *
21797145 CTTCACTCCATTCCACCGTAACCTCAGGGACATTGAGATCCGATACTCATTTTAATCTGATCCAC
1 CTTCACTCCATTCCACTGTAACCTCAAGGACATTGAGATCTGTTACTCATTTTAATCTGATCCAC
* *
21797210 TGCAACTTCAAGGATATAGGATATGGTG
66 TACAACTT-AAGGATATAGGATTTGGTG
** * *
21797238 CTTCACTCCATTCCACT-TAACCTCAAGGACATTGAGATCTGCTT-CGTTGTTTTAATCCGAACC
1 CTTCACTCCATTCCACTGTAACCTCAAGGACATTGAGATCTG-TTAC-TCATTTTAATCTGATCC
* *
21797301 ACTACAACTTAAGGGTAT-GAGATTTGATGTTATAA
64 ACTACAACTTAAGGATATAG-GATTTG--G---T-G
* * * *
21797336 CTTCTCTCCATTCCACTGTAACCT-GAGTGACTTTGAGATCTGTTACTCATTTTGATCTGATCCA
1 CTTCACTCCATTCCACTGTAACCTCAAG-GACATTGAGATCTGTTACTCATTTTAATCTGATCCA
*
21797400 CTAAAACTTAAGGATATAGGATTTGGTG
65 CTACAACTTAAGGATATAGGATTTGGTG
* * *
21797428 CTTCACTCTATTTCACTGTAACCTTAAGGACATTGAGATCTG
1 CTTCACTCCATTCCACTGTAACCTCAAGGACATTGAGATCTG
21797470 CTTCATTGTT
Statistics
Matches: 190, Mismatches: 28, Indels: 29
0.77 0.11 0.12
Matches are distributed among these distances:
91 1 0.01
92 69 0.36
93 42 0.22
94 1 0.01
96 1 0.01
97 1 0.01
98 54 0.28
99 21 0.11
ACGTcount: A:0.27, C:0.23, G:0.16, T:0.34
Consensus pattern (92 bp):
CTTCACTCCATTCCACTGTAACCTCAAGGACATTGAGATCTGTTACTCATTTTAATCTGATCCAC
TACAACTTAAGGATATAGGATTTGGTG
Found at i:21797501 original size:191 final size:191
Alignment explanation
Indices: 21797142--21797485 Score: 528
Period size: 191 Copynumber: 1.8 Consensus size: 191
21797132 TGTGGTGACG
21797142 TAACTTCACTCCATTCCACCGTAACCTCAGGGACATTGAGATCCGATACTCATTTTAATCTGATC
1 TAACTTCACTCCATTCCACCGTAACCTCAGGGACATTGAGATCCGATACTCATTTTAATCTGATC
**
21797207 CACTGCAACTTCAAGGATATAGGATATGGTGCTTCACTCCATTCCACTTAACCTCAAGGACATTG
66 CACTAAAACTTCAAGGATATAGGATATGGTGCTTCACTCCATTCCACTTAACCTCAAGGACATTG
* *
21797272 AGATCTGCTTCGTTGTTTTAATCCGAACCACTACAACTTAAGGGTATGAGATTTGATGTTA
131 AGATCTGCTTCATTGTTTTAATACGAACCACTACAACTTAAGGGTATGAGATTTGATGTTA
* * * * * * * *
21797333 TAACTTCTCTCCATTCCACTGTAACCTGAGTGACTTTGAGATCTGTTACTCATTTTGATCTGATC
1 TAACTTCACTCCATTCCACCGTAACCTCAGGGACATTGAGATCCGATACTCATTTTAATCTGATC
* * * *
21797398 CACTAAAACTT-AAGGATATAGGATTTGGTGCTTCACTCTATTTCACTGTAACCTTAAGGACATT
66 CACTAAAACTTCAAGGATATAGGATATGGTGCTTCACTCCATTCCACT-TAACCTCAAGGACATT
21797462 GAGATCTGCTTCATTGTTTTAATA
130 GAGATCTGCTTCATTGTTTTAATA
21797486 TGCTTCACTA
Statistics
Matches: 136, Mismatches: 16, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
190 33 0.24
191 103 0.76
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.35
Consensus pattern (191 bp):
TAACTTCACTCCATTCCACCGTAACCTCAGGGACATTGAGATCCGATACTCATTTTAATCTGATC
CACTAAAACTTCAAGGATATAGGATATGGTGCTTCACTCCATTCCACTTAACCTCAAGGACATTG
AGATCTGCTTCATTGTTTTAATACGAACCACTACAACTTAAGGGTATGAGATTTGATGTTA
Found at i:21797735 original size:49 final size:49
Alignment explanation
Indices: 21797680--21797915 Score: 222
Period size: 49 Copynumber: 4.8 Consensus size: 49
21797670 TTATCTTTAG
* * **
21797680 GGTATAAGATTCACCGTTGTGGCTTCAATTTTTCCCTTCACATCTCTAA
1 GGTATAAGATTCGCCGTTGCGGCTTCAACCTTTCCCTTCACATCTCTAA
* * * * *
21797729 GTTATAAGGTTCGTCGTTGCGGCTTCAACCTTTCCCTCCACATCTCTAG
1 GGTATAAGATTCGCCGTTGCGGCTTCAACCTTTCCCTTCACATCTCTAA
* * * * * *
21797778 GGTATAAGGTTCGTCGTTGCGGTTTCAACTTTTCCC-TCTATATCTCTAG
1 GGTATAAGATTCGCCGTTGCGGCTTCAACCTTTCCCTTC-ACATCTCTAA
* * * * *
21797827 GGTACAAGATTCGCCATTACGGCTTCAATCTCTCCCTTCACATCTCTAA
1 GGTATAAGATTCGCCGTTGCGGCTTCAACCTTTCCCTTCACATCTCTAA
* * ** * *
21797876 GATATAAGATTCACTATTGTGGCTTCAAACTTTCCCTTCA
1 GGTATAAGATTCGCCGTTGCGGCTTCAACCTTTCCCTTCA
21797916 TGTCTTCTAG
Statistics
Matches: 152, Mismatches: 33, Indels: 4
0.80 0.17 0.02
Matches are distributed among these distances:
48 1 0.01
49 149 0.98
50 2 0.01
ACGTcount: A:0.21, C:0.27, G:0.16, T:0.36
Consensus pattern (49 bp):
GGTATAAGATTCGCCGTTGCGGCTTCAACCTTTCCCTTCACATCTCTAA
Found at i:21797785 original size:98 final size:98
Alignment explanation
Indices: 21797672--21797915 Score: 256
Period size: 98 Copynumber: 2.5 Consensus size: 98
21797662 ACTTTTCCTT
* * * *
21797672 ATCTTTAGGGTATAAGATTCACCGTTGTGGCTTCAATTTTTCCCTTCACATCTCTAAGTTATAAG
1 ATCTCTAGGGTATAAGATTCACCGTTGTGGCTTCAAATTTTCCCTTCACATCTCTAAGGTACAAG
* * * * *
21797737 GTTCGTCGTTGCGGCTTCAACCTTTCCCTCCAC
66 ATTCGCCATTACGGCTTCAACCTCTCCCTCCAC
* ** * * * * *
21797770 ATCTCTAGGGTATAAGGTTCGTCGTTGCGGTTTCAACTTTTCCC-TCTATATCTCTAGGGTACAA
1 ATCTCTAGGGTATAAGATTCACCGTTGTGGCTTCAAATTTTCCCTTC-ACATCTCTAAGGTACAA
* *
21797834 GATTCGCCATTACGGCTTCAATCTCTCCCTTCAC
65 GATTCGCCATTACGGCTTCAACCTCTCCCTCCAC
* * ** *
21797868 ATCTCTAAGATATAAGATTCACTATTGTGGCTTCAAACTTTCCCTTCA
1 ATCTCTAGGGTATAAGATTCACCGTTGTGGCTTCAAATTTTCCCTTCA
21797916 TGTCTTCTAG
Statistics
Matches: 115, Mismatches: 29, Indels: 4
0.78 0.20 0.03
Matches are distributed among these distances:
97 2 0.02
98 111 0.97
99 2 0.02
ACGTcount: A:0.21, C:0.26, G:0.16, T:0.37
Consensus pattern (98 bp):
ATCTCTAGGGTATAAGATTCACCGTTGTGGCTTCAAATTTTCCCTTCACATCTCTAAGGTACAAG
ATTCGCCATTACGGCTTCAACCTCTCCCTCCAC
Found at i:21798566 original size:115 final size:112
Alignment explanation
Indices: 21798365--21798584 Score: 314
Period size: 115 Copynumber: 1.9 Consensus size: 112
21798355 TATCGTTAAA
* * *
21798365 CCACTAACCGTTACTTCAATGCAAAAATGCTTGAATAAGGTTGTATGGTGGATAAAATTGAATTT
1 CCACTAACCGTTACTTCAATGCAAAAATGATTGAACAAGGTTGTAAGGTGGATAAAATTGAATTT
* *
21798430 TATCGGAGGCAAAGCTCGCATGAATGAAAAGATTAAAAATCATTAGT
66 TATCAGAGGCAAAACTCGCATGAATGAAAAGATTAAAAATCATTAGT
* * *
21798477 CCACTAACTGTTATTTCAATGCAAAAAAAGTGATTGAACAGGGTTGTAAGGTGGATAAAATTGAA
1 CCACTAACCGTTACTTCAATGC--AAAAA-TGATTGAACAAGGTTGTAAGGTGGATAAAATTGAA
* * *
21798542 TTTTATTAGAGGCAAAACTTGCATGAATGAAAATATTAAAAAT
63 TTTTATCAGAGGCAAAACTCGCATGAATGAAAAGATTAAAAAT
21798585 GGAAAACATT
Statistics
Matches: 94, Mismatches: 11, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
112 20 0.21
114 5 0.05
115 69 0.73
ACGTcount: A:0.40, C:0.11, G:0.19, T:0.29
Consensus pattern (112 bp):
CCACTAACCGTTACTTCAATGCAAAAATGATTGAACAAGGTTGTAAGGTGGATAAAATTGAATTT
TATCAGAGGCAAAACTCGCATGAATGAAAAGATTAAAAATCATTAGT
Found at i:21798922 original size:13 final size:14
Alignment explanation
Indices: 21798898--21798928 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
21798888 CTCCTTTTTC
21798898 TTTTCTTCTTCTTT
1 TTTTCTTCTTCTTT
21798912 TTTTCTT-TTCTTT
1 TTTTCTTCTTCTTT
21798925 TTTT
1 TTTT
21798929 TTGGGTGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.59
14 7 0.41
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (14 bp):
TTTTCTTCTTCTTT
Found at i:21800958 original size:15 final size:17
Alignment explanation
Indices: 21800938--21800969 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
21800928 TCAAAACGTT
21800938 GGCTTG-AA-TGGTTAG
1 GGCTTGCAAGTGGTTAG
21800953 GGCTTGCAAGTGGTTAG
1 GGCTTGCAAGTGGTTAG
21800970 CCACTTCTCG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 2 0.13
17 7 0.47
ACGTcount: A:0.19, C:0.09, G:0.41, T:0.31
Consensus pattern (17 bp):
GGCTTGCAAGTGGTTAG
Found at i:21803721 original size:17 final size:18
Alignment explanation
Indices: 21803699--21803734 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
21803689 TAAATGAGTT
21803699 AATTAAGAT-TAAATTGG
1 AATTAAGATATAAATTGG
*
21803716 AATTAAGGTATAAATTGG
1 AATTAAGATATAAATTGG
21803734 A
1 A
21803735 TAGAAATTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.47, C:0.00, G:0.19, T:0.33
Consensus pattern (18 bp):
AATTAAGATATAAATTGG
Found at i:21805527 original size:18 final size:20
Alignment explanation
Indices: 21805491--21805527 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
21805481 TAAATTAAAT
21805491 ACAAGAATAAAATAAATAAC
1 ACAAGAATAAAATAAATAAC
21805511 ACAA-AATAAAA-AAATAA
1 ACAAGAATAAAATAAATAA
21805528 TTAATAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
19 7 0.41
20 4 0.24
ACGTcount: A:0.76, C:0.08, G:0.03, T:0.14
Consensus pattern (20 bp):
ACAAGAATAAAATAAATAAC
Found at i:21805641 original size:27 final size:28
Alignment explanation
Indices: 21805580--21805665 Score: 77
Period size: 27 Copynumber: 3.0 Consensus size: 28
21805570 AAGAAAAGAG
*
21805580 TAAAATGATTGAATTTTAAAAAAATAAA
1 TAAAAAGATTGAATTTTAAAAAAATAAA
* *
21805608 AATAAAAGATTTAA-TTT-AAAAAATAGAA
1 TA-AAAAGATTGAATTTTAAAAAAATA-AA
** *
21805636 TAAAAAGGGTAAATTTTAAAAGAAATAAA
1 TAAAAAGATTGAATTTTAAAA-AAATAAA
21805665 T
1 T
21805666 TAATCAAGGA
Statistics
Matches: 46, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
27 16 0.35
28 10 0.22
29 15 0.33
30 5 0.11
ACGTcount: A:0.62, C:0.00, G:0.09, T:0.29
Consensus pattern (28 bp):
TAAAAAGATTGAATTTTAAAAAAATAAA
Found at i:21818009 original size:6 final size:6
Alignment explanation
Indices: 21818000--21818028 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
21817990 TTGGTTTTGG
21818000 TTTTTA TTTTTA TTTTTA TTTTTA TTTTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTT
21818029 TACACTGGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTTA
Found at i:21818015 original size:18 final size:18
Alignment explanation
Indices: 21817994--21818028 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
21817984 TAAATTTTGG
*
21817994 TTTTGGTTTTTATTTTTA
1 TTTTGATTTTTATTTTTA
*
21818012 TTTTTATTTTTATTTTT
1 TTTTGATTTTTATTTTT
21818029 TACACTGGTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.11, C:0.00, G:0.06, T:0.83
Consensus pattern (18 bp):
TTTTGATTTTTATTTTTA
Found at i:21818397 original size:32 final size:31
Alignment explanation
Indices: 21818331--21818394 Score: 94
Period size: 32 Copynumber: 2.1 Consensus size: 31
21818321 AATCTCAAAA
21818331 TTATATATAAATTTTGATTAAATGTATATTT
1 TTATATATAAATTTTGATTAAATGTATATTT
* *
21818362 TTATATATGAAATTTTGATTTAATTTA-ATTT
1 TTATATAT-AAATTTTGATTAAATGTATATTT
21818393 TT
1 TT
21818395 TATTGATTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 14 0.47
32 16 0.53
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (31 bp):
TTATATATAAATTTTGATTAAATGTATATTT
Found at i:21820869 original size:138 final size:138
Alignment explanation
Indices: 21820582--21820995 Score: 710
Period size: 138 Copynumber: 3.0 Consensus size: 138
21820572 AGTAGGAGGC
*
21820582 TCTGGATCATATTGTCTATATCCAATGGTATTAGTTTCGTTATTATTAACAGCATTCACCTGCCT
1 TCTGGATCATATTGTCTATATCCAATGGTATTAGTTTCATTATTATTAACAGCATTCACCTGCCT
*
21820647 CGAGTTTGAAGCAGACAAATCAGA---TCCTCCATCTTTCTTGGCCCAATTCCTCATCTTTTCCG
66 CGAGTTTGAAGCAGACAAATCAGATCCTCCTCCATCTTTCTTGGCCCAATTCCTCGTCTTTTCCG
21820709 GTTTTTCT
131 GTTTTTCT
* *
21820717 TCTGGATCATATTGTCTATATCCAACGGCATTAGTTTCATTATTATTAACAGCATTCACCTGCCT
1 TCTGGATCATATTGTCTATATCCAATGGTATTAGTTTCATTATTATTAACAGCATTCACCTGCCT
* * *
21820782 CAAGTTTGAAGCAGA-ATTATCGGATCCTCCTCCATCTTTCTTGGCCCAATTCCTCGTCTTTTCC
66 CGAGTTTGAAGCAGACA-AATCAGATCCTCCTCCATCTTTCTTGGCCCAATTCCTCGTCTTTTCC
21820846 GGTTTTTCT
130 GGTTTTTCT
*
21820855 TCTGGATCATATTGTCTATATCCAATGGTATCAGTTTCATTATTATTAACAGCATTCACCTGCCT
1 TCTGGATCATATTGTCTATATCCAATGGTATTAGTTTCATTATTATTAACAGCATTCACCTGCCT
*
21820920 CGAGTTTGAAGCAGACAAATCAGATCCTCCTCCATCTTTCTTGGCCCAATTCCTCGTCTTTTCCA
66 CGAGTTTGAAGCAGACAAATCAGATCCTCCTCCATCTTTCTTGGCCCAATTCCTCGTCTTTTCCG
21820985 GTTTTTCT
131 GTTTTTCT
21820993 TCT
1 TCT
21820996 CTAGTTGCTT
Statistics
Matches: 260, Mismatches: 14, Indels: 7
0.93 0.05 0.02
Matches are distributed among these distances:
134 1 0.00
135 81 0.31
138 177 0.68
139 1 0.00
ACGTcount: A:0.22, C:0.26, G:0.14, T:0.39
Consensus pattern (138 bp):
TCTGGATCATATTGTCTATATCCAATGGTATTAGTTTCATTATTATTAACAGCATTCACCTGCCT
CGAGTTTGAAGCAGACAAATCAGATCCTCCTCCATCTTTCTTGGCCCAATTCCTCGTCTTTTCCG
GTTTTTCT
Found at i:21825247 original size:83 final size:83
Alignment explanation
Indices: 21825059--21825467 Score: 646
Period size: 83 Copynumber: 5.0 Consensus size: 83
21825049 CTCATGAGAG
* * * * * *
21825059 TGTTC-CCAAATAAGGTCATAAAAAATGACAACTTCAAATAAATTAAAAGTAATTAAA-AGCATA
1 TGTTCACCAAATAAGTTCATAAAAAATAACAATTTAAAATAAATTAAAAGCAATTAAATA-TATA
21825122 CATTAACCAAATTCAATT-
65 CATTAACCAAATTCAATTA
*
21825140 TGTTCACCAAATAAGTTCATAAAAAATAACAATTTAAAATAAATTAAAAGCCATTAAATATATAC
1 TGTTCACCAAATAAGTTCATAAAAAATAACAATTTAAAATAAATTAAAAGCAATTAAATATATAC
21825205 ATTAACCAAATTCAATTA
66 ATTAACCAAATTCAATTA
* * * *
21825223 TGTTCACCAAATAAGTTCATAAAAAATAACAATTTAAAATGAATTAAAAACCATTAAATACATAC
1 TGTTCACCAAATAAGTTCATAAAAAATAACAATTTAAAATAAATTAAAAGCAATTAAATATATAC
21825288 ATTAACCAAATTCAATTA
66 ATTAACCAAATTCAATTA
*
21825306 TGTTCACCAAATAAGTTCATAAAAAATAACAATTTAAAATAAATTAAAAGCAATTAAATATATAA
1 TGTTCACCAAATAAGTTCATAAAAAATAACAATTTAAAATAAATTAAAAGCAATTAAATATATAC
*
21825371 ATCAACCAAATTCAATTA
66 ATTAACCAAATTCAATTA
*
21825389 TGTTCACCAAATAAGTTCAT-AAAAATGACAATTTAAAATAAATTAAAAGCAATTAAATATATAC
1 TGTTCACCAAATAAGTTCATAAAAAATAACAATTTAAAATAAATTAAAAGCAATTAAATATATAC
*
21825453 ATTAACCGAATTCAA
66 ATTAACCAAATTCAA
21825468 ATTGCCGCAT
Statistics
Matches: 305, Mismatches: 20, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
81 5 0.02
82 122 0.40
83 178 0.58
ACGTcount: A:0.53, C:0.13, G:0.05, T:0.29
Consensus pattern (83 bp):
TGTTCACCAAATAAGTTCATAAAAAATAACAATTTAAAATAAATTAAAAGCAATTAAATATATAC
ATTAACCAAATTCAATTA
Found at i:21829367 original size:12 final size:12
Alignment explanation
Indices: 21829350--21829397 Score: 51
Period size: 12 Copynumber: 3.7 Consensus size: 12
21829340 ACCCAATTCC
*
21829350 ATTTTTCTTATT
1 ATTTTTATTATT
21829362 ATTTTTATTTATTT
1 ATTTTTA-TTA-TT
21829376 ATTTATTTATTATT
1 A-TT-TTTATTATT
21829390 ATTTTTAT
1 ATTTTTAT
21829398 GAACATAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
12 11 0.35
13 5 0.16
14 6 0.19
15 5 0.16
16 4 0.13
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.75
Consensus pattern (12 bp):
ATTTTTATTATT
Found at i:21829432 original size:63 final size:65
Alignment explanation
Indices: 21829358--21829521 Score: 237
Period size: 63 Copynumber: 2.5 Consensus size: 65
21829348 CCATTTTTCT
*
21829358 TATTATTTTTA-TTTATTTATTTATTTATTATTATTTTTATGAACATAAATAAAT-A-TAAAATA
1 TATTAATTTTATTTTA-TTATTTATTTATTATTATTTTTATGAACATAAATAAATAAGTAAAATA
21829420 A
65 A
*
21829421 TATTAATTTTATTTTATTATTTATTTATTTATTA-TTTTATGAATATAAATAAATAAATGTAAAA
1 TATTAATTTTATTTTATTATTTATTTA-TTATTATTTTTATGAACATAAATAAAT-AA-GTAAAA
21829485 TAA
63 TAA
*
21829488 TATTAATTTTGTTTTATTATTTATTTATTATTAT
1 TATTAATTTTATTTTATTATTTATTTATTATTAT
21829522 AAATAAATAA
Statistics
Matches: 91, Mismatches: 3, Indels: 10
0.88 0.03 0.10
Matches are distributed among these distances:
63 40 0.44
64 10 0.11
65 1 0.01
66 6 0.07
67 34 0.37
ACGTcount: A:0.39, C:0.01, G:0.02, T:0.58
Consensus pattern (65 bp):
TATTAATTTTATTTTATTATTTATTTATTATTATTTTTATGAACATAAATAAATAAGTAAAATAA
Found at i:21829478 original size:67 final size:63
Alignment explanation
Indices: 21829358--21829521 Score: 224
Period size: 67 Copynumber: 2.5 Consensus size: 63
21829348 CCATTTTTCT
* *
21829358 TATTATTTTTA-TTTATTTATTTATTTATTATTATTTTTATGAACATAAATAAATATAAAATAA
1 TATTAATTTTATTTTA-TTATTTATTTATTATTATTTTTATGAAAATAAATAAATATAAAATAA
*
21829421 TATTAATTTTATTTTATTATTTATTTATTTATTA-TTTTATGAATATAAATAAATAAATGTAAAA
1 TATTAATTTTATTTTATTATTTATTTA-TTATTATTTTTATG---A-AAATAAATAAATATAAAA
21829485 TAA
61 TAA
*
21829488 TATTAATTTTGTTTTATTATTTATTTATTATTAT
1 TATTAATTTTATTTTATTATTTATTTATTATTAT
21829522 AAATAAATAA
Statistics
Matches: 90, Mismatches: 4, Indels: 10
0.87 0.04 0.10
Matches are distributed among these distances:
63 28 0.31
64 10 0.11
66 7 0.08
67 45 0.50
ACGTcount: A:0.39, C:0.01, G:0.02, T:0.58
Consensus pattern (63 bp):
TATTAATTTTATTTTATTATTTATTTATTATTATTTTTATGAAAATAAATAAATATAAAATAA
Found at i:21829532 original size:63 final size:67
Alignment explanation
Indices: 21829364--21829539 Score: 220
Period size: 67 Copynumber: 2.7 Consensus size: 67
21829354 TTCTTATTAT
***
21829364 TTTTATTTATTTATTTATTTATTATT--ATTTTTATGAACATAAATAAATATAAAATAATATTAA
1 TTTTA-TTATTTATTTATTTATTATTAAATGAATAT-AA-ATAAATAAATATAAAATAATATTAA
21829427 TTTTA
63 TTTTA
** *
21829432 TTTTATTATTTATTTATTTATTATTTTATGAATATAAATAAATAAATGTAAAATAATATTAATTT
1 TTTTATTATTTATTTATTTATTATTAAATGAATATAAATAAATAAATATAAAATAATATTAATTT
*
21829497 TG
66 TA
21829499 TTTTATTATTTATTTA-TTATTA-TAAAT-AA-ATAAATAAATAA
1 TTTTATTATTTATTTATTTATTATTAAATGAATATAAATAAATAA
21829540 CAAACCAAAA
Statistics
Matches: 99, Mismatches: 7, Indels: 9
0.86 0.06 0.08
Matches are distributed among these distances:
63 12 0.12
64 2 0.02
65 3 0.03
66 6 0.06
67 64 0.65
68 7 0.07
69 5 0.05
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.54
Consensus pattern (67 bp):
TTTTATTATTTATTTATTTATTATTAAATGAATATAAATAAATAAATATAAAATAATATTAATTT
TA
Found at i:21829861 original size:11 final size:11
Alignment explanation
Indices: 21829845--21829879 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
21829835 CTCTCTAGCT
*
21829845 TTTCCCCTTCA
1 TTTCCCCTCCA
21829856 TTTCCCCTCCA
1 TTTCCCCTCCA
*
21829867 TTTCCCTTCCA
1 TTTCCCCTCCA
21829878 TT
1 TT
21829880 CTTTTGTCGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.09, C:0.46, G:0.00, T:0.46
Consensus pattern (11 bp):
TTTCCCCTCCA
Found at i:21834547 original size:6 final size:6
Alignment explanation
Indices: 21834538--21834588 Score: 57
Period size: 6 Copynumber: 8.0 Consensus size: 6
21834528 AAAAAATTAA
* *
21834538 AAAAAG AAAAAAG AAAAAG ACAAAG AAAAGG AAAAAG AAGAAAAG AAAAAG
1 AAAAAG -AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG -A-AAAAG AAAAAG
21834589 GGGAGGTCGA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
6 25 0.66
7 8 0.21
8 5 0.13
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:21835574 original size:50 final size:50
Alignment explanation
Indices: 21835511--21835656 Score: 186
Period size: 50 Copynumber: 2.9 Consensus size: 50
21835501 ATCTTTTACC
*
21835511 CCTAAAGCGGTGGAGGTGCAGATTGAAACTGCAATGGTAAATCTCATACA
1 CCTAAAGCTGTGGAGGTGCAGATTGAAACTGCAATGGTAAATCTCATACA
* **
21835561 CCTAAAGCTGTGGAGGTGTAGATTGAAACCACAAT-GTCAAATCTCATACA
1 CCTAAAGCTGTGGAGGTGCAGATTGAAACTGCAATGGT-AAATCTCATACA
* * * * * *
21835611 CCTAAAGCTGTAGAGGGGCAGAATGAAGCTGTAATGGGAAATCTCA
1 CCTAAAGCTGTGGAGGTGCAGATTGAAACTGCAATGGTAAATCTCA
21835657 AAAGTGTGCA
Statistics
Matches: 81, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
49 2 0.02
50 78 0.96
51 1 0.01
ACGTcount: A:0.35, C:0.18, G:0.25, T:0.22
Consensus pattern (50 bp):
CCTAAAGCTGTGGAGGTGCAGATTGAAACTGCAATGGTAAATCTCATACA
Found at i:21836223 original size:16 final size:16
Alignment explanation
Indices: 21836202--21836233 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
21836192 CTCTTTCCTC
*
21836202 ATATTGTGCTGTTAAA
1 ATATTGTGCTATTAAA
21836218 ATATTGTGCTATTAAA
1 ATATTGTGCTATTAAA
21836234 GCAGCATTAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.06, G:0.16, T:0.44
Consensus pattern (16 bp):
ATATTGTGCTATTAAA
Found at i:21841164 original size:85 final size:84
Alignment explanation
Indices: 21841021--21841190 Score: 295
Period size: 85 Copynumber: 2.0 Consensus size: 84
21841011 ATGCGCTTTA
* *
21841021 CAAAAGCGCTTCCACATCAATGCGTTTTTTCTTGTCCCAACGATAAATTCCAACAGCTATTTGAA
1 CAAAAGCGCTTCCACATAAATACGTTTTTTCTTGTCCCAACGATAAATTCCAACAGCTATTTGAA
21841086 ATAGACATTGGACCCCTCCC
66 ATAGACATTGGA-CCCTCCC
* *
21841106 CAAAAGCGCTTCCACATAAATACGTTTTTTCTTGTCCCAACGGTCAATTCCAACAGCTATTTGAA
1 CAAAAGCGCTTCCACATAAATACGTTTTTTCTTGTCCCAACGATAAATTCCAACAGCTATTTGAA
21841171 ATAGACATTGGACCCTCCC
66 ATAGACATTGGACCCTCCC
21841190 C
1 C
21841191 CCCAATGGTA
Statistics
Matches: 81, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
84 8 0.10
85 73 0.90
ACGTcount: A:0.29, C:0.29, G:0.13, T:0.28
Consensus pattern (84 bp):
CAAAAGCGCTTCCACATAAATACGTTTTTTCTTGTCCCAACGATAAATTCCAACAGCTATTTGAA
ATAGACATTGGACCCTCCC
Found at i:21846365 original size:157 final size:158
Alignment explanation
Indices: 21846078--21846557 Score: 687
Period size: 158 Copynumber: 3.0 Consensus size: 158
21846068 ATTTCTGAAT
* * * * * ** * * *
21846078 CATGTAGTTCTCACACAAGCTATGAAATGGGTCTGCTCACGCGAGCTGTGGGTCGAGCTGTTAGG
1 CATGTAATGCTCACACGAGCTGTGAAGTGGACCTGCTCACACGAGCTGTGGGTCGAGATGTTAAG
** *
21846143 CTACGCAATGCTGCTCACACGAGCTGTGGAGAATCTACAACAAATGCC-AGATCTCAACCATTGG
66 CTACGCAATGCTGCTCACACGAGCTGTGGAGAATCCGCAACAAATGCCGA-ATCTCAGCCATTGG
21846207 TAGAACATCTAAGACCAGCACCCATATAA
130 TAGAACATCTAAGACCAGCACCCATATAA
21846236 CATGTAATGCTCACACGAGCTGTGAAGTGGACCTGCTCACACGAGCTGTGGGTCGAGATGTTAAG
1 CATGTAATGCTCACACGAGCTGTGAAGTGGACCTGCTCACACGAGCTGTGGGTCGAGATGTTAAG
* * *
21846301 CTAC-CAATGCTGCTCACACGAGCTGAGGAGAATCCGCAACAAATGCCGAATCTTAGCTATTGGT
66 CTACGCAATGCTGCTCACACGAGCTGTGGAGAATCCGCAACAAATGCCGAATCTCAGCCATTGGT
21846365 AGAACATCTAAGACCAGCACCCATATAA
131 AGAACATCTAAGACCAGCACCCATATAA
* * * * * *
21846393 CATGTAATGCTTACATGAGCTGTGAAGTAGACCTTCTCACACGAGTTGTGGGTTGAGATGTTAAG
1 CATGTAATGCTCACACGAGCTGTGAAGTGGACCTGCTCACACGAGCTGTGGGTCGAGATGTTAAG
* * *
21846458 CTACGCAATGCTGCTCACACGAGTTGTGGAGAATCCGCAACAAATGTCTG-ATCTCAGCCATCGG
66 CTACGCAATGCTGCTCACACGAGCTGTGGAGAATCCGCAACAAATG-CCGAATCTCAGCCATTGG
*
21846522 TAGAACATCTAAGACCAACACCCATATAA
130 TAGAACATCTAAGACCAGCACCCATATAA
21846551 CATGTAA
1 CATGTAA
21846558 ATCCCGAAAT
Statistics
Matches: 290, Mismatches: 29, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
157 143 0.49
158 145 0.50
159 2 0.01
ACGTcount: A:0.30, C:0.24, G:0.23, T:0.23
Consensus pattern (158 bp):
CATGTAATGCTCACACGAGCTGTGAAGTGGACCTGCTCACACGAGCTGTGGGTCGAGATGTTAAG
CTACGCAATGCTGCTCACACGAGCTGTGGAGAATCCGCAACAAATGCCGAATCTCAGCCATTGGT
AGAACATCTAAGACCAGCACCCATATAA
Found at i:21852504 original size:20 final size:21
Alignment explanation
Indices: 21852474--21852512 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
21852464 GGGTTTATAA
21852474 AAAAGAGTCAACAATCAACCC
1 AAAAGAGTCAACAATCAACCC
*
21852495 AAAA-AGTCAACGATCAAC
1 AAAAGAGTCAACAATCAAC
21852513 GGTCAATGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.54, C:0.26, G:0.10, T:0.10
Consensus pattern (21 bp):
AAAAGAGTCAACAATCAACCC
Found at i:21854604 original size:43 final size:42
Alignment explanation
Indices: 21854533--21854634 Score: 143
Period size: 43 Copynumber: 2.4 Consensus size: 42
21854523 ATCATTTTCT
*
21854533 CCTAAAACCCTAAAACCATAATTAATAAAAACA-ATAAAATTA
1 CCTAAAACACTAAAACCATAATTAATAAAAACATA-AAAATTA
*
21854575 CCTAAAACACTAAAATCCATAATTAATAAAAACTTAAAAATTA
1 CCTAAAACACTAAAA-CCATAATTAATAAAAACATAAAAATTA
**
21854618 AATAAAACACTAAAACC
1 CCTAAAACACTAAAACC
21854635 TTAAACCTAA
Statistics
Matches: 54, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
42 16 0.30
43 37 0.69
44 1 0.02
ACGTcount: A:0.60, C:0.19, G:0.00, T:0.22
Consensus pattern (42 bp):
CCTAAAACACTAAAACCATAATTAATAAAAACATAAAAATTA
Found at i:21854738 original size:23 final size:21
Alignment explanation
Indices: 21854668--21854746 Score: 72
Period size: 22 Copynumber: 3.6 Consensus size: 21
21854658 AAATAATTCC
21854668 CTAAACCTTAA-TTTAAAATACA
1 CTAAACC-TAATTTTAAAA-ACA
* *
21854690 CTAACCCTAATTTAAAAAATCA
1 CTAAACCTAATTTTAAAAA-CA
21854712 -TAAATCCTAATTTTAATAAACA
1 CTAAA-CCTAATTTTAA-AAACA
21854734 CTAAACCTTAATT
1 CTAAACC-TAATT
21854747 ATCAATTAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 11
0.76 0.06 0.18
Matches are distributed among these distances:
21 7 0.15
22 28 0.60
23 12 0.26
ACGTcount: A:0.48, C:0.19, G:0.00, T:0.33
Consensus pattern (21 bp):
CTAAACCTAATTTTAAAAACA
Found at i:21861226 original size:31 final size:31
Alignment explanation
Indices: 21861185--21861243 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
21861175 ATTTGAGGTG
* * *
21861185 GAGGGTTTAATTGATTTTTTAATTATTTTAT
1 GAGGGCTTAATTAATTTTGTAATTATTTTAT
21861216 GAGGGCTTAATTAATTTTGTAATTATTT
1 GAGGGCTTAATTAATTTTGTAATTATTT
21861244 AAGCTTAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.27, C:0.02, G:0.17, T:0.54
Consensus pattern (31 bp):
GAGGGCTTAATTAATTTTGTAATTATTTTAT
Found at i:21861335 original size:37 final size:38
Alignment explanation
Indices: 21861277--21861360 Score: 93
Period size: 37 Copynumber: 2.2 Consensus size: 38
21861267 TATAAAATTT
*
21861277 TAAAATTATAGAAAATCTAT-AAAATTAATTAAATATCA
1 TAAAATTATAGAAAATCTATAAAAACT-ATTAAATATCA
* *
21861315 TAAAATTTTA-AAACAT-TATAAAAACTATTAAATATTA
1 TAAAATTATAGAAA-ATCTATAAAAACTATTAAATATCA
21861352 TAAATATTA
1 TAAA-ATTA
21861361 CTAAGATCTT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
37 20 0.51
38 19 0.49
ACGTcount: A:0.57, C:0.05, G:0.01, T:0.37
Consensus pattern (38 bp):
TAAAATTATAGAAAATCTATAAAAACTATTAAATATCA
Found at i:21861351 original size:19 final size:18
Alignment explanation
Indices: 21861294--21861386 Score: 62
Period size: 19 Copynumber: 4.9 Consensus size: 18
21861284 ATAGAAAATC
*
21861294 TATAAAATTAATTAAATAT
1 TATAAAAAT-ATTAAATAT
* * *
21861313 CAT-AAAATTTTAAAACAT
1 TATAAAAATATT-AAATAT
21861331 TATAAAAACTATTAAATAT
1 TATAAAAA-TATTAAATAT
* * *
21861350 TATAAATATTACTAAGATCT
1 TATAAA-AATATTAA-ATAT
*
21861370 TATGAAAATATTAAATA
1 TATAAAAATATTAAATA
21861387 GATATTATAA
Statistics
Matches: 55, Mismatches: 14, Indels: 11
0.69 0.17 0.14
Matches are distributed among these distances:
17 2 0.04
18 13 0.24
19 28 0.51
20 12 0.22
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.38
Consensus pattern (18 bp):
TATAAAAATATTAAATAT
Found at i:21861402 original size:11 final size:10
Alignment explanation
Indices: 21861249--21861398 Score: 72
Period size: 10 Copynumber: 15.5 Consensus size: 10
21861239 TATTTAAGCT
21861249 TAAAA-ATTA
1 TAAAATATTA
*
21861258 TTAAAACATTA
1 -TAAAATATTA
21861269 TAAAAT-TT-
1 TAAAATATTA
21861277 T-AAA-ATTA
1 TAAAATATTA
21861285 TAGAAA-ATCTA
1 TA-AAATAT-TA
*
21861296 TAAAAT-TAA
1 TAAAATATTA
* *
21861305 TTAAATATCA
1 TAAAATATTA
21861315 TAAAAT-TT-
1 TAAAATATTA
*
21861323 TAAAACATTA
1 TAAAATATTA
*
21861333 TAAAA-ACTA
1 TAAAATATTA
*
21861342 TTAAATATTA
1 TAAAATATTA
21861352 T-AAATATTA
1 TAAAATATTA
* *
21861361 CTAAGATCTTA
1 -TAAAATATTA
21861372 TGAAAATATTA
1 T-AAAATATTA
21861383 -AATAGATATTA
1 TAA-A-ATATTA
21861394 TAAAA
1 TAAAA
21861399 ATATAGAAAA
Statistics
Matches: 109, Mismatches: 14, Indels: 34
0.69 0.09 0.22
Matches are distributed among these distances:
7 5 0.05
8 7 0.06
9 28 0.26
10 39 0.36
11 28 0.26
12 2 0.02
ACGTcount: A:0.56, C:0.05, G:0.03, T:0.37
Consensus pattern (10 bp):
TAAAATATTA
Found at i:21861478 original size:9 final size:9
Alignment explanation
Indices: 21861249--21861480 Score: 89
Period size: 9 Copynumber: 24.0 Consensus size: 9
21861239 TATTTAAGCT
21861249 TAAAAATTA
1 TAAAAATTA
21861258 TTAAAACATTA
1 -TAAAA-ATTA
21861269 T-AAAATT-
1 TAAAAATTA
*
21861276 TTAAAATTA
1 TAAAAATTA
21861285 TAGAAAATCTA
1 TA-AAAAT-TA
21861296 T-AAAATTAA
1 TAAAAATT-A
* *
21861305 TTAAATATCA
1 -TAAAAATTA
*
21861315 T-AAAATTT
1 TAAAAATTA
21861323 TAAAACATTA
1 TAAAA-ATTA
*
21861333 TAAAAACTA
1 TAAAAATTA
*
21861342 TTAAATATTA
1 -TAAAAATTA
*
21861352 TAAATATTA
1 TAAAAATTA
**
21861361 CTAAGATCTTA
1 -TAA-AAATTA
21861372 TGAAAATATTA
1 T-AAAA-ATTA
21861383 -AATAGATATTA
1 TAA-A-A-ATTA
21861394 TAAAAA-TA
1 TAAAAATTA
*
21861402 TAGAAAATAA
1 TA-AAAATTA
* *
21861412 TTAAAATGA
1 TAAAAATTA
21861421 TAAAAATCTA
1 TAAAAAT-TA
21861431 TAAAAATGTTA
1 TAAAAA--TTA
21861442 TAAAAACTTA
1 TAAAAA-TTA
* *
21861452 TTAGAAGTATA
1 -TAAAAAT-TA
*
21861463 AAAAAATTA
1 TAAAAATTA
21861472 TAAAAATTA
1 TAAAAATTA
21861481 AATACATATA
Statistics
Matches: 172, Mismatches: 25, Indels: 51
0.69 0.10 0.21
Matches are distributed among these distances:
7 1 0.01
8 19 0.11
9 55 0.32
10 52 0.30
11 42 0.24
12 3 0.02
ACGTcount: A:0.58, C:0.04, G:0.04, T:0.34
Consensus pattern (9 bp):
TAAAAATTA
Found at i:21861733 original size:8 final size:8
Alignment explanation
Indices: 21861720--21861769 Score: 55
Period size: 8 Copynumber: 6.0 Consensus size: 8
21861710 TTTTTAATTA
21861720 AAAATTTT
1 AAAATTTT
21861728 AAAATTTT
1 AAAATTTT
21861736 AAAATTATT
1 AAAATT-TT
21861745 AAAATTATT
1 AAAATT-TT
* *
21861754 AGAATATT
1 AAAATTTT
*
21861762 ATAATTTT
1 AAAATTTT
21861770 TTAAGAAAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
8 22 0.59
9 15 0.41
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (8 bp):
AAAATTTT
Found at i:21861739 original size:17 final size:17
Alignment explanation
Indices: 21861720--21861769 Score: 59
Period size: 17 Copynumber: 3.0 Consensus size: 17
21861710 TTTTTAATTA
21861720 AAAATT-TTAAAATTTT
1 AAAATTATTAAAATTTT
21861736 AAAATTATTAAAATTATT
1 AAAATTATTAAAATT-TT
* *
21861754 AGAA-TATTATAATTTT
1 AAAATTATTAAAATTTT
21861770 TTAAGAAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
16 8 0.27
17 17 0.57
18 5 0.17
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (17 bp):
AAAATTATTAAAATTTT
Found at i:21861946 original size:31 final size:33
Alignment explanation
Indices: 21861880--21861950 Score: 101
Period size: 33 Copynumber: 2.2 Consensus size: 33
21861870 TAAAATTTAT
* *
21861880 TTAAGCCCTCCTAGAATAATTAAAAAAAGTCAA
1 TTAAGCCATCCTAAAATAATTAAAAAAAGTCAA
*
21861913 TTAAGCCATCGTAAAATAATT-AAAAAAGT-AA
1 TTAAGCCATCCTAAAATAATTAAAAAAAGTCAA
21861944 TTAAGCC
1 TTAAGCC
21861951 CTACACATCA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
31 9 0.26
32 8 0.23
33 18 0.51
ACGTcount: A:0.49, C:0.15, G:0.10, T:0.25
Consensus pattern (33 bp):
TTAAGCCATCCTAAAATAATTAAAAAAAGTCAA
Found at i:21868794 original size:10 final size:10
Alignment explanation
Indices: 21868779--21868826 Score: 51
Period size: 10 Copynumber: 4.7 Consensus size: 10
21868769 TGTGACACTT
*
21868779 TTAAATTAAA
1 TTAAAATAAA
*
21868789 TTAAATTAAA
1 TTAAAATAAA
*
21868799 TTATAAAAAAA
1 TTA-AAATAAA
*
21868810 TAAAAATAAA
1 TTAAAATAAA
21868820 TTAAAAT
1 TTAAAAT
21868827 TTTTTATTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
10 25 0.78
11 7 0.22
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (10 bp):
TTAAAATAAA
Found at i:21869939 original size:29 final size:28
Alignment explanation
Indices: 21869886--21869941 Score: 69
Period size: 30 Copynumber: 2.0 Consensus size: 28
21869876 TACTTGCGAC
*
21869886 AAAAAAAAAGTTTAGGTATTAATTTTAG
1 AAAAAAAAAGTTTAGGTATCAATTTTAG
*
21869914 AAAAAAACATAGTTTAGGTA-CCATTTTA
1 AAAAAAA-A-AGTTTAGGTATCAATTTTA
21869942 TAGTTTAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 7 0.29
29 7 0.29
30 10 0.42
ACGTcount: A:0.48, C:0.05, G:0.12, T:0.34
Consensus pattern (28 bp):
AAAAAAAAAGTTTAGGTATCAATTTTAG
Found at i:21870341 original size:18 final size:18
Alignment explanation
Indices: 21870315--21870350 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
21870305 AATGTGTTCT
*
21870315 AAATTATATAATATAAAA
1 AAATAATATAATATAAAA
21870333 AAATAATATAATATAAAA
1 AAATAATATAATATAAAA
21870351 TATTATAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
AAATAATATAATATAAAA
Found at i:21871024 original size:53 final size:52
Alignment explanation
Indices: 21870920--21871024 Score: 133
Period size: 53 Copynumber: 2.0 Consensus size: 52
21870910 TTTTAGCTGG
* * *
21870920 GGGTTTATTGGATTTAGGGTTTTGGGCTAGGAATTAGGAACTTAATTAATCA
1 GGGTTTATTGGATATAGGGTTTTGGGCTAGGAATTAGGAACGTAATGAATCA
*
21870972 GGGTTTATTGGGTATAGGGTTTTTGGGC-AGTGAATTCA-GAACGTAATGAATCA
1 GGGTTTATTGGATATAGGG-TTTTGGGCTAG-GAATT-AGGAACGTAATGAATCA
21871025 CATTTCTATT
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
52 19 0.41
53 26 0.57
54 1 0.02
ACGTcount: A:0.27, C:0.07, G:0.30, T:0.36
Consensus pattern (52 bp):
GGGTTTATTGGATATAGGGTTTTGGGCTAGGAATTAGGAACGTAATGAATCA
Found at i:21877606 original size:21 final size:19
Alignment explanation
Indices: 21877566--21877607 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 19
21877556 ACATCATAAC
*
21877566 CAAATAAGTTAACAAGTTA
1 CAAATAAATTAACAAGTTA
21877585 CAAACTAAATTAACATAGTTA
1 CAAA-TAAATTAACA-AGTTA
21877606 CA
1 CA
21877608 TTGAAAACTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 4 0.20
20 9 0.45
21 7 0.35
ACGTcount: A:0.52, C:0.14, G:0.07, T:0.26
Consensus pattern (19 bp):
CAAATAAATTAACAAGTTA
Found at i:21895527 original size:3 final size:3
Alignment explanation
Indices: 21895467--21895507 Score: 66
Period size: 3 Copynumber: 14.0 Consensus size: 3
21895457 TGAACATCAA
*
21895467 ATT ATT GTT ATT -TT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
21895508 TAATTTTTTC
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 2 0.06
3 33 0.94
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.68
Consensus pattern (3 bp):
ATT
Found at i:21898731 original size:41 final size:41
Alignment explanation
Indices: 21898626--21898853 Score: 206
Period size: 42 Copynumber: 5.5 Consensus size: 41
21898616 GGTGTATAAA
* * * * *
21898626 AAGGAAGACTCATGTCTCGGGTTGAGCATGAGA-AATTGTAT
1 AAGGAAGACTCATGTCTCGAGATGAGAATGAGATTA-TGAAT
* * *
21898667 AAATGAAGACTCATGTCTTGAGATGAAAATGAGATTATGAAT
1 -AAGGAAGACTCATGTCTCGAGATGAGAATGAGATTATGAAT
21898709 AAGGAAGACTCATGTCTCGAGATGAGAATGAGATTATGAAT
1 AAGGAAGACTCATGTCTCGAGATGAGAATGAGATTATGAAT
* * * * * * * *
21898750 ATGGAAGACTCATGCCTCAAAAATAAGAATGATATTTTGATT
1 AAGGAAGACTCATGTCTC-GAGATGAGAATGAGATTATGAAT
* * * **
21898792 AAGGAAGACTCATGTCTCAAGTTGAGAATGAGAATATGGTT
1 AAGGAAGACTCATGTCTCGAGATGAGAATGAGATTATGAAT
* *
21898833 AAAGGAAGACTTATGACTCGA
1 -AAGGAAGACTCATGTCTCGA
21898854 AAGAGCATAA
Statistics
Matches: 152, Mismatches: 31, Indels: 6
0.80 0.16 0.03
Matches are distributed among these distances:
41 70 0.46
42 81 0.53
43 1 0.01
ACGTcount: A:0.39, C:0.11, G:0.24, T:0.27
Consensus pattern (41 bp):
AAGGAAGACTCATGTCTCGAGATGAGAATGAGATTATGAAT
Found at i:21905170 original size:51 final size:51
Alignment explanation
Indices: 21905052--21905290 Score: 300
Period size: 51 Copynumber: 4.6 Consensus size: 51
21905042 TTTCATTTAA
* * * *
21905052 TACTCACGATGAC-TTATAGTCATCGGACCTCTTATTCTGTAAAGGAATTCATA
1 TACTCACGATGACACT-TAGTCATCGGACCT-TTAATCCGTAAAGG-ATTCATT
* * * * *
21905105 TACTCACGATGACACTGAGTCATTGGACCTTTAATCCATCATGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
* * *
21905156 TACTCACGATGACACTTAGTCATTGGATCTTTAATTCGTAAAGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
* * *
21905207 TACTCATGATGACACTTAGTCGTCGGACCTTTAATCCGTAAAGGATTCGTT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
21905258 TACTCACGATGACACTTAGTCATCGGATCCTTT
1 TACTCACGATGACACTTAGTCATCGGA-CCTTT
21905291 CGTTTATAGC
Statistics
Matches: 161, Mismatches: 23, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
51 121 0.75
52 14 0.09
53 25 0.16
54 1 0.01
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.34
Consensus pattern (51 bp):
TACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
Found at i:21907868 original size:16 final size:16
Alignment explanation
Indices: 21907847--21907877 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
21907837 CGAAAGCGTG
21907847 TCCAACTTGATGCGCA
1 TCCAACTTGATGCGCA
*
21907863 TCCAACTTGGTGCGC
1 TCCAACTTGATGCGC
21907878 TTTCAGAACA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.19, C:0.32, G:0.23, T:0.26
Consensus pattern (16 bp):
TCCAACTTGATGCGCA
Found at i:21910421 original size:12 final size:12
Alignment explanation
Indices: 21910404--21910432 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
21910394 ATAATATCAT
21910404 AGTTTTATTGTA
1 AGTTTTATTGTA
21910416 AGTTTTATTGTA
1 AGTTTTATTGTA
21910428 AGTTT
1 AGTTT
21910433 CATCCTTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.17, T:0.59
Consensus pattern (12 bp):
AGTTTTATTGTA
Found at i:21914602 original size:21 final size:21
Alignment explanation
Indices: 21914578--21914639 Score: 97
Period size: 21 Copynumber: 3.0 Consensus size: 21
21914568 ATGCATGACA
*
21914578 TGTATCGGTAAAACTTATACT
1 TGTATCGGTAGAACTTATACT
*
21914599 TGTATCGGTAGAACTTATGCT
1 TGTATCGGTAGAACTTATACT
*
21914620 TGTATCGGTAGAACTAATAC
1 TGTATCGGTAGAACTTATAC
21914640 AGGTAACAGT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.35
Consensus pattern (21 bp):
TGTATCGGTAGAACTTATACT
Found at i:21920991 original size:51 final size:51
Alignment explanation
Indices: 21920922--21921152 Score: 304
Period size: 51 Copynumber: 4.5 Consensus size: 51
21920912 CGAAAGGATT
21920922 CGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTAAAGGTC
1 CGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTAAAGGTC
21920973 CGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTAAAGGTC
1 CGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTAAAGGTC
* * * * * *
21921024 CGATAACTATGTGTCATCGTGAGTAAATGAATCCATGATGGATTAAAGGTT
1 CGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTAAAGGTC
* * * **
21921075 CGATGACTCAA-TGTCCTCGTGAGTATATGAATTCCTATACGGAACAAGAGGTC
1 CGATGACT-AAGTGTCATCGTGAGTAAATGAA-TCCTTTACGGATTAA-AGGTC
*
21921128 CGATGACTATA-TGTCATTGTGAGTA
1 CGATGACTA-AGTGTCATCGTGAGTA
21921153 TTAAATGAAA
Statistics
Matches: 157, Mismatches: 19, Indels: 6
0.86 0.10 0.03
Matches are distributed among these distances:
51 121 0.77
52 11 0.07
53 25 0.16
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Consensus pattern (51 bp):
CGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTAAAGGTC
Found at i:21924551 original size:62 final size:64
Alignment explanation
Indices: 21924463--21924643 Score: 185
Period size: 52 Copynumber: 3.1 Consensus size: 64
21924453 CAAGGTTGGT
* * *
21924463 TTCAGTTCGCATTTGGTAACTCACGATGACACGGAGTCATCGGACCT-TTAATCCGTAATAGGA
1 TTCAGTTCGCATTTGATAACTCACGATGACACAGAGTCATCGGACCTCATAATCCGTAATAGGA
* * *
21924526 TTCATTTCTCATTTGAT-ACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAA-A--A
1 TTCAGTTCGCATTTGATAACTCACGATGACACAGAGTCATCGGACCTCATAATCCGTAATAGGA
* *
21924586 ---AATT--CA--T-AT-ACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAA-AGGA
1 TTCAGTTCGCATTTGATAACTCACGATGACACAGAGTCATCGGACCTCATAATCCGTAATAGGA
21924640 TTCA
1 TTCA
21924644 TATACTCACG
Statistics
Matches: 105, Mismatches: 7, Indels: 18
0.81 0.05 0.14
Matches are distributed among these distances:
52 44 0.42
53 1 0.01
54 1 0.01
55 2 0.02
57 4 0.04
60 1 0.01
62 28 0.27
63 24 0.23
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.29
Consensus pattern (64 bp):
TTCAGTTCGCATTTGATAACTCACGATGACACAGAGTCATCGGACCTCATAATCCGTAATAGGA
Found at i:21924619 original size:52 final size:52
Alignment explanation
Indices: 21924541--21924675 Score: 243
Period size: 52 Copynumber: 2.6 Consensus size: 52
21924531 TTCTCATTTG
21924541 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAAAATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAAAATTCAT
**
21924593 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAAAATTCAT
*
21924645 ATACTCACGATGACACATAGTCATTGGACCT
1 ATACTCACGATGACACATAGTCATCGGACCT
21924676 TTTGTATTTA
Statistics
Matches: 80, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 80 1.00
ACGTcount: A:0.36, C:0.25, G:0.14, T:0.25
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAAAATTCAT
Found at i:21925235 original size:11 final size:11
Alignment explanation
Indices: 21925216--21925253 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
21925206 CCTCAATACC
21925216 ATTTC-ATTTCA
1 ATTTCAATTT-A
21925227 ATTT-AATTTA
1 ATTTCAATTTA
21925237 ATTTCAATTTA
1 ATTTCAATTTA
21925248 ATTTCA
1 ATTTCA
21925254 TTCCTCAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 5 0.20
11 20 0.80
ACGTcount: A:0.34, C:0.11, G:0.00, T:0.55
Consensus pattern (11 bp):
ATTTCAATTTA
Found at i:21925235 original size:16 final size:16
Alignment explanation
Indices: 21925216--21925267 Score: 77
Period size: 16 Copynumber: 3.1 Consensus size: 16
21925206 CCTCAATACC
21925216 ATTTCATTTCAATTTA
1 ATTTCATTTCAATTTA
*
21925232 ATTTAATTTCAATTTA
1 ATTTCATTTCAATTTA
21925248 ATTTCATTCCTCAATTTA
1 ATTTCATT--TCAATTTA
21925266 AT
1 AT
21925268 ATTTACTAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
16 22 0.69
18 10 0.31
ACGTcount: A:0.33, C:0.13, G:0.00, T:0.54
Consensus pattern (16 bp):
ATTTCATTTCAATTTA
Found at i:21925704 original size:16 final size:16
Alignment explanation
Indices: 21925680--21925712 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
21925670 TCCTTACAAA
*
21925680 TTTATTCCTTTAACAT
1 TTTAGTCCTTTAACAT
21925696 TTTAGTCCTTTAACAT
1 TTTAGTCCTTTAACAT
21925712 T
1 T
21925713 AAAATCATCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.24, C:0.18, G:0.03, T:0.55
Consensus pattern (16 bp):
TTTAGTCCTTTAACAT
Found at i:21932789 original size:18 final size:18
Alignment explanation
Indices: 21932766--21932822 Score: 69
Period size: 18 Copynumber: 3.2 Consensus size: 18
21932756 ATTCAGATTG
*
21932766 ACCCGACCCGTTGACTTA
1 ACCCGACCCGTTGACCTA
* *
21932784 ACCCGACTCGTTGACCTG
1 ACCCGACCCGTTGACCTA
* *
21932802 ACTCGACCCGTTGACCCA
1 ACCCGACCCGTTGACCTA
21932820 ACC
1 ACC
21932823 GTTGACCGTT
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.21, C:0.42, G:0.18, T:0.19
Consensus pattern (18 bp):
ACCCGACCCGTTGACCTA
Found at i:21933891 original size:5 final size:5
Alignment explanation
Indices: 21933881--21933906 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
21933871 AATTATAGAA
21933881 TATTT TATTT TATTT TATTT TATTT T
1 TATTT TATTT TATTT TATTT TATTT T
21933907 TGGGTTTCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TATTT
Found at i:21939857 original size:6 final size:6
Alignment explanation
Indices: 21939840--21939868 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
21939830 ACCTAACATT
21939840 AAACCC -AACCC AAACCC AAACCC AAACCC
1 AAACCC AAACCC AAACCC AAACCC AAACCC
21939869 TTAGCCTAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.23
6 17 0.77
ACGTcount: A:0.48, C:0.52, G:0.00, T:0.00
Consensus pattern (6 bp):
AAACCC
Found at i:21940131 original size:7 final size:7
Alignment explanation
Indices: 21940004--21940113 Score: 98
Period size: 7 Copynumber: 16.0 Consensus size: 7
21939994 TGATCCGACT
21940004 CGTTGAC
1 CGTTGAC
21940011 C--TGAC
1 CGTTGAC
* *
21940016 TGTTAAC
1 CGTTGAC
21940023 CGTTGAC
1 CGTTGAC
*
21940030 AGTTGAC
1 CGTTGAC
*
21940037 CATTGAC
1 CGTTGAC
*
21940044 CGTTGAT
1 CGTTGAC
21940051 CGTTGAC
1 CGTTGAC
21940058 CGTTGAC
1 CGTTGAC
* *
21940065 AGTTGAT
1 CGTTGAC
21940072 CGTTGAC
1 CGTTGAC
*
21940079 CATTGAC
1 CGTTGAC
*
21940086 CATTGAC
1 CGTTGAC
*
21940093 CGTTAAC
1 CGTTGAC
*
21940100 CGTCGAC
1 CGTTGAC
*
21940107 TGTTGAC
1 CGTTGAC
21940114 TTTTGGGTTG
Statistics
Matches: 80, Mismatches: 21, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
5 4 0.05
7 76 0.95
ACGTcount: A:0.21, C:0.25, G:0.24, T:0.31
Consensus pattern (7 bp):
CGTTGAC
Found at i:21941163 original size:5 final size:5
Alignment explanation
Indices: 21941153--21941195 Score: 59
Period size: 5 Copynumber: 8.2 Consensus size: 5
21941143 AATTATAGAA
*
21941153 TATTT TATTT TAACTTT TATTT TATTT GATTT TATTT TATTT T
1 TATTT TATTT T-A-TTT TATTT TATTT TATTT TATTT TATTT T
21941196 GGGTTTCATA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
5 28 0.82
6 2 0.06
7 4 0.12
ACGTcount: A:0.21, C:0.02, G:0.02, T:0.74
Consensus pattern (5 bp):
TATTT
Found at i:21942763 original size:22 final size:21
Alignment explanation
Indices: 21942738--21942785 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 21
21942728 ATAATCCGTT
*
21942738 TCATCTCAATTCTATTTTCATA
1 TCATCTC-ATTCTAGTTTCATA
* *
21942760 TCATTCTCATTTTAGTTTCATT
1 TCA-TCTCATTCTAGTTTCATA
21942782 TCAT
1 TCAT
21942786 AACCAAATCA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
21 1 0.05
22 17 0.77
23 4 0.18
ACGTcount: A:0.23, C:0.21, G:0.02, T:0.54
Consensus pattern (21 bp):
TCATCTCATTCTAGTTTCATA
Found at i:21943805 original size:20 final size:20
Alignment explanation
Indices: 21943753--21943806 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 20
21943743 TCTTTTACTT
21943753 TTATAATAATAATAATAATTA
1 TTATAATAA-AATAATAATTA
* *
21943774 TTATTATTAAATAATAATTA
1 TTATAATAAAATAATAATTA
21943794 TT-TAATGAAAATA
1 TTATAAT-AAAATA
21943807 TCAACGAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
19 3 0.11
20 18 0.64
21 7 0.25
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (20 bp):
TTATAATAAAATAATAATTA
Found at i:21944312 original size:20 final size:23
Alignment explanation
Indices: 21944287--21944340 Score: 78
Period size: 23 Copynumber: 2.5 Consensus size: 23
21944277 ACGGTTAATG
21944287 GTCAATGG-TC-A-TCGGTCAAA
1 GTCAATGGTTCGATTCGGTCAAA
21944307 GTCAATGGTTCGATTCGGTCAAA
1 GTCAATGGTTCGATTCGGTCAAA
*
21944330 GTCAACGGTTC
1 GTCAATGGTTC
21944341 AGGTTGGGTT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 8 0.27
21 2 0.07
22 1 0.03
23 19 0.63
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.28
Consensus pattern (23 bp):
GTCAATGGTTCGATTCGGTCAAA
Found at i:21946060 original size:41 final size:41
Alignment explanation
Indices: 21945829--21946064 Score: 309
Period size: 41 Copynumber: 5.8 Consensus size: 41
21945819 CTTTATAAAC
* *
21945829 AATCTTATGCTC-TACCAAGTCAT--GTCTTCCTTTAAACAT
1 AATCTCATGCTCATTCCAAGTCATGAGTCTTCC-TTAAACAT
* * *
21945868 AATCTCATGCTCATTTCGAGTCACGAGTCTTCCTTAAACAT
1 AATCTCATGCTCATTCCAAGTCATGAGTCTTCCTTAAACAT
* * *
21945909 AATCTCATGCTCATTCCAAATCATGAGCCTTCCTTAAGCAT
1 AATCTCATGCTCATTCCAAGTCATGAGTCTTCCTTAAACAT
21945950 AATCTCATGCTCATTCCGAA-TCATGAGTCTTCCTTAAACAT
1 AATCTCATGCTCATTCC-AAGTCATGAGTCTTCCTTAAACAT
* * *
21945991 AATCTCATGCTCATTTCGAGTCACGAGTCTTCCTTAAACAT
1 AATCTCATGCTCATTCCAAGTCATGAGTCTTCCTTAAACAT
* *
21946032 AATCTCATGCTCATCCCAAGACATGAGTCTTCC
1 AATCTCATGCTCATTCCAAGTCATGAGTCTTCC
21946065 ATTTACACAT
Statistics
Matches: 171, Mismatches: 21, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
39 11 0.06
40 8 0.05
41 143 0.84
42 9 0.05
ACGTcount: A:0.28, C:0.28, G:0.11, T:0.33
Consensus pattern (41 bp):
AATCTCATGCTCATTCCAAGTCATGAGTCTTCCTTAAACAT
Found at i:21975413 original size:21 final size:20
Alignment explanation
Indices: 21975387--21975451 Score: 67
Period size: 21 Copynumber: 3.1 Consensus size: 20
21975377 GTATCGGTAA
21975387 AAGTAAAACTTGTTTCAGTAG
1 AAGTAAAACTTGTTTC-GTAG
*
21975408 AAGTAAGACTTGTTTCGATAG
1 AAGTAAAACTTGTTTCG-TAG
* * *
21975429 AAGTTACACTTGTATCGGTAG
1 AAGTAAAACTTGTTTC-GTAG
21975450 AA
1 AA
21975452 CTTTCCCAAG
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
20 1 0.03
21 36 0.95
22 1 0.03
ACGTcount: A:0.35, C:0.11, G:0.22, T:0.32
Consensus pattern (20 bp):
AAGTAAAACTTGTTTCGTAG
Found at i:21990353 original size:3 final size:3
Alignment explanation
Indices: 21990345--21990379 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
21990335 TAAACGTTCA
21990345 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
21990380 ATATTTACAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:21991365 original size:20 final size:19
Alignment explanation
Indices: 21991342--21991381 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
21991332 AATAAATCAC
21991342 AATTCAAAAAAATTATAAAA
1 AATTC-AAAAAATTATAAAA
* *
21991362 AATTCATAAAATTTTAAAA
1 AATTCAAAAAATTATAAAA
21991381 A
1 A
21991382 TATTAACACG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (19 bp):
AATTCAAAAAATTATAAAA
Found at i:21999910 original size:20 final size:20
Alignment explanation
Indices: 21999885--21999938 Score: 81
Period size: 22 Copynumber: 2.6 Consensus size: 20
21999875 AAATAATACA
*
21999885 TAGCACGTTTCTCTGCTTTG
1 TAGCACGTTTCTCTACTTTG
21999905 TAGCACGGTTCTCTCTACTTTG
1 TAGCAC-GTT-TCTCTACTTTG
21999927 TAGCACGTTTCT
1 TAGCACGTTTCT
21999939 TGGCTAGGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 9 0.29
21 6 0.19
22 16 0.52
ACGTcount: A:0.13, C:0.26, G:0.19, T:0.43
Consensus pattern (20 bp):
TAGCACGTTTCTCTACTTTG
Found at i:22004955 original size:52 final size:52
Alignment explanation
Indices: 22004877--22005062 Score: 232
Period size: 52 Copynumber: 3.6 Consensus size: 52
22004867 TGAAAAAGGA
* *
22004877 TCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTACGAGG
1 TCCGATGACTAAGTGTCATCGTGAGTATATGAATCCCTTACGGATTACGAGG
* *
22004929 TCCGATGACTCAA-TGTCATCGAGAGTATATGAAATCCCTTATGGATTTAC-AGG
1 TCCGATGACT-AAGTGTCATCGTGAGTATATG-AATCCCTTACGGA-TTACGAGG
* * * * *
22004982 TCTGATGACTAAGTGTTATCGTGAGTATATGCATCCCTTACGGATTAAGATG
1 TCCGATGACTAAGTGTCATCGTGAGTATATGAATCCCTTACGGATTACGAGG
**
22005034 TCCGATGACTCTGTGTCATCGTGAGTATA
1 TCCGATGACTAAGTGTCATCGTGAGTATA
22005063 CAAATCTCTC
Statistics
Matches: 114, Mismatches: 15, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
51 3 0.03
52 66 0.58
53 41 0.36
54 4 0.04
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.32
Consensus pattern (52 bp):
TCCGATGACTAAGTGTCATCGTGAGTATATGAATCCCTTACGGATTACGAGG
Found at i:22011974 original size:52 final size:50
Alignment explanation
Indices: 22011770--22012014 Score: 229
Period size: 52 Copynumber: 4.7 Consensus size: 50
22011760 AATGAAAAAG
* * * * *
22011770 GGTCCGATGACTAAGTGTCATCATGAGTAAATGAATCCTTTACGGATTACGA
1 GGTCCGATGACTATGTGTCATCGTGAGTATATGAATCC-TTATGGATTA-AA
* * *
22011822 GGTTCGATGATTCTGTGTCATCGTGAGTATATGAAATCCTTTATGGATTTAAA
1 GGTCCGATGACTATGTGTCATCGTGAGTATATG-AATCC-TTATGGA-TTAAA
* * * * *
22011875 GGTCTGATGACTAAGTGTTATCGTGAGTATATGCATCCCTTACGGATTAAGA
1 GGTCCGATGACTATGTGTCATCGTGAGTATATGAAT-CCTTATGGATTAA-A
* * **
22011927 GGTCCGATGACTCTGTGTCATCGTGAGTATACGAATCTCTCGTGGATTATAA
1 GGTCCGATGACTATGTGTCATCGTGAGTATATGAATC-CTTATGGATTA-AA
* * *
22011979 GGTCCGGTGGCTATGTGTCATCATGAGTATATGAAT
1 GGTCCGATGACTATGTGTCATCGTGAGTATATGAAT
22012015 GAAGTGAAAT
Statistics
Matches: 157, Mismatches: 30, Indels: 12
0.79 0.15 0.06
Matches are distributed among these distances:
51 5 0.03
52 106 0.68
53 43 0.27
54 3 0.02
ACGTcount: A:0.26, C:0.16, G:0.25, T:0.33
Consensus pattern (50 bp):
GGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTATGGATTAAA
Found at i:22017852 original size:31 final size:31
Alignment explanation
Indices: 22017817--22017878 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
22017807 TTTTATTTTG
22017817 GTCATTGAACTATTCGAAAGTTTTCATTTAA
1 GTCATTGAACTATTCGAAAGTTTTCATTTAA
* *
22017848 GTCATTGAACTATTTGAAAGTTTTTATTTAA
1 GTCATTGAACTATTCGAAAGTTTTCATTTAA
22017879 ACCATTGGAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.32, C:0.10, G:0.13, T:0.45
Consensus pattern (31 bp):
GTCATTGAACTATTCGAAAGTTTTCATTTAA
Found at i:22017885 original size:31 final size:31
Alignment explanation
Indices: 22017819--22017885 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 31
22017809 TTATTTTGGT
**
22017819 CATTGAACTATTCGAAAGTTTTCATTTAAGT
1 CATTGAACTATTCGAAAGTTTTCATTTAAAC
* *
22017850 CATTGAACTATTTGAAAGTTTTTATTTAAAC
1 CATTGAACTATTCGAAAGTTTTCATTTAAAC
22017881 CATTG
1 CATTG
22017886 GACTGTTAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.43
Consensus pattern (31 bp):
CATTGAACTATTCGAAAGTTTTCATTTAAAC
Found at i:22020553 original size:16 final size:16
Alignment explanation
Indices: 22020532--22020598 Score: 89
Period size: 16 Copynumber: 4.2 Consensus size: 16
22020522 TGAAATACTG
*
22020532 ATTACAACCCTATTCC
1 ATTACAACTCTATTCC
* *
22020548 ATTACAGCTCTATTAC
1 ATTACAACTCTATTCC
22020564 ATTACAACTCTATTCC
1 ATTACAACTCTATTCC
* *
22020580 ATTATAGCTCTATTCC
1 ATTACAACTCTATTCC
22020596 ATT
1 ATT
22020599 CCATTCAACC
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 44 1.00
ACGTcount: A:0.30, C:0.28, G:0.03, T:0.39
Consensus pattern (16 bp):
ATTACAACTCTATTCC
Done.