Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-JGI_221_v2.0
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: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 125 of 226
Found at i:42099580 original size:4 final size:4
Alignment explanation
Indices: 42099571--42099596 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
42099561 TATTTTATAT
42099571 TAAA TAAA TAAA TAAA TAAA TAAA TA
1 TAAA TAAA TAAA TAAA TAAA TAAA TA
42099597 TTAGTTTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (4 bp):
TAAA
Found at i:42103811 original size:44 final size:44
Alignment explanation
Indices: 42103763--42103865 Score: 118
Period size: 44 Copynumber: 2.3 Consensus size: 44
42103753 CACTGTAATA
* * **
42103763 TCAGGGAGATAGGATTTGCTTCT-TCAATCTGCCCCACTGTGACT
1 TCAGGGAGATAAGACTTG-TTCTCTCAATCTGCCCCACTGCAACT
* * * *
42103807 TCAGGGGGATAAGACTTGTTTTCTCAGTCTGCTCCACTGCAACT
1 TCAGGGAGATAAGACTTGTTCTCTCAATCTGCCCCACTGCAACT
42103851 TCAGGGAGATAAGAC
1 TCAGGGAGATAAGAC
42103866 CCGATGCGAT
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
43 3 0.06
44 46 0.94
ACGTcount: A:0.23, C:0.23, G:0.24, T:0.29
Consensus pattern (44 bp):
TCAGGGAGATAAGACTTGTTCTCTCAATCTGCCCCACTGCAACT
Found at i:42104259 original size:87 final size:87
Alignment explanation
Indices: 42104111--42104442 Score: 547
Period size: 87 Copynumber: 3.8 Consensus size: 87
42104101 GCTAGTGCTT
* * * *
42104111 AGGAAGGCAAGATCTGTTATCTTTAACTAGCTCCACTACAATCGATGGTGGCAAGGCTTCGTTTT
1 AGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTACAACCGATGGAGGCAAGGCTTCGTTTT
* *
42104176 CGATCTGCTTCGTTGTTAATGC
66 CGATCTGCTTCGCTGTTAACGC
*
42104198 AAGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTACAACCGATGGAGGCAAGGCTTCGTTTT
1 AGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTACAACCGATGGAGGCAAGGCTTCGTTTT
42104263 CGATCTGCTTCGCTGTTAACGC
66 CGATCTGCTTCGCTGTTAACGC
* * *
42104285 AGGAAGGCAAGATCTGCTATCTTTAACTAACTCCACTACAACTGATGGAGGCAAGGCTTCGTTTT
1 AGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTACAACCGATGGAGGCAAGGCTTCGTTTT
*
42104350 CGATCTGCTTCACTGTTAACGC
66 CGATCTGCTTCGCTGTTAACGC
* *
42104372 AGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTACAACTGATGGAGGCAAGGCTTTGTTTT
1 AGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTACAACCGATGGAGGCAAGGCTTCGTTTT
42104437 CGATCT
66 CGATCT
42104443 TCACTGATCT
Statistics
Matches: 230, Mismatches: 15, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
87 230 1.00
ACGTcount: A:0.25, C:0.23, G:0.22, T:0.29
Consensus pattern (87 bp):
AGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTACAACCGATGGAGGCAAGGCTTCGTTTT
CGATCTGCTTCGCTGTTAACGC
Found at i:42104382 original size:43 final size:43
Alignment explanation
Indices: 42104246--42104382 Score: 104
Period size: 43 Copynumber: 3.2 Consensus size: 43
42104236 CAACCGATGG
*
42104246 AGGCAAGGCTTCGTTTTCGATCTGCTTCGCTGTTAACGCAGGA
1 AGGCAAGGCTTCGTTTTCGATCTGCTTCACTGTTAACGCAGGA
* * * * * * **
42104289 AGGCAAGATCTGC-TATCTT-TAACTAACTCCACT-ACAACTG-ATGG-
1 AGGCAAG-GCTTCGT-T-TTCGATCT-GCTTCACTGTTAAC-GCA-GGA
42104333 AGGCAAGGCTTCGTTTTCGATCTGCTTCACTGTTAACGCAGGA
1 AGGCAAGGCTTCGTTTTCGATCTGCTTCACTGTTAACGCAGGA
42104376 AGGCAAG
1 AGGCAAG
42104383 ATCTGCTATC
Statistics
Matches: 66, Mismatches: 17, Indels: 22
0.63 0.16 0.21
Matches are distributed among these distances:
42 11 0.17
43 26 0.39
44 19 0.29
45 10 0.15
ACGTcount: A:0.25, C:0.23, G:0.24, T:0.28
Consensus pattern (43 bp):
AGGCAAGGCTTCGTTTTCGATCTGCTTCACTGTTAACGCAGGA
Found at i:42108710 original size:34 final size:34
Alignment explanation
Indices: 42108660--42108727 Score: 100
Period size: 34 Copynumber: 2.0 Consensus size: 34
42108650 AATAATTTCG
42108660 TTACGGACTCTGTAATGTGAGAGAACAAGATGGT
1 TTACGGACTCTGTAATGTGAGAGAACAAGATGGT
* * * *
42108694 TTACTGACTCTTTAATGTGAGAGAATAAGCTGGT
1 TTACGGACTCTGTAATGTGAGAGAACAAGATGGT
42108728 CTTCAAATGA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.31, C:0.12, G:0.26, T:0.31
Consensus pattern (34 bp):
TTACGGACTCTGTAATGTGAGAGAACAAGATGGT
Found at i:42110918 original size:44 final size:44
Alignment explanation
Indices: 42110855--42110948 Score: 152
Period size: 44 Copynumber: 2.1 Consensus size: 44
42110845 TAATGTGCGC
* * *
42110855 AATGTGTGCGGTTAAAACCTTGAACTTCAATTTTGGTCCGTTAT
1 AATGTGCGCAGTTAAAACCTTCAACTTCAATTTTGGTCCGTTAT
*
42110899 AATGTGCGCAGTTAAAACCTTCAACTTCAATTTTGGTCTGTTAT
1 AATGTGCGCAGTTAAAACCTTCAACTTCAATTTTGGTCCGTTAT
42110943 AATGTG
1 AATGTG
42110949 GATACATATA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.27, C:0.16, G:0.19, T:0.38
Consensus pattern (44 bp):
AATGTGCGCAGTTAAAACCTTCAACTTCAATTTTGGTCCGTTAT
Found at i:42121662 original size:24 final size:23
Alignment explanation
Indices: 42121629--42121685 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
42121619 TGACACTAAG
* * *
42121629 TGGTGCGTAGGGTTGGATGAAAGA
1 TGGTGTGTAGGGATGG-TCAAAGA
*
42121653 TGGTGTGTAGGGATGGTCAGAGA
1 TGGTGTGTAGGGATGGTCAAAGA
42121676 TGGTGTGTAG
1 TGGTGTGTAG
42121686 TAGATAGGGG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
23 15 0.52
24 14 0.48
ACGTcount: A:0.21, C:0.04, G:0.47, T:0.28
Consensus pattern (23 bp):
TGGTGTGTAGGGATGGTCAAAGA
Found at i:42123693 original size:26 final size:26
Alignment explanation
Indices: 42123662--42123729 Score: 118
Period size: 26 Copynumber: 2.6 Consensus size: 26
42123652 CAATATTGCT
42123662 GCAAAGCTGCCAGTAATAATGACGCA
1 GCAAAGCTGCCAGTAATAATGACGCA
* *
42123688 GTAAAGCTGCCAGTAATAATGATGCA
1 GCAAAGCTGCCAGTAATAATGACGCA
42123714 GCAAAGCTGCCAGTAA
1 GCAAAGCTGCCAGTAA
42123730 CAGTAACACA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.38, C:0.21, G:0.24, T:0.18
Consensus pattern (26 bp):
GCAAAGCTGCCAGTAATAATGACGCA
Found at i:42123970 original size:27 final size:28
Alignment explanation
Indices: 42123936--42124078 Score: 179
Period size: 27 Copynumber: 5.3 Consensus size: 28
42123926 AGGGTATAAT
*
42123936 AGTCATTTTACCCTA-CGGGGGTATTTC
1 AGTCATTTTACCCTATCGAGGGTATTTC
* * * *
42123963 GGTTATTTTA-CCTTTCTAGGGTATTTC
1 AGTCATTTTACCCTATCGAGGGTATTTC
*
42123990 GGTCATTTTACCC-ATCGAGGGTATTTC
1 AGTCATTTTACCCTATCGAGGGTATTTC
*
42124017 AATCATTTTACCC-ATCGAGGGTATTTC
1 AGTCATTTTACCCTATCGAGGGTATTTC
*
42124044 AGTCATTTTA-TCTATCGAGGGTATTTC
1 AGTCATTTTACCCTATCGAGGGTATTTC
42124071 AGTCATTT
1 AGTCATTT
42124079 GCCCACGAAT
Statistics
Matches: 101, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
26 4 0.04
27 95 0.94
28 2 0.02
ACGTcount: A:0.20, C:0.19, G:0.19, T:0.42
Consensus pattern (28 bp):
AGTCATTTTACCCTATCGAGGGTATTTC
Found at i:42132165 original size:28 final size:28
Alignment explanation
Indices: 42132115--42132252 Score: 136
Period size: 28 Copynumber: 5.0 Consensus size: 28
42132105 CATGCAGTGG
* * * * *
42132115 CAGTCTGGGCCTGAGCACTATACAGCAA
1 CAGTGTGGGCCTTAGCCCAATACAGTAA
*
42132143 CAGTGTGGGCCTTAGCCCAATACAATAA
1 CAGTGTGGGCCTTAGCCCAATACAGTAA
* * *
42132171 TA--GTGGGCTTTAGCCCAATATAGTAA
1 CAGTGTGGGCCTTAGCCCAATACAGTAA
* *
42132197 CAGTGTGGGCCTTAGCCCCATATAGTAA
1 CAGTGTGGGCCTTAGCCCAATACAGTAA
* * *
42132225 TAGTATGGGCCATAGCCCAATACAGTAA
1 CAGTGTGGGCCTTAGCCCAATACAGTAA
42132253 GAGTACAATG
Statistics
Matches: 90, Mismatches: 18, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
26 22 0.24
28 68 0.76
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.23
Consensus pattern (28 bp):
CAGTGTGGGCCTTAGCCCAATACAGTAA
Found at i:42132205 original size:54 final size:55
Alignment explanation
Indices: 42132134--42132252 Score: 159
Period size: 54 Copynumber: 2.2 Consensus size: 55
42132124 CCTGAGCACT
* **
42132134 ATACAGCAACAGTGTGGGCCTTAGCCCAATACAATAATAG-TGGGCTTTAGCCCA
1 ATACAGTAACAGTGTGGGCCTTAGCCCAATACAATAATAGATGGGCCATAGCCCA
* * * *
42132188 ATATAGTAACAGTGTGGGCCTTAGCCCCATATAGTAATAGTATGGGCCATAGCCCA
1 ATACAGTAACAGTGTGGGCCTTAGCCCAATACAATAATAG-ATGGGCCATAGCCCA
42132244 ATACAGTAA
1 ATACAGTAA
42132253 GAGTACAATG
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
54 35 0.64
56 20 0.36
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.24
Consensus pattern (55 bp):
ATACAGTAACAGTGTGGGCCTTAGCCCAATACAATAATAGATGGGCCATAGCCCA
Found at i:42132432 original size:26 final size:26
Alignment explanation
Indices: 42132372--42132464 Score: 107
Period size: 26 Copynumber: 3.6 Consensus size: 26
42132362 CGCAACAAAT
* * * *
42132372 CTGCGAGTAATAGTGATGCAGCAAAG
1 CTGCTAGTAACAGTAATGCAGTAAAG
*
42132398 C-GGTCAGTAACAGTAATGCAGTAAAG
1 CTGCT-AGTAACAGTAATGCAGTAAAG
* *
42132424 CTGCTAGTAACAGTATTTCAGTAAAG
1 CTGCTAGTAACAGTAATGCAGTAAAG
42132450 CTGCTAGTAACAGTA
1 CTGCTAGTAACAGTA
42132465 TATGTGGCAA
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
25 1 0.02
26 54 0.95
27 2 0.04
ACGTcount: A:0.35, C:0.16, G:0.25, T:0.24
Consensus pattern (26 bp):
CTGCTAGTAACAGTAATGCAGTAAAG
Found at i:42132465 original size:26 final size:26
Alignment explanation
Indices: 42132403--42132465 Score: 108
Period size: 26 Copynumber: 2.4 Consensus size: 26
42132393 CAAAGCGGTC
*
42132403 AGTAACAGTAATGCAGTAAAGCTGCT
1 AGTAACAGTATTGCAGTAAAGCTGCT
*
42132429 AGTAACAGTATTTCAGTAAAGCTGCT
1 AGTAACAGTATTGCAGTAAAGCTGCT
42132455 AGTAACAGTAT
1 AGTAACAGTAT
42132466 ATGTGGCAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.38, C:0.14, G:0.21, T:0.27
Consensus pattern (26 bp):
AGTAACAGTATTGCAGTAAAGCTGCT
Found at i:42132674 original size:27 final size:27
Alignment explanation
Indices: 42132658--42132809 Score: 223
Period size: 27 Copynumber: 5.6 Consensus size: 27
42132648 TACCTTATGG
* **
42132658 GGGTATTTCGGTAATTTTACCTTTCGA
1 GGGTATTTCGGTCATTTTACCCATCGA
* *
42132685 GGGTATTTCGGTCAATTTACCCATTGA
1 GGGTATTTCGGTCATTTTACCCATCGA
**
42132712 GGGTATTTCAATCATTTTACCCATCGA
1 GGGTATTTCGGTCATTTTACCCATCGA
42132739 GGGTATTTCGGTCATTTTACCCATCGA
1 GGGTATTTCGGTCATTTTACCCATCGA
*
42132766 GGGTATTTCGGTCATTTTACGCATCGA
1 GGGTATTTCGGTCATTTTACCCATCGA
*
42132793 GGGTATTTCAGTCATTT
1 GGGTATTTCGGTCATTT
42132810 GCCCACGAAT
Statistics
Matches: 112, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 112 1.00
ACGTcount: A:0.20, C:0.18, G:0.22, T:0.39
Consensus pattern (27 bp):
GGGTATTTCGGTCATTTTACCCATCGA
Found at i:42135353 original size:9 final size:9
Alignment explanation
Indices: 42135324--42135360 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
42135314 TGAGTTTTCG
42135324 AATTCGAAT
1 AATTCGAAT
*
42135333 AACTCGAAT
1 AATTCGAAT
42135342 AATTCGAAT
1 AATTCGAAT
*
42135351 AATTTGAAT
1 AATTCGAAT
42135360 A
1 A
42135361 TTAAACTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (9 bp):
AATTCGAAT
Found at i:42135657 original size:28 final size:29
Alignment explanation
Indices: 42135599--42135657 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 29
42135589 TTTTTATTTT
* *
42135599 CCCCTAAAATTTTTACTCCCTCTCACTTC
1 CCCCTAAAACTTTTACTCCCTCTCACATC
*
42135628 CCCCTAAAACTTTTACTCCC-CTCCCATC
1 CCCCTAAAACTTTTACTCCCTCTCACATC
42135656 CC
1 CC
42135658 ACTCCCCATC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 8 0.30
29 19 0.70
ACGTcount: A:0.20, C:0.47, G:0.00, T:0.32
Consensus pattern (29 bp):
CCCCTAAAACTTTTACTCCCTCTCACATC
Found at i:42152373 original size:26 final size:26
Alignment explanation
Indices: 42152253--42152375 Score: 84
Period size: 26 Copynumber: 5.0 Consensus size: 26
42152243 TTAAAAGTTA
* *
42152253 TTTGTGAACTTCCTGAT-TATGGCTC
1 TTTGTGAGCTTCCTGTTATATGGCTC
* *
42152278 -TTATGAGCTTCCTGTTATATAGC-C
1 TTTGTGAGCTTCCTGTTATATGGCTC
** *
42152302 -CAGATAAGCTTCCTG--ATA-GGCTC
1 TTTG-TGAGCTTCCTGTTATATGGCTC
*
42152325 TTTTTGAGCTT-CTAGATTA-ATGGCTC
1 TTTGTGAGCTTCCT-G-TTATATGGCTC
42152351 TTTGTGAGCTTCCTGTTATATGGCT
1 TTTGTGAGCTTCCTGTTATATGGCT
42152376 TGAGAGAGGT
Statistics
Matches: 73, Mismatches: 14, Indels: 21
0.68 0.13 0.19
Matches are distributed among these distances:
22 4 0.05
23 11 0.15
24 14 0.19
25 19 0.26
26 23 0.32
27 2 0.03
ACGTcount: A:0.19, C:0.20, G:0.20, T:0.41
Consensus pattern (26 bp):
TTTGTGAGCTTCCTGTTATATGGCTC
Found at i:42159036 original size:26 final size:26
Alignment explanation
Indices: 42159007--42159163 Score: 100
Period size: 26 Copynumber: 6.3 Consensus size: 26
42158997 ATCCGAAGCA
*
42159007 CCTGATTAAAGGCTCTTCGTGAGCTT
1 CCTGATTAAAGGCTCTTTGTGAGCTT
* * * **
42159033 CCTGATTAAAAGTTATTTGTGAAATT
1 CCTGATTAAAGGCTCTTTGTGAGCTT
* *
42159059 CCTGATT-ATGGCTC-TTATGAGCTT
1 CCTGATTAAAGGCTCTTTGTGAGCTT
** *
42159083 CCTG-TTATATA-GC-C-CGGATAAGCTT
1 CCTGATTA-A-AGGCTCTTTG-TGAGCTT
42159108 CCTGA-T--AGGCTCTTTGTGAGCTT
1 CCTGATTAAAGGCTCTTTGTGAGCTT
* *
42159131 CCCGATTAATGGCTCTTTGTGAGCTT
1 CCTGATTAAAGGCTCTTTGTGAGCTT
42159157 CCT-ATTA
1 CCTGATTA
42159164 TATGGCTTGA
Statistics
Matches: 96, Mismatches: 24, Indels: 23
0.67 0.17 0.16
Matches are distributed among these distances:
21 1 0.01
22 2 0.02
23 13 0.14
24 14 0.15
25 21 0.22
26 45 0.47
ACGTcount: A:0.21, C:0.20, G:0.20, T:0.38
Consensus pattern (26 bp):
CCTGATTAAAGGCTCTTTGTGAGCTT
Found at i:42160969 original size:28 final size:28
Alignment explanation
Indices: 42160937--42160990 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
42160927 CTCTATTGTC
*
42160937 CATTCTATATTTCTTTTAGTTTTATATT
1 CATTCTATATTTCTTTTAATTTTATATT
42160965 CATTCTATATTTCTTTTAATTTTATA
1 CATTCTATATTTCTTTTAATTTTATA
42160991 ACATATATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.24, C:0.11, G:0.02, T:0.63
Consensus pattern (28 bp):
CATTCTATATTTCTTTTAATTTTATATT
Found at i:42169141 original size:27 final size:26
Alignment explanation
Indices: 42169102--42169253 Score: 133
Period size: 27 Copynumber: 5.7 Consensus size: 26
42169092 AATGTTTGTT
* * *
42169102 AAATGACTGAATTACCCCCGAGAGGTA
1 AAATGACCGAATTA-CCCCTAAAGGTA
* * * *
42169129 AAGTGACCAAATTACTCCTATAGGATA
1 AAATGACCGAATTACCCCTAAAGG-TA
42169156 AAATGACCGAATTACCCCTAAAGGGTA
1 AAATGACCGAATTACCCCTAAA-GGTA
*
42169183 AAATGACCGAATTACCCCCAAAGGGTA
1 AAATGACCGAATTACCCCTAAA-GGTA
* * **
42169210 AAATGATCGAATTACCCTTGATGGGTA
1 AAATGACCGAATTACCCCT-AAAGGTA
* *
42169237 AAATGATCGAAATACCC
1 AAATGACCGAATTACCC
42169254 TCGATGGGTA
Statistics
Matches: 105, Mismatches: 17, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
26 7 0.07
27 95 0.90
28 3 0.03
ACGTcount: A:0.39, C:0.21, G:0.18, T:0.21
Consensus pattern (26 bp):
AAATGACCGAATTACCCCTAAAGGTA
Found at i:42169236 original size:54 final size:53
Alignment explanation
Indices: 42169102--42169469 Score: 271
Period size: 54 Copynumber: 6.8 Consensus size: 53
42169092 AATGTTTGTT
* * * * *
42169102 AAATGACTGAATTACCCCCGA-GAGGTAAAGTGACC-AAATTACTCCT-ATAGGATA
1 AAATGAC-GAAATACCCCTGATG-GGTAAAATGACCGAAA-TAC-CCTCAAAGGGTA
* * * * *
42169156 AAATGACCGAATTACCCCTAAAGGGTAAAATGACCGAATTACCCCCAAAGGGTA
1 AAATGA-CGAAATACCCCTGATGGGTAAAATGACCGAAATACCCTCAAAGGGTA
* * * * *
42169210 AAATGATCGAATTACCCTTGATGGGTAAAATGATCGAAATACCCTCGATGGGTA
1 AAATGA-CGAAATACCCCTGATGGGTAAAATGACCGAAATACCCTCAAAGGGTA
* * ** * * * * *
42169264 AAATTACTAAAATACCCCCAATCGATAAAATGATCGAAATACCCTCGATGGGTA
1 AAATGAC-GAAATACCCCTGATGGGTAAAATGACCGAAATACCCTCAAAGGGTA
* * * * *
42169318 AAATGACTGAAATACCCTTGATGGGTAAAATTACTGAAATACCCTCGATGGGTA
1 AAATGAC-GAAATACCCCTGATGGGTAAAATGACCGAAATACCCTCAAAGGGTA
* *
42169372 AAATGATCGAAATA-CCCTCGAGGGGTAAAATTACCGAAATACCCTCAATA-GGTA
1 AAATGA-CGAAATACCCCT-GATGGGTAAAATGACCGAAATACCCTCAA-AGGGTA
* * *
42169426 AAATGACCGTAATGCCCCTG-TAGGGTAAAATGACCGTAATACCC
1 AAATGA-CGAAATACCCCTGAT-GGGTAAAATGACCGAAATACCC
42169470 CTATAGGGTT
Statistics
Matches: 259, Mismatches: 45, Indels: 20
0.80 0.14 0.06
Matches are distributed among these distances:
53 6 0.02
54 244 0.94
55 9 0.03
ACGTcount: A:0.39, C:0.21, G:0.19, T:0.22
Consensus pattern (53 bp):
AAATGACGAAATACCCCTGATGGGTAAAATGACCGAAATACCCTCAAAGGGTA
Found at i:42169254 original size:27 final size:27
Alignment explanation
Indices: 42169154--42169493 Score: 310
Period size: 27 Copynumber: 12.6 Consensus size: 27
42169144 TCCTATAGGA
* * *
42169154 TAAAATGACCGAATTACCC-CTAAAGGG
1 TAAAATGACCGAAATACCCTC-GATGGG
* * * *
42169181 TAAAATGACCGAATTACCCCCAAAGGG
1 TAAAATGACCGAAATACCCTCGATGGG
* * *
42169208 TAAAATGATCGAATTACCCTTGATGGG
1 TAAAATGACCGAAATACCCTCGATGGG
*
42169235 TAAAATGATCGAAATACCCTCGATGGG
1 TAAAATGACCGAAATACCCTCGATGGG
* ** * * * *
42169262 TAAAATTACTAAAATACCCCCAATCGA
1 TAAAATGACCGAAATACCCTCGATGGG
*
42169289 TAAAATGATCGAAATACCCTCGATGGG
1 TAAAATGACCGAAATACCCTCGATGGG
* *
42169316 TAAAATGACTGAAATACCCTTGATGGG
1 TAAAATGACCGAAATACCCTCGATGGG
* *
42169343 TAAAATTACTGAAATACCCTCGATGGG
1 TAAAATGACCGAAATACCCTCGATGGG
* *
42169370 TAAAATGATCGAAATACCCTCGAGGGG
1 TAAAATGACCGAAATACCCTCGATGGG
* * *
42169397 TAAAATTACCGAAATACCCTCAATAGG
1 TAAAATGACCGAAATACCCTCGATGGG
* *
42169424 TAAAATGACCGTAATGCCC-CTG-TAGGG
1 TAAAATGACCGAAATACCCTC-GAT-GGG
* *
42169451 TAAAATGACCGTAATACCC-CTATAGGG
1 TAAAATGACCGAAATACCCTCGAT-GGG
* *
42169478 TTAAATAACCGAAATA
1 TAAAATGACCGAAATA
42169494 TCCTTGTAAG
Statistics
Matches: 262, Mismatches: 47, Indels: 8
0.83 0.15 0.03
Matches are distributed among these distances:
26 2 0.01
27 259 0.99
28 1 0.00
ACGTcount: A:0.39, C:0.20, G:0.19, T:0.22
Consensus pattern (27 bp):
TAAAATGACCGAAATACCCTCGATGGG
Found at i:42169507 original size:54 final size:54
Alignment explanation
Indices: 42169124--42169513 Score: 201
Period size: 54 Copynumber: 7.2 Consensus size: 54
42169114 TACCCCCGAG
* * * *
42169124 AGGTAAAGTGACC-AAATTACTCCT--ATAGGATAAAATGACCGAATTACCCCT-AA
1 AGGTAAAATGACCGAAA-TAC-CCTCAATAGG-TAAAATAACCGAAATACCCCTGTA
* * * * * *
42169177 AGGGTAAAATGACCGAATTACCCCCAA-AGGGTAAAATGATCGAATTACCCTTG-A
1 A-GGTAAAATGACCGAAATACCCTCAATA-GGTAAAATAACCGAAATACCCCTGTA
* * * * * ** *
42169231 TGGGTAAAATGATCGAAATACCCTCGATGGGTAAAATTACTAAAATACCCC--CA
1 -AGGTAAAATGACCGAAATACCCTCAATAGGTAAAATAACCGAAATACCCCTGTA
* * * * * * *
42169284 ATCGATAAAATGATCGAAATACCCTCGATGGGTAAAATGACTGAAATACCCTTG-A
1 A--GGTAAAATGACCGAAATACCCTCAATAGGTAAAATAACCGAAATACCCCTGTA
* * * * * * *
42169339 TGGGTAAAATTACTGAAATACCCTCGATGGGTAAAATGATCGAAATA-CCCTCG-A
1 -AGGTAAAATGACCGAAATACCCTCAATAGGTAAAATAACCGAAATACCCCT-GTA
* * * * *
42169393 GGGGTAAAATTACCGAAATACCCTCAATAGGTAAAATGACCGTAATGCCCCTGTA
1 -AGGTAAAATGACCGAAATACCCTCAATAGGTAAAATAACCGAAATACCCCTGTA
* * * * * *
42169448 GGGTAAAATGACCGTAATACCC-CTATAGGGTTAAATAACCGAAATATCCTTGTA
1 AGGTAAAATGACCGAAATACCCTCAATA-GGTAAAATAACCGAAATACCCCTGTA
42169502 AGGTAAAATGAC
1 AGGTAAAATGAC
42169514 AATAATGCCC
Statistics
Matches: 272, Mismatches: 47, Indels: 35
0.77 0.13 0.10
Matches are distributed among these distances:
53 11 0.04
54 250 0.92
55 11 0.04
ACGTcount: A:0.39, C:0.19, G:0.19, T:0.23
Consensus pattern (54 bp):
AGGTAAAATGACCGAAATACCCTCAATAGGTAAAATAACCGAAATACCCCTGTA
Found at i:42169510 original size:27 final size:27
Alignment explanation
Indices: 42169102--42169513 Score: 131
Period size: 27 Copynumber: 15.3 Consensus size: 27
42169092 AATGTTTGTT
* * *
42169102 AAATGACTGAATTACCCCCG-AGAGGTA
1 AAATGACCGAAATACCCCTGTA-AGGTA
* * *
42169129 AAGTGACC-AAATTACTCCTAT-AGGATA
1 AAATGACCGAAA-TACCCCTGTAAGG-TA
* *
42169156 AAATGACCGAATTACCCCT-AAAGGGTA
1 AAATGACCGAAATACCCCTGTAA-GGTA
* **
42169183 AAATGACCGAATTACCCC-CAAAGGGTA
1 AAATGACCGAAATACCCCTGTAA-GGTA
* * * *
42169210 AAATGATCGAATTACCCTTG-ATGGGTA
1 AAATGACCGAAATACCCCTGTA-AGGTA
* *
42169237 AAATGATCGAAATA-CCCTCG-ATGGGTA
1 AAATGACCGAAATACCCCT-GTA-AGGTA
* ** * *
42169264 AAATTACTAAAATACCCC--CAATCGATA
1 AAATGACCGAAATACCCCTGTAA--GGTA
* *
42169291 AAATGATCGAAATA-CCCTCG-ATGGGTA
1 AAATGACCGAAATACCCCT-GTA-AGGTA
* * *
42169318 AAATGACTGAAATACCCTTG-ATGGGTA
1 AAATGACCGAAATACCCCTGTA-AGGTA
* * *
42169345 AAATTACTGAAATA-CCCTCG-ATGGGTA
1 AAATGACCGAAATACCCCT-GTA-AGGTA
* *
42169372 AAATGATCGAAATA-CCCTCG-AGGGGTA
1 AAATGACCGAAATACCCCT-GTA-AGGTA
* **
42169399 AAATTACCGAAATA-CCCTCAATAGGTA
1 AAATGACCGAAATACCCCTGTA-AGGTA
* * *
42169426 AAATGACCGTAATGCCCCTGTAGGGTA
1 AAATGACCGAAATACCCCTGTAAGGTA
* * * *
42169453 AAATGACCGTAATACCCCTATAGGGTT
1 AAATGACCGAAATACCCCTGTAAGGTA
* * *
42169480 AAATAACCGAAATATCCTTGTAAGGTA
1 AAATGACCGAAATACCCCTGTAAGGTA
42169507 AAATGAC
1 AAATGAC
42169514 AATAATGCCC
Statistics
Matches: 304, Mismatches: 59, Indels: 44
0.75 0.14 0.11
Matches are distributed among these distances:
26 15 0.05
27 273 0.90
28 16 0.05
ACGTcount: A:0.39, C:0.20, G:0.19, T:0.23
Consensus pattern (27 bp):
AAATGACCGAAATACCCCTGTAAGGTA
Found at i:42169611 original size:24 final size:24
Alignment explanation
Indices: 42169584--42169641 Score: 73
Period size: 24 Copynumber: 2.4 Consensus size: 24
42169574 CGTGATGTAA
42169584 ATGACTGATCTT-TCTGTGATTGGT
1 ATGACTGAT-TTGTCTGTGATTGGT
* * *
42169608 ATGATTGATTTGTTTGTGATTTGT
1 ATGACTGATTTGTCTGTGATTGGT
42169632 ATGACTGATT
1 ATGACTGATT
42169642 CTCACCATGG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
23 2 0.07
24 27 0.93
ACGTcount: A:0.19, C:0.07, G:0.24, T:0.50
Consensus pattern (24 bp):
ATGACTGATTTGTCTGTGATTGGT
Found at i:42169742 original size:27 final size:26
Alignment explanation
Indices: 42169705--42169755 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 26
42169695 ATGGAGGAAG
42169705 CACTGTACTGGTGGCTCT-GCCACAAT
1 CACTGTACTGGTGGCT-TGGCCACAAT
42169731 CACTGTTACTGGTGGCTTGGCCACA
1 CACTG-TACTGGTGGCTTGGCCACA
42169756 CGGACAGCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
26 6 0.26
27 17 0.74
ACGTcount: A:0.18, C:0.29, G:0.25, T:0.27
Consensus pattern (26 bp):
CACTGTACTGGTGGCTTGGCCACAAT
Found at i:42169812 original size:26 final size:26
Alignment explanation
Indices: 42169760--42169813 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
42169750 GCCACACGGA
* *
42169760 CAGCTTTGCTGCGATACTATTGCTGG
1 CAGCTTTGCTGCGATACTACTGATGG
*
42169786 CAGCTTTGCTGCGATGCTACTGATGG
1 CAGCTTTGCTGCGATACTACTGATGG
42169812 CA
1 CA
42169814 TTGTACCGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.17, C:0.24, G:0.28, T:0.31
Consensus pattern (26 bp):
CAGCTTTGCTGCGATACTACTGATGG
Found at i:42169844 original size:32 final size:31
Alignment explanation
Indices: 42169803--42169943 Score: 158
Period size: 32 Copynumber: 4.5 Consensus size: 31
42169793 GCTGCGATGC
*
42169803 TACTGATGGCATTGTACCGATCATATTACCGT
1 TACTGATGGC-TTGTGCCGATCATATTACCGT
*
42169835 TACTGATGGCTTTGTGCCGATCATATTACCAT
1 TACTGATGGC-TTGTGCCGATCATATTACCGT
* * * *
42169867 TACTAATGGCTCTGTGCCGATCATATCACTGC
1 TACTGATGGCT-TGTGCCGATCATATTACCGT
* *
42169899 TACTGATGGCTTTGTGCCAATCATATTACTG-
1 TACTGATGGC-TTGTGCCGATCATATTACCGT
*
42169930 TACTTATGGCTTGT
1 TACTGATGGCTTGT
42169944 AGCCATTCTG
Statistics
Matches: 95, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
30 4 0.04
31 10 0.11
32 80 0.84
33 1 0.01
ACGTcount: A:0.22, C:0.22, G:0.19, T:0.37
Consensus pattern (31 bp):
TACTGATGGCTTGTGCCGATCATATTACCGT
Found at i:42171178 original size:23 final size:23
Alignment explanation
Indices: 42171144--42171190 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
42171134 CAACCTTGTA
42171144 CCTAAGGATTTATACAGCTTCTT
1 CCTAAGGATTTATACAGCTTCTT
* *
42171167 CCTAAGGCTTTATACAGTTTCTT
1 CCTAAGGATTTATACAGCTTCTT
42171190 C
1 C
42171191 AAAAATCTCG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.23, C:0.23, G:0.13, T:0.40
Consensus pattern (23 bp):
CCTAAGGATTTATACAGCTTCTT
Found at i:42181791 original size:27 final size:26
Alignment explanation
Indices: 42181753--42181816 Score: 92
Period size: 27 Copynumber: 2.4 Consensus size: 26
42181743 TATTTTAAAG
* *
42181753 TTATTAGTTTATCGATAAATGAATATT
1 TTATTAATTTATCAATAAATGAATA-T
*
42181780 TTATTAATTTATCAATAAATTAATAT
1 TTATTAATTTATCAATAAATGAATAT
42181806 TTATTAATTTA
1 TTATTAATTTA
42181817 GAGAATATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
26 12 0.35
27 22 0.65
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.52
Consensus pattern (26 bp):
TTATTAATTTATCAATAAATGAATAT
Found at i:42189301 original size:15 final size:15
Alignment explanation
Indices: 42189281--42189327 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
42189271 GGTAATGGTG
42189281 GAAAAATCTTAGTTT
1 GAAAAATCTTAGTTT
* *
42189296 GAAAAA-C-T-GGTG
1 GAAAAATCTTAGTTT
42189308 GAAAAATCTTAGTTT
1 GAAAAATCTTAGTTT
42189323 GAAAA
1 GAAAA
42189328 TAGTTTTCTT
Statistics
Matches: 25, Mismatches: 4, Indels: 6
0.71 0.11 0.17
Matches are distributed among these distances:
12 8 0.32
13 2 0.08
14 2 0.08
15 13 0.52
ACGTcount: A:0.45, C:0.06, G:0.19, T:0.30
Consensus pattern (15 bp):
GAAAAATCTTAGTTT
Found at i:42189314 original size:27 final size:27
Alignment explanation
Indices: 42189276--42189327 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
42189266 GCCATGGTAA
42189276 TGGTGGAAAAATCTTAGTTTGAAAAAC
1 TGGTGGAAAAATCTTAGTTTGAAAAAC
42189303 TGGTGGAAAAATCTTAGTTTGAAAA
1 TGGTGGAAAAATCTTAGTTTGAAAA
42189328 TAGTTTTCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.40, C:0.06, G:0.23, T:0.31
Consensus pattern (27 bp):
TGGTGGAAAAATCTTAGTTTGAAAAAC
Found at i:42216918 original size:92 final size:92
Alignment explanation
Indices: 42216761--42216944 Score: 323
Period size: 92 Copynumber: 2.0 Consensus size: 92
42216751 TAATTACACA
** * *
42216761 AACTTACCTTAAACTCATACGGAGAAATACGATTTTTTAGTCCACGACTTTATCCTTTCCCCGAT
1 AACTTACCTTAAACTCATACGGAGAAATACGATCGTTTAGTCCACGACTTCATCATTTCCCCGAT
42216826 TTAATTTCGAATGTTGCTTTTCTTGAT
66 TTAATTTCGAATGTTGCTTTTCTTGAT
*
42216853 AACTTACCTTAAACTCGTACGGAGAAATACGATCGTTTAGTCCACGACTTCATCATTTCCCCGAT
1 AACTTACCTTAAACTCATACGGAGAAATACGATCGTTTAGTCCACGACTTCATCATTTCCCCGAT
42216918 TTAATTTCGAATGTTGCTTTTCTTGAT
66 TTAATTTCGAATGTTGCTTTTCTTGAT
42216945 CTATATAATC
Statistics
Matches: 87, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
92 87 1.00
ACGTcount: A:0.26, C:0.22, G:0.13, T:0.39
Consensus pattern (92 bp):
AACTTACCTTAAACTCATACGGAGAAATACGATCGTTTAGTCCACGACTTCATCATTTCCCCGAT
TTAATTTCGAATGTTGCTTTTCTTGAT
Found at i:42224509 original size:19 final size:19
Alignment explanation
Indices: 42224485--42224524 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
42224475 ATATAATCAG
*
42224485 AAAAAATAA-TAAAATTATT
1 AAAAAA-AACTAAAAATATT
42224504 AAAAAAAACTAAAAATATT
1 AAAAAAAACTAAAAATATT
42224523 AA
1 AA
42224525 CATTAATGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 2 0.11
19 17 0.89
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.25
Consensus pattern (19 bp):
AAAAAAAACTAAAAATATT
Found at i:42225438 original size:31 final size:31
Alignment explanation
Indices: 42225370--42225441 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 31
42225360 TTTTAACTCA
* * *
42225370 ATTGTGAGAATAATTACCTAATTCAGGCCTC
1 ATTGTGAAAACAATTACCTAATTCAAGCCTC
* * **
42225401 AATGTGAAAACAATTACCTAATTTAAGTTTC
1 ATTGTGAAAACAATTACCTAATTCAAGCCTC
42225432 ATTGTGAAAA
1 ATTGTGAAAA
42225442 ACCCTAAATA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.33
Consensus pattern (31 bp):
ATTGTGAAAACAATTACCTAATTCAAGCCTC
Found at i:42229480 original size:20 final size:20
Alignment explanation
Indices: 42229446--42229487 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
42229436 AATTATTTAA
** *
42229446 ATAATATTATTTGAATAGTT
1 ATAATATTAAATGAATAATT
42229466 ATAATATTAAATGAATAATT
1 ATAATATTAAATGAATAATT
42229486 AT
1 AT
42229488 GTGTTTATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (20 bp):
ATAATATTAAATGAATAATT
Found at i:42236823 original size:21 final size:21
Alignment explanation
Indices: 42236799--42236851 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
42236789 CATTGTTTCT
* *
42236799 AATCTCACCGCTACAGTATCC
1 AATCTCACCGCTACAGAAACC
*
42236820 AATCTCACCGCTACAGAAACT
1 AATCTCACCGCTACAGAAACC
42236841 AATCTCACCGC
1 AATCTCACCGC
42236852 CACCGTTGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.32, C:0.38, G:0.09, T:0.21
Consensus pattern (21 bp):
AATCTCACCGCTACAGAAACC
Found at i:42248000 original size:18 final size:18
Alignment explanation
Indices: 42247968--42248015 Score: 51
Period size: 20 Copynumber: 2.6 Consensus size: 18
42247958 TCTTGAGAAC
* *
42247968 TTTTTAGAATTTTTAATATT
1 TTTTTAAAATTTAT-ATA-T
*
42247988 TTTTTAAAATTTATCTAT
1 TTTTTAAAATTTATATAT
42248006 TTTTTAAAAT
1 TTTTTAAAAT
42248016 ATAAAATTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 11 0.44
19 2 0.08
20 12 0.48
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (18 bp):
TTTTTAAAATTTATATAT
Found at i:42248048 original size:10 final size:10
Alignment explanation
Indices: 42248035--42248063 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
42248025 GAAAATTTAT
42248035 AATTATTTTG
1 AATTATTTTG
42248045 AATTATTTTG
1 AATTATTTTG
42248055 AATT-TTTTG
1 AATTATTTTG
42248064 TTAAAAGAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 5 0.26
10 14 0.74
ACGTcount: A:0.28, C:0.00, G:0.10, T:0.62
Consensus pattern (10 bp):
AATTATTTTG
Found at i:42254179 original size:13 final size:13
Alignment explanation
Indices: 42254158--42254192 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
42254148 ATAAGTTGCT
* *
42254158 GTTAGTTAAATTA
1 GTTAATTAAATAA
42254171 GTTAATTAAATAA
1 GTTAATTAAATAA
42254184 GTTAATTAA
1 GTTAATTAA
42254193 TTTGTTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.46, C:0.00, G:0.11, T:0.43
Consensus pattern (13 bp):
GTTAATTAAATAA
Found at i:42255274 original size:14 final size:14
Alignment explanation
Indices: 42255255--42255296 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
42255245 TAGTTTAATG
42255255 ATTTTTATTTTTTT
1 ATTTTTATTTTTTT
*
42255269 ATTTTTATTTATTT
1 ATTTTTATTTTTTT
42255283 ATTTCTTAGTTTTT
1 ATTT-TTA-TTTTT
42255297 AAGTTAGATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 17 0.71
15 3 0.12
16 4 0.17
ACGTcount: A:0.17, C:0.02, G:0.02, T:0.79
Consensus pattern (14 bp):
ATTTTTATTTTTTT
Found at i:42256090 original size:12 final size:13
Alignment explanation
Indices: 42256066--42256103 Score: 55
Period size: 11 Copynumber: 3.2 Consensus size: 13
42256056 AAAAGAGAAG
42256066 AAATTCGAAAAAA
1 AAATTCGAAAAAA
42256079 AAATTC--AAAAA
1 AAATTCGAAAAAA
42256090 AAA-TCGAAAAAA
1 AAATTCGAAAAAA
42256102 AA
1 AA
42256104 GGAAAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
10 2 0.09
11 8 0.35
12 7 0.30
13 6 0.26
ACGTcount: A:0.74, C:0.08, G:0.05, T:0.13
Consensus pattern (13 bp):
AAATTCGAAAAAA
Found at i:42268071 original size:29 final size:29
Alignment explanation
Indices: 42268017--42268102 Score: 136
Period size: 29 Copynumber: 3.0 Consensus size: 29
42268007 CAACTGTGCA
* *
42268017 TTCGAACCAATAGTTTGGATATCACTTGG
1 TTCGAACCAATAGCTTGGATACCACTTGG
* *
42268046 TTCGAACCAATAGCTCGAATACCACTTGG
1 TTCGAACCAATAGCTTGGATACCACTTGG
42268075 TTCGAACCAATAGCTTGGATACCACTTG
1 TTCGAACCAATAGCTTGGATACCACTTG
42268103 TCATGGGGCC
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 51 1.00
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (29 bp):
TTCGAACCAATAGCTTGGATACCACTTGG
Found at i:42270519 original size:14 final size:14
Alignment explanation
Indices: 42270496--42270529 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
42270486 ATATAAAAAG
42270496 AATA-TTTTTTATA
1 AATATTTTTTTATA
42270509 AATATTTTTTTATA
1 AATATTTTTTTATA
42270523 AATATTT
1 AATATTT
42270530 AGTATTATGT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.20
14 16 0.80
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
AATATTTTTTTATA
Found at i:42270606 original size:11 final size:11
Alignment explanation
Indices: 42270592--42270622 Score: 55
Period size: 10 Copynumber: 2.9 Consensus size: 11
42270582 AGTATTTTTA
42270592 TTAAATTAAAT
1 TTAAATTAAAT
42270603 TTAAATT-AAT
1 TTAAATTAAAT
42270613 TTAAATTAAA
1 TTAAATTAAA
42270623 ATTGACTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.53
11 9 0.47
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (11 bp):
TTAAATTAAAT
Found at i:42270610 original size:16 final size:16
Alignment explanation
Indices: 42270591--42270625 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
42270581 AAGTATTTTT
*
42270591 ATTAAATTAAATTTAA
1 ATTAAATTAAATTAAA
*
42270607 ATTAATTTAAATTAAA
1 ATTAAATTAAATTAAA
42270623 ATT
1 ATT
42270626 GACTATTAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
ATTAAATTAAATTAAA
Found at i:42275427 original size:45 final size:45
Alignment explanation
Indices: 42275376--42275499 Score: 132
Period size: 43 Copynumber: 2.8 Consensus size: 45
42275366 AGTTGGTTAG
* *
42275376 TACGGTGTGGATAAACCATTCATTGGTGCATATAAAAGC-T-ACTAA
1 TACGGTGTGGATAAACCACTCATTGGTGCAGATAAAA-CTTGA-TAA
* *
42275421 TAC-G-GTGAATAAACCACTCATTGTTGCAGATAAAACTTGATAA
1 TACGGTGTGGATAAACCACTCATTGGTGCAGATAAAACTTGATAA
* *
42275464 TACGATGTGGATAAACCACTCAATT-GTGTAGATAAA
1 TACGGTGTGGATAAACCACTC-ATTGGTGCAGATAAA
42275500 TTACTCACAC
Statistics
Matches: 66, Mismatches: 8, Indels: 10
0.79 0.10 0.12
Matches are distributed among these distances:
42 1 0.02
43 34 0.52
44 2 0.03
45 26 0.39
46 3 0.05
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.28
Consensus pattern (45 bp):
TACGGTGTGGATAAACCACTCATTGGTGCAGATAAAACTTGATAA
Found at i:42277628 original size:16 final size:17
Alignment explanation
Indices: 42277595--42277634 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
42277585 GCTCTTTTTG
*
42277595 TTTTTTATTGTTAAATA
1 TTTTTTATTATTAAATA
*
42277612 TTTTTTATTATT-TATA
1 TTTTTTATTATTAAATA
42277628 TTTTTTA
1 TTTTTTA
42277635 CTAAGTTGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 10 0.48
17 11 0.52
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72
Consensus pattern (17 bp):
TTTTTTATTATTAAATA
Found at i:42281895 original size:12 final size:13
Alignment explanation
Indices: 42281866--42281895 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
42281856 GAAGAGTGTG
42281866 AAATTAAAACATT
1 AAATTAAAACATT
42281879 AAATTAAAACA-T
1 AAATTAAAACATT
42281891 AAATT
1 AAATT
42281896 TGCATTTACA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.35
13 11 0.65
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (13 bp):
AAATTAAAACATT
Found at i:42291740 original size:16 final size:17
Alignment explanation
Indices: 42291713--42291747 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
42291703 CATAATTGAG
*
42291713 TTGAGTAAATTATTTAA
1 TTGAGTAAATTAATTAA
42291730 TTGAG-AAATTAATTAA
1 TTGAGTAAATTAATTAA
42291746 TT
1 TT
42291748 AATTAATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.43, C:0.00, G:0.11, T:0.46
Consensus pattern (17 bp):
TTGAGTAAATTAATTAA
Found at i:42294094 original size:49 final size:50
Alignment explanation
Indices: 42294033--42294177 Score: 176
Period size: 49 Copynumber: 3.0 Consensus size: 50
42294023 TCGAATAAGG
*
42294033 AAAT-ATAATTTAATTATTATTTAAAAGAGTTTTAGATAAATA-ATAATT
1 AAATAATAATTTAATTATTATTTAAAAGAGTTTTAGATAAATAGATAATC
*
42294081 AAA-ACATAATTTAATTATTATTTAAAAGCA-TTTTAAATAAA-AGATAATC
1 AAATA-ATAATTTAATTATTATTTAAAAG-AGTTTTAGATAAATAGATAATC
* * *
42294130 AAATAGT-ATTTAAATTATTATTTAAAAGAGTTTTAGATATATATATAA
1 AAATAATAATTT-AATTATTATTTAAAAGAGTTTTAGATAAATAGATAA
42294178 CTTCAAATCC
Statistics
Matches: 83, Mismatches: 6, Indels: 14
0.81 0.06 0.14
Matches are distributed among these distances:
48 9 0.11
49 67 0.81
50 7 0.08
ACGTcount: A:0.50, C:0.02, G:0.06, T:0.41
Consensus pattern (50 bp):
AAATAATAATTTAATTATTATTTAAAAGAGTTTTAGATAAATAGATAATC
Found at i:42297210 original size:21 final size:21
Alignment explanation
Indices: 42297184--42297225 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
42297174 GCAATTTTGT
42297184 AATTAAA-TGGAAATTAAAACA
1 AATTAAAGT-GAAATTAAAACA
42297205 AATTAAAGTGAAATTAAAACA
1 AATTAAAGTGAAATTAAAACA
42297226 TTTTAACTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 19 0.95
22 1 0.05
ACGTcount: A:0.62, C:0.05, G:0.10, T:0.24
Consensus pattern (21 bp):
AATTAAAGTGAAATTAAAACA
Found at i:42298174 original size:35 final size:35
Alignment explanation
Indices: 42298128--42298225 Score: 169
Period size: 35 Copynumber: 2.8 Consensus size: 35
42298118 TACTCTCTAT
42298128 TTGGCGTGTTTTGGTTGGATTAGCTCTTTTGAGCA
1 TTGGCGTGTTTTGGTTGGATTAGCTCTTTTGAGCA
42298163 TTGGCGTGTTTTGGTTGGATTAGCTCTTTTGAGCA
1 TTGGCGTGTTTTGGTTGGATTAGCTCTTTTGAGCA
* * *
42298198 ATGGCGTGTTTTGGTTGGACTAACTCTT
1 TTGGCGTGTTTTGGTTGGATTAGCTCTT
42298226 ATAGGTACTT
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 60 1.00
ACGTcount: A:0.12, C:0.12, G:0.31, T:0.45
Consensus pattern (35 bp):
TTGGCGTGTTTTGGTTGGATTAGCTCTTTTGAGCA
Found at i:42308748 original size:32 final size:31
Alignment explanation
Indices: 42308680--42308818 Score: 104
Period size: 32 Copynumber: 4.4 Consensus size: 31
42308670 AAATGGTTAC
* * *
42308680 AAGCCATAAGTACAGTAATATGATTGGCACA
1 AAGCCATCAGTACAGTAACATGATCGGCACA
* *
42308711 AAGCCATCAGTAGCAGTGACATGATCGTCACA
1 AAGCCATCAGTA-CAGTAACATGATCGGCACA
* * *
42308743 CAGCCATCTA-TA-ATGGTAATATGACCGGCACA
1 AAGCCATC-AGTACA--GTAACATGATCGGCACA
* * *
42308775 AAGCCATCAGTA-ACGATAATATGATTGGCATA
1 AAGCCATCAGTACA-G-TAACATGATCGGCACA
42308807 AAGCCATCAGTA
1 AAGCCATCAGTA
42308819 ACATCGCAGC
Statistics
Matches: 87, Mismatches: 15, Indels: 11
0.77 0.13 0.10
Matches are distributed among these distances:
30 1 0.01
31 13 0.15
32 72 0.83
33 1 0.01
ACGTcount: A:0.38, C:0.21, G:0.19, T:0.22
Consensus pattern (31 bp):
AAGCCATCAGTACAGTAACATGATCGGCACA
Found at i:42308812 original size:64 final size:64
Alignment explanation
Indices: 42308694--42308814 Score: 145
Period size: 64 Copynumber: 1.9 Consensus size: 64
42308684 CATAAGTACA
** * * * *
42308694 GTAATATGATTGGCACAAAGCCATCAGTAGCAGTGACATGATCGTCACACAGCCATCTATAATG
1 GTAATATGACCGGCACAAAGCCATCAGTAACAGTAACATGATCGGCACAAAGCCATCTATAATG
* * *
42308758 GTAATATGACCGGCACAAAGCCATCAGTAAC-GATAATATGATTGGCATAAAGCCATC
1 GTAATATGACCGGCACAAAGCCATCAGTAACAG-TAACATGATCGGCACAAAGCCATC
42308815 AGTAACATCG
Statistics
Matches: 47, Mismatches: 9, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
63 1 0.02
64 46 0.98
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.22
Consensus pattern (64 bp):
GTAATATGACCGGCACAAAGCCATCAGTAACAGTAACATGATCGGCACAAAGCCATCTATAATG
Found at i:42308819 original size:32 final size:32
Alignment explanation
Indices: 42308695--42308820 Score: 121
Period size: 32 Copynumber: 3.9 Consensus size: 32
42308685 ATAAGTACAG
* *
42308695 TAATATGATTGGCACAAAGCCATCAGTAGC-A
1 TAATATGATCGGCACAAAGCCATCAGTAACGA
* * * * * *
42308726 GTGACATGATCGTCACACAGCCATCTA-TAATGG
1 -TAATATGATCGGCACAAAGCCATC-AGTAACGA
*
42308759 TAATATGACCGGCACAAAGCCATCAGTAACGA
1 TAATATGATCGGCACAAAGCCATCAGTAACGA
* *
42308791 TAATATGATTGGCATAAAGCCATCAGTAAC
1 TAATATGATCGGCACAAAGCCATCAGTAAC
42308821 ATCGCAGCAA
Statistics
Matches: 73, Mismatches: 18, Indels: 6
0.75 0.19 0.06
Matches are distributed among these distances:
31 1 0.01
32 71 0.97
33 1 0.01
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.22
Consensus pattern (32 bp):
TAATATGATCGGCACAAAGCCATCAGTAACGA
Found at i:42308856 original size:14 final size:14
Alignment explanation
Indices: 42308837--42308882 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
42308827 GCAAAGCTGC
42308837 CAGCAATAGTATCG
1 CAGCAATAGTATCG
***
42308851 CAGCAA-AGCGGC-
1 CAGCAATAGTATCG
42308863 CAGCAATAGTATCG
1 CAGCAATAGTATCG
42308877 CAGCAA
1 CAGCAA
42308883 AGCTGCCTAT
Statistics
Matches: 24, Mismatches: 6, Indels: 4
0.71 0.18 0.12
Matches are distributed among these distances:
12 6 0.25
13 6 0.25
14 12 0.50
ACGTcount: A:0.37, C:0.26, G:0.24, T:0.13
Consensus pattern (14 bp):
CAGCAATAGTATCG
Found at i:42308900 original size:26 final size:26
Alignment explanation
Indices: 42308821--42308889 Score: 129
Period size: 26 Copynumber: 2.7 Consensus size: 26
42308811 CATCAGTAAC
42308821 ATCGCAGCAAAGCTGCCAGCAATAGT
1 ATCGCAGCAAAGCTGCCAGCAATAGT
*
42308847 ATCGCAGCAAAGCGGCCAGCAATAGT
1 ATCGCAGCAAAGCTGCCAGCAATAGT
42308873 ATCGCAGCAAAGCTGCC
1 ATCGCAGCAAAGCTGCC
42308890 TATAATAGTA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 41 1.00
ACGTcount: A:0.33, C:0.29, G:0.25, T:0.13
Consensus pattern (26 bp):
ATCGCAGCAAAGCTGCCAGCAATAGT
Found at i:42309073 original size:24 final size:24
Alignment explanation
Indices: 42309015--42309099 Score: 100
Period size: 24 Copynumber: 3.5 Consensus size: 24
42309005 CCATGCTCAG
** *
42309015 AATCAGTCATACAAATCACAGATA
1 AATCAGTCATTTAAATCACAGAAA
*
42309039 AATCAGTCATTTAAATCACAGACA
1 AATCAGTCATTTAAATCACAGAAA
*
42309063 AATCAGTCATTTACATCAC-GAAAA
1 AATCAGTCATTTAAATCACAG-AAA
*
42309087 AATCAATCATTTA
1 AATCAGTCATTTA
42309100 CACTCGAGGG
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
23 1 0.02
24 53 0.98
ACGTcount: A:0.47, C:0.20, G:0.07, T:0.26
Consensus pattern (24 bp):
AATCAGTCATTTAAATCACAGAAA
Found at i:42309169 original size:27 final size:27
Alignment explanation
Indices: 42309124--42309333 Score: 192
Period size: 27 Copynumber: 7.9 Consensus size: 27
42309114 AATAGTATCT
* * * *
42309124 AGGGGCATTATGGTTATTTTACCTTAC
1 AGGGGTATTACGGTCATTTTACCCTAC
* *
42309151 AGGGGTATTTCGGTCATTTAACCCTA-
1 AGGGGTATTACGGTCATTTTACCCTAC
* *
42309177 TGGGGTATTACGGTCATTTTACCCTAT
1 AGGGGTATTACGGTCATTTTACCCTAC
* * *
42309204 AGGGGCACTACGATCATTTTACCCTA-
1 AGGGGTATTACGGTCATTTTACCCTAC
* * * * *
42309230 TGGGGTTTTTCAGTCACTTTACCCTAC
1 AGGGGTATTACGGTCATTTTACCCTAC
42309257 AGGGGTATTACGGTCATTTTACCCTAC
1 AGGGGTATTACGGTCATTTTACCCTAC
* * *
42309284 AGGGGCATTATGGTC-TTTCTACCCTAG
1 AGGGGTATTACGGTCATTT-TACCCTAC
* * *
42309311 AGGGGCATTACAGTTATTTTACC
1 AGGGGTATTACGGTCATTTTACC
42309334 TATTTTAAGG
Statistics
Matches: 147, Mismatches: 32, Indels: 8
0.79 0.17 0.04
Matches are distributed among these distances:
26 44 0.30
27 100 0.68
28 3 0.02
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.36
Consensus pattern (27 bp):
AGGGGTATTACGGTCATTTTACCCTAC
Found at i:42309221 original size:53 final size:53
Alignment explanation
Indices: 42309125--42309317 Score: 172
Period size: 53 Copynumber: 3.6 Consensus size: 53
42309115 ATAGTATCTA
* * * * * * * * *
42309125 GGGGCATTATGGTTATTTTACCTTACAGGGGTATTTCGGTCATTTAACCCTAT
1 GGGGTATTACGGTCATTTTACCCTACAGGGGCACTACGATCATTTTACCCTAT
*
42309178 GGGGTATTACGGTCATTTTACCCTATAGGGGCACTACGATCATTTTACCCTAT
1 GGGGTATTACGGTCATTTTACCCTACAGGGGCACTACGATCATTTTACCCTAT
* * * * * * * *
42309231 GGGGTTTTTCAGTCACTTTACCCTACAGGGGTATTACGGTCATTTTACCCTACA
1 GGGGTATTACGGTCATTTTACCCTACAGGGGCACTACGATCATTTTACCCTA-T
* * *
42309285 GGGGCATTATGGTC-TTTCTACCCTAGAGGGGCA
1 GGGGTATTACGGTCATTT-TACCCTACAGGGGCA
42309318 TTACAGTTAT
Statistics
Matches: 111, Mismatches: 27, Indels: 3
0.79 0.19 0.02
Matches are distributed among these distances:
53 89 0.80
54 22 0.20
ACGTcount: A:0.21, C:0.21, G:0.23, T:0.35
Consensus pattern (53 bp):
GGGGTATTACGGTCATTTTACCCTACAGGGGCACTACGATCATTTTACCCTAT
Found at i:42309307 original size:80 final size:79
Alignment explanation
Indices: 42309124--42309329 Score: 227
Period size: 80 Copynumber: 2.6 Consensus size: 79
42309114 AATAGTATCT
* * * *
42309124 AGGGGCATTATGGTTATTTTACCTTACAGGGGTATTTCGGTCATTTAACCCTATGGGGTATTACG
1 AGGGGCATTATGG-TCTTTTACCCTACAGGGGTATTTCAGTCATTTAACCCTAAGGGGTATTACG
*
42309189 GTCATTTTACCCTAT
65 GTCATTTTACCCTAC
* * * * *
42309204 AGGGGCACTACGATCATTTTACCCTA-TGGGGTTTTTCAGTCACTTT-ACCCTACAGGGGTATTA
1 AGGGGCATTATGGTC-TTTTACCCTACAGGGGTATTTCAGTCA-TTTAACCCTA-AGGGGTATTA
42309267 CGGTCATTTTACCCTAC
63 CGGTCATTTTACCCTAC
* * * *
42309284 AGGGGCATTATGGTCTTTCTACCCTAGAGGGGCATTACAGTTATTT
1 AGGGGCATTATGGTCTTT-TACCCTACAGGGGTATTTCAGTCATTT
42309330 TACCTATTTT
Statistics
Matches: 103, Mismatches: 18, Indels: 10
0.79 0.14 0.08
Matches are distributed among these distances:
79 23 0.22
80 69 0.67
81 11 0.11
ACGTcount: A:0.21, C:0.20, G:0.22, T:0.36
Consensus pattern (79 bp):
AGGGGCATTATGGTCTTTTACCCTACAGGGGTATTTCAGTCATTTAACCCTAAGGGGTATTACGG
TCATTTTACCCTAC
Found at i:42331380 original size:27 final size:27
Alignment explanation
Indices: 42331350--42331404 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
42331340 ATCATAAAAG
42331350 AACATATCTAATGGTATAGCTAACTGA
1 AACATATCTAATGGTATAGCTAACTGA
42331377 AACATATCTAATGGTATAGCTAACTGA
1 AACATATCTAATGGTATAGCTAACTGA
42331404 A
1 A
42331405 GTCACCTTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.29
Consensus pattern (27 bp):
AACATATCTAATGGTATAGCTAACTGA
Found at i:42333488 original size:73 final size:73
Alignment explanation
Indices: 42333369--42333513 Score: 220
Period size: 73 Copynumber: 2.0 Consensus size: 73
42333359 AACAATAGAT
* *
42333369 AAATAAAAGAGACTTGATAGAGTTCAAAATGTTGATGTCCAAAGGATCTCGCAACCTAACATAAT
1 AAATAAAAGAGACTTGATAGAGTTCAAAAAGTTGATGTCCAAAGGATCTCGCAACCTAACAGAAT
42333434 GGTTAAGA
66 GGTTAAGA
* * * *
42333442 AAAT-AAAGAAGACTTGATAGATTTTAAAAAGTTGATGTCCAAAGGATCTTGCAACCTAACAGAC
1 AAATAAAAG-AGACTTGATAGAGTTCAAAAAGTTGATGTCCAAAGGATCTCGCAACCTAACAGAA
42333506 TGGTTAAG
65 TGGTTAAG
42333514 TCAGGTAAAA
Statistics
Matches: 65, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
72 4 0.06
73 61 0.94
ACGTcount: A:0.42, C:0.13, G:0.19, T:0.26
Consensus pattern (73 bp):
AAATAAAAGAGACTTGATAGAGTTCAAAAAGTTGATGTCCAAAGGATCTCGCAACCTAACAGAAT
GGTTAAGA
Found at i:42334869 original size:3 final size:3
Alignment explanation
Indices: 42334861--42334887 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
42334851 ACCACTGGGA
42334861 GGT GGT GGT GGT GGT GGT GGT GGT GGT
1 GGT GGT GGT GGT GGT GGT GGT GGT GGT
42334888 AGTAGGCGGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.67, T:0.33
Consensus pattern (3 bp):
GGT
Found at i:42336150 original size:27 final size:27
Alignment explanation
Indices: 42336115--42336204 Score: 164
Period size: 27 Copynumber: 3.4 Consensus size: 27
42336105 ATAAAAAATA
42336115 ACCAAAATATTATAAATTTTTTTATTT
1 ACCAAAATATTATAAATTTTTTTATTT
42336142 ACCAAAATATTATAAA-TTTTTTATTT
1 ACCAAAATATTATAAATTTTTTTATTT
*
42336168 ACCAAAATATTATAACTTTTTTTATTT
1 ACCAAAATATTATAAATTTTTTTATTT
42336195 ACCAAAATAT
1 ACCAAAATAT
42336205 ACCAAAAAAA
Statistics
Matches: 61, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
26 25 0.41
27 36 0.59
ACGTcount: A:0.42, C:0.10, G:0.00, T:0.48
Consensus pattern (27 bp):
ACCAAAATATTATAAATTTTTTTATTT
Found at i:42336293 original size:27 final size:26
Alignment explanation
Indices: 42336270--42336366 Score: 131
Period size: 27 Copynumber: 3.6 Consensus size: 26
42336260 CACATTGGAA
42336270 GCACCAAAGGTGCCAATGTGATTGGCG
1 GCACCAAAGGTGCCAATGTGATTGG-G
*
42336297 CCACCAAAGGTGCCAATGTGATTGGCG
1 GCACCAAAGGTGCCAATGTGATTGG-G
* *
42336324 GCACCAATGGTGCCAATGTGATTTGTG
1 GCACCAAAGGTGCCAATGTGA-TTGGG
*
42336351 GCACCAATGGTGCCAA
1 GCACCAAAGGTGCCAA
42336367 AGGACTAAAA
Statistics
Matches: 65, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
27 62 0.95
28 3 0.05
ACGTcount: A:0.26, C:0.24, G:0.30, T:0.21
Consensus pattern (26 bp):
GCACCAAAGGTGCCAATGTGATTGGG
Found at i:42336579 original size:22 final size:21
Alignment explanation
Indices: 42336554--42336606 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 21
42336544 ATAACTCTAT
**
42336554 TTTAATTTATTAAATTTAATAG
1 TTTAATTTA-TAAATAGAATAG
* *
42336576 TTTATGTTTATAGATAGAATAG
1 TTTA-ATTTATAAATAGAATAG
42336598 TTTAATTTA
1 TTTAATTTA
42336607 ATAACTCTAT
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
21 4 0.16
22 17 0.68
23 4 0.16
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (21 bp):
TTTAATTTATAAATAGAATAG
Found at i:42336622 original size:19 final size:19
Alignment explanation
Indices: 42336598--42336663 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
42336588 GATAGAATAG
42336598 TTTAATTTAATAACTCTAT
1 TTTAATTTAATAACTCTAT
* *
42336617 TTTAATGTAATAA-ACTAT
1 TTTAATTTAATAACTCTAT
* *
42336635 TCTCATTTAATAACTCTAT
1 TTTAATTTAATAACTCTAT
42336654 TTTAATTTAA
1 TTTAATTTAA
42336664 AAAAATTAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
18 14 0.37
19 24 0.63
ACGTcount: A:0.38, C:0.11, G:0.02, T:0.50
Consensus pattern (19 bp):
TTTAATTTAATAACTCTAT
Found at i:42336840 original size:82 final size:82
Alignment explanation
Indices: 42336744--42336908 Score: 321
Period size: 82 Copynumber: 2.0 Consensus size: 82
42336734 AAAAGGAAAA
42336744 AAATAACGGAAACATAAACTATTTTATCTATTTATAAATTTAATATATTCTTAATAGACTTATAA
1 AAATAACGGAAACATAAACTATTTTATCTATTTATAAATTTAATATATTCTTAATAGACTTATAA
42336809 CATAAACATGTTAGACT
66 CATAAACATGTTAGACT
*
42336826 AAATAATGGAAACATAAACTATTTTATCTATTTATAAATTTAATATATTCTTAATAGACTTATAA
1 AAATAACGGAAACATAAACTATTTTATCTATTTATAAATTTAATATATTCTTAATAGACTTATAA
42336891 CATAAACATGTTAGACT
66 CATAAACATGTTAGACT
42336908 A
1 A
42336909 TTTTAATTAA
Statistics
Matches: 82, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
82 82 1.00
ACGTcount: A:0.45, C:0.10, G:0.06, T:0.38
Consensus pattern (82 bp):
AAATAACGGAAACATAAACTATTTTATCTATTTATAAATTTAATATATTCTTAATAGACTTATAA
CATAAACATGTTAGACT
Found at i:42337001 original size:19 final size:18
Alignment explanation
Indices: 42336977--42337072 Score: 97
Period size: 19 Copynumber: 5.2 Consensus size: 18
42336967 TTTTTATATT
42336977 TTAAATGCAAATAGAGTTA
1 TTAAATG-AAATAGAGTTA
*
42336996 TTAAATGAGAATAG-TTTA
1 TTAAATGA-AATAGAGTTA
*
42337014 TTAAATTAAAATAGAGTTA
1 TTAAA-TGAAATAGAGTTA
*
42337033 TTAAATGAGAATAG-TTTA
1 TTAAATGA-AATAGAGTTA
*
42337051 TTAAATTAAAATAGAGTTA
1 TTAAA-TGAAATAGAGTTA
42337070 TTA
1 TTA
42337073 CTTAATTAGA
Statistics
Matches: 64, Mismatches: 7, Indels: 12
0.77 0.08 0.14
Matches are distributed among these distances:
18 29 0.45
19 35 0.55
ACGTcount: A:0.48, C:0.01, G:0.14, T:0.38
Consensus pattern (18 bp):
TTAAATGAAATAGAGTTA
Found at i:42337018 original size:37 final size:37
Alignment explanation
Indices: 42336985--42337072 Score: 176
Period size: 37 Copynumber: 2.4 Consensus size: 37
42336975 TTTTAAATGC
42336985 AAATAGAGTTATTAAATGAGAATAGTTTATTAAATTA
1 AAATAGAGTTATTAAATGAGAATAGTTTATTAAATTA
42337022 AAATAGAGTTATTAAATGAGAATAGTTTATTAAATTA
1 AAATAGAGTTATTAAATGAGAATAGTTTATTAAATTA
42337059 AAATAGAGTTATTA
1 AAATAGAGTTATTA
42337073 CTTAATTAGA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.14, T:0.38
Consensus pattern (37 bp):
AAATAGAGTTATTAAATGAGAATAGTTTATTAAATTA
Found at i:42337077 original size:18 final size:19
Alignment explanation
Indices: 42336985--42337072 Score: 108
Period size: 18 Copynumber: 4.7 Consensus size: 19
42336975 TTTTAAATGC
*
42336985 AAATAGAGTTATTAAATGA
1 AAATAGAGTTATTAAATTA
* *
42337004 GAATAG-TTTATTAAATTA
1 AAATAGAGTTATTAAATTA
*
42337022 AAATAGAGTTATTAAATGA
1 AAATAGAGTTATTAAATTA
* *
42337041 GAATAG-TTTATTAAATTA
1 AAATAGAGTTATTAAATTA
42337059 AAATAGAGTTATTA
1 AAATAGAGTTATTA
42337073 CTTAATTAGA
Statistics
Matches: 56, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
18 30 0.54
19 26 0.46
ACGTcount: A:0.49, C:0.00, G:0.14, T:0.38
Consensus pattern (19 bp):
AAATAGAGTTATTAAATTA
Found at i:42337830 original size:29 final size:29
Alignment explanation
Indices: 42337805--42337868 Score: 103
Period size: 29 Copynumber: 2.2 Consensus size: 29
42337795 GTTTTTTTGT
*
42337805 ATATTTTGGTAAATAAAAAAAATTTTATA
1 ATATTTTGATAAATAAAAAAAATTTTATA
*
42337834 ATATTTTGATAAATAAAAAAAA-GTTATA
1 ATATTTTGATAAATAAAAAAAATTTTATA
42337862 ATATTTT
1 ATATTTT
42337869 AATTATTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
28 12 0.36
29 21 0.64
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (29 bp):
ATATTTTGATAAATAAAAAAAATTTTATA
Found at i:42338239 original size:16 final size:16
Alignment explanation
Indices: 42338220--42338269 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
42338210 TATTTTTGAA
42338220 TAACATTTAAATAATT
1 TAACATTTAAATAATT
* *
42338236 TAACA-TAATAATAAAT
1 TAACATTTA-AATAATT
*
42338252 T-ATATTTAAATAATT
1 TAACATTTAAATAATT
42338267 TAA
1 TAA
42338270 TATAATAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 6
0.70 0.14 0.16
Matches are distributed among these distances:
15 11 0.42
16 15 0.58
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (16 bp):
TAACATTTAAATAATT
Found at i:42338261 original size:31 final size:30
Alignment explanation
Indices: 42338224--42338292 Score: 102
Period size: 31 Copynumber: 2.3 Consensus size: 30
42338214 TTTGAATAAC
*
42338224 ATTTAAATAATTTAACATAATAATAAATTA
1 ATTTAAATAATTTAACATAATAAAAAATTA
*
42338254 TATTTAAATAATTTAATATAATAAAAAATTA
1 -ATTTAAATAATTTAACATAATAAAAAATTA
*
42338285 ATCTAAAT
1 ATTTAAAT
42338293 TTATAAATAC
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
30 7 0.20
31 28 0.80
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.41
Consensus pattern (30 bp):
ATTTAAATAATTTAACATAATAAAAAATTA
Found at i:42338677 original size:16 final size:17
Alignment explanation
Indices: 42338644--42338677 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
42338634 TATTCTCTCA
*
42338644 ATTCTCTCAAATTATTT
1 ATTCTCTCAAACTATTT
42338661 ATTCTCTC-AACTATTT
1 ATTCTCTCAAACTATTT
42338677 A
1 A
42338678 GTTCCCAATT
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:0.29, C:0.21, G:0.00, T:0.50
Consensus pattern (17 bp):
ATTCTCTCAAACTATTT
Found at i:42347437 original size:16 final size:16
Alignment explanation
Indices: 42347416--42347446 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
42347406 AAACAACAAC
*
42347416 TATGTTTTCAAAATTG
1 TATGTTTTAAAAATTG
42347432 TATGTTTTAAAAATT
1 TATGTTTTAAAAATT
42347447 TCTATTGCAA
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:0.35, C:0.03, G:0.10, T:0.52
Consensus pattern (16 bp):
TATGTTTTAAAAATTG
Found at i:42359154 original size:10 final size:10
Alignment explanation
Indices: 42359119--42359152 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
42359109 CAAATCTGTC
*
42359119 AAAAATAATC
1 AAAAATAATT
42359129 AAAAATAATT
1 AAAAATAATT
*
42359139 AAAATTAATT
1 AAAAATAATT
42359149 AAAA
1 AAAA
42359153 TTCAACATGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (10 bp):
AAAAATAATT
Found at i:42360148 original size:15 final size:15
Alignment explanation
Indices: 42360128--42360157 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
42360118 TTGCCTAAAT
42360128 CATTTTCAACTTCCC
1 CATTTTCAACTTCCC
42360143 CATTTTCAACTTCCC
1 CATTTTCAACTTCCC
42360158 ATGCTTTCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.40, G:0.00, T:0.40
Consensus pattern (15 bp):
CATTTTCAACTTCCC
Found at i:42361527 original size:20 final size:20
Alignment explanation
Indices: 42361502--42361542 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
42361492 ATACCTTTGC
42361502 TAGTGGTGTCAAATATTCTT
1 TAGTGGTGTCAAATATTCTT
42361522 TAGTGGTGTCAAATATTCTT
1 TAGTGGTGTCAAATATTCTT
42361542 T
1 T
42361543 GCGACAAGTG
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:0.24, C:0.10, G:0.20, T:0.46
Consensus pattern (20 bp):
TAGTGGTGTCAAATATTCTT
Found at i:42362109 original size:17 final size:18
Alignment explanation
Indices: 42362079--42362125 Score: 69
Period size: 17 Copynumber: 2.6 Consensus size: 18
42362069 TTTAATTAGT
*
42362079 ATAAAATATTAATAATTAA
1 ATAAAAT-TAAATAATTAA
42362098 AT-AAATTAAATAATTAA
1 ATAAAATTAAATAATTAA
42362115 ATAAAATTAAA
1 ATAAAATTAAA
42362126 ATTTAAGAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 12 0.46
18 12 0.46
19 2 0.08
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
ATAAAATTAAATAATTAA
Found at i:42362112 original size:8 final size:8
Alignment explanation
Indices: 42362089--42362118 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
42362079 ATAAAATATT
42362089 AATAATTA
1 AATAATTA
42362097 AATAAATTA
1 AAT-AATTA
42362106 AATAATTA
1 AATAATTA
42362114 AATAA
1 AATAA
42362119 AATTAAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 13 0.62
9 8 0.38
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (8 bp):
AATAATTA
Found at i:42372588 original size:10 final size:10
Alignment explanation
Indices: 42372569--42372615 Score: 51
Period size: 10 Copynumber: 4.6 Consensus size: 10
42372559 AAATCTATCG
42372569 AAAA-TAATC
1 AAAATTAATC
42372578 AAAATTAATC
1 AAAATTAATC
*
42372588 AAAATTAATTAT
1 AAAATTAA-T-C
*
42372600 AAAATTAATT
1 AAAATTAATC
42372610 AAAATT
1 AAAATT
42372616 CAACATATTA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
9 4 0.12
10 20 0.59
11 2 0.06
12 8 0.24
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (10 bp):
AAAATTAATC
Found at i:42376326 original size:20 final size:19
Alignment explanation
Indices: 42376279--42376328 Score: 52
Period size: 20 Copynumber: 2.7 Consensus size: 19
42376269 CTAGATAAAC
42376279 ATTAAATT--TAATTTAAG
1 ATTAAATTAATAATTTAAG
*
42376296 ATTAAGA-TAATAATTTTAAT
1 ATTAA-ATTAATAA-TTTAAG
42376316 ATTAAATTAATAA
1 ATTAAATTAATAA
42376329 AATACTATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
17 6 0.22
18 1 0.04
19 4 0.15
20 16 0.59
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (19 bp):
ATTAAATTAATAATTTAAG
Found at i:42376332 original size:25 final size:25
Alignment explanation
Indices: 42376285--42376332 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
42376275 AAACATTAAA
*
42376285 TTTAATTTAAGATTAAGATAATAAT
1 TTTAATTTAAGATTAAGAAAATAAT
*
42376310 TTTAATATTAA-ATTAATAAAATA
1 TTTAAT-TTAAGATTAAGAAAATA
42376333 CTATTAAGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 16 0.80
26 4 0.20
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (25 bp):
TTTAATTTAAGATTAAGAAAATAAT
Found at i:42376373 original size:37 final size:37
Alignment explanation
Indices: 42376296--42376385 Score: 103
Period size: 37 Copynumber: 2.4 Consensus size: 37
42376286 TTAATTTAAG
42376296 ATTAAGATAATAATTTTAATATTAAATTAATAAAATACT
1 ATTAAGATAAT-A-TTTAATATTAAATTAATAAAATACT
* *
42376335 ATTAAGATAAATATTTAAT-TTAATTTAATATTAA-ACT
1 ATTAAGAT-AATATTTAATATTAAATTAATA-AAATACT
*
42376372 ATTAAAATAATATT
1 ATTAAGATAATATT
42376386 ATTTTTGGAA
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
36 6 0.13
37 20 0.43
38 8 0.17
39 9 0.20
40 3 0.07
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (37 bp):
ATTAAGATAATATTTAATATTAAATTAATAAAATACT
Found at i:42380130 original size:66 final size:65
Alignment explanation
Indices: 42379982--42380159 Score: 204
Period size: 66 Copynumber: 2.8 Consensus size: 65
42379972 AAAACTTGCG
* * *
42379982 GACCTACGCTCCCAGCTGATTATTAAGGTTAGCAGAGTTAA----GCAACTCCCAGACAGCTAGT
1 GACCTAAGCTCCCAGCTGATTATTAAGGTTA-CAGAGTTAAGCTCGCAACTCCCAAACAACTAGT
*
42380043 G
65 A
*
42380044 GACCTACAG-TCCCAGTTGATTATTAAGGTTACAAGAGTTAAGCTCGCAACTCCCAAACAACTAG
1 GACCTA-AGCTCCCAGCTGATTATTAAGGTTAC-AGAGTTAAGCTCGCAACTCCCAAACAACTAG
42380108 TA
64 TA
* * * *
42380110 GACCTATGCTCCTAACTGATTATTAAGGTTAGTAGAGTTAAGCTCGCAAC
1 GACCTAAGCTCCCAGCTGATTATTAAGGTTA-CAGAGTTAAGCTCGCAAC
42380160 CTTTGGTCTT
Statistics
Matches: 98, Mismatches: 10, Indels: 12
0.82 0.08 0.10
Matches are distributed among these distances:
61 1 0.01
62 35 0.36
63 1 0.01
65 1 0.01
66 60 0.61
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (65 bp):
GACCTAAGCTCCCAGCTGATTATTAAGGTTACAGAGTTAAGCTCGCAACTCCCAAACAACTAGTA
Found at i:42384998 original size:13 final size:12
Alignment explanation
Indices: 42384977--42385015 Score: 53
Period size: 11 Copynumber: 3.2 Consensus size: 12
42384967 TTTTTTAAAA
*
42384977 AAAATTAAATCT
1 AAAATTAAATCC
42384989 AAAATCTAAATCC
1 AAAAT-TAAATCC
42385002 AAAA-TAAATCC
1 AAAATTAAATCC
42385013 AAA
1 AAA
42385016 CAGTCCGGAG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
11 10 0.40
12 5 0.20
13 10 0.40
ACGTcount: A:0.62, C:0.15, G:0.00, T:0.23
Consensus pattern (12 bp):
AAAATTAAATCC
Found at i:42386526 original size:31 final size:30
Alignment explanation
Indices: 42386478--42386538 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
42386468 AAATACCTAA
42386478 AATCCCCTGACAACTCCCCCACTAACAACAT
1 AATCCCCTGACAACT-CCCCACTAACAACAT
* *
42386509 AATCCCCTGA-ATCCTCCCCACTAACCACAT
1 AATCCCCTGACA-ACTCCCCACTAACAACAT
42386539 CCAACTACCT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
30 15 0.56
31 12 0.44
ACGTcount: A:0.33, C:0.46, G:0.03, T:0.18
Consensus pattern (30 bp):
AATCCCCTGACAACTCCCCACTAACAACAT
Found at i:42387456 original size:12 final size:12
Alignment explanation
Indices: 42387439--42387463 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
42387429 AACTCTGTAA
42387439 CTAGTTTAAATT
1 CTAGTTTAAATT
42387451 CTAGTTTAAATT
1 CTAGTTTAAATT
42387463 C
1 C
42387464 GATTTTTAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.12, G:0.08, T:0.48
Consensus pattern (12 bp):
CTAGTTTAAATT
Found at i:42387500 original size:13 final size:13
Alignment explanation
Indices: 42387482--42387547 Score: 63
Period size: 13 Copynumber: 5.5 Consensus size: 13
42387472 AATTTCAAAT
42387482 TATTTAGTAATAA
1 TATTTAGTAATAA
42387495 TATTTAG-AAT--
1 TATTTAGTAATAA
*
42387505 TATTTAGTGATAA
1 TATTTAGTAATAA
42387518 TATTTAG-AAT--
1 TATTTAGTAATAA
* *
42387528 TATTTGGTGATAA
1 TATTTAGTAATAA
42387541 TATTTAG
1 TATTTAG
42387548 GAAAAATCTA
Statistics
Matches: 42, Mismatches: 5, Indels: 12
0.71 0.08 0.20
Matches are distributed among these distances:
10 13 0.31
11 4 0.10
12 5 0.12
13 20 0.48
ACGTcount: A:0.38, C:0.00, G:0.14, T:0.48
Consensus pattern (13 bp):
TATTTAGTAATAA
Found at i:42387505 original size:23 final size:23
Alignment explanation
Indices: 42387479--42387547 Score: 120
Period size: 23 Copynumber: 3.0 Consensus size: 23
42387469 TTAAATTTCA
*
42387479 AATTATTTAGTAATAATATTTAG
1 AATTATTTAGTGATAATATTTAG
42387502 AATTATTTAGTGATAATATTTAG
1 AATTATTTAGTGATAATATTTAG
*
42387525 AATTATTTGGTGATAATATTTAG
1 AATTATTTAGTGATAATATTTAG
42387548 GAAAAATCTA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.39, C:0.00, G:0.13, T:0.48
Consensus pattern (23 bp):
AATTATTTAGTGATAATATTTAG
Found at i:42389143 original size:36 final size:36
Alignment explanation
Indices: 42389095--42389165 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 36
42389085 ATCAAAGGCT
*
42389095 ATAATTAAAAGCTGTATACAATTAGAACTCTAAGAC
1 ATAATTAAAAGCTGTATACAATTAAAACTCTAAGAC
*
42389131 ATAATTAGAAGCTGTATACAATTAAAACTCTAAGA
1 ATAATTAAAAGCTGTATACAATTAAAACTCTAAGA
42389166 TTAAATAATC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.48, C:0.13, G:0.11, T:0.28
Consensus pattern (36 bp):
ATAATTAAAAGCTGTATACAATTAAAACTCTAAGAC
Found at i:42393396 original size:36 final size:36
Alignment explanation
Indices: 42393348--42393418 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 36
42393338 ATCAAAGGCT
*
42393348 ATAATTAAAAGCTGTATACAATTAGAACTCTAAGAC
1 ATAATTAAAAGCTGTATACAATTAAAACTCTAAGAC
*
42393384 ATAATTAGAAGCTGTATACAATTAAAACTCTAAGA
1 ATAATTAAAAGCTGTATACAATTAAAACTCTAAGA
42393419 TTAAATAATC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.48, C:0.13, G:0.11, T:0.28
Consensus pattern (36 bp):
ATAATTAAAAGCTGTATACAATTAAAACTCTAAGAC
Found at i:42395344 original size:22 final size:24
Alignment explanation
Indices: 42395318--42395371 Score: 58
Period size: 22 Copynumber: 2.3 Consensus size: 24
42395308 TTATAAATTC
*
42395318 AATTTAAAGGATA-TAAT-ACAAT
1 AATTTAAAGCATATTAATAACAAT
**
42395340 AATTTCCAGCATATTTAATAACAAT
1 AATTTAAAGCATA-TTAATAACAAT
42395365 AATTTAA
1 AATTTAA
42395372 TCATAAAAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
22 10 0.42
24 4 0.17
25 10 0.42
ACGTcount: A:0.50, C:0.09, G:0.06, T:0.35
Consensus pattern (24 bp):
AATTTAAAGCATATTAATAACAAT
Found at i:42400527 original size:21 final size:22
Alignment explanation
Indices: 42400488--42400529 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
42400478 CATTAGTTGA
42400488 AAAAAAATAAATATGTACATAAG
1 AAAAAAATAAATA-GTACATAAG
*
42400511 AAAACAATAAATA-TACATA
1 AAAAAAATAAATAGTACATA
42400530 TATATATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 6 0.33
23 12 0.67
ACGTcount: A:0.67, C:0.07, G:0.05, T:0.21
Consensus pattern (22 bp):
AAAAAAATAAATAGTACATAAG
Found at i:42402376 original size:44 final size:44
Alignment explanation
Indices: 42402319--42402436 Score: 157
Period size: 44 Copynumber: 2.7 Consensus size: 44
42402309 GATATGATCT
* * *
42402319 ACTCTACTGCAACTTCAGAGAGATAAGATCT-GTGGTTTTAATCC
1 ACTCCACTGCAACTTCAGGGAGATAAGAT-TAGTGGCTTTAATCC
* * *
42402363 ACTCCACTGCAACTTCAGGGAGATAGGATTATTGGCTTTAATCT
1 ACTCCACTGCAACTTCAGGGAGATAAGATTAGTGGCTTTAATCC
*
42402407 GCTCCACTGCAACTTCAGGGAGATAAGATT
1 ACTCCACTGCAACTTCAGGGAGATAAGATT
42402437 CGCCATCTTC
Statistics
Matches: 65, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
43 1 0.02
44 64 0.98
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.30
Consensus pattern (44 bp):
ACTCCACTGCAACTTCAGGGAGATAAGATTAGTGGCTTTAATCC
Found at i:42402575 original size:100 final size:100
Alignment explanation
Indices: 42402443--42402632 Score: 274
Period size: 100 Copynumber: 1.9 Consensus size: 100
42402433 GATTCGCCAT
* * * *
42402443 CTTCAGTCTTTTAAATTGCAATGTTGGTGAAACAAAATTTGCTATCGTAGCTTCAATCTGTTCTA
1 CTTCAATCTTTTAAATTGCAATGTTGGTGAAACAAAATTCGCCATCGTAGCTTCAATCTGTTCCA
42402508 CTACACCGCCAAGGGAATAAGATTCACCGTTGCAG
66 CTACACCGCCAAGGGAATAAGATTCACCGTTGCAG
* ** *
42402543 CTTCAATCTTTTTAATTGCAATGTTGAG-GAAACAAGGTTCGCCGTCGTAGCTTCAATCTGTTCC
1 CTTCAATCTTTTAAATTGCAATGTTG-GTGAAACAAAATTCGCCATCGTAGCTTCAATCTGTTCC
* *
42402607 ACTACACCGCCAGGGGAGTAAGATTC
65 ACTACACCGCCAAGGGAATAAGATTC
42402633 GCCATTGTGG
Statistics
Matches: 79, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
100 78 0.99
101 1 0.01
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.31
Consensus pattern (100 bp):
CTTCAATCTTTTAAATTGCAATGTTGGTGAAACAAAATTCGCCATCGTAGCTTCAATCTGTTCCA
CTACACCGCCAAGGGAATAAGATTCACCGTTGCAG
Found at i:42402882 original size:167 final size:167
Alignment explanation
Indices: 42402580--42402991 Score: 558
Period size: 167 Copynumber: 2.5 Consensus size: 167
42402570 GGAAACAAGG
* * * * * * *
42402580 TTCGCCGTCGTAGCTTCAATCTGTTCCACTACACCGCCAGGGGAGTAAGATTCGCCATTGTGGCT
1 TTCGCCGTCGTGGCTTCAATCTGCTCCGCTACAACGCCAGGGAAGTAAGATTCGCCGTCGTGGCT
** *
42402645 T-TAATCCGTTCCACTGTAATGCCAAAGAGATAGGATTCGTTGCCCACAGCTTTAATACACTCTA
66 TCT-ATCTTTTCCACTGTAATGCCAAAGAGATAGGATTCGCTGCCCACAGCTTTAATACACTCTA
**
42402709 CTTCAGCTAATCCAAGTCTTAACGCCAGGGAGATAAGA
130 CTTCAGCTAATCCAAGTCTTAAAACCAGGGAGATAAGA
* * *
42402747 TTCGCCATCGTGGCTTCAATCTGCTCCGCTACAACGCTAGGGAAGTAAGATTCACCGTCGTGGCT
1 TTCGCCGTCGTGGCTTCAATCTGCTCCGCTACAACGCCAGGGAAGTAAGATTCGCCGTCGTGGCT
* * * *
42402812 TCTATCTTTTCCACTGTAATGCCAAAGAGATAGGTTTCGCTGCCCACATCTTTAAT-CTGCTCTT
66 TCTATCTTTTCCACTGTAATGCCAAAGAGATAGGATTCGCTGCCCACAGCTTTAATAC-ACTCTA
**
42402876 CTTCAGCTAATCCAAGTCTTAAAATTAGGGAGATAAGA
130 CTTCAGCTAATCCAAGTCTTAAAACCAGGGAGATAAGA
* * * *
42402914 TTCGCCGTCGTGGCTTCAATCTGCTCCGCTATAATGCCAGGAAAGTAAGATTCGCTGTCGTGGCT
1 TTCGCCGTCGTGGCTTCAATCTGCTCCGCTACAACGCCAGGGAAGTAAGATTCGCCGTCGTGGCT
*
42402979 TCAATCTTTTCCA
66 TCTATCTTTTCCA
42402992 TTGCAACGTC
Statistics
Matches: 214, Mismatches: 29, Indels: 4
0.87 0.12 0.02
Matches are distributed among these distances:
166 1 0.00
167 212 0.99
168 1 0.00
ACGTcount: A:0.25, C:0.26, G:0.20, T:0.29
Consensus pattern (167 bp):
TTCGCCGTCGTGGCTTCAATCTGCTCCGCTACAACGCCAGGGAAGTAAGATTCGCCGTCGTGGCT
TCTATCTTTTCCACTGTAATGCCAAAGAGATAGGATTCGCTGCCCACAGCTTTAATACACTCTAC
TTCAGCTAATCCAAGTCTTAAAACCAGGGAGATAAGA
Found at i:42403123 original size:88 final size:88
Alignment explanation
Indices: 42403020--42403192 Score: 247
Period size: 88 Copynumber: 2.0 Consensus size: 88
42403010 AAGACCAATG
* * * * *
42403020 TCTTCGATCTGCTTCACTGCCAGCACAGGAAGGCGAGATCTGCTATCTTCAACCTACTCCACTGC
1 TCTTCGATCTACTTCACTGCCAACACAGGAAGACAAGATCTGCTATCTTCAACATACTCCACTGC
42403085 TGCTCAGGGAAACAAGGCTGGTA
66 TGCTCAGGGAAACAAGGCTGGTA
* * * *
42403108 TCTTCGATCTACTTCATTTCCAATACAGGAAGACAAGATCTGCTATTTTCAACATACTCCACTGC
1 TCTTCGATCTACTTCACTGCCAACACAGGAAGACAAGATCTGCTATCTTCAACATACTCCACTGC
* *
42403173 TGCTCAGGGAGATAAGGCTG
66 TGCTCAGGGAAACAAGGCTG
42403193 AAGTTTCACC
Statistics
Matches: 74, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
88 74 1.00
ACGTcount: A:0.26, C:0.27, G:0.20, T:0.27
Consensus pattern (88 bp):
TCTTCGATCTACTTCACTGCCAACACAGGAAGACAAGATCTGCTATCTTCAACATACTCCACTGC
TGCTCAGGGAAACAAGGCTGGTA
Found at i:42415474 original size:21 final size:22
Alignment explanation
Indices: 42415434--42415476 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
42415424 AACATTAGTT
42415434 GAAAAAAATAAATATGTACATAA
1 GAAAAAAATAAATA-GTACATAA
*
42415457 GAAAATAATAAATA-TACATA
1 GAAAAAAATAAATAGTACATA
42415477 TATATATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 6 0.32
23 13 0.68
ACGTcount: A:0.65, C:0.05, G:0.07, T:0.23
Consensus pattern (22 bp):
GAAAAAAATAAATAGTACATAA
Found at i:42418700 original size:29 final size:29
Alignment explanation
Indices: 42418622--42418701 Score: 92
Period size: 29 Copynumber: 2.8 Consensus size: 29
42418612 GTATAACATG
* *
42418622 GATAAATT-AAAAGGTTAAAATAAATTTGA
1 GATAAATTAAAAATGTTAAAAT-AAGTTGA
* * *
42418651 -ATAAATTAACAATATTGAAATAAGTTGA
1 GATAAATTAAAAATGTTAAAATAAGTTGA
42418679 GATAAATTAAAAATGTTAAAATA
1 GATAAATTAAAAATGTTAAAATA
42418702 GTGGAAAGAG
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
28 13 0.32
29 28 0.68
ACGTcount: A:0.56, C:0.01, G:0.11, T:0.31
Consensus pattern (29 bp):
GATAAATTAAAAATGTTAAAATAAGTTGA
Found at i:42420896 original size:17 final size:20
Alignment explanation
Indices: 42420874--42420962 Score: 57
Period size: 21 Copynumber: 4.6 Consensus size: 20
42420864 TTAAATTTAA
42420874 ATTTAA-AT-TTAAAA-ATT
1 ATTTAATATATTAAAATATT
42420891 ATTTAATATATTAAAATATT
1 ATTTAATATATTAAAATATT
* * *
42420911 AATATAAAATATT-ATA-ATT
1 -ATTTAATATATTAAAATATT
*
42420930 -TTTAATATTATTAAACATACAT
1 ATTTAATA-TATTAAA-ATA-TT
42420952 ATTTAAT-TATT
1 ATTTAATATATT
42420963 TTCAATAATT
Statistics
Matches: 55, Mismatches: 7, Indels: 16
0.71 0.09 0.21
Matches are distributed among these distances:
17 11 0.20
18 6 0.11
19 10 0.18
20 6 0.11
21 15 0.27
22 1 0.02
23 6 0.11
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.48
Consensus pattern (20 bp):
ATTTAATATATTAAAATATT
Found at i:42420992 original size:16 final size:16
Alignment explanation
Indices: 42420968--42421009 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
42420958 TTATTTTCAA
*
42420968 TAATTTAATAAATTAT
1 TAATATAATAAATTAT
*
42420984 TAATATAATAATTTAT
1 TAATATAATAAATTAT
*
42421000 TAAAATAATA
1 TAATATAATA
42421010 GTACAAATGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TAATATAATAAATTAT
Found at i:42421839 original size:20 final size:19
Alignment explanation
Indices: 42421802--42421840 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
42421792 AATTTTAAAA
*
42421802 TATTTTTAAAATACTTTTT
1 TATTTTTAAAATAATTTTT
42421821 TATTTTTAAAATAAATTTTT
1 TATTTTTAAAAT-AATTTTT
42421841 GATGTTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (19 bp):
TATTTTTAAAATAATTTTT
Found at i:42421848 original size:20 final size:19
Alignment explanation
Indices: 42421806--42421848 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
42421796 TTAAAATATT
* * *
42421806 TTTAAAATACTTTTTTATT
1 TTTAAAATAATTTTTGATG
42421825 TTTAAAATAAATTTTTGATG
1 TTTAAAAT-AATTTTTGATG
42421845 TTTA
1 TTTA
42421849 TTAAAAAATG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.35, C:0.02, G:0.05, T:0.58
Consensus pattern (19 bp):
TTTAAAATAATTTTTGATG
Found at i:42423969 original size:4 final size:4
Alignment explanation
Indices: 42423937--42423999 Score: 56
Period size: 4 Copynumber: 15.2 Consensus size: 4
42423927 ACGATGGATC
* * * *
42423937 ATAA AGTAA ATTA ATAA GATTA A-AA ATAA ATAA CTAA CAAAA ATAA ATAA
1 ATAA A-TAA ATAA ATAA -ATAA ATAA ATAA ATAA ATAA -ATAA ATAA ATAA
42423987 ATAA ATAA ATAA A
1 ATAA ATAA ATAA A
42424000 GACACATAAA
Statistics
Matches: 47, Mismatches: 8, Indels: 8
0.75 0.13 0.13
Matches are distributed among these distances:
3 2 0.04
4 36 0.77
5 9 0.19
ACGTcount: A:0.70, C:0.03, G:0.03, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:42423980 original size:17 final size:16
Alignment explanation
Indices: 42423958--42423999 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 16
42423948 TAATAAGATT
*
42423958 AAAAATAAATAACTAA
1 AAAAATAAATAAATAA
42423974 CAAAAATAAATAAATAA
1 -AAAAATAAATAAATAA
*
42423991 ATAAATAAA
1 AAAAATAAA
42424000 GACACATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 8 0.35
17 15 0.65
ACGTcount: A:0.76, C:0.05, G:0.00, T:0.19
Consensus pattern (16 bp):
AAAAATAAATAAATAA
Found at i:42427005 original size:8 final size:8
Alignment explanation
Indices: 42426989--42427054 Score: 51
Period size: 8 Copynumber: 7.4 Consensus size: 8
42426979 TTTTAATTTC
42426989 TTTTAAAT
1 TTTTAAAT
*
42426997 TTTTGAAT
1 TTTTAAAT
42427005 TTTCTATATAT
1 TTT-TA-A-AT
42427016 TTTTAAAT
1 TTTTAAAT
*
42427024 ATTTATAAT
1 TTTTA-AAT
42427033 TTTATAAAAT
1 TTT-T-AAAT
42427043 TTTTAATAT
1 TTTTAA-AT
42427052 TTT
1 TTT
42427055 GAGTTTTTAT
Statistics
Matches: 47, Mismatches: 4, Indels: 13
0.73 0.06 0.20
Matches are distributed among these distances:
8 18 0.38
9 13 0.28
10 10 0.21
11 6 0.13
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.62
Consensus pattern (8 bp):
TTTTAAAT
Found at i:42427017 original size:19 final size:18
Alignment explanation
Indices: 42426977--42427071 Score: 72
Period size: 19 Copynumber: 5.3 Consensus size: 18
42426967 ATTAGATACC
* *
42426977 ATTTTT-AATTTCTTTTAA
1 ATTTTTAAATTT-TTATAT
*
42426995 ATTTTTGAATTTTCTATAT
1 ATTTTTAAATTTT-TATAT
*
42427014 ATTTTTAAATATTTATA-
1 ATTTTTAAATTTTTATAT
42427031 ATTTTATAAAATTTTTA-AT
1 ATTTT-T-AAATTTTTATAT
* *
42427050 A-TTTTGAGTTTTTATAT
1 ATTTTTAAATTTTTATAT
42427067 ATTTT
1 ATTTT
42427072 CTTAAAATAT
Statistics
Matches: 63, Mismatches: 7, Indels: 14
0.75 0.08 0.17
Matches are distributed among these distances:
16 7 0.11
17 9 0.14
18 19 0.30
19 28 0.44
ACGTcount: A:0.32, C:0.02, G:0.03, T:0.63
Consensus pattern (18 bp):
ATTTTTAAATTTTTATAT
Found at i:42427027 original size:10 final size:9
Alignment explanation
Indices: 42426977--42427054 Score: 54
Period size: 9 Copynumber: 8.6 Consensus size: 9
42426967 ATTAGATACC
42426977 ATTTTTAAT
1 ATTTTTAAT
*
42426986 TTCTTTTAA-
1 AT-TTTTAAT
42426995 ATTTTTGAAT
1 ATTTTT-AAT
*
42427005 -TTTCTATAT
1 ATTTTTA-AT
42427014 ATTTTTAAAT
1 ATTTTT-AAT
*
42427024 ATTTATAAT
1 ATTTTTAAT
* *
42427033 -TTTATAAA
1 ATTTTTAAT
42427041 ATTTTTAAT
1 ATTTTTAAT
42427050 ATTTT
1 ATTTT
42427055 GAGTTTTTAT
Statistics
Matches: 54, Mismatches: 8, Indels: 14
0.71 0.11 0.18
Matches are distributed among these distances:
8 12 0.22
9 24 0.44
10 17 0.31
11 1 0.02
ACGTcount: A:0.33, C:0.03, G:0.01, T:0.63
Consensus pattern (9 bp):
ATTTTTAAT
Found at i:42427044 original size:17 final size:17
Alignment explanation
Indices: 42426990--42427054 Score: 53
Period size: 17 Copynumber: 3.7 Consensus size: 17
42426980 TTTAATTTCT
* *
42426990 TTTA-AATTTTTGAATT
1 TTTATAATTTTTAAATA
42427006 TTCTATATATTTTTAAATA
1 TT-TATA-ATTTTTAAATA
42427025 TTTATAATTTTATAAA-A
1 TTTATAATTTT-TAAATA
*
42427042 TTTTTAATATTTT
1 TTTATAAT-TTTT
42427055 GAGTTTTTAT
Statistics
Matches: 41, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
16 2 0.05
17 16 0.39
18 12 0.29
19 11 0.27
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.62
Consensus pattern (17 bp):
TTTATAATTTTTAAATA
Found at i:42427044 original size:27 final size:28
Alignment explanation
Indices: 42426989--42427071 Score: 86
Period size: 26 Copynumber: 3.1 Consensus size: 28
42426979 TTTTAATTTC
* *
42426989 TTTTAAAT-TTTTGAATTTTCTATATAT
1 TTTTAAATATTTTGAATTTTATATAAAT
42427016 TTTTAAATATTTAT-AATTTTATA-AAAT
1 TTTTAAATATTT-TGAATTTTATATAAAT
* *
42427043 TTTT-AATATTTTGAGTTTT-TATATAT
1 TTTTAAATATTTTGAATTTTATATAAAT
42427069 TTT
1 TTT
42427072 CTTAAAATAT
Statistics
Matches: 48, Mismatches: 4, Indels: 9
0.79 0.07 0.15
Matches are distributed among these distances:
25 3 0.06
26 18 0.38
27 15 0.31
28 11 0.23
29 1 0.02
ACGTcount: A:0.33, C:0.01, G:0.04, T:0.63
Consensus pattern (28 bp):
TTTTAAATATTTTGAATTTTATATAAAT
Found at i:42427134 original size:21 final size:21
Alignment explanation
Indices: 42427109--42427153 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
42427099 AATTTTGAAA
42427109 TTTTCTAAGATTT-TAAATAAG
1 TTTTC-AAGATTTATAAATAAG
**
42427130 TTTTCAATTTTTATAAATAAG
1 TTTTCAAGATTTATAAATAAG
42427151 TTT
1 TTT
42427154 GAAATTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.36, C:0.04, G:0.07, T:0.53
Consensus pattern (21 bp):
TTTTCAAGATTTATAAATAAG
Found at i:42427159 original size:21 final size:21
Alignment explanation
Indices: 42427122--42427162 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
42427112 TCTAAGATTT
**
42427122 TAAATAAGTTTTCAATTTTTA
1 TAAATAAGTTTGAAATTTTTA
42427143 TAAATAAGTTTGAAATTTTT
1 TAAATAAGTTTGAAATTTTT
42427163 TTATATTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.39, C:0.02, G:0.07, T:0.51
Consensus pattern (21 bp):
TAAATAAGTTTGAAATTTTTA
Found at i:42428042 original size:46 final size:46
Alignment explanation
Indices: 42427989--42428080 Score: 166
Period size: 46 Copynumber: 2.0 Consensus size: 46
42427979 ACCCTATTTT
*
42427989 AGGGTTATTAATTGAGTAGTTTACTCAAAATACTATTACCATCTTG
1 AGGGTTATTAATTGAGTAATTTACTCAAAATACTATTACCATCTTG
*
42428035 AGGGTTATTAATTGAGTAATTTACTCAAAATACTATTACTATCTTG
1 AGGGTTATTAATTGAGTAATTTACTCAAAATACTATTACCATCTTG
42428081 TTTTTGAAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.34, C:0.12, G:0.14, T:0.40
Consensus pattern (46 bp):
AGGGTTATTAATTGAGTAATTTACTCAAAATACTATTACCATCTTG
Found at i:42431048 original size:18 final size:17
Alignment explanation
Indices: 42431016--42431049 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
42431006 TTGTTATTAA
*
42431016 AATTTTATTTTTAATTG
1 AATTTTATATTTAATTG
42431033 AATTTTACTATTTAATT
1 AATTTTA-TATTTAATT
42431050 TTAATTTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (17 bp):
AATTTTATATTTAATTG
Found at i:42431722 original size:28 final size:27
Alignment explanation
Indices: 42431656--42431724 Score: 68
Period size: 28 Copynumber: 2.5 Consensus size: 27
42431646 TTTAGAATAA
42431656 AAAATTATAAAAATTATTAAAAATTTAT
1 AAAATTATAAAAATTATTAAAAA-TTAT
* * *
42431684 AAAACTCTAAAATATATTTTAAAAA-TAT
1 AAAATTATAAAA-AT-TATTAAAAATTAT
*
42431712 GAAATTATAAAAA
1 AAAATTATAAAAA
42431725 AAATGTTGAA
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
27 1 0.03
28 22 0.67
29 2 0.06
30 8 0.24
ACGTcount: A:0.61, C:0.03, G:0.01, T:0.35
Consensus pattern (27 bp):
AAAATTATAAAAATTATTAAAAATTAT
Found at i:42432183 original size:22 final size:22
Alignment explanation
Indices: 42432165--42432236 Score: 117
Period size: 22 Copynumber: 3.3 Consensus size: 22
42432155 GAACTAAACC
42432165 CTCATGGCTAACGTACTAAGCT
1 CTCATGGCTAACGTACTAAGCT
42432187 CTCATGGCTAACGTACTAAGCT
1 CTCATGGCTAACGTACTAAGCT
** *
42432209 CTCATGTTTCACGTACTAAGCT
1 CTCATGGCTAACGTACTAAGCT
42432231 CTCATG
1 CTCATG
42432237 TTCTTTCCCT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 47 1.00
ACGTcount: A:0.25, C:0.28, G:0.17, T:0.31
Consensus pattern (22 bp):
CTCATGGCTAACGTACTAAGCT
Done.