Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 ID=Chr02-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: 62769430
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1067035 characters in sequence are not A, C, G, or T
File 98 of 206
Found at i:28688043 original size:24 final size:25
Alignment explanation
Indices: 28688007--28688058 Score: 70
Period size: 24 Copynumber: 2.1 Consensus size: 25
28687997 ATTGTTTAAA
*
28688007 TTTATCATATATTATCATTTTAAGT
1 TTTATCATATATTATCATTCTAAGT
* *
28688032 TTTAT-ATGTATTATTATTCTAAGT
1 TTTATCATATATTATCATTCTAAGT
28688056 TTT
1 TTT
28688059 CATGTGTAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 19 0.79
25 5 0.21
ACGTcount: A:0.29, C:0.06, G:0.06, T:0.60
Consensus pattern (25 bp):
TTTATCATATATTATCATTCTAAGT
Found at i:28688122 original size:24 final size:23
Alignment explanation
Indices: 28688067--28688122 Score: 55
Period size: 23 Copynumber: 2.4 Consensus size: 23
28688057 TTCATGTGTA
*
28688067 ATTACTTT-TTTTAATTTATCGT
1 ATTATTTTATTTTAATTTATCGT
28688089 A-TATTATTATTTTAATTTCCATC-T
1 ATTATT-TTATTTTAATTT--ATCGT
28688113 ATTATTTTAT
1 ATTATTTTAT
28688123 ATAGTTTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
21 3 0.11
22 3 0.11
23 9 0.32
24 6 0.21
25 7 0.25
ACGTcount: A:0.27, C:0.09, G:0.02, T:0.62
Consensus pattern (23 bp):
ATTATTTTATTTTAATTTATCGT
Found at i:28692084 original size:2 final size:2
Alignment explanation
Indices: 28692077--28692139 Score: 74
Period size: 2 Copynumber: 31.5 Consensus size: 2
28692067 AAAATTCAGC
** *
28692077 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T CGG CT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
*
28692119 AA AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
28692140 GAATCTATGC
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
1 1 0.02
2 52 0.98
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:28694183 original size:50 final size:50
Alignment explanation
Indices: 28694104--28694275 Score: 247
Period size: 50 Copynumber: 3.4 Consensus size: 50
28694094 TATCCTAGAT
** * * *
28694104 ATGGTCTTACATGGGAGTTCTCGTATCGGTGTCC-ATGCCATGTCCCAAAC
1 ATGGTCTTACATGGGACCTCTCATCTCGGTG-CCAACGCCATGTCCCAAAC
** *
28694154 ATGGTCTTACGGGGGACCTCTCATCTCGGTGCCAACGCGATGTCCCAAAC
1 ATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAAAC
*
28694204 ATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGAC
1 ATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAAAC
28694254 ATGGTCTTACATGGGACCTCTC
1 ATGGTCTTACATGGGACCTCTC
28694276 GTAATCTCAA
Statistics
Matches: 109, Mismatches: 12, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
49 2 0.02
50 107 0.98
ACGTcount: A:0.20, C:0.30, G:0.24, T:0.26
Consensus pattern (50 bp):
ATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAAAC
Found at i:28700489 original size:14 final size:14
Alignment explanation
Indices: 28700470--28700498 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
28700460 TTTTTGACTT
28700470 TGTTATATAGATTA
1 TGTTATATAGATTA
28700484 TGTTATATAGATTA
1 TGTTATATAGATTA
28700498 T
1 T
28700499 TATTTATCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.52
Consensus pattern (14 bp):
TGTTATATAGATTA
Found at i:28701032 original size:2 final size:2
Alignment explanation
Indices: 28701025--28701063 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
28701015 AGTGTAATTT
28701025 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
28701064 TTTTATTTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:28703503 original size:31 final size:29
Alignment explanation
Indices: 28703468--28703564 Score: 94
Period size: 31 Copynumber: 3.3 Consensus size: 29
28703458 ATATTTAATG
28703468 TATTATTATGTTAAATTATTTAAATATTATT
1 TATTATTATGTTAAATT-TTTAAA-ATTATT
* *
28703499 TATTATTATATTTAATTTTTAAAATTATT
1 TATTATTATGTTAAATTTTTAAAATTATT
*
28703528 TCATGTA-TA-GTTAAA--TTTAAAATAATT
1 T-AT-TATTATGTTAAATTTTTAAAATTATT
28703555 TATTAATTAT
1 TATT-ATTAT
28703565 TAAAAAGTAT
Statistics
Matches: 56, Mismatches: 5, Indels: 13
0.76 0.07 0.18
Matches are distributed among these distances:
25 1 0.02
26 3 0.05
27 14 0.25
29 11 0.20
30 10 0.18
31 17 0.30
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.56
Consensus pattern (29 bp):
TATTATTATGTTAAATTTTTAAAATTATT
Found at i:28712454 original size:31 final size:28
Alignment explanation
Indices: 28712379--28712459 Score: 83
Period size: 30 Copynumber: 2.7 Consensus size: 28
28712369 TTTAAATCAC
*
28712379 AAAATAGTATCTAAATTATATAATTTTTT
1 AAAATGGTATCTAAATTATAT-ATTTTTT
*
28712408 AAAATTGATATCTAAATTATAT-TTTGTTACCT
1 AAAA-TGGTATCTAAATTATATATTT-TT---T
28712440 AAAATGGTATCTAAATTATA
1 AAAATGGTATCTAAATTATA
28712460 CTTAGTTATT
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
28 3 0.07
29 6 0.14
30 15 0.34
31 15 0.34
32 5 0.11
ACGTcount: A:0.43, C:0.06, G:0.06, T:0.44
Consensus pattern (28 bp):
AAAATGGTATCTAAATTATATATTTTTT
Found at i:28713056 original size:5 final size:5
Alignment explanation
Indices: 28713021--28713090 Score: 56
Period size: 5 Copynumber: 14.0 Consensus size: 5
28713011 AATGAAAAGT
* * * *
28713021 TTTAA TATAA TTAAA TTTGA TTT-T TTATAA TTTAA TTTAA TTTAA TTCT--
1 TTTAA TTTAA TTTAA TTTAA TTTAA TT-TAA TTTAA TTTAA TTTAA TT-TAA
28713070 TTTAA TTTAA TTTTAA TTTAA
1 TTTAA TTTAA -TTTAA TTTAA
28713091 AAGTACCATG
Statistics
Matches: 52, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
3 1 0.02
4 4 0.08
5 39 0.75
6 8 0.15
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.60
Consensus pattern (5 bp):
TTTAA
Found at i:28713057 original size:25 final size:24
Alignment explanation
Indices: 28713020--28713090 Score: 79
Period size: 25 Copynumber: 2.9 Consensus size: 24
28713010 AAATGAAAAG
* * *
28713020 TTTTAATATAATTAAATTTGATTT
1 TTTTAATTTAATTAAATTTAATTC
*
28713044 TTTATAATTTAATTTAATTTAATTC
1 TTT-TAATTTAATTAAATTTAATTC
*
28713069 TTTTAATTTAATTTTAATTTAA
1 TTTTAATTTAA-TTAAATTTAA
28713091 AAGTACCATG
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
24 11 0.27
25 30 0.73
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.61
Consensus pattern (24 bp):
TTTTAATTTAATTAAATTTAATTC
Found at i:28713183 original size:31 final size:31
Alignment explanation
Indices: 28713148--28713210 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
28713138 GCTGAGGTAA
*
28713148 TTTGGGTAATAGAGTATAATTTAGGTACCAC
1 TTTGGGTAATAGAATATAATTTAGGTACCAC
* *
28713179 TTTGGGTAATATAATATAGTTTAGGTACCAC
1 TTTGGGTAATAGAATATAATTTAGGTACCAC
28713210 T
1 T
28713211 AGTAACTAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.32, C:0.10, G:0.21, T:0.38
Consensus pattern (31 bp):
TTTGGGTAATAGAATATAATTTAGGTACCAC
Found at i:28713309 original size:22 final size:20
Alignment explanation
Indices: 28713266--28713305 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
28713256 ATAACTTAGG
28713266 GTACCACTTGTGATAAAAAA
1 GTACCACTTGTGATAAAAAA
28713286 GTACCACTTGTGATAAAAAA
1 GTACCACTTGTGATAAAAAA
28713306 AAGTTTAGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.45, C:0.15, G:0.15, T:0.25
Consensus pattern (20 bp):
GTACCACTTGTGATAAAAAA
Found at i:28719090 original size:29 final size:29
Alignment explanation
Indices: 28718953--28719290 Score: 224
Period size: 29 Copynumber: 11.8 Consensus size: 29
28718943 TAAAGTGAGA
* * *
28718953 CTTTGTAGTTATCTCTGTTAAAAGTAAGT
1 CTTTGTGGCTATCTCTGTTAAAAGGAAGT
** *
28718982 CTTTGTGGCTATCTCTACTAAAATGAAGT
1 CTTTGTGGCTATCTCTGTTAAAAGGAAGT
* * * **
28719011 CTTTATGGCTATATATACTAAAAGGAAGT
1 CTTTGTGGCTATCTCTGTTAAAAGGAAGT
*
28719040 CTTTGTGGCTATCTCTGCTAAAAGGAAGT
1 CTTTGTGGCTATCTCTGTTAAAAGGAAGT
* * *
28719069 CTTTGTGGCGATCTTTGTT-AAA-GAAAT
1 CTTTGTGGCTATCTCTGTTAAAAGGAAGT
* * * * * * *
28719096 CCCTTGTTGTTATCCCTATTAAAAGAAATT
1 -CTTTGTGGCTATCTCTGTTAAAAGGAAGT
* * *
28719126 CTTTTGTGGCAATCTTTGTT-AAAGGAAGC
1 C-TTTGTGGCTATCTCTGTTAAAAGGAAGT
* **
28719155 CTTTGTGGCTATCCCTAATAAAAGGAA-T
1 CTTTGTGGCTATCTCTGTTAAAAGGAAGT
* * * * *
28719183 CCTTTGTAGCGATCTCTATT-AAAGGATGC
1 -CTTTGTGGCTATCTCTGTTAAAAGGAAGT
* *
28719212 CTTCGTGGCTATCTCTGTTAAAAGGAAGC
1 CTTTGTGGCTATCTCTGTTAAAAGGAAGT
* *
28719241 CTTCT-TGGCAATCTCTGTT-AAAGGATG-
1 CTT-TGTGGCTATCTCTGTTAAAAGGAAGT
* *
28719268 CATTTGTGGTTATCTCAGTTAAA
1 C-TTTGTGGCTATCTCTGTTAAA
28719291 TGAATGCCTT
Statistics
Matches: 237, Mismatches: 60, Indels: 24
0.74 0.19 0.07
Matches are distributed among these distances:
27 6 0.03
28 69 0.29
29 148 0.62
30 14 0.06
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.37
Consensus pattern (29 bp):
CTTTGTGGCTATCTCTGTTAAAAGGAAGT
Found at i:28719177 original size:115 final size:114
Alignment explanation
Indices: 28719031--28719281 Score: 272
Period size: 115 Copynumber: 2.2 Consensus size: 114
28719021 ATATATACTA
* * ** * * *
28719031 AAAGGAAGTCTTTGTGGCTATCTCTGCTAAAAGGAAGT-CTTTGTGGCGATCTTTGTTAAAGAAA
1 AAAGGAAGCCTTTGTGGCTATCCCTAATAAAAGGAA-TCCTTTGTAGCGATCTCTATTAAAG-AA
* * ** * *
28719095 TCCCTT-GTTGTTATCCCTATTAAAAGAAATTCTTTTGTGGCAATCTTTGTT
64 TCCCTTCGTGGCTATCCCTATTAAAAGAAAGCCTTCT-TGGCAATCTCTGTT
* *
28719146 AAAGGAAGCCTTTGTGGCTATCCCTAATAAAAGGAATCCTTTGTAGCGATCTCTATTAAAGGATG
1 AAAGGAAGCCTTTGTGGCTATCCCTAATAAAAGGAATCCTTTGTAGCGATCTCTATTAAAGAATC
* * *
28719211 CCTTCGTGGCTATCTCTGTTAAAAGGAAGCCTTCTTGGCAATCTCTGTT
66 CCTTCGTGGCTATCCCTATTAAAAGAAAGCCTTCTTGGCAATCTCTGTT
* * *
28719260 AAAGGATGCATTTGTGGTTATC
1 AAAGGAAGCCTTTGTGGCTATC
28719282 TCAGTTAAAT
Statistics
Matches: 113, Mismatches: 21, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
114 39 0.35
115 74 0.65
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.36
Consensus pattern (114 bp):
AAAGGAAGCCTTTGTGGCTATCCCTAATAAAAGGAATCCTTTGTAGCGATCTCTATTAAAGAATC
CCTTCGTGGCTATCCCTATTAAAAGAAAGCCTTCTTGGCAATCTCTGTT
Found at i:28719255 original size:57 final size:57
Alignment explanation
Indices: 28718963--28719290 Score: 228
Period size: 57 Copynumber: 5.7 Consensus size: 57
28718953 CTTTGTAGTT
* * * ** * * * *
28718963 ATCTCTGTTAAAAGTAAGTCTTTGTGGCTATCTCTACTAAAATGAAGTCTTTATGGCT
1 ATCTCTGTT-AAAGGATGCCTTTGTGGCTATCTCTGTTAAAAGGAAGCCTTTGTGGCA
* * * * * * * * *
28719021 ATATATACTAAAAGGAAGTCTTTGTGGCTATCTCTGCTAAAAGGAAGTCTTTGTGGCG
1 ATCTCT-GTTAAAGGATGCCTTTGTGGCTATCTCTGTTAAAAGGAAGCCTTTGTGGCA
* * * * * * * * * *
28719079 ATCTTTGTTAAAGAAAT-CCCTTGTTGTTATCCCTATTAAAAGAAATTCTTTTGTGGCA
1 ATCTCTGTTAAAG-GATGCCTTTGTGGCTATCTCTGTTAAAAGGAA-GCCTTTGTGGCA
* * * ** * * *
28719137 ATCTTTGTTAAAGGAAGCCTTTGTGGCTATCCCTAATAAAAGGAATCCTTTGTAGCG
1 ATCTCTGTTAAAGGATGCCTTTGTGGCTATCTCTGTTAAAAGGAAGCCTTTGTGGCA
* *
28719194 ATCTCTATTAAAGGATGCCTTCGTGGCTATCTCTGTTAAAAGGAAGCCTTCT-TGGCA
1 ATCTCTGTTAAAGGATGCCTTTGTGGCTATCTCTGTTAAAAGGAAGCCTT-TGTGGCA
* * *
28719251 ATCTCTGTTAAAGGATGCATTTGTGGTTATCTCAGTTAAA
1 ATCTCTGTTAAAGGATGCCTTTGTGGCTATCTCTGTTAAA
28719291 TGAATGCCTT
Statistics
Matches: 213, Mismatches: 52, Indels: 11
0.77 0.19 0.04
Matches are distributed among these distances:
57 115 0.54
58 97 0.46
59 1 0.00
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.37
Consensus pattern (57 bp):
ATCTCTGTTAAAGGATGCCTTTGTGGCTATCTCTGTTAAAAGGAAGCCTTTGTGGCA
Found at i:28732424 original size:16 final size:17
Alignment explanation
Indices: 28732395--28732427 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
28732385 GACACATCAA
*
28732395 CAAATAATTTAAAAATT
1 CAAATAATTCAAAAATT
28732412 CAAA-AATTCAAAAATT
1 CAAATAATTCAAAAATT
28732428 TTATAAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.61, C:0.09, G:0.00, T:0.30
Consensus pattern (17 bp):
CAAATAATTCAAAAATT
Found at i:28734208 original size:21 final size:22
Alignment explanation
Indices: 28734184--28734230 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
28734174 TACAGGGAGG
*
28734184 AAAAAGCTAACTATAGGGA-TA
1 AAAAAGATAACTATAGGGACTA
* *
28734205 AAAAATATAATTATAGGGACTA
1 AAAAAGATAACTATAGGGACTA
28734227 AAAA
1 AAAA
28734231 TTCATATTAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 16 0.73
22 6 0.27
ACGTcount: A:0.57, C:0.06, G:0.15, T:0.21
Consensus pattern (22 bp):
AAAAAGATAACTATAGGGACTA
Found at i:28734412 original size:56 final size:53
Alignment explanation
Indices: 28734348--28734493 Score: 185
Period size: 48 Copynumber: 2.8 Consensus size: 53
28734338 AGTTACGTAT
28734348 GAATCAAATTACTAAAAGATAATATCCCATAATAATATCCTATAATATCCTATTAA
1 GAATCAAATTACTAAAAGATAATATCCCATAATAATATCC--T-ATATCCTATTAA
* *
28734404 GAATCAAATTACTAAGAGATAATAT-CC-T-ATAATATCC--TATCCTATTAT
1 GAATCAAATTACTAAAAGATAATATCCCATAATAATATCCTATATCCTATTAA
* * *
28734452 GAATCAATTTGCTAAAAGATAATATCCTATAATAATATCCTA
1 GAATCAAATTACTAAAAGATAATATCCCATAATAATATCCTA
28734494 ACACCCCCTC
Statistics
Matches: 79, Mismatches: 6, Indels: 13
0.81 0.06 0.13
Matches are distributed among these distances:
48 32 0.41
49 1 0.01
50 1 0.01
51 9 0.11
53 9 0.11
54 1 0.01
55 2 0.03
56 24 0.30
ACGTcount: A:0.45, C:0.16, G:0.05, T:0.34
Consensus pattern (53 bp):
GAATCAAATTACTAAAAGATAATATCCCATAATAATATCCTATATCCTATTAA
Found at i:28738307 original size:18 final size:18
Alignment explanation
Indices: 28738286--28738324 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
28738276 ATGAAGTCGG
28738286 TCATGCTCATGACATTGT
1 TCATGCTCATGACATTGT
28738304 TCATGCTCATGACATTGT
1 TCATGCTCATGACATTGT
28738322 TCA
1 TCA
28738325 AGCATCTTCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.23, C:0.23, G:0.15, T:0.38
Consensus pattern (18 bp):
TCATGCTCATGACATTGT
Found at i:28739095 original size:43 final size:43
Alignment explanation
Indices: 28739033--28739136 Score: 172
Period size: 43 Copynumber: 2.4 Consensus size: 43
28739023 ATATTCCATA
* *
28739033 ATAATATCTTATAATATCCTATTAGGAATCAATTTGCTAAGAG
1 ATAATATCCTATAATATCCTATTAGGAATCAATTTGCTAAAAG
*
28739076 TTAATATCCTATAATATCCTATTAGGAATCAATTTGCTAAAAG
1 ATAATATCCTATAATATCCTATTAGGAATCAATTTGCTAAAAG
*
28739119 ATAATATCCCATAATATC
1 ATAATATCCTATAATATC
28739137 TTAACATGGG
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 56 1.00
ACGTcount: A:0.40, C:0.14, G:0.09, T:0.37
Consensus pattern (43 bp):
ATAATATCCTATAATATCCTATTAGGAATCAATTTGCTAAAAG
Found at i:28739348 original size:7 final size:7
Alignment explanation
Indices: 28739338--28739366 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
28739328 TTTTAGATTT
28739338 ACTTTGG
1 ACTTTGG
28739345 ACTTTGG
1 ACTTTGG
28739352 ACTTTGG
1 ACTTTGG
28739359 ACTTTGG
1 ACTTTGG
28739366 A
1 A
28739367 GATGAAAGGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.17, C:0.14, G:0.28, T:0.41
Consensus pattern (7 bp):
ACTTTGG
Found at i:28746277 original size:14 final size:15
Alignment explanation
Indices: 28746258--28746298 Score: 57
Period size: 14 Copynumber: 2.7 Consensus size: 15
28746248 AAGTTTTATT
28746258 TTTATTTTTATTTA-
1 TTTATTTTTATTTAG
*
28746272 TTTATTTTTACTTAG
1 TTTATTTTTATTTAG
28746287 TTTAATTTTTAT
1 TTT-ATTTTTAT
28746299 GTAAATATTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
14 13 0.57
15 3 0.13
16 7 0.30
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.73
Consensus pattern (15 bp):
TTTATTTTTATTTAG
Found at i:28748535 original size:14 final size:14
Alignment explanation
Indices: 28748516--28748554 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
28748506 TGATTGCCAA
28748516 TAAAATGTTTTCTG
1 TAAAATGTTTTCTG
*
28748530 TAAAATGATTTCTG
1 TAAAATGTTTTCTG
*
28748544 GAAAATGTTTT
1 TAAAATGTTTT
28748555 ACTTTTTTGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.05, G:0.15, T:0.46
Consensus pattern (14 bp):
TAAAATGTTTTCTG
Found at i:28748594 original size:14 final size:15
Alignment explanation
Indices: 28748557--28748596 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
28748547 AATGTTTTAC
28748557 TTTTTTGTAAAATAA
1 TTTTTTGTAAAATAA
**
28748572 TTTACTGTAAAAT-A
1 TTTTTTGTAAAATAA
28748586 TTTTTTGTAAA
1 TTTTTTGTAAA
28748597 TTTCCAGCGT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
14 10 0.48
15 11 0.52
ACGTcount: A:0.38, C:0.03, G:0.07, T:0.53
Consensus pattern (15 bp):
TTTTTTGTAAAATAA
Found at i:28749997 original size:21 final size:21
Alignment explanation
Indices: 28749968--28750008 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
28749958 AGGATTGTTA
*
28749968 TGTGTTGCTGTTACGAGCATC
1 TGTGCTGCTGTTACGAGCATC
28749989 TGTGCTGCTGTTACGAGCAT
1 TGTGCTGCTGTTACGAGCAT
28750009 TTTTTGTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.15, C:0.20, G:0.29, T:0.37
Consensus pattern (21 bp):
TGTGCTGCTGTTACGAGCATC
Found at i:28751418 original size:20 final size:21
Alignment explanation
Indices: 28751367--28751424 Score: 63
Period size: 18 Copynumber: 3.0 Consensus size: 21
28751357 AAATCATTGC
28751367 AATATATGTAAAAA-TAATTT
1 AATATATGTAAAAATTAATTT
* *
28751387 AA-A-ATATAAAAATTTA-TT
1 AATATATGTAAAAATTAATTT
28751405 AATATATGTAAAAA-TAATTT
1 AATATATGTAAAAATTAATTT
28751425 TTTTCGGAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
18 12 0.40
19 6 0.20
20 12 0.40
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (21 bp):
AATATATGTAAAAATTAATTT
Found at i:28751515 original size:14 final size:15
Alignment explanation
Indices: 28751493--28751569 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
28751483 CAATCAAATA
28751493 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
28751507 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
28751522 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
28751542 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
**
28751556 ATAGAAAA-CATTTT
1 CCAGAAAATCATTTT
28751570 ACTAGCAATC
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 22 0.44
15 14 0.28
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.18
ACGTcount: A:0.44, C:0.14, G:0.08, T:0.34
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:28751534 original size:20 final size:20
Alignment explanation
Indices: 28751509--28751548 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
28751499 AATATTTTCC
*
28751509 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
28751529 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
28751549 TCATTTTATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:28751554 original size:34 final size:35
Alignment explanation
Indices: 28751497--28751563 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
28751487 CAAATACCAG
*
28751497 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
28751532 AAAACATTTTCCAG-AAATCATTTTATAGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
28751564 CATTTTACTA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.48, C:0.12, G:0.07, T:0.33
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:28751570 original size:14 final size:14
Alignment explanation
Indices: 28751532--28751571 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
28751522 ACAGAAAAGT
*
28751532 AAAACATTTTCCAG
1 AAAACATTTTACAG
* *
28751546 AAATCATTTTATAG
1 AAAACATTTTACAG
28751560 AAAACATTTTAC
1 AAAACATTTTAC
28751572 TAGCAATCAA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.45, C:0.15, G:0.05, T:0.35
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:28753735 original size:49 final size:48
Alignment explanation
Indices: 28753639--28753735 Score: 149
Period size: 48 Copynumber: 2.0 Consensus size: 48
28753629 TTTCTTTGCT
* *
28753639 TAAAAACACCTAAGTCAGCCTAACTTGCAATGATAACGAATTCAACAG
1 TAAAAACACCTAAGTCAGCCTAACTCGCAATGATAAAGAATTCAACAG
* *
28753687 TAAAAACACCTAAGTCAGCTTAATCTCGCAATGATAAAGGATTCAACAG
1 TAAAAACACCTAAGTCAGCCTAA-CTCGCAATGATAAAGAATTCAACAG
28753736 AATTCCATCA
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
48 22 0.50
49 22 0.50
ACGTcount: A:0.43, C:0.22, G:0.13, T:0.22
Consensus pattern (48 bp):
TAAAAACACCTAAGTCAGCCTAACTCGCAATGATAAAGAATTCAACAG
Found at i:28753988 original size:36 final size:36
Alignment explanation
Indices: 28753929--28753999 Score: 108
Period size: 36 Copynumber: 2.0 Consensus size: 36
28753919 ATCAAGGGCT
28753929 ACAATTAAAAGCTGCATACAATTAGAACTCTAAGAC
1 ACAATTAAAAGCTGCATACAATTAGAACTCTAAGAC
* *
28753965 ACAATTAGAAA-CTGTATATAATTAGAACTCTAAGA
1 ACAATTA-AAAGCTGCATACAATTAGAACTCTAAGA
28754000 TTTTATAATC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
36 29 0.91
37 3 0.09
ACGTcount: A:0.48, C:0.15, G:0.11, T:0.25
Consensus pattern (36 bp):
ACAATTAAAAGCTGCATACAATTAGAACTCTAAGAC
Found at i:28757935 original size:36 final size:36
Alignment explanation
Indices: 28757895--28757968 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
28757885 GCTTTGGAGA
28757895 AAAGTTTGAGTGAACACTCTCAAAATTCTTATTAAC
1 AAAGTTTGAGTGAACACTCTCAAAATTCTTATTAAC
28757931 AAAGTTTGAGTGAACACTCTCAAAATTCTTATTAAC
1 AAAGTTTGAGTGAACACTCTCAAAATTCTTATTAAC
28757967 AA
1 AA
28757969 CTGAATGCCT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.41, C:0.16, G:0.11, T:0.32
Consensus pattern (36 bp):
AAAGTTTGAGTGAACACTCTCAAAATTCTTATTAAC
Found at i:28758075 original size:36 final size:36
Alignment explanation
Indices: 28758035--28758105 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 36
28758025 ATCAAGGGCT
*
28758035 ACAATTAAAAGTTGTATACAATTAGAACTCTAAGAC
1 ACAATTAAAAGCTGTATACAATTAGAACTCTAAGAC
*
28758071 ACAATTAGAAGCTGTATACAATTAGAACTCTAAGA
1 ACAATTAAAAGCTGTATACAATTAGAACTCTAAGA
28758106 TTTTATAATC
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:0.46, C:0.14, G:0.13, T:0.27
Consensus pattern (36 bp):
ACAATTAAAAGCTGTATACAATTAGAACTCTAAGAC
Found at i:28758076 original size:19 final size:19
Alignment explanation
Indices: 28758052--28758105 Score: 60
Period size: 17 Copynumber: 2.9 Consensus size: 19
28758042 AAAGTTGTAT
28758052 ACAATTAGAACTCTAAGAC
1 ACAATTAGAACTCTAAGAC
* *
28758071 ACAATTAGAA-GCT--GTAT
1 ACAATTAGAACTCTAAG-AC
28758088 ACAATTAGAACTCTAAGA
1 ACAATTAGAACTCTAAGA
28758106 TTTTATAATC
Statistics
Matches: 28, Mismatches: 3, Indels: 8
0.72 0.08 0.21
Matches are distributed among these distances:
16 1 0.04
17 11 0.39
18 4 0.14
19 11 0.39
20 1 0.04
ACGTcount: A:0.46, C:0.17, G:0.13, T:0.24
Consensus pattern (19 bp):
ACAATTAGAACTCTAAGAC
Found at i:28758093 original size:17 final size:17
Alignment explanation
Indices: 28758034--28758097 Score: 58
Period size: 17 Copynumber: 3.6 Consensus size: 17
28758024 CATCAAGGGC
* *
28758034 TACAATTAAAAGTTGTA
1 TACAATTAGAAGCTGTA
*
28758051 TACAATTAGAA-CTCTAAGA
1 TACAATTAGAAGCTGT---A
*
28758070 CACAATTAGAAGCTGTA
1 TACAATTAGAAGCTGTA
28758087 TACAATTAGAA
1 TACAATTAGAA
28758098 CTCTAAGATT
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
16 2 0.05
17 21 0.57
19 11 0.30
20 3 0.08
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.28
Consensus pattern (17 bp):
TACAATTAGAAGCTGTA
Found at i:28763016 original size:18 final size:20
Alignment explanation
Indices: 28762995--28763031 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
28762985 ATTTTAATAT
28762995 TTTAAAAA-T-AATTATTAA
1 TTTAAAAATTAAATTATTAA
28763013 TTTAAAAATTAAATTATTA
1 TTTAAAAATTAAATTATTA
28763032 GTATCACTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.47
19 1 0.06
20 8 0.47
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
TTTAAAAATTAAATTATTAA
Found at i:28764235 original size:58 final size:59
Alignment explanation
Indices: 28764161--28764332 Score: 195
Period size: 58 Copynumber: 2.9 Consensus size: 59
28764151 TTGTTATTAA
* * * *
28764161 ATTTTAACATGATTATTATTAAATATAATTTAATAAAAATAATAATA-AATTTAATCAT
1 ATTTTAATATAATTATTATTAAATATAATTTAATAAAAATAATAATATAATTTAATAAC
* * * *
28764219 ATTTTAATATAATTATTATCAAAAACAATTTAATAAAAATGATAATATATAATTTAATAAC
1 ATTTTAATATAATTATTATTAAATATAATTTAATAAAAATAAT-A-ATATAATTTAATAAC
* *
28764280 ATTCTTAATATAATTATTATTAAAATATGAA-TTAATAAAAATCATAACATAAT
1 ATT-TTAATATAATTATTATT-AAATAT-AATTTAATAAAAATAATAATATAAT
28764333 CTCATGGGAT
Statistics
Matches: 95, Mismatches: 13, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
58 37 0.39
59 1 0.01
60 3 0.03
61 18 0.19
62 17 0.18
63 17 0.18
64 2 0.02
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.41
Consensus pattern (59 bp):
ATTTTAATATAATTATTATTAAATATAATTTAATAAAAATAATAATATAATTTAATAAC
Found at i:28767116 original size:143 final size:147
Alignment explanation
Indices: 28766931--28767200 Score: 311
Period size: 147 Copynumber: 1.9 Consensus size: 147
28766921 TCGTTTTGCC
* * * *** *
28766931 AATGGTATTAGTGGCGTTTTTTTGGAAATGCCACAAGCTTGAGTTAAATG-T-C-G-TTTGACTT
1 AATGGTATTAGTGGCGTTTTTTTGAAAACGCCACAAGCTTGAGGTAAATGTTGCTGAAGCGACTG
* * * *
28766992 CG-TTTGATCTTATATTTAGTGGCGCTT-CACTTAAAACGCCGCAACATTGTTCTAACATTTATA
66 CGTTTTGAT-TTATAGTTAGTGGCGCTTGAAC-TAAAACGCCGCAAAAATGTTCTAACATTTATA
28767055 GAAACACTGCCGTTTTTTA
129 GAAACACTGCCGTTTTTTA
* ** * *
28767074 AATGTTATTAGTGGCGATTTTTTT-AAAACGCCACGGGTTTGAGGTAAGTGTTGCTGAAGCGACT
1 AATGGTATTAGTGGCG-TTTTTTTGAAAACGCCACAAGCTTGAGGTAAATGTTGCTGAAGCGACT
*
28767138 GCGTTTTGATTTATAGTTAGTGGCGCTTGAACTAAAACGCCGCAAAAATGTTTTAACATTTAT
65 GCGTTTTGATTTATAGTTAGTGGCGCTTGAACTAAAACGCCGCAAAAATGTTCTAACATTTAT
28767201 CTATACGAGG
Statistics
Matches: 103, Mismatches: 17, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
143 34 0.33
144 8 0.08
145 1 0.01
146 1 0.01
147 51 0.50
148 8 0.08
ACGTcount: A:0.27, C:0.15, G:0.21, T:0.37
Consensus pattern (147 bp):
AATGGTATTAGTGGCGTTTTTTTGAAAACGCCACAAGCTTGAGGTAAATGTTGCTGAAGCGACTG
CGTTTTGATTTATAGTTAGTGGCGCTTGAACTAAAACGCCGCAAAAATGTTCTAACATTTATAGA
AACACTGCCGTTTTTTA
Found at i:28767214 original size:147 final size:146
Alignment explanation
Indices: 28766994--28767329 Score: 331
Period size: 146 Copynumber: 2.3 Consensus size: 146
28766984 TTTGACTTCG
* * * *
28766994 TTTGATCTTATATTTAGTGGCGCTTCACTTAAAACGCCGCAACATTGTTCTAACATTTATAGAAA
1 TTTGAT-TTATAGTTAGTGGCGCTTAACTTAAAACGCCGCAAAAATGTTCTAACATTTATAGAAA
* * * ** * * *
28767059 CACTGCCGTTTT-TTAAATGTTATTAGTGGCGATTT-TTTTAAAACGCCACGGGTTTGAGGTAAG
65 CACGGCCGTTTTGCT--ATATTATTAGTGGCG-TTTATTCAAAAACGCCACAGGTGTGAGCTAAG
* *
28767122 TGTTGCTGAAGCGACTGCGT
127 TGTTGATGAAACGACTGCGT
* ** *
28767142 TTTGATTTATAGTTAGTGGCGCTTGAAC-TAAAACGCCGCAAAAATGTTTTAACATTTATCTATA
1 TTTGATTTATAGTTAGTGGCGCTT-AACTTAAAACGCCGCAAAAATGTTCTAACATTTATAGAAA
* * **
28767206 CGA-GGCCGTTTTGCTGTATTATTAGTGGCGTTTATTCAAAAACGCCACAGGTGTGCGCTATTTG
65 C-ACGGCCGTTTTGCTATATTATTAGTGGCGTTTATTCAAAAACGCCACAGGTGTGAGCTAAGTG
28767270 TTGATGAAACGACTGCGT
129 TTGATGAAACGACTGCGT
* * * * *
28767288 TTCGACTTATAGTTAGTGGTGCTT-ATTTATAAACACCGCAAA
1 TTTGATTTATAGTTAGTGGCGCTTAACTTA-AAACGCCGCAAA
28767330 TGGTTAATTT
Statistics
Matches: 155, Mismatches: 27, Indels: 14
0.79 0.14 0.07
Matches are distributed among these distances:
144 1 0.01
145 5 0.03
146 83 0.54
147 56 0.36
148 10 0.06
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.36
Consensus pattern (146 bp):
TTTGATTTATAGTTAGTGGCGCTTAACTTAAAACGCCGCAAAAATGTTCTAACATTTATAGAAAC
ACGGCCGTTTTGCTATATTATTAGTGGCGTTTATTCAAAAACGCCACAGGTGTGAGCTAAGTGTT
GATGAAACGACTGCGT
Found at i:28769090 original size:16 final size:16
Alignment explanation
Indices: 28769064--28769114 Score: 77
Period size: 16 Copynumber: 3.1 Consensus size: 16
28769054 TTGGATGTGC
28769064 TTTAGCTTATGTTTCAT
1 TTTA-CTTATGTTTCAT
28769081 TTTACTTATGTTTCAT
1 TTTACTTATGTTTCAT
28769097 TTTACTTAT-TTTACAT
1 TTTACTTATGTTT-CAT
28769113 TT
1 TT
28769115 NNNNNNNNNN
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
15 3 0.09
16 26 0.79
17 4 0.12
ACGTcount: A:0.20, C:0.12, G:0.06, T:0.63
Consensus pattern (16 bp):
TTTACTTATGTTTCAT
Found at i:28769849 original size:13 final size:13
Alignment explanation
Indices: 28769821--28769872 Score: 61
Period size: 13 Copynumber: 4.0 Consensus size: 13
28769811 ACTTATTACT
28769821 AATATATATA-TTA
1 AATATAT-TACTTA
*
28769834 AATTTATTACTTA
1 AATATATTACTTA
*
28769847 AATATGTTACTTA
1 AATATATTACTTA
*
28769860 AATACATTACTTA
1 AATATATTACTTA
28769873 CTAAAATTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
12 2 0.06
13 31 0.94
ACGTcount: A:0.44, C:0.08, G:0.02, T:0.46
Consensus pattern (13 bp):
AATATATTACTTA
Found at i:28769932 original size:63 final size:63
Alignment explanation
Indices: 28769844--28770156 Score: 554
Period size: 63 Copynumber: 5.0 Consensus size: 63
28769834 AATTTATTAC
*
28769844 TTAAATATGTTACTTAAATACATTACTTACTAAAATTTAAGTAAGTTTACTTATATGTAAAAT
1 TTAAGTATGTTACTTAAATACATTACTTACTAAAATTTAAGTAAGTTTACTTATATGTAAAAT
* *** **
28769907 TTAAGTATGTTGCGGGAATACATTACTTACTAAAATTTAAGTAAGTTTACTTATATGTAACTT
1 TTAAGTATGTTACTTAAATACATTACTTACTAAAATTTAAGTAAGTTTACTTATATGTAAAAT
*
28769970 TTAAGTATGTTACTTAAATACATTACTTACTAAAATTTAAGCAAGTTTACTTATATGTAAAAT
1 TTAAGTATGTTACTTAAATACATTACTTACTAAAATTTAAGTAAGTTTACTTATATGTAAAAT
28770033 TTAAGTATGTTACTTAAATACATTACTTACTAAAATTTAAGTAAGTTTACTTATATGTAAAAT
1 TTAAGTATGTTACTTAAATACATTACTTACTAAAATTTAAGTAAGTTTACTTATATGTAAAAT
28770096 TTAAGTATGTTACTTAAATACATTACTTACTAAAATTTAAGTAAGTTTACTTATATGTAAA
1 TTAAGTATGTTACTTAAATACATTACTTACTAAAATTTAAGTAAGTTTACTTATATGTAAA
28770157 CTTACATAAT
Statistics
Matches: 235, Mismatches: 15, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
63 235 1.00
ACGTcount: A:0.40, C:0.09, G:0.09, T:0.42
Consensus pattern (63 bp):
TTAAGTATGTTACTTAAATACATTACTTACTAAAATTTAAGTAAGTTTACTTATATGTAAAAT
Found at i:28770069 original size:36 final size:36
Alignment explanation
Indices: 28770027--28770148 Score: 129
Period size: 36 Copynumber: 3.6 Consensus size: 36
28770017 TACTTATATG
28770027 TAAAATTTAAGTATGTTACTTAAATACATTACTTAC
1 TAAAATTTAAGTATGTTACTTAAATACATTACTTAC
* *
28770063 TAAAATTTAAGTA----AGTT---TAC-TTA--TATG
1 TAAAATTTAAGTATGTTACTTAAATACATTACTTA-C
28770090 TAAAATTTAAGTATGTTACTTAAATACATTACTTAC
1 TAAAATTTAAGTATGTTACTTAAATACATTACTTAC
*
28770126 TAAAATTTAAGTAAGTTTACTTA
1 TAAAATTTAAGTATG-TTACTTA
28770149 TATGTAAACT
Statistics
Matches: 69, Mismatches: 5, Indels: 23
0.71 0.05 0.24
Matches are distributed among these distances:
26 2 0.03
27 13 0.19
28 3 0.04
29 3 0.04
31 3 0.04
32 3 0.04
34 3 0.04
35 3 0.04
36 27 0.39
37 9 0.13
ACGTcount: A:0.42, C:0.08, G:0.07, T:0.43
Consensus pattern (36 bp):
TAAAATTTAAGTATGTTACTTAAATACATTACTTAC
Found at i:28770185 original size:23 final size:23
Alignment explanation
Indices: 28770155--28770198 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
28770145 CTTATATGTA
*
28770155 AACTTACATAATACATTACTTTT
1 AACTTACATAATACATAACTTTT
28770178 AACTTACATAATACATAACTT
1 AACTTACATAATACATAACTT
28770199 ATAAAAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.43, C:0.18, G:0.00, T:0.39
Consensus pattern (23 bp):
AACTTACATAATACATAACTTTT
Found at i:28770213 original size:126 final size:126
Alignment explanation
Indices: 28769844--28770214 Score: 383
Period size: 126 Copynumber: 2.9 Consensus size: 126
28769834 AATTTATTAC
* *
28769844 TTAAATATGTTACTTAAATACATTACTTACTAAAATTTAAGTAAGTTTACTTATATGTAAAATTT
1 TTAAGTATGTTACTTAAATACATTACTTACTAAAATTTAAGCAAGTTTACTTATATGTAAAATTT
** * *** * * * **** **
28769909 AAGTATGTTGCGGGAATACATTACTTACTAAAATTTAAGTAAGTTTACTTATATGTAACTT
66 AAGTACATTACTTAAATACATTACATAATAAAACTTAAGTAAAAAAACTTATATGTAAAAT
28769970 TTAAGTATGTTACTTAAATACATTACTTACTAAAATTTAAGCAAGTTTACTTATATGTAAAATTT
1 TTAAGTATGTTACTTAAATACATTACTTACTAAAATTTAAGCAAGTTTACTTATATGTAAAATTT
** * * * ****
28770035 AAGTATGTTACTTAAATACATTACTTACTAAAATTTAAGTAAGTTTACTTATATGTAAAAT
66 AAGTACATTACTTAAATACATTACATAATAAAACTTAAGTAAAAAAACTTATATGTAAAAT
* *
28770096 TTAAGTATGTTACTTAAATACATTACTTACTAAAATTTAAGTAAGTTTACTTATATGTAAACTTA
1 TTAAGTATGTTACTTAAATACATTACTTACTAAAATTTAAGCAAGTTTACTTATATGTAAAATT-
** *
28770161 CATAA-TACATTACTTTTA-AC-TTACATAATACATAACTT-A-TAAAAAAATTTATAT
65 --TAAGTACATTACTTAAATACATTACATAATA-A-AACTTAAGTAAAAAAACTTATAT
28770215 AAACTTACAT
Statistics
Matches: 218, Mismatches: 22, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
126 198 0.91
127 4 0.02
128 13 0.06
129 3 0.01
ACGTcount: A:0.41, C:0.09, G:0.08, T:0.42
Consensus pattern (126 bp):
TTAAGTATGTTACTTAAATACATTACTTACTAAAATTTAAGCAAGTTTACTTATATGTAAAATTT
AAGTACATTACTTAAATACATTACATAATAAAACTTAAGTAAAAAAACTTATATGTAAAAT
Found at i:28770221 original size:38 final size:38
Alignment explanation
Indices: 28770178--28770269 Score: 121
Period size: 38 Copynumber: 2.4 Consensus size: 38
28770168 CATTACTTTT
28770178 AACTTACATAATACATAACTTATAAAAAAATTTATATA
1 AACTTACATAATACATAACTTATAAAAAAATTTATATA
* ******
28770216 AACTTACATGATACATAACTTATATTTTTTTTTATATA
1 AACTTACATAATACATAACTTATAAAAAAATTTATATA
28770254 AACTTACATAATACAT
1 AACTTACATAATACAT
28770270 TTAACTTACA
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
38 46 1.00
ACGTcount: A:0.47, C:0.12, G:0.01, T:0.40
Consensus pattern (38 bp):
AACTTACATAATACATAACTTATAAAAAAATTTATATA
Found at i:28770285 original size:9 final size:9
Alignment explanation
Indices: 28770254--28770785 Score: 385
Period size: 9 Copynumber: 60.0 Consensus size: 9
28770244 TTTTTATATA
28770254 AACTTACAT
1 AACTTACAT
28770263 AA--TACATTT
1 AACTTACA--T
28770272 AACTTACAT
1 AACTTACAT
28770281 AACTTACAT
1 AACTTACAT
*
28770290 AACTTACAC
1 AACTTACAT
28770299 AACTTACAT
1 AACTTACAT
28770308 AACATT-CAT
1 AAC-TTACAT
28770317 AA--TACATTT
1 AACTTACA--T
28770326 AACTTACAT
1 AACTTACAT
28770335 AACTTACAT
1 AACTTACAT
*
28770344 AACTGACAT
1 AACTTACAT
28770353 AACTTACAT
1 AACTTACAT
* *
28770362 AA--TGCAA
1 AACTTACAT
28770369 AACTTACAT
1 AACTTACAT
28770378 AACAACTTACAT
1 ---AACTTACAT
*
28770390 AACATACATT
1 AACTTACA-T
**
28770400 AA-TTTGAT
1 AACTTACAT
28770408 AACTTACAT
1 AACTTACAT
28770417 AACTTACAT
1 AACTTACAT
* *
28770426 AA--TGCAA
1 AACTTACAT
*
28770433 AACTCATA-AC
1 AACT--TACAT
28770443 AACTTACAT
1 AACTTACAT
*
28770452 AACATACAT
1 AACTTACAT
* **
28770461 TACTTTGAT
1 AACTTACAT
28770470 AACTTACAT
1 AACTTACAT
28770479 AACTTACAT
1 AACTTACAT
* *
28770488 AA--TGCAA
1 AACTTACAT
28770495 AACTTACAT
1 AACTTACAT
*
28770504 AAC-AAC-T
1 AACTTACAT
*
28770511 TACTTACAT
1 AACTTACAT
*
28770520 AACATACAT
1 AACTTACAT
* *
28770529 TACTTA-AA
1 AACTTACAT
*
28770537 ATATTTACAT
1 A-ACTTACAT
28770547 AA--TACAT
1 AACTTACAT
28770554 AACTTAGTACAT
1 AAC-T--TACAT
28770566 AACTTACAT
1 AACTTACAT
**
28770575 AA-TT-TTT
1 AACTTACAT
** *
28770582 TTC-TAAAT
1 AACTTACAT
**
28770590 TGCTTACAT
1 AACTTACAT
* *
28770599 AAATTATAT
1 AACTTACAT
28770608 AACTTACAT
1 AACTTACAT
28770617 AACTTACATT
1 AACTTACA-T
*
28770627 AA-TTAAAT
1 AACTTACAT
28770635 AACTTACAT
1 AACTTACAT
28770644 AACTTACAT
1 AACTTACAT
*
28770653 AACTTAAAT
1 AACTTACAT
28770662 AACTTACAT
1 AACTTACAT
28770671 AACTTACAT
1 AACTTACAT
*
28770680 ATCTTACAT
1 AACTTACAT
*
28770689 AACTTATAT
1 AACTTACAT
* *
28770698 AAATTAAAT
1 AACTTACAT
28770707 AACTTACAT
1 AACTTACAT
28770716 AACTTACAT
1 AACTTACAT
28770725 AACTTACAT
1 AACTTACAT
*
28770734 AAATTACAT
1 AACTTACAT
28770743 AACTTACAT
1 AACTTACAT
28770752 AACTTACAT
1 AACTTACAT
28770761 -A-TTACAT
1 AACTTACAT
*
28770768 AACCTT-CCT
1 AA-CTTACAT
28770777 AACTTACAT
1 AACTTACAT
28770786 TATTGTTTAA
Statistics
Matches: 410, Mismatches: 71, Indels: 84
0.73 0.13 0.15
Matches are distributed among these distances:
6 1 0.00
7 39 0.10
8 23 0.06
9 303 0.74
10 17 0.04
11 10 0.02
12 17 0.04
ACGTcount: A:0.45, C:0.19, G:0.02, T:0.34
Consensus pattern (9 bp):
AACTTACAT
Found at i:28770386 original size:12 final size:12
Alignment explanation
Indices: 28770369--28770393 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28770359 CATAATGCAA
28770369 AACTTACATAAC
1 AACTTACATAAC
28770381 AACTTACATAAC
1 AACTTACATAAC
28770393 A
1 A
28770394 TACATTAATT
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:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (12 bp):
AACTTACATAAC
Found at i:28776361 original size:12 final size:12
Alignment explanation
Indices: 28776344--28776371 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
28776334 GCAGAGGCCA
28776344 CAGCGAGAGAAG
1 CAGCGAGAGAAG
28776356 CAGCGAGAGAAG
1 CAGCGAGAGAAG
28776368 CAGC
1 CAGC
28776372 AATAGAAGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.39, C:0.21, G:0.39, T:0.00
Consensus pattern (12 bp):
CAGCGAGAGAAG
Found at i:28776913 original size:43 final size:42
Alignment explanation
Indices: 28776852--28776976 Score: 153
Period size: 43 Copynumber: 2.9 Consensus size: 42
28776842 ATTTTTAAAC
* * *
28776852 AAGCGCGGCTATAGAACATTA-CTTTTAGCGGCGTTTTCTTCCA
1 AAGCGCCGCTAAAGAACATGATC-TTTAGCGGCGTTTT-TTCCA
* *
28776895 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTATTTTCT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTT-TTTCCA
* *
28776938 TAGCGCCGGTAAAGAACATGATCTTTAGCGGCGTTTTTT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTT
28776977 TCTGTAAGCG
Statistics
Matches: 73, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
42 3 0.04
43 68 0.93
44 2 0.03
ACGTcount: A:0.24, C:0.21, G:0.22, T:0.33
Consensus pattern (42 bp):
AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTCCA
Found at i:28778287 original size:20 final size:21
Alignment explanation
Indices: 28778264--28778311 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
28778254 ACATTTTATC
28778264 AATACTTGGT-AAAAGGTATT
1 AATACTTGGTGAAAAGGTATT
**
28778284 AATACTTTTTGAAAAGGTATT
1 AATACTTGGTGAAAAGGTATT
28778305 AATACTT
1 AATACTT
28778312 TTTATAATTG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 8 0.32
21 17 0.68
ACGTcount: A:0.40, C:0.06, G:0.15, T:0.40
Consensus pattern (21 bp):
AATACTTGGTGAAAAGGTATT
Found at i:28778300 original size:21 final size:21
Alignment explanation
Indices: 28778274--28778314 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
28778264 AATACTTGGT
28778274 AAAAGGTATTAATACTTTTTG
1 AAAAGGTATTAATACTTTTTG
28778295 AAAAGGTATTAATACTTTTT
1 AAAAGGTATTAATACTTTTT
28778315 ATAATTGTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.39, C:0.05, G:0.12, T:0.44
Consensus pattern (21 bp):
AAAAGGTATTAATACTTTTTG
Found at i:28778561 original size:20 final size:20
Alignment explanation
Indices: 28778536--28778578 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
28778526 GGGAGCAATT
* *
28778536 TTTCAATTGATTTAAAAATG
1 TTTCAATTGAGTTAAAAAAG
28778556 TTTCAATTGAGTTAAAAAAG
1 TTTCAATTGAGTTAAAAAAG
28778576 TTT
1 TTT
28778579 AAACCATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.40, C:0.05, G:0.12, T:0.44
Consensus pattern (20 bp):
TTTCAATTGAGTTAAAAAAG
Found at i:28784698 original size:18 final size:18
Alignment explanation
Indices: 28784671--28784710 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
28784661 ATATAAAAAA
*
28784671 ATTTAATTTTTATAAA-T
1 ATTTAATTTTTAAAAATT
28784688 ATTTGAATTTTTAAAAATT
1 ATTT-AATTTTTAAAAATT
28784707 ATTT
1 ATTT
28784711 TGAAACTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 4 0.20
18 11 0.55
19 5 0.25
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (18 bp):
ATTTAATTTTTAAAAATT
Found at i:28786691 original size:22 final size:21
Alignment explanation
Indices: 28786653--28786693 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
28786643 TAGACATAAA
**
28786653 TATTTTAAAAATTATATTTAT
1 TATTTTAAAAAAAATATTTAT
28786674 TATTTTATAAAAAAATATTT
1 TATTTTA-AAAAAAATATTT
28786694 TAATAAGTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
TATTTTAAAAAAAATATTTAT
Found at i:28786920 original size:30 final size:30
Alignment explanation
Indices: 28786886--28786944 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
28786876 AAATATAAAA
* *
28786886 TTATACATGAATTTTTTATTTTA-TTCAATT
1 TTATACATGAA-ATTTTAATTTAGTTCAATT
28786916 TTATACATGAAATTTTAATTTAGTTCAAT
1 TTATACATGAAATTTTAATTTAGTTCAAT
28786945 GTTCACAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 9 0.35
30 17 0.65
ACGTcount: A:0.34, C:0.07, G:0.05, T:0.54
Consensus pattern (30 bp):
TTATACATGAAATTTTAATTTAGTTCAATT
Found at i:28788251 original size:27 final size:27
Alignment explanation
Indices: 28788182--28788288 Score: 69
Period size: 28 Copynumber: 3.9 Consensus size: 27
28788172 GCTTAAATTT
*
28788182 TATTTAAATATGAAT-A-ATTAATTTAA
1 TATTTAAATAT-AATAATATTTATTTAA
*
28788208 GCTCATTTAAATTTAATAATATTT-TTTAA
1 --T-ATTTAAATATAATAATATTTATTTAA
* *
28788237 TATTTCAAATATAATTATTTTTATTTAA
1 TATTT-AAATATAATAATATTTATTTAA
* *
28788265 TACTT-AATATTTATATATATTTAT
1 TATTTAAATA-TAATA-ATATTTAT
28788289 CATTAAATAC
Statistics
Matches: 63, Mismatches: 9, Indels: 14
0.73 0.10 0.16
Matches are distributed among these distances:
26 8 0.13
27 17 0.27
28 20 0.32
29 15 0.24
30 3 0.05
ACGTcount: A:0.41, C:0.04, G:0.02, T:0.53
Consensus pattern (27 bp):
TATTTAAATATAATAATATTTATTTAA
Found at i:28789757 original size:24 final size:24
Alignment explanation
Indices: 28789724--28789886 Score: 150
Period size: 25 Copynumber: 6.6 Consensus size: 24
28789714 TACATGTATA
28789724 CTCATACGAGCTGTAAACGGTAAG
1 CTCATACGAGCTGTAAACGGTAAG
* * *
28789748 CTCTTCCGAGCTGAATAACGGTAAG
1 CTCATACGAGCTGTA-AACGGTAAG
*
28789773 CTCATACGAGCTATAAATCAGG-AAG
1 CTCATACGAGCTGTAAA-C-GGTAAG
* * *
28789798 CTCATATGAGCTATAAATCGGGAAG
1 CTCATACGAGCTGTAAA-CGGTAAG
* * *
28789823 CTCATACGAGTTGCAAATCGGGAAG
1 CTCATACGAGCTGTAAA-CGGTAAG
*
28789848 CTCATACGAGCTGCAAATCGAG-AAG
1 CTCATACGAGCTGTAAA-CG-GTAAG
28789873 CTCATACGAGCTGT
1 CTCATACGAGCTGT
28789887 GGTGTGTCTG
Statistics
Matches: 120, Mismatches: 14, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
24 16 0.13
25 101 0.84
26 3 0.03
ACGTcount: A:0.33, C:0.21, G:0.24, T:0.21
Consensus pattern (24 bp):
CTCATACGAGCTGTAAACGGTAAG
Found at i:28797203 original size:25 final size:24
Alignment explanation
Indices: 28797175--28797230 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 24
28797165 AAGCTCTTCT
*
28797175 GAGCTGAATAGCGATAAGCTCATAC
1 GAGCTGAA-AGCGAGAAGCTCATAC
*
28797200 GAGCTAGAAATCGAGAAGCTCATAC
1 GAGCT-GAAAGCGAGAAGCTCATAC
28797225 GAGCTG
1 GAGCTG
28797231 TGGTGTGTCC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
24 1 0.04
25 24 0.86
26 3 0.11
ACGTcount: A:0.36, C:0.20, G:0.27, T:0.18
Consensus pattern (24 bp):
GAGCTGAAAGCGAGAAGCTCATAC
Found at i:28799948 original size:28 final size:25
Alignment explanation
Indices: 28799917--28799985 Score: 75
Period size: 27 Copynumber: 2.6 Consensus size: 25
28799907 ATTAACAAAT
28799917 ATTTTTATATTTTTATACTTTTTTAATA
1 ATTTTTATATTTTTAT--TTTTTTAA-A
* *
28799945 ATTTTAATGATTTTTATTTTTTTTAA
1 ATTTTTAT-ATTTTTATTTTTTTAAA
28799971 ATATTTTATATTTTT
1 AT-TTTTATATTTTT
28799986 TGAATTTCTA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
26 9 0.25
27 12 0.33
28 7 0.19
29 8 0.22
ACGTcount: A:0.28, C:0.01, G:0.01, T:0.70
Consensus pattern (25 bp):
ATTTTTATATTTTTATTTTTTTAAA
Found at i:28799986 original size:9 final size:9
Alignment explanation
Indices: 28799918--28799986 Score: 52
Period size: 9 Copynumber: 7.6 Consensus size: 9
28799908 TTAACAAATA
28799918 TTTTTATA-
1 TTTTTATAT
28799926 TTTTTATACT
1 TTTTTATA-T
*
28799936 TTTTTAATAA
1 TTTTT-ATAT
*
28799946 TTTTAATGA-
1 TTTTTAT-AT
*
28799955 TTTTTATTT
1 TTTTTATAT
*
28799964 TTTTTAAAT
1 TTTTTATAT
*
28799973 ATTTTATAT
1 TTTTTATAT
28799982 TTTTT
1 TTTTT
28799987 GAATTTCTAA
Statistics
Matches: 47, Mismatches: 9, Indels: 9
0.72 0.14 0.14
Matches are distributed among these distances:
8 8 0.17
9 26 0.55
10 10 0.21
11 3 0.06
ACGTcount: A:0.26, C:0.01, G:0.01, T:0.71
Consensus pattern (9 bp):
TTTTTATAT
Found at i:28799986 original size:28 final size:29
Alignment explanation
Indices: 28799913--28799986 Score: 86
Period size: 28 Copynumber: 2.7 Consensus size: 29
28799903 TTAAATTAAC
28799913 AAATATTTT-TATATTTTTATACTTTTTT
1 AAATATTTTATATATTTTTATACTTTTTT
*
28799941 -AATAATTTTA-ATGATTTTTAT-TTTTTTT
1 AAAT-ATTTTATAT-ATTTTTATACTTTTTT
28799969 AAATATTTTATAT-TTTTT
1 AAATATTTTATATATTTTT
28799987 GAATTTCTAA
Statistics
Matches: 40, Mismatches: 1, Indels: 11
0.77 0.02 0.21
Matches are distributed among these distances:
27 8 0.20
28 19 0.47
29 13 0.32
ACGTcount: A:0.30, C:0.01, G:0.01, T:0.68
Consensus pattern (29 bp):
AAATATTTTATATATTTTTATACTTTTTT
Found at i:28802800 original size:25 final size:24
Alignment explanation
Indices: 28802772--28802839 Score: 91
Period size: 24 Copynumber: 2.8 Consensus size: 24
28802762 GTACATAAAT
28802772 GGGAAGCTCATGTGAGCCATGTAAC
1 GGGAAGCTCATGTGAGCCAT-TAAC
** *
28802797 GGGAAGCTCCGGAGAGCCATTAAC
1 GGGAAGCTCATGTGAGCCATTAAC
*
28802821 GGGAAGCTCATATGAGCCA
1 GGGAAGCTCATGTGAGCCA
28802840 ATTTTGGGAA
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
24 19 0.53
25 17 0.47
ACGTcount: A:0.29, C:0.22, G:0.32, T:0.16
Consensus pattern (24 bp):
GGGAAGCTCATGTGAGCCATTAAC
Found at i:28802848 original size:24 final size:24
Alignment explanation
Indices: 28802772--28802878 Score: 81
Period size: 25 Copynumber: 4.4 Consensus size: 24
28802762 GTACATAAAT
* * *
28802772 GGGAAGCTCATGTGAGCCATGTAAC
1 GGGAAGCTCAAGTGAGCCA-ATATC
** * * *
28802797 GGGAAGCTCCGGAGAGCCATTAAC
1 GGGAAGCTCAAGTGAGCCAATATC
* *
28802821 GGGAAGCTCATA-TGAGCCAATTTT
1 GGGAAGCTCA-AGTGAGCCAATATC
*
28802845 GGGAAGGTTCAAGTGAGCCAATATC
1 GGGAA-GCTCAAGTGAGCCAATATC
28802870 GGGAAGCTC
1 GGGAAGCTC
28802879 TGGAGAGCCA
Statistics
Matches: 64, Mismatches: 15, Indels: 7
0.74 0.17 0.08
Matches are distributed among these distances:
24 29 0.45
25 35 0.55
ACGTcount: A:0.29, C:0.20, G:0.32, T:0.20
Consensus pattern (24 bp):
GGGAAGCTCAAGTGAGCCAATATC
Found at i:28803036 original size:24 final size:24
Alignment explanation
Indices: 28803003--28803055 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
28802993 CACAACCAAT
* * *
28803003 CGGGATGCTCCGGAGAGCTATTAA
1 CGGGAAGCTCAGGAGAGCTAATAA
*
28803027 CGGGAAGCTCATGAGAGCTAATAA
1 CGGGAAGCTCAGGAGAGCTAATAA
28803051 CGGGA
1 CGGGA
28803056 TGCGCTTTCG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.30, C:0.19, G:0.34, T:0.17
Consensus pattern (24 bp):
CGGGAAGCTCAGGAGAGCTAATAA
Found at i:28806963 original size:32 final size:31
Alignment explanation
Indices: 28806926--28806988 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 31
28806916 CATTCAATGG
*
28806926 ACCATTC-AATACTAGGTGTTCACACCCAAAGA
1 ACCATTCAAATACGA-GTGTTCACA-CCAAAGA
*
28806958 ACCATTCAAATCCGAGTGTTCACACCAAAGA
1 ACCATTCAAATACGAGTGTTCACACCAAAGA
28806989 TCCTTCGGGC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 7 0.25
32 16 0.57
33 5 0.18
ACGTcount: A:0.38, C:0.29, G:0.13, T:0.21
Consensus pattern (31 bp):
ACCATTCAAATACGAGTGTTCACACCAAAGA
Found at i:28812971 original size:24 final size:24
Alignment explanation
Indices: 28812887--28812972 Score: 68
Period size: 25 Copynumber: 3.5 Consensus size: 24
28812877 TTCGGGAATA
*
28812887 CTCATACGAGCACATAAACAGGAAG
1 CTCATACGAGC-CATTAACAGGAAG
*** **
28812912 CTCACGTGAGCCATGTAATTGGAAG
1 CTCATACGAGCCAT-TAACAGGAAG
28812937 CTC-TGGA-GAGCCATTAACAGGAAG
1 CTCAT--ACGAGCCATTAACAGGAAG
28812961 CTCATACGAGCC
1 CTCATACGAGCC
28812973 GGTTTCGGGA
Statistics
Matches: 46, Mismatches: 10, Indels: 11
0.69 0.15 0.16
Matches are distributed among these distances:
23 1 0.02
24 19 0.41
25 26 0.57
ACGTcount: A:0.34, C:0.24, G:0.24, T:0.17
Consensus pattern (24 bp):
CTCATACGAGCCATTAACAGGAAG
Found at i:28813022 original size:24 final size:24
Alignment explanation
Indices: 28812932--28813022 Score: 60
Period size: 24 Copynumber: 3.8 Consensus size: 24
28812922 CCATGTAATT
* * *
28812932 GGAAGCTCTGGAGAGCCATTAACA
1 GGAAGCTCTAGAGAGCCAGTATCA
* * * *
28812956 GGAAGCTCATA-CGAGCCGGTTTCG
1 GGAAGCTC-TAGAGAGCCAGTATCA
* *
28812980 GGAAG-TTTCAGGTGAGCCAGTATCA
1 GGAAGCTCT-A-GAGAGCCAGTATCA
28813005 GGAAGCTCTAGAGAGCCA
1 GGAAGCTCTAGAGAGCCA
28813023 ATTAATCGGG
Statistics
Matches: 48, Mismatches: 14, Indels: 10
0.67 0.19 0.14
Matches are distributed among these distances:
22 1 0.02
23 2 0.04
24 27 0.56
25 16 0.33
26 2 0.04
ACGTcount: A:0.29, C:0.21, G:0.32, T:0.19
Consensus pattern (24 bp):
GGAAGCTCTAGAGAGCCAGTATCA
Found at i:28814927 original size:25 final size:25
Alignment explanation
Indices: 28814898--28815076 Score: 78
Period size: 25 Copynumber: 7.6 Consensus size: 25
28814888 ATTCTATTTG
*
28814898 GCCTTTGTGGTGTATTTTGTATGTT
1 GCCTTTGTGGCGTATTTTGTATGTT
*
28814923 GCCTTTGTGGCGTACTTTG-ATAG-T
1 GCCTTTGTGGCGTATTTTGTAT-GTT
*
28814947 --CTTTGTGGTGTA-TTT-TAT-TT
1 GCCTTTGTGGCGTATTTTGTATGTT
* *
28814967 GACCTTTGTGACGTATTATGTATGTT
1 G-CCTTTGTGGCGTATTTTGTATGTT
* * * ** * * *
28814993 TCATTTATGGCAAACTCTG-A--TA
1 GCCTTTGTGGCGTATTTTGTATGTT
* * *
28815015 GCCTTTTGTGGCATATTCTG-A--TA
1 GCC-TTTGTGGCGTATTTTGTATGTT
* *
28815038 GCCTTTGTGGCGTATTCTATATGTT
1 GCCTTTGTGGCGTATTTTGTATGTT
28815063 GCCTTTGTGGCGTA
1 GCCTTTGTGGCGTA
28815077 CCCTGATAAG
Statistics
Matches: 118, Mismatches: 23, Indels: 26
0.71 0.14 0.16
Matches are distributed among these distances:
20 1 0.01
21 5 0.04
22 27 0.23
23 30 0.25
24 6 0.05
25 47 0.40
26 2 0.02
ACGTcount: A:0.15, C:0.14, G:0.24, T:0.47
Consensus pattern (25 bp):
GCCTTTGTGGCGTATTTTGTATGTT
Found at i:28815047 original size:22 final size:23
Alignment explanation
Indices: 28815008--28815055 Score: 80
Period size: 22 Copynumber: 2.1 Consensus size: 23
28814998 TATGGCAAAC
28815008 TCTGATAGCCTTTTGTGGCATAT
1 TCTGATAGCCTTTTGTGGCATAT
*
28815031 TCTGATAGCC-TTTGTGGCGTAT
1 TCTGATAGCCTTTTGTGGCATAT
28815053 TCT
1 TCT
28815056 ATATGTTGCC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 14 0.58
23 10 0.42
ACGTcount: A:0.15, C:0.19, G:0.23, T:0.44
Consensus pattern (23 bp):
TCTGATAGCCTTTTGTGGCATAT
Found at i:28815083 original size:70 final size:69
Alignment explanation
Indices: 28814898--28815084 Score: 187
Period size: 70 Copynumber: 2.7 Consensus size: 69
28814888 ATTCTATTTG
* * * * ** *
28814898 GCCTTTGTGGTGTATTTTGTATGTTGCCTTTGTGGCGTACTTTGATAGTCTTTGTGGTGTATTTT
1 GCCTTTGTGGCGTATTATGTATGTTGCCTTTGTGGCGTACTCTGATAGCCTTTGTGGCATATTTG
*
28814963 ATTT
66 ATTA
* * * * **
28814967 GACCTTTGTGACGTATTATGTATGTTTCATTTATGGCAAACTCTGATAGCCTTTTGTGGCATATT
1 G-CCTTTGTGGCGTATTATGTATGTTGCCTTTGTGGCGTACTCTGATAGCC-TTTGTGGCATATT
28815032 CTGA-TA
64 -TGATTA
* * *
28815038 GCCTTTGTGGCGTATTCTATATGTTGCCTTTGTGGCGTACCCTGATA
1 GCCTTTGTGGCGTATTATGTATGTTGCCTTTGTGGCGTACTCTGATA
28815085 AGTCTATGTT
Statistics
Matches: 92, Mismatches: 23, Indels: 5
0.77 0.19 0.04
Matches are distributed among these distances:
69 1 0.01
70 76 0.83
71 13 0.14
72 2 0.02
ACGTcount: A:0.16, C:0.15, G:0.24, T:0.46
Consensus pattern (69 bp):
GCCTTTGTGGCGTATTATGTATGTTGCCTTTGTGGCGTACTCTGATAGCCTTTGTGGCATATTTG
ATTA
Found at i:28819978 original size:45 final size:45
Alignment explanation
Indices: 28819912--28820014 Score: 136
Period size: 45 Copynumber: 2.3 Consensus size: 45
28819902 GTAACGGTAG
* ** *
28819912 CAGTAACAATAATAGTAACAGTATTCAACACACAAAGTG-CTGAAT
1 CAGTAACAGTAACGGTAACAGTATCCAACACACAAAGTGTC-GAAT
* *
28819957 CTGTAACAGTAACGGTAACAGTATCCGACACACAAAGTGTCGAAT
1 CAGTAACAGTAACGGTAACAGTATCCAACACACAAAGTGTCGAAT
28820002 CAGTAACAGTAAC
1 CAGTAACAGTAAC
28820015 AGTAGTCGGC
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
45 49 0.98
46 1 0.02
ACGTcount: A:0.43, C:0.20, G:0.17, T:0.20
Consensus pattern (45 bp):
CAGTAACAGTAACGGTAACAGTATCCAACACACAAAGTGTCGAAT
Found at i:28820264 original size:40 final size:40
Alignment explanation
Indices: 28820218--28820304 Score: 104
Period size: 40 Copynumber: 2.2 Consensus size: 40
28820208 AATTCATTAC
* *
28820218 TTCAGTAA-TTGCACAGTTCAATGCAGTACACATAACAAGA
1 TTCAGTAACTT-CACAATTCAATGCAGTACACAAAACAAGA
* * * *
28820258 TTCAGTAACTTCACAATTCAATTCAGTACTCAAAATAATA
1 TTCAGTAACTTCACAATTCAATGCAGTACACAAAACAAGA
28820298 TTCAGTA
1 TTCAGTA
28820305 TTCCATAATG
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
40 38 0.95
41 2 0.05
ACGTcount: A:0.40, C:0.20, G:0.10, T:0.30
Consensus pattern (40 bp):
TTCAGTAACTTCACAATTCAATGCAGTACACAAAACAAGA
Found at i:28821271 original size:30 final size:29
Alignment explanation
Indices: 28821237--28821293 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 29
28821227 TTATCAAATA
28821237 AATAAA-ATCTTTTAATATAATAATTTAATC
1 AATAAATATCTTTTAAT-TAA-AATTTAATC
* *
28821267 AATAAATTTCTTTTACTTAAAATTTAA
1 AATAAATATCTTTTAATTAAAATTTAA
28821294 GAAAATATAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 7 0.29
30 9 0.38
31 8 0.33
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.46
Consensus pattern (29 bp):
AATAAATATCTTTTAATTAAAATTTAATC
Found at i:28821414 original size:17 final size:16
Alignment explanation
Indices: 28821385--28821428 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
28821375 GGATTTATTA
28821385 ATAATATAATATCATT
1 ATAATATAATATCATT
*
28821401 ATAATTTAATTATCATT
1 ATAATATAA-TATCATT
*
28821418 AATTATATAAT
1 -ATAATATAAT
28821429 TAAAACAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
16 8 0.35
17 8 0.35
18 7 0.30
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (16 bp):
ATAATATAATATCATT
Found at i:28827476 original size:45 final size:45
Alignment explanation
Indices: 28827400--28827506 Score: 151
Period size: 45 Copynumber: 2.4 Consensus size: 45
28827390 TAATCAGTAA
* *
28827400 CGGTAACAATAACAGTAACAATATTCAACACACAAAGTGCTGAAT
1 CGGTAACAGTAACAGTAACAATATCCAACACACAAAGTGCTGAAT
* * * * *
28827445 CTGTAACAGTAACGGTAACAGTATCCGACACACAAAGTGTTGAAT
1 CGGTAACAGTAACAGTAACAATATCCAACACACAAAGTGCTGAAT
28827490 CGGTAACAGTAACAGTA
1 CGGTAACAGTAACAGTA
28827507 GTCAGCATAT
Statistics
Matches: 53, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 53 1.00
ACGTcount: A:0.42, C:0.20, G:0.18, T:0.21
Consensus pattern (45 bp):
CGGTAACAGTAACAGTAACAATATCCAACACACAAAGTGCTGAAT
Found at i:28827752 original size:40 final size:41
Alignment explanation
Indices: 28827706--28827793 Score: 99
Period size: 40 Copynumber: 2.2 Consensus size: 41
28827696 AATTCATTAC
* *
28827706 TTCAGTAA-TTGCACAGTTCAATGCAGTACAC-ATAACAATA
1 TTCAGTAACTT-CACAATTCAATGCAGTACACAAAAACAATA
* ** *
28827746 TTCAGTAACTTCACAATTTAATTTAGTACTCAAAAACAATA
1 TTCAGTAACTTCACAATTCAATGCAGTACACAAAAACAATA
28827787 TTCAGTA
1 TTCAGTA
28827794 TTCCATAATA
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
40 23 0.57
41 17 0.43
ACGTcount: A:0.41, C:0.18, G:0.09, T:0.32
Consensus pattern (41 bp):
TTCAGTAACTTCACAATTCAATGCAGTACACAAAAACAATA
Found at i:28828909 original size:17 final size:16
Alignment explanation
Indices: 28828878--28828921 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
28828868 GATTTATTTA
28828878 ATAATATAATATCATT
1 ATAATATAATATCATT
*
28828894 ATAATTTAATTATCATT
1 ATAATATAA-TATCATT
*
28828911 AATTATATAAT
1 -ATAATATAAT
28828922 TAAAACAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
16 8 0.35
17 8 0.35
18 7 0.30
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (16 bp):
ATAATATAATATCATT
Found at i:28833856 original size:13 final size:13
Alignment explanation
Indices: 28833838--28833862 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28833828 GATTATTTCA
28833838 TAAAAATTAAATT
1 TAAAAATTAAATT
28833851 TAAAAATTAAAT
1 TAAAAATTAAAT
28833863 AAAGAGGTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
TAAAAATTAAATT
Found at i:28836737 original size:18 final size:17
Alignment explanation
Indices: 28836714--28836752 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
28836704 ATATTTCATG
*
28836714 TTATTTTTTATAATTCTT
1 TTATTTTCTATAATT-TT
*
28836732 TTATTTTCTATCATTTT
1 TTATTTTCTATAATTTT
28836749 TTAT
1 TTAT
28836753 CATGAAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.21, C:0.08, G:0.00, T:0.72
Consensus pattern (17 bp):
TTATTTTCTATAATTTT
Found at i:28842419 original size:1 final size:1
Alignment explanation
Indices: 28842413--28842485 Score: 65
Period size: 1 Copynumber: 73.0 Consensus size: 1
28842403 CCGTGGAGGC
* * * * * * * *
28842413 AAAAAAAATAAAAAAACAAAAAAAAGAAAACAAGAAAATAAAAAAATAAAAAAAAAACAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
*
28842478 TAAAAAAA
1 AAAAAAAA
28842486 CCTCTACCGG
Statistics
Matches: 54, Mismatches: 18, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 54 1.00
ACGTcount: A:0.88, C:0.04, G:0.03, T:0.05
Consensus pattern (1 bp):
A
Found at i:28842463 original size:27 final size:27
Alignment explanation
Indices: 28842414--28842485 Score: 99
Period size: 27 Copynumber: 2.6 Consensus size: 27
28842404 CGTGGAGGCA
28842414 AAAAAAATAAAAAAACAAAAAAAAGAAAAC
1 AAAAAAAT-AAAAAA-AAAAAAAA-AAAAC
* *
28842444 AAGAAAATAAAAAAATAAAAAAAAAAC
1 AAAAAAATAAAAAAAAAAAAAAAAAAC
28842471 AAAAAAATAAAAAAA
1 AAAAAAATAAAAAAA
28842486 CCTCTACCGG
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
27 19 0.49
28 7 0.18
29 6 0.15
30 7 0.18
ACGTcount: A:0.88, C:0.04, G:0.03, T:0.06
Consensus pattern (27 bp):
AAAAAAATAAAAAAAAAAAAAAAAAAC
Found at i:28842938 original size:16 final size:17
Alignment explanation
Indices: 28842916--28842965 Score: 59
Period size: 16 Copynumber: 3.0 Consensus size: 17
28842906 ATACTTCACT
*
28842916 TGAAAAAGAAACGAAAA
1 TGAAAAAGAAAAGAAAA
*
28842933 -GAAAAA-AAAATAAAA
1 TGAAAAAGAAAAGAAAA
28842948 TGAAAAAGAAAAAGAAAA
1 TGAAAAAG-AAAAGAAAA
28842966 AGGAGAGGCC
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
15 7 0.26
16 12 0.44
18 8 0.30
ACGTcount: A:0.78, C:0.02, G:0.14, T:0.06
Consensus pattern (17 bp):
TGAAAAAGAAAAGAAAA
Found at i:28843989 original size:90 final size:91
Alignment explanation
Indices: 28843877--28844147 Score: 440
Period size: 90 Copynumber: 3.0 Consensus size: 91
28843867 TGAAGTCATC
*
28843877 ATAGCAAGTCTTGTCTTCCTGTATTGGCAGCGAAGTAGACTGAAAG-TAGCAGATCTTGTCTTCC
1 ATAGCAAGTCTTGTCTTCCTGTATTGGCAGCGAAGTAGACTGAAAGATAACAGATCTTGTCTTCC
28843941 TGTATTGACAGCGAAGTAGATCGAAG
66 TGTATTGACAGCGAAGTAGATCGAAG
* *
28843967 ATAGCAAGTCTTGTCTTCCTGTATTGGTAGTGAAGTAGACT-AAAGATAACAGATCTTGTCTTCC
1 ATAGCAAGTCTTGTCTTCCTGTATTGGCAGCGAAGTAGACTGAAAGATAACAGATCTTGTCTTCC
* *
28844031 TATATTGGCAGCGAAGTAGATCGAAG
66 TGTATTGACAGCGAAGTAGATCGAAG
*
28844057 ATAGCAAGTCTTGTCTTCCTGTATTGGCAGCGAAGTAGACTG-AAGATAACAGATCTTGCCTTCC
1 ATAGCAAGTCTTGTCTTCCTGTATTGGCAGCGAAGTAGACTGAAAGATAACAGATCTTGTCTTCC
** *
28844121 TGTATTGATGGCGAAGCAGATCGAAG
66 TGTATTGACAGCGAAGTAGATCGAAG
28844147 A
1 A
28844148 CACCATAGTT
Statistics
Matches: 166, Mismatches: 13, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
89 4 0.02
90 162 0.98
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.29
Consensus pattern (91 bp):
ATAGCAAGTCTTGTCTTCCTGTATTGGCAGCGAAGTAGACTGAAAGATAACAGATCTTGTCTTCC
TGTATTGACAGCGAAGTAGATCGAAG
Found at i:28844127 original size:135 final size:135
Alignment explanation
Indices: 28843885--28844127 Score: 370
Period size: 135 Copynumber: 1.8 Consensus size: 135
28843875 TCATAGCAAG
*
28843885 TCTTGTCTTCCTGTATTGGCAGCGAAGTAGACTGAAAGTAGCAGATCTTGTCTTCCTGTATTGAC
1 TCTTGTCTTCCTATATTGGCAGCGAAGTAGACTGAAAGTAGCAGATCTTGTCTTCCTGTATTGAC
* *
28843950 AGCGAAGTAGATCGAAGATAGCAAGTCTTGTCTTCCTGTATTGGTAGTGAAGTAGACTAAAGATA
66 AGCGAAGTAGATCGAAGATAACAAGTCTTGCCTTCCTGTATTGGTAGTGAAGTAGACTAAAGATA
28844015 ACAGA
131 ACAGA
28844020 TCTTGTCTTCCTATATTGGCAGCGAAGTAGA-TCG-AAGATAGCA-AGTCTTGTCTTCCTGTATT
1 TCTTGTCTTCCTATATTGGCAGCGAAGTAGACT-GAAAG-TAGCAGA-TCTTGTCTTCCTGTATT
*
28844082 GGCAGCGAAGTAGA-CTGAAGATAAC-AGATCTTGCCTTCCTGTATTG
63 GACAGCGAAGTAGATC-GAAGATAACAAG-TCTTGCCTTCCTGTATTG
28844128 ATGGCGAAGC
Statistics
Matches: 99, Mismatches: 4, Indels: 10
0.88 0.04 0.09
Matches are distributed among these distances:
134 8 0.08
135 91 0.92
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (135 bp):
TCTTGTCTTCCTATATTGGCAGCGAAGTAGACTGAAAGTAGCAGATCTTGTCTTCCTGTATTGAC
AGCGAAGTAGATCGAAGATAACAAGTCTTGCCTTCCTGTATTGGTAGTGAAGTAGACTAAAGATA
ACAGA
Found at i:28844136 original size:45 final size:45
Alignment explanation
Indices: 28843877--28844127 Score: 334
Period size: 45 Copynumber: 5.6 Consensus size: 45
28843867 TGAAGTCATC
28843877 ATAGCA-AGTCTTGTCTTCCTGTATTGGCAGCGAAGTAGACTGAA-
1 ATAGCAGA-TCTTGTCTTCCTGTATTGGCAGCGAAGTAGACTGAAG
*
28843921 AGTAGCAGATCTTGTCTTCCTGTATTGACAGCGAAGTAGA-TCGAAG
1 A-TAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGACT-GAAG
* * *
28843967 ATAGCA-AGTCTTGTCTTCCTGTATTGGTAGTGAAGTAGACTAAAG
1 ATAGCAGA-TCTTGTCTTCCTGTATTGGCAGCGAAGTAGACTGAAG
* *
28844012 ATAACAGATCTTGTCTTCCTATATTGGCAGCGAAGTAGA-TCGAAG
1 ATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGACT-GAAG
28844057 ATAGCA-AGTCTTGTCTTCCTGTATTGGCAGCGAAGTAGACTGAAG
1 ATAGCAGA-TCTTGTCTTCCTGTATTGGCAGCGAAGTAGACTGAAG
* *
28844102 ATAACAGATCTTGCCTTCCTGTATTG
1 ATAGCAGATCTTGTCTTCCTGTATTG
28844128 ATGGCGAAGC
Statistics
Matches: 182, Mismatches: 14, Indels: 21
0.84 0.06 0.10
Matches are distributed among these distances:
44 5 0.03
45 171 0.94
46 6 0.03
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.31
Consensus pattern (45 bp):
ATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGACTGAAG
Found at i:28844328 original size:99 final size:99
Alignment explanation
Indices: 28844168--28844760 Score: 654
Period size: 99 Copynumber: 6.0 Consensus size: 99
28844158 TGCAGCAAAG
* * * * *
28844168 AAGATTGAAGCCGCAACGGTGAATCTTACCTCCCTGGC-AGTGCAGTGGAACATATTGAAGCTAC
1 AAGATTGAAGCCGCAACGGCGAATCTTACTTTCCTGGCGA-TGCAGTGGATCAGATTGAAGCTAC
* *
28844232 AACAGTGAATCTTATTCCTCGACATTGCAATTTAA
65 AACGGTGAATCTTATTCCCCGACATTGCAATTTAA
* * *
28844267 AAGATTGAAGCCGCAACGGCGAATCTTACTTTCCTAGCGATACAATGGATCAGATTGAAGCTACA
1 AAGATTGAAGCCGCAACGGCGAATCTTACTTTCCTGGCGATGCAGTGGATCAGATTGAAGCTACA
* *
28844332 ACGGTGAATCTCATTCCCCGACATTCCAATTTAA
66 ACGGTGAATCTTATTCCCCGACATTGCAATTTAA
* * ** * * * * *
28844366 AAGACTGAAGCCGCAACGGTGAATCTTACTTTTTTGGTGGTGCAGTGGACCAGATTAAAGCTACG
1 AAGATTGAAGCCGCAACGGCGAATCTTACTTTCCTGGCGATGCAGTGGATCAGATTGAAGCTACA
* *
28844431 ACGGTGAATCTTGCTTCCCCGACATTGCAATTAAA
66 ACGGTGAATCTT-ATTCCCCGACATTGCAATTTAA
* *
28844466 AAGATTGAAGCCGCAAGGGCGAATCTTACTTTCCTGGCGATGCAGTGGATTAGATTGAAGCTACA
1 AAGATTGAAGCCGCAACGGCGAATCTTACTTTCCTGGCGATGCAGTGGATCAGATTGAAGCTACA
*
28844531 ACGGCGAATCTTATTCCCCGACATTGCAA-TTAA
66 ACGGTGAATCTTATTCCCCGACATTGCAATTTAA
* * * * * * * *
28844564 AAGGATTGAAGCCACAACGGTGAATCTCACTTCCCTGGC-AGTACAATGGAGCAGATTAAAGCTA
1 AA-GATTGAAGCCGCAACGGCGAATCTTACTTTCCTGGCGA-TGCAGTGGATCAGATTGAAGCTA
* * * *
28844628 CGACGGTGAATCTTGCTTCCCTGAAATTGCAATTTAA
64 CAACGGTGAATCTT-ATTCCCCGACATTGCAATTTAA
* * * * * *
28844665 AATATTGAAGCCGCAACAGCGAATCTTACTTCCCTGG-TAGTGCAGTGGAACAGATTCAAGCTAC
1 AAGATTGAAGCCGCAACGGCGAATCTTACTTTCCTGGCGA-TGCAGTGGATCAGATTGAAGCTAC
* * * * * *
28844729 GACTGCGAATCGTGTTCCCTGACATTGCAATT
65 AACGGTGAATCTTATTCCCCGACATTGCAATT
28844761 GAGGTCGCAA
Statistics
Matches: 416, Mismatches: 71, Indels: 14
0.83 0.14 0.03
Matches are distributed among these distances:
98 6 0.01
99 243 0.58
100 161 0.39
101 6 0.01
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.26
Consensus pattern (99 bp):
AAGATTGAAGCCGCAACGGCGAATCTTACTTTCCTGGCGATGCAGTGGATCAGATTGAAGCTACA
ACGGTGAATCTTATTCCCCGACATTGCAATTTAA
Found at i:28844471 original size:50 final size:50
Alignment explanation
Indices: 28844168--28844700 Score: 288
Period size: 50 Copynumber: 10.7 Consensus size: 50
28844158 TGCAGCAAAG
** * * * * **
28844168 AAGATTGAAGCCGCAACGGTGAATCTTACCTCCCTGGCAGTGCAGTGGAA
1 AAGATTGAAGCTACAACGGTGAATCTTACTTCCCTGACATTGCAATTAAA
* * * *
28844218 CATATTGAAGCTACAACAGTGAATCTTA-TT-CCTCGACATTGCAATTTAA
1 AAGATTGAAGCTACAACGGTGAATCTTACTTCCCT-GACATTGCAATTAAA
** * * * ** *
28844267 AAGATTGAAGCCGCAACGGCGAATCTTACTTTCCT-AGCGA-TACAATGGAT
1 AAGATTGAAGCTACAACGGTGAATCTTACTTCCCTGA-C-ATTGCAATTAAA
* * * * *
28844317 CAGATTGAAGCTACAACGGTGAATCTCA-TTCCCCGACATTCCAATTTAA
1 AAGATTGAAGCTACAACGGTGAATCTTACTTCCCTGACATTGCAATTAAA
* ** *** **** * ** *
28844366 AAGACTGAAGCCGCAACGGTGAATCTTACTTTTTTGGTGGTGCAGTGGAC
1 AAGATTGAAGCTACAACGGTGAATCTTACTTCCCTGACATTGCAATTAAA
* * * * *
28844416 CAGATTAAAGCTACGACGGTGAATCTTGCTTCCCCGACATTGCAATTAAA
1 AAGATTGAAGCTACAACGGTGAATCTTACTTCCCTGACATTGCAATTAAA
** * * * * * ** *
28844466 AAGATTGAAGCCGCAAGGGCGAATCTTACTTTCCTGGCGA-TGCAGTGGAT
1 AAGATTGAAGCTACAACGGTGAATCTTACTTCCCTGAC-ATTGCAATTAAA
* * *
28844516 TAGATTGAAGCTACAACGGCGAATCTTA-TTCCCCGACATTGCAATTAAA
1 AAGATTGAAGCTACAACGGTGAATCTTACTTCCCTGACATTGCAATTAAA
* * * * * * ** *
28844565 AGGATTGAAGCCACAACGGTGAATCTCACTTCCCTGGCAGTACAATGGAG
1 AAGATTGAAGCTACAACGGTGAATCTTACTTCCCTGACATTGCAATTAAA
* * * * * *
28844615 CAGATTAAAGCTACGACGGTGAATCTTGCTTCCCTGAAATTGCAATTTAA
1 AAGATTGAAGCTACAACGGTGAATCTTACTTCCCTGACATTGCAATTAAA
* ** * *
28844665 AATATTGAAGCCGCAACAGCGAATCTTACTTCCCTG
1 AAGATTGAAGCTACAACGGTGAATCTTACTTCCCTG
28844701 GTAGTGCAGT
Statistics
Matches: 342, Mismatches: 130, Indels: 22
0.69 0.26 0.04
Matches are distributed among these distances:
48 5 0.01
49 103 0.30
50 229 0.67
51 5 0.01
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.26
Consensus pattern (50 bp):
AAGATTGAAGCTACAACGGTGAATCTTACTTCCCTGACATTGCAATTAAA
Found at i:28844523 original size:199 final size:198
Alignment explanation
Indices: 28844168--28844739 Score: 761
Period size: 199 Copynumber: 2.9 Consensus size: 198
28844158 TGCAGCAAAG
* * * *
28844168 AAGATTGAAGCCGCAACGGTGAATCTTACCTCCCTGGCAGTGCAGTGGAACATATTGAAGCTACA
1 AAGATTGAAGCCGCAACGGTGAATCTTACTTCCCTGGCAGTGCAGTGGAACAGATTAAAGCTACG
* * *
28844233 ACAGTGAATCTT-ATTCCTCGACATTGCAATTTAAAAGATTGAAGCCGCAACGGCGAATCTTACT
66 ACGGTGAATCTTGCTTCCCCGACATTGCAATTTAAAAGATTGAAGCCGCAACGGCGAATCTTACT
* * * *
28844297 TTCCTAGCGATACAATGGATCAGATTGAAGCTACAACGGTGAATCTCATTCCCCGACATTCCAAT
131 TTCCTGGCGATGCAGTGGATCAGATTGAAGCTACAACGGCGAATCTCATTCCCCGACATTCCAA-
28844362 TTAA
195 TTAA
* *** ** *
28844366 AAGACTGAAGCCGCAACGGTGAATCTTACTTTTTTGGTGGTGCAGTGGACCAGATTAAAGCTACG
1 AAGATTGAAGCCGCAACGGTGAATCTTACTTCCCTGGCAGTGCAGTGGAACAGATTAAAGCTACG
* *
28844431 ACGGTGAATCTTGCTTCCCCGACATTGCAATTAAAAAGATTGAAGCCGCAAGGGCGAATCTTACT
66 ACGGTGAATCTTGCTTCCCCGACATTGCAATTTAAAAGATTGAAGCCGCAACGGCGAATCTTACT
* * *
28844496 TTCCTGGCGATGCAGTGGATTAGATTGAAGCTACAACGGCGAATCTTATTCCCCGACATTGCAAT
131 TTCCTGGCGATGCAGTGGATCAGATTGAAGCTACAACGGCGAATCTCATTCCCCGACATTCCAAT
28844561 TAA
196 TAA
* * * * *
28844564 AAGGATTGAAGCCACAACGGTGAATCTCACTTCCCTGGCAGTACAATGGAGCAGATTAAAGCTAC
1 AA-GATTGAAGCCGCAACGGTGAATCTTACTTCCCTGGCAGTGCAGTGGAACAGATTAAAGCTAC
* * * *
28844629 GACGGTGAATCTTGCTTCCCTGAAATTGCAATTTAAAATATTGAAGCCGCAACAGCGAATCTTAC
65 GACGGTGAATCTTGCTTCCCCGACATTGCAATTTAAAAGATTGAAGCCGCAACGGCGAATCTTAC
* * * * * *
28844694 TTCCCTGG-TAGTGCAGTGGAACAGATTCAAGCTACGACTGCGAATC
130 TTTCCTGGCGA-TGCAGTGGATCAGATTGAAGCTACAACGGCGAATC
28844740 GTGTTCCCTG
Statistics
Matches: 324, Mismatches: 47, Indels: 5
0.86 0.12 0.01
Matches are distributed among these distances:
198 72 0.22
199 252 0.78
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.25
Consensus pattern (198 bp):
AAGATTGAAGCCGCAACGGTGAATCTTACTTCCCTGGCAGTGCAGTGGAACAGATTAAAGCTACG
ACGGTGAATCTTGCTTCCCCGACATTGCAATTTAAAAGATTGAAGCCGCAACGGCGAATCTTACT
TTCCTGGCGATGCAGTGGATCAGATTGAAGCTACAACGGCGAATCTCATTCCCCGACATTCCAAT
TAA
Found at i:28844844 original size:44 final size:44
Alignment explanation
Indices: 28844776--28845082 Score: 211
Period size: 44 Copynumber: 7.1 Consensus size: 44
28844766 CGCAATGGCG
*
28844776 AATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACTACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACTACA
* * * * * * *
28844820 AATCTTATCTCTCTAAAGTTGCAGTAGAGTAGG--TCACA-T-CC
1 AATCTTATCTCCCTGAAGTTGCAGTGGAG-CGGATTAAAACTACA
* * * * * *
28844861 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGCTACT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACTACA
* * * *
28844905 AATCCTATCTCCTTGAAGTTGCAGTGGAGCGGATTAAGACCACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACTACA
* ** * * *** *
28844949 GATCTTATCTATCTGAAGTTGTAGTAGAGC--A-TATCGC-ATCC
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACTA-CA
* * * *
28844990 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACATAAGAA--ACC
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCGGA-TTAA-AACTACA
* *
28845034 AATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACTACA
28845078 AATCT
1 AATCT
28845083 CGTCCCCATA
Statistics
Matches: 196, Mismatches: 54, Indels: 26
0.71 0.20 0.09
Matches are distributed among these distances:
40 2 0.01
41 54 0.28
42 6 0.03
43 8 0.04
44 121 0.62
45 5 0.03
ACGTcount: A:0.30, C:0.22, G:0.21, T:0.27
Consensus pattern (44 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACTACA
Found at i:28844933 original size:129 final size:129
Alignment explanation
Indices: 28844776--28845082 Score: 472
Period size: 129 Copynumber: 2.4 Consensus size: 129
28844766 CGCAATGGCG
* *
28844776 AATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACTACAAATCTTATCTCTCTAAAGTTG
1 AATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCACAAATCTTATCTATCTAAAGTTG
* * ** *
28844841 CAGTAGAGTAGGTCACATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGAC-TGAAGCTACT
66 CAGTAGAGCAGATCACATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAT-AAGAAACC
* * * *
28844905 AATCCTATCTCCTTGAAGTTGCAGTGGAGCGGATTAAGACCACAGATCTTATCTATCTGAAGTTG
1 AATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCACAAATCTTATCTATCTAAAGTTG
* * *
28844970 TAGTAGAGCATATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACATAAGAAACC
66 CAGTAGAGCAGATCACATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACATAAGAAACC
28845034 AATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCACAAATCT
1 AATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCACAAATCT
28845083 CGTCCCCATA
Statistics
Matches: 160, Mismatches: 17, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
129 159 0.99
130 1 0.01
ACGTcount: A:0.30, C:0.22, G:0.21, T:0.27
Consensus pattern (129 bp):
AATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCACAAATCTTATCTATCTAAAGTTG
CAGTAGAGCAGATCACATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACATAAGAAACC
Found at i:28849067 original size:56 final size:56
Alignment explanation
Indices: 28848999--28849151 Score: 227
Period size: 56 Copynumber: 2.7 Consensus size: 56
28848989 AGTAATTACA
*
28848999 TAGGAATTAAATTGCTAAAAGATAATATCTCATAATAATATCCTATAATATCCCAT
1 TAGGAATCAAATTGCTAAAAGATAATATCTCATAATAATATCCTATAATATCCCAT
* * * *
28849055 TAGGAATCAAATTGCTAAGAGATAATATCCCATAATAATACCCTATAATATCCTAT
1 TAGGAATCAAATTGCTAAAAGATAATATCTCATAATAATATCCTATAATATCCCAT
* *
28849111 TAGGGATCAAATTGCAAAAAGATAATATCAT-ATAATAATAT
1 TAGGAATCAAATTGCTAAAAGATAATATC-TCATAATAATAT
28849152 TCTAACTTAT
Statistics
Matches: 86, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
56 86 1.00
ACGTcount: A:0.46, C:0.14, G:0.09, T:0.31
Consensus pattern (56 bp):
TAGGAATCAAATTGCTAAAAGATAATATCTCATAATAATATCCTATAATATCCCAT
Found at i:28852753 original size:42 final size:42
Alignment explanation
Indices: 28852640--28852786 Score: 152
Period size: 42 Copynumber: 3.4 Consensus size: 42
28852630 ATCCGATATG
* * *
28852640 TGATATCGTGTAAGACCATGTTTGGGACGTTGGCATCG-ATT
1 TGATTTCGTGTAAGACCATGTTTGGGACATTGACATCGTATT
* ** *
28852681 TGAGATTTATGTGTAAGACCATGTCCGGGACATTGACATCGTATA
1 T--GATTT-CGTGTAAGACCATGTTTGGGACATTGACATCGTATT
* *
28852726 TGATTTCGTGTAAGACCCTGTTTGGGACAGTGACATCGTTATT
1 TGATTTCGTGTAAGACCATGTTTGGGACATTGACATCG-TATT
* *
28852769 TGATTACATGTAAGACCA
1 TGATTTCGTGTAAGACCA
28852787 CGTCTAGGAC
Statistics
Matches: 85, Mismatches: 16, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
41 1 0.01
42 27 0.32
43 27 0.32
44 27 0.32
45 3 0.04
ACGTcount: A:0.26, C:0.16, G:0.25, T:0.33
Consensus pattern (42 bp):
TGATTTCGTGTAAGACCATGTTTGGGACATTGACATCGTATT
Found at i:28854655 original size:34 final size:34
Alignment explanation
Indices: 28854612--28854683 Score: 135
Period size: 34 Copynumber: 2.1 Consensus size: 34
28854602 ATACTTGCCA
28854612 TCATCGACCCAAAACTCGAATGAAATTTATATTT
1 TCATCGACCCAAAACTCGAATGAAATTTATATTT
*
28854646 TCATCGACCCAAAGCTCGAATGAAATTTATATTT
1 TCATCGACCCAAAACTCGAATGAAATTTATATTT
28854680 TCAT
1 TCAT
28854684 GCTAATGATA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.36, C:0.21, G:0.10, T:0.33
Consensus pattern (34 bp):
TCATCGACCCAAAACTCGAATGAAATTTATATTT
Found at i:28857835 original size:50 final size:50
Alignment explanation
Indices: 28857781--28857907 Score: 139
Period size: 50 Copynumber: 2.5 Consensus size: 50
28857771 CCAAGAAGAT
* * * * *
28857781 TTTACAGAGAGTTCGCCACAAAGGCTTCATAGA-ATATTCGCTACAAAGGG
1 TTTACAGAGAATTTGCCACAAAGGCTTCATAGAGA-ATTCACCACAAAGGC
* * * *
28857831 TTTACAAAGAATTTGCCACAAAGACTTTATAGAGAATTCACCACAAAGTC
1 TTTACAGAGAATTTGCCACAAAGGCTTCATAGAGAATTCACCACAAAGGC
* *
28857881 TTTATAGAGAATTTACCACAAAGGCTT
1 TTTACAGAGAATTTGCCACAAAGGCTT
28857908 TCCAGAGAAT
Statistics
Matches: 63, Mismatches: 13, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
50 62 0.98
51 1 0.02
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.27
Consensus pattern (50 bp):
TTTACAGAGAATTTGCCACAAAGGCTTCATAGAGAATTCACCACAAAGGC
Found at i:28857851 original size:25 final size:25
Alignment explanation
Indices: 28857823--28857917 Score: 109
Period size: 25 Copynumber: 3.8 Consensus size: 25
28857813 AATATTCGCT
* * * *
28857823 ACAAAGGGTTTACAAAGAATTTGCC
1 ACAAAGGCTTTATAGAGAATTTACC
* *
28857848 ACAAAGACTTTATAGAGAATTCACC
1 ACAAAGGCTTTATAGAGAATTTACC
*
28857873 ACAAAGTCTTTATAGAGAATTTACC
1 ACAAAGGCTTTATAGAGAATTTACC
**
28857898 ACAAAGGCTTTCCAGAGAAT
1 ACAAAGGCTTTATAGAGAAT
28857918 CCGTGTTTAC
Statistics
Matches: 59, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 59 1.00
ACGTcount: A:0.41, C:0.18, G:0.16, T:0.25
Consensus pattern (25 bp):
ACAAAGGCTTTATAGAGAATTTACC
Found at i:28860023 original size:30 final size:30
Alignment explanation
Indices: 28859989--28860051 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
28859979 ACTTATTTTA
28859989 TTGTTAATTTTGTTATTATTTTAAAGACAT
1 TTGTTAATTTTGTTATTATTTTAAAGACAT
* *
28860019 TTGTTAATTTTGTTATTATTTTAGAGGCAT
1 TTGTTAATTTTGTTATTATTTTAAAGACAT
28860049 TTG
1 TTG
28860052 CTTGTTAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.25, C:0.03, G:0.14, T:0.57
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAAAGACAT
Found at i:28862224 original size:16 final size:16
Alignment explanation
Indices: 28862198--28862236 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
28862188 CAGAATCGAG
*
28862198 TTAAGAAAATTATTTAA
1 TTAA-AAAATTAATTAA
28862215 TTAAAAAATTAATTAA
1 TTAAAAAATTAATTAA
28862231 TTAAAA
1 TTAAAA
28862237 TTAAATTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 17 0.81
17 4 0.19
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (16 bp):
TTAAAAAATTAATTAA
Found at i:28866171 original size:37 final size:37
Alignment explanation
Indices: 28866102--28866207 Score: 178
Period size: 37 Copynumber: 2.8 Consensus size: 37
28866092 ACCAAAAATT
*
28866102 TATTTTAAAAATAAAAAAATAAAAAAAGTATTTTAAAAA
1 TATTTTAAAATTAAAAAAAT-AAAAAA-TATTTTAAAAA
28866141 TATTTTAAAATTAAAAAAATAAAAAATATTTTAAAAA
1 TATTTTAAAATTAAAAAAATAAAAAATATTTTAAAAA
28866178 TATTTTAAAATTAAAAAAAT-AAAAATATTT
1 TATTTTAAAATTAAAAAAATAAAAAATATTT
28866208 ATTATATTCA
Statistics
Matches: 66, Mismatches: 1, Indels: 3
0.94 0.01 0.04
Matches are distributed among these distances:
36 10 0.15
37 31 0.47
38 6 0.09
39 19 0.29
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (37 bp):
TATTTTAAAATTAAAAAAATAAAAAATATTTTAAAAA
Found at i:28866188 original size:10 final size:11
Alignment explanation
Indices: 28866162--28866187 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
28866152 TAAAAAAATA
28866162 AAAAATATTTT
1 AAAAATATTTT
28866173 AAAAATATTTT
1 AAAAATATTTT
28866184 AAAA
1 AAAA
28866188 TTAAAAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:28866930 original size:20 final size:20
Alignment explanation
Indices: 28866905--28866953 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
28866895 ATATTATTAC
* *
28866905 AAAAAATGTAAGAGAATTGT
1 AAAAAATATAAAAGAATTGT
*
28866925 AAAAAATATAAAAGTATTGT
1 AAAAAATATAAAAGAATTGT
28866945 AAAAAATAT
1 AAAAAATAT
28866954 TTCTAAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.61, C:0.00, G:0.12, T:0.27
Consensus pattern (20 bp):
AAAAAATATAAAAGAATTGT
Found at i:28867203 original size:30 final size:30
Alignment explanation
Indices: 28867144--28867204 Score: 70
Period size: 30 Copynumber: 2.0 Consensus size: 30
28867134 TTTTAACTTG
*
28867144 TTTTAAATTTTTATATATTATATATTATAT
1 TTTTAAATTTTTATATAATATATATTATAT
*
28867174 TTTTACATTTTTA-ATCAATATAATATATATA
1 TTTTAAATTTTTATAT-AATAT-ATAT-TATA
28867205 ATATTAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
29 2 0.08
30 16 0.62
31 4 0.15
32 4 0.15
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.57
Consensus pattern (30 bp):
TTTTAAATTTTTATATAATATATATTATAT
Found at i:28867388 original size:20 final size:20
Alignment explanation
Indices: 28867359--28867396 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
28867349 TAATTTTCTA
*
28867359 TTTTAATTTAACTTTAATAC
1 TTTTAATTTAAATTTAATAC
*
28867379 TTTTATTTTAAATTTAAT
1 TTTTAATTTAAATTTAAT
28867397 TGTCACTTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (20 bp):
TTTTAATTTAAATTTAATAC
Found at i:28868693 original size:103 final size:103
Alignment explanation
Indices: 28868475--28868905 Score: 666
Period size: 103 Copynumber: 4.2 Consensus size: 103
28868465 ACACTCCGTT
* *
28868475 TTGTGGATGAACCACCAGTAATGTGCAGATAAACTGCCAGTAAAAAAAATTGTGGATGAACCACT
1 TTGTGGATGAACCACCAGTAATTTGCAGATAAACTGCCAGT---AAAAATTGTGGATGAACCACC
* *
28868540 AGTG-TTCAGATAAAAAGTTTGCAGACAAGCTGCCAATAAG
63 AGTGTTTTAGATAAAAAGTTTGCAGACAAGCTGCCAGTAAG
*
28868580 TTTTGGATGAACCACCAGTAATTTGCAGATAAACTGCCAGTAAAAATTGTGGATGAACCACCAGT
1 TTGTGGATGAACCACCAGTAATTTGCAGATAAACTGCCAGTAAAAATTGTGGATGAACCACCAGT
* * *
28868645 GTTTTAGATAAAAAATTTGCAGACAAGCTTCTAGTAAG
66 GTTTTAGATAAAAAGTTTGCAGACAAGCTGCCAGTAAG
* *** *
28868683 TTGTGGATGAACCACCAGTAATTTGCAAATAAACTGTTTGTAAAAATTGTGGATGAACCACCAAT
1 TTGTGGATGAACCACCAGTAATTTGCAGATAAACTGCCAGTAAAAATTGTGGATGAACCACCAGT
* * *
28868748 GTTTTAGATAAAAAGTTTGTAGATAAGCTGTCAGTAAG
66 GTTTTAGATAAAAAGTTTGCAGACAAGCTGCCAGTAAG
* *
28868786 TTGTGGATGAACCACCAGTAATTTGCAGATAAACTGCCAGTAAAAATTATGGATGGACCACCAGT
1 TTGTGGATGAACCACCAGTAATTTGCAGATAAACTGCCAGTAAAAATTGTGGATGAACCACCAGT
28868851 GTTTTAGATAAAAAGTTTGCAGACAAGCTGCCAGTAAG
66 GTTTTAGATAAAAAGTTTGCAGACAAGCTGCCAGTAAG
28868889 TTGTGGATGAACCACCA
1 TTGTGGATGAACCACCA
28868906 ATGTTTGTAG
Statistics
Matches: 295, Mismatches: 30, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
102 24 0.08
103 232 0.79
105 39 0.13
ACGTcount: A:0.37, C:0.15, G:0.21, T:0.27
Consensus pattern (103 bp):
TTGTGGATGAACCACCAGTAATTTGCAGATAAACTGCCAGTAAAAATTGTGGATGAACCACCAGT
GTTTTAGATAAAAAGTTTGCAGACAAGCTGCCAGTAAG
Found at i:28868911 original size:57 final size:59
Alignment explanation
Indices: 28868807--28868917 Score: 145
Period size: 57 Copynumber: 1.9 Consensus size: 59
28868797 CCACCAGTAA
* * *
28868807 TTTGCAGATAAACTGCCAGTAAAAATTATGGATGGACCACCAGTGTTT-TAGATAAAAAG
1 TTTGCAGACAAACTGCCAGT-AAAATTATGGATGAACCACCAATGTTTGTAGATAAAAAG
* * *
28868866 TTTGCAGACAAGCTGCCAGT-AAGTTGTGGATGAACCACCAATGTTTGTAGAT
1 TTTGCAGACAAACTGCCAGTAAAATTATGGATGAACCACCAATGTTTGTAGAT
28868918 TGTTAACTGC
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
57 22 0.49
58 5 0.11
59 18 0.40
ACGTcount: A:0.34, C:0.15, G:0.23, T:0.28
Consensus pattern (59 bp):
TTTGCAGACAAACTGCCAGTAAAATTATGGATGAACCACCAATGTTTGTAGATAAAAAG
Found at i:28870037 original size:23 final size:25
Alignment explanation
Indices: 28870000--28870045 Score: 69
Period size: 23 Copynumber: 1.9 Consensus size: 25
28869990 AATAGGGTGC
*
28870000 AAGAATAAGAGAAAAGAG-GAGAAA
1 AAGAATAAGAAAAAAGAGAGAGAAA
28870024 AAGAA-AAGAAAAAAGAGAGAGA
1 AAGAATAAGAAAAAAGAGAGAGA
28870046 GAGCAAATTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.70, C:0.00, G:0.28, T:0.02
Consensus pattern (25 bp):
AAGAATAAGAAAAAAGAGAGAGAAA
Found at i:28871406 original size:31 final size:31
Alignment explanation
Indices: 28871371--28871429 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
28871361 ATAGCCGAGA
28871371 GACTTAAATAAAAACTTTTGAATAGTTCGAT
1 GACTTAAATAAAAACTTTTGAATAGTTCGAT
*
28871402 GACTTAAATGAAAACTTTTGAATAGTTC
1 GACTTAAATAAAAACTTTTGAATAGTTC
28871430 AACGATCATT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.36
Consensus pattern (31 bp):
GACTTAAATAAAAACTTTTGAATAGTTCGAT
Found at i:28871585 original size:18 final size:19
Alignment explanation
Indices: 28871549--28871586 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
28871539 AAATATATTT
* *
28871549 TTTATTAAAATTTATAAAA
1 TTTATTAAAATATAAAAAA
28871568 TTTA-TAAAATATAAAAAA
1 TTTATTAAAATATAAAAAA
28871586 T
1 T
28871587 ATAGAAATTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
TTTATTAAAATATAAAAAA
Found at i:28873846 original size:2 final size:2
Alignment explanation
Indices: 28873839--28873901 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
28873829 CAAAAAGTAA
28873839 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
28873881 AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG A
28873902 ACAATATTAA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:28880810 original size:12 final size:12
Alignment explanation
Indices: 28880793--28880850 Score: 54
Period size: 12 Copynumber: 5.1 Consensus size: 12
28880783 TTTTAATAAG
28880793 ATTTAATATTAA
1 ATTTAATATTAA
28880805 ATTTAATA-TAA
1 ATTTAATATTAA
28880816 TATTT-A-A-TAA
1 -ATTTAATATTAA
*
28880826 ATATT-AGATTAA
1 AT-TTAATATTAA
28880838 ATTTAATATTAA
1 ATTTAATATTAA
28880850 A
1 A
28880851 GTGATTAAGT
Statistics
Matches: 40, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
9 2 0.05
10 7 0.17
11 7 0.17
12 24 0.60
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (12 bp):
ATTTAATATTAA
Found at i:28887673 original size:23 final size:23
Alignment explanation
Indices: 28887610--28887693 Score: 73
Period size: 24 Copynumber: 3.6 Consensus size: 23
28887600 AACAACAGGT
*
28887610 AAAAAGGAAA-AAATAA-AGAAG
1 AAAAAGGAAAGAAAAAACAGAAG
* * *
28887631 AAGAAAAGACAATAACAAACAGAAG
1 AA-AAAGGA-AAGAAAAAACAGAAG
*
28887656 AAAAAGGAAAGAAAAAACAGGAAA
1 AAAAAGGAAAGAAAAAACA-GAAG
*
28887680 AAAAAGAAAAGAAA
1 AAAAAGGAAAGAAA
28887694 GAAAGAAAGA
Statistics
Matches: 50, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
21 2 0.04
22 5 0.10
23 11 0.22
24 25 0.50
25 7 0.14
ACGTcount: A:0.75, C:0.05, G:0.18, T:0.02
Consensus pattern (23 bp):
AAAAAGGAAAGAAAAAACAGAAG
Found at i:28887690 original size:24 final size:23
Alignment explanation
Indices: 28887647--28887709 Score: 67
Period size: 24 Copynumber: 2.8 Consensus size: 23
28887637 AGACAATAAC
* *
28887647 AAACAGAAGAAAAAGGAAAGAAA
1 AAACAGAAAAAAAAGAAAAGAAA
28887670 AAACAGGAAAAAAAAGAAAAGAAA
1 AAACA-GAAAAAAAAGAAAAGAAA
* *
28887694 GAA-AG-AAAGAAAGAAA
1 AAACAGAAAAAAAAGAAA
28887710 TAACATGTCA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
21 10 0.29
22 1 0.03
23 6 0.17
24 18 0.51
ACGTcount: A:0.76, C:0.03, G:0.21, T:0.00
Consensus pattern (23 bp):
AAACAGAAAAAAAAGAAAAGAAA
Found at i:28908986 original size:22 final size:22
Alignment explanation
Indices: 28908961--28909035 Score: 105
Period size: 22 Copynumber: 3.4 Consensus size: 22
28908951 TAACGTGAAA
28908961 CATGAGAGCTTAGTACGTTAGC
1 CATGAGAGCTTAGTACGTTAGC
28908983 CATGAGAGCTTAGTACGTTAGC
1 CATGAGAGCTTAGTACGTTAGC
* * * **
28909005 CATGAGGGTTTAGTTCGTTAAA
1 CATGAGAGCTTAGTACGTTAGC
28909027 CATGAGAGC
1 CATGAGAGC
28909036 GTCAGATACC
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 46 1.00
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.28
Consensus pattern (22 bp):
CATGAGAGCTTAGTACGTTAGC
Found at i:28912875 original size:22 final size:22
Alignment explanation
Indices: 28912850--28912894 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
28912840 GCCTTAAAAA
28912850 TTTTGCGACATTACCTTTACGG
1 TTTTGCGACATTACCTTTACGG
28912872 TTTTGCGACATTACCTTTACGG
1 TTTTGCGACATTACCTTTACGG
28912894 T
1 T
28912895 GAAAAATATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.18, C:0.22, G:0.18, T:0.42
Consensus pattern (22 bp):
TTTTGCGACATTACCTTTACGG
Found at i:28913078 original size:39 final size:41
Alignment explanation
Indices: 28913033--28913169 Score: 137
Period size: 40 Copynumber: 3.5 Consensus size: 41
28913023 GGCGTTTGAA
28913033 TAAAAAACGCCGCTAAAAATCAATCATTAGCGGCGC-TATC
1 TAAAAAACGCCGCTAAAAATCAATCATTAGCGGCGCTTATC
* * * *
28913073 TAAAAAACACCGCTAAAGATCGAGT-ATTAGCGGCGCTTTTC
1 TAAAAAACGCCGCTAAAAATC-AATCATTAGCGGCGCTTATC
* *
28913114 T-AAAAACGCCGCTAAAAAT-GAGCATTAGCGGCG-TT-T-
1 TAAAAAACGCCGCTAAAAATCAATCATTAGCGGCGCTTATC
28913150 TACAAAAAGCGCCGC-AAAAA
1 TA-AAAAA-CGCCGCTAAAAA
28913170 CCTAAATCTA
Statistics
Matches: 82, Mismatches: 9, Indels: 14
0.78 0.09 0.13
Matches are distributed among these distances:
36 1 0.01
37 1 0.01
38 12 0.15
39 16 0.20
40 46 0.56
41 6 0.07
ACGTcount: A:0.39, C:0.23, G:0.18, T:0.20
Consensus pattern (41 bp):
TAAAAAACGCCGCTAAAAATCAATCATTAGCGGCGCTTATC
Found at i:28913866 original size:15 final size:15
Alignment explanation
Indices: 28913846--28913877 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
28913836 TATTTTAAGG
28913846 TTTAGGGAGTATGGA
1 TTTAGGGAGTATGGA
*
28913861 TTTAGGGATTATGGA
1 TTTAGGGAGTATGGA
28913876 TT
1 TT
28913878 AGCGATTATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.00, G:0.34, T:0.41
Consensus pattern (15 bp):
TTTAGGGAGTATGGA
Found at i:28913884 original size:14 final size:15
Alignment explanation
Indices: 28913855--28913892 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
28913845 GTTTAGGGAG
*
28913855 TATGGATTTAGGGAT
1 TATGGATTTAGCGAT
28913870 TATGGA-TTAGCGAT
1 TATGGATTTAGCGAT
28913884 TATGG-TTTA
1 TATGGATTTA
28913893 AGGGTTGTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.26, C:0.03, G:0.29, T:0.42
Consensus pattern (15 bp):
TATGGATTTAGCGAT
Found at i:28913911 original size:21 final size:21
Alignment explanation
Indices: 28913887--28913956 Score: 72
Period size: 21 Copynumber: 3.3 Consensus size: 21
28913877 TAGCGATTAT
*
28913887 GGTTTAAGGGTTGTGATTTAA
1 GGTTTAAGGGTTGAGATTTAA
*
28913908 GGTTT-AGGGATT-AGATGTTAG
1 GGTTTAAGGG-TTGAGAT-TTAA
*
28913929 GGTTTAAGAGTTAGAGATTTAA
1 GGTTTAAGGGTT-GAGATTTAA
28913951 GGTTTA
1 GGTTTA
28913957 GGGATTCAGG
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
20 7 0.17
21 17 0.43
22 12 0.30
23 4 0.10
ACGTcount: A:0.27, C:0.00, G:0.33, T:0.40
Consensus pattern (21 bp):
GGTTTAAGGGTTGAGATTTAA
Found at i:28913957 original size:15 final size:15
Alignment explanation
Indices: 28913901--28913962 Score: 60
Period size: 15 Copynumber: 4.3 Consensus size: 15
28913891 TAAGGGTTGT
28913901 GATTTAAGGTTTAGG
1 GATTTAAGGTTTAGG
*
28913916 GA-TT-AGATGTTAGG
1 GATTTAAGGT-TTAGG
*
28913930 G-TTTAAGAG-TTAGA
1 GATTTAAG-GTTTAGG
28913944 GATTTAAGGTTTAGG
1 GATTTAAGGTTTAGG
28913959 GATT
1 GATT
28913963 CAGGGGTCAG
Statistics
Matches: 37, Mismatches: 4, Indels: 12
0.70 0.08 0.23
Matches are distributed among these distances:
13 3 0.08
14 16 0.43
15 18 0.49
ACGTcount: A:0.29, C:0.00, G:0.32, T:0.39
Consensus pattern (15 bp):
GATTTAAGGTTTAGG
Done.