Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold216
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: 960516
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.32
Warning! 50240 characters in sequence are not A, C, G, or T
File 2 of 4
Found at i:292733 original size:63 final size:63
Alignment explanation
Indices: 292661--292789 Score: 258
Period size: 63 Copynumber: 2.0 Consensus size: 63
292651 TCTTTGCAGC
292661 TGTTGCCAATGCCATCCAGTGAGCTGATGAGATGGTTAATCTAATGTTTTGATTAAACAAAGA
1 TGTTGCCAATGCCATCCAGTGAGCTGATGAGATGGTTAATCTAATGTTTTGATTAAACAAAGA
292724 TGTTGCCAATGCCATCCAGTGAGCTGATGAGATGGTTAATCTAATGTTTTGATTAAACAAAGA
1 TGTTGCCAATGCCATCCAGTGAGCTGATGAGATGGTTAATCTAATGTTTTGATTAAACAAAGA
292787 TGT
1 TGT
292790 AAAATCATAA
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 66 1.00
ACGTcount: A:0.31, C:0.14, G:0.22, T:0.33
Consensus pattern (63 bp):
TGTTGCCAATGCCATCCAGTGAGCTGATGAGATGGTTAATCTAATGTTTTGATTAAACAAAGA
Found at i:292887 original size:13 final size:13
Alignment explanation
Indices: 292869--292899 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
292859 TGAGCAGATG
*
292869 TTCTGATAAAATA
1 TTCTGATAAAACA
292882 TTCTGATAAAACA
1 TTCTGATAAAACA
292895 TTCTG
1 TTCTG
292900 CTATATTTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.39, C:0.13, G:0.10, T:0.39
Consensus pattern (13 bp):
TTCTGATAAAACA
Found at i:293818 original size:18 final size:17
Alignment explanation
Indices: 293792--293827 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
293782 TTTGGTTATA
293792 TTTAATTTTCGATATGTT
1 TTTAATTTT-GATATGTT
*
293810 TTTATTTTTGATATGTT
1 TTTAATTTTGATATGTT
293827 T
1 T
293828 CATTTAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.19, C:0.03, G:0.11, T:0.67
Consensus pattern (17 bp):
TTTAATTTTGATATGTT
Found at i:294811 original size:45 final size:44
Alignment explanation
Indices: 294731--294818 Score: 133
Period size: 45 Copynumber: 2.0 Consensus size: 44
294721 CAATATCATT
*
294731 CCATTCAACCAAACACAATAATACTATTATAGCTCTATTCCATC
1 CCATTCAACCAAACACAATAATACTATTACAGCTCTATTCCATC
*
294775 CCATTCAACCAAAC-CATTGAATTACTATTACAGCTCTATTCCAT
1 CCATTCAACCAAACACAAT-AA-TACTATTACAGCTCTATTCCAT
294819 TACAGCTCTT
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
43 3 0.08
44 16 0.40
45 21 0.52
ACGTcount: A:0.36, C:0.30, G:0.03, T:0.31
Consensus pattern (44 bp):
CCATTCAACCAAACACAATAATACTATTACAGCTCTATTCCATC
Found at i:294822 original size:16 final size:16
Alignment explanation
Indices: 294801--294839 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
294791 TTGAATTACT
294801 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTCC
*
294817 ATTACAGCTCTTTTCC
1 ATTACAGCTCTATTCC
294833 ATTACAG
1 ATTACAG
294840 TGAACCAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.26, C:0.28, G:0.08, T:0.38
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:295061 original size:28 final size:28
Alignment explanation
Indices: 295029--295085 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
295019 GACATGAGAG
*
295029 TTAGTTGAATTTCCCAAAAGGAAGAAAT
1 TTAGTTGAATTTCCCAAAAGAAAGAAAT
295057 TTAGTTGAATTTCCCAAAAGAAAGAAAT
1 TTAGTTGAATTTCCCAAAAGAAAGAAAT
295085 T
1 T
295086 GGTCAGATGT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.44, C:0.11, G:0.16, T:0.30
Consensus pattern (28 bp):
TTAGTTGAATTTCCCAAAAGAAAGAAAT
Found at i:302156 original size:14 final size:13
Alignment explanation
Indices: 302116--302163 Score: 66
Period size: 14 Copynumber: 3.8 Consensus size: 13
302106 AAGAAATAAG
302116 TATTTTTTTCT-C
1 TATTTTTTTCTCC
302128 TA--TTTTTCTCC
1 TATTTTTTTCTCC
302139 TATTTTTTTCTCC
1 TATTTTTTTCTCC
302152 TTATTTTTTTCT
1 -TATTTTTTTCT
302164 TTCTTTTTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
10 7 0.22
11 3 0.09
12 2 0.06
13 9 0.28
14 11 0.34
ACGTcount: A:0.08, C:0.19, G:0.00, T:0.73
Consensus pattern (13 bp):
TATTTTTTTCTCC
Found at i:305745 original size:43 final size:43
Alignment explanation
Indices: 305688--306081 Score: 464
Period size: 43 Copynumber: 9.3 Consensus size: 43
305678 TTTTTCACAT
* *
305688 AAACGCCGTTAAAGAACATGACCTTTAGCGGCACTTTTGTCAC
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCACTTTTATCAC
* * *
305731 AATCGTCGCTAAAGAACATGACCTTTAGCGGCA-TTTTCATGAC
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCACTTTT-ATCAC
* * * *
305774 AAACGGCGCTAAAGAACATGACCTTTAGTGGCGCTTTTATTAC
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCACTTTTATCAC
*
305817 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTATCAC
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCACTTTTATCAC
* ** * *
305860 AAACGCCGCTAAAGAACATGACCTTTAGTGGTGCTTTTAGCAT
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCACTTTTATCAC
*
305903 AAACGCTGCTAAAGAACATGACCTTTAGC-G-ACTTTTTATCAC
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCAC-TTTTATCAC
* **
305945 AAACGCCACTAAAGAACAT---CTTTAGC-AAAGCTTTTATCAC
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCA-CTTTTATCAC
* * * * *
305985 AAACGCCGCTAAAAAATATGACCTTTAACGGCGCTTTTAGCAC
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCACTTTTATCAC
* *
306028 AAACGCCGCTAAATAACATGACCTTTAGCGGC-GTTTT-TCAC
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCACTTTTATCAC
306069 AAACGCCGCTAAA
1 AAACGCCGCTAAA
306082 AGTACCGTTC
Statistics
Matches: 304, Mismatches: 38, Indels: 20
0.84 0.10 0.06
Matches are distributed among these distances:
39 7 0.02
40 26 0.09
41 18 0.06
42 33 0.11
43 216 0.71
44 4 0.01
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.26
Consensus pattern (43 bp):
AAACGCCGCTAAAGAACATGACCTTTAGCGGCACTTTTATCAC
Found at i:306124 original size:168 final size:168
Alignment explanation
Indices: 305688--306081 Score: 470
Period size: 168 Copynumber: 2.3 Consensus size: 168
305678 TTTTTCACAT
* * * * *
305688 AAACGCCGTTAAAGAACATGACCTTTAGCGGCACTTTT-GTCACAATCGTCGCTAAAGAACATGA
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTAG-CACAAACGCCGCTAAAGAACACGA
* * * * * * **** *
305752 CCTTTAGCGGCATTTTCATGACAAACGGCGCTAAAGAACATGACCTTTAGTGGCGCTTTTATTAC
65 CCTTTAGCGAC-TTTTTATCAAAAACGCCACTAAAGAACAT---CTTTAGCAAAGCTTTTATCAC
* * *
305817 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTATCAC
126 AAACGCCGCTAAAAAACATGACCTTTAACGGCGCTTTTAGCAC
* * * * *
305860 AAACGCCGCTAAAGAACATGACCTTTAGTGGTGCTTTTAGCATAAACGCTGCTAAAGAACATGAC
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTAGCACAAACGCCGCTAAAGAACACGAC
*
305925 CTTTAGCGACTTTTTATCACAAACGCCACTAAAGAACATCTTTAGCAAAGCTTTTATCACAAACG
66 CTTTAGCGACTTTTTATCAAAAACGCCACTAAAGAACATCTTTAGCAAAGCTTTTATCACAAACG
*
305990 CCGCTAAAAAATATGACCTTTAACGGCGCTTTTAGCAC
131 CCGCTAAAAAACATGACCTTTAACGGCGCTTTTAGCAC
* *
306028 AAACGCCGCTAAATAACATGACCTTTAGCGGCG-TTTT-TCACAAACGCCGCTAAA
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTAGCACAAACGCCGCTAAA
306082 AGTACCGTTC
Statistics
Matches: 193, Mismatches: 28, Indels: 8
0.84 0.12 0.03
Matches are distributed among these distances:
166 14 0.07
167 4 0.02
168 85 0.44
171 25 0.13
172 64 0.33
173 1 0.01
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.26
Consensus pattern (168 bp):
AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTAGCACAAACGCCGCTAAAGAACACGAC
CTTTAGCGACTTTTTATCAAAAACGCCACTAAAGAACATCTTTAGCAAAGCTTTTATCACAAACG
CCGCTAAAAAACATGACCTTTAACGGCGCTTTTAGCAC
Found at i:309065 original size:34 final size:34
Alignment explanation
Indices: 309022--309090 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
309012 TGTTAGAAGA
309022 TAAACAAATTATAATTGATGAATATTTATCAAAT
1 TAAACAAATTATAATTGATGAATATTTATCAAAT
309056 TAAACAAATTATAATTGATGAATATTTATCAAAT
1 TAAACAAATTATAATTGATGAATATTTATCAAAT
309090 T
1 T
309091 CTAGAACTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.49, C:0.06, G:0.06, T:0.39
Consensus pattern (34 bp):
TAAACAAATTATAATTGATGAATATTTATCAAAT
Found at i:310735 original size:20 final size:20
Alignment explanation
Indices: 310693--310735 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
310683 ACCTCCTCCT
**
310693 AAATTTAGCCTAACAGTCCA
1 AAATTTAGCCTAACAGTAAA
*
310713 AAATTTAGCTTAACAGTAAA
1 AAATTTAGCCTAACAGTAAA
310733 AAA
1 AAA
310736 AAATGTTCAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.49, C:0.16, G:0.09, T:0.26
Consensus pattern (20 bp):
AAATTTAGCCTAACAGTAAA
Found at i:312210 original size:8 final size:7
Alignment explanation
Indices: 312193--312503 Score: 78
Period size: 7 Copynumber: 43.7 Consensus size: 7
312183 CTAATTAATT
312193 TAAACCC
1 TAAACCC
312200 TAAACCCC
1 TAAA-CCC
*
312208 TAAGCCC
1 TAAACCC
**
312215 TATCCCC
1 TAAACCC
*
312222 TAAACTC
1 TAAACCC
* * *
312229 TGAATCA
1 TAAACCC
* *
312236 TAAAACA
1 TAAACCC
* *
312243 TAAAACA
1 TAAACCC
*
312250 TAAACCT
1 TAAACCC
*
312257 TAAACCT
1 TAAACCC
312264 TAAACCCC
1 TAAA-CCC
*
312272 TAACCCC
1 TAAACCC
*
312279 TAAACCT
1 TAAACCC
*
312286 TAAACCT
1 TAAACCC
312293 TAAACCC
1 TAAACCC
* *
312300 -CAACCTT
1 TAAACC-C
*
312307 TAAACCA
1 TAAACCC
*
312314 TAAACCA
1 TAAACCC
*
312321 TAAACCA
1 TAAACCC
*
312328 TAATCCC
1 TAAACCC
312335 TAAACCC
1 TAAACCC
312342 -ATAACCC
1 TA-AACCC
*
312349 ATAAACCT
1 -TAAACCC
**
312357 TAAAATAC
1 T-AAACCC
*
312365 T-AACTCT
1 TAAAC-CC
*
312372 TAAACCT
1 TAAACCC
*
312379 TAAACCA
1 TAAACCC
*
312386 TAAACCA
1 TAAACCC
*
312393 TAAACCA
1 TAAACCC
* *
312400 TTATCCC
1 TAAACCC
312407 TAAACCC
1 TAAACCC
* *
312414 ATAATCCA
1 -TAAACCC
*
312422 TAAACCT
1 TAAACCC
*
312429 TAAA--A
1 TAAACCC
*
312434 TAGTAACTCT
1 TA--AAC-CC
*
312444 TAAACCT
1 TAAACCC
312451 TAAACCC
1 TAAACCC
312458 TAAA--C
1 TAAACCC
*
312463 TATTACCC
1 TA-AACCC
*
312471 TAAACCA
1 TAAACCC
*
312478 TAAACCG
1 TAAACCC
**
312485 TAAACTA
1 TAAACCC
312492 TAAACCC
1 TAAACCC
312499 TAAAC
1 TAAAC
312504 TATAATGATA
Statistics
Matches: 231, Mismatches: 54, Indels: 38
0.72 0.17 0.12
Matches are distributed among these distances:
5 5 0.02
6 8 0.03
7 178 0.77
8 37 0.16
9 1 0.00
10 2 0.01
ACGTcount: A:0.45, C:0.32, G:0.01, T:0.22
Consensus pattern (7 bp):
TAAACCC
Found at i:312267 original size:14 final size:14
Alignment explanation
Indices: 312234--312508 Score: 121
Period size: 14 Copynumber: 19.4 Consensus size: 14
312224 AACTCTGAAT
* *
312234 CATAAAACATAAAA
1 CATAAACCATAAAC
*
312248 CATAAACCTTAAAC
1 CATAAACCATAAAC
* * *
312262 CTTAAACCCCTAACC
1 CATAAA-CCATAAAC
* *
312277 CCTAAACCTTAAAC
1 CATAAACCATAAAC
* **
312291 CTTAAACC-CCAAC
1 CATAAACCATAAAC
*
312304 CTTTAAACCATAAAC
1 C-ATAAACCATAAAC
*
312319 CATAAACCATAATC
1 CATAAACCATAAAC
* *
312333 CCTAAACCCATAACC
1 CATAAA-CCATAAAC
*
312348 CATAAACCTTAAA-
1 CATAAACCATAAAC
*
312361 -ATACTAACTCTTAAAC
1 CATA--AAC-CATAAAC
*
312377 CTTAAACCATAAAC
1 CATAAACCATAAAC
* *
312391 CATAAACCATTATC
1 CATAAACCATAAAC
* *
312405 CCTAAACCCATAATC
1 CATAAA-CCATAAAC
*
312420 CATAAACCTTAAA-
1 CATAAACCATAAAC
*
312433 -ATAGTAACTCTTAAAC
1 CATA--AAC-CATAAAC
* *
312449 CTTAAACCCTAAAC
1 CATAAACCATAAAC
* * *
312463 TAT-TACCCTAAAC
1 CATAAACCATAAAC
*
312476 CATAAACCGTAAAC
1 CATAAACCATAAAC
* *
312490 TATAAACCCTAAAC
1 CATAAACCATAAAC
*
312504 TATAA
1 CATAA
312509 TGATAATTAA
Statistics
Matches: 204, Mismatches: 41, Indels: 32
0.74 0.15 0.12
Matches are distributed among these distances:
12 6 0.03
13 15 0.07
14 122 0.60
15 57 0.28
17 4 0.02
ACGTcount: A:0.47, C:0.30, G:0.01, T:0.23
Consensus pattern (14 bp):
CATAAACCATAAAC
Found at i:312298 original size:22 final size:22
Alignment explanation
Indices: 312257--312398 Score: 93
Period size: 22 Copynumber: 6.6 Consensus size: 22
312247 ACATAAACCT
* *
312257 TAAACCTTAAACCCCT-AACCCC
1 TAAACCTTAAA-CCTTAAACCCA
312279 TAAACCTTAAACCTTAAACCC-
1 TAAACCTTAAACCTTAAACCCA
* *
312300 -CAACCTTTAAACCATAAA-CCA
1 TAAACC-TTAAACCTTAAACCCA
* * *
312321 TAAACCATAATCCCTAAACCCA
1 TAAACCTTAAACCTTAAACCCA
* *
312343 TAACCCATAAACCTTAAA---A
1 TAAACCTTAAACCTTAAACCCA
312362 TACTAACTCTTAAACCTTAAA-CCA
1 TA--AAC-CTTAAACCTTAAACCCA
*
312386 TAAACCATAAACC
1 TAAACCTTAAACC
312399 ATTATCCCTA
Statistics
Matches: 97, Mismatches: 13, Indels: 21
0.74 0.10 0.16
Matches are distributed among these distances:
19 3 0.03
20 6 0.06
21 32 0.33
22 53 0.55
24 3 0.03
ACGTcount: A:0.45, C:0.34, G:0.00, T:0.21
Consensus pattern (22 bp):
TAAACCTTAAACCTTAAACCCA
Found at i:312406 original size:72 final size:72
Alignment explanation
Indices: 312301--312462 Score: 279
Period size: 72 Copynumber: 2.2 Consensus size: 72
312291 CTTAAACCCC
312301 AACCTTTAAACCATAAACCATAAACCATAATCCCTAAACCCATAACCCATAAACCTTAAAATACT
1 AACC-TTAAACCATAAACCATAAACCATAATCCCTAAACCCATAACCCATAAACCTTAAAATACT
312366 AACTCTTA
65 AACTCTTA
* * *
312374 AACCTTAAACCATAAACCATAAACCATTATCCCTAAACCCATAATCCATAAACCTTAAAATAGTA
1 AACCTTAAACCATAAACCATAAACCATAATCCCTAAACCCATAACCCATAAACCTTAAAATACTA
312439 ACTCTTA
66 ACTCTTA
*
312446 AACCTTAAACCCTAAAC
1 AACCTTAAACCATAAAC
312463 TATTACCCTA
Statistics
Matches: 85, Mismatches: 4, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
72 81 0.95
73 4 0.05
ACGTcount: A:0.46, C:0.30, G:0.01, T:0.23
Consensus pattern (72 bp):
AACCTTAAACCATAAACCATAAACCATAATCCCTAAACCCATAACCCATAAACCTTAAAATACTA
ACTCTTA
Found at i:312481 original size:27 final size:28
Alignment explanation
Indices: 312243--312508 Score: 98
Period size: 29 Copynumber: 9.4 Consensus size: 28
312233 TCATAAAACA
* *
312243 TAAAACATAAACCTTAAACCT-TAAACCCC
1 TAAACCATAAACCCTAAA-CTATAAA-CCC
* * *
312272 TAACCCCTAAACCTTAAACCT-TAAACCC
1 TAAACCATAAACCCTAAA-CTATAAACCC
* * * * *
312300 -CAACCTTTAAACCATAAACCATAAACCA
1 TAAACC-ATAAACCCTAAACTATAAACCC
* * * * *
312328 TAATCCCTAAACCCATAACCCATAAACCT
1 TAAACCATAAACCC-TAAACTATAAACCC
* *
312357 TAAA--ATACTAACTCTTAAACCT-TAAACCA
1 TAAACCATA--AAC-CCTAAA-CTATAAACCC
* * * **
312386 TAAACCATAAACCATTATCCCTAAACCC
1 TAAACCATAAACCCTAAACTATAAACCC
* * * *
312414 ATAATCCATAAACCTTAAAATAGT-AACTCT
1 -TAAACCATAAACCCTAAACTA-TAAAC-CC
* *
312444 TAAACCTTAAACCCTAAACTAT-TACCC
1 TAAACCATAAACCCTAAACTATAAACCC
*
312471 TAAACCATAAACCGTAAACTATAAACCC
1 TAAACCATAAACCCTAAACTATAAACCC
*
312499 TAAACTATAA
1 TAAACCATAA
312509 TGATAATTAA
Statistics
Matches: 178, Mismatches: 44, Indels: 31
0.70 0.17 0.12
Matches are distributed among these distances:
27 28 0.16
28 50 0.28
29 93 0.52
30 4 0.02
31 3 0.02
ACGTcount: A:0.46, C:0.30, G:0.01, T:0.23
Consensus pattern (28 bp):
TAAACCATAAACCCTAAACTATAAACCC
Found at i:312868 original size:40 final size:39
Alignment explanation
Indices: 312812--312916 Score: 124
Period size: 40 Copynumber: 2.6 Consensus size: 39
312802 TCTTTTGCGA
*
312812 CGTTTTTCCAAAAGCGCCGCTAATGGTCGACC-TGTAGTGG
1 CGTTTTT-CAAAAGCGCCGCTAATGGTCGACCAT-TAGCGG
312852 CGTTTTTCAAAGAGCGCCGCTAAAT-GTCGACCATTAGCGG
1 CGTTTTTCAAA-AGCGCCGCT-AATGGTCGACCATTAGCGG
* *
312892 CGTTTTTTAAAAAGCGTCGCTAATG
1 CG-TTTTTCAAAAGCGCCGCTAATG
312917 CCACTAAAGT
Statistics
Matches: 57, Mismatches: 3, Indels: 10
0.81 0.04 0.14
Matches are distributed among these distances:
39 7 0.12
40 38 0.67
41 12 0.21
ACGTcount: A:0.24, C:0.23, G:0.25, T:0.29
Consensus pattern (39 bp):
CGTTTTTCAAAAGCGCCGCTAATGGTCGACCATTAGCGG
Found at i:313026 original size:40 final size:40
Alignment explanation
Indices: 312964--313085 Score: 131
Period size: 40 Copynumber: 3.1 Consensus size: 40
312954 ATTTTTTTTT
* * * * *
312964 GCGGCGATTT-CAGAAAGTGCCGCTAATTGTCTACCTATA
1 GCGGCGTTTTCCAAAAAGCGCCGCTAATAGTCGACCTATA
* ** *
313003 GCGGCGTTTTTCAAGTAGCGCCGCTAATAGTCGATCTATA
1 GCGGCGTTTTCCAAAAAGCGCCGCTAATAGTCGACCTATA
*
313043 GCGGCGTTTTCCAAAAAGCGCCGCTAA-AGCTCGATCTATA
1 GCGGCGTTTTCCAAAAAGCGCCGCTAATAG-TCGACCTATA
313083 GCG
1 GCG
313086 ATATTTTTTC
Statistics
Matches: 70, Mismatches: 11, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
39 11 0.16
40 59 0.84
ACGTcount: A:0.25, C:0.25, G:0.25, T:0.26
Consensus pattern (40 bp):
GCGGCGTTTTCCAAAAAGCGCCGCTAATAGTCGACCTATA
Found at i:321440 original size:77 final size:78
Alignment explanation
Indices: 321337--321493 Score: 307
Period size: 77 Copynumber: 2.0 Consensus size: 78
321327 TTTAAAAATA
321337 TATTTTGCAATTATATTAAATTATTTTTTATTCATTTAAATTCAAGTTAAATAGTACAAAATCTA
1 TATTTTGCAATTATATTAAATTATTTTTTATTCATTTAAATTCAAGTTAAATAGTACAAAATCTA
321402 AAATTTATCTATT
66 AAATTTATCTATT
321415 TATTTTGCAA-TATATTAAATTATTTTTTATTCATTTAAATTCAAGTTAAATAGTACAAAATCTA
1 TATTTTGCAATTATATTAAATTATTTTTTATTCATTTAAATTCAAGTTAAATAGTACAAAATCTA
321479 AAATTTATCTATT
66 AAATTTATCTATT
321492 TA
1 TA
321494 AACTCGACTC
Statistics
Matches: 79, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
77 69 0.87
78 10 0.13
ACGTcount: A:0.40, C:0.08, G:0.04, T:0.48
Consensus pattern (78 bp):
TATTTTGCAATTATATTAAATTATTTTTTATTCATTTAAATTCAAGTTAAATAGTACAAAATCTA
AAATTTATCTATT
Found at i:323246 original size:29 final size:28
Alignment explanation
Indices: 323164--323244 Score: 90
Period size: 31 Copynumber: 2.7 Consensus size: 28
323154 GAATTGGATC
323164 AAATCAAAATTTCATGTATAAAATTGCACA
1 AAATCAAAATTT-ATGTAT-AAATTGCACA
* *
323194 AAATTAAAATTTATATATACAATTGCACA
1 AAATCAAAATTTATGTATA-AATTGCACA
*
323223 TTAAATCATAATTTATGTATAA
1 --AAATCAAAATTTATGTATAA
323245 TTTTAAAATT
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
28 1 0.02
29 14 0.33
30 12 0.28
31 16 0.37
ACGTcount: A:0.49, C:0.10, G:0.05, T:0.36
Consensus pattern (28 bp):
AAATCAAAATTTATGTATAAATTGCACA
Found at i:325446 original size:14 final size:14
Alignment explanation
Indices: 325424--325459 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
325414 CATAGGTATC
325424 TAAAAAAATGGAAA
1 TAAAAAAATGGAAA
* *
325438 TAAATAAATGTAAA
1 TAAAAAAATGGAAA
325452 TAAAAAAA
1 TAAAAAAA
325460 AAGTAAATAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.72, C:0.00, G:0.08, T:0.19
Consensus pattern (14 bp):
TAAAAAAATGGAAA
Found at i:325617 original size:23 final size:23
Alignment explanation
Indices: 325589--325633 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
325579 ATATATTTGG
325589 ACTATA-AAATATACATAAAACAA
1 ACTATACAAATAT-CATAAAACAA
*
325612 ACTATACAAATATTATAAAACA
1 ACTATACAAATATCATAAAACA
325634 GAAATATATG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.62, C:0.13, G:0.00, T:0.24
Consensus pattern (23 bp):
ACTATACAAATATCATAAAACAA
Found at i:328233 original size:44 final size:44
Alignment explanation
Indices: 328061--328233 Score: 104
Period size: 44 Copynumber: 3.9 Consensus size: 44
328051 NNNNNNNNNN
* *
328061 AAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAG
1 AAGATCTGAAATCTTCAATCTACTCCACTGCTGCCCAGGG-AG-AC
* * * * **
328107 AA-TTACTG---GCTTCAATGTACTCCACTG-TAACCACAGGGAGGT
1 AAGAT-CTGAAATCTTCAATCTACTCCACTGCT-GCC-CAGGGAGAC
* ** ** * * **
328149 AAAATCTGTCATCTTTGATCTGCTCCACTACTGCTTAGGGAGAC
1 AAGATCTGAAATCTTCAATCTACTCCACTGCTGCCCAGGGAGAC
*
328193 AAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGA
1 AAGATCTGAAATCTTCAATCTACTCCACTGCTGCCCAGGGA
328234 AGTAGAATTA
Statistics
Matches: 90, Mismatches: 29, Indels: 18
0.66 0.21 0.13
Matches are distributed among these distances:
42 6 0.07
43 21 0.23
44 42 0.47
45 15 0.17
46 6 0.07
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (44 bp):
AAGATCTGAAATCTTCAATCTACTCCACTGCTGCCCAGGGAGAC
Found at i:328301 original size:132 final size:132
Alignment explanation
Indices: 328061--328302 Score: 457
Period size: 132 Copynumber: 1.8 Consensus size: 132
328051 NNNNNNNNNN
328061 AAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATGTA
1 AAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATGTA
* *
328126 CTCCACTGTAACCACAGGGAGGTAAAATCTGTCATCTTTGATCTGCTCCACTACTGCTTAGGGAG
66 CTCCACTATAACCACAGGGAGGTAAAATCTGTCATCTTCGATCTGCTCCACTACTGCTTAGGGAG
328191 AC
131 AC
*
328193 AAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTATTGGCTTCAATGTA
1 AAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATGTA
328258 CTCCACTATAACCACAGGGAGGTAAAATCTGTCATCTTCGATCTG
66 CTCCACTATAACCACAGGGAGGTAAAATCTGTCATCTTCGATCTG
328303 TTCTCTGTAA
Statistics
Matches: 107, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
132 107 1.00
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.29
Consensus pattern (132 bp):
AAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATGTA
CTCCACTATAACCACAGGGAGGTAAAATCTGTCATCTTCGATCTGCTCCACTACTGCTTAGGGAG
AC
Found at i:329553 original size:23 final size:24
Alignment explanation
Indices: 329526--329571 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
329516 TCTCCATTTA
*
329526 ACTTTTCCATTTTTCAT-TTTTTC
1 ACTTTTCCATTTCTCATCTTTTTC
*
329549 ACTTTTTCATTTCTCATCTTTTT
1 ACTTTTCCATTTCTCATCTTTTT
329572 TTTTTTTGCG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.13, C:0.22, G:0.00, T:0.65
Consensus pattern (24 bp):
ACTTTTCCATTTCTCATCTTTTTC
Found at i:330065 original size:10 final size:10
Alignment explanation
Indices: 330050--330133 Score: 61
Period size: 9 Copynumber: 8.5 Consensus size: 10
330040 CAGTAGAGGT
330050 TTTTTGTTTC
1 TTTTTGTTTC
*
330060 TTTTTGTTTTT
1 TTTTTG-TTTC
*
330071 TGTTTTTTGTTC
1 T-TTTTGT-TTC
330083 TTTTTG-TTC
1 TTTTTGTTTC
330092 TTTTTG-TTC
1 TTTTTGTTTC
330101 TCTTTT-TTTC
1 T-TTTTGTTTC
*
330111 TTTTT-TCTC
1 TTTTTGTTTC
*
330120 TTTTT-TTCC
1 TTTTTGTTTC
330129 TTTTT
1 TTTTT
330134 TCTTTTTTTT
Statistics
Matches: 62, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
9 32 0.52
10 14 0.23
11 9 0.15
12 7 0.11
ACGTcount: A:0.00, C:0.12, G:0.07, T:0.81
Consensus pattern (10 bp):
TTTTTGTTTC
Found at i:330078 original size:9 final size:9
Alignment explanation
Indices: 330049--330145 Score: 53
Period size: 9 Copynumber: 10.7 Consensus size: 9
330039 CCAGTAGAGG
330049 TTTTTTGTT
1 TTTTTTGTT
330058 TCTTTTTG--
1 T-TTTTTGTT
330066 TTTTTTG--
1 TTTTTTGTT
330073 TTTTTTGTT
1 TTTTTTGTT
*
330082 CTTTTTGTT
1 TTTTTTGTT
*
330091 CTTTTTGTT
1 TTTTTTGTT
330100 CTCTTTTT-TT
1 -T-TTTTTGTT
*
330110 CTTTTTTCTCT
1 -TTTTTTGT-T
*
330121 TTTTTTCCTT
1 TTTTTT-GTT
330131 TTTTCTT-TT
1 TTTT-TTGTT
330140 TTTTTT
1 TTTTTT
330146 TTGAACTGAA
Statistics
Matches: 77, Mismatches: 2, Indels: 19
0.79 0.02 0.19
Matches are distributed among these distances:
7 13 0.17
8 3 0.04
9 29 0.38
10 22 0.29
11 10 0.13
ACGTcount: A:0.00, C:0.11, G:0.06, T:0.82
Consensus pattern (9 bp):
TTTTTTGTT
Found at i:330083 original size:23 final size:25
Alignment explanation
Indices: 330048--330148 Score: 88
Period size: 25 Copynumber: 4.0 Consensus size: 25
330038 CCCAGTAGAG
330048 GTTTTTTGTTTCTTTTTGTT-TTTT
1 GTTTTTTGTTTCTTTTTGTTCTTTT
330072 GTTTTTTG-TTCTTTTTGTTCTTTTT
1 GTTTTTTGTTTCTTTTTGTTC-TTTT
*
330097 GTTCTCTTTTTTTCTTTTT-TCTCTTTT
1 GTT-T-TTTGTTTCTTTTTGT-TCTTTT
*
330124 -TTTCCTTT-TTTCTTTTT-TTTTTTT
1 GTTT--TTTGTTTCTTTTTGTTCTTTT
330148 G
1 G
330149 AACTGAATCT
Statistics
Matches: 67, Mismatches: 2, Indels: 15
0.80 0.02 0.18
Matches are distributed among these distances:
23 11 0.16
24 13 0.19
25 18 0.27
26 7 0.10
27 8 0.12
28 10 0.15
ACGTcount: A:0.00, C:0.11, G:0.08, T:0.81
Consensus pattern (25 bp):
GTTTTTTGTTTCTTTTTGTTCTTTT
Found at i:330087 original size:18 final size:16
Alignment explanation
Indices: 330049--330147 Score: 81
Period size: 17 Copynumber: 5.8 Consensus size: 16
330039 CCAGTAGAGG
* *
330049 TTTTTTGTTTCTTTTTG
1 TTTTTT-TTTTTTTTTC
*
330066 TTTTTTGTTTTTTGTTC
1 TTTTTT-TTTTTTTTTC
330083 TTTTTGTTCTTTTTGTTCTC
1 TTTTT-TT-TTTTT-TT-TC
*
330103 TTTTTTTCTTTTTTCTC
1 TTTTTTT-TTTTTTTTC
**
330120 TTTTTTTCCTTTTTTC
1 TTTTTTTTTTTTTTTC
330136 TTTTTTTTTTTT
1 TTTTTTTTTTTT
330148 GAACTGAATC
Statistics
Matches: 68, Mismatches: 10, Indels: 9
0.78 0.11 0.10
Matches are distributed among these distances:
16 16 0.24
17 29 0.43
18 7 0.10
19 9 0.13
20 7 0.10
ACGTcount: A:0.00, C:0.11, G:0.06, T:0.83
Consensus pattern (16 bp):
TTTTTTTTTTTTTTTC
Found at i:334541 original size:16 final size:16
Alignment explanation
Indices: 334520--334550 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
334510 AAAACATTTA
*
334520 TAATATATATGTATAT
1 TAATATATATATATAT
334536 TAATATATATATATA
1 TAATATATATATATA
334551 GGCGCACACA
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:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (16 bp):
TAATATATATATATAT
Found at i:334578 original size:3 final size:3
Alignment explanation
Indices: 334570--334603 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
334560 ATATAAATAC
*
334570 AAT AAT AAT AAT -AT AAT AAT AAT TAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
334604 ACAATATAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:338486 original size:3 final size:3
Alignment explanation
Indices: 338478--338586 Score: 69
Period size: 3 Copynumber: 35.3 Consensus size: 3
338468 GTGAATAAAT
* * *
338478 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA CTA CTC TTA TTTA TTTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA -TTA
* * * * * *
338525 TTTA CTA CTA TTA TTC GT- TTA TTA AT- TTA TGA TTA TTTA TTA TTA
1 -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA
*
338570 TTC TTA GTTA TTA TTA T
1 TTA TTA -TTA TTA TTA T
338587 CACTATGTAA
Statistics
Matches: 86, Mismatches: 15, Indels: 10
0.77 0.14 0.09
Matches are distributed among these distances:
2 2 0.02
3 67 0.78
4 17 0.20
ACGTcount: A:0.28, C:0.06, G:0.03, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:343900 original size:50 final size:50
Alignment explanation
Indices: 343836--344082 Score: 149
Period size: 50 Copynumber: 4.9 Consensus size: 50
343826 TTTGGCATTA
* *
343836 TAGTGGAATGGATTGAAGCCACAACGGTGAATCTTTTTTCCCTGGCGGTG
1 TAGTGGAATAGATTGAAGCCACAACGGTGAATCTTGTTTCCCTGGCGGTG
* * * * * *** *
343886 TAGTGGAATAGATTGAAGCCACGACAGCGGATCTGGTTTCCCCAAC-ATCG
1 TAGTGGAATAGATTGAAGCCACAACGGTGAATCTTGTTTCCCTGGCGGT-G
* ** ** * *
343936 CAGTTAAATAGATTGAAGCCACAACGGTGAATCTTACCTTCCTTCGCGGTG
1 TAGTGGAATAGATTGAAGCCACAACGGTGAATCTT-GTTTCCCTGGCGGTG
* * * * * **
343987 TAGTGGAACAGATTGAAGTCACGACAGG-G-ATCTTGTTTCCCCGACATTG
1 TAGTGGAATAGATTGAAGCCACAAC-GGTGAATCTTGTTTCCCTGGCGGTG
* * ** * * * *
344036 CAATTAAATAGATTGAACCCACAATGGTGAATCTTATTTTCCTGGCG
1 TAGTGGAATAGATTGAAGCCACAACGGTGAATCTTGTTTCCCTGGCG
344083 TTGCAGCAGA
Statistics
Matches: 137, Mismatches: 54, Indels: 12
0.67 0.27 0.06
Matches are distributed among these distances:
48 2 0.01
49 25 0.18
50 81 0.59
51 26 0.19
52 3 0.02
ACGTcount: A:0.27, C:0.21, G:0.24, T:0.28
Consensus pattern (50 bp):
TAGTGGAATAGATTGAAGCCACAACGGTGAATCTTGTTTCCCTGGCGGTG
Found at i:344078 original size:100 final size:101
Alignment explanation
Indices: 343846--344078 Score: 344
Period size: 100 Copynumber: 2.3 Consensus size: 101
343836 TAGTGGAATG
* * *
343846 GATTGAAGCCACAACGGTGAATCTT-TTTTCCCTGGCGGTGTAGTGGAATAGATTGAAGCCACGA
1 GATTGAAGCCACAACGGTGAATCTTATTTTCCTTCGCGGTGTAGTGGAACAGATTGAAGCCACGA
*
343910 CAGCGGATCTGGTTTCCCCAACATCGCAGTTAAATA
66 CAGCGGATCTGGTTTCCCCAACATCGCAATTAAATA
** *
343946 GATTGAAGCCACAACGGTGAATCTTACCTTCCTTCGCGGTGTAGTGGAACAGATTGAAGTCACGA
1 GATTGAAGCCACAACGGTGAATCTTATTTTCCTTCGCGGTGTAGTGGAACAGATTGAAGCCACGA
* * *
344011 CAG-GGATCTTGTTTCCCCGACATTGCAATTAAATA
66 CAGCGGATCTGGTTTCCCCAACATCGCAATTAAATA
* *
344046 GATTGAACCCACAATGGTGAATCTTATTTTCCT
1 GATTGAAGCCACAACGGTGAATCTTATTTTCCT
344079 GGCGTTGCAG
Statistics
Matches: 118, Mismatches: 14, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
100 82 0.69
101 36 0.31
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.28
Consensus pattern (101 bp):
GATTGAAGCCACAACGGTGAATCTTATTTTCCTTCGCGGTGTAGTGGAACAGATTGAAGCCACGA
CAGCGGATCTGGTTTCCCCAACATCGCAATTAAATA
Found at i:344120 original size:100 final size:98
Alignment explanation
Indices: 343846--344112 Score: 313
Period size: 100 Copynumber: 2.7 Consensus size: 98
343836 TAGTGGAATG
* *
343846 GATTGAAGCCACAACGGTGAATCTT-TTTTCCCTGGCGGTGTAGTGGAATAGATTGAAGCCACGA
1 GATTGAAGCCACAACGGTGAATCTTATTTT-CCTGGCGGTGTAGTGGAACAGATTGAATCCACGA
* * * *
343910 CAGCGGATCTGGTTTCCCCAACATCGCAGTTAAATA
65 C-G-GGATCTTGTTTCCCCGACATTGCAATTAAATA
** *
343946 GATTGAAGCCACAACGGTGAATCTTACCTTCCTTCGCGGTGTAGTGGAACAGATTGAAGT-CACG
1 GATTGAAGCCACAACGGTGAATCTTATTTTCC-TGGCGGTGTAGTGGAACAGATTGAA-TCCACG
344010 ACAGGGATCTTGTTTCCCCGACATTGCAATTAAATA
64 AC-GGGATCTTGTTTCCCCGACATTGCAATTAAATA
* * * * ** * *
344046 GATTGAACCCACAATGGTGAATCTTATTTTCCTGGCGTTGCAGCAGAGCAGATTGAATCCGCGAC
1 GATTGAAGCCACAACGGTGAATCTTATTTTCCTGGCGGTGTAGTGGAACAGATTGAATCCACGAC
344111 GG
66 GG
344113 TGAATCTTAT
Statistics
Matches: 143, Mismatches: 20, Indels: 10
0.83 0.12 0.06
Matches are distributed among these distances:
98 3 0.02
99 24 0.17
100 83 0.58
101 33 0.23
ACGTcount: A:0.27, C:0.22, G:0.25, T:0.26
Consensus pattern (98 bp):
GATTGAAGCCACAACGGTGAATCTTATTTTCCTGGCGGTGTAGTGGAACAGATTGAATCCACGAC
GGGATCTTGTTTCCCCGACATTGCAATTAAATA
Found at i:344715 original size:129 final size:129
Alignment explanation
Indices: 344485--345010 Score: 718
Period size: 129 Copynumber: 4.1 Consensus size: 129
344475 TGCAGCTATA
* * * **
344485 AGTCTTATCTCCCTGAAGTTGCAGTGGAACAGATTA-AAGCCAAT-AATCTTATCTCTTTGAAGT
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAACAGA-CAGAAG-AAATAAATCCTATCTCCCTGAAGT
* * * *
344548 TGCAATGGAGTGGATTAAGACCATAGATCTTATCTCTCTGACGTTGTAGTAGAGCAGATCGCATC
64 TGCAGTGGAGTGGATTAAAACCACAGATCTTATCTCTCTGACGTTGCAGTAGAGCAGATCGCATC
344613 C
129 C
*
344614 AGTCTTATCTCCCTGAAGTTGCAGTGGAACAGACAGAAGAAATCAATCCTATCTCCCTGAAGTTG
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAACAGACAGAAGAAATAAATCCTATCTCCCTGAAGTTG
* *
344679 CAGTGGAGTGGATTAAAACCACAGATCTTATCTCTCTGACATTGTAGTAGAGCAGATCGCATCC
66 CAGTGGAGTGGATTAAAACCACAGATCTTATCTCTCTGACGTTGCAGTAGAGCAGATCGCATCC
* * *
344743 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATAAATCCTATCTCCCTGAAGTTA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAACAGACAGAAGAAATAAATCCTATCTCCCTGAAGTTG
* * * *
344808 CAGTGCAGCGGATTAAAACCACAGATCTTATCTATCTGACGTTGCAGTAGAGTAGATCGCATCC
66 CAGTGGAGTGGATTAAAACCACAGATCTTATCTCTCTGACGTTGCAGTAGAGCAGATCGCATCC
* * *
344872 AGTCTTATCTCCCTAAAGTTGCAGTAGAGCAGACAGAAGAAATAAATCCTATCTCCCTGAAGTTG
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAACAGACAGAAGAAATAAATCCTATCTCCCTGAAGTTG
* * * * * * *
344937 CAGTGAAGTGGATTAAAAGGTC-CAGATCTTATCTTTCTGAAGTTGCAGTAAAGTAGATTGCAT-
66 CAGTGGAGTGGATTAAAA--CCACAGATCTTATCTCTCTGACGTTGCAGTAGAGCAGATCGCATC
345000 C
129 C
*
345001 AGACTTATCT
1 AGTCTTATCT
345011 TTAAAGTTAC
Statistics
Matches: 362, Mismatches: 31, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
128 4 0.01
129 320 0.88
130 37 0.10
131 1 0.00
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.28
Consensus pattern (129 bp):
AGTCTTATCTCCCTGAAGTTGCAGTGGAACAGACAGAAGAAATAAATCCTATCTCCCTGAAGTTG
CAGTGGAGTGGATTAAAACCACAGATCTTATCTCTCTGACGTTGCAGTAGAGCAGATCGCATCC
Found at i:344840 original size:44 final size:43
Alignment explanation
Indices: 344487--344985 Score: 214
Period size: 44 Copynumber: 11.5 Consensus size: 43
344477 CAGCTATAAG
* * *
344487 TCTTATCTCCCTGAAGTTGCAGTGGAACAGATTAAAGCCA-ATAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TAAAACCACA-GA
** * ** * *
344531 TCTTATCTCTTTGAAGTTGCAATGGAGTGGATTAAGACCATAGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TAAAACCACAGA
* * * * *** *
344575 TCTTATCTCTCTGACGTTGTAGTAGAGCAGATCGCATC-CAG-
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATAAAACCACAGA
* * *
344616 TCTTATCTCCCTGAAGTTGCAGTGGAACAGACAGAAGA-AATCA-A
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATA-AA-ACCA-CAGA
* **
344660 TCCTATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAACCACAGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TAAAACCACAGA
* * * *** *
344704 TCTTATCTCTCTGACA-TTGTAGTAGAGCAGATCGCATC-CA-A
1 TCTTATCTCCCTGA-AGTTGCAGTGGAGCAGATAAAACCACAGA
* * * *
344745 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGA-AATAAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATA-AA-ACCACAGA
* * * *
344789 TCCTATCTCCCTGAAGTTACAGTGCAGCGGATTAAAACCACAGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TAAAACCACAGA
** * * * *** *
344833 TCTTATCTATCTGACGTTGCAGTAGAGTAGATCGCATC-CAG-
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATAAAACCACAGA
* * * * * *
344874 TCTTATCTCCCTAAAGTTGCAGTAGAGCAGACAGAAGA-AATAAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATA-AA-ACCACAGA
* * ** *
344918 TCCTATCTCCCTGAAGTTGCAGTGAAGTGGATTAAAAGGTC-CAGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TAAAA--CCACAGA
**
344963 TCTTATCTTTCTGAAGTTGCAGT
1 TCTTATCTCCCTGAAGTTGCAGT
344986 AAAGTAGATT
Statistics
Matches: 328, Mismatches: 102, Indels: 49
0.68 0.21 0.10
Matches are distributed among these distances:
40 1 0.00
41 79 0.24
42 7 0.02
43 19 0.06
44 195 0.59
45 27 0.08
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (43 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATAAAACCACAGA
Found at i:346433 original size:3 final size:3
Alignment explanation
Indices: 346425--346466 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
346415 GTAAATAAAT
*
346425 TTA TTA TTA TTA TTA TTG TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
346467 NNNNNNNNNN
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:351477 original size:15 final size:17
Alignment explanation
Indices: 351457--351489 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
351447 GATTTTTATT
351457 TATATTT-TTA-ATAAA
1 TATATTTATTACATAAA
351472 TATATTTATTACATAAA
1 TATATTTATTACATAAA
351489 T
1 T
351490 TTTTCATTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 3 0.19
17 6 0.38
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (17 bp):
TATATTTATTACATAAA
Found at i:352126 original size:20 final size:20
Alignment explanation
Indices: 352083--352126 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
352073 AATTTAGTTG
352083 ATAA-ATAAATAAAATAAAC
1 ATAATATAAATAAAATAAAC
352102 A-AATATAATATAAAATAAA-
1 ATAATATAA-ATAAAATAAAC
352121 ATAATA
1 ATAATA
352127 ACAGATTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
18 2 0.09
19 6 0.27
20 14 0.64
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (20 bp):
ATAATATAAATAAAATAAAC
Found at i:353798 original size:21 final size:21
Alignment explanation
Indices: 353773--353813 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
353763 ATCTGTTAAA
*
353773 TATGTAAATAATACATTTAGT
1 TATGTAAATAATAAATTTAGT
353794 TATGTAAATAATAAATTTAG
1 TATGTAAATAATAAATTTAG
353814 GAGAGAAGTT
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:0.46, C:0.02, G:0.10, T:0.41
Consensus pattern (21 bp):
TATGTAAATAATAAATTTAGT
Found at i:363248 original size:17 final size:17
Alignment explanation
Indices: 363226--363259 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
363216 ATATATTTTT
363226 TAAAA-TTAGAAAATATA
1 TAAAATTTA-AAAATATA
363243 TAAAATTTAAAAATATA
1 TAAAATTTAAAAATATA
363260 AATTAATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 13 0.81
18 3 0.19
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (17 bp):
TAAAATTTAAAAATATA
Found at i:365550 original size:22 final size:22
Alignment explanation
Indices: 365519--365570 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
365509 TTTAGAAAAA
*
365519 TTTTAAAA-TTTTTTAATATATT
1 TTTTAAAATTTTTTTAAGA-ATT
*
365541 TTTTAGAATTTTTTTAAGAATT
1 TTTTAAAATTTTTTTAAGAATT
365563 TTTTAAAA
1 TTTTAAAA
365571 AATATAAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
22 17 0.65
23 9 0.35
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.60
Consensus pattern (22 bp):
TTTTAAAATTTTTTTAAGAATT
Found at i:365553 original size:11 final size:12
Alignment explanation
Indices: 365519--365566 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
365509 TTTAGAAAAA
365519 TTTTAA-AA-TT
1 TTTTAAGAATTT
*
365529 TTTTAA-TATATT
1 TTTTAAGAAT-TT
365541 TTTT-AGAATTT
1 TTTTAAGAATTT
365552 TTTTAAGAATTT
1 TTTTAAGAATTT
365564 TTT
1 TTT
365567 AAAAAATATA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
10 7 0.22
11 7 0.22
12 18 0.56
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (12 bp):
TTTTAAGAATTT
Found at i:365567 original size:11 final size:11
Alignment explanation
Indices: 365519--365568 Score: 59
Period size: 11 Copynumber: 4.5 Consensus size: 11
365509 TTTAGAAAAA
365519 TTTTAA-AATT
1 TTTTAAGAATT
*
365529 TTTTAATATATT
1 TTTTAAGA-ATT
365541 TTTT-AGAATTT
1 TTTTAAGAA-TT
365552 TTTTAAGAATT
1 TTTTAAGAATT
365563 TTTTAA
1 TTTTAA
365569 AAAATATAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
10 7 0.20
11 17 0.49
12 11 0.31
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (11 bp):
TTTTAAGAATT
Found at i:378310 original size:28 final size:26
Alignment explanation
Indices: 378266--378317 Score: 86
Period size: 28 Copynumber: 1.9 Consensus size: 26
378256 ATATTATTAA
378266 TATAATATATATATGTTATAATAAGG
1 TATAATATATATATGTTATAATAAGG
378292 TATAATATATTATTATGTTATAATAA
1 TATAATATA-TA-TATGTTATAATAA
378318 ACATTAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
26 9 0.38
27 2 0.08
28 13 0.54
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (26 bp):
TATAATATATATATGTTATAATAAGG
Found at i:379991 original size:41 final size:41
Alignment explanation
Indices: 379946--380037 Score: 112
Period size: 41 Copynumber: 2.2 Consensus size: 41
379936 GGCTCAGTGC
* * **
379946 CTAGCAGGCTTGATGCCAGTGATATGTTTCAGACTTTAAGT
1 CTAGCAGGCTTGACGCCAGTGAAACATTTCAGACTTTAAGT
* * * *
379987 CTAGCAGGCTTGACGCCGGTGAAACATTTTATACTTTATGT
1 CTAGCAGGCTTGACGCCAGTGAAACATTTCAGACTTTAAGT
380028 CTAGCAGGCT
1 CTAGCAGGCT
380038 AAGTGCCAGT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.33
Consensus pattern (41 bp):
CTAGCAGGCTTGACGCCAGTGAAACATTTCAGACTTTAAGT
Found at i:382776 original size:44 final size:44
Alignment explanation
Indices: 382710--383227 Score: 393
Period size: 44 Copynumber: 11.7 Consensus size: 44
382700 AGTTATCGTG
* * * * *
382710 ACAAATCTTATCTCCCTAAAGTTGCAGTGGAGTAAATTCAAGCA
1 ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCT
* * * * *
382754 ACAAATCTTATCTCCCTGAAGTTACAATAGAGCGGATTGAAGAT
1 ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCT
** ** * * * * *
382798 AGTGAATCTTATCTCTTTGAAGTTGCAGTAGAGTAGATTAAAACC
1 A-CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCT
** * * *
382843 ACAAATCTTATCTCTTTGAAGTTG-TGTAGAGCAGATTAAAGCT
1 ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCT
* * * * * *
382886 ACAAACCTTATCTCCATGATGTTGGAGTGGAGCACATTGAAGTT
1 ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCT
* * *
382930 ACAAA-CTTTATCTCCCTGAAGTTGTAGTGTAGCAGATTGAAGTT
1 ACAAATC-TTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCT
* * *
382974 ACAAATCTTATCTCCTTGAAGTTGCAGTGGAGCATATTGAAGTT
1 ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCT
* * * * *
383018 ACAAATCTCATCCCCCTGAAGTTGCAGTGGAGCAAATTAAAGCG
1 ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCT
* * * * * * *
383062 ACAAATCCTATAC-CTCGGAAGTTACAGTGG-GTCGGATTAAATCAAGT
1 ACAAATCTTAT-CTCCCTGAAGTTGCAGTGGAG-CAGATTGAAGC---T
383109 CACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCT
1 -ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCT
* * * *
383154 ACAAA-CTTTATCTCCCTAAAGTTGTAGTGGAGTAGATTAAAG-T
1 ACAAATC-TTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCT
* * *
383197 AACAAATCATATAC-CTCAGAAGTTGCAGTGG
1 -ACAAATCTTAT-CTCCCTGAAGTTGCAGTGG
383228 GTTAGAATGA
Statistics
Matches: 380, Mismatches: 78, Indels: 32
0.78 0.16 0.07
Matches are distributed among these distances:
43 39 0.10
44 270 0.71
45 37 0.10
47 1 0.00
48 32 0.08
49 1 0.00
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Consensus pattern (44 bp):
ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCT
Found at i:383139 original size:136 final size:136
Alignment explanation
Indices: 382969--383229 Score: 371
Period size: 136 Copynumber: 1.9 Consensus size: 136
382959 TAGCAGATTG
* * * *
382969 AAGTTACAAATCTTATCTCCTTGAAGTTGCAGTGGAGCATATTGAAGTTACAAA-TCTCATCCCC
1 AAGTCACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTACAAACT-TCATCCCC
* * * *
383033 CTGAAGTTGCAGTGGAGCAAATTAAAGCGACAAATCCTATACCTCGGAAGTTACAGTGGGTCGGA
65 CTAAAGTTGCAGTGGAGCAAATTAAAGCAACAAATCATATACCTCAGAAGTTACAGTGGGTCGGA
383098 TTAAATC
130 TTAAATC
* *
383105 AAGTCACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTACAAACTTTATCTCCC
1 AAGTCACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTACAAACTTCATCCCCC
* * * * *
383170 TAAAGTTGTAGTGGAGTAGATTAAAGTAACAAATCATATACCTCAGAAGTTGCAGTGGGT
66 TAAAGTTGCAGTGGAGCAAATTAAAGCAACAAATCATATACCTCAGAAGTTACAGTGGGT
383230 TAGAATGAAG
Statistics
Matches: 109, Mismatches: 15, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
136 108 0.99
137 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.28
Consensus pattern (136 bp):
AAGTCACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTACAAACTTCATCCCCC
TAAAGTTGCAGTGGAGCAAATTAAAGCAACAAATCATATACCTCAGAAGTTACAGTGGGTCGGAT
TAAATC
Found at i:384695 original size:18 final size:18
Alignment explanation
Indices: 384650--384695 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 18
384640 ACCCAATGCA
384650 ATGCAATATACAAATATGAC
1 ATGC-ATATACAAATAT-AC
384670 ATGC-TATACATAATAT-C
1 ATGCATATACA-AATATAC
384687 ATGCATATA
1 ATGCATATA
384696 AACCGGCATA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
17 5 0.21
18 10 0.42
19 5 0.21
20 4 0.17
ACGTcount: A:0.46, C:0.15, G:0.09, T:0.30
Consensus pattern (18 bp):
ATGCATATACAAATATAC
Found at i:385788 original size:57 final size:57
Alignment explanation
Indices: 385719--385835 Score: 225
Period size: 57 Copynumber: 2.1 Consensus size: 57
385709 GCGGCAAGGT
*
385719 GAGGAATTGAGGAATGAAAATGGTAGAGATGGGGAAAGAAATCATCAGGAAGATGGA
1 GAGGAATTGAGGAATGAAAATGGTAGAGATGGGGAAAGAAATCATCAAGAAGATGGA
385776 GAGGAATTGAGGAATGAAAATGGTAGAGATGGGGAAAGAAATCATCAAGAAGATGGA
1 GAGGAATTGAGGAATGAAAATGGTAGAGATGGGGAAAGAAATCATCAAGAAGATGGA
385833 GAG
1 GAG
385836 AAAACTGACT
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 59 1.00
ACGTcount: A:0.44, C:0.03, G:0.37, T:0.15
Consensus pattern (57 bp):
GAGGAATTGAGGAATGAAAATGGTAGAGATGGGGAAAGAAATCATCAAGAAGATGGA
Found at i:386314 original size:15 final size:15
Alignment explanation
Indices: 386294--386324 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
386284 TCAAAGGTGA
386294 TCTTTTATTTATTTT
1 TCTTTTATTTATTTT
*
386309 TCTTTTTTTTATTTT
1 TCTTTTATTTATTTT
386324 T
1 T
386325 TAATCTGTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.10, C:0.06, G:0.00, T:0.84
Consensus pattern (15 bp):
TCTTTTATTTATTTT
Found at i:387040 original size:174 final size:174
Alignment explanation
Indices: 386750--387097 Score: 696
Period size: 174 Copynumber: 2.0 Consensus size: 174
386740 TGATCAAGCT
386750 CTAGGATCTGCGTGTTTTTGAACTGAGGGTCTATTTACTCTTTCGGTCCTTCCGCTTTTTCACTA
1 CTAGGATCTGCGTGTTTTTGAACTGAGGGTCTATTTACTCTTTCGGTCCTTCCGCTTTTTCACTA
386815 TTTCTCAATCTCGTCCTATTGCTATTTATTATTTCTTTTAATTTATCATTTTTATTCTATTTTTT
66 TTTCTCAATCTCGTCCTATTGCTATTTATTATTTCTTTTAATTTATCATTTTTATTCTATTTTTT
386880 GTGCAATTTGATCCCCCGATTGTTTCCCTTGGGGAAGGACACGC
131 GTGCAATTTGATCCCCCGATTGTTTCCCTTGGGGAAGGACACGC
386924 CTAGGATCTGCGTGTTTTTGAACTGAGGGTCTATTTACTCTTTCGGTCCTTCCGCTTTTTCACTA
1 CTAGGATCTGCGTGTTTTTGAACTGAGGGTCTATTTACTCTTTCGGTCCTTCCGCTTTTTCACTA
386989 TTTCTCAATCTCGTCCTATTGCTATTTATTATTTCTTTTAATTTATCATTTTTATTCTATTTTTT
66 TTTCTCAATCTCGTCCTATTGCTATTTATTATTTCTTTTAATTTATCATTTTTATTCTATTTTTT
387054 GTGCAATTTGATCCCCCGATTGTTTCCCTTGGGGAAGGACACGC
131 GTGCAATTTGATCCCCCGATTGTTTCCCTTGGGGAAGGACACGC
387098 ATCTAGGAAC
Statistics
Matches: 174, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
174 174 1.00
ACGTcount: A:0.17, C:0.21, G:0.16, T:0.47
Consensus pattern (174 bp):
CTAGGATCTGCGTGTTTTTGAACTGAGGGTCTATTTACTCTTTCGGTCCTTCCGCTTTTTCACTA
TTTCTCAATCTCGTCCTATTGCTATTTATTATTTCTTTTAATTTATCATTTTTATTCTATTTTTT
GTGCAATTTGATCCCCCGATTGTTTCCCTTGGGGAAGGACACGC
Found at i:387463 original size:33 final size:34
Alignment explanation
Indices: 387420--387494 Score: 84
Period size: 33 Copynumber: 2.2 Consensus size: 34
387410 CTTTGTTCAT
*
387420 TTATTATTATTATTGTCATTATTATT-TT-ATTT-
1 TTATTTTTATTATTGTCATT-TTATTATTCATTTA
* *
387452 TTAATTTTTATTCTTGTTATTTTATTATTCATTTA
1 TT-ATTTTTATTATTGTCATTTTATTATTCATTTA
387487 TTATTTTT
1 TTATTTTT
387495 GGCACTCTCA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
32 7 0.19
33 17 0.47
34 10 0.28
35 2 0.06
ACGTcount: A:0.23, C:0.04, G:0.03, T:0.71
Consensus pattern (34 bp):
TTATTTTTATTATTGTCATTTTATTATTCATTTA
Found at i:396316 original size:25 final size:25
Alignment explanation
Indices: 396269--396316 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 25
396259 GAAATATAAC
396269 AATTAATGATAACAATAAAAAGATT
1 AATTAATGATAACAATAAAAAGATT
396294 AATTAATTG-TAA-AATAAATAAGA
1 AATTAA-TGATAACAATAAA-AAGA
396317 AGCCAACATG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 6 0.29
25 13 0.62
26 2 0.10
ACGTcount: A:0.60, C:0.02, G:0.08, T:0.29
Consensus pattern (25 bp):
AATTAATGATAACAATAAAAAGATT
Found at i:400048 original size:71 final size:69
Alignment explanation
Indices: 399965--400351 Score: 369
Period size: 71 Copynumber: 5.5 Consensus size: 69
399955 TTATTTTAGG
* * * * *
399965 GGCTGCGATTTTTCACCTGCGAGCCTTAAAATGAAAATTAGGATTTTGTAACTCTTGCTAACTGT
1 GGCTGCGGTTTTTCACCTGCGAGCCTTAATATGACAGTT-GGATTTT-TAACTCTCGCTAACTGT
400030 GTTGGA
64 GTTGGA
* * * * * * * *
400036 GGTTGCGATTTTTCACTTGCGAGCCTTAATATGAGAGTTAGGGGTTTTTAACTCTCTCTAGCTAT
1 GGCTGCGGTTTTTCACCTGCGAGCCTTAATATGACAGTT--GGATTTTTAACTCTCGCTAACTGT
400101 GTTGGA
64 GTTGGA
** *
400107 GGCTGCGGTTTTTCATTTGCGAGCCTTAATATGACAGTTGTGAGTTTGTAACTCTCGCTAACTGT
1 GGCTGCGGTTTTTCACCTGCGAGCCTTAATATGACAGTTG-GA-TTTTTAACTCTCGCTAACTGT
* *
400172 ATTAGA
64 GTTGGA
* * * * * * *
400178 GGCTGTGGTTTTTCACTTGCAAGCCTTAATATGACTGTTGGGAGTTTTCAACTCTAGCTAATTGT
1 GGCTGCGGTTTTTCACCTGCGAGCCTTAATATGACAGTT-GGA-TTTTTAACTCTCGCTAACTGT
*
400243 GTTGAA
64 GTTGGA
** * * * * *
400249 GGCTATGGTTCTTCACCTGTGAGCCTTAATATGATAGCTGAGAGTTTTTAACTCTCGTTAACTGT
1 GGCTGCGGTTTTTCACCTGCGAGCCTTAATATGACAGTTG-GA-TTTTTAACTCTCGCTAACTGT
400314 GTTGGA
64 GTTGGA
* *
400320 GGCTACGGTTTTTCACCTGCGAGCCTTGATAT
1 GGCTGCGGTTTTTCACCTGCGAGCCTTAATAT
400352 AATAGCTATG
Statistics
Matches: 261, Mismatches: 50, Indels: 10
0.81 0.16 0.03
Matches are distributed among these distances:
69 1 0.00
70 2 0.01
71 251 0.96
72 7 0.03
ACGTcount: A:0.21, C:0.17, G:0.24, T:0.38
Consensus pattern (69 bp):
GGCTGCGGTTTTTCACCTGCGAGCCTTAATATGACAGTTGGATTTTTAACTCTCGCTAACTGTGT
TGGA
Found at i:400225 original size:142 final size:141
Alignment explanation
Indices: 399965--400351 Score: 425
Period size: 142 Copynumber: 2.7 Consensus size: 141
399955 TTATTTTAGG
* * * * *
399965 GGCTGCGATTTTTCACCTGCGAGCCTTAAAATGAAAATTAGGATTTTGTAACTCTTGCTAACTGT
1 GGCTGCGGTTTTTCACCTGCGAGCCTTAATATGAAAGTT-GGAGTTTGTAACTCTCGCTAACTGT
* * * * **
400030 GTTGGAGGTTGCGATTTTTCACTTGCGAGCCTTAATATGAGAGTTAGGGGTTTTTAACTCTCTCT
65 GTTGGAGGCTGCGGTTTTTCACTTGCGAGCCTTAATATGACAGTTAGGGGTTTTCAACTCTAGCT
* *
400095 AGCTATGTTGGA
130 AACTATGTTGAA
** *
400107 GGCTGCGGTTTTTCATTTGCGAGCCTTAATATGACAGTTGTGAGTTTGTAACTCTCGCTAACTGT
1 GGCTGCGGTTTTTCACCTGCGAGCCTTAATATGAAAGTTG-GAGTTTGTAACTCTCGCTAACTGT
* * * * *
400172 ATTAGAGGCTGTGGTTTTTCACTTGCAAGCCTTAATATGACTGTT-GGGAGTTTTCAACTCTAGC
65 GTTGGAGGCTGCGGTTTTTCACTTGCGAGCCTTAATATGACAGTTAGGG-GTTTTCAACTCTAGC
* *
400236 TAATTGTGTTGAA
129 TAACTATGTTGAA
** * * * * * *
400249 GGCTATGGTTCTTCACCTGTGAGCCTTAATATGATAGCTGAGAGTTTTTAACTCTCGTTAACTGT
1 GGCTGCGGTTTTTCACCTGCGAGCCTTAATATGAAAGTTG-GAGTTTGTAACTCTCGCTAACTGT
* * *
400314 GTTGGAGGCTACGGTTTTTCACCTGCGAGCCTTGATAT
65 GTTGGAGGCTGCGGTTTTTCACTTGCGAGCCTTAATAT
400352 AATAGCTATG
Statistics
Matches: 202, Mismatches: 41, Indels: 4
0.82 0.17 0.02
Matches are distributed among these distances:
141 4 0.02
142 198 0.98
ACGTcount: A:0.21, C:0.17, G:0.24, T:0.38
Consensus pattern (141 bp):
GGCTGCGGTTTTTCACCTGCGAGCCTTAATATGAAAGTTGGAGTTTGTAACTCTCGCTAACTGTG
TTGGAGGCTGCGGTTTTTCACTTGCGAGCCTTAATATGACAGTTAGGGGTTTTCAACTCTAGCTA
ACTATGTTGAA
Found at i:405945 original size:51 final size:51
Alignment explanation
Indices: 405889--405993 Score: 192
Period size: 51 Copynumber: 2.1 Consensus size: 51
405879 CTACTTACAG
405889 CAGCAACATTATCCAGTCCATCTGATGTTGCAAAATCACCAGCATATTCAT
1 CAGCAACATTATCCAGTCCATCTGATGTTGCAAAATCACCAGCATATTCAT
* *
405940 CAGCAACATTATTCATTCCATCTGATGTTGCAAAATCACCAGCATATTCAT
1 CAGCAACATTATCCAGTCCATCTGATGTTGCAAAATCACCAGCATATTCAT
405991 CAG
1 CAG
405994 TAGCAACTTC
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.33, C:0.27, G:0.11, T:0.29
Consensus pattern (51 bp):
CAGCAACATTATCCAGTCCATCTGATGTTGCAAAATCACCAGCATATTCAT
Found at i:406221 original size:33 final size:33
Alignment explanation
Indices: 406163--406233 Score: 92
Period size: 33 Copynumber: 2.2 Consensus size: 33
406153 CCTTTTCCAA
* *
406163 ATCA-CTTCACCATCAGATTCTACCCCTTCATC
1 ATCACCTTCACCATCAGATTCCACCCCTTCAAC
*
406195 ATCACCTTCCCCATCA-ACTTCCACCCCTTCAAC
1 ATCACCTTCACCATCAGA-TTCCACCCCTTCAAC
406228 ATCACC
1 ATCACC
406234 CTCCTTAGTA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
32 5 0.15
33 29 0.85
ACGTcount: A:0.25, C:0.46, G:0.01, T:0.27
Consensus pattern (33 bp):
ATCACCTTCACCATCAGATTCCACCCCTTCAAC
Found at i:407212 original size:17 final size:16
Alignment explanation
Indices: 407190--407221 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
407180 AAATGTTATG
407190 GATTTGGGGAATTTTAC
1 GATTTGGGG-ATTTTAC
407207 GATTTGGGGATTTTA
1 GATTTGGGGATTTTA
407222 GAAGTTGGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.22, C:0.03, G:0.31, T:0.44
Consensus pattern (16 bp):
GATTTGGGGATTTTAC
Found at i:413526 original size:22 final size:22
Alignment explanation
Indices: 413495--413556 Score: 88
Period size: 22 Copynumber: 2.8 Consensus size: 22
413485 CCCACTGCCT
413495 CTAGTACTGACATTCTCTATCC
1 CTAGTACTGACATTCTCTATCC
* * *
413517 CTAGTGCTGACATTCTTTGTCC
1 CTAGTACTGACATTCTCTATCC
*
413539 CTAGTACTAACATTCTCT
1 CTAGTACTGACATTCTCT
413557 GTGGACTCTA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.21, C:0.29, G:0.11, T:0.39
Consensus pattern (22 bp):
CTAGTACTGACATTCTCTATCC
Found at i:414826 original size:27 final size:27
Alignment explanation
Indices: 414624--414818 Score: 263
Period size: 27 Copynumber: 7.2 Consensus size: 27
414614 GAATTATTTC
*
414624 TGACTGAAATACCCGCATAGGGTAAAA
1 TGACTGAAATACCCTCATAGGGTAAAA
* *
414651 TGA-TCAAAATACCCCCATAGGGTAAAA
1 TGACT-GAAATACCCTCATAGGGTAAAA
414678 TGA-TCGAAATACCC-CTATAGGGTAAAA
1 TGACT-GAAATACCCTC-ATAGGGTAAAA
*
414705 TGACTGAAATACCCCCATAGGGTAAAA
1 TGACTGAAATACCCTCATAGGGTAAAA
414732 TGA-TCGAAATACCCTCATAGGGTAAAA
1 TGACT-GAAATACCCTCATAGGGTAAAA
** *
414759 TGACCAAAATACCATCATAGGGTAAAA
1 TGACTGAAATACCCTCATAGGGTAAAA
414786 TGACTGAAATACCCTCATAGGGTAAAA
1 TGACTGAAATACCCTCATAGGGTAAAA
414813 TGACTG
1 TGACTG
414819 TTATACCCCT
Statistics
Matches: 152, Mismatches: 10, Indels: 12
0.87 0.06 0.07
Matches are distributed among these distances:
26 3 0.02
27 147 0.97
28 2 0.01
ACGTcount: A:0.42, C:0.19, G:0.18, T:0.21
Consensus pattern (27 bp):
TGACTGAAATACCCTCATAGGGTAAAA
Found at i:414826 original size:81 final size:81
Alignment explanation
Indices: 414624--414815 Score: 305
Period size: 81 Copynumber: 2.4 Consensus size: 81
414614 GAATTATTTC
* * * *
414624 TGACTGAAATACCCGCATAGGGTAAAATGATCAAAATACCCCCATAGGGTAAAATGATCGAAATA
1 TGACTGAAATACCCCCATAGGGTAAAATGATCGAAATACCCCCATAGGGTAAAATGACCAAAATA
414689 CCCCTATAGGGTAAAA
66 CCCCTATAGGGTAAAA
*
414705 TGACTGAAATACCCCCATAGGGTAAAATGATCGAAATACCCTCATAGGGTAAAATGACCAAAATA
1 TGACTGAAATACCCCCATAGGGTAAAATGATCGAAATACCCCCATAGGGTAAAATGACCAAAATA
*
414770 -CCATCATAGGGTAAAA
66 CCCCT-ATAGGGTAAAA
*
414786 TGACTGAAATACCCTCATAGGGTAAAATGA
1 TGACTGAAATACCCCCATAGGGTAAAATGA
414816 CTGTTATACC
Statistics
Matches: 103, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
80 3 0.03
81 100 0.97
ACGTcount: A:0.42, C:0.19, G:0.18, T:0.20
Consensus pattern (81 bp):
TGACTGAAATACCCCCATAGGGTAAAATGATCGAAATACCCCCATAGGGTAAAATGACCAAAATA
CCCCTATAGGGTAAAA
Found at i:417825 original size:19 final size:20
Alignment explanation
Indices: 417793--417841 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
417783 TTTATTTTTA
* *
417793 TTAATTTATCTATTTGTA-T
1 TTAATTTTTATATTTGTAGT
* *
417812 TTTATTTTTATATTTTTAGT
1 TTAATTTTTATATTTGTAGT
417832 TTAATTTTTA
1 TTAATTTTTA
417842 CATTCTAATT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.24, C:0.02, G:0.04, T:0.69
Consensus pattern (20 bp):
TTAATTTTTATATTTGTAGT
Found at i:421124 original size:29 final size:30
Alignment explanation
Indices: 421079--421135 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
421069 GTACACGACA
* * *
421079 GTGTGTGCCATATGGCCT-GGCACACGGCT
1 GTGTGTGCCACACGGCCTAGACACACGGCT
421108 GTGTGTGCCACACGGCCTAGACACACGG
1 GTGTGTGCCACACGGCCTAGACACACGG
421136 GCATGTCTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 16 0.67
30 8 0.33
ACGTcount: A:0.18, C:0.30, G:0.33, T:0.19
Consensus pattern (30 bp):
GTGTGTGCCACACGGCCTAGACACACGGCT
Found at i:422072 original size:12 final size:12
Alignment explanation
Indices: 422046--422097 Score: 54
Period size: 12 Copynumber: 4.4 Consensus size: 12
422036 TTTATTTTAT
422046 TTATTTATGATTC
1 TTATTTAT-ATTC
*
422059 TTATTTCTATTC
1 TTATTTATATTC
422071 TTATTTAT-TTC
1 TTATTTATATTC
* *
422082 -TATTTGTTTTC
1 TTATTTATATTC
422093 TTATT
1 TTATT
422098 CTTATTTTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
10 6 0.18
11 6 0.18
12 15 0.44
13 7 0.21
ACGTcount: A:0.17, C:0.10, G:0.04, T:0.69
Consensus pattern (12 bp):
TTATTTATATTC
Found at i:422103 original size:28 final size:30
Alignment explanation
Indices: 422037--422104 Score: 83
Period size: 28 Copynumber: 2.4 Consensus size: 30
422027 TTCCCTTATT
422037 TTATT-TTATTTATTTATGATTCTTATTTC
1 TTATTCTTATTTATTTATGATTCTTATTTC
*
422066 -TATTCTTATTTATTTCT-ATT-TGT-TTTC
1 TTATTCTTATTTATTTATGATTCT-TATTTC
422093 TTATTCTTATTT
1 TTATTCTTATTT
422105 TTATGTGCTT
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
27 5 0.14
28 19 0.54
29 11 0.31
ACGTcount: A:0.18, C:0.09, G:0.03, T:0.71
Consensus pattern (30 bp):
TTATTCTTATTTATTTATGATTCTTATTTC
Found at i:423683 original size:6 final size:6
Alignment explanation
Indices: 423669--423755 Score: 70
Period size: 6 Copynumber: 14.3 Consensus size: 6
423659 ATGATGATCA
* * * * * *
423669 TTTAGT TTTATT TTT-TT TCT-TT TTTCTT TTTAGT TTTCTT TTTCTT
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT
*
423715 TTTCTT TTTAGTTGT TTTATT TTTATT TTTATT TTTATT TT
1 TTTATT TTTA--T-T TTTATT TTTATT TTTATT TTTATT TT
423756 CTTAGACTTC
Statistics
Matches: 69, Mismatches: 8, Indels: 8
0.81 0.09 0.09
Matches are distributed among these distances:
5 8 0.12
6 54 0.78
7 1 0.01
8 1 0.01
9 5 0.07
ACGTcount: A:0.09, C:0.06, G:0.05, T:0.80
Consensus pattern (6 bp):
TTTATT
Found at i:423731 original size:27 final size:27
Alignment explanation
Indices: 423669--423751 Score: 84
Period size: 27 Copynumber: 3.1 Consensus size: 27
423659 ATGATGATCA
*
423669 TTTAGTT-TTATTTTTTTTCTTTTTTCTT
1 TTTAGTTGTT-TTATTTTTC-TTTTTCTT
*
423697 TTTA---GTTTTCTTTTTCTTTTTCTT
1 TTTAGTTGTTTTATTTTTCTTTTTCTT
* *
423721 TTTAGTTGTTTTATTTTTATTTTTATT
1 TTTAGTTGTTTTATTTTTCTTTTTCTT
423748 TTTA
1 TTTA
423752 TTTTCTTAGA
Statistics
Matches: 47, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
24 12 0.26
25 8 0.17
26 2 0.04
27 21 0.45
28 4 0.09
ACGTcount: A:0.10, C:0.06, G:0.05, T:0.80
Consensus pattern (27 bp):
TTTAGTTGTTTTATTTTTCTTTTTCTT
Found at i:428046 original size:21 final size:21
Alignment explanation
Indices: 428020--428078 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
428010 TGCACATCCA
428020 TGTGGCAGAAACACAC-ACTCG
1 TGTGGCAGAAACACACGA-TCG
* * *
428041 TTTGGCAGAGATACACGATCG
1 TGTGGCAGAAACACACGATCG
*
428062 TGTGGCTGAAACACACG
1 TGTGGCAGAAACACACG
428079 CCCGTGTGTG
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
21 29 0.97
22 1 0.03
ACGTcount: A:0.31, C:0.24, G:0.27, T:0.19
Consensus pattern (21 bp):
TGTGGCAGAAACACACGATCG
Found at i:428712 original size:25 final size:25
Alignment explanation
Indices: 428658--428706 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
428648 GTCACATAGC
*
428658 CGTGTCACACGCCCATGTGCCAGGT
1 CGTGTCACACGCCCATATGCCAGGT
* *
428683 CGTGTCACATGCCCGTATGCCAGG
1 CGTGTCACACGCCCATATGCCAGG
428707 CAGTGTAACT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.16, C:0.35, G:0.29, T:0.20
Consensus pattern (25 bp):
CGTGTCACACGCCCATATGCCAGGT
Found at i:448524 original size:12 final size:13
Alignment explanation
Indices: 448500--448528 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
448490 GGGCTATAAC
448500 TATTGCATTTATT
1 TATTGCATTTATT
448513 TATTGC-TTTATT
1 TATTGCATTTATT
448525 TATT
1 TATT
448529 CATCTATGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.21, C:0.07, G:0.07, T:0.66
Consensus pattern (13 bp):
TATTGCATTTATT
Found at i:454962 original size:18 final size:19
Alignment explanation
Indices: 454927--454962 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
454917 ATGTAGCACA
*
454927 ATTTTTCATTAATATAAAG
1 ATTTTCCATTAATATAAAG
454946 ATTTTCCATTAAT-TAAA
1 ATTTTCCATTAATATAAA
454963 TTTAATTGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.42, C:0.08, G:0.03, T:0.47
Consensus pattern (19 bp):
ATTTTCCATTAATATAAAG
Found at i:467941 original size:20 final size:21
Alignment explanation
Indices: 467904--467949 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
467894 CGAAATGCAA
467904 TCAACCTAAAATGAATTAAAT
1 TCAACCTAAAATGAATTAAAT
* *
467925 TCAAGCTAAATTG-ATTAAAT
1 TCAACCTAAAATGAATTAAAT
467945 T-AACC
1 TCAACC
467950 ATTCCAACAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 3 0.14
20 8 0.36
21 11 0.50
ACGTcount: A:0.48, C:0.15, G:0.07, T:0.30
Consensus pattern (21 bp):
TCAACCTAAAATGAATTAAAT
Found at i:468617 original size:11 final size:12
Alignment explanation
Indices: 468599--468632 Score: 61
Period size: 11 Copynumber: 2.9 Consensus size: 12
468589 ATTAAATTGG
468599 ATTATGAATTAT
1 ATTATGAATTAT
468611 A-TATGAATTAT
1 ATTATGAATTAT
468622 ATTATGAATTA
1 ATTATGAATTA
468633 ATACTTATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.44, C:0.00, G:0.09, T:0.47
Consensus pattern (12 bp):
ATTATGAATTAT
Found at i:472187 original size:27 final size:27
Alignment explanation
Indices: 472168--472444 Score: 369
Period size: 27 Copynumber: 10.3 Consensus size: 27
472158 GGGTATAACA
* *
472168 GTCATTTTACCCTGTGGGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTCG
472195 GTCATTTTACCCTATGGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* *
472222 G-CCTTTTACCCTATGGGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTCG
* *
472248 GTCATTTTACCCTATGGTGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTCG
* *
472275 GTCATTTTACCCTATAGGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTCG
* *
472302 ATCATTTTACCTTATGGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* * * *
472329 GTTATTTTA-CTTATGAGGGTATTTCA
1 GTCATTTTACCCTATGGGGGTATTTCG
* *
472355 GTCATTTTACCCTATGAGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTCG
*
472382 ATCATTTTACCCTATGGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* *
472409 ATCATTTTACCCTATGGGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTCG
472436 GTCATTTTA
1 GTCATTTTA
472445 TCTATTTTAG
Statistics
Matches: 223, Mismatches: 25, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
26 47 0.21
27 176 0.79
ACGTcount: A:0.17, C:0.15, G:0.23, T:0.45
Consensus pattern (27 bp):
GTCATTTTACCCTATGGGGGTATTTCG
Found at i:472295 original size:80 final size:80
Alignment explanation
Indices: 472168--472444 Score: 396
Period size: 80 Copynumber: 3.5 Consensus size: 80
472158 GGGTATAACA
* * * *
472168 GTCATTTTACCCTGTGGGGGTATTTTGGTCATTTTACCCTATGGGGGTATTTCG-GCCTTTTACC
1 GTCATTTTACCCTATGGGGGTATTTTGGTCATTTTACCCTAT-GGGGTATTTTGATCATTTTACC
*
472232 CTATGGGGGTATTTTG
65 CTATGGGGGTATTTCG
*
472248 GTCATTTTACCCTATGGTGGTATTTTGGTCATTTTACCCTATAGGGGTATTTTGATCATTTTACC
1 GTCATTTTACCCTATGGGGGTATTTTGGTCATTTTACCCTAT-GGGGTATTTTGATCATTTTACC
*
472313 TTATGGGGGTATTTCG
65 CTATGGGGGTATTTCG
* * * **
472329 GTTATTTTA-CTTATGAGGGTATTTCAGTCATTTTACCCTATGAGGGTATTTTGATCATTTTACC
1 GTCATTTTACCCTATGGGGGTATTTTGGTCATTTTACCCTATG-GGGTATTTTGATCATTTTACC
472393 CTATGGGGGTATTTCG
65 CTATGGGGGTATTTCG
*
472409 ATCATTTTACCCTATGGGGGTATTTTGGTCATTTTA
1 GTCATTTTACCCTATGGGGGTATTTTGGTCATTTTA
472445 TCTATTTTAG
Statistics
Matches: 173, Mismatches: 21, Indels: 5
0.87 0.11 0.03
Matches are distributed among these distances:
79 1 0.01
80 120 0.69
81 52 0.30
ACGTcount: A:0.17, C:0.15, G:0.23, T:0.45
Consensus pattern (80 bp):
GTCATTTTACCCTATGGGGGTATTTTGGTCATTTTACCCTATGGGGTATTTTGATCATTTTACCC
TATGGGGGTATTTCG
Found at i:472327 original size:107 final size:107
Alignment explanation
Indices: 472168--472449 Score: 406
Period size: 107 Copynumber: 2.6 Consensus size: 107
472158 GGGTATAACA
* * *
472168 GTCATTTTACCCTGTGGGGGTATTTTGGTCATTTTACCCTATGGGGGTATTTCGG-CCTTTTACC
1 GTCATTTTACCCTATGGGGGTATTTTGATCATTTTACCCTATGGGGGTATTTCGGTCATTTTA-C
* **
472232 CTATGGGGGTATTTTGGTCATTTTACCCTATG-GTGGTATTTTG
65 CTATGAGGGTATTTCAGTCATTTTACCCTATGAG-GGTATTTTG
* * * *
472275 GTCATTTTACCCTATAGGGGTATTTTGATCATTTTACCTTATGGGGGTATTTCGGTTATTTTACT
1 GTCATTTTACCCTATGGGGGTATTTTGATCATTTTACCCTATGGGGGTATTTCGGTCATTTTACC
472340 TATGAGGGTATTTCAGTCATTTTACCCTATGAGGGTATTTTG
66 TATGAGGGTATTTCAGTCATTTTACCCTATGAGGGTATTTTG
* * * *
472382 ATCATTTTACCCTATGGGGGTATTTCGATCATTTTACCCTATGGGGGTATTTTGGTCATTTTATC
1 GTCATTTTACCCTATGGGGGTATTTTGATCATTTTACCCTATGGGGGTATTTCGGTCATTTTACC
472447 TAT
66 TAT
472450 TTTAGGGTCT
Statistics
Matches: 155, Mismatches: 18, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
107 149 0.96
108 6 0.04
ACGTcount: A:0.17, C:0.15, G:0.23, T:0.45
Consensus pattern (107 bp):
GTCATTTTACCCTATGGGGGTATTTTGATCATTTTACCCTATGGGGGTATTTCGGTCATTTTACC
TATGAGGGTATTTCAGTCATTTTACCCTATGAGGGTATTTTG
Found at i:515730 original size:28 final size:28
Alignment explanation
Indices: 515690--515748 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
515680 ATGTTCATTG
515690 TAGGGTGTGACACTACTAGGCCCAATTT
1 TAGGGTGTGACACTACTAGGCCCAATTT
515718 TAGGGTGTGACACTACTAGGCCCAATTT
1 TAGGGTGTGACACTACTAGGCCCAATTT
515746 TAG
1 TAG
515749 CCCACTTAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.29
Consensus pattern (28 bp):
TAGGGTGTGACACTACTAGGCCCAATTT
Found at i:522042 original size:17 final size:17
Alignment explanation
Indices: 522020--522058 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
522010 GGTTTGAATG
522020 CAAGGTTGAAAGTTCTT
1 CAAGGTTGAAAGTTCTT
522037 CAAGGTTGAAAGTTCTT
1 CAAGGTTGAAAGTTCTT
522054 CAAGG
1 CAAGG
522059 GAAAATCCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.31, C:0.13, G:0.26, T:0.31
Consensus pattern (17 bp):
CAAGGTTGAAAGTTCTT
Found at i:523020 original size:29 final size:29
Alignment explanation
Indices: 522952--523029 Score: 72
Period size: 29 Copynumber: 2.8 Consensus size: 29
522942 AAGGAAATCA
**
522952 CACACGAGTTGGTACACGACAGTGCGTGC
1 CACACGACCTGGTACACGACAGTGCGTGC
* * * *
522981 CATACGACCTGGTACACGGCTGTGTGTGC
1 CACACGACCTGGTACACGACAGTGCGTGC
523010 CACAC-ATCCTGG-ACAC-ACAG
1 CACACGA-CCTGGTACACGACAG
523030 GCATGTCTGA
Statistics
Matches: 39, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
27 2 0.05
28 5 0.13
29 32 0.82
ACGTcount: A:0.24, C:0.31, G:0.27, T:0.18
Consensus pattern (29 bp):
CACACGACCTGGTACACGACAGTGCGTGC
Found at i:523952 original size:28 final size:29
Alignment explanation
Indices: 523918--523983 Score: 86
Period size: 28 Copynumber: 2.4 Consensus size: 29
523908 CATATTTTAT
523918 TTATTTATTAT-TATTATTATTTC-TATTC
1 TTATTTATTATCTATT-TTATTTCTTATTC
*
523946 TTATTTATT-TCTATTTTTTTTCTTATTC
1 TTATTTATTATCTATTTTATTTCTTATTC
523974 TTATTT-TTAT
1 TTATTTATTAT
523984 GTGTTTCATT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
27 9 0.26
28 25 0.74
ACGTcount: A:0.20, C:0.08, G:0.00, T:0.73
Consensus pattern (29 bp):
TTATTTATTATCTATTTTATTTCTTATTC
Found at i:523953 original size:16 final size:15
Alignment explanation
Indices: 523892--523962 Score: 72
Period size: 16 Copynumber: 4.4 Consensus size: 15
523882 ACTTTTTCCT
523892 TATTTTATTTTATTTAC
1 TATTTTA-TTTATTT-C
*
523909 ATATTTTATTTATTTAT
1 -TATTTTATTTATTT-C
523926 TATTATTA-TTATTTC
1 TATT-TTATTTATTTC
523941 TATTCTTATTTATTTC
1 TATT-TTATTTATTTC
523957 TATTTT
1 TATTTT
523963 TTTTCTTATT
Statistics
Matches: 48, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
15 9 0.19
16 21 0.44
17 11 0.23
18 7 0.15
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.70
Consensus pattern (15 bp):
TATTTTATTTATTTC
Found at i:523978 original size:6 final size:5
Alignment explanation
Indices: 523891--523966 Score: 52
Period size: 6 Copynumber: 14.4 Consensus size: 5
523881 CACTTTTTCC
523891 TTATT TTATT TTATT TACATATT TTA-T TTA-T TTATT ATTATT ATTATT
1 TTATT TTATT TTATT T---TATT TTATT TTATT TTATT -TTATT -TTATT
523939 TCTATT CTTA-T TTATT TCTATT TT-TT TT
1 T-TATT -TTATT TTATT T-TATT TTATT TT
523967 CTTATTCTTA
Statistics
Matches: 62, Mismatches: 0, Indels: 19
0.77 0.00 0.23
Matches are distributed among these distances:
4 15 0.24
5 19 0.31
6 22 0.35
7 1 0.02
8 5 0.08
ACGTcount: A:0.22, C:0.05, G:0.00, T:0.72
Consensus pattern (5 bp):
TTATT
Found at i:525626 original size:19 final size:20
Alignment explanation
Indices: 525591--525650 Score: 65
Period size: 19 Copynumber: 3.1 Consensus size: 20
525581 ATGGGGATCA
* *
525591 TTTAGTTTTATTTTTTTCTT
1 TTTAGTTTTACTTTTTTATT
525611 TTTAGTTTT-CTTTTTTATT
1 TTTAGTTTTACTTTTTTATT
525630 TTTA-TGTTTA--TTTTTATT
1 TTTAGT-TTTACTTTTTTATT
525648 TTT
1 TTT
525651 TTCTTTTGGT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
18 12 0.33
19 15 0.42
20 9 0.25
ACGTcount: A:0.12, C:0.03, G:0.05, T:0.80
Consensus pattern (20 bp):
TTTAGTTTTACTTTTTTATT
Found at i:525677 original size:5 final size:6
Alignment explanation
Indices: 525603--525683 Score: 65
Period size: 6 Copynumber: 12.7 Consensus size: 6
525593 TAGTTTTATT
* * *
525603 TTTTTC TTTTTA GTTTTCT- TTTTTA TTTTTA TGTTTA TTTTTA TTTTTT
1 TTTTTA TTTTTA -TTTT-TA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA
*
525652 TCTTTTGGT TGTTTTA TTTTTA TTTTTA TTTT
1 T-TTTT--A T-TTTTA TTTTTA TTTTTA TTTT
525684 CTTAGACTTC
Statistics
Matches: 63, Mismatches: 6, Indels: 12
0.78 0.07 0.15
Matches are distributed among these distances:
5 1 0.02
6 46 0.73
7 9 0.14
8 1 0.02
9 6 0.10
ACGTcount: A:0.10, C:0.04, G:0.06, T:0.80
Consensus pattern (6 bp):
TTTTTA
Found at i:530510 original size:93 final size:93
Alignment explanation
Indices: 530351--530535 Score: 352
Period size: 93 Copynumber: 2.0 Consensus size: 93
530341 ATTCCTAAGG
* *
530351 TTCAACCGAGACTGGATATCCGACATAGCATTGATATGTTTATACATCGATCCATTCACATTATA
1 TTCAACCGAGACTCGATATCCAACATAGCATTGATATGTTTATACATCGATCCATTCACATTATA
530416 AATAACATAATAACATTCAATTTAAATT
66 AATAACATAATAACATTCAATTTAAATT
530444 TTCAACCGAGACTCGATATCCAACATAGCATTGATATGTTTATACATCGATCCATTCACATTATA
1 TTCAACCGAGACTCGATATCCAACATAGCATTGATATGTTTATACATCGATCCATTCACATTATA
530509 AATAACATAATAACATTCAATTTAAAT
66 AATAACATAATAACATTCAATTTAAAT
530536 AACATTAAAA
Statistics
Matches: 90, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
93 90 1.00
ACGTcount: A:0.39, C:0.19, G:0.09, T:0.33
Consensus pattern (93 bp):
TTCAACCGAGACTCGATATCCAACATAGCATTGATATGTTTATACATCGATCCATTCACATTATA
AATAACATAATAACATTCAATTTAAATT
Found at i:552346 original size:37 final size:37
Alignment explanation
Indices: 552305--552379 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
552295 ACAAAATTAA
552305 TGATGTTTTAAGAGTTTTTCTTGAAATCTATAGAGAT
1 TGATGTTTTAAGAGTTTTTCTTGAAATCTATAGAGAT
552342 TGATGTTTTAAGAGTTTTTCTTGAAATCTATAGAGAT
1 TGATGTTTTAAGAGTTTTTCTTGAAATCTATAGAGAT
552379 T
1 T
552380 TATTGATTGG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.29, C:0.05, G:0.19, T:0.47
Consensus pattern (37 bp):
TGATGTTTTAAGAGTTTTTCTTGAAATCTATAGAGAT
Found at i:558373 original size:22 final size:21
Alignment explanation
Indices: 558338--558379 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
558328 CACATTTAAC
558338 ACTTAACAAAATTAACTAAAT
1 ACTTAACAAAATTAACTAAAT
*
558359 ACTTAAACTAAATTAACTAAA
1 ACTT-AACAAAATTAACTAAA
558380 ATTTATTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.57, C:0.14, G:0.00, T:0.29
Consensus pattern (21 bp):
ACTTAACAAAATTAACTAAAT
Found at i:568735 original size:21 final size:21
Alignment explanation
Indices: 568702--568741 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
568692 CATAGAAAAC
* * *
568702 TCAACTACTCTCGTTTCTTTT
1 TCAACAACACTCGTCTCTTTT
568723 TCAACAACACTCGTCTCTT
1 TCAACAACACTCGTCTCTT
568742 GCATACTTTC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.20, C:0.33, G:0.05, T:0.42
Consensus pattern (21 bp):
TCAACAACACTCGTCTCTTTT
Found at i:568821 original size:15 final size:15
Alignment explanation
Indices: 568784--568823 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
568774 TCTTTTTCAA
*
568784 TTTCTTTCTCTTTTT
1 TTTCTTTTTCTTTTT
*
568799 CTTCTTTTTCTTTTT
1 TTTCTTTTTCTTTTT
568814 TTTCTTTTTC
1 TTTCTTTTTC
568824 AATTTCTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (15 bp):
TTTCTTTTTCTTTTT
Found at i:568831 original size:12 final size:11
Alignment explanation
Indices: 568774--568848 Score: 50
Period size: 12 Copynumber: 6.7 Consensus size: 11
568764 AGTCTCACTC
568774 TCTTTTTCAATT
1 TCTTTTTC-ATT
*
568786 TCTTTCTC-TT
1 TCTTTTTCATT
* *
568796 T-TTCTTCTTTT
1 TCTTTTTC-ATT
568807 TCTTTTT--TT
1 TCTTTTTCATT
568816 TCTTTTTCAATT
1 TCTTTTTC-ATT
568828 TCTTTTTCACTT
1 TCTTTTTCA-TT
568840 TCATTTTTC
1 TC-TTTTTC
568849 TCTTCCCATC
Statistics
Matches: 51, Mismatches: 4, Indels: 15
0.73 0.06 0.21
Matches are distributed among these distances:
9 13 0.25
10 3 0.06
11 4 0.08
12 25 0.49
13 6 0.12
ACGTcount: A:0.08, C:0.20, G:0.00, T:0.72
Consensus pattern (11 bp):
TCTTTTTCATT
Found at i:570268 original size:17 final size:18
Alignment explanation
Indices: 570248--570289 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
570238 AATTTATTTT
570248 TTTCTAATATTTTT-TA-A
1 TTTC-AATATTTTTGTATA
570265 TTTCAAT-TTTTTGTATA
1 TTTCAATATTTTTGTATA
570282 TTTCAATA
1 TTTCAATA
570290 AAATAATAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 5 0.23
16 5 0.23
17 12 0.55
ACGTcount: A:0.29, C:0.07, G:0.02, T:0.62
Consensus pattern (18 bp):
TTTCAATATTTTTGTATA
Found at i:571720 original size:22 final size:21
Alignment explanation
Indices: 571689--571730 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
571679 CACATTTAAC
* *
571689 ACTTAACTAAATTAATTAAAT
1 ACTTAACTAAAGTAACTAAAT
571710 ACTTAAACTAAAGTAACTAAA
1 ACTT-AACTAAAGTAACTAAA
571731 ATTTATTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.55, C:0.12, G:0.02, T:0.31
Consensus pattern (21 bp):
ACTTAACTAAAGTAACTAAAT
Found at i:574581 original size:11 final size:10
Alignment explanation
Indices: 574554--574580 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
574544 TTGAAATTAT
574554 AAAAAAATTC
1 AAAAAAATTC
574564 AAAAAAATTC
1 AAAAAAATTC
574574 AAAAAAA
1 AAAAAAA
574581 AAAGAAGTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.78, C:0.07, G:0.00, T:0.15
Consensus pattern (10 bp):
AAAAAAATTC
Found at i:574623 original size:3 final size:3
Alignment explanation
Indices: 574615--574662 Score: 89
Period size: 3 Copynumber: 16.3 Consensus size: 3
574605 TGCAAGTTCT
574615 TTA TTA TTA TTA -TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
574662 T
1 T
574663 NNNNNNNNNN
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.05
3 42 0.95
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:575736 original size:21 final size:22
Alignment explanation
Indices: 575712--575757 Score: 62
Period size: 20 Copynumber: 2.2 Consensus size: 22
575702 AATATGGAAT
575712 GAAAATGAGA-AAAGAA-AAAAA
1 GAAAATGAGAGAAA-AAGAAAAA
575733 G-AAATGAGAGAAAAAGAAAAA
1 GAAAATGAGAGAAAAAGAAAAA
575754 GAAA
1 GAAA
575758 GTAAAAAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
20 10 0.45
21 10 0.45
22 2 0.09
ACGTcount: A:0.74, C:0.00, G:0.22, T:0.04
Consensus pattern (22 bp):
GAAAATGAGAGAAAAAGAAAAA
Found at i:575739 original size:20 final size:21
Alignment explanation
Indices: 575714--575757 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
575704 TATGGAATGA
575714 AAATGAGA-AAAGAA-AAAAAG
1 AAATGAGAGAAA-AAGAAAAAG
575734 AAATGAGAGAAAAAGAAAAAG
1 AAATGAGAGAAAAAGAAAAAG
575755 AAA
1 AAA
575758 GTAAAAAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 10 0.45
21 12 0.55
ACGTcount: A:0.75, C:0.00, G:0.20, T:0.05
Consensus pattern (21 bp):
AAATGAGAGAAAAAGAAAAAG
Found at i:575746 original size:17 final size:17
Alignment explanation
Indices: 575722--575793 Score: 60
Period size: 17 Copynumber: 4.2 Consensus size: 17
575712 GAAAATGAGA
575722 AAAGAAAAAAAGAAATG
1 AAAGAAAAAAAGAAATG
*
575739 AGAGAAAAAGAA-AAA-G
1 AAAGAAAAA-AAGAAATG
*
575755 AAAGTAAAAAAGAAATTG
1 AAAGAAAAAAAGAAA-TG
*
575773 CAAA-AGAAAAAGAAATCG
1 -AAAGAAAAAAAGAAAT-G
575791 AAA
1 AAA
575794 AAGTGAGAGA
Statistics
Matches: 44, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
15 2 0.05
16 11 0.25
17 15 0.34
18 13 0.30
19 3 0.07
ACGTcount: A:0.72, C:0.03, G:0.18, T:0.07
Consensus pattern (17 bp):
AAAGAAAAAAAGAAATG
Found at i:575795 original size:18 final size:18
Alignment explanation
Indices: 575761--575796 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
575751 AAAGAAAGTA
* *
575761 AAAAAGAAATTGCAAAAG
1 AAAAAGAAATCGAAAAAG
575779 AAAAAGAAATCGAAAAAG
1 AAAAAGAAATCGAAAAAG
575797 TGAGAGAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.69, C:0.06, G:0.17, T:0.08
Consensus pattern (18 bp):
AAAAAGAAATCGAAAAAG
Found at i:575808 original size:30 final size:30
Alignment explanation
Indices: 575712--575812 Score: 82
Period size: 30 Copynumber: 3.4 Consensus size: 30
575702 AATATGGAAT
* *
575712 GAAAATGAGAAAAGAAA--AAAAGAAATGAGA
1 GAAAAAGA-AAAAGAAAGTAAAA-AAGTGAGA
** **
575742 GAAAAAGAAAAAGAAAGTAAAAAAGAAATT
1 GAAAAAGAAAAAGAAAGTAAAAAAGTGAGA
* *
575772 GCAAAAGAAAAAGAAA-TCGAAAAAGTGAGA
1 GAAAAAGAAAAAGAAAGT-AAAAAAGTGAGA
575802 GAAAAAGAAAA
1 GAAAAAGAAAA
575813 CAAAGAAAAC
Statistics
Matches: 55, Mismatches: 13, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
29 9 0.16
30 42 0.76
31 4 0.07
ACGTcount: A:0.70, C:0.02, G:0.21, T:0.07
Consensus pattern (30 bp):
GAAAAAGAAAAAGAAAGTAAAAAAGTGAGA
Found at i:575858 original size:17 final size:18
Alignment explanation
Indices: 575826--575859 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
575816 AGAAAACAAA
575826 ATTGAAAAAGAAATTGAG
1 ATTGAAAAAGAAATTGAG
*
575844 ATTGAGAAA-AAATTGA
1 ATTGAAAAAGAAATTGA
575860 AAGAGAAAAA
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:0.56, C:0.00, G:0.21, T:0.24
Consensus pattern (18 bp):
ATTGAAAAAGAAATTGAG
Found at i:575877 original size:29 final size:28
Alignment explanation
Indices: 575823--575881 Score: 66
Period size: 29 Copynumber: 2.1 Consensus size: 28
575813 CAAAGAAAAC
**
575823 AAAATTGAAAAAGAAATTGAGATTGAGAA
1 AAAATTGAAAAAGAAAAAGAGATTGA-AA
*
575852 AAAATTGAAAGAGAAAAAGATG-TTGAAA
1 AAAATTGAAAAAGAAAAAGA-GATTGAAA
575880 AA
1 AA
575882 GAAACGAAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
28 4 0.15
29 21 0.81
30 1 0.04
ACGTcount: A:0.61, C:0.00, G:0.20, T:0.19
Consensus pattern (28 bp):
AAAATTGAAAAAGAAAAAGAGATTGAAA
Found at i:577624 original size:11 final size:11
Alignment explanation
Indices: 577589--577627 Score: 55
Period size: 10 Copynumber: 3.7 Consensus size: 11
577579 AGCTCGATCC
*
577589 AGCTCAA-TCG
1 AGCTCAATTCT
577599 AGCTCAATT-T
1 AGCTCAATTCT
577609 AGCTCAATTCT
1 AGCTCAATTCT
577620 AGCTCAAT
1 AGCTCAAT
577628 GAGCTCGTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
10 16 0.62
11 10 0.38
ACGTcount: A:0.31, C:0.26, G:0.13, T:0.31
Consensus pattern (11 bp):
AGCTCAATTCT
Found at i:577625 original size:21 final size:20
Alignment explanation
Indices: 577589--577627 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
577579 AGCTCGATCC
577589 AGCTCAATCGAGCTCAATTT
1 AGCTCAATCGAGCTCAATTT
*
577609 AGCTCAATTCTAGCTCAAT
1 AGCTCAA-TCGAGCTCAAT
577628 GAGCTCGTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.31, C:0.26, G:0.13, T:0.31
Consensus pattern (20 bp):
AGCTCAATCGAGCTCAATTT
Found at i:577632 original size:20 final size:20
Alignment explanation
Indices: 577589--577633 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
577579 AGCTCGATCC
*
577589 AGCTCAATCGAGCTCAATTT
1 AGCTCAATCGAGCTCAATTG
*
577609 AGCTCAATTCTAGCTCAA-TG
1 AGCTCAA-TCGAGCTCAATTG
577629 AGCTC
1 AGCTC
577634 GTTCCTAGCT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.29
Consensus pattern (20 bp):
AGCTCAATCGAGCTCAATTG
Found at i:579610 original size:36 final size:37
Alignment explanation
Indices: 579542--579628 Score: 113
Period size: 36 Copynumber: 2.4 Consensus size: 37
579532 ACCACTCCGA
* * *
579542 CCACCCTGCACACTACAATTGGGCTATGGTAGGCCCAT
1 CCACCCTGCACACCACAA-TAGGCTATAGTAGGCCCAT
579580 CCACCCTGCACACCACAA-AGGCTATAGTAGGCCCAT
1 CCACCCTGCACACCACAATAGGCTATAGTAGGCCCAT
* *
579616 CCACACTACACAC
1 CCACCCTGCACAC
579629 TACGATAGTG
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
36 27 0.61
38 17 0.39
ACGTcount: A:0.29, C:0.39, G:0.16, T:0.16
Consensus pattern (37 bp):
CCACCCTGCACACCACAATAGGCTATAGTAGGCCCAT
Found at i:581379 original size:21 final size:21
Alignment explanation
Indices: 581353--581415 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
581343 TTGGTATTTG
581353 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
*
581374 GGAATTGGTATGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
581395 GGTATTTGGTACGAATTGGTA
1 GG-AATTGGTACGAAATGGTA
581416 ATGGTTCAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 22 0.59
22 15 0.41
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.33
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:582373 original size:30 final size:30
Alignment explanation
Indices: 582315--582373 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
582305 TTGAAAAGGT
* *
582315 TTGAGCTGAAGTTGAGCTAATTCGAGCTCA
1 TTGAGCTGAAATGGAGCTAATTCGAGCTCA
*
582345 TTGAGCTGAAATGGAAGTTAATTC-AGCTC
1 TTGAGCTGAAATGG-AGCTAATTCGAGCTC
582374 GTATTAAAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 17 0.68
31 8 0.32
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.31
Consensus pattern (30 bp):
TTGAGCTGAAATGGAGCTAATTCGAGCTCA
Found at i:583881 original size:18 final size:18
Alignment explanation
Indices: 583858--583896 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
583848 AAATTTTTTT
*
583858 TATTATAATATGTATACA
1 TATTATAATATGTATAAA
583876 TATTATAATATGTATAAA
1 TATTATAATATGTATAAA
583894 TAT
1 TAT
583897 ATACCTATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (18 bp):
TATTATAATATGTATAAA
Found at i:584011 original size:8 final size:8
Alignment explanation
Indices: 583998--584027 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
583988 TATATTATGC
583998 TTATATTT
1 TTATATTT
584006 TTATATTT
1 TTATATTT
*
584014 TTATCTTT
1 TTATATTT
584022 TTATAT
1 TTATAT
584028 AAGTCTTTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.73
Consensus pattern (8 bp):
TTATATTT
Found at i:586148 original size:30 final size:30
Alignment explanation
Indices: 586114--586184 Score: 142
Period size: 30 Copynumber: 2.4 Consensus size: 30
586104 CTTTAAATTA
586114 AAATCAAAGTTTTATGTGTATAATTGTACC
1 AAATCAAAGTTTTATGTGTATAATTGTACC
586144 AAATCAAAGTTTTATGTGTATAATTGTACC
1 AAATCAAAGTTTTATGTGTATAATTGTACC
586174 AAATCAAAGTT
1 AAATCAAAGTT
586185 CATGTATCTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.38
Consensus pattern (30 bp):
AAATCAAAGTTTTATGTGTATAATTGTACC
Found at i:606181 original size:117 final size:118
Alignment explanation
Indices: 605988--606222 Score: 269
Period size: 117 Copynumber: 2.0 Consensus size: 118
605978 TGACGATATT
* *
605988 TTGAATGTTATTCCTCGGGATAGGCACACGTATTTGTTTTCAGCAACCATGACCAAAAAGGTATG
1 TTGAACGTTATTCCTCGGGATAGGCACAC-TATTTGTTTTCAGCAACCATGACCAAAAAGGTATA
** *
606053 TGGGGGAAAACAAACATTTTACATATTATATAAGAAATATGTCCATATACTATC
65 ACGGGGAAAACAAACATTTTACATATTATATAAGAAACATGTCCATATACTATC
* * * **
606107 TTGAACGTTGTTCCTCGTGG-TAGGCACA-TGTTTGTTTTCTGTGACCATGACCAGAAAAGGTAT
1 TTGAACGTTATTCCTCG-GGATAGGCACACTATTTGTTTTCAGCAACCATGACCA-AAAAGGTAT
* * ** * * *
606170 AACTGGG-AAACAAATATTTTATGTATTCTGTAAGAAACATGTCCATATGCTAT
64 AACGGGGAAAACAAACATTTTACATATTATATAAGAAACATGTCCATATACTAT
606223 TTTCTGTTTC
Statistics
Matches: 97, Mismatches: 17, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
117 60 0.62
118 12 0.12
119 23 0.24
120 2 0.02
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Consensus pattern (118 bp):
TTGAACGTTATTCCTCGGGATAGGCACACTATTTGTTTTCAGCAACCATGACCAAAAAGGTATAA
CGGGGAAAACAAACATTTTACATATTATATAAGAAACATGTCCATATACTATC
Found at i:606600 original size:19 final size:19
Alignment explanation
Indices: 606576--606614 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
606566 TGGAAGTTTG
606576 ACTACAATGTTGATTTTAT
1 ACTACAATGTTGATTTTAT
606595 ACTACAATGTTGATTTTAT
1 ACTACAATGTTGATTTTAT
606614 A
1 A
606615 GGTGAAGAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.33, C:0.10, G:0.10, T:0.46
Consensus pattern (19 bp):
ACTACAATGTTGATTTTAT
Found at i:609708 original size:30 final size:30
Alignment explanation
Indices: 609674--609735 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
609664 GCAGGCTAAA
609674 CAAAACATCGATATCAGCATATATAAACCC
1 CAAAACATCGATATCAGCATATATAAACCC
609704 CAAAACATCGATATCAGCATATATAAACCC
1 CAAAACATCGATATCAGCATATATAAACCC
609734 CA
1 CA
609736 CTTGCACTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.47, C:0.27, G:0.06, T:0.19
Consensus pattern (30 bp):
CAAAACATCGATATCAGCATATATAAACCC
Found at i:614615 original size:17 final size:18
Alignment explanation
Indices: 614578--614616 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
614568 ACTTTGATGT
614578 GCTCACAACTTGGGTTGA
1 GCTCACAACTTGGGTTGA
* *
614596 GCTCACATCTTTGG-TGA
1 GCTCACAACTTGGGTTGA
614613 GCTC
1 GCTC
614617 GTGTTTTTGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.18, C:0.26, G:0.26, T:0.31
Consensus pattern (18 bp):
GCTCACAACTTGGGTTGA
Found at i:615947 original size:22 final size:23
Alignment explanation
Indices: 615921--615973 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
615911 AATGGTTTGG
*
615921 TTATATTTTTAATTA-CTTCAAA
1 TTATATTTTTAATTATATTCAAA
* * *
615943 TTATATTCTTACTTATATTTAAA
1 TTATATTTTTAATTATATTCAAA
615966 TTATATTT
1 TTATATTT
615974 ATATTTATTG
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
22 13 0.52
23 12 0.48
ACGTcount: A:0.34, C:0.08, G:0.00, T:0.58
Consensus pattern (23 bp):
TTATATTTTTAATTATATTCAAA
Found at i:617387 original size:20 final size:20
Alignment explanation
Indices: 617349--617386 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
617339 TCGGTTAAGT
617349 TAAATTAAAAATATTTTTTA
1 TAAATTAAAAATATTTTTTA
617369 TAAATT-AAAATATTTTTT
1 TAAATTAAAAATATTTTTT
617387 TTTGTCTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
TAAATTAAAAATATTTTTTA
Found at i:622092 original size:43 final size:41
Alignment explanation
Indices: 622029--622234 Score: 198
Period size: 42 Copynumber: 4.9 Consensus size: 41
622019 TACCGTAACA
* * * *
622029 ATGCCATATCCCAGATATGGTCTTACATGTAATCTCATATTG
1 ATGCCATAGCCCAGACATGGTCTTACACG-AATCTCATATCG
* * *
622071 ATGCCAATAGCCCAGCCATGGTCTTACACGAAATCACATATCA
1 ATGCC-ATAGCCCAGACATGGTCTTACACG-AATCTCATATCG
622114 ATGCCA-ATGTCCCAGACATGGTCTTACACGAATTCTCATATCG
1 ATGCCATA-G-CCCAGACATGGTCTTACACGAA-TCTCATATCG
* * * * *
622157 ATGTCATATCCCAAATATGGTCTTACACGAATTCTCATATTG
1 ATGCCATAGCCCAGACATGGTCTTACACGAA-TCTCATATCG
** *
622199 ATGCCATATTCCAGATATGGTCTTACACGTAATCTC
1 ATGCCATAGCCCAGACATGGTCTTACACG-AATCTC
622235 GATAACCCTA
Statistics
Matches: 139, Mismatches: 19, Indels: 12
0.82 0.11 0.07
Matches are distributed among these distances:
41 1 0.01
42 69 0.50
43 68 0.49
44 1 0.01
ACGTcount: A:0.30, C:0.25, G:0.14, T:0.31
Consensus pattern (41 bp):
ATGCCATAGCCCAGACATGGTCTTACACGAATCTCATATCG
Found at i:622182 original size:42 final size:42
Alignment explanation
Indices: 622029--622227 Score: 238
Period size: 43 Copynumber: 4.7 Consensus size: 42
622019 TACCGTAACA
* *
622029 ATGCCATATCCCAGATATGGTCTTACATGTAA-TCTCATATTG
1 ATGCCATATCCCAGATATGGTCTTACACG-AATTCTCATATCG
* ** * * *
622071 ATGCCAATAGCCCAGCCATGGTCTTACACGAAATCACATATCA
1 ATGCC-ATATCCCAGATATGGTCTTACACGAATTCTCATATCG
* *
622114 ATGCCAATGTCCCAGACATGGTCTTACACGAATTCTCATATCG
1 ATGCC-ATATCCCAGATATGGTCTTACACGAATTCTCATATCG
* * *
622157 ATGTCATATCCCAAATATGGTCTTACACGAATTCTCATATTG
1 ATGCCATATCCCAGATATGGTCTTACACGAATTCTCATATCG
*
622199 ATGCCATATTCCAGATATGGTCTTACACG
1 ATGCCATATCCCAGATATGGTCTTACACG
622228 TAATCTCGAT
Statistics
Matches: 134, Mismatches: 21, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
42 66 0.49
43 68 0.51
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.30
Consensus pattern (42 bp):
ATGCCATATCCCAGATATGGTCTTACACGAATTCTCATATCG
Done.