Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011520.1 Kokia drynarioides strain JFW-HI SEQ_126506, whole genome shotgun sequence
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: 653816
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Warning! 73 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:181 original size:4 final size:4
Alignment explanation
Indices: 172--206 Score: 52
Period size: 4 Copynumber: 8.8 Consensus size: 4
162 TTTGCCTCAT
* *
172 ATTC ATTC ATTC ATTC ATTC ACTC ATTC ACTC ATT
1 ATTC ATTC ATTC ATTC ATTC ATTC ATTC ATTC ATT
207 TGTTTATTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.26, C:0.29, G:0.00, T:0.46
Consensus pattern (4 bp):
ATTC
Found at i:8432 original size:10 final size:10
Alignment explanation
Indices: 8415--8467 Score: 58
Period size: 10 Copynumber: 5.5 Consensus size: 10
8405 GTTTAAATTA
8415 AGAAAAAAAT
1 AGAAAAAAAT
*
8425 ACAAAAAAGA-
1 AGAAAAAA-AT
8435 AGAAAAAAA-
1 AGAAAAAAAT
*
8444 A-AAGAAAAT
1 AGAAAAAAAT
8453 AGAAAAAAAT
1 AGAAAAAAAT
8463 AGAAA
1 AGAAA
8468 GAGAGAGCAA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
8 6 0.17
9 3 0.08
10 26 0.72
11 1 0.03
ACGTcount: A:0.81, C:0.02, G:0.11, T:0.06
Consensus pattern (10 bp):
AGAAAAAAAT
Found at i:8439 original size:20 final size:19
Alignment explanation
Indices: 8414--8463 Score: 59
Period size: 18 Copynumber: 2.6 Consensus size: 19
8404 TGTTTAAATT
8414 AAGAAAAAAATACAA-AAAA
1 AAGAAAAAAATA-AAGAAAA
8433 GAAGAAAAAAA-AAAGAAAA
1 -AAGAAAAAAATAAAGAAAA
*
8452 TAGAAAAAAATA
1 AAGAAAAAAATA
8464 GAAAGAGAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 11 0.41
19 6 0.22
20 10 0.37
ACGTcount: A:0.82, C:0.02, G:0.10, T:0.06
Consensus pattern (19 bp):
AAGAAAAAAATAAAGAAAA
Found at i:8443 original size:21 final size:20
Alignment explanation
Indices: 8417--8461 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
8407 TTAAATTAAG
*
8417 AAAAAAATACAAAAAAGAAGA
1 AAAAAAAAACAAAAAAGAA-A
* *
8438 AAAAAAAAAGAAAATAGAAA
1 AAAAAAAAACAAAAAAGAAA
8458 AAAA
1 AAAA
8462 TAGAAAGAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.84, C:0.02, G:0.09, T:0.04
Consensus pattern (20 bp):
AAAAAAAAACAAAAAAGAAA
Found at i:8468 original size:21 final size:20
Alignment explanation
Indices: 8414--8469 Score: 57
Period size: 19 Copynumber: 2.9 Consensus size: 20
8404 TGTTTAAATT
8414 AAGAAAAAAATACAAA-AAAG
1 AAGAAAAAAATA-AAAGAAAG
8434 AAG-AAAAAA-AAAAGAAA-
1 AAGAAAAAAATAAAAGAAAG
8451 ATAGAAAAAAATAGAAAGA
1 A-AGAAAAAAATA-AAAGA
8470 GAGAGCAAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
17 4 0.13
18 6 0.19
19 12 0.39
20 4 0.13
21 5 0.16
ACGTcount: A:0.80, C:0.02, G:0.12, T:0.05
Consensus pattern (20 bp):
AAGAAAAAAATAAAAGAAAG
Found at i:9555 original size:42 final size:42
Alignment explanation
Indices: 8869--9553 Score: 941
Period size: 42 Copynumber: 16.5 Consensus size: 42
8859 AAAGAAAGCA
*
8869 TTCATTGCATTTAGAGGCCTAGGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * *
8911 TTCATTGCATTCAGAGGCCTAGGTGTGGAGGCCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * * *
8953 TTCATTGCATTTAAAGGCCTAAGTGTGGAGGTCCATTTATTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* *
8995 TTCATTGCATTCAGAGGCCTAGGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
*
9037 TTCATTGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* *
9079 TTCATTGCATTTAAAGGCCCAGGTGTGGAGGCCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * *
9121 TTCATTGCATTTAGAGGCCCAAGTGTGGAGGTTCATTTATTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
9163 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * * * * *
9205 TTCACTGCATTCAGATGCCCAGGTATAGAGGTCCATTTGCTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* *
9247 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTTCATTTACCT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
*
9289 TTCATTGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * ** *
9331 TTCATTGTATTTAGAGGCTCAGGTGTAAAGGTTCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* *
9373 TTCATCGCATTT--A-G---AGGTGTGGAGGCCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * * *
9409 TTCATCGCATTTAGAGGCCTAGGTATGAAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * * *
9451 TCCATTGCATTTAGCGGCCCAGGGGTGGAGGTCCATTTATTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* *
9493 TTCATTGCATTCAGAGGCCTAGGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
*
9535 TTCATTGCAATTAGAGGCC
1 TTCATTGCATTTAGAGGCC
9554 TAAACATAGA
Statistics
Matches: 564, Mismatches: 73, Indels: 12
0.87 0.11 0.02
Matches are distributed among these distances:
36 30 0.05
38 1 0.00
39 2 0.00
40 1 0.00
42 530 0.94
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.36
Consensus pattern (42 bp):
TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
Found at i:9902 original size:10 final size:11
Alignment explanation
Indices: 9877--9907 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
9867 AAATAGAGGT
9877 TTTTCTTTTTC
1 TTTTCTTTTTC
9888 TTTTCTTTTTC
1 TTTTCTTTTTC
9899 -TTTCTTTTT
1 TTTTCTTTTT
9908 TGGGTTTATC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTCTTTTTC
Found at i:9964 original size:3 final size:3
Alignment explanation
Indices: 9958--9984 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
9948 CATCATCATC
9958 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
9985 TAGGGTTGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:11080 original size:149 final size:148
Alignment explanation
Indices: 10409--11374 Score: 1411
Period size: 151 Copynumber: 6.4 Consensus size: 148
10399 TTTGGAAAAT
* * *
10409 ATTTTGATTTTTTTTAAACAATTTCGAAATAAAAGCTTTGATTTTTTTATGCAAAATAGTGATTT
1 ATTTTGATTTTTTTT-AACTATTTCGAAATAAAAG-TTTGA--TTTTTAAGTAAAATAGTGATTT
* *
10474 TCTTT-AAAAAAGAGAAAGTTTATATTTTAAAAAATAAAAATCTATTTTTTAGTTATTTTAAAGA
62 TCTTTAAAAAAAGAGAAAGTTTATATTTTTAAAAATAAAAATCTGTTTTTTAGTTATTTTAAAGA
*
10538 AAAAGTTTATATTTTTAACAAA
127 AAAAGTTTAAATTTTTAACAAA
* *
10560 GTTTTGATTTTTCTTAACTATTTCGAAATAAAAGTTTGGATTTTTAAGTAAAATAGTGATTTTCT
1 ATTTTGATTTTTTTTAACTATTTCGAAATAAAAGTTT-GATTTTTAAGTAAAATAGTGATTTTCT
*
10625 TT-AAAAAAGATAAAGTTTATATTTTTAAAAATAAAAATCTGTTTTTTAGTTATTTTAAAGAAAA
65 TTAAAAAAAGAGAAAGTTTATATTTTTAAAAATAAAAATCTGTTTTTTAGTTATTTTAAAGAAAA
10689 AGTTTAAATTTTTAACAAA
130 AGTTTAAATTTTTAACAAA
* * *
10708 GTTTTGTTTTTTTTTTTTTAACTATTTCGAAATAAAAGTTTGGATTTTTAAGTAAAATATTGATT
1 ATTTTG----ATTTTTTTTAACTATTTCGAAATAAAAGTTT-GATTTTTAAGTAAAATAGTGATT
** * *
10773 TT-TTTTTAAAAAGAGAAAGTTTATATTTTT-AGAATAAAAATATGTTTTTTAGTTATTTTAAAG
61 TTCTTTAAAAAAAGAGAAAGTTTATATTTTTAAAAATAAAAATCTGTTTTTTAGTTATTTTAAAG
*
10836 AAAAATTTTAAATTTTTAACAAA
126 AAAAAGTTTAAATTTTTAACAAA
*
10859 GTTTT-ACTTCTTTTTTTTTAACTATTTCGAAATAAAAGTTTAGATTTTTAAGTAAAATAGTGAT
1 ATTTTGA-----TTTTTTTTAACTATTTCGAAATAAAAGTTT-GATTTTTAAGTAAAATAGTGAT
10923 TTTCTTTAAAAAAAGAGAAAGTTTATATTTTTAAAAATAAAAATCTGTTTTTTAGTTATTTTAAA
60 TTTCTTTAAAAAAAGAGAAAGTTTATATTTTTAAAAATAAAAATCTGTTTTTTAGTTATTTTAAA
10988 GAAAAAGTTTAAATTTTTAACAAA
125 GAAAAAGTTTAAATTTTTAACAAA
* *
11012 ATTTTGAATTTTTTTAACTATTTCGAAATAAAAGTTTGGAATTTTAAGTAAAATAGTGATTTTCT
1 ATTTTGATTTTTTTTAACTATTTCGAAATAAAAGTTT-GATTTTTAAGTAAAATAGTGATTTTCT
* * *
11077 TTAAAAAAAGAAAAAGTTTATATTTTTAAAAATAAAAATATGTTTTTTAGTTATCTTAAAGAAAA
65 TTAAAAAAAGAGAAAGTTTATATTTTTAAAAATAAAAATCTGTTTTTTAGTTATTTTAAAGAAAA
*
11142 AGTTTAAATTTTTAATAAA
130 AGTTTAAATTTTTAACAAA
* *
11161 ATTTTGATTTTTTTTAACTATTTCGAAATAAATGCTTGAATTTTTAAGTAAAATAGTGATTTTCT
1 ATTTTGATTTTTTTTAACTATTTCGAAATAAAAGTTTG-ATTTTTAAGTAAAATAGTGATTTTCT
* *
11226 TTAAAAAAAGAGAAAGTTTAGATTTTTTAAAAAATAAAAATCTGTTTTTTAGTTATTTTAAATAA
65 TTAAAAAAAGAGAAAGTTTATA-TTTTT-AAAAATAAAAATCTGTTTTTTAGTTATTTTAAAGAA
*
11291 AAAGTTTAAATTTTTGACAAA
128 AAAGTTTAAATTTTTAACAAA
* * * *
11312 ATTTTGATTATTTTTAACTATTTCAAAATAAAAGTTTGAATTTTTAAGTAAAGTAGTAATTTT
1 ATTTTGATTTTTTTTAACTATTTCGAAATAAAAGTTTG-ATTTTTAAGTAAAATAGTGATTTT
11375 TGTTTAATCA
Statistics
Matches: 748, Mismatches: 50, Indels: 34
0.90 0.06 0.04
Matches are distributed among these distances:
148 109 0.15
149 217 0.29
150 25 0.03
151 237 0.32
152 102 0.14
153 57 0.08
154 1 0.00
ACGTcount: A:0.41, C:0.04, G:0.10, T:0.46
Consensus pattern (148 bp):
ATTTTGATTTTTTTTAACTATTTCGAAATAAAAGTTTGATTTTTAAGTAAAATAGTGATTTTCTT
TAAAAAAAGAGAAAGTTTATATTTTTAAAAATAAAAATCTGTTTTTTAGTTATTTTAAAGAAAAA
GTTTAAATTTTTAACAAA
Found at i:11174 original size:51 final size:50
Alignment explanation
Indices: 10518--11363 Score: 238
Period size: 51 Copynumber: 16.8 Consensus size: 50
10508 TAAAAATCTA
* * * *
10518 TTTTTTAGTTATTTTAAAGAAAAAGTTTATATTTTTAACAAAGTTTTGATT
1 TTTTTTAGTTA-TTTAAAGAAAAAGTTTAAATTTTTAATAAAATATTGATT
* ** * ** *
10569 TTTCTTAACTATTTCGAAA-TAAAAGTTTGGATTTTTAAGTAAAATAGTGATT
1 TTTTTTAGTTATTT--AAAGAAAAAGTTTAAATTTTTAA-TAAAATATTGATT
* * * * ***
10621 TTCTTTA---A--AAAAGATAAAGTTTATATTTTT-A-AAAATAAAAATCT
1 TTTTTTAGTTATTTAAAGAAAAAGTTTAAATTTTTAATAAAATATTGAT-T
* * * *
10665 GTTTTTTAGTTATTTTAAAGAAAAAGTTTAAATTTTTAACAAAGTTTTGTTTTTTT
1 -TTTTTTAGTTA-TTTAAAGAAAAAGTTTAAATTTTTAATAAAATATTG----ATT
** * **
10721 TTTTTTAACTATTTCGAAA-TAAAAGTTTGGATTTTTAAGTAAAATATTGA-T
1 TTTTTTAGTTATTT--AAAGAAAAAGTTTAAATTTTTAA-TAAAATATTGATT
* * * *
10772 TTTTTT--TTA--AAAAGAGAAAGTTTATATTTTTAGAATAAAA-A-T-ATG
1 TTTTTTAGTTATTTAAAGAAAAAGTTTAAATTTTT--AATAAAATATTGATT
* * * **
10817 TTTTTTAGTTATTTTAAAGAAAAATTTTAAATTTTTAACAAAGTTTTACTTCTTT
1 TTTTTTAGTTA-TTTAAAGAAAAAGTTTAAATTTTTAATAAA---ATA-TTGATT
** * * *
10872 TTTTTTAACTATTTCGAAA-TAAAAGTTTAGATTTTTAAGTAAAATAGTGATT
1 TTTTTTAGTTATTT--AAAGAAAAAGTTTAAATTTTTAA-TAAAATATTGATT
* ** * * ***
10924 TTCTTTA---A-AAAAAGAGAAAGTTTATATTTTT-A-AAAATAAAAATCT
1 TTTTTTAGTTATTTAAAGAAAAAGTTTAAATTTTTAATAAAATATTGAT-T
* * *
10969 GTTTTTTAGTTATTTTAAAGAAAAAGTTTAAATTTTTAACAAAATTTTGAAT
1 -TTTTTTAGTTA-TTTAAAGAAAAAGTTTAAATTTTTAATAAAATATTGATT
** * * *
11021 TTTTTTAACTATTTCGAAA-TAAAAGTTTGGAA-TTTTAAGTAAAATAGTGATT
1 TTTTTTAGTTATTT--AAAGAAAAAGTTT-AAATTTTTAA-TAAAATATTGATT
* ** * * * * *
11073 TTCTTTA---A-AAAAAGAAAAAGTTTATATTTTTAAAAATAAAAAT-ATG
1 TTTTTTAGTTATTTAAAGAAAAAGTTTAAATTTTTAATAA-AATATTGATT
*
11119 TTTTTTAGTTATCTTAAAGAAAAAGTTTAAATTTTTAATAAAATTTTGATT
1 TTTTTTAGTTAT-TTAAAGAAAAAGTTTAAATTTTTAATAAAATATTGATT
** * * * * *
11170 TTTTTTAACTATTTCGAAA-TAAATGCTTGAATTTTTAAGTAAAATAGTGATT
1 TTTTTTAGTTATTT--AAAGAAAAAGTTTAAATTTTTAA-TAAAATATTGATT
* ** * * ***
11222 TTCTTTA---A-AAAAAGAGAAAGTTTAGATTTTTTAA-AAAATAAAAATCT
1 TTTTTTAGTTATTTAAAGAAAAAGTTTA-AATTTTTAATAAAATATTGAT-T
* * * *
11269 GTTTTTTAGTTATTTTAAATAAAAAGTTTAAATTTTTGACAAAATTTTGATT
1 -TTTTTTAGTTA-TTTAAAGAAAAAGTTTAAATTTTTAATAAAATATTGATT
* ** *
11321 ATTTTTAACTATTTCAAA-ATAAAAGTTTGAATTTTTAAGTAAA
1 TTTTTTAGTTATTT-AAAGA-AAAAGTTTAAATTTTTAA-TAAA
11364 GTAGTAATTT
Statistics
Matches: 569, Mismatches: 147, Indels: 157
0.65 0.17 0.18
Matches are distributed among these distances:
43 8 0.01
44 10 0.02
45 21 0.04
46 62 0.11
47 46 0.08
48 22 0.04
49 8 0.01
50 33 0.06
51 171 0.30
52 81 0.14
53 31 0.05
54 7 0.01
55 51 0.09
56 17 0.03
57 1 0.00
ACGTcount: A:0.41, C:0.03, G:0.09, T:0.46
Consensus pattern (50 bp):
TTTTTTAGTTATTTAAAGAAAAAGTTTAAATTTTTAATAAAATATTGATT
Found at i:11273 original size:300 final size:295
Alignment explanation
Indices: 10409--11374 Score: 1400
Period size: 300 Copynumber: 3.2 Consensus size: 295
10399 TTTGGAAAAT
* * * * *
10409 ATTTTGATTTTTTTTAAACAATTTCGAAATAAAAGCTTTGATTTTTTTATGCAAAATAGTGATTT
1 ATTTTGAATTTTTTT-AACTATTTCGAAATAAAAG-TTTGA--ATTTTAAGTAAAATAGTGATTT
* * *
10474 TCTTTAAAAAAGAGAAAGTTTATATTTTAAAAAATAAAAATCTATTTTTTAGTTATTTTAAAGAA
62 TCTTTAAAAAAGAGAAAGTTTATATTTTTAAAAATAAAAATATGTTTTTTAGTTATTTTAAAGAA
* * *
10539 AAAGTTTATATTTTTAACAAAGTTTTGATTTTTCTTAACTATTTCGAAATAAAAGTTTGGATTTT
127 AAAGTTTAAATTTTTAACAAAGTTTTGATTTTTTTTAACTATTTCGAAATAAAAG-TTGAATTTT
*
10604 TAAGTAAAATAGTGATTTTCTTT-AAAAAAGATAAAGTTTATATTTTTAAAAATAAAAATCTGTT
191 TAAGTAAAATAGTGATTTTCTTTAAAAAAAGAGAAAGTTTATATTTTTAAAAATAAAAATCTGTT
10668 TTTTAGTTATTTTAAAGAAAAAGTTTAAATTTTTAACAAA
256 TTTTAGTTATTTTAAAGAAAAAGTTTAAATTTTTAACAAA
* ** * *
10708 GTTTTGTTTTTTTTTTTTTAACTATTTCGAAATAAAAGTTTGGATTTTTAAGTAAAATATTGATT
1 ATTTTG----AATTTTTTTAACTATTTCGAAATAAAAGTTT-GAATTTTAAGTAAAATAGTGATT
* * *
10773 TTTTTTTAAAAAGAGAAAGTTTATATTTTT-AGAATAAAAATATGTTTTTTAGTTATTTTAAAGA
61 TTCTTTAAAAAAGAGAAAGTTTATATTTTTAAAAATAAAAATATGTTTTTTAGTTATTTTAAAGA
* *
10837 AAAATTTTAAATTTTTAACAAAGTTTT-ACTTCTTTTTTTTTAACTATTTCGAAATAAAAGTTTA
126 AAAAGTTTAAATTTTTAACAAAGTTTTGA-----TTTTTTTTAACTATTTCGAAATAAAAGTTGA
10901 GATTTTTAAGTAAAATAGTGATTTTCTTTAAAAAAAGAGAAAGTTTATATTTTTAAAAATAAAAA
186 -ATTTTTAAGTAAAATAGTGATTTTCTTTAAAAAAAGAGAAAGTTTATATTTTTAAAAATAAAAA
10966 TCTGTTTTTTAGTTATTTTAAAGAAAAAGTTTAAATTTTTAACAAA
250 TCTGTTTTTTAGTTATTTTAAAGAAAAAGTTTAAATTTTTAACAAA
11012 ATTTTGAATTTTTTTAACTATTTCGAAATAAAAGTTTGGAATTTTAAGTAAAATAGTGATTTTCT
1 ATTTTGAATTTTTTTAACTATTTCGAAATAAAAGTTT-GAATTTTAAGTAAAATAGTGATTTTCT
* *
11077 TTAAAAAAAGAAAAAGTTTATATTTTTAAAAATAAAAATATGTTTTTTAGTTATCTTAAAGAAAA
65 TT-AAAAAAGAGAAAGTTTATATTTTTAAAAATAAAAATATGTTTTTTAGTTATTTTAAAGAAAA
* * *
11142 AGTTTAAATTTTTAATAAAATTTTGATTTTTTTTAACTATTTCGAAATAAATGCTTGAATTTTTA
129 AGTTTAAATTTTTAACAAAGTTTTGATTTTTTTTAACTATTTCGAAATAAAAG-TTGAATTTTTA
*
11207 AGTAAAATAGTGATTTTCTTTAAAAAAAGAGAAAGTTTAGATTTTTTAAAAAATAAAAATCTGTT
193 AGTAAAATAGTGATTTTCTTTAAAAAAAGAGAAAGTTTATA-TTTTT-AAAAATAAAAATCTGTT
* *
11272 TTTTAGTTATTTTAAATAAAAAGTTTAAATTTTTGACAAA
256 TTTTAGTTATTTTAAAGAAAAAGTTTAAATTTTTAACAAA
* * *
11312 ATTTTG-ATTATTTTTAACTATTTCAAAATAAAAGTTTGAATTTTTAAGTAAAGTAGTAATTTT
1 ATTTTGAATT-TTTTTAACTATTTCGAAATAAAAGTTTGAA-TTTTAAGTAAAATAGTGATTTT
11375 TGTTTAATCA
Statistics
Matches: 608, Mismatches: 39, Indels: 39
0.89 0.06 0.06
Matches are distributed among these distances:
298 74 0.12
299 75 0.12
300 208 0.34
301 25 0.04
302 78 0.13
303 63 0.10
304 85 0.14
ACGTcount: A:0.41, C:0.04, G:0.10, T:0.46
Consensus pattern (295 bp):
ATTTTGAATTTTTTTAACTATTTCGAAATAAAAGTTTGAATTTTAAGTAAAATAGTGATTTTCTT
TAAAAAAGAGAAAGTTTATATTTTTAAAAATAAAAATATGTTTTTTAGTTATTTTAAAGAAAAAG
TTTAAATTTTTAACAAAGTTTTGATTTTTTTTAACTATTTCGAAATAAAAGTTGAATTTTTAAGT
AAAATAGTGATTTTCTTTAAAAAAAGAGAAAGTTTATATTTTTAAAAATAAAAATCTGTTTTTTA
GTTATTTTAAAGAAAAAGTTTAAATTTTTAACAAA
Found at i:12837 original size:241 final size:239
Alignment explanation
Indices: 12407--12890 Score: 736
Period size: 241 Copynumber: 2.0 Consensus size: 239
12397 AAATATTTTA
* *
12407 AAATCATAATAATGATAAAAGATCGAATAAGTTGTAGATGAATTTTAATATTTCTCTTAATTCAT
1 AAATCAGAATAATGATAAAAGACCGAATAAGTTGTAGATGAATTTTAATATTTCTCTTAATTCAT
* * *
12472 TAGTAACTTTTAGGCTTTTTTTTAGGATTTTAAAATATAAATAATTTTAAGAATTGAAGGTATTT
66 TAGTAACTTTTAGGCTTTTTTTTAGGATTCTAAAATAGAAATAATTTTAAGAATAGAAGGTATTT
* *
12537 TACTAAAATTATTTAAGTATCTTTTAGGATTATCGTTAGAAGTAAAAATCTCTAATTTAAGTTTT
131 TACTAAAATTATTTAAGTATCCTTTAGGATTATCATTAGAAGTAAAAATCTCTAATTTAAGTTTT
*
12602 AAATTAGATAAGTTTGGAGAACACGTCTTAGTTAAGTTACAAGT
196 AAATTAGATAAGTTTGGAGAACACGTCTTAGTCAAGTTACAAGT
* *
12646 AAATCAGATTAATGATAAAAGACCGAATAAGTTGTAGATGAGTTTTAATATTTCTCTTAATTCAT
1 AAATCAGAATAATGATAAAAGACCGAATAAGTTGTAGATGAATTTTAATATTTCTCTTAATTCAT
* * *
12711 TAGTAATTTTTTTTAGG-TTTTTTTTAGGATTCTAAAATAGAATTAATTTTAAGGATAGAAGGTA
66 TAGTAA---CTTTTAGGCTTTTTTTTAGGATTCTAAAATAGAAATAATTTTAAGAATAGAAGGTA
* * * * * * *
12775 TTTTACTAGAATTATTTAGGTATCCTTTAGGGTTCTTATTAGGAGTAAAACTCTCTAATTTAAGT
128 TTTTACTAAAATTATTTAAGTATCCTTTAGGATTATCATTAGAAGTAAAAATCTCTAATTTAAGT
* *
12840 TTTAAATTAGATAAGTTTGGTGAACACGTCTTAGTCAAGTTATAAGT
193 TTTAAATTAGATAAGTTTGGAGAACACGTCTTAGTCAAGTTACAAGT
12887 AAAT
1 AAAT
12891 TGGAGGCATT
Statistics
Matches: 220, Mismatches: 22, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
239 67 0.30
241 146 0.66
242 7 0.03
ACGTcount: A:0.37, C:0.07, G:0.15, T:0.42
Consensus pattern (239 bp):
AAATCAGAATAATGATAAAAGACCGAATAAGTTGTAGATGAATTTTAATATTTCTCTTAATTCAT
TAGTAACTTTTAGGCTTTTTTTTAGGATTCTAAAATAGAAATAATTTTAAGAATAGAAGGTATTT
TACTAAAATTATTTAAGTATCCTTTAGGATTATCATTAGAAGTAAAAATCTCTAATTTAAGTTTT
AAATTAGATAAGTTTGGAGAACACGTCTTAGTCAAGTTACAAGT
Found at i:13682 original size:23 final size:23
Alignment explanation
Indices: 13652--13721 Score: 88
Period size: 23 Copynumber: 3.0 Consensus size: 23
13642 ATTAAATGTG
* *
13652 TTAAAAGTAAATGTGATTAATGC
1 TTAAAAGTTAATGTGATTTATGC
*
13675 TTGAAAGTTAAT-TCGATTTATGC
1 TTAAAAGTTAATGT-GATTTATGC
*
13698 CTAAAAGTTAATGTGATTTATGC
1 TTAAAAGTTAATGTGATTTATGC
13721 T
1 T
13722 CAAATGATGA
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
22 1 0.03
23 37 0.95
24 1 0.03
ACGTcount: A:0.36, C:0.07, G:0.17, T:0.40
Consensus pattern (23 bp):
TTAAAAGTTAATGTGATTTATGC
Found at i:19133 original size:18 final size:18
Alignment explanation
Indices: 19110--19148 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
19100 TGAAAAAGAT
*
19110 AAAGAAGGATTAAAT-TGA
1 AAAGAA-GATAAAATCTGA
19128 AAAGAAGATAAAATCTGA
1 AAAGAAGATAAAATCTGA
19146 AAA
1 AAA
19149 AAAATATGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.62, C:0.03, G:0.18, T:0.18
Consensus pattern (18 bp):
AAAGAAGATAAAATCTGA
Found at i:30455 original size:6 final size:6
Alignment explanation
Indices: 30413--30452 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
30403 ACATCTCTCT
* *
30413 TCTTCA TCTTCA TCTTCA TCTT-A TCTTCT TCTTCT TCTTC
1 TCTTCA TCTTCA TCTTCA TCTTCA TCTTCA TCTTCA TCTTC
30453 TTCCTTTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
5 5 0.16
6 27 0.84
ACGTcount: A:0.10, C:0.33, G:0.00, T:0.57
Consensus pattern (6 bp):
TCTTCA
Found at i:34878 original size:4 final size:4
Alignment explanation
Indices: 34869--34893 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
34859 CTCATTTTAG
34869 AAGA AAGA AAGA AAGA AAGA AAGA A
1 AAGA AAGA AAGA AAGA AAGA AAGA A
34894 GAAGAAGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:35030 original size:29 final size:29
Alignment explanation
Indices: 34960--35031 Score: 101
Period size: 29 Copynumber: 2.5 Consensus size: 29
34950 GAGTAATTTA
*
34960 AAAATAATTATGATTATCTCTTAAATTAT
1 AAAATAATTATTATTATCTCTTAAATTAT
*
34989 AAAATAATAATTATTATCTCTTAAACTT-T
1 AAAATAATTATTATTATCTCTTAAA-TTAT
*
35018 AAAATTATTATTAT
1 AAAATAATTATTAT
35032 AAACTTTCCC
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
29 36 0.95
30 2 0.05
ACGTcount: A:0.46, C:0.07, G:0.01, T:0.46
Consensus pattern (29 bp):
AAAATAATTATTATTATCTCTTAAATTAT
Found at i:45285 original size:29 final size:29
Alignment explanation
Indices: 45236--45310 Score: 87
Period size: 29 Copynumber: 2.6 Consensus size: 29
45226 CTAAAAATTA
* *
45236 TGAAAATGTTATATCCGAATGAATATTTT
1 TGAAAAGGTTATATCCAAATGAATATTTT
* **
45265 TGGAAAGGTTATATCCAAATGGGTATTTT
1 TGAAAAGGTTATATCCAAATGAATATTTT
*
45294 TGAAAAGGATATTATCC
1 TGAAAAGGTTA-TATCC
45311 GGAAGGATAA
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
29 33 0.87
30 5 0.13
ACGTcount: A:0.36, C:0.08, G:0.19, T:0.37
Consensus pattern (29 bp):
TGAAAAGGTTATATCCAAATGAATATTTT
Found at i:45337 original size:40 final size:40
Alignment explanation
Indices: 45293--45381 Score: 133
Period size: 40 Copynumber: 2.2 Consensus size: 40
45283 ATGGGTATTT
* * *
45293 TTGAAAAGGATATTATCCGGAAGGATAATAAATTAAAAGG
1 TTGAAAAGGATATTATCCGAAAGGATAATAAATGAAAAAG
*
45333 TTGAAAAGGATATTATCCGAAAGGGTAATAAATGAAAAAG
1 TTGAAAAGGATATTATCCGAAAGGATAATAAATGAAAAAG
*
45373 TCGAAAAGG
1 TTGAAAAGG
45382 TAAATTTATT
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 44 1.00
ACGTcount: A:0.48, C:0.06, G:0.24, T:0.22
Consensus pattern (40 bp):
TTGAAAAGGATATTATCCGAAAGGATAATAAATGAAAAAG
Found at i:48580 original size:16 final size:15
Alignment explanation
Indices: 48543--48581 Score: 60
Period size: 16 Copynumber: 2.5 Consensus size: 15
48533 ATATGATTAG
48543 CCTATACACCATTCA
1 CCTATACACCATTCA
48558 CCTTATACACCATTCA
1 CC-TATACACCATTCA
48574 CTCTATAC
1 C-CTATAC
48582 CAACCAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 2 0.09
16 19 0.86
17 1 0.05
ACGTcount: A:0.31, C:0.38, G:0.00, T:0.31
Consensus pattern (15 bp):
CCTATACACCATTCA
Found at i:49423 original size:17 final size:17
Alignment explanation
Indices: 49397--49430 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
49387 AATATATATA
*
49397 ACTTGTTTCGAATTTGT
1 ACTTGCTTCGAATTTGT
49414 ACTTGCTTCGAATTTGT
1 ACTTGCTTCGAATTTGT
49431 GCAAGACCGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.18, C:0.15, G:0.18, T:0.50
Consensus pattern (17 bp):
ACTTGCTTCGAATTTGT
Found at i:51407 original size:24 final size:24
Alignment explanation
Indices: 51371--51439 Score: 102
Period size: 24 Copynumber: 2.9 Consensus size: 24
51361 ACACTAATTG
51371 CAGCAGCATTTTCATCAGTAAAAT
1 CAGCAGCATTTTCATCAGTAAAAT
* *
51395 CAGTAGCATTTTCATCAGCAAAAT
1 CAGCAGCATTTTCATCAGTAAAAT
* *
51419 TAGCAGCATATTCATCAGTAA
1 CAGCAGCATTTTCATCAGTAA
51440 CTTCATCAGC
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.38, C:0.20, G:0.13, T:0.29
Consensus pattern (24 bp):
CAGCAGCATTTTCATCAGTAAAAT
Found at i:51449 original size:24 final size:24
Alignment explanation
Indices: 51374--51450 Score: 77
Period size: 24 Copynumber: 3.2 Consensus size: 24
51364 CTAATTGCAG
*
51374 CAGCATTTTCATCAGTAAAATCAGT
1 CAGCATTTTCATCAGTAAATTCA-T
* *
51399 -AGCATTTTCATCAGCAAAATT-AG
1 CAGCATTTTCATCAG-TAAATTCAT
* *
51422 CAGCATATTCATCAGTAACTTCAT
1 CAGCATTTTCATCAGTAAATTCAT
51446 CAGCA
1 CAGCA
51451 ACATTATCCA
Statistics
Matches: 42, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
23 4 0.10
24 34 0.81
25 4 0.10
ACGTcount: A:0.36, C:0.22, G:0.12, T:0.30
Consensus pattern (24 bp):
CAGCATTTTCATCAGTAAATTCAT
Found at i:51627 original size:33 final size:33
Alignment explanation
Indices: 51585--51651 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
51575 CAATAGTAGA
*
51585 CCCTCTTACATCACCCTCCACATCAGCTTCTAC
1 CCCTCTTACATCACCCTCCACAACAGCTTCTAC
* **
51618 CCCTCTTACATCACCTTCCTTAACAGCTTCTAC
1 CCCTCTTACATCACCCTCCACAACAGCTTCTAC
51651 C
1 C
51652 TTTTCCAGAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.21, C:0.46, G:0.03, T:0.30
Consensus pattern (33 bp):
CCCTCTTACATCACCCTCCACAACAGCTTCTAC
Found at i:52670 original size:16 final size:15
Alignment explanation
Indices: 52646--52706 Score: 59
Period size: 16 Copynumber: 3.8 Consensus size: 15
52636 CGTTCTTAGG
52646 TTAGGGATTCAATGAT
1 TTAGGGATTCAAT-AT
*
52662 TTGGGGATTTCAATAT
1 TTAGGGA-TTCAATAT
*
52678 TTAGGGATTTTAATATT
1 TTAGGGA-TTCAATA-T
*
52695 TTAAGGATTCAA
1 TTAGGGATTCAA
52707 AGAAGATTTC
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
16 25 0.66
17 13 0.34
ACGTcount: A:0.31, C:0.05, G:0.21, T:0.43
Consensus pattern (15 bp):
TTAGGGATTCAATAT
Found at i:52675 original size:17 final size:16
Alignment explanation
Indices: 52646--52695 Score: 66
Period size: 16 Copynumber: 3.1 Consensus size: 16
52636 CGTTCTTAGG
52646 TTAGGGA-TTCAATGAT
1 TTAGGGATTTCAAT-AT
*
52662 TTGGGGATTTCAATAT
1 TTAGGGATTTCAATAT
*
52678 TTAGGGATTTTAATAT
1 TTAGGGATTTCAATAT
52694 TT
1 TT
52696 TAAGGATTCA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
16 24 0.80
17 6 0.20
ACGTcount: A:0.28, C:0.04, G:0.22, T:0.46
Consensus pattern (16 bp):
TTAGGGATTTCAATAT
Found at i:66503 original size:49 final size:49
Alignment explanation
Indices: 66445--66542 Score: 178
Period size: 49 Copynumber: 2.0 Consensus size: 49
66435 TCGAACTCCA
*
66445 CACACTACATTTACTACAAGTAACATGCAAATCGAACTCTAATTTCGGG
1 CACACTACATTTACTACAAGTAACATGCAAATCCAACTCTAATTTCGGG
*
66494 CACATTACATTTACTACAAGTAACATGCAAATCCAACTCTAATTTCGGG
1 CACACTACATTTACTACAAGTAACATGCAAATCCAACTCTAATTTCGGG
66543 TATGGATAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 47 1.00
ACGTcount: A:0.37, C:0.24, G:0.11, T:0.28
Consensus pattern (49 bp):
CACACTACATTTACTACAAGTAACATGCAAATCCAACTCTAATTTCGGG
Found at i:70979 original size:2 final size:2
Alignment explanation
Indices: 70974--71003 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
70964 ATTACCTCTA
70974 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
71004 TATGTTTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:76212 original size:15 final size:15
Alignment explanation
Indices: 76192--76221 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
76182 CAATTAGAAG
*
76192 TCCTTAATTTTAGTT
1 TCCTTAATTATAGTT
76207 TCCTTAATTATAGTT
1 TCCTTAATTATAGTT
76222 CTCATTCTTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.13, G:0.07, T:0.57
Consensus pattern (15 bp):
TCCTTAATTATAGTT
Found at i:79533 original size:33 final size:33
Alignment explanation
Indices: 79495--79595 Score: 118
Period size: 33 Copynumber: 3.1 Consensus size: 33
79485 AAAATTGGTA
79495 AAGAGTTAACAAGATGTGTTAAGCATTCAACCT
1 AAGAGTTAACAAGATGTGTTAAGCATTCAACCT
* * * *
79528 TAGAGTTAGCAAGATGTGTTAA-AAGTCTAACCT
1 AAGAGTTAACAAGATGTGTTAAGCATTC-AACCT
79561 AAGCA-TTAACAAGAT-TGGTTAAGCATTCAACCT
1 AAG-AGTTAACAAGATGT-GTTAAGCATTCAACCT
79594 AA
1 AA
79596 AACCAATTGG
Statistics
Matches: 56, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
32 4 0.07
33 48 0.86
34 4 0.07
ACGTcount: A:0.40, C:0.15, G:0.18, T:0.28
Consensus pattern (33 bp):
AAGAGTTAACAAGATGTGTTAAGCATTCAACCT
Found at i:89347 original size:50 final size:51
Alignment explanation
Indices: 89272--89381 Score: 195
Period size: 50 Copynumber: 2.2 Consensus size: 51
89262 AATATTGAAG
89272 AAGAAGAAGAGATTATTTCTCTAAAAATCTCTAGAG-TTTTTGTTTCTCAA
1 AAGAAGAAGAGATTATTTCTCTAAAAATCTCTAGAGTTTTTTGTTTCTCAA
*
89322 AAGAAGAAGAGATTATTTCTCTAAAAATCTCTAGAGTTTTTTGTTTTTCAA
1 AAGAAGAAGAGATTATTTCTCTAAAAATCTCTAGAGTTTTTTGTTTCTCAA
89373 AAGAGAGAA
1 AAGA-AGAA
89382 TCAAAGAAGA
Statistics
Matches: 57, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
50 36 0.63
51 17 0.30
52 4 0.07
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.36
Consensus pattern (51 bp):
AAGAAGAAGAGATTATTTCTCTAAAAATCTCTAGAGTTTTTTGTTTCTCAA
Found at i:89357 original size:25 final size:25
Alignment explanation
Indices: 89279--89357 Score: 70
Period size: 25 Copynumber: 3.2 Consensus size: 25
89269 AAGAAGAAGA
89279 AGAGATTATTTCTCTAAAAATCTCT
1 AGAGATTATTTCTCTAAAAATCTCT
* * * *****
89304 AGAG-TTTTTGTTTCTCAAAAGAAGA
1 AGAGATTATT-TCTCTAAAAATCTCT
89329 AGAGATTATTTCTCTAAAAATCTCT
1 AGAGATTATTTCTCTAAAAATCTCT
89354 AGAG
1 AGAG
89358 TTTTTTGTTT
Statistics
Matches: 36, Mismatches: 16, Indels: 4
0.64 0.29 0.07
Matches are distributed among these distances:
24 4 0.11
25 28 0.78
26 4 0.11
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.37
Consensus pattern (25 bp):
AGAGATTATTTCTCTAAAAATCTCT
Found at i:89424 original size:66 final size:65
Alignment explanation
Indices: 89333--89461 Score: 222
Period size: 65 Copynumber: 2.0 Consensus size: 65
89323 AGAAGAAGAG
*
89333 ATTATTTCTCTAAAAATCTCTAGAGTTTTTTGTTTTTCAAAAGAGAGAATCAAAGAAGAAGAAAC
1 ATTATTTCTCTAAAAATCTCTAGAG-TTTTTGTTTCTCAAAAGAGAGAATCAAAGAAGAAGAAAC
89398 A
65 A
* *
89399 ATTATTTCTCTAAAAATCTCTAGAGTTTTTGTTTCTCAAAAGAGAGAATCGAAGAAGATGAAA
1 ATTATTTCTCTAAAAATCTCTAGAGTTTTTGTTTCTCAAAAGAGAGAATCAAAGAAGAAGAAA
89462 AAAAGAAGAA
Statistics
Matches: 60, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
65 35 0.58
66 25 0.42
ACGTcount: A:0.41, C:0.11, G:0.15, T:0.33
Consensus pattern (65 bp):
ATTATTTCTCTAAAAATCTCTAGAGTTTTTGTTTCTCAAAAGAGAGAATCAAAGAAGAAGAAACA
Found at i:91392 original size:5 final size:5
Alignment explanation
Indices: 91382--91407 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
91372 AGCTTCAAGA
91382 GTGAT GTGAT GTGAT GTGAT GTGAT G
1 GTGAT GTGAT GTGAT GTGAT GTGAT G
91408 AGAGGTCCCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.42, T:0.38
Consensus pattern (5 bp):
GTGAT
Found at i:91754 original size:22 final size:22
Alignment explanation
Indices: 91695--91982 Score: 317
Period size: 22 Copynumber: 12.4 Consensus size: 22
91685 GTGCTGGGGA
*
91695 AACAGAAGCACA-AAAGTGCTGGG
1 AACAGAAGCACACACAGTGCT--G
*
91718 AAACAGTAGACACACACAGTGCTG
1 -AACAGAAG-CACACACAGTGCTG
*
91742 AACAGAAGCACACACAATGCTG
1 AACAGAAGCACACACAGTGCTG
* *
91764 AAGAAAAGCACACACAGTGCTG
1 AACAGAAGCACACACAGTGCTG
91786 AACAGAAGCACACACAGTGCTG
1 AACAGAAGCACACACAGTGCTG
* *
91808 AACAAAAGCACACACAATGCTGGG
1 AACAGAAGCACACACAGTGCT--G
*
91832 TAACAGAAGCACACACAGTGTTGGG
1 -AACAGAAGCACACACAGTGCT--G
* *
91857 TAATAGAAGCACACACAATGCTG
1 -AACAGAAGCACACACAGTGCTG
91880 AACAGAAGCACACACAGTGCTGGG
1 AACAGAAGCACACACAGTGCT--G
* *
91904 TAACAGAAGCACACAAAGTACTG
1 -AACAGAAGCACACACAGTGCTG
91927 AACAGAAGCACACACAGTGCTGGG
1 AACAGAAGCACACACAGTGCT--G
91951 TAACAGAAGCACACACAGTGCTG
1 -AACAGAAGCACACACAGTGCTG
91974 AACAGAAGC
1 AACAGAAGC
91983 GTGCTAGCGT
Statistics
Matches: 230, Mismatches: 23, Indels: 24
0.83 0.08 0.09
Matches are distributed among these distances:
22 118 0.51
23 10 0.04
24 11 0.05
25 84 0.37
26 7 0.03
ACGTcount: A:0.42, C:0.24, G:0.23, T:0.11
Consensus pattern (22 bp):
AACAGAAGCACACACAGTGCTG
Found at i:91884 original size:47 final size:47
Alignment explanation
Indices: 91695--91982 Score: 358
Period size: 47 Copynumber: 6.2 Consensus size: 47
91685 GTGCTGGGGA
* * * *
91695 AACAGAAGCACA-AAAGTGCTGGGAAACAGTAGACACACACAGTGCTG
1 AACAGAAGCACACACAGTGCTGGGTAACAGAAG-CACACACAATGCTG
* * * *
91742 AACAGAAGCACACACAATGCT--G-AAGAAAAGCACACACAGTGCTG
1 AACAGAAGCACACACAGTGCTGGGTAACAGAAGCACACACAATGCTG
*
91786 AACAGAAGCACACACAGTGCT--G-AACAAAAGCACACACAATGCTGGG
1 AACAGAAGCACACACAGTGCTGGGTAACAGAAGCACACACAATGCT--G
* *
91832 TAACAGAAGCACACACAGTGTTGGGTAATAGAAGCACACACAATGCTG
1 -AACAGAAGCACACACAGTGCTGGGTAACAGAAGCACACACAATGCTG
*
91880 AACAGAAGCACACACAGTGCTGGGTAACAGAAGCACACA-AAGTACTG
1 AACAGAAGCACACACAGTGCTGGGTAACAGAAGCACACACAA-TGCTG
*
91927 AACAGAAGCACACACAGTGCTGGGTAACAGAAGCACACACAGTGCTG
1 AACAGAAGCACACACAGTGCTGGGTAACAGAAGCACACACAATGCTG
91974 AACAGAAGC
1 AACAGAAGC
91983 GTGCTAGCGT
Statistics
Matches: 216, Mismatches: 16, Indels: 18
0.86 0.06 0.07
Matches are distributed among these distances:
44 54 0.25
45 5 0.02
46 4 0.02
47 125 0.58
48 8 0.04
49 1 0.00
50 19 0.09
ACGTcount: A:0.42, C:0.24, G:0.23, T:0.11
Consensus pattern (47 bp):
AACAGAAGCACACACAGTGCTGGGTAACAGAAGCACACACAATGCTG
Found at i:93009 original size:21 final size:19
Alignment explanation
Indices: 92983--93023 Score: 64
Period size: 21 Copynumber: 2.1 Consensus size: 19
92973 AGGCTGATTT
92983 TCTTCTCTTTTCACTCTTTTC
1 TCTTCTCTTTTC-CT-TTTTC
93004 TCTTCTCTTTTCCTTTTTC
1 TCTTCTCTTTTCCTTTTTC
93023 T
1 T
93024 TCAATTTGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 6 0.30
20 2 0.10
21 12 0.60
ACGTcount: A:0.02, C:0.32, G:0.00, T:0.66
Consensus pattern (19 bp):
TCTTCTCTTTTCCTTTTTC
Found at i:96843 original size:25 final size:25
Alignment explanation
Indices: 96816--96990 Score: 197
Period size: 25 Copynumber: 7.3 Consensus size: 25
96806 GAAACGCAAA
* *
96816 AGTGCTGGGGAAACAGAAGCACATA-
1 AGTGCT-GGGTAACAGAAGCACACAC
* *
96841 AGTGCTGGGAAACAGTAGACACACAC
1 AGTGCTGGGTAACAGAAG-CACACAC
96867 AGTGCT--G-AACAGAAGCACACAC
1 AGTGCTGGGTAACAGAAGCACACAC
*
96889 AATGCTGGGTAACAGAAGCACACAC
1 AGTGCTGGGTAACAGAAGCACACAC
* *
96914 AGTGCTGGGTAACGGAAGCACATAC
1 AGTGCTGGGTAACAGAAGCACACAC
96939 AGTGCTGGGTAACAGAA--ACACAC
1 AGTGCTGGGTAACAGAAGCACACAC
*
96962 AGTACT--G-AACAGAAGCACACAC
1 AGTGCTGGGTAACAGAAGCACACAC
96984 AGTGCTG
1 AGTGCTG
96991 AACAGAAGTG
Statistics
Matches: 131, Mismatches: 11, Indels: 18
0.82 0.07 0.11
Matches are distributed among these distances:
20 7 0.05
21 1 0.01
22 23 0.18
23 17 0.13
24 13 0.10
25 64 0.49
26 6 0.05
ACGTcount: A:0.38, C:0.22, G:0.27, T:0.13
Consensus pattern (25 bp):
AGTGCTGGGTAACAGAAGCACACAC
Found at i:96981 original size:95 final size:98
Alignment explanation
Indices: 96816--96990 Score: 268
Period size: 95 Copynumber: 1.8 Consensus size: 98
96806 GAAACGCAAA
*
96816 AGTGCTGGGGAAACAGAAGCACATAAGTGCTGGGAAACAGTAGACACACACAGTGCTGAACAGAA
1 AGTGCTGGGGAAACAGAAGCACATAAGTGCTGGGAAACAGTAGACACACACAGTACTGAACAGAA
96881 GCACACACAATGCTGGGTAACAGAAGCACACAC
66 GCACACACAATGCTGGGTAACAGAAGCACACAC
* * *
96914 AGTGCT-GGGTAACGGAAGCACATACAGTGCTGGGTAACAG-A-A-ACACACAGTACTGAACAGA
1 AGTGCTGGGGAAACAGAAGCACATA-AGTGCTGGGAAACAGTAGACACACACAGTACTGAACAGA
*
96975 AGCACACACAGTGCTG
65 AGCACACACAATGCTG
96991 AACAGAAGTG
Statistics
Matches: 71, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
95 33 0.46
96 1 0.01
97 17 0.24
98 20 0.28
ACGTcount: A:0.38, C:0.22, G:0.27, T:0.13
Consensus pattern (98 bp):
AGTGCTGGGGAAACAGAAGCACATAAGTGCTGGGAAACAGTAGACACACACAGTACTGAACAGAA
GCACACACAATGCTGGGTAACAGAAGCACACAC
Found at i:103165 original size:23 final size:23
Alignment explanation
Indices: 103139--103187 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
103129 TGGAAGATGT
103139 TCTCGTTAAGGTAAATGAGTTAA
1 TCTCGTTAAGGTAAATGAGTTAA
103162 TCTCGTTAAGGTAAATGAGTTAA
1 TCTCGTTAAGGTAAATGAGTTAA
103185 TCT
1 TCT
103188 TTCCTGCAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.33, C:0.10, G:0.20, T:0.37
Consensus pattern (23 bp):
TCTCGTTAAGGTAAATGAGTTAA
Found at i:107917 original size:23 final size:23
Alignment explanation
Indices: 107795--107974 Score: 128
Period size: 23 Copynumber: 7.9 Consensus size: 23
107785 AACCAAAAAG
* * *
107795 AGCCTTTGTGGCATATTTTGATT
1 AGCCTTTATGGCGTATTCTGATT
* *** *
107818 AGCTTTTATAATGTATTCTGAAT
1 AGCCTTTATGGCGTATTCTGATT
** * * *
107841 AAACTTTGTGACGTATTCTAATT
1 AGCCTTTATGGCGTATTCTGATT
* * *
107864 AGCCTTTGTGGCATATTCTAATT
1 AGCCTTTATGGCGTATTCTGATT
* *
107887 AGCTTTTATGGCATATTCTGATT
1 AGCCTTTATGGCGTATTCTGATT
*
107910 AGCCTTTATGGTGTATTCTG-TT
1 AGCCTTTATGGCGTATTCTGATT
** * *
107932 AGTGTTTGTGGTGTATTCTGATT
1 AGCCTTTATGGCGTATTCTGATT
* *
107955 AGTCTTTATGGTGTATTCTG
1 AGCCTTTATGGCGTATTCTG
107975 CTAAGTCTAT
Statistics
Matches: 125, Mismatches: 31, Indels: 2
0.79 0.20 0.01
Matches are distributed among these distances:
22 19 0.15
23 106 0.85
ACGTcount: A:0.21, C:0.12, G:0.20, T:0.48
Consensus pattern (23 bp):
AGCCTTTATGGCGTATTCTGATT
Found at i:107927 original size:46 final size:46
Alignment explanation
Indices: 107799--107973 Score: 158
Period size: 46 Copynumber: 3.8 Consensus size: 46
107789 AAAAAGAGCC
* * ** * *
107799 TTTGTGGCATATTTTGATTAGCTTTTATAATGTATTCTGAATAAAC-
1 TTTGTGGCATATTCTGATTAGCCTTTATGGTGTATTCT-AATTAGCT
* * * * **
107845 TTTGTGACGTATTCTAATTAGCCTTTGTGGCATATTCTAATTAGCT
1 TTTGTGGCATATTCTGATTAGCCTTTATGGTGTATTCTAATTAGCT
* *
107891 TTTATGGCATATTCTGATTAGCCTTTATGGTGTATTCT-GTTAG-T
1 TTTGTGGCATATTCTGATTAGCCTTTATGGTGTATTCTAATTAGCT
** *
107935 GTTTGTGGTGTATTCTGATTAGTCTTTATGGTGTATTCT
1 -TTTGTGGCATATTCTGATTAGCCTTTATGGTGTATTCT
107974 GCTAAGTCTA
Statistics
Matches: 103, Mismatches: 24, Indels: 5
0.78 0.18 0.04
Matches are distributed among these distances:
44 1 0.01
45 43 0.42
46 59 0.57
ACGTcount: A:0.21, C:0.11, G:0.19, T:0.49
Consensus pattern (46 bp):
TTTGTGGCATATTCTGATTAGCCTTTATGGTGTATTCTAATTAGCT
Found at i:109071 original size:6 final size:6
Alignment explanation
Indices: 109062--109086 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
109052 AAAGAAAAAG
109062 AAATAA AAATAA AAATAA AAATAA A
1 AAATAA AAATAA AAATAA AAATAA A
109087 TGTTCCTCGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAATAA
Found at i:110163 original size:33 final size:33
Alignment explanation
Indices: 110126--110197 Score: 90
Period size: 33 Copynumber: 2.2 Consensus size: 33
110116 AATGGTTAAT
* * *
110126 GGGTCGATCAAAGTTAACGGGTCGGGTCAGTTC
1 GGGTCGATCAAAGTCAACAGGTCAGGTCAGTTC
* *
110159 GGGTCGATTAACGTCAACAGGTCAGGTCAGTTC
1 GGGTCGATCAAAGTCAACAGGTCAGGTCAGTTC
*
110192 GAGTCG
1 GGGTCG
110198 GGCTGATACA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.22, C:0.19, G:0.35, T:0.24
Consensus pattern (33 bp):
GGGTCGATCAAAGTCAACAGGTCAGGTCAGTTC
Found at i:116927 original size:19 final size:19
Alignment explanation
Indices: 116876--116948 Score: 78
Period size: 20 Copynumber: 3.7 Consensus size: 19
116866 AAAATTACAA
116876 AAAAGATTCAAAATAATTTT
1 AAAA-ATTCAAAATAATTTT
116896 AAAAAATGT-AAAATAATTTT
1 -AAAAAT-TCAAAATAATTTT
*
116916 TAAAATTCAAAAT-ATTTAT
1 AAAAATTCAAAATAATTT-T
116935 AAAAATTCCAAAAT
1 AAAAATT-CAAAAT
116949 TTTATTTTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 9
0.81 0.04 0.16
Matches are distributed among these distances:
18 5 0.11
19 17 0.37
20 19 0.41
21 5 0.11
ACGTcount: A:0.58, C:0.05, G:0.03, T:0.34
Consensus pattern (19 bp):
AAAAATTCAAAATAATTTT
Found at i:116952 original size:19 final size:19
Alignment explanation
Indices: 116876--116953 Score: 65
Period size: 19 Copynumber: 4.0 Consensus size: 19
116866 AAAATTACAA
116876 AAAAGATTCAAAATAATTT-T
1 AAAA-ATTCAAAAT-ATTTAT
116896 AAAAAATGT-AAAATAATTT-T
1 -AAAAAT-TCAAAAT-ATTTAT
*
116916 TAAAATTCAAAATATTTAT
1 AAAAATTCAAAATATTTAT
116935 AAAAATTCCAAAAT-TTTAT
1 AAAAATT-CAAAATATTTAT
116954 TTTTTAATAA
Statistics
Matches: 51, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
18 5 0.10
19 22 0.43
20 19 0.37
21 5 0.10
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.37
Consensus pattern (19 bp):
AAAAATTCAAAATATTTAT
Found at i:126944 original size:73 final size:74
Alignment explanation
Indices: 126857--127011 Score: 249
Period size: 73 Copynumber: 2.1 Consensus size: 74
126847 AGATGAATGG
*
126857 AAAACTTAAAAATTATTACCATCACCATAATAGTGCTTAGAAGAAACCAAGAAACAGGC-AAAGA
1 AAAA-TTAAAAATTATTACCATCACCATAATAGTGCTTAGAAGAAACCAAGAAACAGCCAAAAGA
126921 AATAAAGCAT
65 AATAAAGCAT
* *
126931 AAAATTAAAAATTATTACCATCACCATAATAGTGCTTAGAGGAAACCAAGAAATAGCCAAAAGAA
1 AAAATTAAAAATTATTACCATCACCATAATAGTGCTTAGAAGAAACCAAGAAACAGCCAAAAGAA
*
126996 ATAATGCAT
66 ATAAAGCAT
*
127005 AACATTA
1 AAAATTA
127012 CCACTGATGA
Statistics
Matches: 75, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
73 51 0.68
74 24 0.32
ACGTcount: A:0.52, C:0.15, G:0.12, T:0.21
Consensus pattern (74 bp):
AAAATTAAAAATTATTACCATCACCATAATAGTGCTTAGAAGAAACCAAGAAACAGCCAAAAGAA
ATAAAGCAT
Found at i:135320 original size:43 final size:43
Alignment explanation
Indices: 135259--135345 Score: 165
Period size: 43 Copynumber: 2.0 Consensus size: 43
135249 AAAAAGAAAG
*
135259 GTTTGCAGCAATAATGGTGGATGTGGTTGTGCAAAACACCATC
1 GTTTGCAGCAATAATGGTGGATGTGATTGTGCAAAACACCATC
135302 GTTTGCAGCAATAATGGTGGATGTGATTGTGCAAAACACCATC
1 GTTTGCAGCAATAATGGTGGATGTGATTGTGCAAAACACCATC
135345 G
1 G
135346 ACACAGTGGG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.29, C:0.16, G:0.28, T:0.28
Consensus pattern (43 bp):
GTTTGCAGCAATAATGGTGGATGTGATTGTGCAAAACACCATC
Found at i:148334 original size:17 final size:17
Alignment explanation
Indices: 148298--148382 Score: 100
Period size: 17 Copynumber: 5.1 Consensus size: 17
148288 TCTATTTTAA
*
148298 ATTTTAAATTTTAA-TT
1 ATTTTAAATTTAAATTT
* *
148314 ATTTTGAGTTTAAATTT
1 ATTTTAAATTTAAATTT
*
148331 ATTTTAAATTTAAACTT
1 ATTTTAAATTTAAATTT
* * *
148348 GTTTTGAGTTTAAATTT
1 ATTTTAAATTTAAATTT
148365 ATTTTAAATTTAAATTT
1 ATTTTAAATTTAAATTT
148382 A
1 A
148383 ATTAAAAAGT
Statistics
Matches: 55, Mismatches: 13, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
16 11 0.20
17 44 0.80
ACGTcount: A:0.35, C:0.01, G:0.06, T:0.58
Consensus pattern (17 bp):
ATTTTAAATTTAAATTT
Found at i:148358 original size:34 final size:33
Alignment explanation
Indices: 148298--148380 Score: 139
Period size: 34 Copynumber: 2.5 Consensus size: 33
148288 TCTATTTTAA
*
148298 ATTTTAAATTTTAATTATTTTGAGTTTAAATTT
1 ATTTTAAATTTAAATTATTTTGAGTTTAAATTT
*
148331 ATTTTAAATTTAAACTTGTTTTGAGTTTAAATTT
1 ATTTTAAATTTAAA-TTATTTTGAGTTTAAATTT
148365 ATTTTAAATTTAAATT
1 ATTTTAAATTTAAATT
148381 TAATTAAAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
33 15 0.32
34 32 0.68
ACGTcount: A:0.35, C:0.01, G:0.06, T:0.58
Consensus pattern (33 bp):
ATTTTAAATTTAAATTATTTTGAGTTTAAATTT
Found at i:148377 original size:40 final size:39
Alignment explanation
Indices: 148290--148383 Score: 117
Period size: 34 Copynumber: 2.5 Consensus size: 39
148280 AAATTGAATC
*
148290 TATTTTAAATTTTAAATTTTAATTATTTTGAGTTTAAATT
1 TATTTTAAA-TTTAAATTTAAATTATTTTGAGTTTAAATT
* *
148330 TATTTTAAATTT--A---AACTTGTTTTGAGTTTAAATT
1 TATTTTAAATTTAAATTTAAATTATTTTGAGTTTAAATT
148364 TATTTTAAATTTAAATTTAA
1 TATTTTAAATTTAAATTTAA
148384 TTAAAAAGTG
Statistics
Matches: 46, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
34 30 0.65
36 1 0.02
37 1 0.02
39 5 0.11
40 9 0.20
ACGTcount: A:0.36, C:0.01, G:0.05, T:0.57
Consensus pattern (39 bp):
TATTTTAAATTTAAATTTAAATTATTTTGAGTTTAAATT
Found at i:149039 original size:16 final size:16
Alignment explanation
Indices: 149015--149062 Score: 62
Period size: 16 Copynumber: 3.0 Consensus size: 16
149005 AATGTATATT
149015 TAATAAATAATTATAA
1 TAATAAATAATTATAA
*
149031 TATTAAATAA-TATTAA
1 TAATAAATAATTA-TAA
*
149047 TAATAAATAATAATAA
1 TAATAAATAATTATAA
149063 AAAGAACTCG
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 2 0.07
16 24 0.89
17 1 0.04
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
TAATAAATAATTATAA
Found at i:150239 original size:30 final size:30
Alignment explanation
Indices: 150197--150376 Score: 190
Period size: 30 Copynumber: 6.2 Consensus size: 30
150187 TATTTTCTTT
*
150197 AAAAATCTCATTTTGACCCCCAAACTTCTC
1 AAAAATCACATTTTGACCCCCAAACTTCTC
* * **
150227 CAAAATTACATTTTGACCTTCAAACTTCTC
1 AAAAATCACATTTTGACCCCCAAACTTCTC
* *
150257 AAAAATCACATTTT--CCCCCGAATTTCT-
1 AAAAATCACATTTTGACCCCCAAACTTCTC
* * *
150284 AAATATCACATTTTTACCCTCAAACTTCTC
1 AAAAATCACATTTTGACCCCCAAACTTCTC
*
150314 AAAAATTACATTTTG-CCCCCAAACTTC-C
1 AAAAATCACATTTTGACCCCCAAACTTCTC
* * *
150342 AAAAATCACATTTTTACCCTCGAACTTCTC
1 AAAAATCACATTTTGACCCCCAAACTTCTC
*
150372 CAAAA
1 AAAAA
150377 CTTCATTTTT
Statistics
Matches: 121, Mismatches: 24, Indels: 10
0.78 0.15 0.06
Matches are distributed among these distances:
27 13 0.11
28 23 0.19
29 31 0.26
30 54 0.45
ACGTcount: A:0.35, C:0.30, G:0.03, T:0.32
Consensus pattern (30 bp):
AAAAATCACATTTTGACCCCCAAACTTCTC
Found at i:150308 original size:57 final size:58
Alignment explanation
Indices: 150197--150376 Score: 227
Period size: 58 Copynumber: 3.1 Consensus size: 58
150187 TATTTTCTTT
* * * * *
150197 AAAAATCTCATTTTGACCCCCAAACTTCTCCAAAATTACATTTTGACCTTCAAACTTCTC
1 AAAAATCACATTTTG-CCCCCAAACTTC-CAAAAATCACATTTTTACCCTCAAACTTCTC
* * * *
150257 AAAAATCACATTTT-CCCCCGAATTTCTAAATATCACATTTTTACCCTCAAACTTCTC
1 AAAAATCACATTTTGCCCCCAAACTTCCAAAAATCACATTTTTACCCTCAAACTTCTC
* *
150314 AAAAATTACATTTTGCCCCCAAACTTCCAAAAATCACATTTTTACCCTCGAACTTCTC
1 AAAAATCACATTTTGCCCCCAAACTTCCAAAAATCACATTTTTACCCTCAAACTTCTC
*
150372 CAAAA
1 AAAAA
150377 CTTCATTTTT
Statistics
Matches: 103, Mismatches: 16, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
57 38 0.37
58 52 0.50
60 13 0.13
ACGTcount: A:0.35, C:0.30, G:0.03, T:0.32
Consensus pattern (58 bp):
AAAAATCACATTTTGCCCCCAAACTTCCAAAAATCACATTTTTACCCTCAAACTTCTC
Found at i:152736 original size:30 final size:30
Alignment explanation
Indices: 152700--152836 Score: 143
Period size: 30 Copynumber: 4.6 Consensus size: 30
152690 AAGAATAGAA
*
152700 CAAAATTACATTTTGACCCTTAAACTTATC
1 CAAAATTACATTTTGACCCTTAAACTTCTC
*
152730 CAAAATTACATTTTGACCATTAAACTTCTC
1 CAAAATTACATTTTGACCCTTAAACTTCTC
* * *
152760 AAAAATCACATTTT-ACCCCTAAACTTC-C
1 CAAAATTACATTTTGACCCTTAAACTTCTC
* * * * **
152788 AAAAATCACATTTTTACACTCGAACTTCTC
1 CAAAATTACATTTTGACCCTTAAACTTCTC
* *
152818 AAAAATTACATTTTTACCC
1 CAAAATTACATTTTGACCC
152837 CCCTAATTTT
Statistics
Matches: 93, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
28 15 0.16
29 20 0.22
30 58 0.62
ACGTcount: A:0.38, C:0.26, G:0.02, T:0.34
Consensus pattern (30 bp):
CAAAATTACATTTTGACCCTTAAACTTCTC
Found at i:152782 original size:29 final size:29
Alignment explanation
Indices: 152701--152862 Score: 141
Period size: 30 Copynumber: 5.4 Consensus size: 29
152691 AGAATAGAAC
* * *
152701 AAAATTACATTTTGACCCTTAAACTTATCC
1 AAAATTACATTTT-ACCCCTAAACTTCTCA
**
152731 AAAATTACATTTTGACCATTAAACTTCTCA
1 AAAATTACATTTT-ACCCCTAAACTTCTCA
*
152761 AAAATCACATTTTACCCCTAAACTTC-CA
1 AAAATTACATTTTACCCCTAAACTTCTCA
* * *
152789 AAAATCACATTTTTA-CACTCGAACTTCTCA
1 AAAATTACA-TTTTACCCCT-AAACTTCTCA
**
152819 AAAATTACATTTTTACCCCCCTAATTTTC-CA
1 AAAATTACA-TTTTA--CCCCTAAACTTCTCA
152850 AAAATTACATTTT
1 AAAATTACATTTT
152863 GATCCTCGAA
Statistics
Matches: 113, Mismatches: 13, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
28 14 0.12
29 22 0.19
30 59 0.52
31 11 0.10
32 4 0.04
33 3 0.03
ACGTcount: A:0.38, C:0.25, G:0.02, T:0.36
Consensus pattern (29 bp):
AAAATTACATTTTACCCCTAAACTTCTCA
Found at i:152882 original size:31 final size:29
Alignment explanation
Indices: 152731--152883 Score: 103
Period size: 30 Copynumber: 5.1 Consensus size: 29
152721 AAACTTATCC
* ** *
152731 AAAATTACATTTTGACCATTAAACTTCTCA
1 AAAATTACATTTTTACC-TCGAACTTCCCA
* * *
152761 AAAATCACA-TTTTACCCCTAAACTT-CCA
1 AAAATTACATTTTTACCTC-GAACTTCCCA
* *
152789 AAAATCACATTTTTACACTCGAACTTCTCA
1 AAAATTACATTTTTAC-CTCGAACTTCCCA
* * * *
152819 AAAATTACATTTTTACCCCCCTAATTTTCCA
1 AAAATTACATTTTTA--CCTCGAACTTCCCA
*
152850 AAAATTACATTTTGATCCTCGAACGTTCCCA
1 AAAATTACATTTTTA-CCTCGAAC-TTCCCA
152881 AAA
1 AAA
152884 TCGTATTTTG
Statistics
Matches: 96, Mismatches: 20, Indels: 13
0.74 0.16 0.10
Matches are distributed among these distances:
28 11 0.11
29 23 0.24
30 31 0.32
31 30 0.31
32 1 0.01
ACGTcount: A:0.37, C:0.26, G:0.03, T:0.33
Consensus pattern (29 bp):
AAAATTACATTTTTACCTCGAACTTCCCA
Found at i:152892 original size:61 final size:61
Alignment explanation
Indices: 152701--152898 Score: 162
Period size: 61 Copynumber: 3.3 Consensus size: 61
152691 AGAATAGAAC
* * * **
152701 AAAATTACATTTTGA--CCCTTAAACTTATCC-AAAATTACATTTTGAC-CATTAAACTTCTCA
1 AAAATCACATTTTGACCCCCCTAAAC-T-TCCAAAAATCACATTTTGACAC-TCGAACTTCTCA
*
152761 AAAATCACATTTT-A--CCCCTAAACTTCCAAAAATCACATTTTTACACTCGAACTTCTCA
1 AAAATCACATTTTGACCCCCCTAAACTTCCAAAAATCACATTTTGACACTCGAACTTCTCA
* * ** * *
152819 AAAATTACATTTTTACCCCCCTAATTTTCCAAAAATTACATTTTGATC-CTCGAACGTTC-CC
1 AAAATCACATTTTGACCCCCCTAAACTTCCAAAAATCACATTTTGA-CACTCGAAC-TTCTCA
**
152880 AAAATCGTATTTTGACCCC
1 AAAATCACATTTTGACCCC
152899 AAACACTCCG
Statistics
Matches: 115, Mismatches: 16, Indels: 13
0.80 0.11 0.09
Matches are distributed among these distances:
57 3 0.03
58 37 0.32
59 11 0.10
60 12 0.10
61 48 0.42
62 4 0.03
ACGTcount: A:0.35, C:0.26, G:0.04, T:0.34
Consensus pattern (61 bp):
AAAATCACATTTTGACCCCCCTAAACTTCCAAAAATCACATTTTGACACTCGAACTTCTCA
Found at i:153147 original size:18 final size:19
Alignment explanation
Indices: 153108--153147 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
153098 TAACTTATCA
*
153108 TTAATTGCATAGCTCGTAT
1 TTAATTGCATAGCTCATAT
*
153127 TTAATTGCAT-GCTCATTT
1 TTAATTGCATAGCTCATAT
153145 TTA
1 TTA
153148 TCCCTATATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.25, C:0.15, G:0.12, T:0.47
Consensus pattern (19 bp):
TTAATTGCATAGCTCATAT
Found at i:156570 original size:16 final size:16
Alignment explanation
Indices: 156549--156581 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
156539 TAGCAGGTGC
156549 ATGCAT-TTTTACTTTT
1 ATGCATATTTTA-TTTT
156565 ATGCATATTTTATTTT
1 ATGCATATTTTATTTT
156581 A
1 A
156582 AATTATTTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.24, C:0.09, G:0.06, T:0.61
Consensus pattern (16 bp):
ATGCATATTTTATTTT
Found at i:160362 original size:17 final size:19
Alignment explanation
Indices: 160342--160377 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
160332 TAGAAAAAGT
160342 AGATTGA-AA-AAAAAAAA
1 AGATTGATAACAAAAAAAA
160359 AGATTGATAACAAAAAAAA
1 AGATTGATAACAAAAAAAA
160378 TCTCAAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.41
18 2 0.12
19 8 0.47
ACGTcount: A:0.72, C:0.03, G:0.11, T:0.14
Consensus pattern (19 bp):
AGATTGATAACAAAAAAAA
Found at i:175127 original size:19 final size:20
Alignment explanation
Indices: 175099--175136 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
175089 TTACTGGTTT
*
175099 TTTTTATTATAATTTTTATG
1 TTTTTATTATAAATTTTATG
175119 TTTTT-TTATAAATTTTAT
1 TTTTTATTATAAATTTTAT
175137 TTATAATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (20 bp):
TTTTTATTATAAATTTTATG
Found at i:175766 original size:31 final size:31
Alignment explanation
Indices: 175691--175780 Score: 103
Period size: 31 Copynumber: 2.9 Consensus size: 31
175681 AAAATTTTTA
*
175691 TATTTTTTCTTAAATTAGTACTTAAACTATAT
1 TATTTTTTC-TAAATTAATACTTAAACTATAT
** *
175723 T-TTATTACCTAAAGTAATA-TATAAACTATAT
1 TATT-TTTTCTAAATTAATACT-TAAACTATAT
175754 TATTTTTTCTAAATTAATACTTAAACT
1 TATTTTTTCTAAATTAATACTTAAACT
175781 TTTTTCTTAA
Statistics
Matches: 47, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
30 1 0.02
31 39 0.83
32 7 0.15
ACGTcount: A:0.39, C:0.10, G:0.02, T:0.49
Consensus pattern (31 bp):
TATTTTTTCTAAATTAATACTTAAACTATAT
Found at i:175893 original size:20 final size:20
Alignment explanation
Indices: 175856--175893 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
175846 TTCATTTGAA
*
175856 AAAAAATATTTTTGAAAAGT
1 AAAAAATATTTTTCAAAAGT
175876 AAAAAAT-TTCTTTCAAAA
1 AAAAAATATT-TTTCAAAA
175894 ATTATTCGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 2 0.12
20 14 0.88
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.34
Consensus pattern (20 bp):
AAAAAATATTTTTCAAAAGT
Found at i:179540 original size:11 final size:12
Alignment explanation
Indices: 179516--179542 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
179506 AAATACACTT
179516 AAAAACATTAAA
1 AAAAACATTAAA
179528 AAAAACATTAAA
1 AAAAACATTAAA
179540 AAA
1 AAA
179543 TAAATAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.78, C:0.07, G:0.00, T:0.15
Consensus pattern (12 bp):
AAAAACATTAAA
Found at i:179722 original size:12 final size:12
Alignment explanation
Indices: 179701--179804 Score: 66
Period size: 12 Copynumber: 8.2 Consensus size: 12
179691 AAAACATCCA
179701 AACAACAAAAAT
1 AACAACAAAAAT
* *
179713 AACAATAAAAAC
1 AACAACAAAAAT
*
179725 AACAGCAAAAAT
1 AACAACAAAAAT
*
179737 AACATCAAACAATATTAAA
1 -A-A-C-AACAA-A--AAT
179756 AACAACAAAAAT
1 AACAACAAAAAT
*
179768 AGCAACAAAAAT
1 AACAACAAAAAT
* *
179780 AACAGCAAAAAC
1 AACAACAAAAAT
*
179792 AAC-ACGAAAAT
1 AACAACAAAAAT
179803 AA
1 AA
179805 TAACCAAAAC
Statistics
Matches: 70, Mismatches: 15, Indels: 15
0.70 0.15 0.15
Matches are distributed among these distances:
11 7 0.10
12 44 0.63
13 1 0.01
14 2 0.03
15 6 0.09
16 5 0.07
17 2 0.03
18 1 0.01
19 2 0.03
ACGTcount: A:0.69, C:0.17, G:0.04, T:0.10
Consensus pattern (12 bp):
AACAACAAAAAT
Found at i:179747 original size:67 final size:66
Alignment explanation
Indices: 179676--179804 Score: 145
Period size: 67 Copynumber: 1.9 Consensus size: 66
179666 ATAATAGTAA
** *
179676 AAACACATAAAAAAAAAAACATCCAA-A-CAACAAAAATAACAATAAAAACAACAGCAAAAATAA
1 AAACA-ATAAAAAAAAAAACA-AAAATAGCAACAAAAATAACAACAAAAACAACA-CAAAAATAA
179739 CATC
63 CATC
** * * *
179743 AAACAATATTAAAAACAACAAAAATAGCAACAAAAATAACAGCAAAAACAACACGAAAATAA
1 AAACAATAAAAAAAAAAACAAAAATAGCAACAAAAATAACAACAAAAACAACACAAAAATAA
179805 TAACCAAAAC
Statistics
Matches: 52, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
65 2 0.04
66 21 0.40
67 29 0.56
ACGTcount: A:0.70, C:0.18, G:0.03, T:0.09
Consensus pattern (66 bp):
AAACAATAAAAAAAAAAACAAAAATAGCAACAAAAATAACAACAAAAACAACACAAAAATAACAT
C
Found at i:179748 original size:31 final size:30
Alignment explanation
Indices: 179713--179781 Score: 77
Period size: 31 Copynumber: 2.3 Consensus size: 30
179703 CAACAAAAAT
* *
179713 AACAATAAAAACAACAGCAAAAATAACATCA
1 AACAATAAAAA-AACAACAAAAATAACAACA
* *
179744 AACAATATTAAAAACAACAAAAATAGCAACA
1 AACAATA-AAAAAACAACAAAAATAACAACA
179775 AA-AATAA
1 AACAATAA
179782 CAGCAAAAAC
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
30 4 0.12
31 25 0.78
32 3 0.09
ACGTcount: A:0.70, C:0.16, G:0.03, T:0.12
Consensus pattern (30 bp):
AACAATAAAAAAACAACAAAAATAACAACA
Found at i:179760 original size:43 final size:43
Alignment explanation
Indices: 179687--179793 Score: 110
Period size: 43 Copynumber: 2.5 Consensus size: 43
179677 AACACATAAA
* * *
179687 AAAAAAAACATCCAAACAACAAAAATAACAATAAAAACAACAGC
1 AAAAATAACAT-CAAACAACAAAAATAACAACAAAAACAACAAC
* * * *
179731 AAAAATAACATCAAACAATATTAAA-AACAACAAAAATAGCAAC
1 AAAAATAACATCAAACAACA-AAAATAACAACAAAAACAACAAC
*
179774 AAAAATAACAGCAAA-AACAA
1 AAAAATAACATCAAACAACAA
179794 CACGAAAATA
Statistics
Matches: 52, Mismatches: 10, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
42 3 0.06
43 36 0.69
44 13 0.25
ACGTcount: A:0.70, C:0.18, G:0.03, T:0.09
Consensus pattern (43 bp):
AAAAATAACATCAAACAACAAAAATAACAACAAAAACAACAAC
Found at i:188463 original size:17 final size:16
Alignment explanation
Indices: 188441--188485 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 16
188431 TATGGTAATA
188441 TTTCTTTTCTTTTCTCT
1 TTTCTTTTCTTTTCT-T
188458 TTTCTTCTTC-TTTCTT
1 TTTCTT-TTCTTTTCTT
188474 TTTC-TTTCTTTT
1 TTTCTTTTCTTTT
188486 TGTGATTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
14 3 0.12
15 4 0.15
16 5 0.19
17 11 0.42
18 3 0.12
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTCTTTTCTTTTCTT
Found at i:188484 original size:10 final size:11
Alignment explanation
Indices: 188441--188486 Score: 60
Period size: 10 Copynumber: 4.3 Consensus size: 11
188431 TATGGTAATA
188441 TTTCTTTTCTT
1 TTTCTTTTCTT
188452 TTCTCTTTTCTT
1 TT-TCTTTTCTT
*
188464 CTTC-TTTCTT
1 TTTCTTTTCTT
188474 TTTC-TTTCTT
1 TTTCTTTTCTT
188484 TTT
1 TTT
188487 GTGATTTTTC
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
10 18 0.56
11 4 0.12
12 10 0.31
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (11 bp):
TTTCTTTTCTT
Found at i:189045 original size:17 final size:18
Alignment explanation
Indices: 189022--189063 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
189012 TATAAGAATA
189022 GAAATGCAACT-AC-AAT
1 GAAATGCAACTAACAAAT
189038 GCAAATGC-ACTAACAAAT
1 G-AAATGCAACTAACAAAT
189056 GAAATGCA
1 GAAATGCA
189064 GTGACAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
16 4 0.18
17 14 0.64
18 4 0.18
ACGTcount: A:0.50, C:0.19, G:0.14, T:0.17
Consensus pattern (18 bp):
GAAATGCAACTAACAAAT
Found at i:191280 original size:25 final size:25
Alignment explanation
Indices: 191252--191305 Score: 108
Period size: 25 Copynumber: 2.2 Consensus size: 25
191242 TCATCATAGA
191252 ATGCGCCGACAAGTTGTGTTTTACG
1 ATGCGCCGACAAGTTGTGTTTTACG
191277 ATGCGCCGACAAGTTGTGTTTTACG
1 ATGCGCCGACAAGTTGTGTTTTACG
191302 ATGC
1 ATGC
191306 ATCGACAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.20, C:0.20, G:0.28, T:0.31
Consensus pattern (25 bp):
ATGCGCCGACAAGTTGTGTTTTACG
Found at i:191311 original size:25 final size:25
Alignment explanation
Indices: 191252--191313 Score: 97
Period size: 25 Copynumber: 2.5 Consensus size: 25
191242 TCATCATAGA
*
191252 ATGCGCCGACAAGTTGTGTTTTACG
1 ATGCACCGACAAGTTGTGTTTTACG
*
191277 ATGCGCCGACAAGTTGTGTTTTACG
1 ATGCACCGACAAGTTGTGTTTTACG
*
191302 ATGCATCGACAA
1 ATGCACCGACAA
191314 AAAGATGACT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (25 bp):
ATGCACCGACAAGTTGTGTTTTACG
Found at i:198011 original size:20 final size:21
Alignment explanation
Indices: 197983--198040 Score: 57
Period size: 20 Copynumber: 2.9 Consensus size: 21
197973 TATTAAAATC
*
197983 AAGTTAAAATTATTTTAAAC-
1 AAGTCAAAATTATTTTAAACT
* * *
198003 ATGTCAAAA-TAATTTGAACT
1 AAGTCAAAATTATTTTAAACT
*
198023 AAGTCAAAATCATTTTAA
1 AAGTCAAAATTATTTTAA
198041 CACTTTAAAA
Statistics
Matches: 28, Mismatches: 8, Indels: 3
0.72 0.21 0.08
Matches are distributed among these distances:
19 8 0.29
20 15 0.54
21 5 0.18
ACGTcount: A:0.48, C:0.09, G:0.07, T:0.36
Consensus pattern (21 bp):
AAGTCAAAATTATTTTAAACT
Found at i:199866 original size:3 final size:3
Alignment explanation
Indices: 199858--199891 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
199848 AAAGATTCCA
199858 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A
199892 GGAAGAAATG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.35, C:0.00, G:0.32, T:0.32
Consensus pattern (3 bp):
ATG
Found at i:206361 original size:20 final size:20
Alignment explanation
Indices: 206316--206417 Score: 73
Period size: 20 Copynumber: 5.0 Consensus size: 20
206306 GTTTGAATCA
* *
206316 AATTTAAAATCAAGTTAAAAT
1 AATTTTAAA-CAAGTCAAAAT
* *
206337 GATTTTAAACATGTCAAAAT
1 AATTTTAAACAAGTCAAAAT
*
206357 AA-TTTGAACTAAGTCAAAAT
1 AATTTTAAAC-AAGTCAAAAT
* **
206377 CATTTT-AACACTTCAAAAT
1 AATTTTAAACAAGTCAAAAT
**
206396 GTTTTTCAAACAAGTCAAAAT
1 AATTTT-AAACAAGTCAAAAT
206417 A
1 A
206418 GCTTCAGGCC
Statistics
Matches: 62, Mismatches: 15, Indels: 8
0.73 0.18 0.09
Matches are distributed among these distances:
19 18 0.29
20 23 0.37
21 21 0.34
ACGTcount: A:0.48, C:0.12, G:0.07, T:0.33
Consensus pattern (20 bp):
AATTTTAAACAAGTCAAAAT
Found at i:214601 original size:12 final size:12
Alignment explanation
Indices: 214584--214608 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
214574 CTTGAGTTTC
214584 TTCAATTATATT
1 TTCAATTATATT
214596 TTCAATTATATT
1 TTCAATTATATT
214608 T
1 T
214609 CTTATGTTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.08, G:0.00, T:0.60
Consensus pattern (12 bp):
TTCAATTATATT
Found at i:228171 original size:16 final size:17
Alignment explanation
Indices: 228140--228172 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
228130 GATTTAATTC
228140 AATAATTGTCAAGGTAA
1 AATAATTGTCAAGGTAA
*
228157 AATAA-TGTCATGGTAA
1 AATAATTGTCAAGGTAA
228173 TGTCAATGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.45, C:0.06, G:0.18, T:0.30
Consensus pattern (17 bp):
AATAATTGTCAAGGTAA
Found at i:228189 original size:16 final size:17
Alignment explanation
Indices: 228160--228193 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
228150 AAGGTAAAAT
228160 AATGTCATGGTAATGTC
1 AATGTCATGGTAATGTC
*
228177 AATGT-ATGTTAATGTC
1 AATGTCATGGTAATGTC
228193 A
1 A
228194 TGACTCTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.32, C:0.09, G:0.21, T:0.38
Consensus pattern (17 bp):
AATGTCATGGTAATGTC
Found at i:228304 original size:17 final size:17
Alignment explanation
Indices: 228254--228305 Score: 61
Period size: 17 Copynumber: 3.0 Consensus size: 17
228244 AAAGTAATAT
*
228254 ATATATAAAGAATAAAA
1 ATATATAAAGAATAGAA
*
228271 ATATA-ATAAGTATTAGAA
1 ATATATA-AAG-AATAGAA
228289 ATATATAAAGAATAGAA
1 ATATATAAAGAATAGAA
228306 TAATACGTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
16 1 0.03
17 14 0.48
18 13 0.45
19 1 0.03
ACGTcount: A:0.63, C:0.00, G:0.10, T:0.27
Consensus pattern (17 bp):
ATATATAAAGAATAGAA
Found at i:228510 original size:14 final size:15
Alignment explanation
Indices: 228475--228537 Score: 69
Period size: 15 Copynumber: 4.3 Consensus size: 15
228465 TGGTGCGAGA
228475 AAAATAAA-TGC-AG
1 AAAATAAAGTGCAAG
*
228488 AAATTTAAA-TGCAAG
1 AAA-ATAAAGTGCAAG
228503 AAAATAAAGTGCAAG
1 AAAATAAAGTGCAAG
* *
228518 AAAGTAAAGTGTAAG
1 AAAATAAAGTGCAAG
228533 AAAAT
1 AAAAT
228538 CAATTGCATG
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
13 3 0.07
14 11 0.26
15 28 0.67
ACGTcount: A:0.59, C:0.05, G:0.17, T:0.19
Consensus pattern (15 bp):
AAAATAAAGTGCAAG
Found at i:233170 original size:13 final size:13
Alignment explanation
Indices: 233152--233176 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
233142 TAAATATAAA
233152 ATGCTAAAAATGT
1 ATGCTAAAAATGT
233165 ATGCTAAAAATG
1 ATGCTAAAAATG
233177 ATACAAAAGA
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:0.48, C:0.08, G:0.16, T:0.28
Consensus pattern (13 bp):
ATGCTAAAAATGT
Found at i:242877 original size:18 final size:18
Alignment explanation
Indices: 242851--242885 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
242841 GTTTGACCTT
242851 CAAAAATGTCGACGCAAC
1 CAAAAATGTCGACGCAAC
* *
242869 CAAAGATGTCGATGCAA
1 CAAAAATGTCGACGCAA
242886 TCTGATGTAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.23, G:0.20, T:0.14
Consensus pattern (18 bp):
CAAAAATGTCGACGCAAC
Found at i:244642 original size:15 final size:16
Alignment explanation
Indices: 244622--244657 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
244612 GTCACATAAA
244622 AAAAAGAGAAAAG-AG
1 AAAAAGAGAAAAGAAG
*
244637 AAAAAGGGAAAAGAAG
1 AAAAAGAGAAAAGAAG
244653 AAAAA
1 AAAAA
244658 TTATATATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 12 0.63
16 7 0.37
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (16 bp):
AAAAAGAGAAAAGAAG
Found at i:251214 original size:27 final size:26
Alignment explanation
Indices: 251184--251252 Score: 68
Period size: 26 Copynumber: 2.6 Consensus size: 26
251174 GCCATGTCCA
* *
251184 CTAGTGATCCCCAGTTCGTA-AGGCCTT
1 CTAGTGA-CCCCAGTTC-AACAAGCCTT
* *
251211 CTAGTGAACCCAGTTCAACAATCCTT
1 CTAGTGACCCCAGTTCAACAAGCCTT
251237 CTAGTGAACCCCAGTT
1 CTAGTG-ACCCCAGTT
251253 TGCCAAGCCC
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
25 1 0.03
26 19 0.54
27 15 0.43
ACGTcount: A:0.25, C:0.30, G:0.17, T:0.28
Consensus pattern (26 bp):
CTAGTGACCCCAGTTCAACAAGCCTT
Found at i:279562 original size:18 final size:18
Alignment explanation
Indices: 279541--279575 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
279531 AATGATATAT
*
279541 TAATTAATAATAATATTA
1 TAATAAATAATAATATTA
279559 TAATAAATAATAATATT
1 TAATAAATAATAATATT
279576 TTATTATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
TAATAAATAATAATATTA
Found at i:282204 original size:15 final size:15
Alignment explanation
Indices: 282184--282220 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
282174 GATAGACACC
282184 GTACCGATGGTTAGG
1 GTACCGATGGTTAGG
282199 GTACCGATGGTTAGG
1 GTACCGATGGTTAGG
282214 GTACCGA
1 GTACCGA
282221 ATATGTTATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.22, C:0.16, G:0.38, T:0.24
Consensus pattern (15 bp):
GTACCGATGGTTAGG
Found at i:285218 original size:19 final size:19
Alignment explanation
Indices: 285194--285233 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
285184 CATATAGAAT
285194 GACACCAATTGAGTTGAAA
1 GACACCAATTGAGTTGAAA
285213 GACACCAATTGAGTTGAAA
1 GACACCAATTGAGTTGAAA
285232 GA
1 GA
285234 ATTAAAAGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.42, C:0.15, G:0.23, T:0.20
Consensus pattern (19 bp):
GACACCAATTGAGTTGAAA
Found at i:288158 original size:18 final size:18
Alignment explanation
Indices: 288132--288170 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
288122 ATGCATTTTA
* *
288132 TTTAGTTGTCATTGTATT
1 TTTAGTTGTCACTGCATT
*
288150 TTTATTTGTCACTGCATT
1 TTTAGTTGTCACTGCATT
288168 TTT
1 TTT
288171 CATATTAGTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.15, C:0.10, G:0.13, T:0.62
Consensus pattern (18 bp):
TTTAGTTGTCACTGCATT
Found at i:288776 original size:19 final size:19
Alignment explanation
Indices: 288739--288776 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
288729 AATGTTGAAT
*
288739 GAGAAAAAGAAAAGGAAAA
1 GAGAAAAAGAAAAGAAAAA
288758 GAGAAAAAGAGAAA-AAAAA
1 GAGAAAAAGA-AAAGAAAAA
288777 AAAAGAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 14 0.82
20 3 0.18
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (19 bp):
GAGAAAAAGAAAAGAAAAA
Found at i:302066 original size:17 final size:18
Alignment explanation
Indices: 302045--302086 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
302035 TATAAGAATG
302045 GAAATGCAACT-AC-AAT
1 GAAATGCAACTAACAAAT
302061 GCAAATGC-ACTAACAAAT
1 G-AAATGCAACTAACAAAT
302079 GAAATGCA
1 GAAATGCA
302087 GTGACAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
16 4 0.18
17 14 0.64
18 4 0.18
ACGTcount: A:0.50, C:0.19, G:0.14, T:0.17
Consensus pattern (18 bp):
GAAATGCAACTAACAAAT
Found at i:302255 original size:21 final size:21
Alignment explanation
Indices: 302231--302274 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
302221 GCCTTCCTCT
302231 TTGCAC-TTCTTCTTCTTATCC
1 TTGCACTTTC-TCTTCTTATCC
* *
302252 TTGCGCTTTCTCTTCTTGTCC
1 TTGCACTTTCTCTTCTTATCC
302273 TT
1 TT
302275 CGAGTCGACC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 17 0.85
22 3 0.15
ACGTcount: A:0.05, C:0.32, G:0.09, T:0.55
Consensus pattern (21 bp):
TTGCACTTTCTCTTCTTATCC
Found at i:315170 original size:19 final size:19
Alignment explanation
Indices: 315122--315170 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
315112 GTTTCTCGAA
* * *
315122 AAAGTCAACGATCAAATTC
1 AAAGTTAACGGTCAAAGTC
315141 AAAGTTAACGGTCAAAGTC
1 AAAGTTAACGGTCAAAGTC
315160 AAAGTTAACGG
1 AAAGTTAACGG
315171 GTCTGGGTCG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.45, C:0.16, G:0.18, T:0.20
Consensus pattern (19 bp):
AAAGTTAACGGTCAAAGTC
Found at i:315223 original size:20 final size:20
Alignment explanation
Indices: 315198--315240 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
315188 TAACGGTCGA
* *
315198 GTTCGAGTCGGGTCAGTCAG
1 GTTCGAGTAGGGCCAGTCAG
*
315218 GTTCGAGTAGGGCCAGTCGG
1 GTTCGAGTAGGGCCAGTCAG
315238 GTT
1 GTT
315241 TAGGTCGGGC
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:0.14, C:0.19, G:0.42, T:0.26
Consensus pattern (20 bp):
GTTCGAGTAGGGCCAGTCAG
Found at i:344458 original size:16 final size:16
Alignment explanation
Indices: 344437--344479 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
344427 TATTTTTTCG
344437 CATTTTGTTTTCATTT
1 CATTTTGTTTTCATTT
* *
344453 CATTTTATTTTTATTT
1 CATTTTGTTTTCATTT
*
344469 AATTTTAGTTT
1 CATTTT-GTTT
344480 ATGACTAGAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 19 0.86
17 3 0.14
ACGTcount: A:0.19, C:0.07, G:0.05, T:0.70
Consensus pattern (16 bp):
CATTTTGTTTTCATTT
Found at i:352804 original size:16 final size:17
Alignment explanation
Indices: 352783--352816 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
352773 TTTAAAACAC
*
352783 TAAATA-CTAACCATTA
1 TAAATACCTAAACATTA
352799 TAAATACCTAAACATTA
1 TAAATACCTAAACATTA
352816 T
1 T
352817 TCTAACTCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.50, C:0.18, G:0.00, T:0.32
Consensus pattern (17 bp):
TAAATACCTAAACATTA
Found at i:358030 original size:14 final size:14
Alignment explanation
Indices: 358011--358044 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
358001 GATTACTTTG
*
358011 ATTCTTATTTGATT
1 ATTCTTATCTGATT
*
358025 ATTCTTATCTGTTT
1 ATTCTTATCTGATT
358039 ATTCTT
1 ATTCTT
358045 GGACTTAACT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.18, C:0.12, G:0.06, T:0.65
Consensus pattern (14 bp):
ATTCTTATCTGATT
Found at i:371367 original size:19 final size:20
Alignment explanation
Indices: 371237--371424 Score: 87
Period size: 19 Copynumber: 9.9 Consensus size: 20
371227 GAAACAATAA
* *
371237 ATAAATTTTTAT-ATTTTTT
1 ATAAGTTTTTATAAATTTTT
* *
371256 ATAAG-TTAT-TAATTTTTT
1 ATAAGTTTTTATAAATTTTT
*
371274 ATAAAGTTTTTA-ATA-TTTT
1 AT-AAGTTTTTATAAATTTTT
* **
371293 A-AACTTTTTATTTATTTTT
1 ATAAGTTTTTATAAATTTTT
* * *
371312 ACAACTTTATATAAA-TTTT
1 ATAAGTTTTTATAAATTTTT
* * * *
371331 AAAACTGTTGTA-ATATTTTT
1 ATAAGT-TTTTATAAATTTTT
*
371351 ATTA-TTTTTATAAATTTTT
1 ATAAGTTTTTATAAATTTTT
*
371370 ATAA-TTTATTA-GAATTTTT
1 ATAAGTTT-TTATAAATTTTT
*
371389 A-AAGATTTTATAAA-TTTT
1 ATAAGTTTTTATAAATTTTT
*
371407 ATAAGTTTATATAAATTT
1 ATAAGTTTTTATAAATTT
371425 CCGATATTTT
Statistics
Matches: 131, Mismatches: 23, Indels: 29
0.72 0.13 0.16
Matches are distributed among these distances:
17 9 0.07
18 28 0.21
19 65 0.50
20 29 0.22
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.58
Consensus pattern (20 bp):
ATAAGTTTTTATAAATTTTT
Found at i:371453 original size:10 final size:9
Alignment explanation
Indices: 371240--371460 Score: 87
Period size: 9 Copynumber: 23.7 Consensus size: 9
371230 ACAATAAATA
371240 AATTTTTAT
1 AATTTTTAT
*
371249 ATTTTTTAT
1 AATTTTTAT
*
371258 AAGTTATTA-
1 AA-TTTTTAT
*
371267 ATTTTTTAT
1 AATTTTTAT
*
371276 AAAGTTTT-T
1 -AATTTTTAT
371285 AATATTTTA-
1 AAT-TTTTAT
371294 AACTTTTTATT
1 AA-TTTTTA-T
* *
371305 TATTTTTAC
1 AATTTTTAT
*
371314 AACTTTATAT
1 AA-TTTTTAT
* *
371324 AAATTTTAA
1 AATTTTTAT
*
371333 AACTGTTGTA-
1 AA-T-TTTTAT
371343 ATATTTTTAT
1 A-ATTTTTAT
*
371353 TATTTTTAT
1 AATTTTTAT
371362 AAATTTTTAT
1 -AATTTTTAT
*
371372 AATTTATTAG
1 AATTT-TTAT
371382 AATTTTTA-
1 AATTTTTAT
*
371390 AAGATTTTAT
1 AA-TTTTTAT
*
371400 AAATTTTAT
1 AATTTTTAT
*
371409 AAGTTTATAT
1 AA-TTTTTAT
**
371419 AAATTTCCGAT
1 -AATTT-TTAT
371430 -ATTTTTAT
1 AATTTTTAT
*
371438 GATTTTTAT
1 AATTTTTAT
*
371447 AACTTTTAT
1 AATTTTTAT
371456 -ATTTT
1 AATTTT
371461 CATTAGAAAA
Statistics
Matches: 159, Mismatches: 32, Indels: 43
0.68 0.14 0.18
Matches are distributed among these distances:
8 15 0.09
9 82 0.52
10 52 0.33
11 10 0.06
ACGTcount: A:0.34, C:0.03, G:0.04, T:0.59
Consensus pattern (9 bp):
AATTTTTAT
Found at i:376533 original size:31 final size:31
Alignment explanation
Indices: 376498--376558 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
376488 TAGTACTTAA
376498 TATAAAAT-AGTAATTGATACATAGTACCTGC
1 TATAAAATGA-TAATTGATACATAGTACCTGC
* * *
376529 TATAATATGATCATTGGTACATAGTACCTG
1 TATAAAATGATAATTGATACATAGTACCTG
376559 ATACTTTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 25 0.96
32 1 0.04
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.34
Consensus pattern (31 bp):
TATAAAATGATAATTGATACATAGTACCTGC
Found at i:377457 original size:21 final size:22
Alignment explanation
Indices: 377428--377469 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
377418 GATGAAGATA
377428 ATATCTTTACTTACTTTTTAAC
1 ATATCTTTACTTACTTTTTAAC
* *
377450 ATAT-TTTATTTTCTTTTTAA
1 ATATCTTTACTTACTTTTTAA
377470 TTTAATTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.26, C:0.12, G:0.00, T:0.62
Consensus pattern (22 bp):
ATATCTTTACTTACTTTTTAAC
Found at i:381261 original size:23 final size:23
Alignment explanation
Indices: 381200--381252 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
381190 CTTATTCATA
* *
381200 TTTTTCTATTGCTTTTGGACTAC
1 TTTTTCTGTTGATTTTGGACTAC
**
381223 TTTTTCTGTTGATTTTGGACTGT
1 TTTTTCTGTTGATTTTGGACTAC
381246 TTTTTCT
1 TTTTTCT
381253 TTTTTTTTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.09, C:0.13, G:0.15, T:0.62
Consensus pattern (23 bp):
TTTTTCTGTTGATTTTGGACTAC
Found at i:381349 original size:19 final size:19
Alignment explanation
Indices: 381325--381362 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
381315 TATTTCTGTT
381325 GATTTTTTTGAACGAGTTG
1 GATTTTTTTGAACGAGTTG
381344 GATTTTTTTGAACGAGTTG
1 GATTTTTTTGAACGAGTTG
381363 AATTCATTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.05, G:0.26, T:0.47
Consensus pattern (19 bp):
GATTTTTTTGAACGAGTTG
Found at i:386237 original size:22 final size:23
Alignment explanation
Indices: 386207--386249 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
386197 TAATGTGGGT
386207 CATGCAAATTAAATTAATTAAAG
1 CATGCAAATTAAATTAATTAAAG
* *
386230 CATG-AAATTATATTATTTAA
1 CATGCAAATTAAATTAATTAA
386250 TGGACATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.49, C:0.07, G:0.07, T:0.37
Consensus pattern (23 bp):
CATGCAAATTAAATTAATTAAAG
Found at i:387879 original size:5 final size:5
Alignment explanation
Indices: 387847--387897 Score: 52
Period size: 5 Copynumber: 10.0 Consensus size: 5
387837 AATATATTCT
*
387847 TTTTA -TTTA TTTTCGA TTTGTT TTTTA TTTTA TTTTA -TTTA TTTTA
1 TTTTA TTTTA TTTT--A TTT-TA TTTTA TTTTA TTTTA TTTTA TTTTA
387893 TTTTA
1 TTTTA
387898 CTAACTAATT
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
4 8 0.21
5 23 0.59
6 3 0.08
7 4 0.10
8 1 0.03
ACGTcount: A:0.18, C:0.02, G:0.04, T:0.76
Consensus pattern (5 bp):
TTTTA
Found at i:391371 original size:18 final size:18
Alignment explanation
Indices: 391348--391387 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
391338 CCCAGATAAT
*
391348 ATGCGATCACATAACCAG
1 ATGCGATCACAAAACCAG
*
391366 ATGCGATCACAAAATCAG
1 ATGCGATCACAAAACCAG
391384 ATGC
1 ATGC
391388 ATTCGTATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.40, C:0.25, G:0.17, T:0.17
Consensus pattern (18 bp):
ATGCGATCACAAAACCAG
Found at i:396472 original size:21 final size:20
Alignment explanation
Indices: 396446--396505 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 20
396436 AATGGTGAAG
396446 ACTTCTACGGATACAAGTGAC
1 ACTTCTAC-GATACAAGTGAC
* *
396467 AGTTCTGTCGATACAAGTGAC
1 ACTTCT-ACGATACAAGTGAC
*
396488 ACTTCTACCGAAACAAGT
1 ACTTCTA-CGATACAAGT
396506 CTTACTTCTG
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
21 31 0.97
22 1 0.03
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.25
Consensus pattern (20 bp):
ACTTCTACGATACAAGTGAC
Found at i:401093 original size:18 final size:17
Alignment explanation
Indices: 401070--401155 Score: 75
Period size: 18 Copynumber: 4.8 Consensus size: 17
401060 TTCATTTTGG
*
401070 GTTTAAATTTAGTTTAAA
1 GTTTAAATTTAATTT-AA
**
401088 GTTTAAACTTTTCTTTCAA
1 GTTTAAA-TTTAATTT-AA
*
401107 GTTTAAATTTAAATTAA
1 GTTTAAATTTAATTTAA
*
401124 GTTTAAAATTAATTTGAA
1 GTTTAAATTTAATTT-AA
401142 -TTTAAAATTTAATT
1 GTTT-AAATTTAATT
401156 ATTTAAAATG
Statistics
Matches: 56, Mismatches: 9, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
17 18 0.32
18 23 0.41
19 15 0.27
ACGTcount: A:0.40, C:0.03, G:0.07, T:0.50
Consensus pattern (17 bp):
GTTTAAATTTAATTTAA
Found at i:401127 original size:17 final size:18
Alignment explanation
Indices: 401105--401153 Score: 57
Period size: 17 Copynumber: 2.8 Consensus size: 18
401095 CTTTTCTTTC
401105 AAGTTTAAATTTAAATT-
1 AAGTTTAAATTTAAATTG
* *
401122 AAGTTTAAAATTAATTTG
1 AAGTTTAAATTTAAATTG
401140 AA-TTTAAAATTTAA
1 AAGTTT-AAATTTAA
401154 TTATTTAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
17 18 0.67
18 9 0.33
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.45
Consensus pattern (18 bp):
AAGTTTAAATTTAAATTG
Found at i:401922 original size:15 final size:15
Alignment explanation
Indices: 401902--401939 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
401892 AGTAAATGTT
401902 TTATTAATAATATTA
1 TTATTAATAATATTA
*
401917 TTATTATTAATATTA
1 TTATTAATAATATTA
401932 --ATTAATAA
1 TTATTAATAA
401940 AAAGGGGGGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 7 0.33
15 14 0.67
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TTATTAATAATATTA
Found at i:403121 original size:29 final size:29
Alignment explanation
Indices: 403069--403278 Score: 255
Period size: 29 Copynumber: 7.2 Consensus size: 29
403059 CAGAAATTTT
* * *
403069 ATTTTTACCCTGAAA-TTCCTAAAATCCC
1 ATTTTGACCCCGAAACTTCCAAAAATCCC
* **
403097 ACTTTTGACCTCGAAACTTCCAAAAATTCTA
1 A-TTTTGACCCCGAAACTTCCAAAAA-TCCC
403128 ATTTT-ACCCCTG-AACTTCCAAAAATCCC
1 ATTTTGACCCC-GAAACTTCCAAAAATCCC
*
403156 ATTTTTGACCCCGAAACTTCCAAAAATTCC
1 A-TTTTGACCCCGAAACTTCCAAAAATCCC
* *
403186 ATTTTGACCACGAAACTTCCAAAAATTCC
1 ATTTTGACCCCGAAACTTCCAAAAATCCC
* *
403215 ATTTTGACCCCAAAACTTCCAAAAATTCC
1 ATTTTGACCCCGAAACTTCCAAAAATCCC
403244 ATTTATGACCCCGAAACTTCCAAAAATCCC
1 ATTT-TGACCCCGAAACTTCCAAAAATCCC
403274 ATTTT
1 ATTTT
403279 TTATGACGAA
Statistics
Matches: 159, Mismatches: 15, Indels: 15
0.84 0.08 0.08
Matches are distributed among these distances:
28 4 0.03
29 91 0.57
30 61 0.38
31 3 0.02
ACGTcount: A:0.35, C:0.30, G:0.05, T:0.30
Consensus pattern (29 bp):
ATTTTGACCCCGAAACTTCCAAAAATCCC
Found at i:403162 original size:59 final size:58
Alignment explanation
Indices: 403052--403336 Score: 276
Period size: 59 Copynumber: 4.8 Consensus size: 58
403042 GGAGGTCCCT
* * * * * * *
403052 AAACTTCCAGAAATTTTATTTTTA-CCCTGAAATTCCTAAAATCCCACTTTTGACCTCG
1 AAACTTCCA-AAAATTCAATTTTACCCCTGAACTTCCAAAAATCCCATTTTTGACCCCG
403110 AAACTTCCAAAAATTCTAATTTTACCCCTGAACTTCCAAAAATCCCATTTTTGACCCCG
1 AAACTTCCAAAAATTC-AATTTTACCCCTGAACTTCCAAAAATCCCATTTTTGACCCCG
* * * *
403169 AAACTTCCAAAAATTCCATTTTGACCAC-GAAACTTCCAAAAATTCCA-TTTTGACCCCA
1 AAACTTCCAAAAATTCAATTTT-ACCCCTG-AACTTCCAAAAATCCCATTTTTGACCCCG
* * ***
403227 AAACTTCCAAAAATTCCATTTATGACCCC-GAAACTTCCAAAAATCCCATTTTTTATGACG
1 AAACTTCCAAAAATTCAATTT-T-ACCCCTG-AACTTCCAAAAATCCCATTTTTGACCCCG
* *
403287 AAACTTCCAAAAATTC-CTTTTCCGCCCTCGAACTTCC-AAAATCTCCATTT
1 AAACTTCCAAAAATTCAATTTTAC-CCCT-GAACTTCCAAAAATC-CCATTT
403337 CGCCCTCAAA
Statistics
Matches: 197, Mismatches: 20, Indels: 19
0.83 0.08 0.08
Matches are distributed among these distances:
57 6 0.03
58 62 0.31
59 106 0.54
60 23 0.12
ACGTcount: A:0.34, C:0.29, G:0.06, T:0.31
Consensus pattern (58 bp):
AAACTTCCAAAAATTCAATTTTACCCCTGAACTTCCAAAAATCCCATTTTTGACCCCG
Found at i:403201 original size:88 final size:87
Alignment explanation
Indices: 403069--403336 Score: 319
Period size: 88 Copynumber: 3.0 Consensus size: 87
403059 CAGAAATTTT
* * *
403069 ATTTTT-ACCCTGAAA-TTCCTAAAATCCCACTTTTGACCTCGAAACTTCCAAAAATTCTAATTT
1 ATTTTTGACCCCGAAACTTCCAAAAATCCCACTTTTGACCACGAAACTTCCAAAAATTC--ATTT
403132 TACCCCTGAACTTCCAAAAATCCC
64 TACCCCTGAACTTCCAAAAATCCC
*
403156 ATTTTTGACCCCGAAACTTCCAAAAATTCCA-TTTTGACCACGAAACTTCCAAAAATTCCATTTT
1 ATTTTTGACCCCGAAACTTCCAAAAATCCCACTTTTGACCACGAAACTTCCAAAAATT-CATTTT
** *
403220 GACCCCAAAACTTCCAAAAATTCC
65 -ACCCCTGAACTTCCAAAAATCCC
* * * ** * *
403244 ATTTATGACCCCGAAACTTCCAAAAATCCCATTTTTTATGACGAAACTTCCAAAAATTCCTTTTC
1 ATTTTTGACCCCGAAACTTCCAAAAATCCCACTTTTGACCACGAAACTTCCAAAAATTCATTTTA
403309 CGCCCTCGAACTTCC-AAAATCTCC
66 C-CCCT-GAACTTCCAAAAATC-CC
403333 ATTT
1 ATTT
403337 CGCCCTCAAA
Statistics
Matches: 156, Mismatches: 17, Indels: 14
0.83 0.09 0.07
Matches are distributed among these distances:
87 12 0.08
88 95 0.61
89 49 0.31
ACGTcount: A:0.34, C:0.30, G:0.06, T:0.31
Consensus pattern (87 bp):
ATTTTTGACCCCGAAACTTCCAAAAATCCCACTTTTGACCACGAAACTTCCAAAAATTCATTTTA
CCCCTGAACTTCCAAAAATCCC
Found at i:403320 original size:29 final size:30
Alignment explanation
Indices: 403052--403356 Score: 210
Period size: 29 Copynumber: 10.4 Consensus size: 30
403042 GGAGGTCCCT
* ** **
403052 AAACTTCCAGAAATTTTATTTTTACCCT-G
1 AAACTTCCAAAAATTCCATTTTCGCCCTCG
* * *
403081 AAA-TTCCTAAAATCCCACTTTT-GACCTCG
1 AAACTTCCAAAAATTCCA-TTTTCGCCCTCG
*
403110 AAACTTCCAAAAATTCTAATTTTAC-CCCT-G
1 AAACTTCCAAAAATTC-CATTTT-CGCCCTCG
* *
403140 -AACTTCCAAAAATCCCATTTTTGACCC-CG
1 AAACTTCCAAAAATTCCATTTTCG-CCCTCG
* *
403169 AAACTTCCAAAAATTCCATTTT-GACCACG
1 AAACTTCCAAAAATTCCATTTTCGCCCTCG
*
403198 AAACTTCCAAAAATTCCATTTT-GACCC-CA
1 AAACTTCCAAAAATTCCATTTTCG-CCCTCG
403227 AAACTTCCAAAAATTCCATTTAT-GACCC-CG
1 AAACTTCCAAAAATTCCATTT-TCG-CCCTCG
* ******
403257 AAACTTCCAAAAATCCCATTTTTTATGACG
1 AAACTTCCAAAAATTCCATTTTCGCCCTCG
403287 AAACTTCCAAAAATTCC-TTTTCCGCCCTCG
1 AAACTTCCAAAAATTCCATTTT-CGCCCTCG
*
403317 -AACTTCC-AAAATCTCCA-TTTCGCCCTCA
1 AAACTTCCAAAAAT-TCCATTTTCGCCCTCG
*
403345 AAACTTTCAAAA
1 AAACTTCCAAAA
403357 TTACCCTTTT
Statistics
Matches: 223, Mismatches: 33, Indels: 39
0.76 0.11 0.13
Matches are distributed among these distances:
28 31 0.14
29 101 0.45
30 87 0.39
31 4 0.02
ACGTcount: A:0.34, C:0.30, G:0.06, T:0.30
Consensus pattern (30 bp):
AAACTTCCAAAAATTCCATTTTCGCCCTCG
Found at i:403561 original size:21 final size:20
Alignment explanation
Indices: 403523--403562 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
403513 TGCATTAGTA
* *
403523 TTTTGCATTTTTTGTTTTTT
1 TTTTGCATTTTATCTTTTTT
403543 TTTTGCCATTTTATCTTTTT
1 TTTTG-CATTTTATCTTTTT
403563 ATTTATCTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.07, C:0.10, G:0.07, T:0.75
Consensus pattern (20 bp):
TTTTGCATTTTATCTTTTTT
Found at i:415489 original size:205 final size:204
Alignment explanation
Indices: 415137--415803 Score: 1012
Period size: 205 Copynumber: 3.3 Consensus size: 204
415127 GTGACCATCC
*
415137 ACAAACGATGCGGTCATCTTCCTGATGAGATACCGAGAAGAAGACCAAATCAAACCCACGCTCGA
1 ACAAACGACGCGGTCATCTTCCTGATGAGATACCGAGAAGAAGACCAAATCAAACCCACGCTCGA
* *
415202 TGTGAGTAAATCTTCGAATCTCAGCTTCCTGATGAGACACCAAGAAGCAGATCGAAGCAATAAAC
66 TGTGAGTAAATCTTCGAATCACAGCTTCCTGATGAGACACCGAGAAGCAGATCGAAGCAATAAAC
*
415267 GGTTAGCTTCCTGATGAGATACTGAGAAGTGGATCAAATTCATCTTCCTGATGAGATACAAAGAA
131 GGTTAGCTTCCTGATGAGATACTGAGAAGTGGA-CAAATTCATCTTCCTGATGAGATACAGAGAA
415332 GCGGATTGAA
195 GCGGATTGAA
* * * *
415342 ACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAAAAGACCAAACCAAACCCACGCTCAA
1 ACAAACGACGCGGTCATCTTCCTGATGAGATACCGAGAAGAAGACCAAATCAAACCCACGCTCGA
* *
415407 TGTGAGTAAATCTTCGAATCACAGCTTCCTGATGAGACACCGGGAAGCAGATCGAAGTAATAAAC
66 TGTGAGTAAATCTTCGAATCACAGCTTCCTGATGAGACACCGAGAAGCAGATCGAAGCAATAAAC
*
415472 GGTTAGTTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGA-CTTCCTGATGAGATACAGAGA
131 GGTTAGCTTCCTGATGAGATACTGAGAAGTGGA-CAAATTC-ATCTTCCTGATGAGATACAGAGA
415536 AGCGGATTGAA
194 AGCGGATTGAA
*
415547 ACAAACAACGCGGTCATCTTCCTGATGAGATACCGAGAAGAAGACCAAATCAAACCCACGCTCGA
1 ACAAACGACGCGGTCATCTTCCTGATGAGATACCGAGAAGAAGACCAAATCAAACCCACGCTCGA
* * *
415612 TATGAGTAAATCTTTGAATCCCAGCTTCCTGATGAGACACCGAGAAGCAGATCGAAGCAATAAAC
66 TGTGAGTAAATCTTCGAATCACAGCTTCCTGATGAGACACCGAGAAGCAGATCGAAGCAATAAAC
* * * *
415677 GATTAGCTTCCTGATGAGATACTGAGAAGTGGACCAATTCATCTTCCTGATGAAACACAGAGAAG
131 GGTTAGCTTCCTGATGAGATACTGAGAAGTGGACAAATTCATCTTCCTGATGAGATACAGAGAAG
* ***
415742 TGGAACAAA
196 CGGATTGAA
** *** * * * *
415751 ACAAGTGATATGGTCATCTTCCCGATGAGATACTGAGAAGAAGGCCAAGTCAA
1 ACAAACGACGCGGTCATCTTCCTGATGAGATACCGAGAAGAAGACCAAATCAA
415804 TGAAACCAGA
Statistics
Matches: 419, Mismatches: 41, Indels: 5
0.90 0.09 0.01
Matches are distributed among these distances:
203 1 0.00
204 75 0.18
205 342 0.82
206 1 0.00
ACGTcount: A:0.36, C:0.21, G:0.22, T:0.21
Consensus pattern (204 bp):
ACAAACGACGCGGTCATCTTCCTGATGAGATACCGAGAAGAAGACCAAATCAAACCCACGCTCGA
TGTGAGTAAATCTTCGAATCACAGCTTCCTGATGAGACACCGAGAAGCAGATCGAAGCAATAAAC
GGTTAGCTTCCTGATGAGATACTGAGAAGTGGACAAATTCATCTTCCTGATGAGATACAGAGAAG
CGGATTGAA
Found at i:416242 original size:18 final size:18
Alignment explanation
Indices: 416157--416242 Score: 72
Period size: 17 Copynumber: 4.8 Consensus size: 18
416147 TTCATTTTGG
*
416157 GTTT-AAATTTAGTTTAAA
1 GTTTAAAATTTAATTT-AA
* **
416175 GTTTAAACTTTTCTTTTAA
1 GTTTAAA-ATTTAATTTAA
*
416194 GTTT-AAATTTAAATTAA
1 GTTTAAAATTTAATTTAA
416211 GTTTAAAA-TTAATTTGAA
1 GTTTAAAATTTAATTT-AA
416229 -TTTAAAATTTAATT
1 GTTTAAAATTTAATT
416243 ATTTAAAATG
Statistics
Matches: 55, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
17 24 0.44
18 17 0.31
19 8 0.15
20 6 0.11
ACGTcount: A:0.40, C:0.02, G:0.07, T:0.51
Consensus pattern (18 bp):
GTTTAAAATTTAATTTAA
Found at i:416355 original size:14 final size:15
Alignment explanation
Indices: 416325--416357 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
416315 TTACAAAGGT
416325 CTAAATAAGCACAAA
1 CTAAATAAGCACAAA
*
416340 CTAAATAA-CCCAAA
1 CTAAATAAGCACAAA
416354 CTAA
1 CTAA
416358 CCTAAAACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.58, C:0.24, G:0.03, T:0.15
Consensus pattern (15 bp):
CTAAATAAGCACAAA
Found at i:417807 original size:30 final size:30
Alignment explanation
Indices: 417773--418093 Score: 270
Period size: 30 Copynumber: 10.9 Consensus size: 30
417763 GAGGTCCCTA
*
417773 AACTTCCAAAAATTCTATTTTTTACCCTCG
1 AACTTCCAAAAATTCCATTTTTTACCCTCG
* * * *
417803 AACTTCCAAAAATCCCACTTTTGACCC-AG
1 AACTTCCAAAAATTCCATTTTTTACCCTCG
* * * *
417832 AAACTTCTAAAAATTTC-GTTTTTACCCTTG
1 -AACTTCCAAAAATTCCATTTTTTACCCTCG
** * *
417862 AACTT-TTAAAATCCCATTTTTGA-CCTCG
1 AACTTCCAAAAATTCCATTTTTTACCCTCG
*
417890 AAACTTCCAAAAATTCCA-TTTTTACCC-CTA
1 -AACTTCCAAAAATTCCATTTTTTACCCTC-G
* *
417920 AACTTCCAAAAATTCCATTTTTAACCC-CAA
1 AACTTCCAAAAATTCCATTTTTTACCCTC-G
* * *
417950 AACTTCCAAAAATTCCATTTTTGATCC-CA
1 AACTTCCAAAAATTCCATTTTTTACCCTCG
*
417979 AACTTTCAAAAATTCCATTTTTTACCCTCG
1 AACTTCCAAAAATTCCATTTTTTACCCTCG
* * *
418009 AACTTCCAAAAATCCCGTTTTTTA-TCTCG
1 AACTTCCAAAAATTCCATTTTTTACCCTCG
* *
418038 AAACTTCCAAAAATT--TTGTTTTTGCCCTCG
1 -AACTTCCAAAAATTCCAT-TTTTTACCCTCG
418068 AACTTCC-AAAATCTCCATTTTTTACC
1 AACTTCCAAAAAT-TCCATTTTTTACC
418094 TCAAAACTCT
Statistics
Matches: 236, Mismatches: 40, Indels: 30
0.77 0.13 0.10
Matches are distributed among these distances:
28 17 0.07
29 89 0.38
30 129 0.55
31 1 0.00
ACGTcount: A:0.32, C:0.27, G:0.04, T:0.36
Consensus pattern (30 bp):
AACTTCCAAAAATTCCATTTTTTACCCTCG
Done.