Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015381.1 Kokia drynarioides strain JFW-HI SEQ_130428, 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: 2291099
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Warning! 587 characters in sequence are not A, C, G, or T
File 6 of 8
Found at i:1347572 original size:29 final size:29
Alignment explanation
Indices: 1347484--1347578 Score: 70
Period size: 29 Copynumber: 3.3 Consensus size: 29
1347474 AATTACCTAA
* *
1347484 TTACCCTCGAATGTC-AAAATTTTCATTTT
1 TTACCCCCGAATGTCTAAAA-TTACATTTT
* * * *
1347513 TGA-CCCCGATTTTTCTAAAAATTAC-TATT
1 TTACCCCCGA-ATGTCT-AAAATTACATTTT
*
1347542 TTACCCCCGAATGTCTAAAATTCCATTTT
1 TTACCCCCGAATGTCTAAAATTACATTTT
*
1347571 TTAACCCC
1 TTACCCCC
1347579 AAACTTTCCC
Statistics
Matches: 49, Mismatches: 12, Indels: 10
0.69 0.17 0.14
Matches are distributed among these distances:
28 12 0.24
29 24 0.49
30 9 0.18
31 4 0.08
ACGTcount: A:0.28, C:0.25, G:0.06, T:0.40
Consensus pattern (29 bp):
TTACCCCCGAATGTCTAAAATTACATTTT
Found at i:1358009 original size:30 final size:30
Alignment explanation
Indices: 1357917--1358009 Score: 96
Period size: 30 Copynumber: 3.1 Consensus size: 30
1357907 TCATCCTTTC
* * *
1357917 TCAGTCATCTAGTGTTGAGCATCCTTCGAG
1 TCAGTCACCTAGTGTTGAGCCTTCTTCGAG
* * ** *
1357947 TCAGTTACCTAGTGTTGAGTCTTCCCCAAG
1 TCAGTCACCTAGTGTTGAGCCTTCTTCGAG
* *
1357977 TCAGTCACCTACTGTTGAGCCTTCTTTGAG
1 TCAGTCACCTAGTGTTGAGCCTTCTTCGAG
1358007 TCA
1 TCA
1358010 ACCATTTGGT
Statistics
Matches: 48, Mismatches: 15, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
30 48 1.00
ACGTcount: A:0.19, C:0.26, G:0.20, T:0.34
Consensus pattern (30 bp):
TCAGTCACCTAGTGTTGAGCCTTCTTCGAG
Found at i:1359114 original size:15 final size:15
Alignment explanation
Indices: 1359094--1359124 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1359084 GGTTGAGGAC
1359094 AAAGCAACTTATCAG
1 AAAGCAACTTATCAG
*
1359109 AAAGCAGCTTATCAG
1 AAAGCAACTTATCAG
1359124 A
1 A
1359125 GGTTGATTGG
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:0.45, C:0.19, G:0.16, T:0.19
Consensus pattern (15 bp):
AAAGCAACTTATCAG
Found at i:1364725 original size:5 final size:5
Alignment explanation
Indices: 1364715--1364739 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
1364705 CTTTTTCTTC
1364715 CTTTT CTTTT CTTTT CTTTT CTTTT
1 CTTTT CTTTT CTTTT CTTTT CTTTT
1364740 GCTGATTTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
CTTTT
Found at i:1366288 original size:19 final size:19
Alignment explanation
Indices: 1366264--1366338 Score: 81
Period size: 19 Copynumber: 4.3 Consensus size: 19
1366254 GAGATATGAA
1366264 AATATGTGAAATTGATGTG
1 AATATGTGAAATTGATGTG
* *
1366283 AATATGAGACATTGATGTG
1 AATATGTGAAATTGATGTG
*
1366302 AATATGTG----TCAT-TG
1 AATATGTGAAATTGATGTG
1366316 -ATATGTGAAATTGATGTG
1 AATATGTGAAATTGATGTG
1366334 AATAT
1 AATAT
1366339 CAAATGTGTT
Statistics
Matches: 45, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
13 7 0.16
14 2 0.04
15 3 0.07
17 3 0.07
18 2 0.04
19 28 0.62
ACGTcount: A:0.36, C:0.03, G:0.24, T:0.37
Consensus pattern (19 bp):
AATATGTGAAATTGATGTG
Found at i:1366432 original size:19 final size:19
Alignment explanation
Indices: 1366408--1366452 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
1366398 GACATTAATT
*
1366408 TGAATATGTGAAATTGATG
1 TGAATATGAGAAATTGATG
* *
1366427 TTAATATGAGACATTGATG
1 TGAATATGAGAAATTGATG
1366446 TGAATAT
1 TGAATAT
1366453 CAAATGTGTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.38, C:0.02, G:0.22, T:0.38
Consensus pattern (19 bp):
TGAATATGAGAAATTGATG
Found at i:1372006 original size:23 final size:22
Alignment explanation
Indices: 1371950--1372024 Score: 69
Period size: 23 Copynumber: 3.3 Consensus size: 22
1371940 AATTAGTGAG
* *
1371950 ATTCTCTAGCATGAACAATTAT
1 ATTCTCTAGCATGAACAGTAAT
* * *
1371972 ATTCTTTGGCATGAATAGTAAAT
1 ATTCTCTAGCATGAACAGT-AAT
* *
1371995 ATTCTCTAGCATAAACAGTGAAG
1 ATTCTCTAGCATGAACAGT-AAT
1372018 ATTCTCT
1 ATTCTCT
1372025 TGTAATTTGT
Statistics
Matches: 41, Mismatches: 11, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
22 15 0.37
23 26 0.63
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.36
Consensus pattern (22 bp):
ATTCTCTAGCATGAACAGTAAT
Found at i:1378394 original size:29 final size:29
Alignment explanation
Indices: 1378362--1378512 Score: 96
Period size: 29 Copynumber: 5.1 Consensus size: 29
1378352 AAAATAGAGA
* *
1378362 TTTTAGAGGTTCGAGGGTAAAAATGGAAG
1 TTTTGGAGGTTCGAGGGTAAAAATGGAAT
* *
1378391 TTTTGGAAGTTTTG-GGGTCAAAAATAGG-AT
1 TTTTGG-AGGTTCGAGGGT-AAAAAT-GGAAT
* *
1378421 TTTTGGAAGTTCGAGGCTAAAAATGGAAT
1 TTTTGGAGGTTCGAGGGTAAAAATGGAAT
* * *
1378450 TTTTGGAAGTTTTG-GGGTCAAAAATATG-AT
1 TTTTGG-AGGTTCGAGGGT-AAAAAT-GGAAT
* * *
1378480 TTTTGGAAGTT-TAGGGGTAAAAATTGAAT
1 TTTTGGAGGTTCGA-GGGTAAAAATGGAAT
1378509 TTTT
1 TTTT
1378513 TGATAGTTTA
Statistics
Matches: 95, Mismatches: 16, Indels: 22
0.71 0.12 0.17
Matches are distributed among these distances:
28 4 0.04
29 45 0.47
30 43 0.45
31 3 0.03
ACGTcount: A:0.32, C:0.03, G:0.28, T:0.36
Consensus pattern (29 bp):
TTTTGGAGGTTCGAGGGTAAAAATGGAAT
Found at i:1378501 original size:59 final size:59
Alignment explanation
Indices: 1378339--1378521 Score: 226
Period size: 59 Copynumber: 3.1 Consensus size: 59
1378329 TGATTTTGAG
* * * * * *
1378339 AGTTTTGAGGTCGAAAATAGAGA-TTTTAGAGGTTCGAGGGTAAAAATGGAAGTTTTGGA
1 AGTTTTGGGGTCAAAAATAG-GATTTTTGGAAGTTAGAGGGTAAAAATGGAATTTTTGGA
* *
1378398 AGTTTTGGGGTCAAAAATAGGATTTTTGGAAGTTCGAGGCTAAAAATGGAATTTTTGGA
1 AGTTTTGGGGTCAAAAATAGGATTTTTGGAAGTTAGAGGGTAAAAATGGAATTTTTGGA
* * *
1378457 AGTTTTGGGGTCAAAAATATGATTTTTGGAAGTTTAG-GGGTAAAAATTGAATTTTTTGA
1 AGTTTTGGGGTCAAAAATAGGATTTTTGGAAG-TTAGAGGGTAAAAATGGAATTTTTGGA
1378516 TAGTTT
1 -AGTTT
1378522 AGGGACCTCC
Statistics
Matches: 110, Mismatches: 11, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
58 2 0.02
59 100 0.91
60 8 0.07
ACGTcount: A:0.32, C:0.03, G:0.28, T:0.36
Consensus pattern (59 bp):
AGTTTTGGGGTCAAAAATAGGATTTTTGGAAGTTAGAGGGTAAAAATGGAATTTTTGGA
Found at i:1378522 original size:30 final size:29
Alignment explanation
Indices: 1378376--1378525 Score: 153
Period size: 30 Copynumber: 5.1 Consensus size: 29
1378366 AGAGGTTCGA
* *
1378376 GGGTAAAAATGGAAGTTTTGGAAGTTTTG
1 GGGTAAAAATGGAATTTTTGGAAGTTTAG
*
1378405 GGGTCAAAAATAGG-ATTTTTGGAAG-TTCG
1 GGGT-AAAAAT-GGAATTTTTGGAAGTTTAG
* *
1378434 AGGCTAAAAATGGAATTTTTGGAAGTTTTG
1 -GGGTAAAAATGGAATTTTTGGAAGTTTAG
*
1378464 GGGTCAAAAATATG-ATTTTTGGAAGTTTAG
1 GGGT-AAAAAT-GGAATTTTTGGAAGTTTAG
* *
1378494 GGGTAAAAATTGAATTTTTTGATAGTTTAG
1 GGGTAAAAATGGAATTTTTGGA-AGTTTAG
1378524 GG
1 GG
1378526 ACCTCCAGGG
Statistics
Matches: 104, Mismatches: 8, Indels: 17
0.81 0.06 0.13
Matches are distributed among these distances:
28 4 0.04
29 41 0.39
30 56 0.54
31 3 0.03
ACGTcount: A:0.32, C:0.03, G:0.29, T:0.36
Consensus pattern (29 bp):
GGGTAAAAATGGAATTTTTGGAAGTTTAG
Found at i:1379530 original size:18 final size:18
Alignment explanation
Indices: 1379507--1379542 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1379497 TGGTTCCCTT
*
1379507 TTTTTATTATTATTAATA
1 TTTTTATTAATATTAATA
1379525 TTTTTATTAATATTAATA
1 TTTTTATTAATATTAATA
1379543 AAAATTTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
TTTTTATTAATATTAATA
Found at i:1379531 original size:12 final size:12
Alignment explanation
Indices: 1379511--1379607 Score: 56
Period size: 12 Copynumber: 8.2 Consensus size: 12
1379501 TCCCTTTTTT
1379511 TATTATTATTAA
1 TATTATTATTAA
*
1379523 TATTTTTATTAA
1 TATTATTATTAA
*
1379535 TATTA--ATAAA
1 TATTATTATTAA
*
1379545 AATT-TTATTAA
1 TATTATTATTAA
* * **
1379556 TACCTATTAATGC
1 TA-TTATTATTAA
* * *
1379569 CATTATTGTCAA
1 TATTATTATTAA
1379581 TATTTATTATTAA
1 TA-TTATTATTAA
*
1379594 TGTTATTATTAA
1 TATTATTATTAA
1379606 TA
1 TA
1379608 ATAATATTTA
Statistics
Matches: 58, Mismatches: 22, Indels: 10
0.64 0.24 0.11
Matches are distributed among these distances:
10 7 0.12
11 5 0.09
12 32 0.55
13 14 0.24
ACGTcount: A:0.39, C:0.05, G:0.03, T:0.53
Consensus pattern (12 bp):
TATTATTATTAA
Found at i:1379538 original size:21 final size:21
Alignment explanation
Indices: 1379505--1379566 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 21
1379495 TTTGGTTCCC
*
1379505 TTTTT-TTATTATTATTAATA
1 TTTTTATTAATATTATTAATA
* *
1379525 TTTTTATTAATATTAATAAAA
1 TTTTTATTAATATTATTAATA
* *
1379546 ATTTTATTAATACCTATTAAT
1 TTTTTATTAATA-TTATTAAT
1379567 GCCATTATTG
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
20 5 0.15
21 23 0.70
22 5 0.15
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (21 bp):
TTTTTATTAATATTATTAATA
Found at i:1380264 original size:17 final size:17
Alignment explanation
Indices: 1380244--1380353 Score: 123
Period size: 17 Copynumber: 6.4 Consensus size: 17
1380234 CTTTATTTAT
* *
1380244 TTTAAATTTATAATAAT
1 TTTAAATTTAAAATAAA
1380261 TTTAAATTTGAAAATAAA
1 TTTAAATTT-AAAATAAA
* *
1380279 TTTAAACTTAAATTAAA
1 TTTAAATTTAAAATAAA
1380296 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
* *
1380313 TTTAAATTTTTAAACAAA
1 TTTAAA-TTTAAAATAAA
*
1380331 TTT-AATCCTAAAATAAA
1 TTTAAAT-TTAAAATAAA
1380348 TTTAAA
1 TTTAAA
1380354 ATGAGTTTGG
Statistics
Matches: 78, Mismatches: 11, Indels: 7
0.81 0.11 0.07
Matches are distributed among these distances:
16 1 0.01
17 49 0.63
18 28 0.36
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.43
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:1380289 original size:6 final size:6
Alignment explanation
Indices: 1380244--1380321 Score: 67
Period size: 6 Copynumber: 13.5 Consensus size: 6
1380234 CTTTATTTAT
* * *
1380244 TTTAAA TTTATAA --TAAT TTTAAA TTTGAAA -ATAAA TTTAAA CTTAAA
1 TTTAAA TTTA-AA TTTAAA TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA
*
1380291 -TTAAA TTTAAA TTTAAA -ATAAA TTTAAA TTT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT
1380322 TTAAACAAAT
Statistics
Matches: 58, Mismatches: 7, Indels: 14
0.73 0.09 0.18
Matches are distributed among these distances:
4 1 0.02
5 14 0.24
6 38 0.66
7 5 0.09
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (6 bp):
TTTAAA
Found at i:1380300 original size:11 final size:11
Alignment explanation
Indices: 1380262--1380320 Score: 66
Period size: 11 Copynumber: 5.2 Consensus size: 11
1380252 TATAATAATT
1380262 TTAAATTTGAAA
1 TTAAATTT-AAA
*
1380274 ATAAATTTAAA
1 TTAAATTTAAA
1380285 CTTAAA-TTAAA
1 -TTAAATTTAAA
1380296 TTTAAATTTAAA
1 -TTAAATTTAAA
*
1380308 ATAAATTTAAA
1 TTAAATTTAAA
1380319 TT
1 TT
1380321 TTTAAACAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
11 24 0.60
12 16 0.40
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (11 bp):
TTAAATTTAAA
Found at i:1380311 original size:52 final size:52
Alignment explanation
Indices: 1380244--1380353 Score: 148
Period size: 52 Copynumber: 2.1 Consensus size: 52
1380234 CTTTATTTAT
* * * * *
1380244 TTTAAATTTATAATAATTTTAAATTTGAAAATAAATTTAAACTTAAATTAAA
1 TTTAAATTTAAAATAAATTTAAATTTGAAAACAAATTTAAACCTAAAATAAA
** *
1380296 TTTAAATTTAAAATAAATTTAAATTTTTAAACAAATTTAATCCTAAAATAAA
1 TTTAAATTTAAAATAAATTTAAATTTGAAAACAAATTTAAACCTAAAATAAA
1380348 TTTAAA
1 TTTAAA
1380354 ATGAGTTTGG
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.43
Consensus pattern (52 bp):
TTTAAATTTAAAATAAATTTAAATTTGAAAACAAATTTAAACCTAAAATAAA
Found at i:1380332 original size:35 final size:35
Alignment explanation
Indices: 1380244--1380353 Score: 120
Period size: 35 Copynumber: 3.2 Consensus size: 35
1380234 CTTTATTTAT
* *
1380244 TTTAAATTTAT-AATAATTTTAAATTTGAAAATAAA
1 TTTAAATTTTTAAATAAATTTAAATTT-AAAATAAA
*
1380279 TTTAAA--CTTAAATTAAATTTAAATTTAAAATAAA
1 TTTAAATTTTTAAA-TAAATTTAAATTTAAAATAAA
* *
1380313 TTTAAATTTTTAAACAAATTT-AATCCTAAAATAAA
1 TTTAAATTTTTAAATAAATTTAAAT-TTAAAATAAA
1380348 TTTAAA
1 TTTAAA
1380354 ATGAGTTTGG
Statistics
Matches: 64, Mismatches: 6, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
33 1 0.02
34 19 0.30
35 39 0.61
36 5 0.08
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.43
Consensus pattern (35 bp):
TTTAAATTTTTAAATAAATTTAAATTTAAAATAAA
Found at i:1381176 original size:205 final size:205
Alignment explanation
Indices: 1380746--1381539 Score: 1191
Period size: 205 Copynumber: 3.9 Consensus size: 205
1380736 TTTTATCCAT
* * * * * * *
1380746 TTCTCTGTGTTTCATTAGGAAGACGGATTTGGTTCACTTCTCCGTATCTCATCAGGGAGCTAACC
1 TTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACC
* * * *
1380811 ACTTTATTGCTTCGACCTGCTTCTCAGTGTCTCATCAAGAAGCTGGGGTTCGAAGATTTGCTCAC
66 -CTTTATTGCTTCGCCCTGCTTCTCCGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCAC
1380876 ATCGGGCGTGAGTTTGATTTGG--T-CTTCTCAGTATCTCATCAGGAAGATGACTGCGTCGTTTG
130 ATCGGGCGTGAGTTTGATTTGGTCTCCTTCTCAGTATCTCATCAGGAAGATGACTGCGTCGTTTG
1380938 TTTCAATTCGC
195 TTTCAATTCGC
* *
1380949 TTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATTAGGAAACTAACC
1 TTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACC
** * *
1381014 CTTTATTGCTTCGCCCTGCTTCTCCGTATCTCATCAGGAAGCTAAGGTTCGAAGATTTTCTTACA
66 CTTTATTGCTTCGCCCTGCTTCTCCGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACA
* * *
1381079 TCGGGCGTGAGTTTGATTTGTTCTTCTTCTCAGTATCTCATCAGGAAGATGACTGCATCGTTTGT
131 TCGGGCGTGAGTTTGATTTGGTCTCCTTCTCAGTATCTCATCAGGAAGATGACTGCGTCGTTTGT
1381144 TTCAATTCGC
196 TTCAATTCGC
* * * *
1381154 TCCTCTATATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAATATCTCATCTGGAAGCTAACC
1 TTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACC
* * * *
1381219 CTTTATTGCTTTGCGCTGCTTCTCGGTATCTCATCAGGAAGCT-GGGTTCAAAGATTTGCTCACA
66 CTTTATTGCTTCGCCCTGCTTCTCCGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACA
** * *
1381283 TCGGGCGTGAAATTGATTTGGTCTCCTTCTCAGTATCTCATCGGGAAGATGATTGCGTCGTTTGT
131 TCGGGCGTGAGTTTGATTTGGTCTCCTTCTCAGTATCTCATCAGGAAGATGACTGCGTCGTTTGT
1381348 TTCAATTCGC
196 TTCAATTCGC
* * *
1381358 TTCTCTGTATCTCATCAAGAAGAAGAATTTGGTCCACTTCTTAGTATCTCATCAGGAAGCTAACC
1 TTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACC
* * *
1381423 TTTTATTGCTTCACCTTGCTTCTCCGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACA
66 CTTTATTGCTTCGCCCTGCTTCTCCGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACA
* *
1381488 TCGGGCGTGAGTTTGATTTGGTCTCCTTCTCAGTATCTCATCAAGAAAATGA
131 TCGGGCGTGAGTTTGATTTGGTCTCCTTCTCAGTATCTCATCAGGAAGATGA
1381540 TCGTATCGCT
Statistics
Matches: 529, Mismatches: 58, Indels: 6
0.89 0.10 0.01
Matches are distributed among these distances:
202 77 0.15
203 56 0.11
204 181 0.34
205 215 0.41
ACGTcount: A:0.21, C:0.23, G:0.20, T:0.35
Consensus pattern (205 bp):
TTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACC
CTTTATTGCTTCGCCCTGCTTCTCCGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACA
TCGGGCGTGAGTTTGATTTGGTCTCCTTCTCAGTATCTCATCAGGAAGATGACTGCGTCGTTTGT
TTCAATTCGC
Found at i:1381362 original size:409 final size:408
Alignment explanation
Indices: 1380757--1381539 Score: 1221
Period size: 409 Copynumber: 1.9 Consensus size: 408
1380747 TCTCTGTGTT
* * * ** *
1380757 TCATTAGGAAGACGGATTTGGTTCACTTCTCCGTATCTCATCAGGGAGCTAACCACTTTATTGCT
1 TCATCAGGAAGACGAATTTGGTCCACTTCTCAATATCTCATCAGGAAGCTAACCACTTTATTGCT
* *
1380822 TCGACCTGCTTCTCAGTGTCTCATCAAGAAGCTGGGGTTCGAAGATTTGCTCACATCGGGCGTGA
66 TCGACCTGCTTCTCAGTATCTCATCAAGAAGCTGGGGTTCAAAGATTTGCTCACATCGGGCGTGA
**
1380887 GTTTGATTTGGTCTTCTCAGTATCTCATCAGGAAGATGACTGCGTCGTTTGTTTCAATTCGCTTC
131 AATTGATTTGGTCTTCTCAGTATCTCATCAGGAAGATGACTGCGTCGTTTGTTTCAATTCGCTTC
* * *
1380952 TCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATTAGGAAACTAACCCTT
196 TCTGTATCTCATCAAGAAGAAGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAACTAACCCTT
* * *
1381017 TATTGCTTCGCCCTGCTTCTCCGTATCTCATCAGGAAGCTAAGGTTCGAAGATTTTCTTACATCG
261 TATTGCTTCACCCTGCTTCTCCGTATCTCATCAGGAAGCTAAGGTTCGAAGATTTGCTCACATCG
* * * *
1381082 GGCGTGAGTTTGATTTGTTCTTCTTCTCAGTATCTCATCAGGAAGATGACTGCATCGTTTGTTTC
326 GGCGTGAGTTTGATTTGGTCTCCTTCTCAGTATCTCATCAAGAAAATGACTGCATCGTTTGTTTC
1381147 AATTCGCTCCTCTATATC
391 AATTCGCTCCTCTATATC
*
1381165 TCATCAGGAAGACGAATTTGGTCCACTTCTCAATATCTCATCTGGAAGCTAACC-CTTTATTGCT
1 TCATCAGGAAGACGAATTTGGTCCACTTCTCAATATCTCATCAGGAAGCTAACCACTTTATTGCT
* * *
1381229 TTG-CGCTGCTTCTCGGTATCTCATCAGGAAGCT-GGGTTCAAAGATTTGCTCACATCGGGCGTG
66 TCGAC-CTGCTTCTCAGTATCTCATCAAGAAGCTGGGGTTCAAAGATTTGCTCACATCGGGCGTG
* *
1381292 AAATTGATTTGGTCTCCTTCTCAGTATCTCATCGGGAAGATGATTGCGTCGTTTGTTTCAATTCG
130 AAATTGATTTGG--T-CTTCTCAGTATCTCATCAGGAAGATGACTGCGTCGTTTGTTTCAATTCG
* *
1381357 CTTCTCTGTATCTCATCAAGAAGAAGAATTTGGTCCACTTCTTAGTATCTCATCAGGAAGCTAAC
192 CTTCTCTGTATCTCATCAAGAAGAAGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAACTAAC
* * **
1381422 CTTTTATTGCTTCACCTTGCTTCTCCGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCAC
257 CCTTTATTGCTTCACCCTGCTTCTCCGTATCTCATCAGGAAGCTAAGGTTCGAAGATTTGCTCAC
1381487 ATCGGGCGTGAGTTTGATTTGGTCTCCTTCTCAGTATCTCATCAAGAAAATGA
322 ATCGGGCGTGAGTTTGATTTGGTCTCCTTCTCAGTATCTCATCAAGAAAATGA
1381540 TCGTATCGCT
Statistics
Matches: 339, Mismatches: 32, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
406 40 0.12
407 37 0.11
408 48 0.14
409 214 0.63
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.35
Consensus pattern (408 bp):
TCATCAGGAAGACGAATTTGGTCCACTTCTCAATATCTCATCAGGAAGCTAACCACTTTATTGCT
TCGACCTGCTTCTCAGTATCTCATCAAGAAGCTGGGGTTCAAAGATTTGCTCACATCGGGCGTGA
AATTGATTTGGTCTTCTCAGTATCTCATCAGGAAGATGACTGCGTCGTTTGTTTCAATTCGCTTC
TCTGTATCTCATCAAGAAGAAGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAACTAACCCTT
TATTGCTTCACCCTGCTTCTCCGTATCTCATCAGGAAGCTAAGGTTCGAAGATTTGCTCACATCG
GGCGTGAGTTTGATTTGGTCTCCTTCTCAGTATCTCATCAAGAAAATGACTGCATCGTTTGTTTC
AATTCGCTCCTCTATATC
Found at i:1393049 original size:96 final size:96
Alignment explanation
Indices: 1392872--1393056 Score: 223
Period size: 96 Copynumber: 1.9 Consensus size: 96
1392862 GAAAAGGATG
* ** * * * *
1392872 TTCGATTATCTCGATTTGACGAAAGGTTGCACCTAGTAAGTTAAGGCGTAAATTTTTAGAATCGG
1 TTCGATTATCTCGATTTGAAGAAAAATTACACCTAGTAAGTTAAGCCGCAAATTTTGAGAATCGG
* *
1392937 AGATAAGGACACATTGCCTCGATTATGGGTA
66 AAATAAAGACACATTGCCTCGATTATGGGTA
*
1392968 TTCGATTATTTCGATTTGAAGAAAAATTACACCTAGTAAGTTAAGCCGCAAATTTTCGA-AACTC
1 TTCGATTATCTCGATTTGAAGAAAAATTACACCTAGTAAGTTAAGCCGCAAATTTT-GAGAA-TC
*
1393032 -GAAATAAAAGA-ATATTGCCTCGATT
64 GGAAAT-AAAGACACATTGCCTCGATT
1393057 TTATAGTTTT
Statistics
Matches: 75, Mismatches: 11, Indels: 6
0.82 0.12 0.07
Matches are distributed among these distances:
96 68 0.91
97 7 0.09
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.31
Consensus pattern (96 bp):
TTCGATTATCTCGATTTGAAGAAAAATTACACCTAGTAAGTTAAGCCGCAAATTTTGAGAATCGG
AAATAAAGACACATTGCCTCGATTATGGGTA
Found at i:1393389 original size:30 final size:30
Alignment explanation
Indices: 1393357--1393725 Score: 187
Period size: 30 Copynumber: 12.4 Consensus size: 30
1393347 GAAAGAGTGA
*
1393357 TTTTGAG-AGTTTCGTGGTCAAAAATAGAGA-
1 TTTTGAGAAGTTTCGAGGT-AAAAATAGA-AT
* *
1393387 TTTT-AG-AGGTTC-ATGGGTAAAAATGGAAT
1 TTTTGAGAAGTTTCGA--GGTAAAAATAGAAT
1393416 TTTTG-GAAGTTTCGAGGTTAAAAAT-GACAT
1 TTTTGAGAAGTTTCGAGG-TAAAAATAGA-AT
* *
1393446 TTTTG-GAAG-TTCGGGGGTAAAAATGGAAT
1 TTTTGAGAAGTTTC-GAGGTAAAAATAGAAT
*
1393475 TTTTGA-AAGTTTCGAGGTCAAAAATAGGA-
1 TTTTGAGAAGTTTCGAGGT-AAAAATAGAAT
*
1393504 TTTTCAGAAG-TTCGAGGGTAAAAATAGAAT
1 TTTTGAGAAGTTTCGA-GGTAAAAATAGAAT
**
1393534 TTTTG-GAAGTTTCG-GAGTCAAAAA-ATGGGT
1 TTTTGAGAAGTTTCGAG-GT-AAAAATA-GAAT
1393564 TTTTG-GAAG-TTCGAGGGTAAAAAT-GAAAT
1 TTTTGAGAAGTTTCGA-GGTAAAAATAG-AAT
* *
1393593 TTTTG-GAAGTTT-TAGGGTTAAAAATAGGAT
1 TTTTGAGAAGTTTCGA-GG-TAAAAATAGAAT
* * * * *
1393623 ATTTG-GAAG-TTCAGGGGTAAAAAAAAAAA
1 TTTTGAGAAGTTTC-GAGGTAAAAATAGAAT
* * *
1393652 TTTTG-GAAGTTTTGGGGTCAAAAATAGGATT
1 TTTTGAGAAGTTTCGAGGT-AAAAATA-GAAT
1393683 TTTTG-GAAGTTT-GAGGGTAAAAATAGAAAT
1 TTTTGAGAAGTTTCGA-GGTAAAAATAG-AAT
1393713 TTTTG-GACAGTTT
1 TTTTGAGA-AGTTT
1393726 AGGGACCTTT
Statistics
Matches: 272, Mismatches: 32, Indels: 69
0.73 0.09 0.18
Matches are distributed among these distances:
28 3 0.01
29 121 0.44
30 124 0.46
31 24 0.09
ACGTcount: A:0.35, C:0.04, G:0.27, T:0.34
Consensus pattern (30 bp):
TTTTGAGAAGTTTCGAGGTAAAAATAGAAT
Found at i:1393428 original size:59 final size:56
Alignment explanation
Indices: 1393364--1393725 Score: 339
Period size: 59 Copynumber: 6.1 Consensus size: 56
1393354 TGATTTTGAG
* *
1393364 AGTTTCGTGGTCAAAAATAGAGATTTTAGAGGTTCATGGGTAAAAATGGAATTTTTGGA
1 AGTTTCG-GGTCAAAAATAG-GATTTTGGAAGTTCA-GGGTAAAAATGGAATTTTTGGA
* * * *
1393423 AGTTTCGAGGTTAAAAAT-GACATTTTTGGAAGTTCGGGGGTAAAAATGGAATTTTTGAA
1 AGTTTCG-GGTCAAAAATAG-GA-TTTTGGAAGTTC-AGGGTAAAAATGGAATTTTTGGA
* *
1393482 AGTTTCGAGGTCAAAAATAGGATTTTCAGAAGTTCGAGGGTAAAAATAGAATTTTTGGA
1 AGTTTCG-GGTCAAAAATAGGATTTT-GGAAGTTC-AGGGTAAAAATGGAATTTTTGGA
* * *
1393541 AGTTTCGGAGTCAAAAAATGGGTTTTTGGAAGTTCGAGGGTAAAAATGAAATTTTTGGA
1 AGTTTCGG-GTC-AAAAATAGGATTTTGGAAGTTC-AGGGTAAAAATGGAATTTTTGGA
* * *** *
1393600 AGTTTTAGGGTTAAAAATAGGATATTTGGAAGTTCAGGGGTAAAAAAAAAAATTTTGGA
1 AG-TTTCGGGTCAAAAATAGGAT-TTTGGAAGTTCA-GGGTAAAAATGGAATTTTTGGA
* * *
1393659 AGTTTTGGGGTCAAAAATAGGATTTTTTGGAAGTTTGAGGGTAAAAATAGAAATTTTTGGA
1 AG-TTTCGGGTCAAAAATAGGA--TTTTGGAAG-TTCAGGGTAAAAAT-GGAATTTTTGGA
1393720 CAGTTT
1 -AGTTT
1393726 AGGGACCTTT
Statistics
Matches: 258, Mismatches: 31, Indels: 26
0.82 0.10 0.08
Matches are distributed among these distances:
58 18 0.07
59 186 0.72
60 35 0.14
61 17 0.07
62 2 0.01
ACGTcount: A:0.36, C:0.04, G:0.27, T:0.33
Consensus pattern (56 bp):
AGTTTCGGGTCAAAAATAGGATTTTGGAAGTTCAGGGTAAAAATGGAATTTTTGGA
Found at i:1393486 original size:118 final size:113
Alignment explanation
Indices: 1393357--1393717 Score: 398
Period size: 118 Copynumber: 3.0 Consensus size: 113
1393347 GAAAGAGTGA
* * *
1393357 TTTTGAGAGTTTCGTGGTCAAAAATAGAGATTTTAGAGGTTCATGGGTAAAAATGGAATTTTTGG
1 TTTTGAAAGTTTCG-GGTCAAAAATAG-GATTTTAGAAGTTCA-GGGTAAAAATAGAATTTTTGG
* * *
1393422 AAGTTTCGAGGTTAAAAATGACATTTTTGGAAGTTCGGGGGTAAAAATGGAAT
63 AAGTTTCG-GGTAAAAAATGA-ATTTTTGGAAGTTCGAGGGTAAAAATGAAAT
1393475 TTTTGAAAGTTTCGAGGTCAAAAATAGGATTTTCAGAAGTTCGAGGGTAAAAATAGAATTTTTGG
1 TTTTGAAAGTTTCG-GGTCAAAAATAGGATTTT-AGAAGTTC-AGGGTAAAAATAGAATTTTTGG
**
1393540 AAGTTTCGGAGTCAAAAAATGGGTTTTTGGAAGTTCGAGGGTAAAAATGAAAT
63 AAGTTTCGG-GT-AAAAAATGAATTTTTGGAAGTTCGAGGGTAAAAATGAAAT
* * * * * * *
1393593 TTTTGGAAGTTTTAGGGTTAAAAATAGGATATTTGGAAGTTCAGGGGTAAAAAAAAAAATTTTGG
1 TTTTGAAAG-TTTCGGGTCAAAAATAGGAT-TTTAGAAGTTCA-GGGTAAAAATAGAATTTTTGG
* * * *
1393658 AAGTTTTGGGGTCAAAAATAGGATTTTTTGGAAGTTTGAGGGTAAAAATAGAAAT
63 AAG-TTTCGGGT-AAAAA-ATGAATTTTTGGAAGTTCGAGGGTAAAAAT-GAAAT
1393713 TTTTG
1 TTTTG
1393718 GACAGTTTAG
Statistics
Matches: 212, Mismatches: 21, Indels: 18
0.84 0.08 0.07
Matches are distributed among these distances:
117 8 0.04
118 148 0.70
119 46 0.22
120 10 0.05
ACGTcount: A:0.35, C:0.04, G:0.27, T:0.34
Consensus pattern (113 bp):
TTTTGAAAGTTTCGGGTCAAAAATAGGATTTTAGAAGTTCAGGGTAAAAATAGAATTTTTGGAAG
TTTCGGGTAAAAAATGAATTTTTGGAAGTTCGAGGGTAAAAATGAAAT
Found at i:1393656 original size:29 final size:29
Alignment explanation
Indices: 1393564--1393662 Score: 85
Period size: 29 Copynumber: 3.4 Consensus size: 29
1393554 AAAAATGGGT
** *
1393564 TTTTGGAAGTTC-GAGGGTAAAAATGAAAT
1 TTTTGGAAGTTCAG-GGGTAAAAAAAAAAA
* * * **
1393593 TTTTGGAAGTTTTA-GGGTTAAAAATAGGA
1 TTTTGGAAG-TTCAGGGGTAAAAAAAAAAA
1393622 TATTTGGAAGTTCAGGGGTAAAAAAAAAAA
1 T-TTTGGAAGTTCAGGGGTAAAAAAAAAAA
1393652 TTTTGGAAGTT
1 TTTTGGAAGTT
1393663 TTGGGGTCAA
Statistics
Matches: 54, Mismatches: 12, Indels: 8
0.73 0.16 0.11
Matches are distributed among these distances:
29 32 0.59
30 22 0.41
ACGTcount: A:0.38, C:0.02, G:0.26, T:0.33
Consensus pattern (29 bp):
TTTTGGAAGTTCAGGGGTAAAAAAAAAAA
Found at i:1394765 original size:21 final size:21
Alignment explanation
Indices: 1394735--1394778 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
1394725 CCTTTTTTTT
* *
1394735 TATTATTAATATTTTTATTAA
1 TATTAATAATAATTTTATTAA
1394756 TATTAATAATAATTTTATTAA
1 TATTAATAATAATTTTATTAA
1394777 TA
1 TA
1394779 CCTATTAATG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TATTAATAATAATTTTATTAA
Found at i:1395513 original size:18 final size:17
Alignment explanation
Indices: 1395475--1395550 Score: 73
Period size: 18 Copynumber: 4.4 Consensus size: 17
1395465 CTTTATTTAT
* *
1395475 TTTAAATTTACAATAAT
1 TTTAAATTTAAAATAAA
1395492 TTTAAATTTGAAAATAAA
1 TTTAAATTT-AAAATAAA
* *
1395510 TTTAAATTTTTAAACAAA
1 TTTAAA-TTTAAAATAAA
*
1395528 TTT-AATCCTAAAATAAA
1 TTTAAAT-TTAAAATAAA
1395545 TTTAAA
1 TTTAAA
1395551 ATGAATTTGG
Statistics
Matches: 48, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
16 1 0.02
17 21 0.44
18 23 0.48
19 3 0.06
ACGTcount: A:0.51, C:0.05, G:0.01, T:0.42
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:1395547 original size:17 final size:17
Alignment explanation
Indices: 1395502--1395549 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
1395492 TTTAAATTTG
**
1395502 AAAATAAATTTAAATTTT
1 AAAATAAATTT-AATCCT
* *
1395520 TAAACAAATTTAATCCT
1 AAAATAAATTTAATCCT
1395537 AAAATAAATTTAA
1 AAAATAAATTTAA
1395550 AATGAATTTG
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
17 15 0.62
18 9 0.38
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (17 bp):
AAAATAAATTTAATCCT
Found at i:1401889 original size:22 final size:22
Alignment explanation
Indices: 1401861--1401947 Score: 93
Period size: 23 Copynumber: 3.9 Consensus size: 22
1401851 AAAAAACAAA
*
1401861 ATGAACAGTGAGATTCTCTAGC
1 ATGAACAGTGATATTCTCTAGC
* * *
1401883 ATGAACATTGCTATTCTCTGGC
1 ATGAACAGTGATATTCTCTAGC
* *
1401905 ATGAATAGTAAATATTCTCTAGC
1 ATGAACAGT-GATATTCTCTAGC
*
1401928 ATAAACAGTGAATATTCTCT
1 ATGAACAGTG-ATATTCTCT
1401948 TGTAATTTGT
Statistics
Matches: 51, Mismatches: 12, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
22 25 0.49
23 26 0.51
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Consensus pattern (22 bp):
ATGAACAGTGATATTCTCTAGC
Found at i:1404521 original size:51 final size:51
Alignment explanation
Indices: 1404440--1404625 Score: 273
Period size: 51 Copynumber: 3.6 Consensus size: 51
1404430 GTAATAAACG
*
1404440 AAAGAGTTCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
1 AAAG-GTTCGATGACTAAGTGTCATCGTGAGTAAATAAATCCTTTACGGATT
*
1404492 AAAGGTTCGATGACTAAGTGTTATCGTGAGTAAATAAATCCTTTACGGATT
1 AAAGGTTCGATGACTAAGTGTCATCGTGAGTAAATAAATCCTTTACGGATT
* * * *
1404543 AAAGGTTCGATGACTAAGTGTCATCGTGAATAAATAAATCCATGACGAATT
1 AAAGGTTCGATGACTAAGTGTCATCGTGAGTAAATAAATCCTTTACGGATT
* * * *
1404594 AAAGGTCCGATGACTCAGTGTTATCGTAAGTA
1 AAAGGTTCGATGACTAAGTGTCATCGTGAGTA
1404626 TATGAATTCC
Statistics
Matches: 122, Mismatches: 12, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
51 118 0.97
52 4 0.03
ACGTcount: A:0.34, C:0.13, G:0.22, T:0.30
Consensus pattern (51 bp):
AAAGGTTCGATGACTAAGTGTCATCGTGAGTAAATAAATCCTTTACGGATT
Found at i:1405603 original size:51 final size:51
Alignment explanation
Indices: 1405527--1405806 Score: 294
Period size: 51 Copynumber: 5.4 Consensus size: 51
1405517 AAGAGTCTGT
**
1405527 TGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTAAAGGAACGA
1 TGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTAAAGGTCCGA
*
1405578 TGACTAAGTGTCATCGTCG-GTAAATGAATCCTTTACGGGTTAAAGGTCCGA
1 TGACTAAGTGTCATCGT-GAGTAAATGAATCCTTTACGGATTAAAGGTCCGA
* * * * **
1405629 TGACTAAGTGTCATCGTGAGTGAATGTATCCATGACAAATTAAAGGTCCGA
1 TGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTAAAGGTCCGA
* * * * *
1405680 TGACTAAGTGTCATCATGAGTAAATAAATCCATGACGAATTAAAGGTCCGA
1 TGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTAAAGGTCCGA
* * * * * ** **
1405731 TGACTCATTGTCATTGTGAGTATATGAATTCCTATACGGAACAAAGGGGTTTGA
1 TGACTAAGTGTCATCGTGAGTAAATGAA-TCCTTTACGGATTAAA--GGTCCGA
1405785 TGACTATA-TGTCATCGTGAGTA
1 TGACTA-AGTGTCATCGTGAGTA
1405807 TTAAATGAAA
Statistics
Matches: 192, Mismatches: 31, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
50 1 0.01
51 156 0.81
52 11 0.06
54 23 0.12
55 1 0.01
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.29
Consensus pattern (51 bp):
TGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTAAAGGTCCGA
Found at i:1409522 original size:18 final size:18
Alignment explanation
Indices: 1409499--1409538 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
1409489 CAAAAATTAC
1409499 AAGTCTT-AAAATAAATCA
1 AAGTCTTGAAAA-AAATCA
*
1409517 AAGTCTTGAAAAAAATTA
1 AAGTCTTGAAAAAAATCA
1409535 AAGT
1 AAGT
1409539 TCAATCGTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.55, C:0.07, G:0.10, T:0.28
Consensus pattern (18 bp):
AAGTCTTGAAAAAAATCA
Found at i:1415279 original size:17 final size:17
Alignment explanation
Indices: 1415257--1415289 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1415247 TATAGGATAT
1415257 TATTTATATTTA-ATTTG
1 TATTTA-ATTTAGATTTG
1415274 TATTTAATTTAGATTT
1 TATTTAATTTAGATTT
1415290 ATCTTTTAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (17 bp):
TATTTAATTTAGATTTG
Found at i:1420434 original size:13 final size:13
Alignment explanation
Indices: 1420416--1420443 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1420406 TGGTAAGTTT
1420416 GGGAATGAGTTAA
1 GGGAATGAGTTAA
1420429 GGGAATGAGTTAA
1 GGGAATGAGTTAA
1420442 GG
1 GG
1420444 TATGTTATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.36, C:0.00, G:0.43, T:0.21
Consensus pattern (13 bp):
GGGAATGAGTTAA
Found at i:1422376 original size:31 final size:31
Alignment explanation
Indices: 1422308--1422387 Score: 108
Period size: 32 Copynumber: 2.5 Consensus size: 31
1422298 TAATACTATT
*
1422308 TTTGGCCCTTGTACTACAGTAAAAAATTTTAC
1 TTTGGCCCTTGTACTATAGT-AAAAATTTTAC
*
1422340 TTTGGCCCTTGTACTATAGT-GAAATTTTCAC
1 TTTGGCCCTTGTACTATAGTAAAAATTTT-AC
*
1422371 TTTGGCCTTTGTACTAT
1 TTTGGCCCTTGTACTAT
1422388 TTTTCCGGTC
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
30 7 0.16
31 18 0.41
32 19 0.43
ACGTcount: A:0.24, C:0.19, G:0.15, T:0.42
Consensus pattern (31 bp):
TTTGGCCCTTGTACTATAGTAAAAATTTTAC
Found at i:1423117 original size:20 final size:20
Alignment explanation
Indices: 1423092--1423130 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1423082 AATCTATTTC
*
1423092 AAATTCACTAAAAAATCATT
1 AAATTCACAAAAAAATCATT
*
1423112 AAATTCCCAAAAAAATCAT
1 AAATTCACAAAAAAATCAT
1423131 AATTTTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.56, C:0.18, G:0.00, T:0.26
Consensus pattern (20 bp):
AAATTCACAAAAAAATCATT
Found at i:1423346 original size:21 final size:22
Alignment explanation
Indices: 1423311--1423356 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
1423301 TTAATTTTAG
* *
1423311 TTTTCTGAGAAAATTTTTATAA
1 TTTTATGAGAAAATTTTTAGAA
1423333 TTTTATGA-AAAATTTTTAGAA
1 TTTTATGAGAAAATTTTTAGAA
1423354 TTT
1 TTT
1423357 GATGGTATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 15 0.68
22 7 0.32
ACGTcount: A:0.37, C:0.02, G:0.09, T:0.52
Consensus pattern (22 bp):
TTTTATGAGAAAATTTTTAGAA
Found at i:1426087 original size:19 final size:20
Alignment explanation
Indices: 1426063--1426107 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 20
1426053 GGTAAAAAAA
1426063 TCAACGATCAA-AGTCAAAG
1 TCAACGATCAACAGTCAAAG
1426082 TCAACGATCAACGAGTCAAAG
1 TCAACGATCAAC-AGTCAAAG
1426103 TCAAC
1 TCAAC
1426108 TCGAGTCAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 11 0.46
21 13 0.54
ACGTcount: A:0.44, C:0.24, G:0.16, T:0.16
Consensus pattern (20 bp):
TCAACGATCAACAGTCAAAG
Found at i:1430028 original size:19 final size:20
Alignment explanation
Indices: 1430004--1430048 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 20
1429994 GGTAAAAAAA
1430004 TCAACGATCAA-AGTCAAAG
1 TCAACGATCAACAGTCAAAG
*
1430023 TCAACGATCAACGGGTCAAAG
1 TCAACGATCAAC-AGTCAAAG
1430044 TCAAC
1 TCAAC
1430049 TCGAGTAAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 11 0.48
21 12 0.52
ACGTcount: A:0.42, C:0.24, G:0.18, T:0.16
Consensus pattern (20 bp):
TCAACGATCAACAGTCAAAG
Found at i:1436677 original size:14 final size:15
Alignment explanation
Indices: 1436645--1436677 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1436635 AAAATAACCA
1436645 AATTTTATTATAAAT
1 AATTTTATTATAAAT
*
1436660 AATTTTATT-TATAT
1 AATTTTATTATAAAT
1436674 AATT
1 AATT
1436678 AAACATTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
AATTTTATTATAAAT
Found at i:1439643 original size:21 final size:22
Alignment explanation
Indices: 1439598--1439647 Score: 68
Period size: 21 Copynumber: 2.3 Consensus size: 22
1439588 CCAAATAAAA
1439598 CCAAACCCTTAAAAACCCAAAC
1 CCAAACCCTTAAAAACCCAAAC
*
1439620 CCAAACCCTTTAAAAA-TC-AAC
1 CCAAACCC-TTAAAAACCCAAAC
1439641 CCAAACC
1 CCAAACC
1439648 AAACCCACGT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 10 0.38
22 9 0.35
23 7 0.27
ACGTcount: A:0.48, C:0.40, G:0.00, T:0.12
Consensus pattern (22 bp):
CCAAACCCTTAAAAACCCAAAC
Found at i:1439786 original size:21 final size:21
Alignment explanation
Indices: 1439762--1439821 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
1439752 GACTGACCCA
1439762 TTGACCGA-TGACCGTTGATAG
1 TTGACC-ATTGACCGTTGATAG
* *
1439783 TTGACCATTGATCGTTGATCG
1 TTGACCATTGACCGTTGATAG
*
1439804 TTGA-CAGTTGATCGTTGA
1 TTGACCA-TTGACCGTTGA
1439822 CCATTTACCG
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.09
21 32 0.91
ACGTcount: A:0.22, C:0.17, G:0.27, T:0.35
Consensus pattern (21 bp):
TTGACCATTGACCGTTGATAG
Found at i:1439787 original size:14 final size:14
Alignment explanation
Indices: 1439770--1439821 Score: 59
Period size: 14 Copynumber: 3.7 Consensus size: 14
1439760 CATTGACCGA
1439770 TGACCGTTGATAGT
1 TGACCGTTGATAGT
* *
1439784 TGACCATTGATCGT
1 TGACCGTTGATAGT
* *
1439798 TGATCGTTGACAGT
1 TGACCGTTGATAGT
*
1439812 TGATCGTTGA
1 TGACCGTTGA
1439822 CCATTTACCG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 32 1.00
ACGTcount: A:0.21, C:0.15, G:0.27, T:0.37
Consensus pattern (14 bp):
TGACCGTTGATAGT
Found at i:1445575 original size:14 final size:14
Alignment explanation
Indices: 1445556--1445584 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1445546 ACCAGATATT
1445556 GTTCACGAGTCTAA
1 GTTCACGAGTCTAA
1445570 GTTCACGAGTCTAA
1 GTTCACGAGTCTAA
1445584 G
1 G
1445585 GAGACTATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.28
Consensus pattern (14 bp):
GTTCACGAGTCTAA
Found at i:1446896 original size:22 final size:21
Alignment explanation
Indices: 1446867--1446916 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 21
1446857 TGACCCAATA
1446867 AAACCAAACCC-TTAAAAATCC
1 AAACCAAACCCTTTAAAAAT-C
1446888 AAACTCAAACCCTTTAAAAATC
1 AAAC-CAAACCCTTTAAAAATC
1446910 AAACCAA
1 AAACCAA
1446917 GCTAAACCAG
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
21 7 0.26
22 12 0.44
23 8 0.30
ACGTcount: A:0.54, C:0.30, G:0.00, T:0.16
Consensus pattern (21 bp):
AAACCAAACCCTTTAAAAATC
Found at i:1447039 original size:21 final size:21
Alignment explanation
Indices: 1447013--1447074 Score: 88
Period size: 21 Copynumber: 3.0 Consensus size: 21
1447003 AAACCCGTTG
*
1447013 ACAGTTGACCGTTGACCATTA
1 ACAGTTGATCGTTGACCATTA
* *
1447034 ACAGTTGATCGTTGACCGTTG
1 ACAGTTGATCGTTGACCATTA
*
1447055 ACCGTTGATCGTTGACCATT
1 ACAGTTGATCGTTGACCATT
1447075 TGTCGTTGAC
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.32
Consensus pattern (21 bp):
ACAGTTGATCGTTGACCATTA
Found at i:1447067 original size:7 final size:7
Alignment explanation
Indices: 1447007--1447071 Score: 76
Period size: 7 Copynumber: 9.3 Consensus size: 7
1446997 TTACCTAAAC
1447007 CCGTTGA
1 CCGTTGA
*
1447014 CAGTTGA
1 CCGTTGA
1447021 CCGTTGA
1 CCGTTGA
* *
1447028 CCATTAA
1 CCGTTGA
*
1447035 CAGTTGA
1 CCGTTGA
*
1447042 TCGTTGA
1 CCGTTGA
1447049 CCGTTGA
1 CCGTTGA
1447056 CCGTTGA
1 CCGTTGA
*
1447063 TCGTTGA
1 CCGTTGA
1447070 CC
1 CC
1447072 ATTTGTCGTT
Statistics
Matches: 46, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
7 46 1.00
ACGTcount: A:0.20, C:0.25, G:0.25, T:0.31
Consensus pattern (7 bp):
CCGTTGA
Found at i:1447080 original size:14 final size:14
Alignment explanation
Indices: 1447008--1447084 Score: 59
Period size: 14 Copynumber: 5.5 Consensus size: 14
1446998 TACCTAAACC
* *
1447008 CGTTGACAGTTGAC
1 CGTTGACCGTTGAT
* *
1447022 CGTTGACCATT-AA
1 CGTTGACCGTTGAT
* *
1447035 CAGTTGATCGTTGAC
1 C-GTTGACCGTTGAT
1447050 CGTTGACCGTTGAT
1 CGTTGACCGTTGAT
*
1447064 CGTTGACCATTTG-T
1 CGTTGACC-GTTGAT
1447078 CGTTGAC
1 CGTTGAC
1447085 TTTGACTTTG
Statistics
Matches: 51, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
13 2 0.04
14 44 0.86
15 5 0.10
ACGTcount: A:0.19, C:0.22, G:0.25, T:0.34
Consensus pattern (14 bp):
CGTTGACCGTTGAT
Found at i:1449992 original size:12 final size:12
Alignment explanation
Indices: 1449977--1450003 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1449967 AGTGGTTGTT
1449977 TAAGAACAAAAC
1 TAAGAACAAAAC
1449989 TAAGAACAAAAC
1 TAAGAACAAAAC
1450001 TAA
1 TAA
1450004 CCCTGATAGG
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:0.67, C:0.15, G:0.07, T:0.11
Consensus pattern (12 bp):
TAAGAACAAAAC
Found at i:1454975 original size:90 final size:87
Alignment explanation
Indices: 1454860--1455041 Score: 229
Period size: 90 Copynumber: 2.1 Consensus size: 87
1454850 TTTTCTCAGA
* * *
1454860 TACTTGAACTTTTAAAATGCATCAAAAAAGCCCTCAAACTTTTTCAGAAAAAGCAATTAAGCCCC
1 TACTTAAACTTTTAAAATGCATCAAAAAA-CCCTCAAACTTTTTCA-AAAAAACAATTAAACCCC
* * *
1454925 TGCTTTTATTTTACACTCAATTGGG
64 TGATTTT-TTTTACACACAATTGAG
* * * * *
1454950 TACTTAAACTTTTAAAATGCTTCAAAAAATCCTCAAATTTTTTGAAAAAAACAATTAAACCCTTG
1 TACTTAAACTTTTAAAATGCATCAAAAAACCCTCAAACTTTTTCAAAAAAACAATTAAACCCCTG
*
1455015 ATTTTTTTTGCACACAATTGAG
66 ATTTTTTTTACACACAATTGAG
1455037 TACTT
1 TACTT
1455042 GTACCGCTCT
Statistics
Matches: 80, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
87 19 0.24
88 21 0.26
89 13 0.16
90 27 0.34
ACGTcount: A:0.37, C:0.19, G:0.09, T:0.35
Consensus pattern (87 bp):
TACTTAAACTTTTAAAATGCATCAAAAAACCCTCAAACTTTTTCAAAAAAACAATTAAACCCCTG
ATTTTTTTTACACACAATTGAG
Found at i:1455180 original size:16 final size:17
Alignment explanation
Indices: 1455158--1455239 Score: 62
Period size: 16 Copynumber: 4.8 Consensus size: 17
1455148 CATTCTATAA
*
1455158 ATTTTTTCTAATTTTAT
1 ATTTTTTATAATTTTAT
*
1455175 -TTTTTTATATTTTTAT
1 ATTTTTTATAATTTTAT
*
1455191 A-TTTTTAT-ATTTTTT
1 ATTTTTTATAATTTTAT
* *
1455206 ATTAAAATTTAATATTTTTAT
1 ATT----TTTTATAATTTTAT
1455227 ATTTTTTATAATT
1 ATTTTTTATAATT
1455240 AGGGGTGACT
Statistics
Matches: 49, Mismatches: 9, Indels: 14
0.68 0.12 0.19
Matches are distributed among these distances:
15 6 0.12
16 22 0.45
17 8 0.16
20 5 0.10
21 8 0.16
ACGTcount: A:0.28, C:0.01, G:0.00, T:0.71
Consensus pattern (17 bp):
ATTTTTTATAATTTTAT
Found at i:1455188 original size:24 final size:25
Alignment explanation
Indices: 1455160--1455236 Score: 75
Period size: 28 Copynumber: 3.0 Consensus size: 25
1455150 TTCTATAAAT
*
1455160 TTTTTCTAATTTTAT-TTTTTTATA
1 TTTTTATAATTTTATATTTTTTATA
*
1455184 TTTTTATATTTTTATATTTTTTATTAAA
1 TTTTTATAATTTTATATTTTTTA-T--A
* * *
1455212 ATTTAATATTTTTATATTTTTTATA
1 TTTTTATAATTTTATATTTTTTATA
1455237 ATTAGGGGTG
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
24 13 0.29
25 8 0.18
26 1 0.02
27 1 0.02
28 22 0.49
ACGTcount: A:0.27, C:0.01, G:0.00, T:0.71
Consensus pattern (25 bp):
TTTTTATAATTTTATATTTTTTATA
Found at i:1455230 original size:8 final size:8
Alignment explanation
Indices: 1455169--1455232 Score: 67
Period size: 8 Copynumber: 7.5 Consensus size: 8
1455159 TTTTTTCTAA
*
1455169 TTTTATTT
1 TTTTATAT
1455177 TTTTATAT
1 TTTTATAT
1455185 TTTTATAT
1 TTTTATAT
1455193 TTTTATAT
1 TTTTATAT
1455201 TTTT-TAT
1 TTTTATAT
1455208 TAAAATTTAATAT
1 T----TTT-ATAT
1455221 TTTTATAT
1 TTTTATAT
1455229 TTTT
1 TTTT
1455233 TATAATTAGG
Statistics
Matches: 49, Mismatches: 1, Indels: 12
0.79 0.02 0.19
Matches are distributed among these distances:
7 4 0.08
8 35 0.71
9 3 0.06
11 3 0.06
13 4 0.08
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (8 bp):
TTTTATAT
Found at i:1455505 original size:89 final size:89
Alignment explanation
Indices: 1455360--1455573 Score: 254
Period size: 89 Copynumber: 2.4 Consensus size: 89
1455350 AATCGGGGGC
* *
1455360 TTAATTGCTTTTTTTGAAAACGTTTAAGGGAC-TTTTTGATACATTTTGAAAATTCAAGTACCC-
1 TTAATTGC-TTTTTTGAAAAAGTTTGAGGG-CTTTTTTGATACATTTTGAAAATTCAAGTACCCA
** * **
1455423 AATAGGGTGCAGAATAAAAGCAAGGG-T
64 AAT-GAATGCA-AAAAAAAAAAAGGGAT
* * * * *
1455450 TTAATTGCTCTTTTGAAAAAGTTTGAGGGCTTTTTTTATGCATTTTGAAAGTTCAAGTACTCAAA
1 TTAATTGCTTTTTTGAAAAAGTTTGAGGGCTTTTTTGATACATTTTGAAAATTCAAGTACCCAAA
1455515 TGAATGCAAAAAAAAAAAAGGGAT
66 TGAATGCAAAAAAAAAAAAGGGAT
*
1455539 TTAATTGTTTTTTTGAAAAAGTTTGAGGGCTTTTT
1 TTAATTGCTTTTTTGAAAAAGTTTGAGGGCTTTTT
1455574 ACACCTTAAG
Statistics
Matches: 107, Mismatches: 14, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
88 12 0.11
89 84 0.79
90 11 0.10
ACGTcount: A:0.34, C:0.09, G:0.19, T:0.38
Consensus pattern (89 bp):
TTAATTGCTTTTTTGAAAAAGTTTGAGGGCTTTTTTGATACATTTTGAAAATTCAAGTACCCAAA
TGAATGCAAAAAAAAAAAAGGGAT
Found at i:1456788 original size:89 final size:88
Alignment explanation
Indices: 1456665--1456846 Score: 226
Period size: 89 Copynumber: 2.0 Consensus size: 88
1456655 CATTTCGTTT
* *
1456665 TTTTTTTTGCACTCATTTGGGTACTTGAAATTTTAAAATAG-ATAAAAGAAGA-CCTCAAACCTT
1 TTTTTTTTGCACTCAATTGGATACTTGAAATTTTAAAAT-GCATAAAA-AAGATCCTCAAA--TT
*
1456728 TT-CAAAAAAGGCAATTAAGCCCATAC
62 TTACAAAAAAAGCAATTAAGCCCATAC
* * *
1456754 TTTTTTTTGCACTTAATTGGATACTTGAACTTTTAAAATGCATCAAAAAGATCCTCAAATTTTGA
1 TTTTTTTTGCACTCAATTGGATACTTGAAATTTTAAAATGCATAAAAAAGATCCTCAAATTTT-A
* *
1456819 CAAAAAAAGCAATTAAGCTCATGC
65 CAAAAAAAGCAATTAAGCCCATAC
1456843 TTTT
1 TTTT
1456847 ATTAAAAAAT
Statistics
Matches: 81, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
87 4 0.05
88 5 0.06
89 72 0.89
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (88 bp):
TTTTTTTTGCACTCAATTGGATACTTGAAATTTTAAAATGCATAAAAAAGATCCTCAAATTTTAC
AAAAAAAGCAATTAAGCCCATAC
Found at i:1456929 original size:18 final size:18
Alignment explanation
Indices: 1456908--1456955 Score: 57
Period size: 17 Copynumber: 2.8 Consensus size: 18
1456898 ATTTTAATAA
1456908 AAAATTATTATAAATTAG-
1 AAAATTATTATAAATT-GT
*
1456926 AAAATTA-TAAAAATTGT
1 AAAATTATTATAAATTGT
1456943 AAAATT-TTATAAA
1 AAAATTATTATAAA
1456956 AATCATAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 1 0.04
17 18 0.69
18 7 0.27
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (18 bp):
AAAATTATTATAAATTGT
Found at i:1456940 original size:9 final size:9
Alignment explanation
Indices: 1456907--1456975 Score: 59
Period size: 10 Copynumber: 7.4 Consensus size: 9
1456897 AATTTTAATA
1456907 AAAAATTATT
1 AAAAATTA-T
*
1456917 ATAAATTA-
1 AAAAATTAT
*
1456925 GAAAATTAT
1 AAAAATTAT
*
1456934 AAAAATTGT
1 AAAAATTAT
*
1456943 AAAATTTTAT
1 AAAA-ATTAT
*
1456953 AAAAATCAT
1 AAAAATTAT
1456962 AAAAAATTAT
1 -AAAAATTAT
1456972 AAAA
1 AAAA
1456976 TATATTGAAA
Statistics
Matches: 46, Mismatches: 10, Indels: 7
0.73 0.16 0.11
Matches are distributed among these distances:
8 6 0.13
9 18 0.39
10 22 0.48
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.33
Consensus pattern (9 bp):
AAAAATTAT
Found at i:1456946 original size:17 final size:17
Alignment explanation
Indices: 1456908--1456975 Score: 57
Period size: 19 Copynumber: 3.7 Consensus size: 17
1456898 ATTTTAATAA
*
1456908 AAAATTATTATAAATTAG
1 AAAATTA-TAAAAATTAG
1456926 AAAATTATAAAAATT-G
1 AAAATTATAAAAATTAG
*
1456942 TAAAATTTTATAAAAATCATAA
1 -AAAA--TTATAAAAAT--TAG
1456964 AAAATTATAAAA
1 AAAATTATAAAA
1456976 TATATTGAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
16 1 0.02
17 11 0.26
18 7 0.17
19 18 0.43
21 5 0.12
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.34
Consensus pattern (17 bp):
AAAATTATAAAAATTAG
Found at i:1456954 original size:19 final size:19
Alignment explanation
Indices: 1456929--1457013 Score: 73
Period size: 19 Copynumber: 4.4 Consensus size: 19
1456919 AAATTAGAAA
*
1456929 ATTATAAAAATTGTAAAAT
1 ATTATAAAAATTATAAAAT
* * *
1456948 TTTATAAAAATCATAAAAA
1 ATTATAAAAATTATAAAAT
*
1456967 ATTAT-AAAATATATTGAAAT
1 ATTATAAAAAT-TA-TAAAAT
* *
1456987 ATAAAAAAAATTATAAAAT
1 ATTATAAAAATTATAAAAT
*
1457006 TTTATAAA
1 ATTATAAA
1457014 GTCGTAAGAA
Statistics
Matches: 49, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
18 5 0.10
19 30 0.61
20 9 0.18
21 5 0.10
ACGTcount: A:0.61, C:0.01, G:0.02, T:0.35
Consensus pattern (19 bp):
ATTATAAAAATTATAAAAT
Found at i:1457353 original size:16 final size:17
Alignment explanation
Indices: 1457327--1457380 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 17
1457317 TAAAAAAAAG
1457327 TTTTAATTTTTAATAATT
1 TTTTAA-TTTTAATAATT
* * *
1457345 TTTTATTTTTTAT-TTT
1 TTTTAATTTTAATAATT
*
1457361 TTTTAAATTTAATAATT
1 TTTTAATTTTAATAATT
1457378 TTT
1 TTT
1457381 CTACAATTTA
Statistics
Matches: 28, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
16 12 0.43
17 11 0.39
18 5 0.18
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (17 bp):
TTTTAATTTTAATAATT
Found at i:1457391 original size:34 final size:33
Alignment explanation
Indices: 1457335--1457414 Score: 79
Period size: 34 Copynumber: 2.4 Consensus size: 33
1457325 AGTTTTAATT
*** * *
1457335 TTTAATAATTTTTTATTTTTTATTTTTTTTAAA
1 TTTAATAATTTTTTACAATTTATATTTTATAAA
*
1457368 TTTAATAATTTTTCTACAATTTATATTTTATAAC
1 TTTAATAATTTTT-TACAATTTATATTTTATAAA
**
1457402 TTTTCTAATTTTT
1 TTTAATAATTTTT
1457415 AATAAGAGCA
Statistics
Matches: 38, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
33 13 0.34
34 25 0.66
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (33 bp):
TTTAATAATTTTTTACAATTTATATTTTATAAA
Found at i:1457415 original size:25 final size:26
Alignment explanation
Indices: 1457360--1457416 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 26
1457350 TTTTTTATTT
*
1457360 TTTTTAAATTTAATAATTTTTCTACA
1 TTTTTAAATTTAATAACTTTTCTACA
* * *
1457386 -ATTTATATTTTATAACTTTTCTA-A
1 TTTTTAAATTTAATAACTTTTCTACA
1457410 TTTTTAA
1 TTTTTAA
1457417 TAAGAGCAAG
Statistics
Matches: 24, Mismatches: 6, Indels: 3
0.73 0.18 0.09
Matches are distributed among these distances:
24 1 0.04
25 23 0.96
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (26 bp):
TTTTTAAATTTAATAACTTTTCTACA
Found at i:1457850 original size:90 final size:88
Alignment explanation
Indices: 1457707--1457906 Score: 238
Period size: 90 Copynumber: 2.2 Consensus size: 88
1457697 AAGTCCCTAC
* * * * * * *
1457707 TTTTACACTCACTTGGATACTTGAATTTTCAAAATGCATCAAAAAGGCTCTCAAACTTTTTCAAA
1 TTTTACACTTAATTGGATACTTAAACTTTCAAAATACATCAAAAAGACCCTCAAACTTTTTCAAA
* * * *
1457772 AAATGTAACTAAGCCTTTGCTTTT
66 AAAAGTAACTAAACC-CTGATTTT
* * * *
1457796 ATTTTGCACTTAATTGGGTACTTAAACTTTCGAAATACATCACAAAGACCCTCAAACTTTTTCAA
1 -TTTTACACTTAATTGGATACTTAAACTTTCAAAATACATCAAAAAGACCCTCAAACTTTTTCAA
*
1457861 AAAAAGTAATTAAACCCTGATTTT
65 AAAAAGTAACTAAACCCTGATTTT
1457885 TTTTACACTTAATTGGATACTT
1 TTTTACACTTAATTGGATACTT
1457907 GAATCGCCCC
Statistics
Matches: 92, Mismatches: 18, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
88 20 0.22
89 6 0.07
90 66 0.72
ACGTcount: A:0.35, C:0.18, G:0.10, T:0.37
Consensus pattern (88 bp):
TTTTACACTTAATTGGATACTTAAACTTTCAAAATACATCAAAAAGACCCTCAAACTTTTTCAAA
AAAAGTAACTAAACCCTGATTTT
Found at i:1458313 original size:89 final size:90
Alignment explanation
Indices: 1458220--1458416 Score: 224
Period size: 89 Copynumber: 2.2 Consensus size: 90
1458210 ACCGGGTGCC
* * * * *
1458220 TAATTTTTTTTTTTTTAAATA-TTTGAGGACCTTTTTGATG-ATTTTAAAAGTTCAAATACCCAA
1 TAATTTCTTTTTTTTTAAAAAGTCTGAGGACATTTTT-ATGCATTTTAAAAGCTCAAATACCCAA
*
1458283 TTGAGTGCAAAATAAA-AGT-AAGGACT
65 GTGAGTGCAAAA-AAAGAGTAAAGG-CT
* * * *
1458309 TAATTGC-TTTTTTTGAAAAAGTCTGAGGACATTTTTATGCATTTTGAAAGCTCAAGTACCCAAG
1 TAATTTCTTTTTTTTTAAAAAGTCTGAGGACATTTTTATGCATTTTAAAAGCTCAAATACCCAAG
1458373 TGAGTGCAAAAAAAGAGTAGAAGGCT
66 TGAGTGCAAAAAAAGAGTA-AAGGCT
*
1458399 TAATTACTTTTTTTTTAA
1 TAATTTCTTTTTTTTTAA
1458417 TTGAGAGTTT
Statistics
Matches: 90, Mismatches: 12, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
88 17 0.19
89 52 0.58
90 8 0.09
91 13 0.14
ACGTcount: A:0.35, C:0.10, G:0.16, T:0.39
Consensus pattern (90 bp):
TAATTTCTTTTTTTTTAAAAAGTCTGAGGACATTTTTATGCATTTTAAAAGCTCAAATACCCAAG
TGAGTGCAAAAAAAGAGTAAAGGCT
Found at i:1458462 original size:3 final size:3
Alignment explanation
Indices: 1458454--1458488 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
1458444 AATATATGTA
1458454 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1458489 ATTATAGGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1460910 original size:52 final size:52
Alignment explanation
Indices: 1460823--1461063 Score: 306
Period size: 52 Copynumber: 4.7 Consensus size: 52
1460813 GCCATAAACG
* * *
1460823 AAGAGGTCTGATGTCTAAGTGTCATCATGAGTATATAAATCCTTTACGGATT
1 AAGAGGTCCGATGACTAAGTGTCATCGTGAGTATATAAATCCTTTACGGATT
* * * * * *
1460875 AAGAGATCTGATTACTAAGTGTCATCGTGATTATATGAATTCTTTACGGATT
1 AAGAGGTCCGATGACTAAGTGTCATCGTGAGTATATAAATCCTTTACGGATT
*
1460927 AAGAGGTCCGATGACTAAGTGTCATCGTGAGTATATGAATCCTTTACGGATT
1 AAGAGGTCCGATGACTAAGTGTCATCGTGAGTATATAAATCCTTTACGGATT
* * * *
1460979 AAGAGGTCCAATGACTCTA-TGTCATCGTGAGTATATAAATCCATTGCGGATT
1 AAGAGGTCCGATGACT-AAGTGTCATCGTGAGTATATAAATCCTTTACGGATT
** *
1461031 AA-AGGTCCGATGACTTTGTGTCATCCTGAGTAT
1 AAGAGGTCCGATGACTAAGTGTCATCGTGAGTAT
1461064 CAAATACGAA
Statistics
Matches: 167, Mismatches: 20, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
50 1 0.01
51 26 0.16
52 139 0.83
53 1 0.01
ACGTcount: A:0.29, C:0.15, G:0.22, T:0.34
Consensus pattern (52 bp):
AAGAGGTCCGATGACTAAGTGTCATCGTGAGTATATAAATCCTTTACGGATT
Found at i:1468380 original size:15 final size:15
Alignment explanation
Indices: 1468360--1468388 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1468350 ATTTTGGATA
1468360 ATTTTTAAGAATTTT
1 ATTTTTAAGAATTTT
1468375 ATTTTTAAGAATTT
1 ATTTTTAAGAATTT
1468389 CTCTTGAGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (15 bp):
ATTTTTAAGAATTTT
Found at i:1476067 original size:27 final size:27
Alignment explanation
Indices: 1476004--1476064 Score: 79
Period size: 26 Copynumber: 2.3 Consensus size: 27
1475994 ATTAAAATGG
** * *
1476004 TTATTAAATTATATATTAATTTTATTT
1 TTATTAAATTATATATTAATAATAATC
1476031 TTATTAAATTATAT-TTAATAATAATC
1 TTATTAAATTATATATTAATAATAATC
1476057 TTATTAAA
1 TTATTAAA
1476065 ATTTAATAAC
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
26 16 0.53
27 14 0.47
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.56
Consensus pattern (27 bp):
TTATTAAATTATATATTAATAATAATC
Found at i:1477559 original size:173 final size:173
Alignment explanation
Indices: 1477256--1477601 Score: 525
Period size: 173 Copynumber: 2.0 Consensus size: 173
1477246 TGTTAATCAG
* * *
1477256 TATTTAGCAAATTGAATGTTTTACAACTTGGTGAGAAAACATAATAATTTTGAATGTTGGATGCA
1 TATTTAGCAAATTGAATGTTTTACAACTTGGTGAGAAAACACAATAATTTTGAATATTGAATGCA
* * * *
1477321 AAAATAAATGACTAGGTGCAAAATTATCCTTAATGCAAATTAATCTAAATGTGATGAATAATTAA
66 AAAATAAATGACTAGATGCAAAATGATCCTCAATGCAAATTAATCTAAATGTGATAAATAATTAA
* * *
1477386 AATGGAAGAGATGGATTTAGCAGCATAATTCACAAGATTTCAA
131 AATGGAAGAGATAGATTTAGCAGCAAAATTCAAAAGATTTCAA
* * *
1477429 TATTTTGCAAAATT-AATGTTTTACAACTTGGTGAGAAAGCACAATAATTTTGAATATTGAATGT
1 TATTTAGC-AAATTGAATGTTTTACAACTTGGTGAGAAAACACAATAATTTTGAATATTGAATGC
*
1477493 AAAAATAAATGACTAGATGCAAAATGATTCC-CAATGCAAATTAATTTAAATGTGATAAATAATT
65 AAAAATAAATGACTAGATGCAAAATGA-TCCTCAATGCAAATTAATCTAAATGTGATAAATAATT
*
1477557 AAAATGGATGAGATAGATTTAGCAGCAAAATTCAAAAGATTTCAA
129 AAAATGGAAGAGATAGATTTAGCAGCAAAATTCAAAAGATTTCAA
1477602 CAACTATAAC
Statistics
Matches: 156, Mismatches: 15, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
173 148 0.95
174 8 0.05
ACGTcount: A:0.44, C:0.09, G:0.16, T:0.32
Consensus pattern (173 bp):
TATTTAGCAAATTGAATGTTTTACAACTTGGTGAGAAAACACAATAATTTTGAATATTGAATGCA
AAAATAAATGACTAGATGCAAAATGATCCTCAATGCAAATTAATCTAAATGTGATAAATAATTAA
AATGGAAGAGATAGATTTAGCAGCAAAATTCAAAAGATTTCAA
Found at i:1490602 original size:17 final size:17
Alignment explanation
Indices: 1490580--1490617 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
1490570 AATGATTTTT
1490580 TAATTTT-TTGAAAATAA
1 TAATTTTATT-AAAATAA
1490597 TAATTTTATTAAAATAA
1 TAATTTTATTAAAATAA
1490614 -AATT
1 TAATT
1490618 AATGAATCTG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 4 0.20
17 14 0.70
18 2 0.10
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (17 bp):
TAATTTTATTAAAATAA
Found at i:1492769 original size:27 final size:27
Alignment explanation
Indices: 1492738--1492792 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
1492728 TGAGCACTTG
*
1492738 TAACGTGATCGTCGATCACCATAATGT
1 TAACGTGATCGTCGACCACCATAATGT
1492765 TAACGTGATCGTCGACCACCATAATGT
1 TAACGTGATCGTCGACCACCATAATGT
1492792 T
1 T
1492793 TTACTCCCAG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (27 bp):
TAACGTGATCGTCGACCACCATAATGT
Found at i:1492912 original size:28 final size:28
Alignment explanation
Indices: 1492881--1492956 Score: 102
Period size: 28 Copynumber: 2.8 Consensus size: 28
1492871 GACATTTTTC
*
1492881 ATTTGGAATTAGTTATGTTTATGAATGA
1 ATTTGGAATTAATTATGTTTATGAATGA
**
1492909 ATTTGGAATTAATTATGTTTATGTTTGA
1 ATTTGGAATTAATTATGTTTATGAATGA
*
1492937 ATTT--AATTAATTAAGTTTAT
1 ATTTGGAATTAATTATGTTTAT
1492957 ATTTGTATTT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
26 15 0.34
28 29 0.66
ACGTcount: A:0.33, C:0.00, G:0.16, T:0.51
Consensus pattern (28 bp):
ATTTGGAATTAATTATGTTTATGAATGA
Found at i:1492954 original size:26 final size:26
Alignment explanation
Indices: 1492887--1493001 Score: 140
Period size: 26 Copynumber: 4.3 Consensus size: 26
1492877 TTTCATTTGG
* **
1492887 AATTAGTTATGTTTATGAATGAATTT
1 AATTAATTATGTTTATGTTTGAATTT
1492913 GGAATTAATTATGTTTATGTTTGAATTT
1 --AATTAATTATGTTTATGTTTGAATTT
* * *
1492941 AATTAATTAAGTTTATATTTGTATTT
1 AATTAATTATGTTTATGTTTGAATTT
* *
1492967 CATTAATTATGTTTATGTTTGTATTT
1 AATTAATTATGTTTATGTTTGAATTT
1492993 AATTAATTA
1 AATTAATTA
1493002 GGGTTTAGGG
Statistics
Matches: 77, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
26 54 0.70
28 23 0.30
ACGTcount: A:0.32, C:0.01, G:0.12, T:0.55
Consensus pattern (26 bp):
AATTAATTATGTTTATGTTTGAATTT
Found at i:1498217 original size:20 final size:20
Alignment explanation
Indices: 1498181--1498219 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1498171 AGATAATTGT
*
1498181 AATTTAAATATTAAATTATA
1 AATTTAAATAATAAATTATA
1498201 AATTT-AATAATATAATTAT
1 AATTTAAATAATA-AATTAT
1498220 GATAGAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
AATTTAAATAATAAATTATA
Found at i:1505601 original size:17 final size:17
Alignment explanation
Indices: 1505562--1505615 Score: 74
Period size: 17 Copynumber: 3.1 Consensus size: 17
1505552 CAACTAGAGT
1505562 TAAAAGGTCATCTTCTTAA-
1 TAAAAGGTCA--TTC-TAAC
1505581 TAAAAGGTCATTCTAAC
1 TAAAAGGTCATTCTAAC
1505598 TAAAAGGTCATTCTAAC
1 TAAAAGGTCATTCTAAC
1505615 T
1 T
1505616 GATCTTATAC
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
16 3 0.09
17 21 0.62
19 10 0.29
ACGTcount: A:0.39, C:0.17, G:0.11, T:0.33
Consensus pattern (17 bp):
TAAAAGGTCATTCTAAC
Found at i:1508666 original size:2 final size:2
Alignment explanation
Indices: 1508654--1508706 Score: 88
Period size: 2 Copynumber: 26.5 Consensus size: 2
1508644 TTTATTATTT
* *
1508654 TA TA CA TA TA TA TA TA TA TA CA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1508696 TA TA TA TA TA T
1 TA TA TA TA TA T
1508707 GTATCAAATT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1512113 original size:12 final size:12
Alignment explanation
Indices: 1512096--1512120 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1512086 TGACAAGAAG
1512096 TGCTTGGTGTGA
1 TGCTTGGTGTGA
1512108 TGCTTGGTGTGA
1 TGCTTGGTGTGA
1512120 T
1 T
1512121 AGAAGAGGAG
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:0.08, C:0.08, G:0.40, T:0.44
Consensus pattern (12 bp):
TGCTTGGTGTGA
Found at i:1526350 original size:32 final size:32
Alignment explanation
Indices: 1526290--1526350 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 32
1526280 GCACTTCCAC
* * * * *
1526290 ATTTTTACTTTGTTTTAATTTTGTCCTTTTTT
1 ATTTTTAATTTATGTTAATTTCGCCCTTTTTT
1526322 ATTTTTAATTTATGTTAATTTCGCCCTTT
1 ATTTTTAATTTATGTTAATTTCGCCCTTT
1526351 AATTTTATTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 24 1.00
ACGTcount: A:0.16, C:0.11, G:0.07, T:0.66
Consensus pattern (32 bp):
ATTTTTAATTTATGTTAATTTCGCCCTTTTTT
Found at i:1526573 original size:19 final size:15
Alignment explanation
Indices: 1526535--1526563 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1526525 ATTTTAGTAT
1526535 TTTATTTATTTTTTC
1 TTTATTTATTTTTTC
1526550 TTTATTTATTTTTT
1 TTTATTTATTTTTT
1526564 TGCCATTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.03, G:0.00, T:0.83
Consensus pattern (15 bp):
TTTATTTATTTTTTC
Found at i:1538042 original size:18 final size:19
Alignment explanation
Indices: 1538016--1538053 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
1538006 CGGTTGGCTC
*
1538016 GAGGGACAA-GAAAAGAAA
1 GAGGCACAAGGAAAAGAAA
*
1538034 GAGGCACAAGGGAAAGAAA
1 GAGGCACAAGGAAAAGAAA
1538053 G
1 G
1538054 TGAAGAAGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.55, C:0.08, G:0.37, T:0.00
Consensus pattern (19 bp):
GAGGCACAAGGAAAAGAAA
Found at i:1542868 original size:12 final size:12
Alignment explanation
Indices: 1542851--1542894 Score: 52
Period size: 12 Copynumber: 3.4 Consensus size: 12
1542841 GAAGGAAACT
1542851 GAAGAAGAGAAG
1 GAAGAAGAGAAG
*
1542863 GAAGAAGAGGAGAA
1 GAAGAAGA-GA-AG
1542877 GAATGAAGAGAAG
1 GAA-GAAGAGAAG
1542890 GAAGA
1 GAAGA
1542895 TGCCTCGACA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
12 10 0.37
13 6 0.22
14 6 0.22
15 5 0.19
ACGTcount: A:0.57, C:0.00, G:0.41, T:0.02
Consensus pattern (12 bp):
GAAGAAGAGAAG
Found at i:1543182 original size:17 final size:21
Alignment explanation
Indices: 1543142--1543180 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
1543132 AATTGACTCC
1543142 AAGGACAAGAAAAGAAAGAGG
1 AAGGACAAGAAAAGAAAGAGG
*
1543163 AAGGACAA-AAAAAAAAGA
1 AAGGACAAGAAAAGAAAGA
1543181 AGCACAATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.69, C:0.05, G:0.26, T:0.00
Consensus pattern (21 bp):
AAGGACAAGAAAAGAAAGAGG
Found at i:1547280 original size:3 final size:3
Alignment explanation
Indices: 1547272--1547297 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1547262 AGAGCATCAT
1547272 AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AA
1547298 TATTCTCAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:1553378 original size:18 final size:19
Alignment explanation
Indices: 1553338--1553386 Score: 73
Period size: 18 Copynumber: 2.6 Consensus size: 19
1553328 GGTTGACTCC
1553338 AAGGACAAGAAAGAAAGAAG
1 AAGGACAA-AAAGAAAGAAG
1553358 AAGGACAAAAAGAAA-AAG
1 AAGGACAAAAAGAAAGAAG
*
1553376 AAGCACAAAAA
1 AAGGACAAAAA
1553387 AGAGCACCCA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
18 13 0.46
19 7 0.25
20 8 0.29
ACGTcount: A:0.69, C:0.08, G:0.22, T:0.00
Consensus pattern (19 bp):
AAGGACAAAAAGAAAGAAG
Found at i:1553387 original size:19 final size:20
Alignment explanation
Indices: 1553342--1553389 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
1553332 GACTCCAAGG
* *
1553342 ACAAGAAAGAAAGAAGAAGG
1 ACAAAAAAGAAAGAAGAAGC
1553362 AC-AAAAAGAAA-AAGAAGC
1 ACAAAAAAGAAAGAAGAAGC
1553380 ACAAAAAAGA
1 ACAAAAAAGA
1553390 GCACCCAAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 8 0.32
19 15 0.60
20 2 0.08
ACGTcount: A:0.71, C:0.08, G:0.21, T:0.00
Consensus pattern (20 bp):
ACAAAAAAGAAAGAAGAAGC
Found at i:1559401 original size:23 final size:23
Alignment explanation
Indices: 1559369--1559414 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
1559359 CTGAAAGCAC
* *
1559369 AGTTATAGGAATTGTCAGATAAA
1 AGTTACAGGAATTGTCAAATAAA
1559392 AGTTACAGGAATTGTCAAATAAA
1 AGTTACAGGAATTGTCAAATAAA
1559415 TGTTTCATCC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.46, C:0.07, G:0.20, T:0.28
Consensus pattern (23 bp):
AGTTACAGGAATTGTCAAATAAA
Found at i:1571807 original size:21 final size:21
Alignment explanation
Indices: 1571781--1571827 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
1571771 AAGTTGTTCT
1571781 CATTTGGTCATCCTTAGCATA
1 CATTTGGTCATCCTTAGCATA
1571802 CATTTGGTCATCCTTAGCATA
1 CATTTGGTCATCCTTAGCATA
1571823 CATTT
1 CATTT
1571828 TTAGCATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.23, C:0.23, G:0.13, T:0.40
Consensus pattern (21 bp):
CATTTGGTCATCCTTAGCATA
Found at i:1586227 original size:59 final size:60
Alignment explanation
Indices: 1586156--1586309 Score: 177
Period size: 59 Copynumber: 2.6 Consensus size: 60
1586146 AGGGAAAATT
* *
1586156 GGTGTCAGCCATTGGTTGCCAAACACCAAAAAAATT-ATTTTTTAATTTGTATTTTTATG
1 GGTGTCAGCCATTGGTTGCCAAACACCAAAAAAATTAATTTTTTAATTCGTATTTTTATA
* * * * *
1586215 GGTGTCTGCCATTGGTTGTCAGACACC-AAAAAATTAATTTTTTTATTCGTATTTTTGTA
1 GGTGTCAGCCATTGGTTGCCAAACACCAAAAAAATTAATTTTTTAATTCGTATTTTTATA
* * * * * *
1586274 GGTGTCGGCCATTAGATGGCAAATATCAAAAAAATT
1 GGTGTCAGCCATTGGTTGCCAAACACCAAAAAAATT
1586310 TTGGGGACCT
Statistics
Matches: 79, Mismatches: 14, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
58 8 0.10
59 63 0.80
60 8 0.10
ACGTcount: A:0.31, C:0.14, G:0.18, T:0.38
Consensus pattern (60 bp):
GGTGTCAGCCATTGGTTGCCAAACACCAAAAAAATTAATTTTTTAATTCGTATTTTTATA
Found at i:1586419 original size:114 final size:113
Alignment explanation
Indices: 1586301--1586506 Score: 265
Period size: 113 Copynumber: 1.8 Consensus size: 113
1586291 GGCAAATATC
** ** * *
1586301 AAAAAAATTTTGGGGACCT-AAAAAATGTGATGTCGGTCATTGCTTGGCAGACACCCAAAAA-AA
1 AAAAAAATTTT-GAAACCTAAAAAAATG-G-TGTCAATCATGGCTTGGCAAACACCCAAAAATAA
*
1586364 TAA-TTTTTATTCGTATTTTTTGGGTGTCGATCATGGTTTGATAAACACCCA
63 TAATTTTTTATTCGTA-CTTTTGGGTGTCGATCATGGTTTGATAAACACCCA
*
1586415 AAAAAAATTTTGAAACCTGAAAAAAATGGTGTCAATCATGGCTTGGCAAACATCCAAAAATAATA
1 AAAAAAATTTTGAAACCT-AAAAAAATGGTGTCAATCATGGCTTGGCAAACACCCAAAAATAATA
*
1586480 ATTTTTTATTTGTACTTTTGGGTGTCG
65 ATTTTTTATTCGTACTTTTGGGTGTCG
1586507 GACATAGCTT
Statistics
Matches: 79, Mismatches: 9, Indels: 8
0.82 0.09 0.08
Matches are distributed among these distances:
113 31 0.39
114 29 0.37
115 19 0.24
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (113 bp):
AAAAAAATTTTGAAACCTAAAAAAATGGTGTCAATCATGGCTTGGCAAACACCCAAAAATAATAA
TTTTTTATTCGTACTTTTGGGTGTCGATCATGGTTTGATAAACACCCA
Found at i:1586552 original size:114 final size:113
Alignment explanation
Indices: 1586337--1586561 Score: 253
Period size: 114 Copynumber: 2.0 Consensus size: 113
1586327 GTGATGTCGG
* * * * *
1586337 TCATTGCTTGGCAGACACCCAAAAAAATAATTTTTATTCGTATTTTTTGGGTGTCGATCATGGTT
1 TCATGGCTTGGCAAACACCCAAAAAAATAATTTTTATTCGTATCTTTTGGGTGTCGATCATAGCT
* *
1586402 TGATAAACACCCAAAAAAAATTTTGAAACCTGAAAAAA-ATGGTGTCAA
66 TCACAAACACCCAAAAAAAATTTTGAAA-CTGAAAAAAGATGGTGTCAA
* *
1586450 TCATGGCTTGGCAAACATCCAAAAATAATAATTTTTTATTTGTA-CTTTTGGGTGTCGGA-CATA
1 TCATGGCTTGGCAAACACCCAAAAA-AATAA-TTTTTATTCGTATCTTTTGGGTGTC-GATCATA
**
1586513 GCTTCACAAACA-CCAAAAAAATATTTTTTTAA-TGTAAAAAAGATGGTGT
63 GCTTCACAAACACCCAAAAAAA-A-TTTTGAAACTG-AAAAAAGATGGTGT
1586562 TGGCCATAGA
Statistics
Matches: 94, Mismatches: 11, Indels: 12
0.80 0.09 0.10
Matches are distributed among these distances:
113 33 0.35
114 35 0.37
115 26 0.28
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (113 bp):
TCATGGCTTGGCAAACACCCAAAAAAATAATTTTTATTCGTATCTTTTGGGTGTCGATCATAGCT
TCACAAACACCCAAAAAAAATTTTGAAACTGAAAAAAGATGGTGTCAA
Found at i:1589142 original size:61 final size:58
Alignment explanation
Indices: 1589077--1589204 Score: 152
Period size: 58 Copynumber: 2.2 Consensus size: 58
1589067 TCATCTAATC
*
1589077 GCTGACACCCACAAATGATACGAA-TAAAAAAATAATTTTTTTTCGTATTTGACAACCAATG
1 GCTGACACCCACAAA-AATACGAACT-AAAAAAT-ATTTTTTTT-GTATTTGACAACCAATG
* * * *
1589138 GCTGACACCCATAAAAATATGAACTAAAAAATATTTTTTTTGTGTTTGGCAACCAATG
1 GCTGACACCCACAAAAATACGAACTAAAAAATATTTTTTTTGTATTTGACAACCAATG
1589196 G-TCGACACC
1 GCT-GACACC
1589205 AACTTTCCGT
Statistics
Matches: 60, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
57 1 0.02
58 22 0.37
59 9 0.15
60 13 0.22
61 15 0.25
ACGTcount: A:0.38, C:0.19, G:0.13, T:0.30
Consensus pattern (58 bp):
GCTGACACCCACAAAAATACGAACTAAAAAATATTTTTTTTGTATTTGACAACCAATG
Found at i:1589972 original size:18 final size:18
Alignment explanation
Indices: 1589949--1590001 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
1589939 GTGAAAATGT
1589949 GAAAAAATAATTATTATC
1 GAAAAAATAATTATTATC
* * *
1589967 GAAAAATTAAATATATATT
1 GAAAAAATAATTAT-TATC
*
1589986 GAAAAAATAATAATTA
1 GAAAAAATAATTATTA
1590002 CAAATTAAAG
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
18 14 0.50
19 14 0.50
ACGTcount: A:0.60, C:0.02, G:0.06, T:0.32
Consensus pattern (18 bp):
GAAAAAATAATTATTATC
Found at i:1605591 original size:3 final size:3
Alignment explanation
Indices: 1605585--1605611 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1605575 AATGAAATAC
1605585 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1605612 TCAATTTAAA
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:1605793 original size:25 final size:25
Alignment explanation
Indices: 1605765--1605828 Score: 101
Period size: 25 Copynumber: 2.6 Consensus size: 25
1605755 AAATACTAGC
1605765 TTGAAATTAAAATTATAGTTTAAAA
1 TTGAAATTAAAATTATAGTTTAAAA
* *
1605790 TTGAAATTACAATTATAGTTTAAAT
1 TTGAAATTAAAATTATAGTTTAAAA
*
1605815 TTGAAATAAAAATT
1 TTGAAATTAAAATT
1605829 TAATTTTGGG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.50, C:0.02, G:0.08, T:0.41
Consensus pattern (25 bp):
TTGAAATTAAAATTATAGTTTAAAA
Found at i:1605979 original size:25 final size:25
Alignment explanation
Indices: 1605934--1605993 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
1605924 ATCGTATAAA
** *
1605934 TTTAATTTAAAAATTTTAAATGTAT
1 TTTAATTTAAAAATTAAAAATATAT
1605959 TTTAATTTAAATAA-TAAAAATATAT
1 TTTAATTTAAA-AATTAAAAATATAT
*
1605984 TTCAATTTAA
1 TTTAATTTAA
1605994 GTTTAGAATA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
25 28 0.93
26 2 0.07
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (25 bp):
TTTAATTTAAAAATTAAAAATATAT
Found at i:1606413 original size:13 final size:15
Alignment explanation
Indices: 1606395--1606431 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
1606385 TTTAATAAAC
1606395 TTAAATAAAAA-T-T
1 TTAAATAAAAACTAT
1606408 TTAAATTAAAAACTAT
1 TTAAA-TAAAAACTAT
1606424 TTAAATAA
1 TTAAATAA
1606432 TTTGAATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
13 5 0.24
14 6 0.29
15 4 0.19
16 6 0.29
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (15 bp):
TTAAATAAAAACTAT
Found at i:1608932 original size:21 final size:20
Alignment explanation
Indices: 1608886--1608932 Score: 62
Period size: 18 Copynumber: 2.4 Consensus size: 20
1608876 ATTTAATTTG
*
1608886 TAATTATTAATTTTTCAATA
1 TAATTATTAAATTTTCAATA
1608906 T-A-TATTAAATTTTCAATAA
1 TAATTATTAAATTTTCAAT-A
1608925 TAATTATT
1 TAATTATT
1608933 TCCCCACATT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
18 14 0.61
19 3 0.13
20 2 0.09
21 4 0.17
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (20 bp):
TAATTATTAAATTTTCAATA
Found at i:1611457 original size:52 final size:52
Alignment explanation
Indices: 1611377--1611757 Score: 558
Period size: 52 Copynumber: 7.4 Consensus size: 52
1611367 TGGTTTGATA
*
1611377 ACTATGTGTCATCGTGAGTATATAAATCCTTTACGGATTATGAGGTCCGATG
1 ACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCCGATG
* *
1611429 ACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATAAGGTCTGATG
1 ACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCCGATG
*
1611481 ACTATGTGTCATTGTGAGTATATGAATCCTTTACGGATTATGAGGTCCGATG
1 ACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCCGATG
* *
1611533 ACTATGTGTCGTCGTGAGTATATGAAT-C---ACGAATTATGAGGTCCGATG
1 ACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCCGATG
*
1611581 ACTATGTGTCGTCGTGAGTATATGAATCCTTTACGGATTATGAGGTCCGATG
1 ACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCCGATG
1611633 ACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCCGATG
1 ACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCCGATG
* ** * * * *
1611685 ACACAT-ACTCATCGTGAGCATATGGATCCTTTTTCGGATT-TAAGGTCCGATG
1 AC-TATGTGTCATCGTGAGTATATGAATCC-TTTACGGATTATGAGGTCCGATG
* *
1611737 ACTTTGTGTCATCATGAGTAT
1 ACTATGTGTCATCGTGAGTAT
1611758 TAAATGGGAA
Statistics
Matches: 298, Mismatches: 24, Indels: 14
0.89 0.07 0.04
Matches are distributed among these distances:
48 46 0.15
49 1 0.00
51 2 0.01
52 238 0.80
53 11 0.04
ACGTcount: A:0.25, C:0.15, G:0.24, T:0.35
Consensus pattern (52 bp):
ACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCCGATG
Found at i:1611657 original size:152 final size:154
Alignment explanation
Indices: 1611377--1611686 Score: 525
Period size: 152 Copynumber: 2.0 Consensus size: 154
1611367 TGGTTTGATA
*
1611377 ACTATGTGTCATCGTGAGTATATAAATCCTTTACGGATTATGAGGTCCGATGACTATGTGTCATC
1 ACTATGTGTCATCGTGAGTATATAAATCC--TACGAATTATGAGGTCCGATGACTATGTGTCATC
* *
1611442 GTGAGTATATGAATCCTTTACGGATTATAAGGTCTGATGACTATGTGTCATTGTGAGTATATGAA
64 GTGAGTATATGAATCCTTTACGGATTATAAGGTCCGATGACTATGTGTCATCGTGAGTATATGAA
1611507 TCCTTTACGGATTATGAGGTCCGATG
129 TCCTTTACGGATTATGAGGTCCGATG
* * *
1611533 ACTATGTGTCGTCGTGAGTATATGAAT-C-ACGAATTATGAGGTCCGATGACTATGTGTCGTCGT
1 ACTATGTGTCATCGTGAGTATATAAATCCTACGAATTATGAGGTCCGATGACTATGTGTCATCGT
*
1611596 GAGTATATGAATCCTTTACGGATTATGAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATC
66 GAGTATATGAATCCTTTACGGATTATAAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATC
1611661 CTTTACGGATTATGAGGTCCGATG
131 CTTTACGGATTATGAGGTCCGATG
1611685 AC
1 AC
1611687 ACATACTCAT
Statistics
Matches: 147, Mismatches: 7, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
152 121 0.82
155 1 0.01
156 25 0.17
ACGTcount: A:0.26, C:0.15, G:0.25, T:0.35
Consensus pattern (154 bp):
ACTATGTGTCATCGTGAGTATATAAATCCTACGAATTATGAGGTCCGATGACTATGTGTCATCGT
GAGTATATGAATCCTTTACGGATTATAAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATC
CTTTACGGATTATGAGGTCCGATG
Found at i:1611700 original size:152 final size:154
Alignment explanation
Indices: 1611385--1611757 Score: 511
Period size: 152 Copynumber: 2.4 Consensus size: 154
1611375 TAACTATGTG
* *
1611385 TCATCGTGAGTATATAAATCCTTTACGGATTATGAGGTCCGATGACTATGTGTCATCGTGAGTAT
1 TCATCGTGAGTATATGAATCC--TACGAATTATGAGGTCCGATGACTATGTGTCATCGTGAGTAT
* *
1611450 ATGAATCCTTTACGGATTATAAGGTCTGATGACTATGTGTCATTGTGAGTATATGAATCCTTTAC
64 ATGAATCCTTTACGGATTATAAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTAC
* **
1611515 GGATTATGAGGTCCGATGACTATGTG
129 GGATTATGAGGTCCGATGACCATGAC
* *
1611541 TCGTCGTGAGTATATGAAT-C-ACGAATTATGAGGTCCGATGACTATGTGTCGTCGTGAGTATAT
1 TCATCGTGAGTATATGAATCCTACGAATTATGAGGTCCGATGACTATGTGTCATCGTGAGTATAT
*
1611604 GAATCCTTTACGGATTATGAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGG
66 GAATCCTTTACGGATTATAAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGG
1611669 ATTATGAGGTCCGATGACACAT-AC
131 ATTATGAGGTCCGATGAC-CATGAC
* * * * * * *
1611693 TCATCGTGAGCATATGGATCCTTTTTCGGATT-TAAGGTCCGATGACTTTGTGTCATCATGAGTA
1 TCATCGTGAGTATATGAATCC---TACGAATTATGAGGTCCGATGACTATGTGTCATCGTGAGTA
1611757 T
63 T
1611758 TAAATGGGAA
Statistics
Matches: 192, Mismatches: 19, Indels: 12
0.86 0.09 0.05
Matches are distributed among these distances:
152 137 0.71
153 3 0.02
155 1 0.01
156 46 0.24
157 5 0.03
ACGTcount: A:0.25, C:0.16, G:0.24, T:0.35
Consensus pattern (154 bp):
TCATCGTGAGTATATGAATCCTACGAATTATGAGGTCCGATGACTATGTGTCATCGTGAGTATAT
GAATCCTTTACGGATTATAAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGG
ATTATGAGGTCCGATGACCATGAC
Found at i:1611733 original size:204 final size:204
Alignment explanation
Indices: 1611377--1611757 Score: 595
Period size: 204 Copynumber: 1.9 Consensus size: 204
1611367 TGGTTTGATA
1611377 ACTATGTGTCATCGTGAGTATATAAATCCTTTACGGATTATGAGGTCCGATGACTATGTGTCATC
1 ACTATGTGTCATCGTGAGTATATAAATCCTTTACGGATTATGAGGTCCGATGACTATGTGTCATC
* * ** * *
1611442 GTGAGTATATGAATCCTTTACGGATTATAAGGTCTGATGACTATGTGTCATTGTGAGTATATGAA
66 GTGAGTATATGAATCCTTTACGGATTATAAGGTCCGATGACCATGACTCATCGTGAGCATATGAA
* * *
1611507 TCCTTTACGGATTATGAGGTCCGATGACTATGTGTCGTCGTGAGTATATGAATCACGAATTATGA
131 TCCTTTACGGATTATAAGGTCCGATGACTATGTGTCATCATGAGTATATGAATCACGAATTATGA
1611572 GGTCCGATG
196 GGTCCGATG
* *
1611581 ACTATGTGTCGTCGTGAGTATATGAATCCTTTACGGATTATGAGGTCCGATGACTATGTGTCATC
1 ACTATGTGTCATCGTGAGTATATAAATCCTTTACGGATTATGAGGTCCGATGACTATGTGTCATC
* *
1611646 GTGAGTATATGAATCCTTTACGGATTATGAGGTCCGATGACACAT-ACTCATCGTGAGCATATGG
66 GTGAGTATATGAATCCTTTACGGATTATAAGGTCCGATGAC-CATGACTCATCGTGAGCATATGA
* *
1611710 ATCCTTTTTCGGATT-TAAGGTCCGATGACTTTGTGTCATCATGAGTAT
130 ATCC-TTTACGGATTATAAGGTCCGATGACTATGTGTCATCATGAGTAT
1611758 TAAATGGGAA
Statistics
Matches: 160, Mismatches: 15, Indels: 4
0.89 0.08 0.02
Matches are distributed among these distances:
204 149 0.93
205 11 0.07
ACGTcount: A:0.25, C:0.15, G:0.24, T:0.35
Consensus pattern (204 bp):
ACTATGTGTCATCGTGAGTATATAAATCCTTTACGGATTATGAGGTCCGATGACTATGTGTCATC
GTGAGTATATGAATCCTTTACGGATTATAAGGTCCGATGACCATGACTCATCGTGAGCATATGAA
TCCTTTACGGATTATAAGGTCCGATGACTATGTGTCATCATGAGTATATGAATCACGAATTATGA
GGTCCGATG
Found at i:1613630 original size:112 final size:113
Alignment explanation
Indices: 1613514--1613746 Score: 264
Period size: 113 Copynumber: 2.1 Consensus size: 113
1613504 TATTTGTGGC
* * *
1613514 TGTCGACCAT-TA-AATAGCAAACA-CCAATATATATATATTTTTT-ATTTTTGGGTTTCGGCCA
1 TGTCGACCATCTAGAATAGCAAACACCCAAAAAATATATATTTTTTCA-TTTTGGGTGTCGGCCA
* * *
1613575 TGGGTTGGCAAACATC-CAAAAATATAATTTTTGGTATTTGGAAAAGGGGA
65 TGGGTTGGCAAACACCTCAAAAA-ATAA-TTTTGATATCTGGAAAAGGGGA
* ** * * *
1613625 GTGTCG-GC-TCTAGCTTGGCAGACACCCAAAAAATATATATTTTTTCATTTTGGGTGTCGGTCA
1 -TGTCGACCATCTAGAATAGCAAACACCCAAAAAATATATATTTTTTCATTTTGGGTGTCGGCCA
*
1613688 TGTGTTGGCAAACACCTCAAAAAATAATTTTGATATCTGGAAAAGGGGA
65 TGGGTTGGCAAACACCTCAAAAAATAATTTTGATATCTGGAAAAGGGGA
1613737 TGTCGACCAT
1 TGTCGACCAT
1613747 GAGTTGGTAG
Statistics
Matches: 100, Mismatches: 14, Indels: 13
0.79 0.11 0.10
Matches are distributed among these distances:
110 1 0.01
111 8 0.08
112 33 0.33
113 51 0.51
114 7 0.07
ACGTcount: A:0.31, C:0.15, G:0.21, T:0.33
Consensus pattern (113 bp):
TGTCGACCATCTAGAATAGCAAACACCCAAAAAATATATATTTTTTCATTTTGGGTGTCGGCCAT
GGGTTGGCAAACACCTCAAAAAATAATTTTGATATCTGGAAAAGGGGA
Found at i:1613753 original size:58 final size:56
Alignment explanation
Indices: 1613677--1613829 Score: 152
Period size: 56 Copynumber: 2.7 Consensus size: 56
1613667 TTTCATTTTG
** * *
1613677 GGTGTCGGTCATGTGTTGGCAAACACCTCAAAAAATAATTTTGATATCTGGAAAAGG-
1 GGTGTCGACCATG-GTTGGCAGACACCTCAAAAAAT-ATTTTGATATCTGAAAAAGGA
* * ** *
1613734 GGATGTCGACCATGAGTTGGTAGACACCT-AAAAAATGTTTTTTTATTTGAAAAAGGA
1 GG-TGTCGACCATG-GTTGGCAGACACCTCAAAAAATATTTTGATATCTGAAAAAGGA
1613791 GGTGTCGACCATGGCTTGGCAGACACC-C-AAAAATATTTT
1 GGTGTCGACCATGG-TTGGCAGACACCTCAAAAAATATTTT
1613830 TTTTAGTATA
Statistics
Matches: 80, Mismatches: 12, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
55 11 0.14
56 37 0.46
57 11 0.14
58 21 0.26
ACGTcount: A:0.33, C:0.15, G:0.24, T:0.29
Consensus pattern (56 bp):
GGTGTCGACCATGGTTGGCAGACACCTCAAAAAATATTTTGATATCTGAAAAAGGA
Found at i:1613798 original size:56 final size:56
Alignment explanation
Indices: 1613728--1613892 Score: 160
Period size: 56 Copynumber: 2.9 Consensus size: 56
1613718 TGATATCTGG
1613728 AAAAGGGGATGTCGACCATGAGTTGGTAGACACCTAAAAAATGTTTTTTTATT-TG-A
1 AAAAGGGG-TGTCGACCATGAGTTGGTAGACACCTAAAAAAT-TTTTTTTATTATGAA
* *
1613784 AAAAGGAGGTGTCGACCATG-GCTTGGCAGACACCCAAAAATATTTTTTTTAGTATATGAA
1 AAAAGG-GGTGTCGACCATGAG-TTGGTAGACACCTAAAAA-ATTTTTTTTA-T-TATGAA
* * *
1613844 AAAAGGGGTGT-TAGTCATGACTT-GTCAGACACCTAAAAAATTATTTTTT
1 AAAAGGGGTGTCGA-CCATGAGTTGGT-AGACACCTAAAAAATT-TTTTTT
1613893 TATTCGTATT
Statistics
Matches: 91, Mismatches: 7, Indels: 19
0.78 0.06 0.16
Matches are distributed among these distances:
55 1 0.01
56 41 0.45
57 5 0.05
58 6 0.07
59 31 0.34
60 7 0.08
ACGTcount: A:0.35, C:0.13, G:0.21, T:0.32
Consensus pattern (56 bp):
AAAAGGGGTGTCGACCATGAGTTGGTAGACACCTAAAAAATTTTTTTTATTATGAA
Found at i:1615529 original size:14 final size:15
Alignment explanation
Indices: 1615500--1615542 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
1615490 TAAATCATAT
1615500 TTTATATTAAAAATA
1 TTTATATTAAAAATA
*
1615515 TTTAT-TTAGAAATA
1 TTTATATTAAAAATA
*
1615529 TTTACTGTTAAAAA
1 TTTA-TATTAAAAA
1615543 ACATGCGCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 12 0.50
15 6 0.25
16 6 0.25
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.47
Consensus pattern (15 bp):
TTTATATTAAAAATA
Found at i:1616283 original size:13 final size:13
Alignment explanation
Indices: 1616265--1616289 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1616255 TTTTTGGTCC
1616265 AATTTAATATTTA
1 AATTTAATATTTA
1616278 AATTTAATATTT
1 AATTTAATATTT
1616290 TTCTTAATTT
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
AATTTAATATTTA
Found at i:1618101 original size:32 final size:32
Alignment explanation
Indices: 1618034--1618101 Score: 77
Period size: 32 Copynumber: 2.1 Consensus size: 32
1618024 TCTTGTTGGG
* *
1618034 TTTGATTTTCCTTTGTGGTAGGTCTACGTCGGA
1 TTTGATTTTCCTTTGTGGTAGATCTACG-CAGA
1618067 TTTGA-TTTCCTTTGTGGTAGCATCTATC-CAGA
1 TTTGATTTTCCTTTGTGGTAG-ATCTA-CGCAGA
1618099 TTT
1 TTT
1618102 CATCAGCTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
32 21 0.68
33 9 0.29
34 1 0.03
ACGTcount: A:0.15, C:0.16, G:0.22, T:0.47
Consensus pattern (32 bp):
TTTGATTTTCCTTTGTGGTAGATCTACGCAGA
Found at i:1622296 original size:15 final size:16
Alignment explanation
Indices: 1622276--1622306 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1622266 TATTCAAAAA
1622276 GTAAAA-AAAATTTGT
1 GTAAAAGAAAATTTGT
1622291 GTAAAAGAAAATTTGT
1 GTAAAAGAAAATTTGT
1622307 TGAAAACACA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.52, C:0.00, G:0.16, T:0.32
Consensus pattern (16 bp):
GTAAAAGAAAATTTGT
Found at i:1629757 original size:12 final size:12
Alignment explanation
Indices: 1629740--1629769 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1629730 TGTGGGTATC
1629740 AAGAAGAAAAAG
1 AAGAAGAAAAAG
*
1629752 AAGAAGAGAAAG
1 AAGAAGAAAAAG
1629764 AAGAAG
1 AAGAAG
1629770 GAGAGAAGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (12 bp):
AAGAAGAAAAAG
Found at i:1636522 original size:7 final size:7
Alignment explanation
Indices: 1636510--1636596 Score: 135
Period size: 7 Copynumber: 12.7 Consensus size: 7
1636500 AACAACCTAT
1636510 AAAATAA
1 AAAATAA
1636517 AAAATAA
1 AAAATAA
1636524 AAAATAA
1 AAAATAA
1636531 AAAATAA
1 AAAATAA
1636538 AAAATAA
1 AAAATAA
1636545 AAAAT-A
1 AAAATAA
1636551 AAAATAA
1 AAAATAA
1636558 AAAAT-A
1 AAAATAA
1636564 AAAATAA
1 AAAATAA
1636571 AAAAT-A
1 AAAATAA
1636577 AAAATAA
1 AAAATAA
1636584 GAAAATAA
1 -AAAATAA
*
1636592 CAAAT
1 AAAAT
1636597 TTTTTTGACT
Statistics
Matches: 75, Mismatches: 1, Indels: 8
0.89 0.01 0.10
Matches are distributed among these distances:
6 18 0.24
7 50 0.67
8 7 0.09
ACGTcount: A:0.83, C:0.01, G:0.01, T:0.15
Consensus pattern (7 bp):
AAAATAA
Found at i:1636526 original size:1 final size:1
Alignment explanation
Indices: 1636510--1636580 Score: 52
Period size: 1 Copynumber: 71.0 Consensus size: 1
1636500 AACAACCTAT
* * * * * * * * *
1636510 AAAATAAAAAATAAAAAATAAAAAATAAAAAATAAAAAATAAAAATAAAAAATAAAAATAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
*
1636575 TAAAAA
1 AAAAAA
1636581 TAAGAAAATA
Statistics
Matches: 50, Mismatches: 20, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
1 50 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (1 bp):
A
Found at i:1636532 original size:13 final size:13
Alignment explanation
Indices: 1636510--1636596 Score: 138
Period size: 13 Copynumber: 6.4 Consensus size: 13
1636500 AACAACCTAT
1636510 AAAATAAAAAATAA
1 AAAATAAAAAAT-A
1636524 AAAATAAAAAATAA
1 AAAATAAAAAAT-A
1636538 AAAATAAAAAATA
1 AAAATAAAAAATA
1636551 AAAATAAAAAATA
1 AAAATAAAAAATA
1636564 AAAATAAAAAATA
1 AAAATAAAAAATA
1636577 AAAATAAGAAAATA
1 AAAATAA-AAAATA
1636591 ACAAAT
1 A-AAAT
1636597 TTTTTTGACT
Statistics
Matches: 71, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
13 34 0.48
14 33 0.46
15 4 0.06
ACGTcount: A:0.83, C:0.01, G:0.01, T:0.15
Consensus pattern (13 bp):
AAAATAAAAAATA
Found at i:1638322 original size:107 final size:107
Alignment explanation
Indices: 1638136--1638354 Score: 402
Period size: 107 Copynumber: 2.0 Consensus size: 107
1638126 TTTATTTCCT
*
1638136 CTTAAACGCTGATAAATTCTCATGAACTTAATTGTGTATGGAAATACCTTTTAATTTTAGATCTA
1 CTTAAACGCTGATAAATTCTCATGAACTTAATTGTGTATGGAAAAACCTTTTAATTTTAGATCTA
*
1638201 CTTTGATTTCTGCTCAATTCTTCTTATTTGTTTATCTTTGGA
66 CTTTGATTTCTGCTCAATTCTTCTTATCTGTTTATCTTTGGA
*
1638243 CTTAAACGCTGATAAATTCTCATGAACTTAATTGTGTATGGAAAAAGCTTTTAATTTTAGATCTA
1 CTTAAACGCTGATAAATTCTCATGAACTTAATTGTGTATGGAAAAACCTTTTAATTTTAGATCTA
1638308 CTTTGATTTCTGCTCAATTCTTCTTATCTGTTTATCTTTGGA
66 CTTTGATTTCTGCTCAATTCTTCTTATCTGTTTATCTTTGGA
*
1638350 TTTAA
1 CTTAA
1638355 TTGTTTGATC
Statistics
Matches: 108, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
107 108 1.00
ACGTcount: A:0.27, C:0.15, G:0.12, T:0.46
Consensus pattern (107 bp):
CTTAAACGCTGATAAATTCTCATGAACTTAATTGTGTATGGAAAAACCTTTTAATTTTAGATCTA
CTTTGATTTCTGCTCAATTCTTCTTATCTGTTTATCTTTGGA
Found at i:1648274 original size:15 final size:16
Alignment explanation
Indices: 1648254--1648283 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1648244 TTTAATTTTT
1648254 TTATTT-ACTTTTCAG
1 TTATTTCACTTTTCAG
1648269 TTATTTCACTTTTCA
1 TTATTTCACTTTTCA
1648284 TCGTGTTGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.20, C:0.17, G:0.03, T:0.60
Consensus pattern (16 bp):
TTATTTCACTTTTCAG
Found at i:1657611 original size:12 final size:12
Alignment explanation
Indices: 1657594--1657646 Score: 52
Period size: 12 Copynumber: 4.2 Consensus size: 12
1657584 CAGGTTCAAT
1657594 TTCTTCCTTCTC
1 TTCTTCCTTCTC
1657606 TTCTTCCTTTCCTTC
1 TTCTTCC-TT-C-TC
* *
1657621 TTCTTCTTTTTC
1 TTCTTCCTTCTC
*
1657633 TTCATCCTTCTC
1 TTCTTCCTTCTC
1657645 TT
1 TT
1657647 GATCACCTCT
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
12 20 0.61
13 2 0.06
14 3 0.09
15 8 0.24
ACGTcount: A:0.02, C:0.36, G:0.00, T:0.62
Consensus pattern (12 bp):
TTCTTCCTTCTC
Found at i:1669022 original size:3 final size:3
Alignment explanation
Indices: 1669014--1669059 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
1669004 CCCATAAATT
1669014 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1669060 ATTTTTTCCC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1672384 original size:15 final size:15
Alignment explanation
Indices: 1672364--1672396 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1672354 ATGGTATGAT
1672364 GTCACATTTATCACA
1 GTCACATTTATCACA
*
1672379 GTCACATTTATCATA
1 GTCACATTTATCACA
1672394 GTC
1 GTC
1672397 TCAATCTTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.30, C:0.24, G:0.09, T:0.36
Consensus pattern (15 bp):
GTCACATTTATCACA
Found at i:1673055 original size:13 final size:13
Alignment explanation
Indices: 1673039--1673064 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1673029 ACGATCAAAT
1673039 TCAAAGTCAACAG
1 TCAAAGTCAACAG
1673052 TCAAAGTCAACAG
1 TCAAAGTCAACAG
1673065 GTCGGGTCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.23, G:0.15, T:0.15
Consensus pattern (13 bp):
TCAAAGTCAACAG
Found at i:1686750 original size:30 final size:31
Alignment explanation
Indices: 1686668--1686740 Score: 130
Period size: 31 Copynumber: 2.4 Consensus size: 31
1686658 ATAACTGCCA
1686668 AATGACTTAAATAAAAACTTTTGAATAGTTC
1 AATGACTTAAATAAAAACTTTTGAATAGTTC
1686699 AATGACTTAAATAAAAACTTTTGAATAGTTC
1 AATGACTTAAATAAAAACTTTTGAATAGTTC
*
1686730 GATGAC-TAAAT
1 AATGACTTAAAT
1686741 TGTAACTTTT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
30 5 0.12
31 36 0.88
ACGTcount: A:0.45, C:0.10, G:0.11, T:0.34
Consensus pattern (31 bp):
AATGACTTAAATAAAAACTTTTGAATAGTTC
Found at i:1688523 original size:14 final size:11
Alignment explanation
Indices: 1688493--1688538 Score: 56
Period size: 11 Copynumber: 4.2 Consensus size: 11
1688483 AAACTTTATT
*
1688493 TTTTGTTATTG
1 TTTTGTTGTTG
**
1688504 TTTTGTTGTCA
1 TTTTGTTGTTG
*
1688515 TTTCGTTGTTG
1 TTTTGTTGTTG
1688526 TTTTGTTGTTG
1 TTTTGTTGTTG
1688537 TT
1 TT
1688539 CGCTATTATA
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 28 1.00
ACGTcount: A:0.04, C:0.04, G:0.22, T:0.70
Consensus pattern (11 bp):
TTTTGTTGTTG
Done.