Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010078.1 Corchorus capsularis cultivar CVL-1 contig10099, 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: 184184
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:26291 original size:2 final size:2
Alignment explanation
Indices: 26284--26314 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
26274 TGGAATTTAG
26284 TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
26315 GTGACCATGA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:30326 original size:3 final size:3
Alignment explanation
Indices: 30318--30346 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
30308 AGGTAAGATT
30318 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
30347 GGTAGAATTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:36403 original size:25 final size:25
Alignment explanation
Indices: 36375--36424 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
36365 GCATTAGAAC
36375 CCTATTTAACCAAATTAAAAGCATG
1 CCTATTTAACCAAATTAAAAGCATG
* *
36400 CCTATTTAACCAGATTGAAAGCATG
1 CCTATTTAACCAAATTAAAAGCATG
36425 ATCCCTAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.40, C:0.20, G:0.12, T:0.28
Consensus pattern (25 bp):
CCTATTTAACCAAATTAAAAGCATG
Found at i:36506 original size:17 final size:17
Alignment explanation
Indices: 36486--36524 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
36476 TTCCTAAATT
36486 ATTATTAT-TATTGAAAA
1 ATTATTATCTATTG-AAA
*
36503 ATTAGTATCTATTGAAA
1 ATTATTATCTATTGAAA
36520 ATTAT
1 ATTAT
36525 GCTTCACAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.46
Consensus pattern (17 bp):
ATTATTATCTATTGAAA
Found at i:38388 original size:10 final size:10
Alignment explanation
Indices: 38375--38409 Score: 61
Period size: 10 Copynumber: 3.5 Consensus size: 10
38365 AAAATCTTTT
38375 AAAAAAATTA
1 AAAAAAATTA
38385 AAAAAAATTA
1 AAAAAAATTA
*
38395 AAAAAAAATA
1 AAAAAAATTA
38405 AAAAA
1 AAAAA
38410 GAAAATGGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (10 bp):
AAAAAAATTA
Found at i:38389 original size:11 final size:11
Alignment explanation
Indices: 38375--38415 Score: 57
Period size: 11 Copynumber: 3.7 Consensus size: 11
38365 AAAATCTTTT
38375 AAAAAAATT-A
1 AAAAAAATTAA
38385 AAAAAAATTAA
1 AAAAAAATTAA
*
38396 AAAAAAATAAA
1 AAAAAAATTAA
38407 AAAGAAAAT
1 AAA-AAAAT
38416 GGTTGTAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
10 9 0.32
11 14 0.50
12 5 0.18
ACGTcount: A:0.83, C:0.00, G:0.02, T:0.15
Consensus pattern (11 bp):
AAAAAAATTAA
Found at i:38515 original size:15 final size:14
Alignment explanation
Indices: 38464--38556 Score: 58
Period size: 11 Copynumber: 7.1 Consensus size: 14
38454 TTATGATTAG
*
38464 TTTTAATTAGTTAA
1 TTTTAATTAGTTTA
** *
38478 TTAAAATTA-CTTA
1 TTTTAATTAGTTTA
*
38491 GTTT-ATTAGTTTA
1 TTTTAATTAGTTTA
38504 TGTTTAATTAG--TA
1 T-TTTAATTAGTTTA
*
38517 -TCTAATTAGTTTA
1 TTTTAATTAGTTTA
38530 TTATTAATTAG--TA
1 TT-TTAATTAGTTTA
38543 -TTTAATTAGTTTA
1 TTTTAATTAGTTTA
38556 T
1 T
38557 GATTAAAATG
Statistics
Matches: 58, Mismatches: 11, Indels: 20
0.65 0.12 0.22
Matches are distributed among these distances:
11 16 0.28
12 5 0.09
13 14 0.24
14 11 0.19
15 12 0.21
ACGTcount: A:0.33, C:0.02, G:0.09, T:0.56
Consensus pattern (14 bp):
TTTTAATTAGTTTA
Found at i:38524 original size:26 final size:26
Alignment explanation
Indices: 38495--38562 Score: 102
Period size: 26 Copynumber: 2.6 Consensus size: 26
38485 TACTTAGTTT
38495 ATTAGTTTATGTTTAATTAGTATCTA
1 ATTAGTTTATGTTTAATTAGTATCTA
*
38521 ATTAGTTTAT-TATTAATTAGTATTTA
1 ATTAGTTTATGT-TTAATTAGTATCTA
*
38547 ATTAGTTTATGATTAA
1 ATTAGTTTATGTTTAA
38563 AATGAAGGAA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
25 1 0.03
26 37 0.97
ACGTcount: A:0.34, C:0.01, G:0.10, T:0.54
Consensus pattern (26 bp):
ATTAGTTTATGTTTAATTAGTATCTA
Found at i:38606 original size:24 final size:24
Alignment explanation
Indices: 38572--38636 Score: 100
Period size: 23 Copynumber: 2.8 Consensus size: 24
38562 AAATGAAGGA
38572 AAATGAA-TTTGAAGATTTGTTAG
1 AAATGAAGTTTGAAGATTTGTTAG
38595 AAATGAAGTTTGAAGA-TTGTTAG
1 AAATGAAGTTTGAAGATTTGTTAG
*
38618 AAATGAAGTTT-AGGATTTG
1 AAATGAAGTTTGAAGATTTG
38637 AAGGTTGAGA
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
22 3 0.08
23 28 0.72
24 8 0.21
ACGTcount: A:0.38, C:0.00, G:0.25, T:0.37
Consensus pattern (24 bp):
AAATGAAGTTTGAAGATTTGTTAG
Found at i:38738 original size:21 final size:22
Alignment explanation
Indices: 38698--38742 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
38688 ACAAAAGTGT
38698 AAAAAGGGGAGCGCTATTTAGC
1 AAAAAGGGGAGCGCTATTTAGC
* *
38720 AAAAAGGGG-GCGGTGTTTAGC
1 AAAAAGGGGAGCGCTATTTAGC
38741 AA
1 AA
38743 TCCAGTATAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 12 0.57
22 9 0.43
ACGTcount: A:0.36, C:0.11, G:0.36, T:0.18
Consensus pattern (22 bp):
AAAAAGGGGAGCGCTATTTAGC
Found at i:45882 original size:42 final size:42
Alignment explanation
Indices: 45818--45901 Score: 141
Period size: 42 Copynumber: 2.0 Consensus size: 42
45808 AACGTAGAAT
*
45818 AACGTTAACGTGCTGTATTTTGATGACGATTTAAGAAAAATG
1 AACGATAACGTGCTGTATTTTGATGACGATTTAAGAAAAATG
* *
45860 AACGATAACGTGTTGTATTTTGATGACGATTTATGAAAAATG
1 AACGATAACGTGCTGTATTTTGATGACGATTTAAGAAAAATG
45902 TAATTTTTAA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.36, C:0.08, G:0.21, T:0.35
Consensus pattern (42 bp):
AACGATAACGTGCTGTATTTTGATGACGATTTAAGAAAAATG
Found at i:46099 original size:33 final size:33
Alignment explanation
Indices: 46056--46139 Score: 125
Period size: 33 Copynumber: 2.5 Consensus size: 33
46046 AAATTTATCT
* *
46056 AGCCGCCCTAGTGGGGCGGCTCCACCATGGCT-G
1 AGCCGTCCTAGTGGGGAGGCTCCACCATGG-TGG
*
46089 AGCCGTCCTAGTGGGGAGGCTCCGCCATGGTGG
1 AGCCGTCCTAGTGGGGAGGCTCCACCATGGTGG
46122 AGCCGTCCTAGTGGGGAG
1 AGCCGTCCTAGTGGGGAG
46140 ACTAATGTAA
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
32 1 0.02
33 46 0.98
ACGTcount: A:0.13, C:0.30, G:0.40, T:0.17
Consensus pattern (33 bp):
AGCCGTCCTAGTGGGGAGGCTCCACCATGGTGG
Found at i:49131 original size:30 final size:29
Alignment explanation
Indices: 49064--49135 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
49054 ACACCGAACC
****
49064 GTCAAATAAGCCCCTGAACTATTATTTCA
1 GTCAAATAAGCCCCTGAACTATTAAAAAA
* *
49093 GCCAAATAAGCCCCTGAACTCTTAAAAAA
1 GTCAAATAAGCCCCTGAACTATTAAAAAA
49122 TGTCAAATAAGCCC
1 -GTCAAATAAGCCC
49136 TGTTGACAAG
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
29 23 0.66
30 12 0.34
ACGTcount: A:0.39, C:0.26, G:0.11, T:0.24
Consensus pattern (29 bp):
GTCAAATAAGCCCCTGAACTATTAAAAAA
Found at i:50629 original size:11 final size:11
Alignment explanation
Indices: 50605--50639 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
50595 TTGACAGCGT
50605 AACAAAAACAA
1 AACAAAAACAA
* *
50616 AACGAAAACGA
1 AACAAAAACAA
50627 AACAAAAACAA
1 AACAAAAACAA
50638 AA
1 AA
50640 AATAGAAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.77, C:0.17, G:0.06, T:0.00
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:51409 original size:21 final size:22
Alignment explanation
Indices: 51385--51429 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
51375 TACGTGTTAG
51385 ATTTATTAT-TGTACAGAT-AAA
1 ATTTATT-TCTGTACAGATGAAA
51406 ATTTATTTCTGTACAGATGAAA
1 ATTTATTTCTGTACAGATGAAA
51428 AT
1 AT
51430 ATTTTCGGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 1 0.05
21 16 0.73
22 5 0.23
ACGTcount: A:0.40, C:0.07, G:0.11, T:0.42
Consensus pattern (22 bp):
ATTTATTTCTGTACAGATGAAA
Found at i:51435 original size:21 final size:21
Alignment explanation
Indices: 51394--51435 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
51384 GATTTATTAT
*
51394 TGTACAGATAAAATTTATTTC
1 TGTACAGATAAAATATATTTC
51415 TGTACAGATGAAAATAT-TTTC
1 TGTACAGAT-AAAATATATTTC
51436 GGTGGTTGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.38, C:0.10, G:0.12, T:0.40
Consensus pattern (21 bp):
TGTACAGATAAAATATATTTC
Found at i:65472 original size:11 final size:11
Alignment explanation
Indices: 65456--65498 Score: 68
Period size: 11 Copynumber: 3.9 Consensus size: 11
65446 TATACTATAT
65456 CTAATTAATAG
1 CTAATTAATAG
*
65467 CTAATTAATAT
1 CTAATTAATAG
65478 CTAATTAATAG
1 CTAATTAATAG
*
65489 TTAATTAATA
1 CTAATTAATA
65499 ATGAATAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.47, C:0.07, G:0.05, T:0.42
Consensus pattern (11 bp):
CTAATTAATAG
Found at i:65477 original size:22 final size:22
Alignment explanation
Indices: 65452--65498 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
65442 CCATTATACT
65452 ATATCTAATTAATAGCTAATTA
1 ATATCTAATTAATAGCTAATTA
*
65474 ATATCTAATTAATAGTTAATTA
1 ATATCTAATTAATAGCTAATTA
65496 ATA
1 ATA
65499 ATGAATAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (22 bp):
ATATCTAATTAATAGCTAATTA
Found at i:66153 original size:22 final size:22
Alignment explanation
Indices: 66125--66174 Score: 100
Period size: 22 Copynumber: 2.3 Consensus size: 22
66115 CATCATTCTT
66125 ATCATTGGACTTTTATATAACC
1 ATCATTGGACTTTTATATAACC
66147 ATCATTGGACTTTTATATAACC
1 ATCATTGGACTTTTATATAACC
66169 ATCATT
1 ATCATT
66175 CTAATTGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.32, C:0.18, G:0.08, T:0.42
Consensus pattern (22 bp):
ATCATTGGACTTTTATATAACC
Found at i:70553 original size:2 final size:2
Alignment explanation
Indices: 70546--70579 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
70536 TAGGAAGTAG
70546 TA TA TA TA TA TA TA 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
70580 GTACTGTTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:94046 original size:2 final size:2
Alignment explanation
Indices: 94039--94071 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
94029 CCAATTTAAG
*
94039 GA GA GA GA GA GA GA GA AA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
94072 TGATGATAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
GA
Found at i:106881 original size:325 final size:318
Alignment explanation
Indices: 106329--107643 Score: 1120
Period size: 325 Copynumber: 4.0 Consensus size: 318
106319 AAAAACCCTT
* * * *
106329 CAATATTTTTGGCGTTGAATTATATAT-TTTTATGAGTATTTTAACCAAAAATTGAAGAAATACA
1 CAATCTTTTTGGCGTTGAATTATATATATTTTATGAGTATTTTAGCAAAAAATTGAGGAAATA-A
* * * * *
106393 TTTTCGGTCATTTTTTGCAAAATTTTAGCCGAAAT-TCTA--AACATCACGGTTTTTGGCTAAAA
65 TTTTCGGTCAATTTTTGCAAAATTTTAGTCGAAATCTGTACTAATATCACGGTTTTTGACTAAAA
* * * * * *
106455 AAGCGTTCCAGGGCCCCAGA-TTAGTTTTGCATTATTTTTGGCACCAAGACTCCTTGAGATATCC
130 ACGCGTTCCGGGGCCCC-GACTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCC
* * * * * * *
106519 ACATTCATCTAATTAAATCTCAGCCACATTACATTTAAGGATTTATTTTTATGAGCATTTGCATC
194 ATATTCATCTAATCAAATCTCAGCTACATTGCATTTAAGGATTT-TTTTTACGAGCATCTGAATC
* *
106584 TTGTTTTGATTTAATT-GAAAATTAATTCAGAAAA-AATATGAAAAGCGTGGAAAGTCCTC
258 TTGTTTCGATTTAATTAGAAAATTAATTCAGAAAACAATATGAAAAGCGTGAAAAGTCCTC
* *
106643 CAATCTTTTTGGCGTTAAATTATATATATTTCATGAGTATTTTAGCAAAAAATTGAGGAAA-AAT
1 CAATCTTTTTGGCGTTGAATTATATATATTTTATGAGTATTTTAGCAAAAAATTGAGGAAATAA-
* *
106707 TTTTCTGGTCATTTTTTTGCAAAATTTTAGTCGAAATCATGTACTAACTATCACAGTTTTTTTTT
65 TTTTC-GGTCA-ATTTTTGCAAAATTTTAGTCGAAATC-TGTACTAA-TATCAC-G---GTTTTT
* * **
106772 TACTAAAAACGCGTTTCGGGGCCCCGACTCAGTTTTGCATGATTTTTGGCGTAAAGACTCCTTGA
122 GACTAAAAACGCGTTCCGGGGCCCCGACTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGA
* *
106837 AATATCTATATTCATCTAATCAAATCTCAGCTACATTGCATTTAAGGATTTGTTTTTATGAGCAT
187 AATATCCATATTCATCTAATCAAATCTCAGCTACATTGCATTTAAGGATTT-TTTTTACGAGCAT
* *
106902 CTGAATCTTGTTTCAATTTAATTAGAAATTAATTTAGGAAAATT-ATGAAAAACGAA-ATTAAAA
251 CTGAATCTTGTTTCGATTTAATTAG-AA--AA-TT-----AATTCA-G-AAAAC-AATATGAAAA
106965 GCGTGAAAAGTCCTC
304 GCGTGAAAAGTCCTC
* * *
106980 TAATCTTTTTGGAGTTGAATTATATATATTTTATGAGTATTTTAGAAAAAAATTGA-GAAA-AAT
1 CAATCTTTTTGGCGTTGAATTATATATATTTTATGAGTATTTTAGCAAAAAATTGAGGAAATAA-
* * * * * *
107043 TTATTTCTGGTCAATTTTTACAAAATATTA-TCCGAAATTGTGTACGTTAGTCGAAATCATGATT
65 -T-TTTC-GGTCAATTTTTGCAAAATTTTAGT-CGAAA-TCTGTAC--TA----ATATCACGGTT
* ** * ** * **
107107 TTTGGCTAAAAACGAATTCCGGGGCACCGGTTCAGTGTTGCATGATTTTTGGCGTTGAA-ACTCC
119 TTTGACTAAAAACGCGTTCCGGGGCCCCGACTCAGTTTTGCATGATTTTTGGCG-CCAAGACTCC
* * * * * ***
107171 TTGAAATATCTATATTCATCTTATAACCAAATCTCA-TTCACATTGGATTTAAGGATTTGTAAAA
183 TTGAAATATCCATATTCATC---TAATCAAATCTCAGCT-ACATTGCATTTAAGGATTTTTTTTA
* * * ** * *
107235 CAATCATCTGAATCATGTTTCGATTTAATTAG-AAATTAATTTGGAAAATAATAGGAAAAGCGAA
244 CGAGCATCTGAATCTTGTTTCGATTTAATTAGAAAATTAATTCAGAAAACAATATGAAAAGCG--
*
107299 ATTAGAAGCATGATAAGTCCTT
307 --T----G-A--A-AAGTCCTC
* * * * *
107321 TAATCTTTTTGGCATTGAATTATATA-ATTTTTATGAGTATTGTGGCTAAAAATTGAGGAAATAA
1 CAATCTTTTTGGCGTTGAATTATATATA-TTTTATGAGTATTTTAGCAAAAAATTGAGGAAATAA
* * * * *
107385 CTTTCGAGTCAATTTTTGTAAAATTCTAGTCGATATCCTGTAATAATCATCACGGTTTTTGACTA
65 TTTTCG-GTCAATTTTTGCAAAATTTTAGTCGAAAT-CTGTACTAAT-ATCACGGTTTTTGACTA
* * * * * * *
107450 AAAATGCGTTACGGGGCCCCGGCTAAGTTTTACATGATTTTTGGCGCCAAGACTCTTTGAGATAT
127 AAAACGCGTTCCGGGGCCCCGACTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATAT
* * *
107515 CCATATTCATCTAATCAGATCTCAGCTACATTGGATTTAA-CA-TTTTTTTACGAGCATCTGAAT
192 CCATATTCATCTAATCAAATCTCAGCTACATTGCATTTAAGGATTTTTTTTACGAGCATCTGAAT
* * * *
107578 CTTATTTCGATTTAATTAGAAATTTAATTCAGAAGAACGATATTAAAAGCGTGAAAAGTCCTC
257 CTTGTTTCGATTTAATTAGAAAATTAATTCAGAA-AACAATATGAAAAGCGTGAAAAGTCCTC
107641 CAA
1 CAA
107644 AATTTGACGG
Statistics
Matches: 808, Mismatches: 125, Indels: 130
0.76 0.12 0.12
Matches are distributed among these distances:
313 1 0.00
314 31 0.04
315 34 0.04
316 24 0.03
318 3 0.00
320 11 0.01
321 6 0.01
322 1 0.00
323 1 0.00
324 3 0.00
325 134 0.17
326 1 0.00
327 2 0.00
328 3 0.00
329 14 0.02
330 39 0.05
331 12 0.01
332 36 0.04
333 2 0.00
334 4 0.00
335 80 0.10
336 13 0.02
337 98 0.12
338 89 0.11
339 7 0.01
340 61 0.08
341 87 0.11
342 8 0.01
343 3 0.00
ACGTcount: A:0.33, C:0.14, G:0.15, T:0.37
Consensus pattern (318 bp):
CAATCTTTTTGGCGTTGAATTATATATATTTTATGAGTATTTTAGCAAAAAATTGAGGAAATAAT
TTTCGGTCAATTTTTGCAAAATTTTAGTCGAAATCTGTACTAATATCACGGTTTTTGACTAAAAA
CGCGTTCCGGGGCCCCGACTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCCAT
ATTCATCTAATCAAATCTCAGCTACATTGCATTTAAGGATTTTTTTTACGAGCATCTGAATCTTG
TTTCGATTTAATTAGAAAATTAATTCAGAAAACAATATGAAAAGCGTGAAAAGTCCTC
Found at i:113120 original size:15 final size:16
Alignment explanation
Indices: 113092--113124 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
113082 GAAATAAAAA
113092 TAAAAATAAAAATTAT
1 TAAAAATAAAAATTAT
*
113108 TAAAAA-AATAATTAT
1 TAAAAATAAAAATTAT
113123 TA
1 TA
113125 TATATTCCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
TAAAAATAAAAATTAT
Found at i:113204 original size:14 final size:14
Alignment explanation
Indices: 113171--113216 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
113161 ATCATTAAAA
*
113171 ATATATATAA-ATT
1 ATATTTATAATATT
113184 ATA-TTATAATATT
1 ATATTTATAATATT
**
113197 ATATTTATTTTATT
1 ATATTTATAATATT
113211 ATATTT
1 ATATTT
113217 TATTCAATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
12 5 0.18
13 9 0.32
14 14 0.50
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
ATATTTATAATATT
Found at i:113204 original size:19 final size:19
Alignment explanation
Indices: 113182--113220 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
113172 TATATATAAA
113182 TTATATTATAATATTATAT
1 TTATATTATAATATTATAT
* * *
113201 TTATTTTATTATATTTTAT
1 TTATATTATAATATTATAT
113220 T
1 T
113221 CAATAAGAAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
TTATATTATAATATTATAT
Found at i:117157 original size:16 final size:16
Alignment explanation
Indices: 117136--117187 Score: 59
Period size: 16 Copynumber: 3.1 Consensus size: 16
117126 ATATTATTTC
*
117136 ATAAATTTATAAATAT
1 ATAAATTAATAAATAT
117152 ATAAATTAATAAAATAAT
1 ATAAATTAAT-AAAT-AT
* *
117170 AAAAAATAATAAATAT
1 ATAAATTAATAAATAT
117186 AT
1 AT
117188 TATTTATTTG
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
16 12 0.40
17 8 0.27
18 10 0.33
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
ATAAATTAATAAATAT
Found at i:117560 original size:51 final size:50
Alignment explanation
Indices: 117493--117627 Score: 193
Period size: 48 Copynumber: 2.7 Consensus size: 50
117483 TTGGTGTCCG
*
117493 CCGACATGTATATGGGTTGCTCGGTGGGTCTTGCTGGGTTCAGATTGGTGT
1 CCGACATATATATGGGTTG-TCGGTGGGTCTTGCTGGGTTCAGATTGGTGT
* *
117544 CTGACATATATATGGG-T-TCGGTAGGTCTTGCTGGGTTCAGATTGGTGT
1 CCGACATATATATGGGTTGTCGGTGGGTCTTGCTGGGTTCAGATTGGTGT
* *
117592 CCAACATATATATGGGTTGATCGGTGGGCCTTGCTG
1 CCGACATATATATGGGTTG-TCGGTGGGTCTTGCTG
117628 AAGCAGACAA
Statistics
Matches: 74, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
48 44 0.59
49 1 0.01
50 1 0.01
51 28 0.38
ACGTcount: A:0.16, C:0.16, G:0.34, T:0.35
Consensus pattern (50 bp):
CCGACATATATATGGGTTGTCGGTGGGTCTTGCTGGGTTCAGATTGGTGT
Found at i:124878 original size:17 final size:18
Alignment explanation
Indices: 124851--124885 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
124841 TTCGTATAAT
124851 AATTGTTCATATAATGAA
1 AATTGTTCATATAATGAA
124869 AATT-TTCATATAATGAA
1 AATTGTTCATATAATGAA
124886 TTTTAGCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.46, C:0.06, G:0.09, T:0.40
Consensus pattern (18 bp):
AATTGTTCATATAATGAA
Found at i:129654 original size:74 final size:74
Alignment explanation
Indices: 129533--129671 Score: 260
Period size: 74 Copynumber: 1.9 Consensus size: 74
129523 TATTCTGCAC
*
129533 TGCACTTCAGATAACATTTTATAAATGTGATTTGTCAATTTGCATTAAGAAACTATACAGATATA
1 TGCACTTCAGATAACATTTTATAAATGTGAGTTGTCAATTTGCATTAAGAAACTATACAGATATA
129598 TATAAGTTT
66 TATAAGTTT
*
129607 TGCACTTCAGATGACATTTTATAAATGTGAGTTGTCAATTTGCATTAAGAAACTATACAGATATA
1 TGCACTTCAGATAACATTTTATAAATGTGAGTTGTCAATTTGCATTAAGAAACTATACAGATATA
129672 AGTCAGATCT
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
74 63 1.00
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.37
Consensus pattern (74 bp):
TGCACTTCAGATAACATTTTATAAATGTGAGTTGTCAATTTGCATTAAGAAACTATACAGATATA
TATAAGTTT
Found at i:129987 original size:18 final size:18
Alignment explanation
Indices: 129966--130000 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
129956 ATGAATTAGT
129966 AATAAAAAAATAATAATG
1 AATAAAAAAATAATAATG
* *
129984 AATAAAAGAATTATAAT
1 AATAAAAAAATAATAAT
130001 AACTTTTCTT
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:0.69, C:0.00, G:0.06, T:0.26
Consensus pattern (18 bp):
AATAAAAAAATAATAATG
Found at i:130255 original size:29 final size:31
Alignment explanation
Indices: 130195--130258 Score: 96
Period size: 29 Copynumber: 2.1 Consensus size: 31
130185 AACTTTATGT
* *
130195 TTTCCGATTGTTCCCTTATTTTTAAAACATA
1 TTTCCAATTGTACCCTTATTTTTAAAACATA
130226 TTTCCAATTGTACCC-T-TTTTTAAAACATA
1 TTTCCAATTGTACCCTTATTTTTAAAACATA
130255 TTTC
1 TTTC
130259 TAAATTGACA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 17 0.55
30 1 0.03
31 13 0.42
ACGTcount: A:0.27, C:0.20, G:0.05, T:0.48
Consensus pattern (31 bp):
TTTCCAATTGTACCCTTATTTTTAAAACATA
Found at i:130326 original size:29 final size:29
Alignment explanation
Indices: 130213--130326 Score: 87
Period size: 29 Copynumber: 4.0 Consensus size: 29
130203 TGTTCCCTTA
* **
130213 TTTTTAAAACATATTTC-CAATTGTACCCT
1 TTTTTAAAACATATTTCTAAATTG-ACATT
130242 TTTTTAAAACATATTTCTAAATTGACA--
1 TTTTTAAAACATATTTCTAAATTGACATT
** *
130269 TTACTAAATA-ATATTT-TAATTATT-TCATT
1 TTTTTAAA-ACATATTTCTAA--ATTGACATT
*
130298 TTTTTAAAATATATTTCTAAATTGACATT
1 TTTTTAAAACATATTTCTAAATTGACATT
130327 ATTAAAATTT
Statistics
Matches: 68, Mismatches: 8, Indels: 18
0.72 0.09 0.19
Matches are distributed among these distances:
26 3 0.04
27 14 0.21
28 8 0.12
29 35 0.51
30 8 0.12
ACGTcount: A:0.37, C:0.11, G:0.03, T:0.49
Consensus pattern (29 bp):
TTTTTAAAACATATTTCTAAATTGACATT
Found at i:130331 original size:27 final size:27
Alignment explanation
Indices: 130245--130339 Score: 79
Period size: 27 Copynumber: 3.4 Consensus size: 27
130235 GTACCCTTTT
*
130245 TTAAAACATATTTCTAAATTGACATTA
1 TTAAAATATATTTCTAAATTGACATTA
* * *
130272 CT-AAATAATATTT-TAATTATT-TCATTTTT
1 TTAAAAT-ATATTTCTAA--ATTGACA--TTA
130301 TTAAAATATATTTCTAAATTGACATTA
1 TTAAAATATATTTCTAAATTGACATTA
*
130328 TTAAAATTTATT
1 TTAAAATATATT
130340 ATTTAAAAAT
Statistics
Matches: 52, Mismatches: 8, Indels: 16
0.68 0.11 0.21
Matches are distributed among these distances:
26 6 0.12
27 22 0.42
28 6 0.12
29 11 0.21
30 7 0.13
ACGTcount: A:0.41, C:0.07, G:0.02, T:0.49
Consensus pattern (27 bp):
TTAAAATATATTTCTAAATTGACATTA
Found at i:134222 original size:330 final size:329
Alignment explanation
Indices: 133490--135081 Score: 1622
Period size: 330 Copynumber: 4.8 Consensus size: 329
133480 CCGAAATCTC
* * * * * * * * *
133490 GTTTTACATGATTTTTTGCGCCGAGACTCCTTGAAATATTTTTATTTATCTAATAAAATCTTAGG
1 GTTTTGCATGATTTTTGGCGCCGAAACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGC
* * *
133555 CATATTAGATTTAAGGATTTGTTTTTATGTGAATCTGAATCTTGTTTCGATTTAATTAGAAATTA
66 CACATTAGATTTAAGGATTTGTTTTTACGTGCATCTGAATCTTGTTTCGATTTAATTAGAAATTA
* *
133620 ATTTAGAAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCCTCCAATCCTTTTGATGT-TG
131 ATTT-GAAAAAATATGAAAAACAATATTAAAAGCGTGAAAAGTCCTCCAATCTTTTTGATGTCT-
* * * *
133684 AATTATATATTTTTTATGAGTATTTTCACTATAAATCGAGGAAAAATATTTCGGGTCAATTTTTG
194 AATTATATATTTTTTATGAGTATTTTAACCATAAATTGAGGAAAAATCTTTCGGGTCAATTTTTG
* * * * *
133749 CAAAATTTTA-GCCGAAATCAAGTACTAACCATGACGGTTTTCGACTAAAACCACGTTTCGAGGC
259 CAAAATTTTATG-CGAAATCATGTACTAACCATCACGGTTTTCGGCTAAAAACACG-TTCCAGGC
* *
133813 -CCAGCTCA
322 ACGA-CTCT
* * *
133821 GTTTTGCATGATTTTTGGTGCCAAAACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGC
1 GTTTTGCATGATTTTTGGCGCCGAAACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGC
* * ** * *
133886 CACATTAGATTCACGGATTTGTTTTTACAAGCATCTGAATCTTGTTTCAATTTAATTAAAAATTA
66 CACATTAGATTTAAGGATTTGTTTTTACGTGCATCTGAATCTTGTTTCGATTTAATTAGAAATTA
* * * *
133951 ATTTGAAAAAATA-AAAAAACAATATTAGAAGCGCT-AAAAGTCTTTCAATCTTTTTGATGTCTA
131 ATTTGAAAAAATATGAAAAACAATATTAAAAGCG-TGAAAAGTCCTCCAATCTTTTTGATGTCTA
* * * * *
134014 ATTATATATTTTTTATGAGTATTTGAACCATAAATTGTGGAAATATCTTTCGGGTTAATTTTTAC
195 ATTATATATTTTTTATGAGTATTTTAACCATAAATTGAGGAAAAATCTTTCGGGTCAATTTTTGC
* * * *
134079 AAAATTTT-TGCGAAATCGTGTACTAATCATCACGGTTTTTTGGCTAAAAACGCGTTCCATGGCT
260 AAAATTTTATGCGAAATCATGTACTAACCATCACGG-TTTTCGGCTAAAAACACGTTCCA-GGC-
*
134143 ACGGCTCT
322 ACGACTCT
* *
134151 GTTTTACATGATTTTTGGCGCCGAAACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGA
1 GTTTTGCATGATTTTTGGCGCCGAAACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGC
* *
134216 CACATTAGATTTAAGGATTTGTTTTTA-GTTGAATCTGAATCTTGTTTCAATTTAATTAGAAATT
66 CACATTAGATTTAAGGATTTGTTTTTACG-TGCATCTGAATCTTGTTTCGATTTAATTAGAAATT
* * *
134280 CATTCAGAAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCCTCCAATCCTTTTGACGTTG
130 AATT-TGAAAAAATATGAAAAACAATATTAAAAGCGTGAAAAGTCCTCCAAT-C-TTT----TTG
* * ** ***
134345 AATTATATATATATATATATATATATATTTATGAGTATTTTCGCTGGAAATTGAGGAAAAATCTT
188 ----ATGTCTA-AT-TATATAT-T-T-TTTATGAGTATTTTAACCATAAATTGAGGAAAAATCTT
* ** * * * *
134410 TTGCATCAATTTTTGCAAAATTTTAAT-CGAAATCATTTACCAATCATCATGGTTTTCGGCTAAA
244 TCGGGTCAATTTTTGCAAAATTTT-ATGCGAAATCATGTACTAACCATCACGGTTTTCGGCTAAA
* ** *
134474 ACCGTGTTCCGGGGC-CTGACT-T
308 AACACGTTCC-AGGCAC-GACTCT
* * * * *
134496 AGTTTTGCATGATTTTTTGTGCC-AAGACTCATTGAAATATCTATATTAATCTAACCAAATCTCA
1 -GTTTTGCATGATTTTTGGCGCCGAA-ACTCCTTGAAATATCTATATTCATCTAATCAAATCTCA
* *
134560 GCCACATTAAATTT-AGGA-TTGTTTTTACGAT-CATCTGAATCTTATTTCGATTTAATTAGAAA
64 GCCACATTAGATTTAAGGATTTGTTTTTACG-TGCATCTGAATCTTGTTTCGATTTAATTAGAAA
* * * * * *
134622 TTAATTTG-AAAAATAGGAAAAACAATATTAGAAGAGTTAAAAG-CCATTCAATCTTTTTTATGT
128 TTAATTTGAAAAAATATGAAAAACAATATTAAAAGCGTGAAAAGTCC-TCCAATCTTTTTGATGT
* * * *
134685 CGAATTATATATATTTTATGAGTATTTTAGCCAAAAATTGA-GAAAATATCTTTCGGGTCAAATT
192 CTAATTATATATTTTTTATGAGTATTTTAACCATAAATTGAGGAAAA-ATCTTTCGGGTC-AATT
* * ** *
134749 TTTGCAAAATTTTATCCAAAATTGTGTA-TGAACCATCACGGTTTTTGGCTAAAAACACGTTCCA
255 TTTGCAAAATTTTATGCGAAATCATGTACT-AACCATCACGGTTTTCGGCTAAAAACACGTTCC-
*
134813 AGTCACGACTCT
318 AGGCACGACTCT
* * * * *
134825 GTTTTGCATGATTTTTGTCACCGAGACTCCTTGAAATATCTTTATTCATCTAATCAAATCTCAGG
1 GTTTTGCATGATTTTTGGCGCCGAAACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGC
* * * * *
134890 CGCATTGGATTTAAGGATTTGCTTTTATGTGCATCTGAATCTTATTTCGATTTAATTAGAAATTA
66 CACATTAGATTTAAGGATTTGTTTTTACGTGCATCTGAATCTTGTTTCGATTTAATTAGAAATTA
* * * * * **
134955 ATTCTGAAAAAATATGAAAGACGATATTAAAAGAGTGAGAAGTCCTCCAATCCTTTTGGCGT-TG
131 ATT-TGAAAAAATATGAAAAACAATATTAAAAGCGTGAAAAGTCCTCCAATCTTTTTGATGTCT-
* * ** * *
135019 AATTATTTATATTTTATGAGTATTTTTGCCAAAAATTGAGGAAAAATCTTTTGGGTC-ATTTTT
194 AATTATATATTTTTTATGAGTATTTTAACCATAAATTGAGGAAAAATCTTTCGGGTCAATTTTT
135082 ACCTTCATGG
Statistics
Matches: 1046, Mismatches: 166, Indels: 99
0.80 0.13 0.08
Matches are distributed among these distances:
326 5 0.00
327 34 0.03
328 146 0.14
329 130 0.12
330 193 0.18
331 128 0.12
332 122 0.12
333 8 0.01
334 3 0.00
336 2 0.00
338 3 0.00
340 3 0.00
341 3 0.00
342 40 0.04
343 3 0.00
344 49 0.05
345 11 0.01
346 70 0.07
347 71 0.07
348 21 0.02
349 1 0.00
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.38
Consensus pattern (329 bp):
GTTTTGCATGATTTTTGGCGCCGAAACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGC
CACATTAGATTTAAGGATTTGTTTTTACGTGCATCTGAATCTTGTTTCGATTTAATTAGAAATTA
ATTTGAAAAAATATGAAAAACAATATTAAAAGCGTGAAAAGTCCTCCAATCTTTTTGATGTCTAA
TTATATATTTTTTATGAGTATTTTAACCATAAATTGAGGAAAAATCTTTCGGGTCAATTTTTGCA
AAATTTTATGCGAAATCATGTACTAACCATCACGGTTTTCGGCTAAAAACACGTTCCAGGCACGA
CTCT
Found at i:134355 original size:2 final size:2
Alignment explanation
Indices: 134348--134372 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
134338 GACGTTGAAT
134348 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
134373 TTATGAGTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:134873 original size:674 final size:671
Alignment explanation
Indices: 133490--135031 Score: 2098
Period size: 674 Copynumber: 2.3 Consensus size: 671
133480 CCGAAATCTC
* * * *
133490 GTTTTACATGATTTTT-TGCGCCGAGACTCCTTGAAATATTTTTATTTATCTAATAAAATCTTAG
1 GTTTTACATGATTTTTGT-CGCCGAGACTCCTTGAAATATCTTTATTCATCTAATCAAATCTCAG
*
133554 GCATATTAGATTTAAGGATTTGTTTTTATGTGAATCTGAATCTTGTTTCGATTTAATTAGAAATT
65 GCACATTAGATTTAAGGATTTGTTTTTATGTGAATCTGAATCTTGTTTCGATTTAATTAGAAATT
*
133619 AATTTAGAAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCCTCCAATCCTTTTGA---TG
130 AATTCAGAAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCCTCCAATCCTTTTGACGTTG
* * **
133681 -----TT-GA-ATTATATATTTTTTATGAGTATTTTCACTATAAATCGAGGAAAAATATTTCGGG
195 AATTATTATATATTATATATTTTTTATGAGTATTTTCACTAGAAATCGAGGAAAAATATTTCGCA
* * *
133739 TCAATTTTTGCAAAATTTTAGCCGAAATCAAGTACTAACCATGACGGTTTTCGACTAAAACCACG
260 TCAATTTTTGCAAAATTTTAACCGAAATCAAGTACCAACCATCACGGTTTTCGACTAAAACCACG
* * *
133804 TTTCGAGGCCCAGCTCAGTTTTGCATGATTTTTGGTGCCAAAACTCCTTGAAATATCTATATTCA
325 TTCCGAGGCCCAGCTCAGTTTTGCATGATTTTTGGTGCCAAAACTCATTGAAATATCTATATTAA
* *
133869 TCTAACCAAATCTCAGCCACATTAGATTCACGGATTTGTTTTTACAAGCATCTGAATCTTGTTTC
390 TCTAACCAAATCTCAGCCACATTAAATTCACGGATTTGTTTTTACAAGCATCTGAATCTTATTTC
* * *
133934 AATTTAATTAAAAATTAATTTGAAAAAATAAAAAAACAATATTAGAAGCGCTAAAAGTCTTTCAA
455 AATTTAATTAAAAATTAATTTGAAAAAATAAAAAAACAATATTAGAAGAGCTAAAAGCCATTCAA
* * * * *
133999 TCTTTTTGATGTCTAATTATATATTTTTTATGAGTATTTGAACCATAAATTGTGGAAATATCTTT
520 TCTTTTTGATGTCGAATTATATATATTTTATGAGTATTTGAACCAAAAATTGAGAAAATATCTTT
* * * *
134064 CGGGTTAATTTTTACAAAATTTTTGCGAAATCGTGTACTAATCATCACGGTTTTTTGGCTAAAAA
585 CGGGTAAATTTTTACAAAATTTTTCCAAAATCGTGTACTAACCATCACGGTTTTTTGGCTAAAAA
* * *
134129 CGCGTTCCATGGCTACGGCTCT
650 CACGTTCCAAGGCTACGACTCT
* * * *
134151 GTTTTACATGATTTTTGGCGCCGAAACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGA
1 GTTTTACATGATTTTTGTCGCCGAGACTCCTTGAAATATCTTTATTCATCTAATCAAATCTCAGG
*
134216 CACATTAGATTTAAGGATTTGTTTTTA-GTTGAATCTGAATCTTGTTTCAATTTAATTAGAAATT
66 CACATTAGATTTAAGGATTTGTTTTTATG-TGAATCTGAATCTTGTTTCGATTTAATTAGAAATT
*
134280 CATTCAGAAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCCTCCAATCCTTTTGACGTTG
130 AATTCAGAAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCCTCCAATCCTTTTGACGTTG
* * * *
134345 AATTATATATATATATATATATATATATTTATGAGTATTTTCGCTGGAAATTGAGGAAAAATCTT
195 AATTAT-TATATAT-TATATAT-T-T-TTTATGAGTATTTTCACTAGAAATCGAGGAAAAATATT
* * ** * * *
134410 TTGCATCAATTTTTGCAAAATTTTAATCGAAATCATTTACCAATCATCATGGTTTTCGGCTAAAA
255 TCGCATCAATTTTTGCAAAATTTTAACCGAAATCAAGTACCAACCATCACGGTTTTCGACTAAAA
** * * * * *
134475 CCGTGTTCCG-GGGCCTGACTTAGTTTTGCATGATTTTTTGTGCCAAGACTCATTGAAATATCTA
320 CCACGTTCCGAGGCCCAG-CTCAGTTTTGCATGATTTTTGGTGCCAAAACTCATTGAAATATCTA
* * *
134539 TATTAATCTAACCAAATCTCAGCCACATTAAATTTA-GGA-TTGTTTTTACGATCATCTGAATCT
384 TATTAATCTAACCAAATCTCAGCCACATTAAATTCACGGATTTGTTTTTACAAGCATCTGAATCT
* * * *
134602 TATTTCGATTTAATTAGAAATTAATTTG-AAAAATAGGAAAAACAATATTAGAAGAGTTAAAAGC
449 TATTTCAATTTAATTAAAAATTAATTTGAAAAAATA-AAAAAACAATATTAGAAGAGCTAAAAGC
* * *
134666 CATTCAATCTTTTTTATGTCGAATTATATATATTTTATGAGTATTTTAGCCAAAAATTGAGAAAA
513 CATTCAATCTTTTTGATGTCGAATTATATATATTTTATGAGTATTTGAACCAAAAATTGAGAAAA
* *
134731 TATCTTTCGGGTCAAATTTTTGCAAAATTTTATCCAAAATTGTGTA-TGAACCATCACGG-TTTT
578 TATCTTTCGGGT-AAATTTTTACAAAATTTT-TCCAAAATCGTGTACT-AACCATCACGGTTTTT
*
134794 TGGCTAAAAACACGTTCCAAGTC-ACGACTCT
640 TGGCTAAAAACACGTTCCAAGGCTACGACTCT
* *
134825 GTTTTGCATGATTTTTGTCACCGAGACTCCTTGAAATATCTTTATTCATCTAATCAAATCTCAGG
1 GTTTTACATGATTTTTGTCGCCGAGACTCCTTGAAATATCTTTATTCATCTAATCAAATCTCAGG
* * * * *
134890 CGCATTGGATTTAAGGATTTGCTTTTATGTGCATCTGAATCTTATTTCGATTTAATTAGAAATTA
66 CACATTAGATTTAAGGATTTGTTTTTATGTGAATCTGAATCTTGTTTCGATTTAATTAGAAATTA
* * * * *
134955 ATTCTGAAAAAATATGAAAGACGATATTAAAAGAGTGAGAAGTCCTCCAATCCTTTTGGCGTTGA
131 ATTCAGAAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCCTCCAATCCTTTTGACGTTGA
135020 ATTATT-TATATT
196 ATTATTATATATT
135032 TTATGAGTAT
Statistics
Matches: 770, Mismatches: 88, Indels: 36
0.86 0.10 0.04
Matches are distributed among these distances:
660 1 0.00
661 174 0.23
664 2 0.00
669 1 0.00
670 1 0.00
671 2 0.00
672 7 0.01
673 15 0.02
674 327 0.42
675 51 0.07
676 189 0.25
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.38
Consensus pattern (671 bp):
GTTTTACATGATTTTTGTCGCCGAGACTCCTTGAAATATCTTTATTCATCTAATCAAATCTCAGG
CACATTAGATTTAAGGATTTGTTTTTATGTGAATCTGAATCTTGTTTCGATTTAATTAGAAATTA
ATTCAGAAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCCTCCAATCCTTTTGACGTTGA
ATTATTATATATTATATATTTTTTATGAGTATTTTCACTAGAAATCGAGGAAAAATATTTCGCAT
CAATTTTTGCAAAATTTTAACCGAAATCAAGTACCAACCATCACGGTTTTCGACTAAAACCACGT
TCCGAGGCCCAGCTCAGTTTTGCATGATTTTTGGTGCCAAAACTCATTGAAATATCTATATTAAT
CTAACCAAATCTCAGCCACATTAAATTCACGGATTTGTTTTTACAAGCATCTGAATCTTATTTCA
ATTTAATTAAAAATTAATTTGAAAAAATAAAAAAACAATATTAGAAGAGCTAAAAGCCATTCAAT
CTTTTTGATGTCGAATTATATATATTTTATGAGTATTTGAACCAAAAATTGAGAAAATATCTTTC
GGGTAAATTTTTACAAAATTTTTCCAAAATCGTGTACTAACCATCACGGTTTTTTGGCTAAAAAC
ACGTTCCAAGGCTACGACTCT
Found at i:144280 original size:28 final size:29
Alignment explanation
Indices: 144239--144308 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 29
144229 CTGAGGGAGT
*
144239 AAAAAGTCTCAAAATTGAAGTTCA-GGGGC
1 AAAAAGTC-CAAAATTAAAGTTCAGGGGGC
* *
144268 AAAATGTCCAAAATTAAAGTTTAGGGGGC
1 AAAAAGTCCAAAATTAAAGTTCAGGGGGC
**
144297 AAAGCGTCCAAA
1 AAAAAGTCCAAA
144309 TGCTACAAGT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
28 13 0.37
29 22 0.63
ACGTcount: A:0.43, C:0.14, G:0.23, T:0.20
Consensus pattern (29 bp):
AAAAAGTCCAAAATTAAAGTTCAGGGGGC
Found at i:147128 original size:12 final size:13
Alignment explanation
Indices: 147099--147131 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
147089 CTCACCATAA
147099 TTTCAAAAAACACT
1 TTTC-AAAAACACT
147113 TTTCAAAAACAC-
1 TTTCAAAAACACT
147125 TTTCAAA
1 TTTCAAA
147132 CCAAGGTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.37
13 8 0.42
14 4 0.21
ACGTcount: A:0.48, C:0.21, G:0.00, T:0.30
Consensus pattern (13 bp):
TTTCAAAAACACT
Found at i:149413 original size:14 final size:14
Alignment explanation
Indices: 149394--149423 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
149384 TAAGTTTCTC
149394 TCTTTTTTTCTTTT
1 TCTTTTTTTCTTTT
*
149408 TCTTTTTTTTTTTT
1 TCTTTTTTTCTTTT
149422 TC
1 TC
149424 ACTTTTGTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (14 bp):
TCTTTTTTTCTTTT
Found at i:150122 original size:20 final size:20
Alignment explanation
Indices: 150099--150141 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
150089 TGCAGCTATT
150099 CCAATCAATAAACAGCTCTA
1 CCAATCAATAAACAGCTCTA
150119 CCAATCAATAAACAGCTCTA
1 CCAATCAATAAACAGCTCTA
150139 CCA
1 CCA
150142 TTAGCTATGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.44, C:0.33, G:0.05, T:0.19
Consensus pattern (20 bp):
CCAATCAATAAACAGCTCTA
Found at i:161767 original size:2 final size:2
Alignment explanation
Indices: 161760--161785 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
161750 ATATGTATCC
161760 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
161786 CGATTAATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:163568 original size:3 final size:3
Alignment explanation
Indices: 163560--163598 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
163550 ATCAGTGCAA
163560 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
163599 TTTTCAGTGC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:169288 original size:105 final size:103
Alignment explanation
Indices: 169108--169317 Score: 314
Period size: 105 Copynumber: 2.0 Consensus size: 103
169098 TAAGATACAA
*
169108 CTGAAATAGGTTGATAGATTAACCAACCATCTAGGTCCCCTTCAGAATAAAGCTATACCCCATAA
1 CTGAAATAGGTTGATAGATTAACCAACCATCTAGGCCCCCTTCAGAATAAAGCTATACCCCATAA
169173 AAAGGCCAAATCAGCCATTGAACTTATGGTACATTAAT
66 AAAGGCCAAATCAGCCATTGAACTTATGGTACATTAAT
* *
169211 CTGAAATAGGTTGATAGATTAACTACCCATCTATGGCCCCCCTTCA-AGATAAAGCTATACCCCA
1 CTGAAATAGGTTGATAGATTAACCAACCATCTA-GG-CCCCCTTCAGA-ATAAAGCTATACCCCA
** * * *
169275 TAAGGAGGCCAAATCAGCCATTGAGCTTCTTGTACATTAAT
63 TAAAAAGGCCAAATCAGCCATTGAACTTATGGTACATTAAT
169316 CT
1 CT
169318 ACCCAAGGGA
Statistics
Matches: 96, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
103 31 0.32
104 3 0.03
105 62 0.65
ACGTcount: A:0.35, C:0.24, G:0.15, T:0.26
Consensus pattern (103 bp):
CTGAAATAGGTTGATAGATTAACCAACCATCTAGGCCCCCTTCAGAATAAAGCTATACCCCATAA
AAAGGCCAAATCAGCCATTGAACTTATGGTACATTAAT
Found at i:173406 original size:97 final size:97
Alignment explanation
Indices: 173237--173425 Score: 360
Period size: 97 Copynumber: 1.9 Consensus size: 97
173227 AAGAATAGTC
*
173237 TTTAAATCCAATCAGATTTAAATTTCATGAAAAAACAAACAACAATAGATTCATATTTTACTAAA
1 TTTAAATCCAATCAGATTTAAATTTCATGAAAAAACAAACAACAATAAATTCATATTTTACTAAA
*
173302 TTGTCTTAGATATATATGTAAATTTTACTAAA
66 TTATCTTAGATATATATGTAAATTTTACTAAA
173334 TTTAAATCCAATCAGATTTAAATTTCATGAAAAAACAAACAACAATAAATTCATATTTTACTAAA
1 TTTAAATCCAATCAGATTTAAATTTCATGAAAAAACAAACAACAATAAATTCATATTTTACTAAA
173399 TTATCTTAGATATATATGTAAATTTTA
66 TTATCTTAGATATATATGTAAATTTTA
173426 TAGAATTATT
Statistics
Matches: 90, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
97 90 1.00
ACGTcount: A:0.46, C:0.11, G:0.05, T:0.38
Consensus pattern (97 bp):
TTTAAATCCAATCAGATTTAAATTTCATGAAAAAACAAACAACAATAAATTCATATTTTACTAAA
TTATCTTAGATATATATGTAAATTTTACTAAA
Found at i:173690 original size:38 final size:34
Alignment explanation
Indices: 173609--173672 Score: 103
Period size: 34 Copynumber: 1.9 Consensus size: 34
173599 AAAGTTTTAC
* *
173609 TGTAATTATTATGTTGCTAATTATCCAAAAAAAA
1 TGTAATTATTATGTTGCTAATTAGCAAAAAAAAA
173643 TGTAATTATTATGTTGC-AATTAGCAAAAAA
1 TGTAATTATTATGTTGCTAATTAGCAAAAAA
173673 GAAAAATATG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
33 11 0.39
34 17 0.61
ACGTcount: A:0.44, C:0.08, G:0.11, T:0.38
Consensus pattern (34 bp):
TGTAATTATTATGTTGCTAATTAGCAAAAAAAAA
Found at i:176744 original size:21 final size:21
Alignment explanation
Indices: 176718--176790 Score: 58
Period size: 21 Copynumber: 3.3 Consensus size: 21
176708 TAGAATCAGA
*
176718 TGAAGAATCCGAACCAGGATC
1 TGAAGAAACCGAACCAGGATC
* ** *
176739 TGAAGAAGA-AGAATTAGAATC
1 TGAAGAA-ACCGAACCAGGATC
176760 AGATGAAGAAACCGAACCAGGATC
1 ---TGAAGAAACCGAACCAGGATC
176784 TGAAGAA
1 TGAAGAA
176791 GAAGAAGAAC
Statistics
Matches: 38, Mismatches: 9, Indels: 10
0.67 0.16 0.18
Matches are distributed among these distances:
21 22 0.58
23 1 0.03
24 15 0.39
ACGTcount: A:0.47, C:0.15, G:0.25, T:0.14
Consensus pattern (21 bp):
TGAAGAAACCGAACCAGGATC
Found at i:176775 original size:45 final size:45
Alignment explanation
Indices: 176707--176796 Score: 171
Period size: 45 Copynumber: 2.0 Consensus size: 45
176697 TGTAGTCGAT
*
176707 TTAGAATCAGATGAAGAATCCGAACCAGGATCTGAAGAAGAAGAA
1 TTAGAATCAGATGAAGAAACCGAACCAGGATCTGAAGAAGAAGAA
176752 TTAGAATCAGATGAAGAAACCGAACCAGGATCTGAAGAAGAAGAA
1 TTAGAATCAGATGAAGAAACCGAACCAGGATCTGAAGAAGAAGAA
176797 GAACAGGAAG
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.48, C:0.13, G:0.24, T:0.14
Consensus pattern (45 bp):
TTAGAATCAGATGAAGAAACCGAACCAGGATCTGAAGAAGAAGAA
Found at i:176791 original size:24 final size:24
Alignment explanation
Indices: 176719--176793 Score: 75
Period size: 24 Copynumber: 3.2 Consensus size: 24
176709 AGAATCAGAT
*
176719 GAAGAATCCGAACCAGGATCTGAA
1 GAAGAAACCGAACCAGGATCTGAA
** * * *
176743 GAAG-AA--GAATTAGAATCAGAT
1 GAAGAAACCGAACCAGGATCTGAA
176764 GAAGAAACCGAACCAGGATCTGAA
1 GAAGAAACCGAACCAGGATCTGAA
176788 GAAGAA
1 GAAGAA
176794 GAAGAACAGG
Statistics
Matches: 37, Mismatches: 11, Indels: 6
0.69 0.20 0.11
Matches are distributed among these distances:
21 14 0.38
22 2 0.05
23 1 0.03
24 20 0.54
ACGTcount: A:0.48, C:0.15, G:0.25, T:0.12
Consensus pattern (24 bp):
GAAGAAACCGAACCAGGATCTGAA
Found at i:176817 original size:21 final size:21
Alignment explanation
Indices: 176791--176846 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
176781 ATCTGAAGAA
*
176791 GAAGAAGAACAGGAAGAGACC
1 GAAGAAGAACAAGAAGAGACC
**
176812 GAAGAAG-ACGAAGAAGATTCC
1 GAAGAAGAAC-AAGAAGAGACC
176833 GAAGAAGAACAAGA
1 GAAGAAGAACAAGA
176847 GCAAGAACAG
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 2 0.07
21 26 0.87
22 2 0.07
ACGTcount: A:0.54, C:0.12, G:0.30, T:0.04
Consensus pattern (21 bp):
GAAGAAGAACAAGAAGAGACC
Found at i:179120 original size:69 final size:69
Alignment explanation
Indices: 179037--179176 Score: 253
Period size: 69 Copynumber: 2.0 Consensus size: 69
179027 ATCTAAAGTT
* *
179037 TTCTGTCCTGAGCATTGTGCTTACTTACTATTACATTATTGCAGCATATTTATTAGATTTTATTT
1 TTCTGTCATGAGCATTGTGCTTACTTACTATTACATTATTGCAGCATATTTATTACATTTTATTT
179102 GAAA
66 GAAA
*
179106 TTCTGTCATGAGCATTGTGCTTACTTATTATTACATTATTGCAGCATATTTATTACATTTTATTT
1 TTCTGTCATGAGCATTGTGCTTACTTACTATTACATTATTGCAGCATATTTATTACATTTTATTT
179171 GAAA
66 GAAA
179175 TT
1 TT
179177 GTGCTTACTT
Statistics
Matches: 68, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
69 68 1.00
ACGTcount: A:0.26, C:0.14, G:0.12, T:0.48
Consensus pattern (69 bp):
TTCTGTCATGAGCATTGTGCTTACTTACTATTACATTATTGCAGCATATTTATTACATTTTATTT
GAAA
Found at i:179178 original size:55 final size:55
Alignment explanation
Indices: 179119--179231 Score: 217
Period size: 55 Copynumber: 2.1 Consensus size: 55
179109 TGTCATGAGC
*
179119 ATTGTGCTTACTTATTATTACATTATTGCAGCATATTTATTACATTTTATTTGAA
1 ATTGTGCTTACTTATTATTACATTATTGCAACATATTTATTACATTTTATTTGAA
179174 ATTGTGCTTACTTATTATTACATTATTGCAACATATTTATTACATTTTATTTGAA
1 ATTGTGCTTACTTATTATTACATTATTGCAACATATTTATTACATTTTATTTGAA
179229 ATT
1 ATT
179232 TACTATAGGA
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 57 1.00
ACGTcount: A:0.30, C:0.11, G:0.08, T:0.51
Consensus pattern (55 bp):
ATTGTGCTTACTTATTATTACATTATTGCAACATATTTATTACATTTTATTTGAA
Found at i:179505 original size:12 final size:12
Alignment explanation
Indices: 179490--179515 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
179480 CAAGCATTGA
179490 CTCAAATTCTCC
1 CTCAAATTCTCC
179502 CTCAAATTCTCC
1 CTCAAATTCTCC
179514 CT
1 CT
179516 GGTATGTTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.42, G:0.00, T:0.35
Consensus pattern (12 bp):
CTCAAATTCTCC
Found at i:179829 original size:44 final size:44
Alignment explanation
Indices: 179769--179865 Score: 158
Period size: 44 Copynumber: 2.2 Consensus size: 44
179759 CTTATTTTGT
* *
179769 AGGAATATTTTGTGGTAGGAGATTGAAATCAACTTTATCATTTC
1 AGGATTATTTTATGGTAGGAGATTGAAATCAACTTTATCATTTC
* *
179813 AGGATTATTTTATGGTAGGGGATTGAAATCAACTTTATCATTTT
1 AGGATTATTTTATGGTAGGAGATTGAAATCAACTTTATCATTTC
179857 AGGATTATT
1 AGGATTATT
179866 ATGTAGGAGT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
44 49 1.00
ACGTcount: A:0.31, C:0.07, G:0.21, T:0.41
Consensus pattern (44 bp):
AGGATTATTTTATGGTAGGAGATTGAAATCAACTTTATCATTTC
Found at i:180207 original size:55 final size:55
Alignment explanation
Indices: 180148--180270 Score: 221
Period size: 55 Copynumber: 2.2 Consensus size: 55
180138 GAACAATACT
*
180148 TTGAATTCATAACAACTACG-CTGAACATTAACGCTCTTGTGACGGACAATATAGC
1 TTGAATTCATAACAACTACGAC-GAACATTAACGCTCTTGCGACGGACAATATAGC
180203 TTGAATTCATAACAACTACGACGAACATTAACGCTCTTGCGACGGACAATATAGC
1 TTGAATTCATAACAACTACGACGAACATTAACGCTCTTGCGACGGACAATATAGC
180258 TTGAATTCATAAC
1 TTGAATTCATAAC
180271 TACGACGGAC
Statistics
Matches: 66, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
55 65 0.98
56 1 0.02
ACGTcount: A:0.36, C:0.22, G:0.15, T:0.27
Consensus pattern (55 bp):
TTGAATTCATAACAACTACGACGAACATTAACGCTCTTGCGACGGACAATATAGC
Found at i:182559 original size:21 final size:21
Alignment explanation
Indices: 182511--182565 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
182501 TGTTTTGAGT
* * * *
182511 AAGAAAGAAGCCGAATGGAGA
1 AAGAGAGAAGCTGAAGGGAAA
182532 AAGAGAGAAGCTGAAGGGAAA
1 AAGAGAGAAGCTGAAGGGAAA
*
182553 AATAGAGAAGCTG
1 AAGAGAGAAGCTG
182566 GATTAAAACA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.51, C:0.07, G:0.35, T:0.07
Consensus pattern (21 bp):
AAGAGAGAAGCTGAAGGGAAA
Done.