Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1871
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: 379514
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
File 3 of 3
Found at i:328519 original size:102 final size:104
Alignment explanation
Indices: 328395--328889 Score: 426
Period size: 102 Copynumber: 4.5 Consensus size: 104
328385 GACTAAAAAG
*
328395 TGCCACCAACTCGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAAC
1 TGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAAC
* *
328460 TTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTT-GA-G-GA
66 TTGTGTGGGCTTTAA-AGGGGTCCTGCTCTTTGGACGAAA
328497 TGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAAC
1 TGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAAC
*
328562 TTGTGTGGGCTTCGAAAGGGGTCCTGCTCTTTGGGGACTGAAAAA
66 TTGTGTGGGCTT-TAAAGGGGTCCTGCTCTTT--GGAC-G--AAA
* * * *
328607 TGCCACCAACTTGTGTGGGCTTCGAAAGGGGTCCTGCTCTTTGGGGACT-GAAAGGTGCCACCAA
1 TGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAA
*** *
328671 CTTGTGTGGGCTTTGAAAAGAAAAAACATCCTGCTCTTTGAGGACTGAAGG
65 CTTGTGTGGGCTTT--AAAG-----GGGTCCTGCTCTTT--GGAC-GAA-A
* ** **
328722 TGCCACCAACTTGGGTGGGCTTTAAAAGAAAAGGCAT-CTCGCTCTTTGAGGACT-GAAGGTGCC
1 TGCCACCAACTTGTGTGGGCTTT----G-AAAGGTGTCCT-GCTCTTTGAGGACTGGAAAATGCC
* **
328785 ACCAACTTGTGTGGGCTTTAAAAGAAAATGCGTCCCACTCTTTGAGGACTGAAAAA
60 ACCAACTTGTGTGGGCTTT-AAAG-----GGGTCCTGCTCTTT--GGAC-G--AAA
* *
328841 TGCCACCAACTTGTGTGGGCTTTAAAAGGCGTCCTGCTCTTTGAGGACT
1 TGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACT
328890 AAAAAGCGGA
Statistics
Matches: 337, Mismatches: 29, Indels: 42
0.83 0.07 0.10
Matches are distributed among these distances:
102 91 0.27
103 2 0.01
105 2 0.01
107 1 0.00
109 4 0.01
110 69 0.20
111 4 0.01
114 23 0.07
115 23 0.07
116 18 0.05
118 27 0.08
119 49 0.15
120 24 0.07
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.27
Consensus pattern (104 bp):
TGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAAC
TTGTGTGGGCTTTAAAGGGGTCCTGCTCTTTGGACGAAA
Found at i:328797 original size:119 final size:120
Alignment explanation
Indices: 328588--328868 Score: 362
Period size: 119 Copynumber: 2.4 Consensus size: 120
328578 AGGGGTCCTG
* * * **
328588 CTCTTTGGGGACTGAAAAATGCCACCAACTTGTGTGGGC-TT---CG-AAAGGGGTC-CTGCTCT
1 CTCTTTGAGGACTGAAAAATGCCACCAACTTGGGTGGGCTTTAAAAGAAAAGGCATCTC-GCTCT
* **
328647 TTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAACATCCTG
65 TTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGAAAAAACATCCCA
**
328704 CTCTTTGAGGACTG-AAGGTGCCACCAACTTGGGTGGGCTTTAAAAGAAAAGGCATCTCGCTCTT
1 CTCTTTGAGGACTGAAAAATGCCACCAACTTGGGTGGGCTTTAAAAGAAAAGGCATCTCGCTCTT
** *
328768 TGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAATGCGTCCCA
66 TGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAAACATCCCA
*
328822 CTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTAAAAG
1 CTCTTTGAGGACTGAAAAATGCCACCAACTTGGGTGGGCTTTAAAAG
328869 GCGTCCTGCT
Statistics
Matches: 142, Mismatches: 16, Indels: 11
0.84 0.09 0.07
Matches are distributed among these distances:
115 21 0.15
116 15 0.11
118 27 0.19
119 57 0.40
120 21 0.15
121 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (120 bp):
CTCTTTGAGGACTGAAAAATGCCACCAACTTGGGTGGGCTTTAAAAGAAAAGGCATCTCGCTCTT
TGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAAACATCCCA
Found at i:335590 original size:17 final size:17
Alignment explanation
Indices: 335568--335601 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
335558 ACATCGATTC
*
335568 TTGACTGTGGCTTCCTT
1 TTGACTGTGCCTTCCTT
*
335585 TTGACTTTGCCTTCCTT
1 TTGACTGTGCCTTCCTT
335602 CTTACCTCTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.06, C:0.26, G:0.18, T:0.50
Consensus pattern (17 bp):
TTGACTGTGCCTTCCTT
Found at i:340514 original size:21 final size:21
Alignment explanation
Indices: 340473--340516 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
340463 CTCCCCTTTA
* *
340473 TCTCCCCCGTTTATTAATAAT
1 TCTCCCCCGTTAATCAATAAT
340494 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCGTTAATCAA-TAAT
340515 TC
1 TC
340517 ATATCAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.25, C:0.32, G:0.05, T:0.39
Consensus pattern (21 bp):
TCTCCCCCGTTAATCAATAAT
Found at i:340540 original size:71 final size:71
Alignment explanation
Indices: 340422--340594 Score: 303
Period size: 71 Copynumber: 2.5 Consensus size: 71
340412 AAGTTCGTAC
* * * *
340422 ATTCTCCCCCTTAATAAAGTAGTT-GTAGCAATTTACGCATTCTCCCCTTTATCTCCCCCGTTTA
1 ATTCTCCCCCTTAATCAAGTAATTCATATCAATTTACGCATTCTCCCCTTTATCTCCCCCGTTTA
340486 TTAATA
66 TTAATA
340492 ATTCTCCCCCTTAATCAAGTAATTCATATCAATTTACGCATTCTCCCCTTTATCTCCCCCGTTTA
1 ATTCTCCCCCTTAATCAAGTAATTCATATCAATTTACGCATTCTCCCCTTTATCTCCCCCGTTTA
340557 TTAATA
66 TTAATA
340563 ATTCTCCCCCTTAATCAAGTAATTCATATCAA
1 ATTCTCCCCCTTAATCAAGTAATTCATATCAA
340595 AAATTTATTT
Statistics
Matches: 98, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
70 22 0.22
71 76 0.78
ACGTcount: A:0.27, C:0.29, G:0.06, T:0.38
Consensus pattern (71 bp):
ATTCTCCCCCTTAATCAAGTAATTCATATCAATTTACGCATTCTCCCCTTTATCTCCCCCGTTTA
TTAATA
Found at i:340585 original size:21 final size:21
Alignment explanation
Indices: 340544--340587 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
340534 CTCCCCTTTA
* *
340544 TCTCCCCCGTTTATTAATAAT
1 TCTCCCCCGTTAATCAATAAT
340565 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCGTTAATCAA-TAAT
340586 TC
1 TC
340588 ATATCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.25, C:0.32, G:0.05, T:0.39
Consensus pattern (21 bp):
TCTCCCCCGTTAATCAATAAT
Found at i:342357 original size:13 final size:13
Alignment explanation
Indices: 342339--342364 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
342329 ATAATCACCC
342339 TGTATCGATACAA
1 TGTATCGATACAA
342352 TGTATCGATACAA
1 TGTATCGATACAA
342365 AGAAAAATGT
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:344463 original size:15 final size:15
Alignment explanation
Indices: 344443--344473 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
344433 ATTTCGTTTG
*
344443 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
344458 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
344473 G
1 G
344474 GACATTTTTA
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:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:346307 original size:21 final size:21
Alignment explanation
Indices: 346278--346322 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
346268 AAGTTTTCAT
*
346278 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
346298 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
346320 TTT
1 TTT
346323 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:348557 original size:13 final size:13
Alignment explanation
Indices: 348539--348564 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
348529 CAATTTTTTG
348539 TGTATCGATACAT
1 TGTATCGATACAT
348552 TGTATCGATACAT
1 TGTATCGATACAT
348565 ACTTGCTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:352389 original size:51 final size:50
Alignment explanation
Indices: 352250--352417 Score: 185
Period size: 51 Copynumber: 3.2 Consensus size: 50
352240 GAAATAACGA
* *
352250 GGTTGGAGTATCCTCGATTGTGAAAAAATTGCTGATTTTGGAAATAAAATCG
1 GGTTGGAGTATCCTCGATTGTGGAAAAATTG-TG-TTTTAGAAATAAAATCG
* * ** * *
352302 GAGCTGGAGTATCCCCGATTAAAGG-AAATTTGGTGTTTTAAAAATAAAATCG
1 G-GTTGGAGTATCCTCGATT-GTGGAAAAATT-GTGTTTTAGAAATAAAATCG
*
352354 GGTTGGAGTATCCTCGATTGTGGAAAAATTAGTGTTTTAGCAATAAAATCGG
1 GGTTGGAGTATCCTCGATTGTGGAAAAATT-GTGTTTTAGAAATAAAATC-G
352406 GGTTGGAGTATC
1 GGTTGGAGTATC
352418 GCCGATTATG
Statistics
Matches: 95, Mismatches: 16, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
50 2 0.02
51 38 0.40
52 30 0.32
53 23 0.24
54 2 0.02
ACGTcount: A:0.32, C:0.10, G:0.26, T:0.32
Consensus pattern (50 bp):
GGTTGGAGTATCCTCGATTGTGGAAAAATTGTGTTTTAGAAATAAAATCG
Found at i:352443 original size:51 final size:52
Alignment explanation
Indices: 352337--352469 Score: 141
Period size: 51 Copynumber: 2.6 Consensus size: 52
352327 AAATTTGGTG
* * * * *
352337 TTTTAAAAATAAAATC-GGGTTGGAGTATCCTCGATTGTGGAAAAATTAGTG
1 TTTTAAGAATAAAATCGGGGTTGGAGTATCCTCGATTATGGAAAAATCAATA
*
352388 TTTT-AGCAATAAAATCGGGGTTGGAGTATCGC-CGATTAT-GAGAAATCAATA
1 TTTTAAG-AATAAAATCGGGGTTGGAGTATC-CTCGATTATGGAAAAATCAATA
*
352439 TTTTAAGAAT-AAAGCAGGGGTTGGAGTATCC
1 TTTTAAGAATAAAATC-GGGGTTGGAGTATCC
352470 CCTCGGAAAT
Statistics
Matches: 70, Mismatches: 7, Indels: 11
0.80 0.08 0.12
Matches are distributed among these distances:
50 6 0.09
51 42 0.60
52 21 0.30
53 1 0.01
ACGTcount: A:0.35, C:0.10, G:0.25, T:0.31
Consensus pattern (52 bp):
TTTTAAGAATAAAATCGGGGTTGGAGTATCCTCGATTATGGAAAAATCAATA
Found at i:352460 original size:103 final size:104
Alignment explanation
Indices: 352250--352469 Score: 252
Period size: 103 Copynumber: 2.1 Consensus size: 104
352240 GAAATAACGA
*
352250 GGTTGGAGTATCCTCGATTGTGAAAAAATTGCTGATTTTGGAAATAAAATCGGAGCTGGAGTATC
1 GGTTGGAGTATCCTCGATTGTGAAAAAATTGCTGATTTTAGAAATAAAATCGGAGCTGGAGTATC
*** *
352315 CCCGATTAAAGGAAATTTGGTGTTTTAAAAATAAAATCG
66 CCCGATTAAAGGAAATTCAATATTTTAAAAATAAAATCG
* * * *
352354 GGTTGGAGTATCCTCGATTGTGGAAAAATTAG-TG-TTTTAGCAATAAAATCGGGGTTGGAGTAT
1 GGTTGGAGTATCCTCGATTGTGAAAAAATT-GCTGATTTTAGAAATAAAATCGGAGCTGGAGTAT
* * * *
352417 CGCCGATT-ATGAGAAA-TCAATATTTTAAGAATAAAGCA-GG
65 CCCCGATTAAAG-GAAATTCAATATTTTAAAAATAAA--ATCG
352457 GGTTGGAGTATCC
1 GGTTGGAGTATCC
352470 CCTCGGAAAT
Statistics
Matches: 99, Mismatches: 13, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
102 16 0.16
103 50 0.51
104 32 0.32
105 1 0.01
ACGTcount: A:0.33, C:0.10, G:0.26, T:0.30
Consensus pattern (104 bp):
GGTTGGAGTATCCTCGATTGTGAAAAAATTGCTGATTTTAGAAATAAAATCGGAGCTGGAGTATC
CCCGATTAAAGGAAATTCAATATTTTAAAAATAAAATCG
Found at i:352517 original size:27 final size:28
Alignment explanation
Indices: 352455--352529 Score: 107
Period size: 27 Copynumber: 2.7 Consensus size: 28
352445 GAATAAAGCA
***
352455 GGGGTTGGAGTATCCCCTCGGAAATAAC
1 GGGGTTGGAGTATCCCCGATGAAATAAC
*
352483 GGGGTTGGAGTATCCCCGATG-ATTAAC
1 GGGGTTGGAGTATCCCCGATGAAATAAC
352510 GGGGTTGGAGTATCCCCGAT
1 GGGGTTGGAGTATCCCCGAT
352530 TGTGAAAAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
27 25 0.58
28 18 0.42
ACGTcount: A:0.21, C:0.20, G:0.35, T:0.24
Consensus pattern (28 bp):
GGGGTTGGAGTATCCCCGATGAAATAAC
Found at i:352572 original size:55 final size:52
Alignment explanation
Indices: 352513--352644 Score: 151
Period size: 51 Copynumber: 2.5 Consensus size: 52
352503 GATTAACGGG
* *
352513 GTTGGAGTATCCCCGATTGTGA-AAAATTTGTGTTTTTTTTAAAAATACAATCGGA
1 GTTGGAGTATCCCCGATTGTGAGAAAATTAGTG----TTTTAAAAATAAAATCGGA
* *
352568 GTTGGAGTATCCCCGATTAT-AGAAAATTAGTGTTTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAGAAAATTAGTGTTTTAAAAATAAAATCGGA
* *
352619 GATGGAATATCCCCGATTGTGGAGAA
1 GTTGGAGTATCCCCGATTGT-GAGAA
352645 TTGAGAAACT
Statistics
Matches: 67, Mismatches: 7, Indels: 8
0.82 0.09 0.10
Matches are distributed among these distances:
51 34 0.51
53 4 0.06
54 1 0.01
55 28 0.42
ACGTcount: A:0.33, C:0.11, G:0.23, T:0.33
Consensus pattern (52 bp):
GTTGGAGTATCCCCGATTGTGAGAAAATTAGTGTTTTAAAAATAAAATCGGA
Found at i:352611 original size:263 final size:264
Alignment explanation
Indices: 352140--352641 Score: 688
Period size: 263 Copynumber: 1.9 Consensus size: 264
352130 TCGAAAATAA
* ** * *
352140 CGGGGTTGGAGTATCCCCAATTATGATAAATCAATATTTTGGGAATTAAGCCGGGGTTGGACTAT
1 CGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTAAGAATAAAGCAGGGGTTGGACTAT
* ** * *
352205 CCCCTTAGAGGTAACGGGGTTGGAGTATCCTCGATGAAATAACGAGGTTGGAGTATCCTCGATTG
66 CCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCCCGATTG
** * *
352270 TGAAAAAATTGCTGATTTTGGAAATAAAATCGGAGCTGGAGTATCCCCGATTAAAGGAAATTTGG
131 TGAAAAAATTGCTGATTTTAAAAATAAAATCGGAGCTGGAGTATCCCCGATTAAAGGAAAATTAG
* * *
352335 TGTTTTAAAAATAAAATCGG-GTTGGAGTATCCTCGATTGTGGAAAAATTAGTGTTTTAGCAATA
196 TGTTTTAAAAATAAAATCGGAGATGGAATATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATA
352399 AAAT
261 AAAT
* * *
352403 CGGGGTTGGAGTATCGCCGATTATGAGAAATCAATATTTTAAGAATAAAGCAGGGGTTGGAGTAT
1 CGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTAAGAATAAAGCAGGGGTTGGACTAT
* * *
352468 CCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATG-ATTAACGGGGTTGGAGTATCCCCGATTG
66 CCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCCCGATTG
* * * * *
352532 TGAAAAATTTG-TGTTTTTTTTAAAAATACAATCGGAGTTGGAGTATCCCCGATTATA-GAAAAT
131 TGAAAAAATTGCTG---ATTTTAAAAATAAAATCGGAGCTGGAGTATCCCCGATTAAAGGAAAAT
*
352595 TAGTGTTTTGAAAATAAAATCGGAGATGGAATATCCCCGATTGTGGA
193 TAGTGTTTTAAAAATAAAATCGGAGATGGAATATCCCCGATTGTGGA
352642 GAATTGAGAA
Statistics
Matches: 206, Mismatches: 29, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
261 2 0.01
262 35 0.17
263 114 0.55
264 55 0.27
ACGTcount: A:0.31, C:0.13, G:0.26, T:0.30
Consensus pattern (264 bp):
CGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTAAGAATAAAGCAGGGGTTGGACTAT
CCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCCCGATTG
TGAAAAAATTGCTGATTTTAAAAATAAAATCGGAGCTGGAGTATCCCCGATTAAAGGAAAATTAG
TGTTTTAAAAATAAAATCGGAGATGGAATATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATA
AAAT
Found at i:355015 original size:13 final size:13
Alignment explanation
Indices: 354997--355022 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
354987 ACAAAGATCC
354997 ATGTATCGATACA
1 ATGTATCGATACA
355010 ATGTATCGATACA
1 ATGTATCGATACA
355023 CAGAAAAATG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:355018 original size:33 final size:33
Alignment explanation
Indices: 354976--355042 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
354966 AAAATTTCCA
***
354976 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
355009 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
355042 A
1 A
355043 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:355086 original size:19 final size:18
Alignment explanation
Indices: 355062--355129 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
355052 CAGTAGCTAA
355062 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
355081 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
355096 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
355113 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
355130 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:355102 original size:13 final size:13
Alignment explanation
Indices: 355084--355108 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
355074 ACAATACTTA
355084 TGTATCGATACAT
1 TGTATCGATACAT
355097 TGTATCGATACA
1 TGTATCGATACA
355109 AAACTTATGT
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:355106 original size:32 final size:32
Alignment explanation
Indices: 355065--355127 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
355055 TAGCTAATTA
*
355065 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
355097 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
355128 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:356051 original size:55 final size:55
Alignment explanation
Indices: 355967--356485 Score: 515
Period size: 55 Copynumber: 9.3 Consensus size: 55
355957 ATAAAGCGTA
* * *
355967 TCCTGCTCTTTGAGGACT-AAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACTGGAAAA-TGCCACCAACTTGTGTGGGCTTTGAAAGGCG
*
356022 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAA-AGGCG
*
356077 TCCTGCTCTTT---GA--GG---ATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
* * *
356124 TCCTGCTCTATGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTCGAAAGGGG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
* * * *
356179 TCCTGCTCTTTGGGGACTGAAAAATGCCACCAACTTGTGTGGGCTTCGAAAGGGG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
* * * *
356234 TCTTGCTCTTTGGGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCA
1 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTG-AAAG-----GCG
* * * *
356295 TCCTACTCTTTGAGGACT-GAAAGTGCCACCAACTTGGGTGGGCTTTAAAAGAAAAGGCA
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT----G-AAAGGCG
* ** *
356354 TCCCGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAATGCG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT----G-AAAGGCG
** * * *
356413 TCCCCCTCTTTGAGTACTGAAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGCG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
356468 TCCTGCTCTTTGAGGACT
1 TCCTGCTCTTTGAGGACT
356486 AAAAAGCGAA
Statistics
Matches: 407, Mismatches: 34, Indels: 46
0.84 0.07 0.09
Matches are distributed among these distances:
47 39 0.10
48 2 0.00
50 4 0.01
52 4 0.01
54 5 0.01
55 199 0.49
56 8 0.02
59 72 0.18
60 48 0.12
61 20 0.05
64 6 0.01
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.27
Consensus pattern (55 bp):
TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
Found at i:356114 original size:47 final size:47
Alignment explanation
Indices: 356045--356187 Score: 171
Period size: 47 Copynumber: 2.9 Consensus size: 47
356035 GGACTGGAAA
*
356045 ATGCCACCAACTTGTGTGGGCTTT-AAGAGGTGTCCTGCTCTTTGAGG
1 ATGCCACCAACTTGTGTGGGCTTTGAA-AGGTGTCCTGCTCTATGAGG
356092 ATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTATGAGGACTGG
1 ATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTAT---GA--GG
* *
356144 AAAATGCCACCAACTTGTGTGGGCTTCGAAAGGGGTCCTGCTCT
1 ---ATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCT
356188 TTGGGGACTG
Statistics
Matches: 84, Mismatches: 3, Indels: 10
0.87 0.03 0.10
Matches are distributed among these distances:
47 39 0.46
48 2 0.02
50 2 0.02
52 2 0.02
55 39 0.46
ACGTcount: A:0.20, C:0.22, G:0.29, T:0.29
Consensus pattern (47 bp):
ATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTATGAGG
Found at i:356115 original size:102 final size:104
Alignment explanation
Indices: 355991--356485 Score: 424
Period size: 102 Copynumber: 4.5 Consensus size: 104
355981 GACTAAAAAG
*
355991 TGCCACCAACTCGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAAC
1 TGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAAC
* *
356056 TTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTT-GA-G-GA
66 TTGTGTGGGCTTTAA-AGGGGTCCTGCTCTTTGGACGAAA
*
356093 TGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTATGAGGACTGGAAAATGCCACCAAC
1 TGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAAC
*
356158 TTGTGTGGGCTTCGAAAGGGGTCCTGCTCTTTGGGGACTGAAAAA
66 TTGTGTGGGCTT-TAAAGGGGTCCTGCTCTTT--GGAC-G--AAA
* * * * *
356203 TGCCACCAACTTGTGTGGGCTTCGAAAGGGGTCTTGCTCTTTGGGGACT-GAAAGGTGCCACCAA
1 TGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAA
** *
356267 CTTGTGTGGGCTTTGAAAAGAAAAAGCATCCTACTCTTTGAGGACTGAAA
65 CTTGTGTGGGCTTT--AAAG-----GGGTCCTGCTCTTT--GGAC-GAAA
* ** * **
356317 GTGCCACCAACTTGGGTGGGCTTTAAAAGAAAAGGCATCCCGCTCTTTGAGGACT-GAAGGTGCC
1 -TGCCACCAACTTGTGTGGGCTTT----G-AAAGGTGTCCTGCTCTTTGAGGACTGGAAAATGCC
* **
356381 ACCAACTTGTGTGGGCTTTAAAAGAAAATGCGTCCCCCTCTTTGAGTACTGAAAAA
60 ACCAACTTGTGTGGGCTTT-AAAG-----GGGTCCTGCTCTTTG-G-AC-G--AAA
* *
356437 TGCCACCAACTTGTGTGGGCTTTAAAAGGCGTCCTGCTCTTTGAGGACT
1 TGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACT
356486 AAAAAGCGAA
Statistics
Matches: 334, Mismatches: 32, Indels: 42
0.82 0.08 0.10
Matches are distributed among these distances:
102 90 0.27
103 2 0.01
105 2 0.01
107 1 0.00
109 4 0.01
110 67 0.20
111 4 0.01
114 26 0.08
115 21 0.06
116 19 0.06
117 1 0.00
118 24 0.07
119 47 0.14
120 26 0.08
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.27
Consensus pattern (104 bp):
TGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAAC
TTGTGTGGGCTTTAAAGGGGTCCTGCTCTTTGGACGAAA
Found at i:356366 original size:59 final size:59
Alignment explanation
Indices: 356238--356464 Score: 328
Period size: 59 Copynumber: 3.8 Consensus size: 59
356228 AAGGGGTCTT
* *
356238 GCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCT
1 GCTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTT-AAAAGAAAAAGCATCCC
* * *
356299 ACTCTTTGAGGACTGAAAGTGCCACCAACTTGGGTGGGCTTTAAAAGAAAAGGCATCCC
1 GCTCTTTGAGGACTGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAAGCATCCC
* * *
356358 GCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAATGCGTCCC
1 GCTCTTTGAGGACTGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAAGCATCCC
* * *
356417 CCTCTTTGAGTACTGAAAAATGCCACCAACTTGTGTGGGCTTTAAAAG
1 GCTCTTTGAGGACTG-AAAGTGCCACCAACTTGTGTGGGCTTTAAAAG
356465 GCGTCCTGCT
Statistics
Matches: 151, Mismatches: 14, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
59 82 0.54
60 53 0.35
61 16 0.11
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.25
Consensus pattern (59 bp):
GCTCTTTGAGGACTGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAAGCATCCC
Found at i:356393 original size:119 final size:120
Alignment explanation
Indices: 356184--356464 Score: 369
Period size: 119 Copynumber: 2.4 Consensus size: 120
356174 AGGGGTCCTG
* * * ** **
356184 CTCTTTGGGGACTGAAAAATGCCACCAACTTGTGTGGGC-TT---CG-AAAGGGGTCTTGCTCTT
1 CTCTTTGAGGACTGAAAAATGCCACCAACTTGGGTGGGCTTTAAAAGAAAAGGCATCCCGCTCTT
* *
356244 TGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCTA
66 TGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGAAAAAGCATCCCA
*
356300 CTCTTTGAGGACTG-AAAGTGCCACCAACTTGGGTGGGCTTTAAAAGAAAAGGCATCCCGCTCTT
1 CTCTTTGAGGACTGAAAAATGCCACCAACTTGGGTGGGCTTTAAAAGAAAAGGCATCCCGCTCTT
* * *
356364 TGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAATGCGTCCCC
66 TGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAAGCATCCCA
* *
356418 CTCTTTGAGTACTGAAAAATGCCACCAACTTGTGTGGGCTTTAAAAG
1 CTCTTTGAGGACTGAAAAATGCCACCAACTTGGGTGGGCTTTAAAAG
356465 GCGTCCTGCT
Statistics
Matches: 143, Mismatches: 16, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
115 22 0.15
116 15 0.10
118 27 0.19
119 58 0.41
120 21 0.15
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.26
Consensus pattern (120 bp):
CTCTTTGAGGACTGAAAAATGCCACCAACTTGGGTGGGCTTTAAAAGAAAAGGCATCCCGCTCTT
TGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAAGCATCCCA
Found at i:362892 original size:52 final size:52
Alignment explanation
Indices: 362717--362939 Score: 211
Period size: 52 Copynumber: 4.3 Consensus size: 52
362707 GAAATAACGA
* * * * * *
362717 GGTTGGAGTATCCTCGATTGTGAAAAAATTGGTGTTTTTGGAAATAAAATCAG
1 GGTTGGAGTATCCCCGATTATGGAAAAATTAGTG-TTTTAGAAATAAAATCGG
* * * * * * *
362770 AGCTAGAGTATCCCCGACTAAAGG-AAAATTGGTGTTTTAAAAATAAAATCGG
1 GGTTGGAGTATCCCCGA-TTATGGAAAAATTAGTGTTTTAGAAATAAAATCGG
*
362822 GGTTGGAGTATCCCCGATTATGGAAAAATTAGTGTTTTAGCAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGGAAAAATTAGTGTTTTAGAAATAAAATCGG
* * * * *
362874 GGTTGGAGTATCCCCGATTAT-GAGAAATCAATATTTTA-AGAAT-AAAGCAGG
1 GGTTGGAGTATCCCCGATTATGGAAAAATTAGTGTTTTAGA-AATAAAATC-GG
362925 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
362940 TCGAAAATAA
Statistics
Matches: 141, Mismatches: 25, Indels: 10
0.80 0.14 0.06
Matches are distributed among these distances:
50 4 0.03
51 37 0.26
52 75 0.53
53 23 0.16
54 2 0.01
ACGTcount: A:0.34, C:0.12, G:0.25, T:0.29
Consensus pattern (52 bp):
GGTTGGAGTATCCCCGATTATGGAAAAATTAGTGTTTTAGAAATAAAATCGG
Found at i:363071 original size:134 final size:131
Alignment explanation
Indices: 362819--363073 Score: 293
Period size: 134 Copynumber: 1.9 Consensus size: 131
362809 AAAATAAAAT
* ** * *
362819 CGGGGTTGGAGTATCCCCGATTATGGAAAAATTAGTGTTTTAGCAATAAAATCGGGGTTGGAGTA
1 CGGGGTTGGAGTATCCCCGATTATGAAAAAATTAGTGTTTTAAAAATAAAATCAGAGTTGGAGTA
** * *
362884 TCCCCGATTATGAGAAATCAATATTTTAAGAATAAAGCAGGGGTTGGAGTATCCCCTCGAAAATA
66 TCCCCGATTATGAGAAATCAATATTTTAAGAATAAAGCAGAAGATGGAATATCCCCTCGAAAATA
362949 A
131 A
*
362950 CGGGGTTGGAGTATCCCCGATTGTGAAAAAATT-GTGTTTTTTTTAAAAATAAAATCAGAGTTGG
1 CGGGGTTGGAGTATCCCCGATTATGAAAAAATTAGTG----TTTTAAAAATAAAATCAGAGTTGG
* * * *
363014 AGTATCCCCGATTAT-AGAAAATTAGTGTTTTGAA-AATAAAATC-GAAGATGGAATATCCCC
62 AGTATCCCCGATTATGAG-AAATCAATATTTT-AAGAAT-AAAGCAGAAGATGGAATATCCCC
363074 GATTGCGGAG
Statistics
Matches: 103, Mismatches: 14, Indels: 11
0.80 0.11 0.09
Matches are distributed among these distances:
130 3 0.03
131 31 0.30
133 2 0.02
134 61 0.59
135 6 0.06
ACGTcount: A:0.35, C:0.13, G:0.23, T:0.29
Consensus pattern (131 bp):
CGGGGTTGGAGTATCCCCGATTATGAAAAAATTAGTGTTTTAAAAATAAAATCAGAGTTGGAGTA
TCCCCGATTATGAGAAATCAATATTTTAAGAATAAAGCAGAAGATGGAATATCCCCTCGAAAATA
A
Found at i:364895 original size:10 final size:10
Alignment explanation
Indices: 364882--364911 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
364872 CAATGGAATA
364882 GTGTTTTTTT
1 GTGTTTTTTT
364892 GTGTTTTTTT
1 GTGTTTTTTT
364902 G-GTTTTTTT
1 GTGTTTTTTT
364911 G
1 G
364912 CTAAAGGATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.00, C:0.00, G:0.23, T:0.77
Consensus pattern (10 bp):
GTGTTTTTTT
Found at i:365463 original size:13 final size:13
Alignment explanation
Indices: 365445--365470 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
365435 ACAAAGATCC
365445 ATGTATCGATACA
1 ATGTATCGATACA
365458 ATGTATCGATACA
1 ATGTATCGATACA
365471 CAGAAAAATG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:365466 original size:33 final size:33
Alignment explanation
Indices: 365424--365490 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
365414 AAAATTTCCA
***
365424 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
365457 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
365490 A
1 A
365491 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:367236 original size:98 final size:97
Alignment explanation
Indices: 367018--367257 Score: 243
Period size: 98 Copynumber: 2.5 Consensus size: 97
367008 AATTTTATTT
* * *
367018 ATCGGGGATACTCCAACCCTATTCCTCTAAGGGGATACTCCAACCTCGCTTTTAAACACATCAAA
1 ATCGGGGACACTCCAACCCCATTCCTCTGAGGGGATACTCCAACCTCGCTTTTAAACACATCAAA
* * *
367083 GTTTAAATCTTATTCTCACTTAAATTATCACC
66 CTTGAAATCTTATTCTCACCTAAATTATCACC
* * * * * * * *
367115 ATCGGTGCCACTTCAACCTCATTCCTTTGAGGGGATACTCCAA-CTCCGTTTTTAAA-ACTTGTT
1 ATCGGGGACACTCCAACCCCATTCCTCTGAGGGGATACTCCAACCT-CGCTTTTAAACAC--ATC
** **
367178 AAGACTTGAAA-CTTATTCTTGCCTAAATTATCATT
63 AA-ACTTGAAATCTTATTCTCACCTAAATTATCACC
* *
367213 GTCGGGGACACTCCAACCCCATTCCTCTGAGGGGATACTCTAACC
1 ATCGGGGACACTCCAACCCCATTCCTCTGAGGGGATACTCCAACC
367258 CCATTTTTCA
Statistics
Matches: 113, Mismatches: 25, Indels: 8
0.77 0.17 0.05
Matches are distributed among these distances:
96 4 0.04
97 44 0.39
98 58 0.51
99 7 0.06
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.31
Consensus pattern (97 bp):
ATCGGGGACACTCCAACCCCATTCCTCTGAGGGGATACTCCAACCTCGCTTTTAAACACATCAAA
CTTGAAATCTTATTCTCACCTAAATTATCACC
Found at i:371886 original size:13 final size:13
Alignment explanation
Indices: 371868--371893 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
371858 TACAGCAAGT
371868 ATGTATCGATACA
1 ATGTATCGATACA
371881 ATGTATCGATACA
1 ATGTATCGATACA
371894 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:374151 original size:21 final size:21
Alignment explanation
Indices: 374118--374162 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
374108 TTGCAAGTTG
*
374118 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
374140 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
374160 AAA
1 AAA
374163 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:375948 original size:15 final size:15
Alignment explanation
Indices: 375928--375958 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
375918 TAAAAATGTC
*
375928 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
375943 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
375958 C
1 C
375959 CAAACGAAAT
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:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:378025 original size:20 final size:20
Alignment explanation
Indices: 377955--378032 Score: 68
Period size: 20 Copynumber: 3.6 Consensus size: 20
377945 ATGTCCTAAA
*
377955 TGTATCGATACATGTTT-TT
1 TGTATCGATACATCTTTCTT
**
377974 GTGTATCGATACATCTGGAAATTCAA
1 -TGTATCGATACATCT-----TTCTT
378000 TGTATCGATACATCTTTCTT
1 TGTATCGATACATCTTTCTT
378020 TGTATCGATACAT
1 TGTATCGATACAT
378033 TGTATCGATA
Statistics
Matches: 47, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
20 30 0.64
25 17 0.36
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.42
Consensus pattern (20 bp):
TGTATCGATACATCTTTCTT
Found at i:378058 original size:13 final size:13
Alignment explanation
Indices: 378020--378058 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
378010 CATCTTTCTT
*
378020 TGTATCGATACAT
1 TGTATCGATACAG
378033 TGTATCGATACAG
1 TGTATCGATACAG
378046 TGTATCGATACAG
1 TGTATCGATACAG
378059 GAGGATTATA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.15, G:0.21, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAG
Done.