Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008397.1 Hibiscus syriacus cultivar Beakdansim tig00111166_pilon, 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: 2560905
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 13 of 13
Found at i:2431691 original size:37 final size:34
Alignment explanation
Indices: 2431650--2431772 Score: 120
Period size: 36 Copynumber: 3.4 Consensus size: 34
2431640 GGTCATTTCG
* *
2431650 CTTGAGACTAATTTAGTCAAAACAAAGTTTTGTCTCT
1 CTTGAGAC-AATTT-CTCGAAACAAA-TTTTGTCTCT
* *
2431687 CTTGAGACAGTTTCTCTTGAAACAAATTTTGTCTAT
1 CTTGAGACAATTTCTC--GAAACAAATTTTGTCTCT
* *
2431723 CTTGAGACATTTTCCCTTGAAACAAATTTTGTCTCT
1 CTTGAGACAATTT--CTCGAAACAAATTTTGTCTCT
*
2431759 CTTGAGACAGTTTC
1 CTTGAGACAATTTC
2431773 CCTTGAAGCA
Statistics
Matches: 74, Mismatches: 8, Indels: 11
0.80 0.09 0.12
Matches are distributed among these distances:
34 1 0.01
35 2 0.03
36 54 0.73
37 15 0.20
38 2 0.03
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.40
Consensus pattern (34 bp):
CTTGAGACAATTTCTCGAAACAAATTTTGTCTCT
Found at i:2431726 original size:36 final size:36
Alignment explanation
Indices: 2431669--2431784 Score: 178
Period size: 36 Copynumber: 3.2 Consensus size: 36
2431659 AATTTAGTCA
2431669 AAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTG
1 AAACAAA-TTTTGTCTCTCTTGAGACAGTTTCTCTTG
* * *
2431706 AAACAAATTTTGTCTATCTTGAGACATTTTCCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
*
2431742 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
*
2431778 AAGCAAA
1 AAACAAA
2431785 ATCTTTGAAT
Statistics
Matches: 73, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
36 66 0.90
37 7 0.10
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (36 bp):
AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
Found at i:2431727 original size:21 final size:20
Alignment explanation
Indices: 2431701--2431763 Score: 55
Period size: 21 Copynumber: 3.3 Consensus size: 20
2431691 AGACAGTTTC
2431701 TCTTGAAACAAATTTTGTCT
1 TCTTGAAACAAATTTTGTCT
*
2431721 ATCTTGAGAC--A-TTT-TC-
1 -TCTTGAAACAAATTTTGTCT
*
2431737 CCTTGAAACAAATTTTGTCT
1 TCTTGAAACAAATTTTGTCT
2431757 CTCTTGA
1 -TCTTGA
2431764 GACAGTTTCC
Statistics
Matches: 32, Mismatches: 4, Indels: 12
0.67 0.08 0.25
Matches are distributed among these distances:
15 7 0.22
17 3 0.09
18 6 0.19
19 3 0.09
21 13 0.41
ACGTcount: A:0.27, C:0.19, G:0.11, T:0.43
Consensus pattern (20 bp):
TCTTGAAACAAATTTTGTCT
Found at i:2431880 original size:102 final size:101
Alignment explanation
Indices: 2431702--2431886 Score: 280
Period size: 101 Copynumber: 1.8 Consensus size: 101
2431692 GACAGTTTCT
* *
2431702 CTTGAAACAAATTTTGTCTATCTTGAGACATTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGAC
1 CTTGAAACAAATTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGAC
*
2431767 AGTTTCCCTTGAAGCAAAATCTTTGAATACATCTTC
66 AGTTTCCCTTGAAACAAAATCTTTGAATACATCTTC
* ** * *
2431803 CTTGAAACAAATTTCGTCTCTCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGA
1 CTTGAAACAAATTTCGTCTATCTTGAGACAGTTTCCCTTGAAAC-AAATTTTGTCTCTCTTGAGA
*
2431868 CAGTTTCTCTTGAAACAAA
65 CAGTTTCCCTTGAAACAAA
2431887 TTTTGTCTCT
Statistics
Matches: 74, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
101 38 0.51
102 36 0.49
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.39
Consensus pattern (101 bp):
CTTGAAACAAATTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGAC
AGTTTCCCTTGAAACAAAATCTTTGAATACATCTTC
Found at i:2431917 original size:138 final size:138
Alignment explanation
Indices: 2431669--2431922 Score: 384
Period size: 138 Copynumber: 1.8 Consensus size: 138
2431659 AATTTAGTCA
* *
2431669 AAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTTGTCTATCTTGAGACATT
1 AAACAAAGTTTCGTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTTGTCTATCTTGAGACAGT
* * *
2431734 TTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAGCAAAATCTTTGAATACAT
66 TTCCCTTGAAACAAATTTTGTCTCTCTTAAGACAGTTTCACTTGAAACAAAATCTTTGAATACAT
2431799 CTTCCTTG
131 CTTCCTTG
* * * *
2431807 AAACAAA-TTTCGTCTCTCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAG
1 AAACAAAGTTTCGTCTCTCTTGAGACAGTTTCTCTTGAAAC-AAATTTTGTCTATCTTGAGACAG
* **
2431871 TTTCTCTTGAAACAAATTTTGTCTCTCTTAAGTTAGTTTCACTTGAAACAAA
65 TTTCCCTTGAAACAAATTTTGTCTCTCTTAAGACAGTTTCACTTGAAACAAA
2431923 GTTTTGTCTC
Statistics
Matches: 103, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
137 30 0.29
138 73 0.71
ACGTcount: A:0.28, C:0.19, G:0.13, T:0.40
Consensus pattern (138 bp):
AAACAAAGTTTCGTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTTGTCTATCTTGAGACAGT
TTCCCTTGAAACAAATTTTGTCTCTCTTAAGACAGTTTCACTTGAAACAAAATCTTTGAATACAT
CTTCCTTG
Found at i:2431925 original size:73 final size:73
Alignment explanation
Indices: 2431803--2431959 Score: 233
Period size: 73 Copynumber: 2.2 Consensus size: 73
2431793 ATACATCTTC
* ** * *
2431803 CTTGAAACAAATTTCGTCTCTCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGA
1 CTTGAAACAAATTTCGTCTCTCTTAAGACAGTTTCACTTGAAACAAAGTTTTGTCTCTCTTGAGA
2431868 CAGTTTCT
66 CAGTTTCT
* **
2431876 CTTGAAACAAATTTTGTCTCTCTTAAGTTAGTTTCACTTGAAACAAAGTTTTGTCTCTCTTGAGA
1 CTTGAAACAAATTTCGTCTCTCTTAAGACAGTTTCACTTGAAACAAAGTTTTGTCTCTCTTGAGA
*
2431941 TAGTTTCT
66 CAGTTTCT
2431949 CTTGAAACAAA
1 CTTGAAACAAA
2431960 AAAAAACCTT
Statistics
Matches: 75, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
73 75 1.00
ACGTcount: A:0.26, C:0.18, G:0.15, T:0.41
Consensus pattern (73 bp):
CTTGAAACAAATTTCGTCTCTCTTAAGACAGTTTCACTTGAAACAAAGTTTTGTCTCTCTTGAGA
CAGTTTCT
Found at i:2431959 original size:37 final size:36
Alignment explanation
Indices: 2431803--2431959 Score: 215
Period size: 37 Copynumber: 4.3 Consensus size: 36
2431793 ATACATCTTC
*
2431803 CTTGAAACAAATTTCGTCTCTCTTGAGACAGTTTCT
1 CTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCT
* * *
2431839 TTTGGAACTAAGTTTTGTCTCTCTTGAGACAGTTTCT
1 CTTGAAAC-AAATTTTGTCTCTCTTGAGACAGTTTCT
* ** *
2431876 CTTGAAACAAATTTTGTCTCTCTTAAGTTAGTTTCA
1 CTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCT
*
2431912 CTTGAAACAAAGTTTTGTCTCTCTTGAGATAGTTTCT
1 CTTGAAACAAA-TTTTGTCTCTCTTGAGACAGTTTCT
2431949 CTTGAAACAAA
1 CTTGAAACAAA
2431960 AAAAAACCTT
Statistics
Matches: 105, Mismatches: 14, Indels: 3
0.86 0.11 0.02
Matches are distributed among these distances:
36 40 0.38
37 65 0.62
ACGTcount: A:0.26, C:0.18, G:0.15, T:0.41
Consensus pattern (36 bp):
CTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCT
Found at i:2432417 original size:5 final size:5
Alignment explanation
Indices: 2432407--2432741 Score: 485
Period size: 5 Copynumber: 67.0 Consensus size: 5
2432397 TCTAAAAAAC
2432407 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
2432457 ATTAT ATTAT ATTAT ATTAT A-TAT A-TAT ATTAT ATTAT ATTATAT ATTAT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT A-T-TAT ATTAT
2432507 ATTAT ATTATAT ATTAT ATTAT A-TAT A-TAT ATTAT A-T-T ATTAT ATATAT
1 ATTAT A-T-TAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT AT-TAT
2432556 ATTAT ATTAT A-T-T ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
2432604 ATTAT ATTATAT ATTAT ATTAT ATTAT ATTAT A-TAT ATTAT ATTAT ATTAT
1 ATTAT A-T-TAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
2432655 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
*
2432705 -TTATT ATTATT ATTATT ATTATT ATTAT -TTTT ATTAT
1 ATTA-T ATTA-T ATTA-T ATTA-T ATTAT ATTAT ATTAT
2432742 TTTTTATAGG
Statistics
Matches: 311, Mismatches: 2, Indels: 34
0.90 0.01 0.10
Matches are distributed among these distances:
3 4 0.01
4 30 0.10
5 233 0.75
6 32 0.10
7 12 0.04
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
ATTAT
Found at i:2439154 original size:2 final size:2
Alignment explanation
Indices: 2439147--2439209 Score: 53
Period size: 2 Copynumber: 33.0 Consensus size: 2
2439137 TAATATTCTA
* * * *
2439147 AT AT AT AT AT AT AT AT -T AT TT AT -T CT TT TT A- AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2439185 CAT AT AT AT AT AT AT AT AT AT AT AT
1 -AT AT AT AT AT AT AT AT AT AT AT AT
2439210 TATTTTTACT
Statistics
Matches: 52, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
1 4 0.08
2 46 0.88
3 2 0.04
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (2 bp):
AT
Found at i:2439379 original size:2 final size:2
Alignment explanation
Indices: 2439372--2439398 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2439362 CTTTATTTAT
2439372 TA 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 TA T
2439399 TATTTTTACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2439445 original size:40 final size:37
Alignment explanation
Indices: 2439397--2439482 Score: 93
Period size: 40 Copynumber: 2.2 Consensus size: 37
2439387 ATATATATAT
2439397 ATTATTTTTACTATTATTTTCTTTATTTAT-TTTGTTTGTA
1 ATTATTTTTACTATTA-TTTCTTT-TTTATCTTT-TTT-TA
* *
2439437 ATTATTTTTTATTTTTATTTCTTTTTTATCTTTTTTTA
1 ATTA-TTTTTACTATTATTTCTTTTTTATCTTTTTTTA
*
2439475 TTTATTTT
1 ATTATTTT
2439483 ACTTACTTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
37 4 0.10
38 5 0.12
39 8 0.20
40 14 0.34
41 10 0.24
ACGTcount: A:0.17, C:0.05, G:0.02, T:0.76
Consensus pattern (37 bp):
ATTATTTTTACTATTATTTCTTTTTTATCTTTTTTTA
Found at i:2439503 original size:18 final size:19
Alignment explanation
Indices: 2439475--2439560 Score: 65
Period size: 24 Copynumber: 4.4 Consensus size: 19
2439465 TCTTTTTTTA
2439475 TTTATTTTAC-TTA-CTTT
1 TTTATTTTACTTTATCTTT
2439492 TTTATATTTACTTTATCTTT
1 TTTAT-TTTACTTTATCTTT
2439512 TTTACTCTTTTTTA-TCTTATCTTT
1 TTTA-----TTTTACT-TTATCTTT
*
2439536 TTTATTTCA-TTTAT-TTT
1 TTTATTTTACTTTATCTTT
2439553 TTTATTTT
1 TTTATTTT
2439561 TTCATTTTAA
Statistics
Matches: 58, Mismatches: 2, Indels: 18
0.74 0.03 0.23
Matches are distributed among these distances:
17 15 0.26
18 9 0.16
19 8 0.14
20 8 0.14
23 1 0.02
24 16 0.28
25 1 0.02
ACGTcount: A:0.16, C:0.10, G:0.00, T:0.73
Consensus pattern (19 bp):
TTTATTTTACTTTATCTTT
Found at i:2439504 original size:14 final size:13
Alignment explanation
Indices: 2439413--2439567 Score: 55
Period size: 14 Copynumber: 11.8 Consensus size: 13
2439403 TTTACTATTA
*
2439413 TTTTCTTTATTTAT
1 TTTT-TTTATTTAC
*
2439427 TTTGTTTGTAATTA-
1 TTT-TTT-TATTTAC
*
2439441 TTTTTTATTTTTA-
1 TTTTTT-TATTTAC
*
2439454 TTTCTTT-TTTATC
1 TTTTTTTATTTA-C
2439467 TTTTTTTATTTA-
1 TTTTTTTATTTAC
*
2439479 ---TTTTACTTAC
1 TTTTTTTATTTAC
2439489 TTTTTTATATTTAC
1 TTTTTT-TATTTAC
2439503 TTTATCTTT-TTTAC
1 TTT-T-TTTATTTAC
2439517 TCTTTTTTATCTTA-
1 T-TTTTTTAT-TTAC
2439531 TCTTTTTTATTT-C
1 T-TTTTTTATTTAC
2439544 ATTTATTTT-TTTA-
1 -TTT-TTTTATTTAC
*
2439557 TTTTTTCATTT
1 TTTTTTTATTT
2439568 TAAATTTTCA
Statistics
Matches: 112, Mismatches: 9, Indels: 42
0.69 0.06 0.26
Matches are distributed among these distances:
9 8 0.07
11 7 0.06
12 7 0.06
13 31 0.28
14 44 0.39
15 13 0.12
16 2 0.02
ACGTcount: A:0.15, C:0.08, G:0.01, T:0.75
Consensus pattern (13 bp):
TTTTTTTATTTAC
Found at i:2439507 original size:42 final size:41
Alignment explanation
Indices: 2439461--2439562 Score: 115
Period size: 42 Copynumber: 2.5 Consensus size: 41
2439451 TTATTTCTTT
*
2439461 TTTATCTTTTTTTATTTATTTTA-CTTA-CTTTTTTATATTTA
1 TTTATCTTTTTTTATTT-TTTTATCTTATCTTTTTTAT-TTCA
2439502 CTTTATC-TTTTTTACTCTTTTTTATCTTATCTTTTTTATTTCA
1 -TTTATCTTTTTTTA-T-TTTTTTATCTTATCTTTTTTATTTCA
2439545 TTTA--TTTTTTTATTTTTT
1 TTTATCTTTTTTTATTTTTT
2439563 CATTTTAAAT
Statistics
Matches: 54, Mismatches: 1, Indels: 13
0.79 0.01 0.19
Matches are distributed among these distances:
39 5 0.09
40 1 0.02
41 14 0.26
42 16 0.30
43 9 0.17
44 9 0.17
ACGTcount: A:0.16, C:0.10, G:0.00, T:0.75
Consensus pattern (41 bp):
TTTATCTTTTTTTATTTTTTTATCTTATCTTTTTTATTTCA
Found at i:2439540 original size:9 final size:9
Alignment explanation
Indices: 2439441--2439529 Score: 67
Period size: 9 Copynumber: 9.2 Consensus size: 9
2439431 TTTGTAATTA
2439441 TTTTTTAT-
1 TTTTTTATC
2439449 TTTTATT-TC
1 TTTT-TTATC
2439458 TTTTTTATC
1 TTTTTTATC
2439467 TTTTTTTAT-
1 -TTTTTTATC
2439476 TTATTTTACTTAC
1 TT-TTTTA--T-C
*
2439489 TTTTTTATA
1 TTTTTTATC
2439498 TTTACTTTATC
1 TTT--TTTATC
2439509 TTTTTTACTC
1 TTTTTTA-TC
2439519 TTTTTTATC
1 TTTTTTATC
2439528 TT
1 TT
2439530 ATCTTTTTTA
Statistics
Matches: 67, Mismatches: 2, Indels: 23
0.73 0.02 0.25
Matches are distributed among these distances:
8 9 0.13
9 24 0.36
10 18 0.27
11 9 0.13
12 5 0.07
13 2 0.03
ACGTcount: A:0.15, C:0.10, G:0.00, T:0.75
Consensus pattern (9 bp):
TTTTTTATC
Found at i:2439561 original size:9 final size:9
Alignment explanation
Indices: 2439422--2439562 Score: 54
Period size: 10 Copynumber: 14.1 Consensus size: 9
2439412 ATTTTCTTTA
2439422 TTTATTTTGT
1 TTTATTTT-T
2439432 TTGTAATTATTT
1 TT-T-ATT-TTT
2439444 TTTATTTTT
1 TTTATTTTT
* *
2439453 ATT-TCTTT
1 TTTATTTTT
2439461 TTTATCTTTT
1 TTTAT-TTTT
*
2439471 TTTATTTAT
1 TTTATTTTT
2439480 TTTACTTACTTT
1 TTTA-TT--TTT
*
2439492 TTTATATTTAC
1 TTTAT-TTT-T
*
2439503 TTTATCTTT
1 TTTATTTTT
*
2439512 TTTACTCTTT
1 TTTA-TTTTT
2439522 TTTATCTTATCT
1 TTTAT-TT-T-T
2439534 TTT-TTATTT
1 TTTATT-TTT
2439543 CATTTA-TTTT
1 --TTTATTTTT
2439553 TTTATTTTT
1 TTTATTTTT
2439562 T
1 T
2439563 CATTTTAAAT
Statistics
Matches: 102, Mismatches: 10, Indels: 39
0.68 0.07 0.26
Matches are distributed among these distances:
8 10 0.10
9 24 0.24
10 34 0.33
11 15 0.15
12 17 0.17
13 2 0.02
ACGTcount: A:0.16, C:0.08, G:0.01, T:0.75
Consensus pattern (9 bp):
TTTATTTTT
Found at i:2439575 original size:13 final size:13
Alignment explanation
Indices: 2439559--2439588 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
2439549 TTTTTTTATT
2439559 TTTTCATTTTAAA
1 TTTTCATTTTAAA
2439572 TTTTCATTTTAAA
1 TTTTCATTTTAAA
2439585 TTTT
1 TTTT
2439589 TATTATCTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.27, C:0.07, G:0.00, T:0.67
Consensus pattern (13 bp):
TTTTCATTTTAAA
Found at i:2441237 original size:15 final size:14
Alignment explanation
Indices: 2441213--2441250 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 14
2441203 ATTTTGATTT
2441213 TATAAATAAAAATA
1 TATAAATAAAAATA
2441227 TATAAATTAAAAATA
1 TATAAA-TAAAAATA
2441242 -ATGAAATAA
1 TAT-AAATAA
2441251 TATATTTTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 11 0.50
15 11 0.50
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (14 bp):
TATAAATAAAAATA
Found at i:2449368 original size:140 final size:140
Alignment explanation
Indices: 2449214--2449489 Score: 383
Period size: 140 Copynumber: 2.0 Consensus size: 140
2449204 GAATTCAAAG
* * * * * * * *
2449214 ATTTAGAGACCATTTTAAAATGAAGATCATATTTTTTTAATGAAATTGAAACATTTAAAATGTTC
1 ATTTAGAGACCATTTTAAAATGAAGATCATAATTTGTTAATAAAACTAAAACACTTAAAAAGTTA
*
2449279 GAGGATCTA-ATCAAGAATGAGAAAAATAATTTGATGACAAAGTTAAAATTTTAAGACCAAATTG
66 GAGAATCTATATC-AGAATGAGAAAAATAATTTGATGACAAAGTTAAAATTTTAAGACCAAATTG
2449343 AAATGATCATA
130 AAATGATCATA
*
2449354 ATTTAGAGATCATTTTAAAATGAAGATCATAATTTGTTAATAAAACTAAAACACTTAAAAAGTTA
1 ATTTAGAGACCATTTTAAAATGAAGATCATAATTTGTTAATAAAACTAAAACACTTAAAAAGTTA
* * ** * * *
2449419 GAGAATTTATTTCAGAATGAGAATCATAATTTGATGACGAATTTAAAATTTTAAGACCAACTTGA
66 GAGAATCTATATCAGAATGAGAAAAATAATTTGATGACAAAGTTAAAATTTTAAGACCAAATTGA
2449484 AATGAT
131 AATGAT
2449490 GATCATAATT
Statistics
Matches: 118, Mismatches: 17, Indels: 2
0.86 0.12 0.01
Matches are distributed among these distances:
140 116 0.98
141 2 0.02
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.33
Consensus pattern (140 bp):
ATTTAGAGACCATTTTAAAATGAAGATCATAATTTGTTAATAAAACTAAAACACTTAAAAAGTTA
GAGAATCTATATCAGAATGAGAAAAATAATTTGATGACAAAGTTAAAATTTTAAGACCAAATTGA
AATGATCATA
Found at i:2453286 original size:13 final size:14
Alignment explanation
Indices: 2453264--2453296 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
2453254 AGATAAATAT
*
2453264 AAATAGATAATT-A
1 AAATAAATAATTGA
2453277 AAATAAATAATTGA
1 AAATAAATAATTGA
2453291 AAATAA
1 AAATAA
2453297 GATGTTTTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 11 0.61
14 7 0.39
ACGTcount: A:0.67, C:0.00, G:0.06, T:0.27
Consensus pattern (14 bp):
AAATAAATAATTGA
Found at i:2454755 original size:2 final size:2
Alignment explanation
Indices: 2454750--2454794 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
2454740 TCACACAAAC
2454750 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2454792 AT A
1 AT A
2454795 AATAAAAATA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2470342 original size:24 final size:24
Alignment explanation
Indices: 2470313--2470366 Score: 108
Period size: 24 Copynumber: 2.2 Consensus size: 24
2470303 AAGAATGAAT
2470313 ATTACATAGTGACAATAATTATGA
1 ATTACATAGTGACAATAATTATGA
2470337 ATTACATAGTGACAATAATTATGA
1 ATTACATAGTGACAATAATTATGA
2470361 ATTACA
1 ATTACA
2470367 ATCCGGCTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.46, C:0.09, G:0.11, T:0.33
Consensus pattern (24 bp):
ATTACATAGTGACAATAATTATGA
Found at i:2472561 original size:163 final size:164
Alignment explanation
Indices: 2472358--2472686 Score: 651
Period size: 163 Copynumber: 2.0 Consensus size: 164
2472348 AAAAACCCCG
2472358 AAAAAATCTTTGTTTAAATATCGATAGAGATTATTAAAATAATTATTTTACTATTTCAAACCTTG
1 AAAAAATCTTTGTTTAAATATCGATAGAGATTATTAAAATAATTATTTTACTATTTCAAACCTTG
2472423 ATATAATTTACAACTTAATGGAAGCAAATTATAAATTAGTTGTTAACAAAGTATTAAGGGGATTT
66 ATATAATTTACAACTTAATGGAAGCAAATTATAAATTAGTTGTTAACAAAGTATTAAGGGGATTT
2472488 TAAAAAGCAACTAATACAGAATGGAAAACCTGTA
131 TAAAAAGCAACTAATACAGAATGGAAAACCTGTA
2472522 AAAAAATCTTTGTTT-AATATCGATAGAGATTATTAAAATAATTATTTTACTATTTCAAACCTTG
1 AAAAAATCTTTGTTTAAATATCGATAGAGATTATTAAAATAATTATTTTACTATTTCAAACCTTG
2472586 ATATAATTTACAACTTAATGGAAGCAAATTATAAATTAGTTGTTAACAAAGTATTAAGGGGATTT
66 ATATAATTTACAACTTAATGGAAGCAAATTATAAATTAGTTGTTAACAAAGTATTAAGGGGATTT
2472651 TAAAAAGCAACTAATACAGAATGGAAAACCTGTA
131 TAAAAAGCAACTAATACAGAATGGAAAACCTGTA
2472685 AA
1 AA
2472687 CTTACCGCAA
Statistics
Matches: 165, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
163 150 0.91
164 15 0.09
ACGTcount: A:0.45, C:0.09, G:0.12, T:0.34
Consensus pattern (164 bp):
AAAAAATCTTTGTTTAAATATCGATAGAGATTATTAAAATAATTATTTTACTATTTCAAACCTTG
ATATAATTTACAACTTAATGGAAGCAAATTATAAATTAGTTGTTAACAAAGTATTAAGGGGATTT
TAAAAAGCAACTAATACAGAATGGAAAACCTGTA
Found at i:2477877 original size:27 final size:27
Alignment explanation
Indices: 2477837--2477900 Score: 71
Period size: 27 Copynumber: 2.4 Consensus size: 27
2477827 AATAAAAAAC
2477837 AAATAA-AATAAATAAACGAAT-ATGACT
1 AAATAATAATAAAT-AAC-AATAATGACT
*
2477864 AAATAATAAT-AATAACAATAATGATT
1 AAATAATAATAAATAACAATAATGACT
2477890 AAAGTAATAAT
1 AAA-TAATAAT
2477901 TTAAACATAT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
25 3 0.09
26 11 0.33
27 16 0.48
28 3 0.09
ACGTcount: A:0.62, C:0.05, G:0.06, T:0.27
Consensus pattern (27 bp):
AAATAATAATAAATAACAATAATGACT
Found at i:2508958 original size:3 final size:3
Alignment explanation
Indices: 2508950--2508982 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
2508940 TTATTTATTA
*
2508950 AAT AAT AAT ATT AA- AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
2508983 TGAGACAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:2508968 original size:14 final size:13
Alignment explanation
Indices: 2508945--2508982 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
2508935 TAAAATTATT
2508945 TATTAAATAATAA
1 TATTAAATAATAA
2508958 TATTAAAATAATAA
1 TATT-AAATAATAA
*
2508972 TAAT-AATAATA
1 TATTAAATAATA
2508983 TGAGACAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
12 7 0.30
13 4 0.17
14 12 0.52
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (13 bp):
TATTAAATAATAA
Found at i:2509628 original size:122 final size:122
Alignment explanation
Indices: 2509362--2510044 Score: 833
Period size: 122 Copynumber: 5.7 Consensus size: 122
2509352 TAAGGCAAGA
*
2509362 TTGAACAAATTCTTCTCATTATGAACTTCTTC-TCCTTCTTCAGATGAGTTCTTCTTATTATGAA
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATGAGTTCTTCTCATTATGAA
** * * * *
2509426 CTTTTTCTGGAAATGTTGATGCTGATATATCTCTTT-TTGTGATAGAGTC-ATGCAAAAAG
65 C-ACTTCTGGAAATGTTGATGTTGATCTATCTCTTTCTT-TGATAGAATCGA-GCAAAAGG
* * *
2509485 TTGAACAAATTCTTCTTATTATGAACTTATTCTTCCTCTTCAGATGAGTTCTTCTCATTATGGAC
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAAC
* * * *
2509550 ACTTATGGAAATTTTAATGTTGATCTATCTCTTTCTTTGATAGAATCGAGTAAAAGG
66 ACTTCTGGAAATGTTGATGTTGATCTATCTCTTTCTTTGATAGAATCGAGCAAAAGG
*
2509607 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAAGAAC
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAAC
* * *
2509672 ACTTCTGGAAATTTTGATGTTGATCTATCTCTTTCTTTGATAGAATTGAGTAAAAGG
66 ACTTCTGGAAATGTTGATGTTGATCTATCTCTTTCTTTGATAGAATCGAGCAAAAGG
* * *
2509729 TTAAACAAATTCTTCTCATTATGAACTTCTTTTTCCTCTTCAGATGAGTTCTTCTTATTATGAAC
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAAC
* * * ** *
2509794 TCTTCCGGAAATGTTGA-----A-CCA--TC---GATTGAT-GAATTCAAGCAAAAGG
66 ACTTCTGGAAATGTTGATGTTGATCTATCTCTTTCTTTGATAGAA-TCGAGCAAAAGG
* * *
2509840 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCATATGAGTTCTTCTCATTTTGAA
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATGAGTTCTTCTCATTATGAA
* **
2509905 CACTTCTGGAAATGTTGGTGTTGATCTATCTCCTTT-TGGGATAGAATCGAGCAAAAGG
65 CACTTCTGGAAATGTTGATGTTGATCTATCT-CTTTCTTTGATAGAATCGAGCAAAAGG
* *
2509963 TTGAATAAGTTCTTCTCATTATGAACTTC-TCATTCCTCTTCAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAATTCTTCTCATTATGAACTTCTTC-TTCCTCTTCAGATGAGTTCTTCTCATTATGAA
* *
2510027 CTTCCTCTGGAAATGTTG
65 C-ACTTCTGGAAATGTTG
2510045 GTCCATCGAG
Statistics
Matches: 487, Mismatches: 53, Indels: 40
0.84 0.09 0.07
Matches are distributed among these distances:
110 3 0.01
111 47 0.10
112 40 0.08
114 2 0.00
116 2 0.00
117 2 0.00
118 2 0.00
120 1 0.00
121 1 0.00
122 261 0.54
123 120 0.25
124 6 0.01
ACGTcount: A:0.26, C:0.18, G:0.14, T:0.41
Consensus pattern (122 bp):
TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAAC
ACTTCTGGAAATGTTGATGTTGATCTATCTCTTTCTTTGATAGAATCGAGCAAAAGG
Found at i:2509886 original size:24 final size:23
Alignment explanation
Indices: 2509851--2509895 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 23
2509841 TGAACAAGTT
2509851 CTTCTCATTATGAACTTCTTCTTC
1 CTTCTCATTATG-ACTTCTTCTTC
*
2509875 CTTCTTCA-TATGAGTTCTTCT
1 CTTC-TCATTATGACTTCTTCT
2509896 CATTTTGAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 8 0.42
24 8 0.42
25 3 0.16
ACGTcount: A:0.16, C:0.27, G:0.07, T:0.51
Consensus pattern (23 bp):
CTTCTCATTATGACTTCTTCTTC
Found at i:2510125 original size:36 final size:35
Alignment explanation
Indices: 2510085--2510211 Score: 94
Period size: 36 Copynumber: 3.5 Consensus size: 35
2510075 AGTGAAACTG
2510085 TCTCAAGCGAGACAAATCTTGTTTTAAGAAAAACAA
1 TCTCAAGCGAGACAAAT-TTGTTTTAAGAAAAACAA
* * ** ** **
2510121 TCTCAAGTGAGATAAATTGTTGTTTCGAGTGAAACTG
1 TCTCAAGCGAGACAAA-T-TTGTTTTAAGAAAAACAA
* *
2510158 TCTCAAGCAAGATGC-AGTTTGTTTTAAGAAAAACAA
1 TCTCAAGCGAGA--CAAATTTGTTTTAAGAAAAACAA
* *
2510194 TCTCAAGTGAGATAAATT
1 TCTCAAGCGAGACAAATT
2510212 ACTATTTGAA
Statistics
Matches: 64, Mismatches: 23, Indels: 9
0.67 0.24 0.09
Matches are distributed among these distances:
35 3 0.05
36 36 0.56
37 24 0.38
38 1 0.02
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (35 bp):
TCTCAAGCGAGACAAATTTGTTTTAAGAAAAACAA
Found at i:2510162 original size:37 final size:36
Alignment explanation
Indices: 2510075--2510165 Score: 92
Period size: 36 Copynumber: 2.5 Consensus size: 36
2510065 TTCTGTTTTT
*
2510075 AGTGAAACTGTCTCAAGCGAGACAAATCTTGTTTTA
1 AGTGAAACTGTCTCAAGCGAGACAAATCTTGTTTCA
** ** * * * *
2510111 AGAAAAACAATCTCAAGTGAGATAAATTGTTGTTTCG
1 AGTGAAACTGTCTCAAGCGAGACAAA-TCTTGTTTCA
2510148 AGTGAAACTGTCTCAAGC
1 AGTGAAACTGTCTCAAGC
2510166 AAGATGCAGT
Statistics
Matches: 40, Mismatches: 14, Indels: 1
0.73 0.25 0.02
Matches are distributed among these distances:
36 20 0.50
37 20 0.50
ACGTcount: A:0.36, C:0.15, G:0.20, T:0.29
Consensus pattern (36 bp):
AGTGAAACTGTCTCAAGCGAGACAAATCTTGTTTCA
Found at i:2510180 original size:73 final size:73
Alignment explanation
Indices: 2510075--2510211 Score: 224
Period size: 73 Copynumber: 1.9 Consensus size: 73
2510065 TTCTGTTTTT
*
2510075 AGTGAAACTGTCTCAAGCGAGACAAATCTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTG
1 AGTGAAACTGTCTCAAGCAAGACAAATCTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTG
2510140 TTGTTTCG
66 TTGTTTCG
*
2510148 AGTGAAACTGTCTCAAGCAAGATGC-AGT-TTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAT
1 AGTGAAACTGTCTCAAGCAAGA--CAAATCTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAT
2510211 T
64 T
2510212 ACTATTTGAA
Statistics
Matches: 60, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
73 57 0.95
74 2 0.03
75 1 0.02
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.29
Consensus pattern (73 bp):
AGTGAAACTGTCTCAAGCAAGACAAATCTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTG
TTGTTTCG
Found at i:2515093 original size:32 final size:32
Alignment explanation
Indices: 2515054--2515120 Score: 100
Period size: 32 Copynumber: 2.1 Consensus size: 32
2515044 TGAAGAAATA
* *
2515054 GTTGTTATGCTTATCTGGTA-GAGATACTTCTT
1 GTTGTTATGCTTATCTCGTAGGA-ATACTTCAT
2515086 GTTGTTATGCTTATCTCGTAGGAATACTTCAT
1 GTTGTTATGCTTATCTCGTAGGAATACTTCAT
2515118 GTT
1 GTT
2515121 TCTAGACTCT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
32 30 0.94
33 2 0.06
ACGTcount: A:0.19, C:0.13, G:0.21, T:0.46
Consensus pattern (32 bp):
GTTGTTATGCTTATCTCGTAGGAATACTTCAT
Found at i:2515585 original size:8 final size:8
Alignment explanation
Indices: 2515572--2515634 Score: 67
Period size: 8 Copynumber: 8.0 Consensus size: 8
2515562 TTTGATTCAA
2515572 TTTTTTCT
1 TTTTTTCT
*
2515580 TTTTTTCC
1 TTTTTTCT
**
2515588 TTCCTTCT
1 TTTTTTCT
2515596 TTTTTTCT
1 TTTTTTCT
2515604 TTTTTTC-
1 TTTTTTCT
*
2515611 TTTTTCCT
1 TTTTTTCT
2515619 TTTTTT-T
1 TTTTTTCT
2515626 ATTTTTTCT
1 -TTTTTTCT
2515635 CTTCTTCAAG
Statistics
Matches: 44, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
7 7 0.16
8 36 0.82
9 1 0.02
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (8 bp):
TTTTTTCT
Found at i:2515622 original size:24 final size:26
Alignment explanation
Indices: 2515572--2515641 Score: 85
Period size: 25 Copynumber: 2.8 Consensus size: 26
2515562 TTTGATTCAA
2515572 TTTTTTCTTTTTTTC--CTTCCTTCT
1 TTTTTTCTTTTTTTCTTCTTCCTTCT
*
2515596 TTTTTTCTTTTTTTCTTTTTCCTT-T
1 TTTTTTCTTTTTTTCTTCTTCCTTCT
*
2515621 TTTTTAT-TTTTTCTCTTCTTC
1 TTTTT-TCTTTTTTTCTTCTTC
2515642 AAGTATAATA
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
24 15 0.38
25 18 0.45
26 7 0.17
ACGTcount: A:0.01, C:0.20, G:0.00, T:0.79
Consensus pattern (26 bp):
TTTTTTCTTTTTTTCTTCTTCCTTCT
Found at i:2518497 original size:6 final size:6
Alignment explanation
Indices: 2518424--2518487 Score: 119
Period size: 6 Copynumber: 10.7 Consensus size: 6
2518414 AAAAAATGCA
*
2518424 AAATGC AAATGT AAATGT AAATGT AAATGT AAATGT AAATGT AAATGT
1 AAATGT AAATGT AAATGT AAATGT AAATGT AAATGT AAATGT AAATGT
2518472 AAATGT AAATGT AAAT
1 AAATGT AAATGT AAAT
2518488 ATGTGAATGT
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 57 1.00
ACGTcount: A:0.52, C:0.02, G:0.16, T:0.31
Consensus pattern (6 bp):
AAATGT
Found at i:2520054 original size:17 final size:17
Alignment explanation
Indices: 2520032--2520064 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
2520022 TTGAAAATAA
2520032 AATAAAATAAA-AATATT
1 AATAAAA-AAATAATATT
2520049 AATAAAAAAATAATAT
1 AATAAAAAAATAATAT
2520065 ACATATAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (17 bp):
AATAAAAAAATAATATT
Found at i:2520070 original size:23 final size:22
Alignment explanation
Indices: 2520026--2520075 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 22
2520016 TAATACTTGA
*
2520026 AAATAAAATAAAATAAAAATAT
1 AAATAAAAAAAAATAAAAATAT
* * *
2520048 TAATAAAAAAATAATATACATAT
1 AAATAAAAAAA-AATAAAAATAT
2520071 AAATA
1 AAATA
2520076 TTATGAAAAT
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
22 9 0.41
23 13 0.59
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (22 bp):
AAATAAAAAAAAATAAAAATAT
Found at i:2520074 original size:29 final size:30
Alignment explanation
Indices: 2520038--2520112 Score: 95
Period size: 29 Copynumber: 2.6 Consensus size: 30
2520028 ATAAAATAAA
2520038 ATAAAAATATTAAT-AAAAAAATAA-TATAC
1 ATAAAAATATT-ATGAAAAAAATAAGTATAC
* *
2520067 ATATAAATATTATGAAAATAATAAGTATAC
1 ATAAAAATATTATGAAAAAAATAAGTATAC
2520097 ATAAAAAT-TT-TGAAAA
1 ATAAAAATATTATGAAAA
2520113 GAAAGAATTA
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
28 8 0.20
29 21 0.51
30 12 0.29
ACGTcount: A:0.63, C:0.03, G:0.04, T:0.31
Consensus pattern (30 bp):
ATAAAAATATTATGAAAAAAATAAGTATAC
Found at i:2520098 original size:30 final size:28
Alignment explanation
Indices: 2520041--2520139 Score: 87
Period size: 29 Copynumber: 3.5 Consensus size: 28
2520031 AAATAAAATA
2520041 AAAATATTAAT-AAAAAAATAATATACAT
1 AAAATATT-ATGAAAAAAATAATATACAT
*
2520069 ATAAATATTATGAAAATAATAAGTATACAT
1 A-AAATATTATGAAAAAAATAA-TATACAT
* * *
2520099 AAAA-ATTTTGAAAAGAAAGAATTATAAAT
1 AAAATATTATGAAAA-AAATAA-TATACAT
*
2520128 TAAATA-TATGAA
1 AAAATATTATGAA
2520140 TTTTTAATTT
Statistics
Matches: 58, Mismatches: 8, Indels: 9
0.77 0.11 0.12
Matches are distributed among these distances:
28 12 0.21
29 37 0.64
30 9 0.16
ACGTcount: A:0.62, C:0.02, G:0.06, T:0.30
Consensus pattern (28 bp):
AAAATATTATGAAAAAAATAATATACAT
Found at i:2522289 original size:3 final size:3
Alignment explanation
Indices: 2522283--2522314 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
2522273 TTATTTATTA
2522283 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2522315 ATGAGACAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2533905 original size:124 final size:124
Alignment explanation
Indices: 2533685--2533973 Score: 443
Period size: 124 Copynumber: 2.3 Consensus size: 124
2533675 GGATGGCTTC
* * *
2533685 TTGAGCTTTGAATTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCTAGATATAGATACTACTT
1 TTGAGCTTTGAATTGGATATCCTTCGTTGTGAAGTTGAAATACAATCTAGAGATAGACACTACTT
* *
2533750 ATGGGCACAATATATTTCGTCGTGAAGTTGAAATCGTGGATGGCTCATTCATTGTGAAG
66 ATGGGCACAATATACTTCGTCGTGAAGTTGAAATCGTGGATGACTCATTCATTGTGAAG
* * * * *
2533809 TTGAGCTTTGAATTGGATATCCTTCGTTATGAAGTTGAAATATAATCTAGAGATGGACGCTGCTT
1 TTGAGCTTTGAATTGGATATCCTTCGTTGTGAAGTTGAAATACAATCTAGAGATAGACACTACTT
* * * *
2533874 GTGGGCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGACTCATTCGTTGTGAAG
66 ATGGGCACAATATACTTCGTCGTGAAGTTGAAATCGTGGATGACTCATTCATTGTGAAG
*
2533933 TTGAGCTTTGAATTGGATATCATTCGTTGTGAAGTTGAAAT
1 TTGAGCTTTGAATTGGATATCCTTCGTTGTGAAGTTGAAAT
2533974 TAAAGGGTTA
Statistics
Matches: 149, Mismatches: 16, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
124 149 1.00
ACGTcount: A:0.27, C:0.13, G:0.25, T:0.36
Consensus pattern (124 bp):
TTGAGCTTTGAATTGGATATCCTTCGTTGTGAAGTTGAAATACAATCTAGAGATAGACACTACTT
ATGGGCACAATATACTTCGTCGTGAAGTTGAAATCGTGGATGACTCATTCATTGTGAAG
Found at i:2534091 original size:125 final size:126
Alignment explanation
Indices: 2533933--2534166 Score: 371
Period size: 125 Copynumber: 1.9 Consensus size: 126
2533923 CGTTGTGAAG
* **
2533933 TTGAGCTTTGAATTGGATATCATTCGTTGTGAAGTTGAAATTAAAGGGTTATTTCACCAAATTGG
1 TTGAGCTTTGAATTGGATATCATTCGTTGTGAAGTTGAAATCAAAGAATTATTTCACCAAATTGG
*
2533998 TTTTGAGTTGGATATCCTTCGTCGTGAAGTTGAAATCTAATCTTGAGTAAGTTTCACCAAA
66 CTTTGAGTTGGATATCCTTCGTCGTGAAGTTGAAATCTAATCTTGAGTAAGTTTCACCAAA
* * * *
2534059 TTGA-CTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATCCAAGAATTGTTTCACCAAATTGG
1 TTGAGCTTTGAATTGGATATCATTCGTTGTGAAGTTGAAATCAAAGAATTATTTCACCAAATTGG
* *
2534123 CTTTGAGTTGGCTATCCTTCGTTGTGAAGTTGAAATCTAATCTT
66 CTTTGAGTTGGATATCCTTCGTCGTGAAGTTGAAATCTAATCTT
2534167 TTGTATGTTG
Statistics
Matches: 98, Mismatches: 10, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
125 94 0.96
126 4 0.04
ACGTcount: A:0.26, C:0.13, G:0.21, T:0.39
Consensus pattern (126 bp):
TTGAGCTTTGAATTGGATATCATTCGTTGTGAAGTTGAAATCAAAGAATTATTTCACCAAATTGG
CTTTGAGTTGGATATCCTTCGTCGTGAAGTTGAAATCTAATCTTGAGTAAGTTTCACCAAA
Found at i:2534159 original size:60 final size:60
Alignment explanation
Indices: 2533937--2534159 Score: 284
Period size: 60 Copynumber: 3.6 Consensus size: 60
2533927 GTGAAGTTGA
* * * * *
2533937 GCTTTGAATTGGATATCATTCGTTGTGAAGTTGAAATTAAAGGGTTATTTCACCAAATTG
1 GCTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATCAAAGAGTTGTTTCACCAAATTG
* * * *
2533997 GTTTTGAGTTGGATATCCTTCGTCGTGAAGTTGAAATCTAATCTTGAGTAAGTTTCACCAAATTG
1 GCTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATC-AA---AGAGT-TGTTTCACCAAATTG
* * *
2534062 ACTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATCCAAGAATTGTTTCACCAAATTG
1 GCTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATCAAAGAGTTGTTTCACCAAATTG
*
2534122 GCTTTGAGTTGGCTATCCTTCGTTGTGAAGTTGAAATC
1 GCTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATC
2534160 TAATCTTTTG
Statistics
Matches: 140, Mismatches: 18, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
60 83 0.59
61 5 0.04
64 4 0.03
65 48 0.34
ACGTcount: A:0.26, C:0.13, G:0.22, T:0.38
Consensus pattern (60 bp):
GCTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATCAAAGAGTTGTTTCACCAAATTG
Found at i:2535964 original size:6 final size:6
Alignment explanation
Indices: 2535953--2536004 Score: 52
Period size: 6 Copynumber: 8.5 Consensus size: 6
2535943 CACTTTTTTC
* * *
2535953 TTTGTT TTTGTT TTTGTT TTT-TAT TTTCTC TTTGTTT TTTTTT TTTGTT
1 TTTGTT TTTGTT TTTGTT TTTGT-T TTTGTT TTTG-TT TTTGTT TTTGTT
2536002 TTT
1 TTT
2536005 TTCTTTCTCT
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
5 1 0.03
6 32 0.84
7 5 0.13
ACGTcount: A:0.02, C:0.04, G:0.10, T:0.85
Consensus pattern (6 bp):
TTTGTT
Found at i:2535987 original size:30 final size:30
Alignment explanation
Indices: 2535946--2536016 Score: 101
Period size: 31 Copynumber: 2.4 Consensus size: 30
2535936 TTTCCTTCAC
2535946 TTTTT-TCTTTG-TTTTTGTTTTTGTTTTT
1 TTTTTCTCTTTGTTTTTTGTTTTTGTTTTT
*
2535974 TATTTTCTCTTTGTTTTTTTTTTTTGTTTTT
1 T-TTTTCTCTTTGTTTTTTGTTTTTGTTTTT
2536005 TTCTTTCTCTTT
1 TT-TTTCTCTTT
2536017 TTGTTCTGAT
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
28 1 0.03
29 4 0.11
30 7 0.18
31 26 0.68
ACGTcount: A:0.01, C:0.08, G:0.07, T:0.83
Consensus pattern (30 bp):
TTTTTCTCTTTGTTTTTTGTTTTTGTTTTT
Found at i:2538048 original size:32 final size:32
Alignment explanation
Indices: 2537989--2538050 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
2537979 ATGGAAAATA
* *
2537989 ACACAAATAAAAGAATGGAGATAAGTTAGTGT
1 ACACAAACAAAAGAATGGAAATAAGTTAGTGT
*
2538021 ACACAAACAAAAGAA-GTGAAATTAGTTAGT
1 ACACAAACAAAAGAATG-GAAATAAGTTAGT
2538051 ACATGTAAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 1 0.04
32 25 0.96
ACGTcount: A:0.52, C:0.08, G:0.19, T:0.21
Consensus pattern (32 bp):
ACACAAACAAAAGAATGGAAATAAGTTAGTGT
Found at i:2539158 original size:17 final size:19
Alignment explanation
Indices: 2539118--2539157 Score: 64
Period size: 20 Copynumber: 2.1 Consensus size: 19
2539108 AAAAAATACT
2539118 AAATAAATTAAAGAGAAAAA
1 AAATAAATTAAAGAG-AAAA
2539138 AAATAAATT-AAGAGAAAA
1 AAATAAATTAAAGAGAAAA
2539156 AA
1 AA
2539158 TGTTAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 6 0.30
19 5 0.25
20 9 0.45
ACGTcount: A:0.75, C:0.00, G:0.10, T:0.15
Consensus pattern (19 bp):
AAATAAATTAAAGAGAAAA
Found at i:2539164 original size:20 final size:20
Alignment explanation
Indices: 2539118--2539157 Score: 73
Period size: 19 Copynumber: 2.0 Consensus size: 20
2539108 AAAAAATACT
2539118 AAATAAATTAAAGAGAAAAA
1 AAATAAATTAAAGAGAAAAA
2539138 AAATAAATT-AAGAGAAAAA
1 AAATAAATTAAAGAGAAAAA
2539157 A
1 A
2539158 TGTTAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.75, C:0.00, G:0.10, T:0.15
Consensus pattern (20 bp):
AAATAAATTAAAGAGAAAAA
Found at i:2539181 original size:11 final size:10
Alignment explanation
Indices: 2539152--2539177 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
2539142 AAATTAAGAG
2539152 AAAAAATGTT
1 AAAAAATGTT
2539162 AAAAAATGTT
1 AAAAAATGTT
2539172 AAAAAA
1 AAAAAA
2539178 ATGTGTAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.69, C:0.00, G:0.08, T:0.23
Consensus pattern (10 bp):
AAAAAATGTT
Found at i:2540524 original size:23 final size:23
Alignment explanation
Indices: 2540498--2540581 Score: 123
Period size: 23 Copynumber: 3.7 Consensus size: 23
2540488 CTCGTATAAA
*
2540498 TGCACCAAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
2540521 TGCACCGTAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
* * *
2540544 TGCACCGTAGTGCCGCGTAGAAA
1 TGCACCGAAGTGCCACGTAGAAT
2540567 TGCACCGAAGTGCCA
1 TGCACCGAAGTGCCA
2540582 TATAAGGTTG
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 55 1.00
ACGTcount: A:0.29, C:0.27, G:0.26, T:0.18
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:2542341 original size:65 final size:63
Alignment explanation
Indices: 2542253--2542394 Score: 171
Period size: 65 Copynumber: 2.2 Consensus size: 63
2542243 TCTTTAACAT
* *
2542253 GTGCATCGATGCACTACCCATGCATCGATACACAAATTACCTTCGATGTTTTCATT-TTAAAAGG
1 GTGCATCGATGCACTACCCATGCATCGATACACAAATTACATTCGATG-TTTC-TTCTTAAAAGA
* * * * *
2542317 GATGCATCGATGCACT-CCTTATGCATCGATGCACCAATTGCATTCGATGTTTCTTCTTTAAAGA
1 G-TGCATCGATGCACTACC-CATGCATCGATACACAAATTACATTCGATGTTTCTTCTTAAAAGA
2542381 GTGCATCGATGCAC
1 GTGCATCGATGCAC
2542395 GCACATTCAA
Statistics
Matches: 68, Mismatches: 7, Indels: 7
0.83 0.09 0.09
Matches are distributed among these distances:
63 15 0.22
64 14 0.21
65 39 0.57
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.32
Consensus pattern (63 bp):
GTGCATCGATGCACTACCCATGCATCGATACACAAATTACATTCGATGTTTCTTCTTAAAAGA
Found at i:2543839 original size:12 final size:12
Alignment explanation
Indices: 2543824--2543877 Score: 56
Period size: 12 Copynumber: 4.6 Consensus size: 12
2543814 GTTATTTAAA
2543824 CGGGTATTGGGC
1 CGGGTATTGGGC
*
2543836 CGGGTATTTGG-
1 CGGGTATTGGGC
**
2543847 TTGGTATTGGGC
1 CGGGTATTGGGC
* *
2543859 CGGGAATCGGGC
1 CGGGTATTGGGC
2543871 CGGGTAT
1 CGGGTAT
2543878 ATATATATAT
Statistics
Matches: 32, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
11 8 0.25
12 24 0.75
ACGTcount: A:0.11, C:0.15, G:0.46, T:0.28
Consensus pattern (12 bp):
CGGGTATTGGGC
Found at i:2543935 original size:24 final size:25
Alignment explanation
Indices: 2543875--2543935 Score: 69
Period size: 24 Copynumber: 2.6 Consensus size: 25
2543865 TCGGGCCGGG
2543875 TATATA-TATA-TATTTAAATTAAA
1 TATATATTATATTATTTAAATTAAA
*
2543898 TATATATT-TTTTATTTAAATTAAA
1 TATATATTATATTATTTAAATTAAA
2543922 T-T-TATTAATATTAT
1 TATATATT-ATATTAT
2543936 ATATATATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
22 4 0.12
23 8 0.25
24 20 0.62
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (25 bp):
TATATATTATATTATTTAAATTAAA
Found at i:2550769 original size:18 final size:18
Alignment explanation
Indices: 2550730--2550770 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
2550720 ACCTTGGGCA
* *
2550730 TCATCTTCCTTATCATCG
1 TCATCTTCCTCATCATCC
*
2550748 TCATCTTCCTCATCGTCC
1 TCATCTTCCTCATCATCC
2550766 TCATC
1 TCATC
2550771 GTCGTCGTCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.15, C:0.39, G:0.05, T:0.41
Consensus pattern (18 bp):
TCATCTTCCTCATCATCC
Found at i:2552884 original size:18 final size:18
Alignment explanation
Indices: 2552861--2552898 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
2552851 AAATAATTAA
2552861 TTAGTATAAATGTAATAT
1 TTAGTATAAATGTAATAT
2552879 TTAGTATAAATGTAATAT
1 TTAGTATAAATGTAATAT
2552897 TT
1 TT
2552899 TAGAGATTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.42, C:0.00, G:0.11, T:0.47
Consensus pattern (18 bp):
TTAGTATAAATGTAATAT
Found at i:2559736 original size:87 final size:87
Alignment explanation
Indices: 2559630--2559888 Score: 509
Period size: 87 Copynumber: 3.0 Consensus size: 87
2559620 AGCCTTCTTA
*
2559630 ATTTTGAAGTAAGAATCCCATACCAAGTGAGGATCAATAGTTGGCATTAATTAATTAACTAAACC
1 ATTTTGAAGTAAGAATCCCATACCAAGTGAGGATCAATAGTTGCCATTAATTAATTAACTAAACC
2559695 AACATAAACCTAACTTCATGTG
66 AACATAAACCTAACTTCATGTG
2559717 ATTTTGAAGTAAGAATCCCATACCAAGTGAGGATCAATAGTTGCCATTAATTAATTAACTAAACC
1 ATTTTGAAGTAAGAATCCCATACCAAGTGAGGATCAATAGTTGCCATTAATTAATTAACTAAACC
2559782 AACATAAACCTAACTTCATGTG
66 AACATAAACCTAACTTCATGTG
2559804 ATTTTGAAGTAAGAATCCCATACCAAGTGAGGATCAATAGTTGCCATTAATTAATTAACTAAACC
1 ATTTTGAAGTAAGAATCCCATACCAAGTGAGGATCAATAGTTGCCATTAATTAATTAACTAAACC
2559869 AACATAAACCTAACTTCATG
66 AACATAAACCTAACTTCATG
2559889 GTCACTTGGT
Statistics
Matches: 171, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
87 171 1.00
ACGTcount: A:0.41, C:0.18, G:0.13, T:0.29
Consensus pattern (87 bp):
ATTTTGAAGTAAGAATCCCATACCAAGTGAGGATCAATAGTTGCCATTAATTAATTAACTAAACC
AACATAAACCTAACTTCATGTG
Done.