Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008290.1 Hibiscus syriacus cultivar Beakdansim tig00110954_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: 1890093
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 9
Found at i:609382 original size:16 final size:16
Alignment explanation
Indices: 609361--609504 Score: 146
Period size: 16 Copynumber: 8.9 Consensus size: 16
609351 AGTGTATCAT
609361 TTTATTAGTTTACTAC
1 TTTATTAGTTTACTAC
* *
609377 TTTATTAAAGTGTATTAC
1 TTTATT--AGTTTACTAC
*
609395 TTTATTAATTTACTAC
1 TTTATTAGTTTACTAC
** *
609411 TTTATTAGTTTAGAAA
1 TTTATTAGTTTACTAC
* *
609427 TTGATTAGTTTATTAC
1 TTTATTAGTTTACTAC
*
609443 TTAATTAGTTTTA-TAC
1 TTTATTAG-TTTACTAC
609459 TTTATTAGTTTACTAC
1 TTTATTAGTTTACTAC
* *
609475 TTAATTAGTTTACTAT
1 TTTATTAGTTTACTAC
*
609491 TTTATTAATTTACT
1 TTTATTAGTTTACT
609505 GTTTTGCTTG
Statistics
Matches: 105, Mismatches: 19, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
15 4 0.04
16 83 0.79
17 4 0.04
18 14 0.13
ACGTcount: A:0.30, C:0.08, G:0.07, T:0.56
Consensus pattern (16 bp):
TTTATTAGTTTACTAC
Found at i:609382 original size:34 final size:34
Alignment explanation
Indices: 609344--609417 Score: 121
Period size: 34 Copynumber: 2.2 Consensus size: 34
609334 TATTAACATG
* *
609344 TTATTAAAGTGTATCATTTTATTAGTTTACTACT
1 TTATTAAAGTGTATCACTTTATTAATTTACTACT
*
609378 TTATTAAAGTGTATTACTTTATTAATTTACTACT
1 TTATTAAAGTGTATCACTTTATTAATTTACTACT
609412 TTATTA
1 TTATTA
609418 GTTTAGAAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.31, C:0.08, G:0.07, T:0.54
Consensus pattern (34 bp):
TTATTAAAGTGTATCACTTTATTAATTTACTACT
Found at i:609406 original size:8 final size:8
Alignment explanation
Indices: 609361--609502 Score: 61
Period size: 8 Copynumber: 17.5 Consensus size: 8
609351 AGTGTATCAT
*
609361 TTTATTAG
1 TTTATTAC
*
609369 TTTACTAC
1 TTTATTAC
*
609377 TTTATTAAAG
1 TTTATT--AC
*
609387 TGTATTAC
1 TTTATTAC
*
609395 TTTATTAA
1 TTTATTAC
*
609403 TTTACTAC
1 TTTATTAC
*
609411 TTTATTAG
1 TTTATTAC
** *
609419 TTTAGAAA
1 TTTATTAC
* *
609427 TTGATTAG
1 TTTATTAC
609435 TTTATTAC
1 TTTATTAC
* *
609443 TTAATTAG
1 TTTATTAC
609451 TTT-TATAC
1 TTTAT-TAC
*
609459 TTTATTAG
1 TTTATTAC
*
609467 TTTACTAC
1 TTTATTAC
* *
609475 TTAATTAG
1 TTTATTAC
* *
609483 TTTACTAT
1 TTTATTAC
*
609491 TTTATTAA
1 TTTATTAC
609499 TTTA
1 TTTA
609503 CTGTTTTGCT
Statistics
Matches: 94, Mismatches: 36, Indels: 8
0.68 0.26 0.06
Matches are distributed among these distances:
7 1 0.01
8 86 0.91
9 1 0.01
10 6 0.06
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.56
Consensus pattern (8 bp):
TTTATTAC
Found at i:609568 original size:13 final size:13
Alignment explanation
Indices: 609533--609574 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
609523 TGAAAGTGTA
* *
609533 TTACTTTATTATT
1 TTACTATATTAGT
609546 TTAC-ACTATTAGT
1 TTACTA-TATTAGT
609559 TTACTATATTAGT
1 TTACTATATTAGT
609572 TTA
1 TTA
609575 GTCTTATGCC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
13 24 0.96
14 1 0.04
ACGTcount: A:0.29, C:0.10, G:0.05, T:0.57
Consensus pattern (13 bp):
TTACTATATTAGT
Found at i:609771 original size:40 final size:40
Alignment explanation
Indices: 609716--609794 Score: 140
Period size: 40 Copynumber: 2.0 Consensus size: 40
609706 TAGAAATACA
*
609716 ATGTACACAGAACATTTATGTCCACAAAATCATCAACACG
1 ATGTACACAAAACATTTATGTCCACAAAATCATCAACACG
*
609756 ATGTACACAAAACATTTATGTTCACAAAATCATCAACAC
1 ATGTACACAAAACATTTATGTCCACAAAATCATCAACAC
609795 AAATATCTAC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.44, C:0.24, G:0.08, T:0.24
Consensus pattern (40 bp):
ATGTACACAAAACATTTATGTCCACAAAATCATCAACACG
Found at i:610362 original size:19 final size:19
Alignment explanation
Indices: 610321--610362 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
610311 GGAGGAGAAT
* *
610321 AAACTCTTTTAGACAATCG
1 AAACTCTTTTAGACAACCA
*
610340 AAACTCTTTTTGACAACCA
1 AAACTCTTTTAGACAACCA
610359 AAAC
1 AAAC
610363 CCTACTCTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.40, C:0.24, G:0.07, T:0.29
Consensus pattern (19 bp):
AAACTCTTTTAGACAACCA
Found at i:611221 original size:21 final size:22
Alignment explanation
Indices: 611181--611235 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 22
611171 ACCCCTCTAT
* **
611181 ATATTATTTTTTGAATTAAATCA
1 ATATT-TTTATTGAATTAAAAAA
*
611204 CTATTTTTATTGAA-TAAAAAA
1 ATATTTTTATTGAATTAAAAAA
611225 ATATTTTTATT
1 ATATTTTTATT
611236 ATTTTGGGTC
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 15 0.56
22 8 0.30
23 4 0.15
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.53
Consensus pattern (22 bp):
ATATTTTTATTGAATTAAAAAA
Found at i:611884 original size:3 final size:3
Alignment explanation
Indices: 611876--611916 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
611866 ATTGTAAACT
611876 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
611917 TACAAAGAGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:612164 original size:17 final size:17
Alignment explanation
Indices: 612133--612176 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
612123 TGAGATCATA
*
612133 ATATTAT-TTTTATATT
1 ATATTATATATTATATT
612149 -TATTTATATATTATATT
1 ATA-TTATATATTATATT
612166 ATATTATATAT
1 ATATTATATAT
612177 AAATAAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
15 2 0.08
16 4 0.17
17 16 0.67
18 2 0.08
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
ATATTATATATTATATT
Found at i:617397 original size:2 final size:2
Alignment explanation
Indices: 617390--617441 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
617380 ATTGTTTTAA
617390 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
617432 AT AT AT AT AT
1 AT AT AT AT AT
617442 CATGAGTTTT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:621623 original size:2 final size:2
Alignment explanation
Indices: 621616--621647 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
621606 GCCAATTGAT
621616 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
621648 GCTTAAGCTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:622155 original size:18 final size:18
Alignment explanation
Indices: 622134--622172 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
622124 GAATTTGATA
*
622134 CTCTGGACGAGGTTGTTC
1 CTCTGGACGAGCTTGTTC
* *
622152 CTCTGGAGGTGCTTGTTC
1 CTCTGGACGAGCTTGTTC
622170 CTC
1 CTC
622173 GTGCTGCTCT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.08, C:0.26, G:0.31, T:0.36
Consensus pattern (18 bp):
CTCTGGACGAGCTTGTTC
Found at i:623831 original size:21 final size:22
Alignment explanation
Indices: 623749--623830 Score: 87
Period size: 23 Copynumber: 3.7 Consensus size: 22
623739 AGAACCCCAT
*
623749 GGGGGTATCGATTCCCC-T-ATA
1 GGGGGAATCGATTCCCCTTCA-A
*
623770 GGGGGAATTGATTCCCCTTCAAA
1 GGGGGAATCGATTCCCCTTC-AA
* *
623793 GGGGGAATAGGTTCCCCTTCAA
1 GGGGGAATCGATTCCCCTTCAA
*
623815 GGGGGTATCGATTCCC
1 GGGGGAATCGATTCCC
623831 TCTGCACCAA
Statistics
Matches: 51, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
21 15 0.29
22 16 0.31
23 19 0.37
24 1 0.02
ACGTcount: A:0.21, C:0.23, G:0.30, T:0.26
Consensus pattern (22 bp):
GGGGGAATCGATTCCCCTTCAA
Found at i:630612 original size:45 final size:45
Alignment explanation
Indices: 630561--630652 Score: 175
Period size: 45 Copynumber: 2.0 Consensus size: 45
630551 TTTCGCACTA
630561 TTTTAAAAAAAATCTTTTTCCAAAGTTGATTTCATTTTTCAACTT
1 TTTTAAAAAAAATCTTTTTCCAAAGTTGATTTCATTTTTCAACTT
*
630606 TTTTAAAAAAATTCTTTTTCCAAAGTTGATTTCATTTTTCAACTT
1 TTTTAAAAAAAATCTTTTTCCAAAGTTGATTTCATTTTTCAACTT
630651 TT
1 TT
630653 CTGATAAATG
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.32, C:0.13, G:0.04, T:0.51
Consensus pattern (45 bp):
TTTTAAAAAAAATCTTTTTCCAAAGTTGATTTCATTTTTCAACTT
Found at i:631427 original size:2 final size:2
Alignment explanation
Indices: 631420--631450 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
631410 TTATTATTTA
631420 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
631451 CATTCATGAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:632827 original size:18 final size:18
Alignment explanation
Indices: 632795--632829 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
632785 ATGACCATTG
*
632795 CCAGCATTAGGCCCACTA
1 CCAGCATTAGACCCACTA
*
632813 CCAGCATTTGACCCACT
1 CCAGCATTAGACCCACT
632830 GGTAGCATTC
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:0.26, C:0.40, G:0.14, T:0.20
Consensus pattern (18 bp):
CCAGCATTAGACCCACTA
Found at i:632961 original size:16 final size:16
Alignment explanation
Indices: 632940--633085 Score: 114
Period size: 16 Copynumber: 8.8 Consensus size: 16
632930 GTGTATTATT
632940 TTTATTAGTTTAATAC
1 TTTATTAGTTTAATAC
*
632956 TTTATTAGTTAAAGTGTATTAC
1 TTTATTAG-T----T-TAATAC
* *
632978 TTTATTAATTTACTAC
1 TTTATTAGTTTAATAC
*
632994 TTTATTAGTTTAGA-AA
1 TTTATTAGTTTA-ATAC
* *
633010 TTGATTAGTTTATTAC
1 TTTATTAGTTTAATAC
* * *
633026 TTAATTAGTTTTATAA
1 TTTATTAGTTTAATAC
*
633042 TTTATTAGTTTACTAC
1 TTTATTAGTTTAATAC
*
633058 TTAATTAGTTTAATAC
1 TTTATTAGTTTAATAC
*
633074 TTTTTTAGTTTA
1 TTTATTAGTTTA
633086 CTATTTTAAT
Statistics
Matches: 101, Mismatches: 21, Indels: 16
0.73 0.15 0.12
Matches are distributed among these distances:
16 85 0.84
17 2 0.02
21 2 0.02
22 12 0.12
ACGTcount: A:0.31, C:0.05, G:0.08, T:0.55
Consensus pattern (16 bp):
TTTATTAGTTTAATAC
Found at i:632978 original size:22 final size:21
Alignment explanation
Indices: 632922--632984 Score: 71
Period size: 22 Copynumber: 3.1 Consensus size: 21
632912 CATTAACATG
632922 TTATTAAAGTGTATTA-TTT-
1 TTATTAAAGTGTATTACTTTA
* *
632941 TTATT--AGTTTAATACTTTA
1 TTATTAAAGTGTATTACTTTA
632960 TTAGTTAAAGTGTATTACTTTA
1 TTA-TTAAAGTGTATTACTTTA
632982 TTA
1 TTA
632985 ATTTACTACT
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
17 7 0.20
18 3 0.09
19 8 0.23
20 2 0.06
22 15 0.43
ACGTcount: A:0.32, C:0.03, G:0.10, T:0.56
Consensus pattern (21 bp):
TTATTAAAGTGTATTACTTTA
Found at i:632989 original size:8 final size:8
Alignment explanation
Indices: 632940--633085 Score: 73
Period size: 8 Copynumber: 18.5 Consensus size: 8
632930 GTGTATTATT
632940 TTTATTAG
1 TTTATTAG
* *
632948 TTTAATAC
1 TTTATTAG
632956 TTTATTAG
1 TTTATTAG
*
632964 -TTA-AAG
1 TTTATTAG
* *
632970 TGTATTAC
1 TTTATTAG
*
632978 TTTATTAA
1 TTTATTAG
* *
632986 TTTACTAC
1 TTTATTAG
632994 TTTATTAG
1 TTTATTAG
** *
633002 TTTAGAAA
1 TTTATTAG
*
633010 TTGATTAG
1 TTTATTAG
*
633018 TTTATTAC
1 TTTATTAG
*
633026 TTAATTAG
1 TTTATTAG
*
633034 TTT-TATAA
1 TTTAT-TAG
633042 TTTATTAG
1 TTTATTAG
* *
633050 TTTACTAC
1 TTTATTAG
*
633058 TTAATTAG
1 TTTATTAG
* *
633066 TTTAATAC
1 TTTATTAG
*
633074 TTTTTTAG
1 TTTATTAG
633082 TTTA
1 TTTA
633086 CTATTTTAAT
Statistics
Matches: 94, Mismatches: 40, Indels: 8
0.66 0.28 0.06
Matches are distributed among these distances:
6 2 0.02
7 6 0.06
8 85 0.90
9 1 0.01
ACGTcount: A:0.31, C:0.05, G:0.08, T:0.55
Consensus pattern (8 bp):
TTTATTAG
Found at i:632995 original size:38 final size:39
Alignment explanation
Indices: 632925--633003 Score: 124
Period size: 38 Copynumber: 2.1 Consensus size: 39
632915 TAACATGTTA
* *
632925 TTAAAGTGTATTATTTTTATTAGTTTAATACTTTATTAG
1 TTAAAGTGTATTATCTTTATTAATTTAATACTTTATTAG
*
632964 TTAAAGTGTATTA-CTTTATTAATTTACTACTTTATTAG
1 TTAAAGTGTATTATCTTTATTAATTTAATACTTTATTAG
633002 TT
1 TT
633004 TAGAAATTGA
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
38 24 0.65
39 13 0.35
ACGTcount: A:0.30, C:0.05, G:0.09, T:0.56
Consensus pattern (39 bp):
TTAAAGTGTATTATCTTTATTAATTTAATACTTTATTAG
Found at i:633024 original size:48 final size:48
Alignment explanation
Indices: 632972--633093 Score: 129
Period size: 48 Copynumber: 2.5 Consensus size: 48
632962 AGTTAAAGTG
* * *
632972 TATTACTTTATTAATTTACTACTTTATTAGTTTAGAAATTGATTAGTT
1 TATTACTTTATTAATTTACTAATTTATTAGTTTACAAATTAATTAGTT
* * * *
633020 TATTACTTAATTAGTTTTA-TAATTTATTAGTTTACTACTTAATTAGTT
1 TATTACTTTATTA-ATTTACTAATTTATTAGTTTACAAATTAATTAGTT
* * * *
633068 TAATACTTTTTTAGTTTACTATTTTA
1 TATTACTTTATTAATTTACTAATTTA
633094 ATAAGTTACT
Statistics
Matches: 60, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
47 4 0.07
48 52 0.87
49 4 0.07
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.57
Consensus pattern (48 bp):
TATTACTTTATTAATTTACTAATTTATTAGTTTACAAATTAATTAGTT
Found at i:633497 original size:57 final size:57
Alignment explanation
Indices: 633424--633536 Score: 154
Period size: 57 Copynumber: 2.0 Consensus size: 57
633414 TGTATCCATA
* * * * * *
633424 TAATCATTAATACTAATCAATTTGTTAATATTTTAATCATCAATACAAATGTCCACG
1 TAATCATCAACACTAATCAATTTATTAATAGTTTAATAATCAACACAAATGTCCACG
* *
633481 TAATCATCAACACTAATTAATTTATTAATAGTTTATTAATCAACACAAATGTCCAC
1 TAATCATCAACACTAATCAATTTATTAATAGTTTAATAATCAACACAAATGTCCAC
633537 ATAGCACTTA
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
57 48 1.00
ACGTcount: A:0.42, C:0.17, G:0.04, T:0.37
Consensus pattern (57 bp):
TAATCATCAACACTAATCAATTTATTAATAGTTTAATAATCAACACAAATGTCCACG
Found at i:634029 original size:19 final size:19
Alignment explanation
Indices: 634007--634043 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
633997 GAATAAACTC
*
634007 TTTTAGACAATCGAAACCT
1 TTTTAGACAACCGAAACCT
*
634026 TTTTTGACAACCGAAACC
1 TTTTAGACAACCGAAACC
634044 CTACTCTAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.35, C:0.24, G:0.11, T:0.30
Consensus pattern (19 bp):
TTTTAGACAACCGAAACCT
Found at i:635731 original size:5 final size:5
Alignment explanation
Indices: 635721--635779 Score: 104
Period size: 5 Copynumber: 12.2 Consensus size: 5
635711 ACTTGAGATC
635721 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT A-T-T ATTAT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
635769 ATTAT ATTAT A
1 ATTAT ATTAT A
635780 AATAAATATG
Statistics
Matches: 52, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
3 2 0.04
4 2 0.04
5 48 0.92
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
ATTAT
Found at i:637468 original size:353 final size:348
Alignment explanation
Indices: 636800--638025 Score: 1694
Period size: 346 Copynumber: 3.5 Consensus size: 348
636790 CGACTGTGGA
* ** * * *
636800 TTTAAATGAAAAGATATTTACTTTATTTTTATTTTTTTATCTGCTTAAATTCCGCACTATTTTAA
1 TTTAAAGGAAAAGATATTTACTTTA-TTTTATTTTTCCATTTGCCTAACTTCCGCACTATTTTAA
* *
636865 AAAAATTATTTTTCCAAAATTGATTTCA-TTTTAAACTTTTCTTG-TAAATGCTCCTTTTTTTTC
65 AAAATTTATTTTTCCAAAATTGATTTCATTTTTCAACTTTTC-TGATAAATG--CC------TT-
* * *
636928 TTTTCTTTTCTTTTTTTGCTAAATTTTATCGTAGACTCTTTTCTAATCATTTGTTTAACTTAATT
120 TTTT-TTTTATTTTTTTGCTAAGTTTTATCGTAGACTCTTTCCTAATCATTTGTTTAACTTAATT
*
636993 TTTTTTCATATTTAACTTGATTGGTTTTACTTATTC--ATTT--TTGTTT-TTTTTTAAAAAA--
184 TTTTTCCATATTTAACTTGATTGGTTTTACTTATTCTAATTTGATT-TTTGTTTTTTAAAAAACT
** *
637051 AATTGAAGCAAAAGTGCTTCTTAAACACATGACAACTAATAAGTCTAACCGATACAAATGCAAGC
248 TTTTGAAGCAAAAGTGCTTCTTAAACACATGACAACTAATAAGCCTAACCGATACAAATGCAAGC
* * *
637116 AATCTATAGGGTATCTTTCGCACTATTTGCTTTATTT
313 AATCTATAAGGTATCTTTTGCACTATTTACTTTA-TT
* * * *
637153 TTTAAAGGAAAAAATATTTACTTTTTTTTATTTTTCTATTTGCCTAACTTCCGTACTA-TTTAAA
1 TTTAAAGGAAAAGATATTTACTTTATTTTATTTTTCCATTTGCCTAACTTCCGCACTATTTTAAA
* *
637217 AAA-TTATTTTTCCAAAATTGATTTTATTTTTCAACTTTTCTGATAAATGCACATTTTTTCTAAT
66 AAATTTATTTTTCCAAAATTGATTTCATTTTTCAACTTTTCTGATAAATGC-C-TTTTTT-T-TT
* *
637281 TATTTTTTTTGCTAAGTTTTATCATAGACTCTTTCCTAATCATTTGCTTAACTTAATTTTTTTCC
127 TA-TTTTTTTGCTAAGTTTTATCGTAGACTCTTTCCTAATCATTTGTTTAACTTAATTTTTTTCC
*
637346 ATATTTAACTTGATTGATTTTACTTATTCTAATTTGATTTTTGTTTTTTAAAAAATCTTTTTGAA
191 ATATTTAACTTGATTGGTTTTACTTATTCTAATTTGATTTTTGTTTTTTAAAAAA-CTTTTTGAA
*
637411 GCAAAAGTGCTTCTTAAACACATGACAGCTAATAAGCCTAACCGATACAAATGCAAGCAATCTAT
255 GCAAAAGTGCTTCTTAAACACATGACAACTAATAAGCCTAACCGATACAAATGCAAGCAATCTAT
637476 AAGGTATCTTTTGCACTATTTACTTTATT
320 AAGGTATCTTTTGCACTATTTACTTTATT
* * *
637505 TTTAAAGGAAAAGATATTTACTTTATTTTATTTTTCCATTTGTCTAACTTCTGCACTGTTTTAAA
1 TTTAAAGGAAAAGATATTTACTTTATTTTATTTTTCCATTTGCCTAACTTCCGCACTATTTTAAA
* * * **
637570 AAATTTCTTTTTCCAAAGTTGATTTCATTTTTTAACTTTTCTGATAAATG---TTACTTTTTATT
66 AAATTTATTTTTCCAAAATTGATTTCATTTTTCAACTTTTCTGATAAATGCCTTTTTTTTTTATT
*
637632 TTTTTGCTAAGTTTTATCGTAGACTATTTCCT-A-CATTTGTTTAACTT-ATTTTTTTCCATATT
131 TTTTTGCTAAGTTTTATCGTAGACTCTTTCCTAATCATTTGTTTAACTTAATTTTTTTCCATATT
637694 TAACTTGATTGGTTTTACTTATTCTAATTTGATTTTTGTTTTTTTAAAAAAAACCTTTTTGAAGC
196 TAACTTGATTGGTTTTACTTATTCTAATTTGATTTTTG-TTTTTT--AAAAAA-CTTTTTGAAGC
* *
637759 AAAAGTGCTTCTTAAACACAGGACAACTAATAAGCCTAACCGCTACAAATGCAAGCAATCTATAA
257 AAAAGTGCTTCTTAAACACATGACAACTAATAAGCCTAACCGATACAAATGCAAGCAATCTATAA
637824 GGTATCTTTTGCACTATTTACTTTATT
322 GGTATCTTTTGCACTATTTACTTTATT
* *
637851 TTTAAAGGAAAATATATTTACTTTATTTTATTTTTCCATTTGTCTAACTTCCGCACTATTTTAAA
1 TTTAAAGGAAAAGATATTTACTTTATTTTATTTTTCCATTTGCCTAACTTCCGCACTATTTTAAA
* *
637916 AAATTTCTTTTTCCAAAGTTGATTTCATTTTTCAACTTTTCTGATAAATGCTCCTTTTTATTTTT
66 AAATTTATTTTTCCAAAATTGATTTCATTTTTCAACTTTTCTGATAAATG--CC-TTTT-TTTTT
637981 TATTTTTTTGCTAAGTTTTATCGTAGACTCTTTCCTAATCATTTG
127 TATTTTTTTGCTAAGTTTTATCGTAGACTCTTTCCTAATCATTTG
638026 AAAAAACCTT
Statistics
Matches: 791, Mismatches: 55, Indels: 52
0.88 0.06 0.06
Matches are distributed among these distances:
343 52 0.07
344 25 0.03
345 5 0.01
346 334 0.42
347 3 0.00
348 5 0.01
349 7 0.01
350 39 0.05
351 27 0.03
352 83 0.10
353 162 0.20
354 43 0.05
355 6 0.01
ACGTcount: A:0.29, C:0.14, G:0.08, T:0.49
Consensus pattern (348 bp):
TTTAAAGGAAAAGATATTTACTTTATTTTATTTTTCCATTTGCCTAACTTCCGCACTATTTTAAA
AAATTTATTTTTCCAAAATTGATTTCATTTTTCAACTTTTCTGATAAATGCCTTTTTTTTTTATT
TTTTTGCTAAGTTTTATCGTAGACTCTTTCCTAATCATTTGTTTAACTTAATTTTTTTCCATATT
TAACTTGATTGGTTTTACTTATTCTAATTTGATTTTTGTTTTTTAAAAAACTTTTTGAAGCAAAA
GTGCTTCTTAAACACATGACAACTAATAAGCCTAACCGATACAAATGCAAGCAATCTATAAGGTA
TCTTTTGCACTATTTACTTTATT
Found at i:638678 original size:23 final size:23
Alignment explanation
Indices: 638652--638717 Score: 60
Period size: 23 Copynumber: 2.8 Consensus size: 23
638642 AATCATTTGC
638652 TTAACTTGATTTTTTTTTCATAT
1 TTAACTTGATTTTTTTTTCATAT
* ** * *
638675 TTAACTTAATTGGTTTTACTTAT
1 TTAACTTGATTTTTTTTTCATAT
*
638698 TCTAATTTGATTTTTGTTTT
1 T-TAACTTGATTTTT-TTTT
638718 TTAAAAAAAA
Statistics
Matches: 31, Mismatches: 10, Indels: 2
0.72 0.23 0.05
Matches are distributed among these distances:
23 19 0.61
24 9 0.29
25 3 0.10
ACGTcount: A:0.21, C:0.08, G:0.08, T:0.64
Consensus pattern (23 bp):
TTAACTTGATTTTTTTTTCATAT
Found at i:638899 original size:351 final size:350
Alignment explanation
Indices: 638026--639166 Score: 1460
Period size: 350 Copynumber: 3.3 Consensus size: 350
638016 TAATCATTTG
* *
638026 AAAAAACCTTTTTGAAGTAAAAGTGCTTCTTAAACACAGGACAGCTAATAAGCCTAACCGATACA
1 AAAAAAACTTTTTGAAGCAAAAGTG--TCTTAAACACAGGACAGCTAATAAGCCTAACCGATACA
* * * * *
638091 ACTGCGAGCAATCTATAGGATATCTTTTGCACTATTTGTTTTATTTTTAAAGGAAAAGATATTTA
64 AATACAAGCAATCTATAGG-TATCTTTCGCACTATTTGATTTATTTTTAAAGGAAAAGATATTTA
* **
638156 CTTTATTTTTATTTTTCTATTTGCCTAACTTCCGCACTATTTTAAGAAAATTTCTTTTTCCAAAG
128 CTTTATTTTTATTTTTCTATTTGCCTAACTTCCGCACTA-TTTAAAAAAAAATCTTTTT-CAAAG
* *
638221 TTGATTTCATTTTTCAACTTTTCTAATAAATGCTT-CTTTTTTCTAATTATTTTTTTTGCTAAGT
191 TTGATTTCATTTTTCAACTTTTCTGATAAAT-ATTCCTTTTTTCT-ATT-TTTTTTTTGCTAAGT
* *
638285 TTTACAGTAGACTCTTTCCTAACCATTTGCTTAACTTA-ATTTTTTTCATATTTAACTTGATTGG
253 TTTAC-GTAGACTCTTTCCTAATCATTTGCTTAACTTATTTTTTTTTCATATTTAACTTGATTGG
*
638349 TTTTACTTATTCTAATTTGATTTTTGTTTTTAAA
317 TTTTACTTATTCTAATTTGATTTTTGTTTTTTAA
** * *
638383 AAAAAAACTTTTTGAAGCAAAAGTG-CTT-----C-TTA-AGC--A-AGGGCTAACCGATACAAA
1 AAAAAAACTTTTTGAAGCAAAAGTGTCTTAAACACAGGACAGCTAATAAGCCTAACCGATACAAA
* *
638437 TACAAGCAATCTATAGGTATCTTTCGCACTATTTGCTTTATTTTTAAAGGAAAATATATTTACTT
66 TACAAGCAATCTATAGGTATCTTTCGCACTATTTGATTTATTTTTAAAGGAAAAGATATTTACTT
* *
638502 TATTTTTATTTTTCTATTTTCCTAACTTCCGCACTATTT-TAAAAAAATCTTTTTCTAAAGTTGA
131 TATTTTTATTTTTCTATTTGCCTAACTTCCGCACTATTTAAAAAAAAATCTTTTTC-AAAGTTGA
638566 TTTCATTTTTCAACTTTTCTGATAAATATTCCTTTTTTCT-TTTTTTTTTTGCTAAGTTTTATCG
195 TTTCATTTTTCAACTTTTCTGATAAATATTCCTTTTTTCTATTTTTTTTTTGCTAAGTTTTA-CG
* *
638630 TATACTC-TTCCTAATCATTTGCTTAACTTGATTTTTTTTTCATATTTAACTTAATTGGTTTTAC
259 TAGACTCTTTCCTAATCATTTGCTTAACTT-ATTTTTTTTTCATATTTAACTTGATTGGTTTTAC
638694 TTATTCTAATTTGATTTTTGTTTTTTAA
323 TTATTCTAATTTGATTTTTGTTTTTTAA
* *
638722 AAAAAAACTTTTTTGAAGCAAAAGTG-CTTAAACACGGGACAGTTAAATAAGCCTAACCGATACA
1 AAAAAAAC-TTTTTGAAGCAAAAGTGTCTTAAACACAGGACAGCT-AATAAGCCTAACCGATACA
* * *
638786 AATACAAGCAATTTATAGGTATCTTTCGCACTATTTAATTTATTTTTAACGGAAAAGATATTTAC
64 AATACAAGCAATCTATAGGTATCTTTCGCACTATTTGATTTATTTTTAAAGGAAAAGATATTTAC
638851 TTTA-TTTTATTTTTCTATTTGCCTAACTTCCGCACTATTTAAAAAAAAATC-----C-AAGTTG
129 TTTATTTTTATTTTTCTATTTGCCTAACTTCCGCACTATTTAAAAAAAAATCTTTTTCAAAGTTG
**
638909 ATTTCATTTTTCAACTTTTCTGATAAATGCTCCTTTTTTCTAATTAATTTTTTTTTTGCTAAGTT
194 ATTTCATTTTTCAACTTTTCTGATAAATATTCCTTTTTTC----T-ATTTTTTTTTTGCTAAGTT
* * * *
638974 TTACCGTAGACTCTTTCCGAATCATTTGATTAATTTA-ATTTTTTTCTATATTTAACTTGATTGG
254 TTA-CGTAGACTCTTTCCTAATCATTTGCTTAACTTATTTTTTTTTC-ATATTTAACTTGATTGG
* **
639038 TTTTACCTATTCTAATTTGATTTTTGTTTAAAATAA
317 TTTTACTTATTCTAATTTGATTTTTGTTT--TTTAA
* *
639074 AAAAAAA----TTGAAGCAAAAGTGCTTCTTAAACACAAGACAGCTAATACGCCTAACCGATACA
1 AAAAAAACTTTTTGAAGCAAAAGTG--TCTTAAACACAGGACAGCTAATAAGCCTAACCGATACA
*
639135 AATGCAAGCAATCTATAGGGTATCTTTC-CACT
64 AATACAAGCAATCTATA-GGTATCTTTCGCACT
639167 TGATAAATGA
Statistics
Matches: 698, Mismatches: 54, Indels: 72
0.85 0.07 0.09
Matches are distributed among these distances:
337 21 0.03
338 27 0.04
339 68 0.10
340 23 0.03
341 54 0.08
342 3 0.00
343 80 0.11
344 74 0.11
345 2 0.00
346 2 0.00
347 19 0.03
348 2 0.00
349 46 0.07
350 135 0.19
351 106 0.15
352 10 0.01
354 3 0.00
357 23 0.03
ACGTcount: A:0.31, C:0.15, G:0.10, T:0.45
Consensus pattern (350 bp):
AAAAAAACTTTTTGAAGCAAAAGTGTCTTAAACACAGGACAGCTAATAAGCCTAACCGATACAAA
TACAAGCAATCTATAGGTATCTTTCGCACTATTTGATTTATTTTTAAAGGAAAAGATATTTACTT
TATTTTTATTTTTCTATTTGCCTAACTTCCGCACTATTTAAAAAAAAATCTTTTTCAAAGTTGAT
TTCATTTTTCAACTTTTCTGATAAATATTCCTTTTTTCTATTTTTTTTTTGCTAAGTTTTACGTA
GACTCTTTCCTAATCATTTGCTTAACTTATTTTTTTTTCATATTTAACTTGATTGGTTTTACTTA
TTCTAATTTGATTTTTGTTTTTTAA
Found at i:645204 original size:31 final size:31
Alignment explanation
Indices: 645146--645211 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
645136 GGGGAATGAC
** * *
645146 CTCTAATATTATTTATATATTTGATTTTAGT
1 CTCTAATATTATCGATATATTTAATTTTAAT
645177 CTCTAATATTATCGAT-TCATTTAATTTTAAT
1 CTCTAATATTATCGATAT-ATTTAATTTTAAT
645208 CTCT
1 CTCT
645212 CATCTATTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 1 0.03
31 29 0.97
ACGTcount: A:0.29, C:0.12, G:0.05, T:0.55
Consensus pattern (31 bp):
CTCTAATATTATCGATATATTTAATTTTAAT
Found at i:653978 original size:252 final size:253
Alignment explanation
Indices: 653499--654004 Score: 906
Period size: 252 Copynumber: 2.0 Consensus size: 253
653489 CTCTGAGAAC
* *
653499 TCAATGAAGCTCATCAATTGGGAGGTTCAACATCTGGTAGAGCATTGGTCTTTTTCTACTCTTCA
1 TCAATGAAGCTCATCAATTGGGACGTTAAACATCTGGTAGAGCATTGGTCTTTTTCTACTCTTCA
* * *
653564 GCAAGCGTCTTGAGCGATGGCAATCTCTCTCCGATCCTCCAATATCTGTATAGTCGCATGCTCGG
66 GCAAACCTCTTGAGCGATGGCAATCTCTCTCCGATCCTACAATATCTGTATAGTCGCATGCTCGG
* *
653629 GGGCTTCCTCTATCCAGTACCTATCCTCGTTGTCGTCAATTTCATCGTTGGTTACGAGGTGAGCG
131 GGGCTTCCTCTATCCAGTACCTATCCTCGTTGTCGTCAATTTCATCGTTGGCTACGAGGTGAGCA
653694 ACTCTGTTTCCTTCTCTCGGTGTGAATCTGAAATCACAAGAGTCAAAGCCCTTTGCTA
196 ACTCTGTTTCCTTCTCTCGGTGTGAATCTGAAATCACAAGAGTCAAAGCCCTTTGCTA
*
653752 TCAATGAAGCTCATCAATT-GGACGTTAAACATTTGGTAGAGCATTGGTCTTTTTCTACTCTTCA
1 TCAATGAAGCTCATCAATTGGGACGTTAAACATCTGGTAGAGCATTGGTCTTTTTCTACTCTTCA
* *
653816 GCAAACCTCTTGAGGGATGGCAATCTCTCTCCGATCCTACAATATTTGTATAGTCGCATGCTCGG
66 GCAAACCTCTTGAGCGATGGCAATCTCTCTCCGATCCTACAATATCTGTATAGTCGCATGCTCGG
*
653881 GGGCTTCCTCTATCCAGTACCTATCCTCGTTGTCTTCAATTTCATCGTTGGCTACGAGGTGAGCA
131 GGGCTTCCTCTATCCAGTACCTATCCTCGTTGTCGTCAATTTCATCGTTGGCTACGAGGTGAGCA
653946 ACTCTGTTTCCTTCTCTCGGTGTGAATCTGAAATCACAAGAGTCAAAGCCCTTTGCTA
196 ACTCTGTTTCCTTCTCTCGGTGTGAATCTGAAATCACAAGAGTCAAAGCCCTTTGCTA
654004 T
1 T
654005 TTGTTTGATT
Statistics
Matches: 242, Mismatches: 11, Indels: 1
0.95 0.04 0.00
Matches are distributed among these distances:
252 223 0.92
253 19 0.08
ACGTcount: A:0.22, C:0.25, G:0.20, T:0.33
Consensus pattern (253 bp):
TCAATGAAGCTCATCAATTGGGACGTTAAACATCTGGTAGAGCATTGGTCTTTTTCTACTCTTCA
GCAAACCTCTTGAGCGATGGCAATCTCTCTCCGATCCTACAATATCTGTATAGTCGCATGCTCGG
GGGCTTCCTCTATCCAGTACCTATCCTCGTTGTCGTCAATTTCATCGTTGGCTACGAGGTGAGCA
ACTCTGTTTCCTTCTCTCGGTGTGAATCTGAAATCACAAGAGTCAAAGCCCTTTGCTA
Found at i:658521 original size:28 final size:28
Alignment explanation
Indices: 658481--658536 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
658471 AGTTCCAGCT
*
658481 TTGTTTATTATGTATATTTAATAACAAA
1 TTGTTTAATATGTATATTTAATAACAAA
658509 TTGTTTAATATGTATATTTAATAACAAA
1 TTGTTTAATATGTATATTTAATAACAAA
658537 ATAATTATTG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.41, C:0.04, G:0.07, T:0.48
Consensus pattern (28 bp):
TTGTTTAATATGTATATTTAATAACAAA
Found at i:659674 original size:21 final size:21
Alignment explanation
Indices: 659650--659692 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
659640 TTCTAAGACG
659650 CTAATAACTTTTATGTTGCAA
1 CTAATAACTTTTATGTTGCAA
659671 CTAATAACTTTTATGTTGCAA
1 CTAATAACTTTTATGTTGCAA
659692 C
1 C
659693 GATACACGGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.33, C:0.16, G:0.09, T:0.42
Consensus pattern (21 bp):
CTAATAACTTTTATGTTGCAA
Found at i:660189 original size:38 final size:37
Alignment explanation
Indices: 659946--660191 Score: 257
Period size: 40 Copynumber: 6.4 Consensus size: 37
659936 TTGCAAACGG
*
659946 TTTTTGAAAATACTTATATAATATATAGTTTTTAAAACA
1 TTTTTGAAATTA--TATATAATATATAGTTTTTAAAACA
*
659985 CTTTTGAAA--ACTATATAATATATAGTTTTTAAAACA
1 TTTTTGAAATTA-TATATAATATATAGTTTTTAAAACA
* * *
660021 TTTTAGAAAATATATATAATGTATAGTTTTTAAAATCA
1 TTTTTGAAATTATATATAATATATAGTTTTTAAAA-CA
* *
660059 TTTTTAAAACT-TATATAATATATAGTTTTTTAAAACA
1 TTTTTGAAATTATATATAATATATAG-TTTTTAAAACA
*
660096 TTTTTTTGAGAATT-TATATAATATATAATTTTTAAAAACA
1 --TTTTTGA-AATTATATATAATATATAGTTTTT-AAAACA
* * *
660136 TTTTTGAAAACTTATATATAATATACAATATTTAAAACA
1 TTTTTG-AAA-TTATATATAATATATAGTTTTTAAAACA
660175 TTTTTGGAAATTATATA
1 TTTTT-GAAATTATATA
660192 GTTTTAAAAA
Statistics
Matches: 181, Mismatches: 14, Indels: 25
0.82 0.06 0.11
Matches are distributed among these distances:
36 32 0.18
37 38 0.21
38 35 0.19
39 36 0.20
40 40 0.22
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (37 bp):
TTTTTGAAATTATATATAATATATAGTTTTTAAAACA
Found at i:660268 original size:44 final size:43
Alignment explanation
Indices: 660218--660301 Score: 116
Period size: 44 Copynumber: 1.9 Consensus size: 43
660208 TTTTAACAAT
*
660218 TATATAGTTTTTAAAAAAAAACATTTTT-GAAAATTTATATATAA
1 TATATAGTTTTT--AAAAAAACATTTTTAAAAAATTTATATATAA
*
660262 TATATAGTTTTTAAAGAAACATTTTTAAAAAAATTTATAT
1 TATATAGTTTTTAAAAAAACATTTTT-AAAAAATTTATAT
660302 TATATAGTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
42 13 0.36
44 23 0.64
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (43 bp):
TATATAGTTTTTAAAAAAACATTTTTAAAAAATTTATATATAA
Found at i:660283 original size:42 final size:44
Alignment explanation
Indices: 660218--660327 Score: 119
Period size: 42 Copynumber: 2.6 Consensus size: 44
660208 TTTTAACAAT
*
660218 TATATAGTTTTTAAAAAAAAACATTTTT-GAAAATTTATATATAA
1 TATATAGTTTTT-AAAAAAAACATTTTTAAAAAATTTATATATAA
* *
660262 TATATAGTTTTT-AAAGAAACATTTTTAAAAAAATT-TATAT--
1 TATATAGTTTTTAAAAAAAACATTTTTAAAAAATTTATATATAA
660302 TATATAG--TTTAAAAAAATAC-TTTTTA
1 TATATAGTTTTTAAAAAAA-ACATTTTTA
660328 TTTGTTATTA
Statistics
Matches: 59, Mismatches: 4, Indels: 11
0.80 0.05 0.15
Matches are distributed among these distances:
38 3 0.05
39 11 0.19
40 9 0.15
42 18 0.31
43 6 0.10
44 12 0.20
ACGTcount: A:0.48, C:0.03, G:0.05, T:0.45
Consensus pattern (44 bp):
TATATAGTTTTTAAAAAAAACATTTTTAAAAAATTTATATATAA
Found at i:660340 original size:3 final size:3
Alignment explanation
Indices: 660332--660385 Score: 54
Period size: 3 Copynumber: 16.7 Consensus size: 3
660322 TTTTTATTTG
* *
660332 TTA TTA TTA TTA TTA TTC TTA TTTA TTA TTTA TTTG TTA TTA TTTA TTA
1 TTA TTA TTA TTA TTA TTA TTA -TTA TTA -TTA -TTA TTA TTA -TTA TTA
660381 TTA TT
1 TTA TT
660386 TCTTGTTTAT
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
3 32 0.73
4 12 0.27
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:660357 original size:10 final size:10
Alignment explanation
Indices: 660335--660386 Score: 70
Period size: 10 Copynumber: 5.2 Consensus size: 10
660325 TTATTTGTTA
660335 TTATTATTA-
1 TTATTATTAT
*
660344 TTATTCTTAT
1 TTATTATTAT
660354 TTATTATTTAT
1 TTATTA-TTAT
*
660365 TTGTTATTAT
1 TTATTATTAT
660375 TTATTATTAT
1 TTATTATTAT
660385 TT
1 TT
660387 CTTGTTTATT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
9 8 0.22
10 20 0.54
11 9 0.24
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.71
Consensus pattern (10 bp):
TTATTATTAT
Found at i:660362 original size:7 final size:7
Alignment explanation
Indices: 660325--660382 Score: 61
Period size: 7 Copynumber: 8.7 Consensus size: 7
660315 AAAATACTTT
*
660325 TTATTTG
1 TTATTTA
660332 TTA-TTA
1 TTATTTA
660338 TTA-TTA
1 TTATTTA
*
660344 TTA-TTC
1 TTATTTA
660350 TTATTTA
1 TTATTTA
660357 TTATTTA
1 TTATTTA
660364 TT-TGTTA
1 TTAT-TTA
660371 TTATTTA
1 TTATTTA
660378 TTATT
1 TTATT
660383 ATTTCTTGTT
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
6 17 0.38
7 27 0.60
8 1 0.02
ACGTcount: A:0.24, C:0.02, G:0.03, T:0.71
Consensus pattern (7 bp):
TTATTTA
Found at i:660365 original size:36 final size:37
Alignment explanation
Indices: 660322--660405 Score: 129
Period size: 36 Copynumber: 2.3 Consensus size: 37
660312 AAAAAAATAC
660322 TTTTTATTTGTTATTA-TTATTATTA-TTCTTATTTA
1 TTTTTATTTGTTATTATTTATTATTATTTCTTATTTA
*
660357 TTATTTATTTGTTATTATTTATTATTATTTCTTGTTTA
1 TT-TTTATTTGTTATTATTTATTATTATTTCTTATTTA
660395 TTTTT-TTTGTT
1 TTTTTATTTGTT
660406 CAAGGTCCAA
Statistics
Matches: 45, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
35 2 0.04
36 20 0.44
37 12 0.27
38 11 0.24
ACGTcount: A:0.19, C:0.02, G:0.05, T:0.74
Consensus pattern (37 bp):
TTTTTATTTGTTATTATTTATTATTATTTCTTATTTA
Found at i:660397 original size:21 final size:21
Alignment explanation
Indices: 660324--660389 Score: 65
Period size: 21 Copynumber: 3.5 Consensus size: 21
660314 AAAAATACTT
*
660324 TTTATTTGTTATTA-TTATTA
1 TTTATTTCTTATTATTTATTA
660344 -TTA-TTC---TTATTTATTA
1 TTTATTTCTTATTATTTATTA
*
660360 TTTATTTGTTATTATTTATTA
1 TTTATTTCTTATTATTTATTA
660381 -TTATTTCTT
1 TTTATTTCTT
660390 GTTTATTTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 12
0.71 0.06 0.23
Matches are distributed among these distances:
15 3 0.08
16 6 0.16
17 3 0.08
18 4 0.11
19 3 0.08
20 8 0.22
21 10 0.27
ACGTcount: A:0.23, C:0.03, G:0.03, T:0.71
Consensus pattern (21 bp):
TTTATTTCTTATTATTTATTA
Found at i:660571 original size:16 final size:15
Alignment explanation
Indices: 660550--660579 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
660540 GCTGGCAAAA
660550 ATCCCGGGATTGACCC
1 ATCCCGGGA-TGACCC
660566 ATCCCGGGATGACC
1 ATCCCGGGATGACC
660580 GGCCTCACGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.20, C:0.37, G:0.27, T:0.17
Consensus pattern (15 bp):
ATCCCGGGATGACCC
Found at i:661479 original size:3 final size:3
Alignment explanation
Indices: 661471--661568 Score: 69
Period size: 3 Copynumber: 32.7 Consensus size: 3
661461 ATTTATTTCT
* *
661471 TTA TTA TTA TT- TCT- TTA TTT TTA TTA TTTA CTTA CTTA TTT TTA TTA
1 TTA TTA TTA TTA T-TA TTA TTA TTA TTA -TTA -TTA -TTA TTA TTA TTA
* * * * *
661518 TTA CTA CTA TTA TTC TTA TTC TTA TT- TT- TTA TTT TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
661564 TTA TT
1 TTA TT
661569 TTTCCCTACA
Statistics
Matches: 78, Mismatches: 13, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
2 6 0.08
3 62 0.79
4 10 0.13
ACGTcount: A:0.23, C:0.07, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:661493 original size:6 final size:6
Alignment explanation
Indices: 661457--661571 Score: 52
Period size: 6 Copynumber: 17.7 Consensus size: 6
661447 GATATATACA
* * *
661457 TTTTAT TTATT-T CTTTAT TATTATT TCTTTAT TTTTAT TATTTACT TACTTAT
1 TTTTAT TT-TTAT TTTTAT TTTTA-T T-TTTAT TTTTAT T-TTTA-T T-TTTAT
* * * * *
661510 TTTTAT TATTACTAC TATTAT TCTTAT TCTTATT TTTTAT TTTTAT TATTAT
1 TTTTAT T-TT--TAT TTTTAT TTTTAT TTTTA-T TTTTAT TTTTAT TTTTAT
*
661562 TATTAT TTTT
1 TTTTAT TTTT
661572 CCCTACATTT
Statistics
Matches: 86, Mismatches: 13, Indels: 20
0.72 0.11 0.17
Matches are distributed among these distances:
5 2 0.02
6 52 0.60
7 19 0.22
8 10 0.12
9 3 0.03
ACGTcount: A:0.22, C:0.07, G:0.00, T:0.71
Consensus pattern (6 bp):
TTTTAT
Found at i:661821 original size:7 final size:7
Alignment explanation
Indices: 661809--661839 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
661799 TCAAATCAAA
661809 TTTTAAT
1 TTTTAAT
661816 TTTTAAT
1 TTTTAAT
*
661823 ATTTAAT
1 TTTTAAT
661830 TTTTAAT
1 TTTTAAT
661837 TTT
1 TTT
661840 CACAATTAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (7 bp):
TTTTAAT
Found at i:668568 original size:64 final size:63
Alignment explanation
Indices: 668477--668614 Score: 145
Period size: 64 Copynumber: 2.2 Consensus size: 63
668467 ATTCAATGTG
* * *
668477 CATCGATGCACTCTTTAAAAAAGAAACATCGAATGCAAATGGTGCATCGATGCATAAGG-AGTA
1 CATCGATGCACCCTTTAAAAAAGAAACATAGAAGGCAAATGGTGCATCGATGCAT-AGGTAGTA
* * * * * * *
668540 CATCGATGCATCCCTTT-AAAATGAAAACATAGAAGGTAATTTGTGTATCGATGCATGGGTAGTG
1 CATCGATGCA-CCCTTTAAAAAAG-AAACATAGAAGGCAAATGGTGCATCGATGCATAGGTAGTA
668604 CATCGATGCAC
1 CATCGATGCAC
668615 ATGTTAAAGA
Statistics
Matches: 62, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
63 18 0.29
64 44 0.71
ACGTcount: A:0.36, C:0.17, G:0.22, T:0.25
Consensus pattern (63 bp):
CATCGATGCACCCTTTAAAAAAGAAACATAGAAGGCAAATGGTGCATCGATGCATAGGTAGTA
Found at i:669488 original size:2 final size:2
Alignment explanation
Indices: 669483--669533 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
669473 TGTGTGTATG
669483 TA TA TA TA 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 TA TA TA TA
669525 TA TA TA TA T
1 TA TA TA TA T
669534 GTTATATGTT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:669698 original size:2 final size:2
Alignment explanation
Indices: 669691--669721 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
669681 CATGCATGCA
669691 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
669722 TACATATAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:670537 original size:2 final size:2
Alignment explanation
Indices: 670530--670555 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
670520 ATATTATAAT
670530 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
670556 ATAAAACTTG
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):
TA
Found at i:670724 original size:95 final size:96
Alignment explanation
Indices: 670544--670729 Score: 284
Period size: 95 Copynumber: 1.9 Consensus size: 96
670534 TATATATATA
* * * * *
670544 TATATATATATAATAAAACTTGAGTTGTTCCTCTAAAGCAATTGGTTAAATGTCCCGGCTTTATG
1 TATATATATACAATAAAACTTGAGTTGTCCCTCTAAAGCAATTGGTTAAACGCCCCGACTTTATG
*
670609 GATAAGATTCAACTAGCCTGACAAAGGTGAT
66 GATAAGATTCAACTAACCTGACAAAGGTGAT
*
670640 TATAT-TATACAATAAAACTTGAGTTGTCCCTCTAAGGCAATTGGTTAAACGCCCCGACTTTATG
1 TATATATATACAATAAAACTTGAGTTGTCCCTCTAAAGCAATTGGTTAAACGCCCCGACTTTATG
* *
670704 GATAAGATTCAGCTAACCTGATAAAG
66 GATAAGATTCAACTAACCTGACAAAG
670730 TTGTTTACAT
Statistics
Matches: 81, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
95 76 0.94
96 5 0.06
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (96 bp):
TATATATATACAATAAAACTTGAGTTGTCCCTCTAAAGCAATTGGTTAAACGCCCCGACTTTATG
GATAAGATTCAACTAACCTGACAAAGGTGAT
Found at i:672167 original size:84 final size:83
Alignment explanation
Indices: 671937--672692 Score: 602
Period size: 84 Copynumber: 9.1 Consensus size: 83
671927 ATCATAACTC
* * * * * * * *
671937 AAGGGTTGTCTGTCAGCCAAGACCTTCGAGTTCAACTACGCTAAGCTCTAAGGCACATCATTTGC
1 AAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTGC
* * * * *
672002 AGCATAGCTCAAGGCTAA
66 AGCATAACTTAAGTCGAG
* * * * * * * *
672020 AATGGTTATCTGCC-ACCAAGACCTTCGAGTTTGATTACGCTCAGCTCCAATGTATATCATTTGC
1 AAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTGC
*
672084 AGCATAACTTAAGTTGAG
66 AGCATAACTTAAGTCGAG
* * * * *
672102 AAGGGTTATCTGCCAAACAAAGATCTTCGAGTTTGACTACACTCAGCACTAAAGCACATCATTTG
1 AAGGGTTATCTGCC-AACAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTG
*
672167 CAGCATAACTTAAGTCGAA
65 CAGCATAACTTAAGTCGAG
* * * * * * * * * *
672186 AAAGGTTATTTG---TCAAAGACCCTCGAGTTCGATTACACTCAACTTCGAGGGAACATCATTTA
1 AAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGACTACACTCAGC-TCCAAGGCACATCATTTG
* * * *
672248 CAGCATAACTCAAGGCTAT
65 CAGCATAACTTAAGTCGAG
* * *
672267 AAGGGTTATTTGTGACCAA-AAA-ACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATT
1 AAGGGTTA--TCTG-CCAACAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATT
672330 TGCAGCATAACTTAAGTCGAG
63 TGCAGCATAACTTAAGTCGAG
* *
672351 AAGGGTTATCTGCCAAACAAAGACCTTCGAGTTCGACTACACTCAACTCCAAGGCACATAATTTG
1 AAGGGTTATCTGCC-AACAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTG
* *
672416 CAGCATAGCTTAAGTAGAG
65 CAGCATAACTTAAGTCGAG
* * * * * * * *
672435 AAGGCTTATCT-TC--CAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGTACATCATTTA
1 AAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGACTACACTCAGC-TCCAAGGCACATCATTTG
* *
672497 CAACATAACTTAAGTCGAT
65 CAGCATAACTTAAGTCGAG
* * * * * * * *
672516 AAGGGTTATCTG-C--CAAAGGCCCTCGAGTTCAATTACACTCAGGTTCGAGGGCACATCATTTA
1 AAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGACTACACTCA-GCTCCAAGGCACATCATTTG
* * *
672578 CAGCATAACTCAAGGCTAG
65 CAGCATAACTTAAGTCGAG
* * * ** *
672597 AAGGGTTATCAT-TCACCAAAAGACCTTCTAGTTCGACTATGCTCAGCTCCAAGGAACATCATTT
1 AAGGGTTATC-TGCCAAC-AAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTT
* * * *
672661 GCAACATAGCATAAGTCGAA
64 GCAGCATAACTTAAGTCGAG
*
672681 AAGGGCTATCTG
1 AAGGGTTATCTG
672693 TAACACCCCT
Statistics
Matches: 537, Mismatches: 115, Indels: 41
0.77 0.17 0.06
Matches are distributed among these distances:
80 52 0.10
81 142 0.26
82 74 0.14
83 19 0.04
84 206 0.38
85 41 0.08
86 3 0.01
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.26
Consensus pattern (83 bp):
AAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTGC
AGCATAACTTAAGTCGAG
Found at i:672297 original size:165 final size:163
Alignment explanation
Indices: 671955--672692 Score: 633
Period size: 165 Copynumber: 4.5 Consensus size: 163
671945 TCTGTCAGCC
* * * * * * * * *
671955 AAGACCTTCGAGTTCAACTACGCTAAGCTCTAAGGCACATCATTTGCAGCATAGCTCAAGGCTAA
1 AAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAACATAACTTAAGTCGAA
* * * * * * * ** * * *
672020 AATGGTTATCTGCCACCAAGACCTTCGAGTTTGATTACGCTCAGC-TCCAATGTATATCATTTGC
66 AAGGGTTATCTG--ACAAAGACCCTCGAGTTCGATTACACTCAACTTCGAGGGCACATCATTTAC
* * * *
672084 AGCATAACTTAA-GTTGAGAAGGGTTAT-CTGCCAAACA
129 AGCATAACTCAAGGCT-AGAAGGGTTATATTACC--A-A
* * * * * *
672121 AAGATCTTCGAGTTTGACTACACTCAGCACTAAAGCACATCATTTGCAGCATAACTTAAGTCGAA
1 AAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAACATAACTTAAGTCGAA
* * * *
672186 AAAGGTTATTTGTCAAAGACCCTCGAGTTCGATTACACTCAACTTCGAGGGAACATCATTTACAG
66 AAGGGTTATCTGACAAAGACCCTCGAGTTCGATTACACTCAACTTCGAGGGCACATCATTTACAG
* *
672251 CATAACTCAAGGCTATAAGGGTTATTTGTGACCAA
131 CATAACTCAAGGCTAGAAGGGTTATAT-T-ACCAA
* * * * *
672286 AAAACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTCGAG
1 AAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAACATAACTTAAGTCGAA
* * * * *
672351 AAGGGTTATCTGCCAAACAAAGACCTTCGAGTTCGACTACACTCAAC-TCCAAGGCACATAATTT
66 AAGGGTTATCTG----ACAAAGACCCTCGAGTTCGATTACACTCAACTTCGAGGGCACATCATTT
* * * *** * *
672415 GCAGCATAGCTTAAGTAGAGAAGGCTTATCTT-CC-A
127 ACAGCATAACTCAAGGCTAGAAGGGTTATATTACCAA
* * * * * *
672450 AAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGTACATCATTTACAACATAACTTAAGTCGA
1 AAGACCTTCGAGTTCGACTACACTCAGC-TCCAAGGCACATCATTTGCAACATAACTTAAGTCGA
* * * * **
672515 TAAGGGTTATCTGCCAAAGGCCCTCGAGTTCAATTACACTCAGGTTCGAGGGCACATCATTTACA
65 AAAGGGTTATCTGACAAAGACCCTCGAGTTCGATTACACTCAACTTCGAGGGCACATCATTTACA
672580 GCATAACTCAAGGCTAGAAGGGTTATCATTCACCAA
130 GCATAACTCAAGGCTAGAAGGGTTAT-ATT-ACCAA
* ** * * *
672616 AAGACCTTCTAGTTCGACTATGCTCAGCTCCAAGGAACATCATTTGCAACATAGCATAAGTCGAA
1 AAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAACATAACTTAAGTCGAA
*
672681 AAGGGCTATCTG
66 AAGGGTTATCTG
672693 TAACACCCCT
Statistics
Matches: 458, Mismatches: 99, Indels: 31
0.78 0.17 0.05
Matches are distributed among these distances:
161 24 0.05
162 36 0.08
163 2 0.00
164 50 0.11
165 188 0.41
166 91 0.20
167 2 0.00
168 37 0.08
169 28 0.06
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.26
Consensus pattern (163 bp):
AAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAACATAACTTAAGTCGAA
AAGGGTTATCTGACAAAGACCCTCGAGTTCGATTACACTCAACTTCGAGGGCACATCATTTACAG
CATAACTCAAGGCTAGAAGGGTTATATTACCAA
Found at i:672430 original size:249 final size:248
Alignment explanation
Indices: 671991--672691 Score: 817
Period size: 249 Copynumber: 2.8 Consensus size: 248
671981 GCTCTAAGGC
* * * * ** *
671991 ACATCATTTGCAGCATAGCTCAAGGCTAAAATGGTTATCTGCCACC-AAGACCTTCGAGTTTGAT
1 ACATCATTTACAGCATAACTCAAGGCTATAAGGGTTAT-TGTGACCAAAGACCTTCGAGTTCGAT
* * *
672055 TACGCTCAGCTCCAATGTATATCATTTGCAGCATAACTTAAGTTGAGAAGGGTTATCTGCCAAAC
65 TACGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAAAC
* * * * * *
672120 AAAGATCTTCGAGTTTGACTACACTCAGCACTAAAGCACATCATTTGCAGCATAACTTAAGTCGA
130 AAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGA
*
672185 AAAAGG-TTAT-TTGTCAAAGACCCTCGAGTTCGATTACACTCAACTTCGAGGGA
195 AAAAGGCTTATCTT-CCAAAGACCCTCGAGTTCGATTACACTCAACTTCGAGGGA
*
672238 ACATCATTTACAGCATAACTCAAGGCTATAAGGGTTATTTGTGACCAAAAAACCTTCGAGTTCGA
1 ACATCATTTACAGCATAACTCAAGGCTATAAGGGTTA-TTGTGACC-AAAGACCTTCGAGTTCGA
*
672303 CTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAAA
64 TTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAAA
* * *
672368 CAAAGACCTTCGAGTTCGACTACACTCAACTCCAAGGCACATAATTTGCAGCATAGCTTAAGTAG
129 CAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCG
* * *
672433 -AGAAGGCTTATCTTCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGT
194 AAAAAGGCTTATCTTCCAAAGACCCTCGAGTTCGATTACACTCAACTTCGAGGGA
* * * * * * * *
672487 ACATCATTTACAACATAACTTAAGTCGATAAGGGTTA-TCTG-CCAAAGGCCCTCGAGTTCAATT
1 ACATCATTTACAGCATAACTCAAGGCTATAAGGGTTATTGTGACCAAAGACCTTCGAGTTCGATT
* * * * * * * * * * *
672550 ACACTCAGGTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCAT-TC-AC
66 ACGCTCA-GCTCCAAGGCATATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATC-TGCCAAA
* ** * * *
672613 CAAAAGACCTTCTAGTTCGACTATGCTCAGCTCCAAGGAACATCATTTGCAACATAGCATAAGTC
129 C-AAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTC
*
672678 GAAAAGGGC-TATCT
193 GAAAAAGGCTTATCT
672692 GTAACACCCC
Statistics
Matches: 388, Mismatches: 57, Indels: 19
0.84 0.12 0.04
Matches are distributed among these distances:
245 23 0.06
246 104 0.27
247 47 0.12
248 6 0.02
249 206 0.53
250 2 0.01
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.26
Consensus pattern (248 bp):
ACATCATTTACAGCATAACTCAAGGCTATAAGGGTTATTGTGACCAAAGACCTTCGAGTTCGATT
ACGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAAACA
AAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAA
AAAGGCTTATCTTCCAAAGACCCTCGAGTTCGATTACACTCAACTTCGAGGGA
Found at i:679134 original size:18 final size:18
Alignment explanation
Indices: 679111--679146 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
679101 GTTCAATATT
*
679111 TGTCCCGAATGACCACTA
1 TGTCCCGAAGGACCACTA
679129 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
679147 GATACATCCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.28, C:0.33, G:0.19, T:0.19
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:679159 original size:22 final size:22
Alignment explanation
Indices: 679131--679200 Score: 104
Period size: 22 Copynumber: 3.2 Consensus size: 22
679121 GACCACTATG
*
679131 TCCCGAAGGACCACTAGATACA
1 TCCCGAAGGACCACTGGATACA
* *
679153 TCCCGAATGACCACTGGATACG
1 TCCCGAAGGACCACTGGATACA
*
679175 TCCCGAAGGACTACTGGATACA
1 TCCCGAAGGACCACTGGATACA
679197 TCCC
1 TCCC
679201 AAAAGACTAA
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.30, C:0.33, G:0.20, T:0.17
Consensus pattern (22 bp):
TCCCGAAGGACCACTGGATACA
Found at i:679195 original size:44 final size:40
Alignment explanation
Indices: 679113--679200 Score: 122
Period size: 44 Copynumber: 2.1 Consensus size: 40
679103 TCAATATTTG
679113 TCCCGAATGACCACTATGTCCCGAAGGACCACTAGATACA
1 TCCCGAATGACCACTATGTCCCGAAGGACCACTAGATACA
* *
679153 TCCCGAATGACCACTGGATACGTCCCGAAGGACTACTGGATACA
1 TCCCGAATGACCACT--AT--GTCCCGAAGGACCACTAGATACA
679197 TCCC
1 TCCC
679201 AAAAGACTAA
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
40 15 0.36
42 2 0.05
44 25 0.60
ACGTcount: A:0.30, C:0.33, G:0.19, T:0.18
Consensus pattern (40 bp):
TCCCGAATGACCACTATGTCCCGAAGGACCACTAGATACA
Found at i:679208 original size:22 final size:22
Alignment explanation
Indices: 679131--679209 Score: 86
Period size: 22 Copynumber: 3.6 Consensus size: 22
679121 GACCACTATG
* * *
679131 TCCCGAAGGACCACTAGATACA
1 TCCCGAAAGACTACTGGATACA
* * *
679153 TCCCGAATGACCACTGGATACG
1 TCCCGAAAGACTACTGGATACA
*
679175 TCCCGAAGGACTACTGGATACA
1 TCCCGAAAGACTACTGGATACA
*
679197 TCCCAAAAGACTA
1 TCCCGAAAGACTA
679210 ATATACCCTC
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 49 1.00
ACGTcount: A:0.34, C:0.30, G:0.19, T:0.16
Consensus pattern (22 bp):
TCCCGAAAGACTACTGGATACA
Found at i:679886 original size:160 final size:160
Alignment explanation
Indices: 679622--679942 Score: 633
Period size: 160 Copynumber: 2.0 Consensus size: 160
679612 TACATAGTAA
679622 TACATTGATACTTATCAGCATACGAATTGATATTCCAAACTATTAATCCTTAGGCTAAAAGAAAG
1 TACATTGATACTTATCAGCATACGAATTGATATTCCAAACTATTAATCCTTAGGCTAAAAGAAAG
*
679687 TTATTTCCATCTCTTACTGAAGGTATGCATCGAAGCACTACACCATGTATCGATGCATCCCTTGA
66 TTATTTCCATCTCTTACTGAAGGTATGCATCAAAGCACTACACCATGTATCGATGCATCCCTTGA
679752 CGGGTACATCGATGCACTACCCATGCATCG
131 CGGGTACATCGATGCACTACCCATGCATCG
679782 TACATTGATACTTATCAGCATACGAATTGATATTCCAAACTATTAATCCTTAGGCTAAAAGAAAG
1 TACATTGATACTTATCAGCATACGAATTGATATTCCAAACTATTAATCCTTAGGCTAAAAGAAAG
679847 TTATTTCCATCTCTTACTGAAGGTATGCATCAAAGCACTACACCATGTATCGATGCATCCCTTGA
66 TTATTTCCATCTCTTACTGAAGGTATGCATCAAAGCACTACACCATGTATCGATGCATCCCTTGA
679912 CGGGTACATCGATGCACTACCCATGCATCG
131 CGGGTACATCGATGCACTACCCATGCATCG
679942 T
1 T
679943 GCATAAATCC
Statistics
Matches: 160, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
160 160 1.00
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.30
Consensus pattern (160 bp):
TACATTGATACTTATCAGCATACGAATTGATATTCCAAACTATTAATCCTTAGGCTAAAAGAAAG
TTATTTCCATCTCTTACTGAAGGTATGCATCAAAGCACTACACCATGTATCGATGCATCCCTTGA
CGGGTACATCGATGCACTACCCATGCATCG
Found at i:681538 original size:37 final size:37
Alignment explanation
Indices: 681456--681822 Score: 252
Period size: 37 Copynumber: 10.0 Consensus size: 37
681446 TTTCGTCTAT
* * **
681456 ATATATATATTATATAG-TTTGCAAATAGTTTTTGAAA
1 ATATATATAATATATAGTTTTG-AAAAACATTTTGAAA
681493 ATACGTATATAATATATAGTTTTGAAAAACATTTTGAAA
1 ATA--TATATAATATATAGTTTTGAAAAACATTTTGAAA
*
681532 ATGTATATAATATATAGTTTTG-AAAACACTTTTGAAA
1 ATATATATAATATATAGTTTTGAAAAACA-TTTTGAAA
* **
681569 A-CTATATAATATATAGTTTT-TTAAACATTTTAGAAA
1 ATATATATAATATATAGTTTTGAAAAACATTTT-GAAA
* * *
681605 ATATATATAATATATGGTTTTTAAAATCATTTTGAAA
1 ATATATATAATATATAGTTTTGAAAAACATTTTGAAA
*
681642 ACT-TATATAATATATAGTTTTTG-AAAACATTTTTAAA
1 A-TATATATAATATATAG-TTTTGAAAAACATTTTGAAA
* * *
681679 ACTTATATATAATATATAATTTT-TAAAGCATTTTTG---
1 A--TATATATAATATATAGTTTTGAAAAACA-TTTTGAAA
* * *
681715 -GA-A-AT--TATATAGTTTTAAAAAAACATTTTAAAA
1 ATATATATAATATATAGTTTT-GAAAAACATTTTGAAA
* *
681748 AT-TATATAGT-T-T--TTTTGAAAATCATTTTTGAAA
1 ATATATATAATATATAGTTTTGAAAAACA-TTTTGAAA
* *
681781 ATTTATATATAATATATAGTTTTTAAAGAAACATTTTTAAA
1 A--TATATATAATATATAG-TTTTGAA-AAACATTTTGAAA
681822 A
1 A
681823 AAATTTATAT
Statistics
Matches: 263, Mismatches: 33, Indels: 64
0.73 0.09 0.18
Matches are distributed among these distances:
29 10 0.04
30 4 0.02
31 7 0.03
32 7 0.03
33 13 0.05
34 1 0.00
35 8 0.03
36 42 0.16
37 81 0.31
38 24 0.09
39 44 0.17
40 4 0.02
41 14 0.05
42 4 0.02
ACGTcount: A:0.44, C:0.04, G:0.08, T:0.44
Consensus pattern (37 bp):
ATATATATAATATATAGTTTTGAAAAACATTTTGAAA
Found at i:681625 original size:110 final size:111
Alignment explanation
Indices: 681484--681725 Score: 323
Period size: 110 Copynumber: 2.2 Consensus size: 111
681474 TTGCAAATAG
681484 TTTTTGAAAATACGTATATAATATATAGTTTTGAAAAACATTTTGAAAA-TGTATATAATATATA
1 TTTTTGAAAATA--TATATAATATATAGTTTTGAAAAACATTTTGAAAACT-TATATAATATATA
*
681548 G-TTTTGAAAACACTTTTGAAAAC-TATATAATATATAGTTTTTTAAA-CA
63 GTTTTTGAAAACA-TTTTGAAAACTTATATAATATATA-ATTTTTAAAGCA
* * * *
681596 TTTTAGAAAATATATATAATATATGGTTTTTAAAATCATTTTGAAAACTTATATAATATATAGTT
1 TTTTTGAAAATATATATAATATATAGTTTTGAAAAACATTTTGAAAACTTATATAATATATAGTT
*
681661 TTTGAAAACATTTTTAAAACTTATATATAATATATAATTTTTAAAGCA
66 TTTGAAAACATTTTGAAAAC-T-TATATAATATATAATTTTTAAAGCA
*
681709 TTTTTGGAAAT-TATATA
1 TTTTTGAAAATATATATA
681726 GTTTTAAAAA
Statistics
Matches: 116, Mismatches: 8, Indels: 12
0.85 0.06 0.09
Matches are distributed among these distances:
110 55 0.47
111 12 0.10
112 25 0.22
113 24 0.21
ACGTcount: A:0.43, C:0.05, G:0.08, T:0.44
Consensus pattern (111 bp):
TTTTTGAAAATATATATAATATATAGTTTTGAAAAACATTTTGAAAACTTATATAATATATAGTT
TTTGAAAACATTTTGAAAACTTATATAATATATAATTTTTAAAGCA
Found at i:681878 original size:17 final size:17
Alignment explanation
Indices: 681858--681891 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
681848 AAAAATACTT
*
681858 TTTATTTGTTATTATTA
1 TTTATTTATTATTATTA
681875 TTTATTTATTATTATTA
1 TTTATTTATTATTATTA
681892 ATTCTTATTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (17 bp):
TTTATTTATTATTATTA
Found at i:681885 original size:14 final size:14
Alignment explanation
Indices: 681866--681920 Score: 58
Period size: 13 Copynumber: 3.9 Consensus size: 14
681856 TTTTTATTTG
681866 TTATTATTATTTAT
1 TTATTATTATTTAT
*
681880 TTATTATTA-TTAA
1 TTATTATTATTTAT
*
681893 TTCTTATTCATTTATT
1 TTATTATT-ATTTA-T
*
681909 TTATTTTTATTT
1 TTATTATTATTT
681921 TTTTGTTCAG
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
13 10 0.30
14 10 0.30
15 7 0.21
16 6 0.18
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.71
Consensus pattern (14 bp):
TTATTATTATTTAT
Found at i:683043 original size:37 final size:35
Alignment explanation
Indices: 683002--683097 Score: 97
Period size: 36 Copynumber: 2.6 Consensus size: 35
682992 ATATATTTTA
683002 TTTATTTCTTTTTATTATTATTTAT-TTATTTATTTG
1 TTTATTT-TTTTTATTATTATTTATATTA-TTATTTG
* * *
683038 TTTTATTTTTATTATTACTA-CTATCATTATTATTTG
1 -TTTATTTTTTTTATTATTATTTAT-ATTATTATTTG
683074 TTTATTTGTTTATTATTATTATTT
1 TTTATTT-TTT-TTATTATTATTT
683098 TTTTGTGTTT
Statistics
Matches: 48, Mismatches: 6, Indels: 9
0.76 0.10 0.14
Matches are distributed among these distances:
35 10 0.21
36 19 0.40
37 18 0.38
38 1 0.02
ACGTcount: A:0.22, C:0.04, G:0.03, T:0.71
Consensus pattern (35 bp):
TTTATTTTTTTTATTATTATTTATATTATTATTTG
Found at i:687877 original size:13 final size:13
Alignment explanation
Indices: 687859--687920 Score: 58
Period size: 13 Copynumber: 5.0 Consensus size: 13
687849 TAAAAGGTAA
687859 TTTTTAAATTTAT
1 TTTTTAAATTTAT
*
687872 TTTTT--ATTAAT
1 TTTTTAAATTTAT
*
687883 TTTTTAAAGTTAT
1 TTTTTAAATTTAT
***
687896 TTTTTATCCTTAT
1 TTTTTAAATTTAT
687909 TTTTT-AATTTAT
1 TTTTTAAATTTAT
687921 ATTTATCATT
Statistics
Matches: 38, Mismatches: 9, Indels: 5
0.73 0.17 0.10
Matches are distributed among these distances:
11 10 0.26
12 4 0.11
13 24 0.63
ACGTcount: A:0.26, C:0.03, G:0.02, T:0.69
Consensus pattern (13 bp):
TTTTTAAATTTAT
Found at i:687890 original size:24 final size:25
Alignment explanation
Indices: 687859--687920 Score: 83
Period size: 24 Copynumber: 2.5 Consensus size: 25
687849 TAAAAGGTAA
687859 TTTTTAAATTTATTTTTTAT-TAAT
1 TTTTTAAATTTATTTTTTATCTAAT
* *
687883 TTTTTAAAGTTATTTTTTATCCTTAT
1 TTTTTAAATTTATTTTTTAT-CTAAT
687909 TTTTT-AATTTAT
1 TTTTTAAATTTAT
687921 ATTTATCATT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
24 19 0.58
25 6 0.18
26 8 0.24
ACGTcount: A:0.26, C:0.03, G:0.02, T:0.69
Consensus pattern (25 bp):
TTTTTAAATTTATTTTTTATCTAAT
Found at i:688410 original size:30 final size:30
Alignment explanation
Indices: 688374--688466 Score: 93
Period size: 30 Copynumber: 3.1 Consensus size: 30
688364 TATTGTTAAC
* *
688374 ATATATTTAATAAGTTAA-AGTAAGAATAAA
1 ATATATTTAATAAATTAATA-TAAAAATAAA
*
688404 ATATATTTAATAAATTAATATAAAAATAAT
1 ATATATTTAATAAATTAATATAAAAATAAA
**
688434 ATAT-TTTAAATATTTTAA-ATAAAAATAGAA
1 ATATATTT-AATAAATTAATATAAAAATA-AA
688464 ATA
1 ATA
688467 AAACATATGC
Statistics
Matches: 54, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
29 12 0.22
30 41 0.76
31 1 0.02
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (30 bp):
ATATATTTAATAAATTAATATAAAAATAAA
Found at i:688527 original size:59 final size:57
Alignment explanation
Indices: 688442--688552 Score: 152
Period size: 58 Copynumber: 1.9 Consensus size: 57
688432 ATATATTTTA
688442 AATATTTTAAATAAAAATAGAAATAAAACATATGCTTGATCTTCCAACCATTTTCTTG
1 AATATTTTAAATAAAAATAGAAATAAAACAT-TGCTTGATCTTCCAACCATTTTCTTG
* * * *
688500 AATATTTTTCAATAAAATTA-AGAATAAAATATTGTTTGATCTTCCAACCATTT
1 AATA-TTTTAAATAAAAATAGA-AATAAAACATTGCTTGATCTTCCAACCATTT
688553 CCTTTTCCCA
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
58 25 0.53
59 22 0.47
ACGTcount: A:0.42, C:0.13, G:0.06, T:0.39
Consensus pattern (57 bp):
AATATTTTAAATAAAAATAGAAATAAAACATTGCTTGATCTTCCAACCATTTTCTTG
Found at i:689092 original size:37 final size:37
Alignment explanation
Indices: 689039--689148 Score: 175
Period size: 37 Copynumber: 3.0 Consensus size: 37
689029 AAACAAACGT
* *
689039 TAGAGTTTTAGTAGGATTCAAACTCCTAAAAATATGA
1 TAGAGTTTTACTAGGATTCAAACTCCTAAAAATAGGA
* *
689076 TAGAGTTTTACAAGGATTCAAACTCTTAAAAATAGGA
1 TAGAGTTTTACTAGGATTCAAACTCCTAAAAATAGGA
*
689113 TAGAGTTTTACTATGATTCAAACTCCTAAAAATAGG
1 TAGAGTTTTACTAGGATTCAAACTCCTAAAAATAGG
689149 TTCCACAAGC
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 66 1.00
ACGTcount: A:0.41, C:0.12, G:0.15, T:0.32
Consensus pattern (37 bp):
TAGAGTTTTACTAGGATTCAAACTCCTAAAAATAGGA
Found at i:689706 original size:2 final size:2
Alignment explanation
Indices: 689701--689730 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
689691 ATTTTTTAAG
689701 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
689731 GTTATTTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:689792 original size:2 final size:2
Alignment explanation
Indices: 689787--689813 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
689777 TTATGTTTTT
689787 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
689814 TTTATTTACT
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:689846 original size:9 final size:9
Alignment explanation
Indices: 689811--689854 Score: 51
Period size: 9 Copynumber: 5.3 Consensus size: 9
689801 TATATATATA
689811 TATTTTATT
1 TATTTTATT
*
689820 TACTTT-TT
1 TATTTTATT
689828 TA--TT-TT
1 TATTTTATT
689834 TATTTTATT
1 TATTTTATT
689843 TATTTTATT
1 TATTTTATT
689852 TAT
1 TAT
689855 ATATTTTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
6 6 0.19
8 6 0.19
9 19 0.61
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.77
Consensus pattern (9 bp):
TATTTTATT
Found at i:689846 original size:15 final size:15
Alignment explanation
Indices: 689826--689988 Score: 75
Period size: 17 Copynumber: 10.5 Consensus size: 15
689816 TATTTACTTT
689826 TTTATTTTTATTTTA
1 TTTATTTTTATTTTA
689841 TTTA-TTTTA-TTTA
1 TTTATTTTTATTTTA
* * *
689854 TATATTTTTTTTCTTC
1 TTTATTTTTATT-TTA
*
689870 TTTATATTTTTTCTTTA
1 TTTAT-TTTTAT-TTTA
* *
689887 TATATTTTTTATATTA
1 TTTA-TTTTTATTTTA
* *
689903 CTTACTATTTTATCTTTG
1 TTTA-T-TTTTAT-TTTA
* *
689921 TTT-TCTTTATCTTA
1 TTTATTTTTATTTTA
*
689935 TCTTATCTTTTATTTAA
1 T-TTAT-TTTTATTTTA
*
689952 TTTATTTTT-TCTTCA
1 TTTATTTTTAT-TTTA
*
689967 TTTTAATTTTA-TTTA
1 -TTTATTTTTATTTTA
689982 TTTATTT
1 TTTATTT
689989 CTTACCTTTT
Statistics
Matches: 110, Mismatches: 24, Indels: 29
0.67 0.15 0.18
Matches are distributed among these distances:
13 7 0.06
14 19 0.17
15 22 0.20
16 26 0.24
17 30 0.27
18 6 0.05
ACGTcount: A:0.20, C:0.07, G:0.01, T:0.72
Consensus pattern (15 bp):
TTTATTTTTATTTTA
Found at i:689879 original size:16 final size:15
Alignment explanation
Indices: 689854--689896 Score: 59
Period size: 16 Copynumber: 2.8 Consensus size: 15
689844 ATTTTATTTA
*
689854 TATATTTTTTTTCTT
1 TATATATTTTTTCTT
*
689869 CTTTATATTTTTTCTT
1 -TATATATTTTTTCTT
689885 TATATATTTTTT
1 TATATATTTTTT
689897 ATATTACTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
15 11 0.46
16 13 0.54
ACGTcount: A:0.16, C:0.07, G:0.00, T:0.77
Consensus pattern (15 bp):
TATATATTTTTTCTT
Found at i:689887 original size:46 final size:45
Alignment explanation
Indices: 689783--689894 Score: 120
Period size: 46 Copynumber: 2.4 Consensus size: 45
689773 TTTTTTATGT
* * *
689783 TTTTTATATATATATATATATATATATATATTTTATTTACTTTTTTA
1 TTTTTAT-TTTATATAT-TTTATTTATATATTTTATTTACTTTTTTA
* *
689830 TTTTTATTTTATTTATTTTATTTATATATTTT-TTTTCTTCTTTATA
1 TTTTTATTTTATATATTTTATTTATATATTTTATTTACTT-TTT-TA
689876 TTTTT-TCTTTATATATTTT
1 TTTTTAT-TTTATATATTTT
689895 TTATATTACT
Statistics
Matches: 56, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
44 6 0.11
45 18 0.32
46 25 0.45
47 7 0.12
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.71
Consensus pattern (45 bp):
TTTTTATTTTATATATTTTATTTATATATTTTATTTACTTTTTTA
Found at i:689964 original size:26 final size:26
Alignment explanation
Indices: 689926--689998 Score: 76
Period size: 26 Copynumber: 2.8 Consensus size: 26
689916 CTTTGTTTTC
* *
689926 TTTATCTTATCTTATCTTTTATTTAA
1 TTTATTTTTTCTTATCTTTTATTTAA
* *
689952 TTTATTTTTTCTTCAT-TTTAATTTTA
1 TTTATTTTTTCTT-ATCTTTTATTTAA
*
689978 TTTATTTATTTCTTACCTTTT
1 TTTATTT-TTTCTTATCTTTT
689999 TATCTAACAC
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
26 27 0.71
27 11 0.29
ACGTcount: A:0.19, C:0.11, G:0.00, T:0.70
Consensus pattern (26 bp):
TTTATTTTTTCTTATCTTTTATTTAA
Found at i:692818 original size:9 final size:9
Alignment explanation
Indices: 692804--692837 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
692794 CAATCAGAAC
*
692804 AAAAAGGGA
1 AAAAAGAGA
692813 AAAAAGAGA
1 AAAAAGAGA
692822 AAAAAGAAGA
1 AAAAAG-AGA
692832 AAAAAG
1 AAAAAG
692838 CAAAGAGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 14 0.61
10 9 0.39
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (9 bp):
AAAAAGAGA
Found at i:692896 original size:23 final size:23
Alignment explanation
Indices: 692816--692897 Score: 67
Period size: 23 Copynumber: 3.4 Consensus size: 23
692806 AAAGGGAAAA
* *
692816 AAGAGAAAAAAGAAGAAAAAAGCAA
1 AAGA-AAAAAAAAAGAAAAAAG-AG
*
692841 AGAGAAAATAAAAAATAAAAAAGAG
1 A-AGAAAA-AAAAAAGAAAAAAGAG
* *
692866 AA-ACAAAAATAAAGAAAAAAGTG
1 AAGA-AAAAAAAAAGAAAAAAGAG
692889 AAGAAAAAA
1 AAGAAAAAA
692898 GAAGACAGGA
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
23 21 0.45
24 5 0.11
25 6 0.13
26 15 0.32
ACGTcount: A:0.77, C:0.02, G:0.16, T:0.05
Consensus pattern (23 bp):
AAGAAAAAAAAAAGAAAAAAGAG
Found at i:694673 original size:36 final size:36
Alignment explanation
Indices: 694612--694900 Score: 303
Period size: 36 Copynumber: 8.1 Consensus size: 36
694602 AATTTACCCA
** *
694612 AAACAAAGTTTTAACTCTCTTGAGACAGTTTCCCTTG
1 AAACAAA-TTTTGTCTCTCTTGAGACAGTTTTCCTTG
694649 AAACAAATTTTGTCTCTCTTGAGACAGTTTTCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTTCCTTG
694685 AAACAAATTTTGTCTCTCTTGAGACAGTTTTCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTTCCTTG
* * *
694721 AAATAAA------ATCT-TTGA-ATATGTTTTCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACA-GTTTTCCTTG
* * *
694750 AAACAAATTTCGTCTCCCTTGAGACAG-TTTCTTTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTTC-CTTG
* ** *
694786 GAACTAGGTTTTGTCTCTCTTGATACAG-TTTCTCTTG
1 AAAC-AAATTTTGTCTCTCTTGAGACAGTTTTC-CTTG
* *
694823 AAACAAATTTTGTCTCTCTTGAGACAATTTCCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTTCCTTG
694859 AAACAAAGTTTTGTCTCTCTTGAGACAG-TTTCTCTTG
1 AAACAAA-TTTTGTCTCTCTTGAGACAGTTTTC-CTTG
694896 AAACA
1 AAACA
694901 TAAATCTTTG
Statistics
Matches: 212, Mismatches: 26, Indels: 28
0.80 0.10 0.11
Matches are distributed among these distances:
28 2 0.01
29 20 0.09
30 3 0.01
35 6 0.03
36 112 0.53
37 69 0.33
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.40
Consensus pattern (36 bp):
AAACAAATTTTGTCTCTCTTGAGACAGTTTTCCTTG
Found at i:694814 original size:37 final size:36
Alignment explanation
Indices: 694742--694900 Score: 203
Period size: 37 Copynumber: 4.4 Consensus size: 36
694732 TTGAATATGT
* * *
694742 TTTC-CTTGAAACAAATTTCGTCTCCCTTGAGACAG
1 TTTCTCTTGAAACAAGTTTTGTCTCTCTTGAGACAG
* * * *
694777 TTTCTTTTGGAACTAGGTTTTGTCTCTCTTGATACAG
1 TTTCTCTTGAAAC-AAGTTTTGTCTCTCTTGAGACAG
* *
694814 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAA
1 TTTCTCTTGAAACAAGTTTTGTCTCTCTTGAGACAG
*
694850 TTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAG
1 TTTCTCTTGAAAC-AAGTTTTGTCTCTCTTGAGACAG
694887 TTTCTCTTGAAACA
1 TTTCTCTTGAAACA
694901 TAAATCTTTG
Statistics
Matches: 104, Mismatches: 17, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
35 4 0.04
36 38 0.37
37 62 0.60
ACGTcount: A:0.24, C:0.21, G:0.14, T:0.41
Consensus pattern (36 bp):
TTTCTCTTGAAACAAGTTTTGTCTCTCTTGAGACAG
Found at i:694841 original size:21 final size:21
Alignment explanation
Indices: 694816--694881 Score: 72
Period size: 21 Copynumber: 3.4 Consensus size: 21
694806 TGATACAGTT
694816 TCTCTTGAAACAAATTTTGTC
1 TCTCTTGAAACAAATTTTGTC
*
694837 TCTCTTGAGAC-AA--TT-TC
1 TCTCTTGAAACAAATTTTGTC
694854 -C-CTTGAAACAAAGTTTTGTC
1 TCTCTTGAAACAAA-TTTTGTC
694874 TCTCTTGA
1 TCTCTTGA
694882 GACAGTTTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 13
0.71 0.04 0.25
Matches are distributed among these distances:
15 7 0.19
16 3 0.08
17 2 0.06
18 2 0.06
19 2 0.06
20 4 0.11
21 11 0.31
22 5 0.14
ACGTcount: A:0.26, C:0.21, G:0.12, T:0.41
Consensus pattern (21 bp):
TCTCTTGAAACAAATTTTGTC
Found at i:694870 original size:73 final size:73
Alignment explanation
Indices: 694742--694900 Score: 230
Period size: 73 Copynumber: 2.2 Consensus size: 73
694732 TTGAATATGT
* ** * * *
694742 TTTC-CTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAGGTTTTGTCTCTCT
1 TTTCTCTTGAAACAAATTTCGTCTCCCTTGAGACAATTTCCCTTGAAACAAAGTTTTGTCTCTCT
*
694806 TGATACAG
66 TGAGACAG
* *
694814 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAATTTCCCTTGAAACAAAGTTTTGTCTCTCT
1 TTTCTCTTGAAACAAATTTCGTCTCCCTTGAGACAATTTCCCTTGAAACAAAGTTTTGTCTCTCT
694879 TGAGACAG
66 TGAGACAG
694887 TTTCTCTTGAAACA
1 TTTCTCTTGAAACA
694901 TAAATCTTTG
Statistics
Matches: 77, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
72 4 0.05
73 73 0.95
ACGTcount: A:0.24, C:0.21, G:0.14, T:0.41
Consensus pattern (73 bp):
TTTCTCTTGAAACAAATTTCGTCTCCCTTGAGACAATTTCCCTTGAAACAAAGTTTTGTCTCTCT
TGAGACAG
Found at i:695022 original size:36 final size:35
Alignment explanation
Indices: 694958--695072 Score: 185
Period size: 35 Copynumber: 3.3 Consensus size: 35
694948 AGACAATTTA
* *
694958 TCTTGAAACACGAAAAAAACCTTCGAAATTGTTTC
1 TCTTGAAACACAAAAAAAACCTTTGAAATTGTTTC
*
694993 TTTTGAAACACAAAAAAAACCCTTTGAAATTGTTTC
1 TCTTGAAACACAAAAAAAA-CCTTTGAAATTGTTTC
*
695029 TCTTGAAACACAAAAAAAACCTTTGAAAATGTTTC
1 TCTTGAAACACAAAAAAAACCTTTGAAATTGTTTC
695064 TCTTGAAAC
1 TCTTGAAAC
695073 CCAAGACCTT
Statistics
Matches: 74, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
35 41 0.55
36 33 0.45
ACGTcount: A:0.42, C:0.18, G:0.10, T:0.30
Consensus pattern (35 bp):
TCTTGAAACACAAAAAAAACCTTTGAAATTGTTTC
Found at i:696305 original size:36 final size:35
Alignment explanation
Indices: 696263--696371 Score: 107
Period size: 36 Copynumber: 3.0 Consensus size: 35
696253 ATTACATATA
*
696263 TATATATATGTTATT-TTTTATTATCTGTTTTATTAATT
1 TATATATA-GTTATTATTTT-TTATAT-TTTTATT-ATT
*
696301 TATATATATTTATTATTTTTTATATTTTTATTATT
1 TATATATAGTTATTATTTTTTATATTTTTATTATT
*
696336 TATATATATATATATTA-TTTTTACT-TTTTTATTATT
1 TATATATA-GT-TATTATTTTTTA-TATTTTTATTATT
696372 ATTTTATTTA
Statistics
Matches: 64, Mismatches: 3, Indels: 10
0.83 0.04 0.13
Matches are distributed among these distances:
35 11 0.17
36 25 0.39
37 16 0.25
38 12 0.19
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.68
Consensus pattern (35 bp):
TATATATAGTTATTATTTTTTATATTTTTATTATT
Found at i:696314 original size:4 final size:4
Alignment explanation
Indices: 696291--696519 Score: 65
Period size: 4 Copynumber: 56.8 Consensus size: 4
696281 TATTATCTGT
*
696291 TTTA TTAA TTTA TATATA TTTA -TTA TTT- TTTA TATT- TTTA -TTA TTTA
1 TTTA TTTA TTTA T-T-TA TTTA TTTA TTTA TTTA T-TTA TTTA TTTA TTTA
* * * * *
696338 TATA TATA TATA TTATT TTTA CTTT- TTTA -TTA -TTA TTTTA TTTA TTTGT
1 TTTA TTTA TTTA TT-TA TTTA -TTTA TTTA TTTA TTTA -TTTA TTTA TTT-A
* * *
696387 TTTA TTTA TATA TTT- TTTC TTCTT TTTA TTT- TTTA TTATA TTT- TTTA
1 TTTA TTTA TTTA TTTA TTTA TT-TA TTTA TTTA TTTA TT-TA TTTA TTTA
* * * *
696434 TATTA CTTA -CTA TTTTA TCTT- TTT- TTTC TTTA TCTTA TCT- TTTA
1 T-TTA TTTA TTTA -TTTA T-TTA TTTA TTTA TTTA T-TTA TTTA TTTA
* *
696478 TTTAA TTTA TTT- TTTC TTCA TTTTAA TTTTA TTTA TTTA TTT
1 TTT-A TTTA TTTA TTTA TTTA -TTT-A -TTTA TTTA TTTA TTT
696520 CTTACATTTT
Statistics
Matches: 175, Mismatches: 21, Indels: 58
0.69 0.08 0.23
Matches are distributed among these distances:
3 41 0.23
4 85 0.49
5 41 0.23
6 8 0.05
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (4 bp):
TTTA
Found at i:696314 original size:18 final size:18
Alignment explanation
Indices: 696291--696344 Score: 74
Period size: 18 Copynumber: 3.1 Consensus size: 18
696281 TATTATCTGT
696291 TTTATTAATTTATATATA
1 TTTATTAATTTATATATA
* * *
696309 TTTATTATTTTTTATATT
1 TTTATTAATTTATATATA
696327 TTTATT-ATTTATATATA
1 TTTATTAATTTATATATA
696344 T
1 T
696345 ATATATTATT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
17 9 0.30
18 21 0.70
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (18 bp):
TTTATTAATTTATATATA
Found at i:696328 original size:9 final size:9
Alignment explanation
Indices: 696299--696437 Score: 58
Period size: 9 Copynumber: 14.9 Consensus size: 9
696289 GTTTTATTAA
*
696299 TTTATATATA
1 TTTATAT-TT
696309 TTTATTATTT
1 TTTA-TATTT
696319 TTTATA--T
1 TTTATATTT
*
696326 TTT-TATTA
1 TTTATATTT
*
696334 TTTATATATA
1 TTTATAT-TT
*
696344 TATATATTAT
1 TTTATATT-T
696354 TTT-TACTTT
1 TTTATA-TTT
696363 TTTATTATTAT
1 TTTA-TATT-T
696374 TTTATTTATTT
1 TTTA--TATTT
696385 GTTT-TA-TT
1 -TTTATATTT
*
696393 TATATATTT
1 TTTATATTT
*
696402 TTTCT-TCTT
1 TTTATAT-TT
*
696411 TTTATTTTT
1 TTTATATTT
696420 TATTATATTT
1 T-TTATATTT
696430 TTTATATT
1 TTTATATT
696438 ACTTACTATT
Statistics
Matches: 102, Mismatches: 10, Indels: 35
0.69 0.07 0.24
Matches are distributed among these distances:
6 2 0.02
7 6 0.06
8 8 0.08
9 35 0.34
10 32 0.31
11 11 0.11
12 8 0.08
ACGTcount: A:0.24, C:0.02, G:0.01, T:0.73
Consensus pattern (9 bp):
TTTATATTT
Found at i:696379 original size:83 final size:82
Alignment explanation
Indices: 696258--696427 Score: 204
Period size: 83 Copynumber: 2.1 Consensus size: 82
696248 TTTAGATTAC
*
696258 ATATATATATATATGTTATTTTTTATTATCTGTTTTATTAATTTATATATATTTAT-TATTTTTT
1 ATATATATATATATGTTATTTTTTATTATCTATTTTATTAATTTAT-TATATTTATATATTTTTT
696322 -ATATTTTTATTATTTAT
65 CATATTTTTATTATTTAT
* * * *
696339 ATATATATATATTATTTTTACTTTTTTATTAT-TATTTTATTTATTTGTTTTATTTATATATTTT
1 ATATATATATA-TA-TGTTA-TTTTTTATTATCTATTTTATTAATTTATTATATTTATATATTTT
* * *
696403 TTCTTCTTTTTATTTTTTAT
63 TTCATATTTTTATTATTTAT
696423 -TATAT
1 ATATAT
696428 TTTTTATATT
Statistics
Matches: 76, Mismatches: 8, Indels: 8
0.83 0.09 0.09
Matches are distributed among these distances:
81 11 0.14
82 10 0.13
83 30 0.39
84 25 0.33
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.69
Consensus pattern (82 bp):
ATATATATATATATGTTATTTTTTATTATCTATTTTATTAATTTATTATATTTATATATTTTTTC
ATATTTTTATTATTTAT
Found at i:696392 original size:57 final size:55
Alignment explanation
Indices: 696310--696437 Score: 163
Period size: 57 Copynumber: 2.3 Consensus size: 55
696300 TTATATATAT
696310 TTATTATTTTTTATATTTTTATTATTTATATATATATATATTATTTTTACTTTTTTA
1 TTATTATTTTTTATATTTTTATTATTTATATAT-TATATATTATTTTTA-TTTTTTA
* * * *
696367 TTATTATTTTATT-TATTTGTT-TTATTTATATATTTTTTCTTCTTTTTATTTTTTA
1 TTATTATTTT-TTATATTT-TTATTATTTATATATTATATATTATTTTTATTTTTTA
696422 TTA-TATTTTTTATATT
1 TTATTATTTTTTATATT
696438 ACTTACTATT
Statistics
Matches: 64, Mismatches: 4, Indels: 9
0.83 0.05 0.12
Matches are distributed among these distances:
53 2 0.03
54 10 0.16
55 10 0.16
56 11 0.17
57 27 0.42
58 4 0.06
ACGTcount: A:0.23, C:0.02, G:0.01, T:0.73
Consensus pattern (55 bp):
TTATTATTTTTTATATTTTTATTATTTATATATTATATATTATTTTTATTTTTTA
Found at i:696404 original size:28 final size:28
Alignment explanation
Indices: 696273--696434 Score: 115
Period size: 28 Copynumber: 5.8 Consensus size: 28
696263 TATATATATG
* *
696273 TTATTTTTTAT-TATCTGTTTTATTAATTT
1 TTATTATTTATATAT-T-TTTTATTTATTT
*
696302 ATATATATTTAT-TATTTTTTA--TATTT
1 TTAT-TATTTATATATTTTTTATTTATTT
* *
696328 TTATTATTTATATA-TATATATATTATTT
1 TTATTATTTATATATTTTTTAT-TTATTT
*
696356 TTACTTTTTTAT-TATTATTTTATTTATTT
1 TTA-TTATTTATATATT-TTTTATTTATTT
* *
696385 GTT-TTATTTATATATTTTTT-CTTCTTT
1 -TTATTATTTATATATTTTTTATTTATTT
*
696412 TTATTTTTTATTATATTTTTTAT
1 TTATTATTTA-TATATTTTTTAT
696435 ATTACTTACT
Statistics
Matches: 106, Mismatches: 14, Indels: 26
0.73 0.10 0.18
Matches are distributed among these distances:
25 11 0.10
26 11 0.10
27 11 0.10
28 36 0.34
29 22 0.21
30 15 0.14
ACGTcount: A:0.24, C:0.02, G:0.01, T:0.72
Consensus pattern (28 bp):
TTATTATTTATATATTTTTTATTTATTT
Found at i:696444 original size:84 final size:80
Alignment explanation
Indices: 696276--696518 Score: 206
Period size: 84 Copynumber: 2.9 Consensus size: 80
696266 ATATATGTTA
* * * * *
696276 TTTTTTATTATCTGTTTTATTAATTTATATATATTTATTATTTTTT-ATATTTTTATTATTTATA
1 TTTTTTATTAT-TATTTTATTTATTTAT-TTTATTTATTATTTTTTCTTCTTTTTATT-TTT-TA
*
696340 TATATATATATTATTTTTAC
62 T-TATATTTATTATTTTTAC
*
696360 TTTTTTATTATTATTTTATTTATTTGTTTTATTTATATATTTTTTCTTCTTTTTATTTTTTATTA
1 TTTTTTATTATTATTTTATTTATTTATTTTATTTAT-TATTTTTTCTTCTTTTTATTTTTTATTA
*
696425 TATTTTTTATATTACTTAC
65 TATTTATTAT-TT--TTAC
* * * * *
696444 TATTTTATCT-TTTTTTTCTTTATCTTATCTTTTATTTAATTTATTTTTTCTTCATTTTA-ATTT
1 TTTTTTAT-TATTATTTTATTTAT-TTA--TTTTATTT-A-TTATTTTTTCTTCTTTTTATTTTT
696507 TATT-TATTTATT
60 TATTATATTTATT
696519 TCTTACATTT
Statistics
Matches: 133, Mismatches: 15, Indels: 20
0.79 0.09 0.12
Matches are distributed among these distances:
81 10 0.08
82 13 0.10
83 24 0.18
84 42 0.32
85 3 0.02
86 7 0.05
87 15 0.11
88 18 0.14
89 1 0.01
ACGTcount: A:0.23, C:0.05, G:0.01, T:0.72
Consensus pattern (80 bp):
TTTTTTATTATTATTTTATTTATTTATTTTATTTATTATTTTTTCTTCTTTTTATTTTTTATTAT
ATTTATTATTTTTAC
Found at i:696486 original size:92 final size:91
Alignment explanation
Indices: 696290--696487 Score: 196
Period size: 92 Copynumber: 2.2 Consensus size: 91
696280 TTATTATCTG
696290 TTTTA-TTAATTTATATATATTTATTATTTTTTATATTTTTATTATTTATATATATATATATTAT
1 TTTTATTTAATTTATATATATTTATTATTTTTTATATTTTTATTATTTATATATATATATATTAT
* *
696354 TTTTACTTTTTTATTATTATTTTATT
66 TTTTACTTTTTTATTATTATCTTATC
* * * *
696380 TATTTGTTTTATTTATATAT-TTT-TTCTTCTTTT-TATTTTTTATTATATT-T-TTTATAT-TA
1 T-TTTATTTAATTTATATATATTTATTATT-TTTTATA-TTTTTATTAT-TTATATATATATATA
*
696439 CTTACTATTTTATCTTTTTT-TTCTTTATCTTATC
62 -TTA-T-TTTTA-CTTTTTTATT-ATTATCTTATC
696473 TTTTATTTAATTTAT
1 TTTTATTTAATTTAT
696488 TTTTTCTTCA
Statistics
Matches: 89, Mismatches: 9, Indels: 18
0.77 0.08 0.16
Matches are distributed among these distances:
89 2 0.02
90 16 0.18
91 22 0.25
92 33 0.37
93 16 0.18
ACGTcount: A:0.24, C:0.05, G:0.01, T:0.71
Consensus pattern (91 bp):
TTTTATTTAATTTATATATATTTATTATTTTTTATATTTTTATTATTTATATATATATATATTAT
TTTTACTTTTTTATTATTATCTTATC
Found at i:696492 original size:16 final size:15
Alignment explanation
Indices: 696273--696519 Score: 83
Period size: 15 Copynumber: 16.4 Consensus size: 15
696263 TATATATATG
696273 TTATTTTTTA-TTAT
1 TTATTTTTTATTTAT
* *
696287 CTGTTTTATTAATTTAT
1 TTATTTT-TT-ATTTAT
*
696304 ATATATTTATTATTT-T
1 -T-TATTTTTTATTTAT
696320 TTATATTTTTA-TTAT
1 TTAT-TTTTTATTTAT
* * *
696335 TTA-TATATATATAT
1 TTATTTTTTATTTAT
696349 ATTA-TTTTTACTTT-T
1 -TTATTTTTTA-TTTAT
*
696364 TTA-TTATTATTTTAT
1 TTATTTTTTA-TTTAT
696379 TTATTTGTTTTATTTAT
1 TTA-TT-TTTTATTTAT
* * *
696396 ATATTTTTTCTTCTTT
1 TTATTTTTTATT-TAT
696412 TTATTTTTTA-TTA-
1 TTATTTTTTATTTAT
*
696425 -TATTTTTTATATTAC
1 TTATTTTTTAT-TTAT
* *
696440 TTACTATTTTA--T-C
1 TTA-TTTTTTATTTAT
*
696453 TT-TTTTTTCTTTAT
1 TTATTTTTTATTTAT
*
696467 CTTATCTTTTATTTAAT
1 -TTATTTTTTATTT-AT
* *
696484 TTATTTTTTCTTCAT
1 TTATTTTTTATTTAT
*
696499 TT-TAATTTTATTTAT
1 TTAT-TTTTTATTTAT
696514 TTATTT
1 TTATTT
696520 CTTACATTTT
Statistics
Matches: 171, Mismatches: 34, Indels: 55
0.66 0.13 0.21
Matches are distributed among these distances:
11 5 0.03
12 9 0.05
13 8 0.05
14 30 0.18
15 48 0.28
16 37 0.22
17 24 0.14
18 6 0.04
19 4 0.02
ACGTcount: A:0.23, C:0.05, G:0.01, T:0.72
Consensus pattern (15 bp):
TTATTTTTTATTTAT
Found at i:696506 original size:26 final size:27
Alignment explanation
Indices: 696473--696529 Score: 82
Period size: 26 Copynumber: 2.1 Consensus size: 27
696463 TTATCTTATC
696473 TTTTATTTAATTTATTT-TTTCTT-CA
1 TTTTATTTAATTTATTTATTTCTTACA
*
696498 TTTTAATTTTATTTATTTATTTCTTACA
1 TTTT-ATTTAATTTATTTATTTCTTACA
696526 TTTT
1 TTTT
696530 TATCTAACAC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
25 4 0.14
26 12 0.43
27 6 0.21
28 6 0.21
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.72
Consensus pattern (27 bp):
TTTTATTTAATTTATTTATTTCTTACA
Found at i:697346 original size:43 final size:43
Alignment explanation
Indices: 697285--697372 Score: 131
Period size: 43 Copynumber: 2.0 Consensus size: 43
697275 ATACATCATA
* *
697285 TATAAAAAATATTGTCATGTCAATCTTAAAACAAGCAGAAGCC
1 TATAAAAAATATTGTCATGGCAATCTGAAAACAAGCAGAAGCC
* * *
697328 TATAAACATTATTGTCATGGCAATCTGAAACCAAGCAGAAGCC
1 TATAAAAAATATTGTCATGGCAATCTGAAAACAAGCAGAAGCC
697371 TA
1 TA
697373 GGCTTAGTGG
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.43, C:0.18, G:0.14, T:0.25
Consensus pattern (43 bp):
TATAAAAAATATTGTCATGGCAATCTGAAAACAAGCAGAAGCC
Found at i:705506 original size:24 final size:24
Alignment explanation
Indices: 705479--705549 Score: 99
Period size: 24 Copynumber: 3.0 Consensus size: 24
705469 CACCACAGCT
*
705479 CGTATAAATTGCACCGAAGTGCCA
1 CGTAGAAATTGCACCGAAGTGCCA
* *
705503 CGTAGAATTTGCACCGAAGTGCCG
1 CGTAGAAATTGCACCGAAGTGCCA
*
705527 CGTAGAAA-TGCACCGTAGTGCCA
1 CGTAGAAATTGCACCGAAGTGCCA
705550 TATAATATTG
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
23 13 0.32
24 28 0.68
ACGTcount: A:0.30, C:0.25, G:0.25, T:0.20
Consensus pattern (24 bp):
CGTAGAAATTGCACCGAAGTGCCA
Found at i:711713 original size:24 final size:24
Alignment explanation
Indices: 711686--711756 Score: 90
Period size: 24 Copynumber: 3.0 Consensus size: 24
711676 CACCACAGCT
* *
711686 CGTATAAATTGAACCGAAGTGCCA
1 CGTAGAAATTGCACCGAAGTGCCA
* *
711710 CGTAGAATTTGCACCGAAGTGCCG
1 CGTAGAAATTGCACCGAAGTGCCA
*
711734 CGTAGAAA-TGCACCGTAGTGCCA
1 CGTAGAAATTGCACCGAAGTGCCA
711757 TATAATATTG
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
23 13 0.32
24 27 0.68
ACGTcount: A:0.31, C:0.24, G:0.25, T:0.20
Consensus pattern (24 bp):
CGTAGAAATTGCACCGAAGTGCCA
Found at i:712138 original size:2 final size:2
Alignment explanation
Indices: 712125--712162 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
712115 ACATGGATTC
*
712125 AT AT AA 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
712163 GAATTGTATT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:715162 original size:2 final size:2
Alignment explanation
Indices: 715155--715187 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
715145 TATGTACAAA
715155 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
715188 TTTTGGAGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:717602 original size:19 final size:20
Alignment explanation
Indices: 717580--717617 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
717570 AAAAATCTTG
*
717580 AATTATAAT-AAAAATTTAC
1 AATTACAATCAAAAATTTAC
*
717599 AATTACAATCATAAATTTA
1 AATTACAATCAAAAATTTA
717618 GAACATAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.55, C:0.08, G:0.00, T:0.37
Consensus pattern (20 bp):
AATTACAATCAAAAATTTAC
Found at i:718753 original size:41 final size:41
Alignment explanation
Indices: 718702--718784 Score: 107
Period size: 41 Copynumber: 2.0 Consensus size: 41
718692 TTTTTTGATT
*
718702 TATGTAAAAGAGATAAATTTGATA-ATAT-TAATATATAATAA
1 TATGTAAAAGAGATAAACTT-ATATATATAT-ATATATAATAA
* *
718743 TATGTGAAAGAGATAAACTTATATATATATATATATATTAA
1 TATGTAAAAGAGATAAACTTATATATATATATATATAATAA
718784 T
1 T
718785 TGAATAAATG
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
40 3 0.08
41 33 0.89
42 1 0.03
ACGTcount: A:0.51, C:0.01, G:0.10, T:0.39
Consensus pattern (41 bp):
TATGTAAAAGAGATAAACTTATATATATATATATATAATAA
Found at i:722706 original size:14 final size:15
Alignment explanation
Indices: 722672--722712 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
722662 TTGTGTTATG
*
722672 CTATATATATATACA
1 CTATATAAATATACA
*
722687 CT-TATACATATACA
1 CTATATAAATATACA
722701 -TATATAAATATA
1 CTATATAAATATA
722713 TGTATGTATC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
13 1 0.04
14 20 0.87
15 2 0.09
ACGTcount: A:0.49, C:0.12, G:0.00, T:0.39
Consensus pattern (15 bp):
CTATATAAATATACA
Found at i:724876 original size:152 final size:152
Alignment explanation
Indices: 724593--724905 Score: 574
Period size: 152 Copynumber: 2.1 Consensus size: 152
724583 GCAGTGCGGG
* *
724593 ATAAC-TTAACTACTAATGTCTCTTTTTATTGTTGGTTATGTTGAGCATAATTGTAATAAGGTTC
1 ATAACGTTAACTACTAAGGTCTCTTTTTATTGTTGGTTATGTTGAGCAAAATTGTAATAAGGTTC
*
724657 ACACGTTAGGCTCTTGGGCTCTTAGTTCTGGGCGTACCTTATTTTATGACTCGGTTTGTCCCAAG
66 ACACGTTAGGCTCTTGGGCTCTTAGTTCTGGGCGTACCTTATTTTATGACTCAGTTTGTCCCAAG
724722 GTTATCATATCTGATGTATTCA
131 GTTATCATATCTGATGTATTCA
724744 ATAACGTTAACTACTAAGGTCTCTTTTTATTGTTGGTTATGTTGAGCAAAATTGTAATAAGGTTC
1 ATAACGTTAACTACTAAGGTCTCTTTTTATTGTTGGTTATGTTGAGCAAAATTGTAATAAGGTTC
*
724809 ACACGTTAGGCTCTTGGGCTCTTAGTTCTGGGCGTACCTTATTTTATGACTCAGTTTGTCCCGAG
66 ACACGTTAGGCTCTTGGGCTCTTAGTTCTGGGCGTACCTTATTTTATGACTCAGTTTGTCCCAAG
*
724874 GTTATCCTATCTGATGTATTCA
131 GTTATCATATCTGATGTATTCA
724896 ATAACGTTAA
1 ATAACGTTAA
724906 TTTTGGATAA
Statistics
Matches: 156, Mismatches: 5, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
151 5 0.03
152 151 0.97
ACGTcount: A:0.23, C:0.17, G:0.19, T:0.41
Consensus pattern (152 bp):
ATAACGTTAACTACTAAGGTCTCTTTTTATTGTTGGTTATGTTGAGCAAAATTGTAATAAGGTTC
ACACGTTAGGCTCTTGGGCTCTTAGTTCTGGGCGTACCTTATTTTATGACTCAGTTTGTCCCAAG
GTTATCATATCTGATGTATTCA
Found at i:725003 original size:3 final size:3
Alignment explanation
Indices: 724995--725035 Score: 64
Period size: 3 Copynumber: 13.7 Consensus size: 3
724985 TTTTTCATTC
* *
724995 TAT TAT TAT TAT TAT TAT TAA AAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
725036 CACAAATATT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:728354 original size:36 final size:36
Alignment explanation
Indices: 728307--728378 Score: 99
Period size: 36 Copynumber: 2.0 Consensus size: 36
728297 GAACTATGCA
* * * *
728307 CACAAATATCCTGTTATATTAATATCAAAAGTATTC
1 CACAAAGATCCTGTTAGATTAATACCAAAAGCATTC
*
728343 CACAAAGATCCTGTTAGATTGATACCAAAAGCATTC
1 CACAAAGATCCTGTTAGATTAATACCAAAAGCATTC
728379 TACGACAAGA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.40, C:0.19, G:0.10, T:0.31
Consensus pattern (36 bp):
CACAAAGATCCTGTTAGATTAATACCAAAAGCATTC
Found at i:729018 original size:14 final size:15
Alignment explanation
Indices: 728986--729023 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
728976 CATACATGCA
728986 TTTGCATTTTTCATC
1 TTTGCATTTTTCATC
*
729001 TTTGCATTTTTTAT-
1 TTTGCATTTTTCATC
729015 TTTGCATTT
1 TTTGCATTT
729024 ATACTTTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 9 0.41
15 13 0.59
ACGTcount: A:0.13, C:0.13, G:0.08, T:0.66
Consensus pattern (15 bp):
TTTGCATTTTTCATC
Found at i:731535 original size:7 final size:8
Alignment explanation
Indices: 731508--731544 Score: 56
Period size: 8 Copynumber: 4.6 Consensus size: 8
731498 CTATACTAAA
731508 AAAAAGGG
1 AAAAAGGG
731516 AAAAAGGG
1 AAAAAGGG
*
731524 AAAAAGGA
1 AAAAAGGG
*
731532 AAAAAAGG
1 AAAAAGGG
731540 AAAAA
1 AAAAA
731545 TTGAATCAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (8 bp):
AAAAAGGG
Found at i:735515 original size:54 final size:54
Alignment explanation
Indices: 735402--735626 Score: 303
Period size: 54 Copynumber: 4.1 Consensus size: 54
735392 AAAACTTCAC
*
735402 TTACGAACATCTGGGCAGAAACCACATGGAAA-GAATGAATGTGTTGTCAAATGTT
1 TTACGAACATCTAGGCAGAAACCACAT-GAAATG-ATGAATGTGTTGTCAAATGTT
*
735457 TTACGAACATCTAGGCAGAAGCCACATGAAATGATGAATGTGTTGTCAAATGTT
1 TTACGAACATCTAGGCAGAAACCACATGAAATGATGAATGTGTTGTCAAATGTT
* * * *
735511 TTACGAACATCTATGCA-AAAGCCACAGGAAAGGATGAATGTGTTGTCAATTGTT
1 TTACGAACATCTAGGCAGAAA-CCACATGAAATGATGAATGTGTTGTCAAATGTT
* * * *
735565 TTACTAGCATCT-GAGCATAAACCACATGAAATAATGAATGTGTTGTCAAATGTT
1 TTACGAACATCTAG-GCAGAAACCACATGAAATGATGAATGTGTTGTCAAATGTT
735619 TTACGAAC
1 TTACGAAC
735627 TAGTTATAAT
Statistics
Matches: 150, Mismatches: 16, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
53 2 0.01
54 119 0.79
55 29 0.19
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.28
Consensus pattern (54 bp):
TTACGAACATCTAGGCAGAAACCACATGAAATGATGAATGTGTTGTCAAATGTT
Found at i:736016 original size:22 final size:22
Alignment explanation
Indices: 735988--736085 Score: 171
Period size: 22 Copynumber: 4.5 Consensus size: 22
735978 ATATTTACAT
735988 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
736010 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
*
736032 TCTTCAAAGATGATAGATT-TT
1 TCTTCAAAGATGATAGATTCTC
736053 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
*
736075 TTTTCAAAGAT
1 TCTTCAAAGAT
736086 AAACTTTATT
Statistics
Matches: 72, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
21 20 0.28
22 52 0.72
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.39
Consensus pattern (22 bp):
TCTTCAAAGATGATAGATTCTC
Found at i:736071 original size:43 final size:44
Alignment explanation
Indices: 735988--736085 Score: 171
Period size: 43 Copynumber: 2.2 Consensus size: 44
735978 ATATTTACAT
735988 TCTTCAAAGATGATAGATTCTCTCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTCTCTTCAAAGATGATAGATTCTC
*
736032 TCTTCAAAGATGATAGATT-TTTCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTCTCTTCAAAGATGATAGATTCTC
*
736075 TTTTCAAAGAT
1 TCTTCAAAGAT
736086 AAACTTTATT
Statistics
Matches: 52, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
43 33 0.63
44 19 0.37
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.39
Consensus pattern (44 bp):
TCTTCAAAGATGATAGATTCTCTCTTCAAAGATGATAGATTCTC
Found at i:736897 original size:76 final size:76
Alignment explanation
Indices: 736767--736962 Score: 329
Period size: 76 Copynumber: 2.6 Consensus size: 76
736757 CTACAGTGCA
*
736767 TGATGTTTTTAAAGCCTCCGGGTCATCCATAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTT
1 TGATGTTTTTAAAGCCTCCGGGTCATCCATAAGACCTACAGTGCAGGATATTTTCAAAAAGCCTT
736832 CGGGAGCTTTT
66 CGGGAGCTTTT
*
736843 TGATGTTTTTAAAGCCTCCGGGTCATCCATAAGACCTACAGTGCATGATATTTTCAAAAAGCCTT
1 TGATGTTTTTAAAGCCTCCGGGTCATCCATAAGACCTACAGTGCAGGATATTTTCAAAAAGCCTT
* *
736908 TGGGAGTTTTT
66 CGGGAGCTTTT
* **
736919 TGATGTTTTTAAAGCCTTCGGGTCATCTGTAAGACCTACAGTGC
1 TGATGTTTTTAAAGCCTCCGGGTCATCCATAAGACCTACAGTGC
736963 TAGATGATAA
Statistics
Matches: 113, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
76 113 1.00
ACGTcount: A:0.25, C:0.20, G:0.21, T:0.34
Consensus pattern (76 bp):
TGATGTTTTTAAAGCCTCCGGGTCATCCATAAGACCTACAGTGCAGGATATTTTCAAAAAGCCTT
CGGGAGCTTTT
Found at i:737080 original size:118 final size:118
Alignment explanation
Indices: 736857--737136 Score: 443
Period size: 118 Copynumber: 2.4 Consensus size: 118
736847 GTTTTTAAAG
* * * * * * *
736857 CCTCCGGGTCATCCATAAGACCTACAGTGCATGATATTTTCAAAAAGCCTTTGGGAGTTTTTTGA
1 CCTCAGGGCCATCCGTAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGA
* *
736922 TGTTTTTAAAGCCTTCGGGTCATCTGTAAGACCTACAGTGCTAGATGATAAGA
66 TGTTTTTAAAGCCTCCGGGTCATCTGTAAGACCTACAGTGCAAGATGATAAGA
* *
736975 CCTCAGGGCTATCCGTAAGACCTACAATGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGA
1 CCTCAGGGCCATCCGTAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGA
*
737040 TGTTTTTAAAGCCTCCGGGTTATCTGTAAGACCTACAGTGCAAGATGATAAGA
66 TGTTTTTAAAGCCTCCGGGTCATCTGTAAGACCTACAGTGCAAGATGATAAGA
*
737093 CCTCAGGGCCATCCGTAAGACTTACAGTGCAGGATGTTTTCAAA
1 CCTCAGGGCCATCCGTAAGACCTACAGTGCAGGATGTTTTCAAA
737137 TGAGATTTAA
Statistics
Matches: 147, Mismatches: 15, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
118 147 1.00
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.30
Consensus pattern (118 bp):
CCTCAGGGCCATCCGTAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGA
TGTTTTTAAAGCCTCCGGGTCATCTGTAAGACCTACAGTGCAAGATGATAAGA
Found at i:737392 original size:3 final size:3
Alignment explanation
Indices: 737380--737412 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
737370 TTAATTTTTC
737380 ATT A-T ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
737413 CAAATATTAC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:739160 original size:2 final size:2
Alignment explanation
Indices: 739148--739181 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
739138 ATATCTTATT
*
739148 TA TA AA 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
739182 CTTTATTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:743955 original size:23 final size:23
Alignment explanation
Indices: 743928--744006 Score: 104
Period size: 23 Copynumber: 3.4 Consensus size: 23
743918 GGTTCTACAC
743928 GGTCCTTCGGGACAATTCTATGT
1 GGTCCTTCGGGACAATTCTATGT
* * *
743951 TGTCCTTCGGGACAATTCTACGC
1 GGTCCTTCGGGACAATTCTATGT
* *
743974 GGTCCTTCGAGACAAATCTATGT
1 GGTCCTTCGGGACAATTCTATGT
*
743997 GGTACTTCGG
1 GGTCCTTCGG
744007 TGCATATTCT
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.19, C:0.24, G:0.25, T:0.32
Consensus pattern (23 bp):
GGTCCTTCGGGACAATTCTATGT
Found at i:743988 original size:46 final size:47
Alignment explanation
Indices: 743920--744019 Score: 132
Period size: 46 Copynumber: 2.1 Consensus size: 47
743910 GAGTCAAGGG
* * * * *
743920 TTCTACACGGTCCTTCGGGACAATTCTATGTTGTCCTTCGG-GACA-A
1 TTCTACGCGGTCCTTCGAGACAAATCTATGTGGTACTTCGGTG-CATA
743966 TTCTACGCGGTCCTTCGAGACAAATCTATGTGGTACTTCGGTGCATA
1 TTCTACGCGGTCCTTCGAGACAAATCTATGTGGTACTTCGGTGCATA
744013 TTCTACG
1 TTCTACG
744020 TGCACTTTGG
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
46 38 0.81
47 9 0.19
ACGTcount: A:0.20, C:0.25, G:0.22, T:0.33
Consensus pattern (47 bp):
TTCTACGCGGTCCTTCGAGACAAATCTATGTGGTACTTCGGTGCATA
Found at i:745662 original size:23 final size:23
Alignment explanation
Indices: 745629--745677 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
745619 AAAAAATGAA
**
745629 AAACATACCATAAAGGTAGAGAT
1 AAACATACCATAAAAATAGAGAT
*
745652 AAACATGCCATAAAAATAGAGAT
1 AAACATACCATAAAAATAGAGAT
745675 AAA
1 AAA
745678 TGTATTATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.57, C:0.12, G:0.14, T:0.16
Consensus pattern (23 bp):
AAACATACCATAAAAATAGAGAT
Found at i:752867 original size:491 final size:491
Alignment explanation
Indices: 751945--752927 Score: 1941
Period size: 491 Copynumber: 2.0 Consensus size: 491
751935 GTTTGATTGA
751945 AACAACCGTATTCTGTACCCTCAATTTTATTGGGTAGAACTTCTGTTAGGTTACCAAGCCTATTG
1 AACAACCGTATTCTGTACCCTCAATTTTATTGGGTAGAACTTCTGTTAGGTTACCAAGCCTATTG
752010 GGGATTGCCTTGACATATAAACCGAACAGTTGATTTGCTTTTAGGTATATTTGCCCAGTTTTAAT
66 GGGATTGCCTTGACATATAAACCGAACAGTTGATTTGCTTTTAGGTATATTTGCCCAGTTTTAAT
752075 ACCCTAGTAAAAGGTGGTTGCATATTTCTTCATGGTGGCTTAGTGATCATGCCGCCCTCCCCCTT
131 ACCCTAGTAAAAGGTGGTTGCATATTTCTTCATGGTGGCTTAGTGATCATGCCGCCCTCCCCCTT
752140 TTCTTCTCTTTTCCCTCTTTACGAGAGGTCCTTGGGGTTTGTGAACCGATTTTGTTGTCCTTGTT
196 TTCTTCTCTTTTCCCTCTTTACGAGAGGTCCTTGGGGTTTGTGAACCGATTTTGTTGTCCTTGTT
752205 TCTACTGCTACATTACATGGCTATTAAAAGGCTATTACTAGTGTATGCTGCCTACTTCCCCTTCC
261 TCTACTGCTACATTACATGGCTATTAAAAGGCTATTACTAGTGTATGCTGCCTACTTCCCCTTCC
752270 TTTTAGCATGAGTATGGGTATTCAGTTTCTGCAGTTAAACTATCGTAACGTACTTATGAATTTTA
326 TTTTAGCATGAGTATGGGTATTCAGTTTCTGCAGTTAAACTATCGTAACGTACTTATGAATTTTA
752335 AAAGAAAGAAAATGAAAAATGCTGCTATCTAGACAGAAGCCAATACACAGTGGAGTTATTGTGTA
391 AAAGAAAGAAAATGAAAAATGCTGCTATCTAGACAGAAGCCAATACACAGTGGAGTTATTGTGTA
752400 GCTCACATATATTTGTGGAAATGTAACAGGTAGGAT
456 GCTCACATATATTTGTGGAAATGTAACAGGTAGGAT
*
752436 AACAACCGTATTCTGTACCCTCAATTTTATTGGGTAGAACTTCTGTTATGTTACCAAGCCTATTG
1 AACAACCGTATTCTGTACCCTCAATTTTATTGGGTAGAACTTCTGTTAGGTTACCAAGCCTATTG
752501 GGGATTGCCTTGACATATAAACCGAACAGTTGATTTGCTTTTAGGTATATTTGCCCAGTTTTAAT
66 GGGATTGCCTTGACATATAAACCGAACAGTTGATTTGCTTTTAGGTATATTTGCCCAGTTTTAAT
752566 ACCCTAGTAAAAGGTGGTTGCATATTTCTTCATGGTGGCTTAGTGATCATG-CGCCCTCCCCCTT
131 ACCCTAGTAAAAGGTGGTTGCATATTTCTTCATGGTGGCTTAGTGATCATGCCGCCCTCCCCCTT
752630 TTCTTCTCTTTTCCCTCTTTACGAGAGGTCCTTGGGGTTTGTGAACCGATTTTGTTGTCCTTGTT
196 TTCTTCTCTTTTCCCTCTTTACGAGAGGTCCTTGGGGTTTGTGAACCGATTTTGTTGTCCTTGTT
752695 TCTACTGCTACATTACATGGCTATTAAAAGGCTATTACTAGTGTATGCTGCCTACTTCCCCTTCC
261 TCTACTGCTACATTACATGGCTATTAAAAGGCTATTACTAGTGTATGCTGCCTACTTCCCCTTCC
752760 TTTTAGCATGAGTATGGGTAATTCAGTTTCTGCAGTTAAACTATCGTAACGTACTTATGAATTTT
326 TTTTAGCATGAGTATGGGT-ATTCAGTTTCTGCAGTTAAACTATCGTAACGTACTTATGAATTTT
752825 AAAAGAAAGAAAATGAAAAATGCTGCTATCTAGACAGAAGCCAATACACAGTGGAGTTATTGTGT
390 AAAAGAAAGAAAATGAAAAATGCTGCTATCTAGACAGAAGCCAATACACAGTGGAGTTATTGTGT
752890 AGCTCACATATATTTGTGGAAATGTAACAGGTAGGAT
455 AGCTCACATATATTTGTGGAAATGTAACAGGTAGGAT
752927 A
1 A
752928 TGCTGAGAAA
Statistics
Matches: 490, Mismatches: 1, Indels: 2
0.99 0.00 0.00
Matches are distributed among these distances:
490 162 0.33
491 328 0.67
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.36
Consensus pattern (491 bp):
AACAACCGTATTCTGTACCCTCAATTTTATTGGGTAGAACTTCTGTTAGGTTACCAAGCCTATTG
GGGATTGCCTTGACATATAAACCGAACAGTTGATTTGCTTTTAGGTATATTTGCCCAGTTTTAAT
ACCCTAGTAAAAGGTGGTTGCATATTTCTTCATGGTGGCTTAGTGATCATGCCGCCCTCCCCCTT
TTCTTCTCTTTTCCCTCTTTACGAGAGGTCCTTGGGGTTTGTGAACCGATTTTGTTGTCCTTGTT
TCTACTGCTACATTACATGGCTATTAAAAGGCTATTACTAGTGTATGCTGCCTACTTCCCCTTCC
TTTTAGCATGAGTATGGGTATTCAGTTTCTGCAGTTAAACTATCGTAACGTACTTATGAATTTTA
AAAGAAAGAAAATGAAAAATGCTGCTATCTAGACAGAAGCCAATACACAGTGGAGTTATTGTGTA
GCTCACATATATTTGTGGAAATGTAACAGGTAGGAT
Found at i:755460 original size:12 final size:12
Alignment explanation
Indices: 755428--755467 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
755418 TTCTAAGAAA
755428 TTAAAA-TTA-T
1 TTAAAATTTATT
*
755438 TT-AAATCTATT
1 TTAAAATTTATT
755449 TTAAAATTTATT
1 TTAAAATTTATT
755461 TTAAAAT
1 TTAAAAT
755468 ATGAATTGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
9 3 0.12
10 4 0.16
11 3 0.12
12 15 0.60
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (12 bp):
TTAAAATTTATT
Found at i:755479 original size:22 final size:22
Alignment explanation
Indices: 755454--755975 Score: 760
Period size: 22 Copynumber: 23.7 Consensus size: 22
755444 CTATTTTAAA
*
755454 ATTTATTTTAAAATATGAATTG
1 ATTTATTTTAAAATATGGATTG
755476 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
*
755498 ATTTATTTTAAAATGTGGATTG
1 ATTTATTTTAAAATATGGATTG
*
755520 ATTTATTTTAAAATATGAATTG
1 ATTTATTTTAAAATATGGATTG
755542 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
* ***
755564 ATTTATTTTAAAATATAGAAAA
1 ATTTATTTTAAAATATGGATTG
755586 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
***
755608 ATTTATTTTAAAATATGGAAAA
1 ATTTATTTTAAAATATGGATTG
* *
755630 AATTATTTTAAAATATGGATCG
1 ATTTATTTTAAAATATGGATTG
755652 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
*
755674 ATTTATTTTAAAATATAGATTG
1 ATTTATTTTAAAATATGGATTG
*
755696 ATTTATTTAAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
***
755718 ATTTATTTTAAAATAT-GAAAA
1 ATTTATTTTAAAATATGGATTG
755739 ATTTTATTTTAAAATATGGATTG
1 A-TTTATTTTAAAATATGGATTG
* *
755762 ATTTATTTTAAAAGACGGATTG
1 ATTTATTTTAAAATATGGATTG
*
755784 ATTTATTTTAAAATATGTATTG
1 ATTTATTTTAAAATATGGATTG
*
755806 ATTTATTTTAAAATATGAATTG
1 ATTTATTTTAAAATATGGATTG
755828 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
**
755850 ATTTATTTTAAAATATGGA-AA
1 ATTTATTTTAAAATATGGATTG
755871 ATTTTATTTTAAAATATGGATTG
1 A-TTTATTTTAAAATATGGATTG
* ***
755894 ATTTATTTTAAAATATGAAAAA
1 ATTTATTTTAAAATATGGATTG
*
755916 AATTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
755938 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
755960 ATTTATTTTAAAATAT
1 ATTTATTTTAAAATAT
755976 TTATTATTGT
Statistics
Matches: 443, Mismatches: 53, Indels: 8
0.88 0.11 0.02
Matches are distributed among these distances:
21 4 0.01
22 435 0.98
23 4 0.01
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.48
Consensus pattern (22 bp):
ATTTATTTTAAAATATGGATTG
Found at i:756052 original size:31 final size:31
Alignment explanation
Indices: 755995--756053 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
755985 TAGTTGTATG
* * *
755995 ATTATTTAAATTTTATTATAATAAAACTAAA
1 ATTATTTAAATTTCAGTATAACAAAACTAAA
*
756026 ATTATTTAAATTTCAGTATTACAAAACT
1 ATTATTTAAATTTCAGTATAACAAAACT
756054 CTTTTAAGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.47, C:0.07, G:0.02, T:0.44
Consensus pattern (31 bp):
ATTATTTAAATTTCAGTATAACAAAACTAAA
Found at i:762053 original size:19 final size:19
Alignment explanation
Indices: 762021--762057 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
762011 ATGACCAACA
* *
762021 AAATCGCAATGCGATCTCT
1 AAATCACAACGCGATCTCT
762040 AAATCACAACGCGATCTC
1 AAATCACAACGCGATCTC
762058 CAGTATCGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.35, C:0.30, G:0.14, T:0.22
Consensus pattern (19 bp):
AAATCACAACGCGATCTCT
Found at i:762258 original size:19 final size:19
Alignment explanation
Indices: 762233--762300 Score: 66
Period size: 19 Copynumber: 3.5 Consensus size: 19
762223 TCCAAATTCG
762233 CGTTGCGATTTTTCGAATT
1 CGTTGCGATTTTTCGAATT
* **
762252 TGTTGCGA-TAGTCGAAGTT
1 CGTTGCGATTTTTCGAA-TT
*
762271 CGCGTTGCGATTTTTCAAATT
1 --CGTTGCGATTTTTCGAATT
762292 CGTTGCGAT
1 CGTTGCGAT
762301 AGTCGAAGTT
Statistics
Matches: 38, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
18 6 0.16
19 18 0.47
21 9 0.24
22 5 0.13
ACGTcount: A:0.18, C:0.16, G:0.25, T:0.41
Consensus pattern (19 bp):
CGTTGCGATTTTTCGAATT
Done.