Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009461.1 Hibiscus syriacus cultivar Beakdansim tig00113724_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: 2346588
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 12
Found at i:1207179 original size:7 final size:8
Alignment explanation
Indices: 1207161--1207190 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
1207151 TCTTTCCTTC
1207161 TTTTTGTTT
1 TTTTTG-TT
1207170 TTTTTGTT
1 TTTTTGTT
1207178 TTTTTGTT
1 TTTTTGTT
1207186 TTTTT
1 TTTTT
1207191 TCTTTTATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 15 0.71
9 6 0.29
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (8 bp):
TTTTTGTT
Found at i:1207183 original size:17 final size:17
Alignment explanation
Indices: 1207161--1207196 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
1207151 TCTTTCCTTC
*
1207161 TTTTTGTTTTTTTTGTT
1 TTTTTGTTTTTTTTCTT
1207178 TTTTTGTTTTTTTTCTT
1 TTTTTGTTTTTTTTCTT
1207195 TT
1 TT
1207197 ATTTTCGAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.00, C:0.03, G:0.08, T:0.89
Consensus pattern (17 bp):
TTTTTGTTTTTTTTCTT
Found at i:1207697 original size:29 final size:29
Alignment explanation
Indices: 1207637--1207697 Score: 104
Period size: 29 Copynumber: 2.1 Consensus size: 29
1207627 GAGCTGAAGG
*
1207637 GTCTTGAAACCCTACTTTGAACAGGTTAC
1 GTCTTGAAACCCTACTTTGAACAGGGTAC
*
1207666 GTCTTGAAACCCTACTTTGAACAGGGTGC
1 GTCTTGAAACCCTACTTTGAACAGGGTAC
1207695 GTC
1 GTC
1207698 CTAGGCCGGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.30
Consensus pattern (29 bp):
GTCTTGAAACCCTACTTTGAACAGGGTAC
Found at i:1207864 original size:3 final size:3
Alignment explanation
Indices: 1207856--1207908 Score: 81
Period size: 3 Copynumber: 17.7 Consensus size: 3
1207846 ACAAAATATG
*
1207856 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -ATA TAC
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA
1207901 TAA TAA TA
1 TAA TAA TA
1207909 TTTTTTTAAC
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
2 1 0.02
3 44 0.96
4 1 0.02
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1208447 original size:20 final size:18
Alignment explanation
Indices: 1208405--1208446 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
1208395 ACTTTATATG
1208405 TTATTATATATAATAGTA
1 TTATTATATATAATAGTA
*
1208423 ATATTATATAATAA-A-TA
1 TTATTATAT-ATAATAGTA
1208440 TTATTAT
1 TTATTAT
1208447 TTAAGCTCGA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 8 0.38
18 9 0.43
19 4 0.19
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (18 bp):
TTATTATATATAATAGTA
Found at i:1215861 original size:22 final size:22
Alignment explanation
Indices: 1215827--1215881 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
1215817 CATATCGACA
*
1215827 TTTTGCAAGGATGATAGATTCTC
1 TTTT-CAAAGATGATAGATTCTC
1215850 TTTTCAAAGATGATAGATTCTC
1 TTTTCAAAGATGATAGATTCTC
1215872 TTTTCAAAGA
1 TTTTCAAAGA
1215882 CGAAAGCTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 27 0.87
23 4 0.13
ACGTcount: A:0.31, C:0.13, G:0.16, T:0.40
Consensus pattern (22 bp):
TTTTCAAAGATGATAGATTCTC
Found at i:1216639 original size:99 final size:100
Alignment explanation
Indices: 1216468--1216678 Score: 329
Period size: 99 Copynumber: 2.1 Consensus size: 100
1216458 CACGAATTTG
* * * * *
1216468 TAAATCCT-TCGGGTCATCTGTAAAGCCTCAGGGTAGGATGTTTTTACATGAAAATGAGAAATCC
1 TAAATCCTCTCGGGCCATCTGTAAAACCTCAGAGTAGGATGTTTTCACATGAAAATGAGAAAGCC
1216532 ATTTTCAAAGTTTCTCATTTAATGTTCTAGAAAAT
66 ATTTTCAAAGTTTCTCATTTAATGTTCTAGAAAAT
* * *
1216567 TAAATCCTCT-GGGCCATCTGTAAAACCTCATAGTAGGATGTTTTCGCATGAAAATGAGAAAGCG
1 TAAATCCTCTCGGGCCATCTGTAAAACCTCAGAGTAGGATGTTTTCACATGAAAATGAGAAAGCC
1216631 ATTTTCAAAGTTTCTCATTTAATGTTCTAGAAAAT
66 ATTTTCAAAGTTTCTCATTTAATGTTCTAGAAAAT
1216666 TAAATCCTC-CGGG
1 TAAATCCTCTCGGG
1216679 TTATCCATCA
Statistics
Matches: 102, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
99 101 0.99
100 1 0.01
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34
Consensus pattern (100 bp):
TAAATCCTCTCGGGCCATCTGTAAAACCTCAGAGTAGGATGTTTTCACATGAAAATGAGAAAGCC
ATTTTCAAAGTTTCTCATTTAATGTTCTAGAAAAT
Found at i:1216692 original size:99 final size:99
Alignment explanation
Indices: 1216500--1216780 Score: 312
Period size: 99 Copynumber: 2.7 Consensus size: 99
1216490 AAGCCTCAGG
** * *
1216500 GTAGGATGTTTTTACATGAAAATGAGAAATCCATTTTCAAAGTTTCTCATTTAATGTTCTAGAAA
1 GTAGGATGTTTTCGCATGAAAATGAGAAAGCAATTTTCAAAGTTTCTCATTTAATGTTCTAGAAA
* **
1216565 ATTAAATCCTCTGGGCCATCTGTAAAACCTCAT-A
66 ATTAAATCCTCCGGGCCATCCATAAAACCT-ATGA
*
1216599 GTAGGATGTTTTCGCATGAAAATGAGAAAGCGATTTTCAAAGTTTCTCATTTAATGTTCTAGAAA
1 GTAGGATGTTTTCGCATGAAAATGAGAAAGCAATTTTCAAAGTTTCTCATTTAATGTTCTAGAAA
** * * *
1216664 ATTAAATCCTCCGGGTTATCCATCAAACCTTTGG
66 ATTAAATCCTCCGGGCCATCCATAAAACCTATGA
*
1216698 GTAGGATGTTTACATATGATTTTCGCATGAAAATGAGATAGCAATTTTCAAAGTTTCTCATTTAA
1 GTA-G--G-------ATG-TTTTCGCATGAAAATGAGAAAGCAATTTTCAAAGTTTCTCATTTAA
*
1216763 TGCTCTAGAAAATTAAAT
55 TGTTCTAGAAAATTAAAT
1216781 TTTTTGAAAA
Statistics
Matches: 155, Mismatches: 15, Indels: 13
0.85 0.08 0.07
Matches are distributed among these distances:
98 1 0.01
99 88 0.57
100 1 0.01
102 1 0.01
109 3 0.02
110 61 0.39
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.36
Consensus pattern (99 bp):
GTAGGATGTTTTCGCATGAAAATGAGAAAGCAATTTTCAAAGTTTCTCATTTAATGTTCTAGAAA
ATTAAATCCTCCGGGCCATCCATAAAACCTATGA
Found at i:1217327 original size:55 final size:55
Alignment explanation
Indices: 1217224--1217328 Score: 131
Period size: 55 Copynumber: 1.9 Consensus size: 55
1217214 GTGAAATTAG
* ****
1217224 ATTCTCAGTCTCCACGGAAGAGTAGTGAAATTAGATTTTTTGTCAAAAATCAATC
1 ATTCTCAGTCTCCACGGAAGAGTAGTGAAATCAGATTTTTAAAAAAAAATCAATC
* *
1217279 ATTCTTAGTCTCCACGGAAGAGTAGTGGAA-CAGATTTTTCAAAAAAAAAT
1 ATTCTCAGTCTCCACGGAAGAGTAGTGAAATCAGATTTTT-AAAAAAAAAT
1217329 ATGAGCCTTC
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
54 8 0.19
55 34 0.81
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.30
Consensus pattern (55 bp):
ATTCTCAGTCTCCACGGAAGAGTAGTGAAATCAGATTTTTAAAAAAAAATCAATC
Found at i:1217678 original size:20 final size:18
Alignment explanation
Indices: 1217636--1217677 Score: 61
Period size: 16 Copynumber: 2.4 Consensus size: 18
1217626 ATTATATACG
1217636 TTATTATATATAATAATA
1 TTATTATATATAATAATA
1217654 TTA-T-TATATAATAAATA
1 TTATTATATATAAT-AATA
1217671 TTATTAT
1 TTATTAT
1217678 TTAACCCTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 8 0.38
17 8 0.38
18 4 0.19
19 1 0.05
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
TTATTATATATAATAATA
Found at i:1219424 original size:3 final size:3
Alignment explanation
Indices: 1219418--1219442 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1219408 TAAAAAAAAG
1219418 ACA ACA ACA ACA ACA ACA ACA ACA A
1 ACA ACA ACA ACA ACA ACA ACA ACA A
1219443 AACCCAATTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:1232360 original size:15 final size:15
Alignment explanation
Indices: 1232340--1232370 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1232330 CTACAAATAG
1232340 AATTTTTATATAAAT
1 AATTTTTATATAAAT
*
1232355 AATTTTTATTTAAAT
1 AATTTTTATATAAAT
1232370 A
1 A
1232371 TTTATAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AATTTTTATATAAAT
Found at i:1238052 original size:343 final size:343
Alignment explanation
Indices: 1237422--1238107 Score: 1300
Period size: 343 Copynumber: 2.0 Consensus size: 343
1237412 GAAATCGAGC
1237422 AGGAAGAATCAAAACTAATTTCGGTTTCACCTTTAAAATTCTAAAAATGAGGTACGCGTTTAGAA
1 AGGAAGAATCAAAACTAATTTCGGTTTCACCTTTAAAATTCTAAAAATGAGGTACGCGTTTAGAA
* *
1237487 CCAATTCATTTAGGTACAAAGTGTTGTAAATTGATTTCCACCGAAAGTGGAAAGTGCAAGATTTC
66 CCAATTCATTTAGGTACAAAGCGTTGGAAATTGATTTCCACCGAAAGTGGAAAGTGCAAGATTTC
1237552 AAAAGGTAGGCACTGAATGTGCAAGAAGTCAAGGTGCAATAAATTTTGTTGATTTTTTAAAATGG
131 AAAAGGTAGGCACTGAATGTGCAAGAAGTCAAGGTGCAATAAATTTTGTTGATTTTTTAAAATGG
1237617 GTTAATCACACTTTAGTCATTGCACTTTAGGGTATTTTCAAAGATCAGTCCCTAAGTTTCAACTA
196 GTTAATCACACTTTAGTCATTGCACTTTAGGGTATTTTCAAAGATCAGTCCCTAAGTTTCAACTA
*
1237682 TAAATACCCTAGCTCATTTAGCTTCAAAATCATCCCAAAAATCATTTCTTTCTCCCAATACTAGA
261 TAAATACCCTAGCTCATTTAACTTCAAAATCATCCCAAAAATCATTTCTTTCTCCCAATACTAGA
1237747 GAGCTTTCTTGTGAGTAG
326 GAGCTTTCTTGTGAGTAG
1237765 AGGAAGAATCAAAACTAATTTCGGTTTCACCTTTAAAATTCTAAAAATGAGGTACGCGTTTAGAA
1 AGGAAGAATCAAAACTAATTTCGGTTTCACCTTTAAAATTCTAAAAATGAGGTACGCGTTTAGAA
*
1237830 CCAATTCATTTAGGTACAACGCGTTGGAAATTGATTTCCACCGAAAGTGGAAAGTGCAAGATTTC
66 CCAATTCATTTAGGTACAAAGCGTTGGAAATTGATTTCCACCGAAAGTGGAAAGTGCAAGATTTC
1237895 AAAAGGTAGGCACTGAATGTGCAAGAAGTCAAGGTGCAATAAATTTTGTTGATTTTTTAAAATGG
131 AAAAGGTAGGCACTGAATGTGCAAGAAGTCAAGGTGCAATAAATTTTGTTGATTTTTTAAAATGG
* * * *
1237960 GTTAATCACACTTTAGTCATTGTACTTTAGGGTGTTTTCAAAGATTAGTCCCTAAGTTTTAACTA
196 GTTAATCACACTTTAGTCATTGCACTTTAGGGTATTTTCAAAGATCAGTCCCTAAGTTTCAACTA
1238025 TAAATACCCTAGCTCATTTAACTTCAAAATCATCCCAAAAATCATTTCTTTCTCCCAATACTAGA
261 TAAATACCCTAGCTCATTTAACTTCAAAATCATCCCAAAAATCATTTCTTTCTCCCAATACTAGA
1238090 GAGCTTTCTTGTGAGTAG
326 GAGCTTTCTTGTGAGTAG
1238108 TGAGTGTTTT
Statistics
Matches: 335, Mismatches: 8, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
343 335 1.00
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Consensus pattern (343 bp):
AGGAAGAATCAAAACTAATTTCGGTTTCACCTTTAAAATTCTAAAAATGAGGTACGCGTTTAGAA
CCAATTCATTTAGGTACAAAGCGTTGGAAATTGATTTCCACCGAAAGTGGAAAGTGCAAGATTTC
AAAAGGTAGGCACTGAATGTGCAAGAAGTCAAGGTGCAATAAATTTTGTTGATTTTTTAAAATGG
GTTAATCACACTTTAGTCATTGCACTTTAGGGTATTTTCAAAGATCAGTCCCTAAGTTTCAACTA
TAAATACCCTAGCTCATTTAACTTCAAAATCATCCCAAAAATCATTTCTTTCTCCCAATACTAGA
GAGCTTTCTTGTGAGTAG
Found at i:1238382 original size:16 final size:17
Alignment explanation
Indices: 1238361--1238396 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
1238351 TTACTATTCA
*
1238361 TGTGAATAGT-GAATTT
1 TGTGAATAGTAAAATTT
1238377 TGTGAATAGTAAAATTT
1 TGTGAATAGTAAAATTT
1238394 TGT
1 TGT
1238397 TGGCGATACG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 10 0.56
17 8 0.44
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (17 bp):
TGTGAATAGTAAAATTT
Found at i:1243161 original size:14 final size:14
Alignment explanation
Indices: 1243142--1243175 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1243132 TAACGGAAAG
*
1243142 TAAATTTTGAAAAA
1 TAAATTTCGAAAAA
*
1243156 TAAATTTCGTAAAA
1 TAAATTTCGAAAAA
1243170 TAAATT
1 TAAATT
1243176 ATATTTTATG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.53, C:0.03, G:0.06, T:0.38
Consensus pattern (14 bp):
TAAATTTCGAAAAA
Found at i:1243331 original size:29 final size:29
Alignment explanation
Indices: 1243295--1243371 Score: 70
Period size: 29 Copynumber: 2.7 Consensus size: 29
1243285 CATAAAATAC
1243295 AATA-AATAATATTATTTATTG-AAAAAT
1 AATATAATAATATTATTTATTGTAAAAAT
* * *
1243322 AATAATAATATTATT-TTTAATGTAAGAAT
1 AAT-ATAATAATATTATTTATTGTAAAAAT
* *
1243351 AATTTATTTAATATTATTTAT
1 AATATA-ATAATATTATTTAT
1243372 ATCAATATTA
Statistics
Matches: 38, Mismatches: 7, Indels: 7
0.73 0.13 0.13
Matches are distributed among these distances:
27 3 0.08
28 9 0.24
29 22 0.58
30 4 0.11
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (29 bp):
AATATAATAATATTATTTATTGTAAAAAT
Found at i:1243393 original size:29 final size:30
Alignment explanation
Indices: 1243360--1243419 Score: 79
Period size: 29 Copynumber: 2.0 Consensus size: 30
1243350 TAATTTATTT
*
1243360 AATATTATTTATATCA-ATAT-TAATATTAA
1 AATATTATATATAT-ATATATATAATATTAA
*
1243389 AATATTATATATATATATATATAATTTTAA
1 AATATTATATATATATATATATAATATTAA
1243419 A
1 A
1243420 TAAAAATGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
28 1 0.04
29 17 0.63
30 9 0.33
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (30 bp):
AATATTATATATATATATATATAATATTAA
Found at i:1243483 original size:35 final size:34
Alignment explanation
Indices: 1243435--1243504 Score: 106
Period size: 35 Copynumber: 2.0 Consensus size: 34
1243425 ATGTTAATAT
1243435 TATTATATTTTATTAAAATAA-AATATATAAATTA
1 TATTATATTTTATTAAAATAAGAATA-ATAAATTA
*
1243469 TATTAATATTTTATTAAAATAAGAATAATATATTA
1 TATT-ATATTTTATTAAAATAAGAATAATAAATTA
1243504 T
1 T
1243505 TAACTATATT
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
34 4 0.12
35 25 0.76
36 4 0.12
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (34 bp):
TATTATATTTTATTAAAATAAGAATAATAAATTA
Found at i:1244560 original size:5 final size:5
Alignment explanation
Indices: 1244550--1244604 Score: 67
Period size: 5 Copynumber: 10.8 Consensus size: 5
1244540 GAACCGATAT
* *
1244550 GACCC GACCC GA-CT GACCC GACCC GACCGTT GACCC GACCC GACCC GACCC
1 GACCC GACCC GACCC GACCC GACCC GACC--C GACCC GACCC GACCC GACCC
1244601 GACC
1 GACC
1244605 GTTGACTTCC
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
4 3 0.07
5 36 0.84
7 4 0.09
ACGTcount: A:0.20, C:0.53, G:0.22, T:0.05
Consensus pattern (5 bp):
GACCC
Found at i:1244585 original size:17 final size:15
Alignment explanation
Indices: 1244549--1244604 Score: 78
Period size: 17 Copynumber: 3.7 Consensus size: 15
1244539 CGAACCGATA
1244549 TGACCCGACCCGA-C
1 TGACCCGACCCGACC
1244563 TGACCCGACCCGACC
1 TGACCCGACCCGACC
1244578 GTTGACCCGACCCGACC
1 --TGACCCGACCCGACC
*
1244595 CGACCCGACC
1 TGACCCGACC
1244605 GTTGACTTCC
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
14 13 0.34
15 10 0.26
17 15 0.39
ACGTcount: A:0.20, C:0.52, G:0.21, T:0.07
Consensus pattern (15 bp):
TGACCCGACCCGACC
Found at i:1251596 original size:7 final size:7
Alignment explanation
Indices: 1251584--1251630 Score: 60
Period size: 7 Copynumber: 6.9 Consensus size: 7
1251574 CGACCCGACA
1251584 GTTGACC
1 GTTGACC
1251591 GTTGACC
1 GTTGACC
* *
1251598 ATTGATC
1 GTTGACC
1251605 GTTGACC
1 GTTGACC
*
1251612 GTTGACT
1 GTTGACC
1251619 G-TGACC
1 GTTGACC
1251625 GTTGAC
1 GTTGAC
1251631 TTCCTTTGAC
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
6 5 0.15
7 28 0.85
ACGTcount: A:0.17, C:0.23, G:0.28, T:0.32
Consensus pattern (7 bp):
GTTGACC
Found at i:1251625 original size:13 final size:13
Alignment explanation
Indices: 1251607--1251631 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1251597 CATTGATCGT
1251607 TGACCGTTGACTG
1 TGACCGTTGACTG
1251620 TGACCGTTGACT
1 TGACCGTTGACT
1251632 TCCTTTGACC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.24, G:0.28, T:0.32
Consensus pattern (13 bp):
TGACCGTTGACTG
Found at i:1256199 original size:13 final size:13
Alignment explanation
Indices: 1256181--1256206 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1256171 TAAAAACTTC
1256181 GAATTTTTTTTTT
1 GAATTTTTTTTTT
1256194 GAATTTTTTTTTT
1 GAATTTTTTTTTT
1256207 TTTTTGCAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.08, T:0.77
Consensus pattern (13 bp):
GAATTTTTTTTTT
Found at i:1256571 original size:29 final size:26
Alignment explanation
Indices: 1256528--1256591 Score: 76
Period size: 26 Copynumber: 2.3 Consensus size: 26
1256518 ATTTAATGAT
*
1256528 TAATAT-TTTTATTAAAATGATATTAAAA
1 TAATATATTATATT-AAAT-AT-TTAAAA
1256556 TAATATATTATATTAAATATTTAAAA
1 TAATATATTATATTAAATATTTAAAA
1256582 TAATAATATT
1 TAAT-ATATT
1256592 TTGAGTGTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
26 10 0.30
27 7 0.21
28 10 0.30
29 6 0.18
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (26 bp):
TAATATATTATATTAAATATTTAAAA
Found at i:1256764 original size:14 final size:14
Alignment explanation
Indices: 1256745--1256772 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1256735 CATTAGAAAA
1256745 TAAAAAAAATTATT
1 TAAAAAAAATTATT
1256759 TAAAAAAAATTATT
1 TAAAAAAAATTATT
1256773 ACAGGGAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
TAAAAAAAATTATT
Found at i:1259055 original size:21 final size:21
Alignment explanation
Indices: 1259025--1259266 Score: 171
Period size: 21 Copynumber: 11.6 Consensus size: 21
1259015 GATTTACATA
*
1259025 TTCGCATTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
* *
1259046 TTCGTGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
* ** *
1259067 TTTGCGTTGCGATTTTCCAAA
1 TTCGCGTTGCGATAGTCCAAG
*
1259088 TT--CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
* *
1259107 TTCGCGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
*
1259130 TT--CGTTGCGATAGTCAAAG
1 TTCGCGTTGCGATAGTCCAAG
* *
1259149 TTCGCGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
*
1259172 TT--CGTTGCGATAGTCAAAG
1 TTCGCGTTGCGATAGTCCAAG
* *
1259191 TTCGCGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
*
1259214 TT--CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
* *
1259233 TTCGCATTGCGATTTATTCCAAG
1 TTCGCGTTGCGA--TAGTCCAAG
1259256 TT--CGTTGCGAT
1 TTCGCGTTGCGAT
1259267 TTATTCCAAA
Statistics
Matches: 170, Mismatches: 35, Indels: 34
0.71 0.15 0.14
Matches are distributed among these distances:
19 40 0.24
21 97 0.57
23 33 0.19
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.36
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTCCAAG
Found at i:1259079 original size:42 final size:41
Alignment explanation
Indices: 1259025--1259266 Score: 344
Period size: 42 Copynumber: 5.8 Consensus size: 41
1259015 GATTTACATA
* * *
1259025 TTCGCATTGCGA-TAGTCCAAGTTCGTGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATTATTCCAAATTC--GTTGCGATAGTCGAAG
*
1259067 TTTGCGTTGCGATT-TTCCAAATTCGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATTATTCCAAATTCGTTGCGATAGTCGAAG
*
1259107 TTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCAAAG
1 TTCGCGTTGCGA-TTATTCCAAATTCGTTGCGATAGTCGAAG
*
1259149 TTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCAAAG
1 TTCGCGTTGCGA-TTATTCCAAATTCGTTGCGATAGTCGAAG
1259191 TTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCGAAG
1 TTCGCGTTGCGA-TTATTCCAAATTCGTTGCGATAGTCGAAG
* *
1259233 TTCGCATTGCGATTTATTCCAAGTTCGTTGCGAT
1 TTCGCGTTGCGA-TTATTCCAAATTCGTTGCGAT
1259267 TTATTCCAAA
Statistics
Matches: 188, Mismatches: 9, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
40 27 0.14
41 2 0.01
42 158 0.84
43 1 0.01
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.36
Consensus pattern (41 bp):
TTCGCGTTGCGATTATTCCAAATTCGTTGCGATAGTCGAAG
Found at i:1259922 original size:6 final size:6
Alignment explanation
Indices: 1259911--1259949 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
1259901 TCTCGGTTCG
1259911 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1259950 AATACGTGTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.00, C:0.15, G:0.51, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:1260075 original size:21 final size:21
Alignment explanation
Indices: 1260046--1260258 Score: 135
Period size: 21 Copynumber: 10.3 Consensus size: 21
1260036 ATTTTGGACT
1260046 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAATTTGGAATAA
* * * *
1260067 ATCGGAACGCGAACTTCGACT--
1 ATCGCAA--CGAATTTGGAATAA
1260088 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAATTTGGAATAA
*
1260109 ATCGTAACGAATTTGGAATAA
1 ATCGCAACGAATTTGGAATAA
* * *
1260130 ATCGCAACGCGAACTTCGACT--
1 ATCGCAA--CGAATTTGGAATAA
*
1260151 ATCGCAACGAATTTTG-A-AA
1 ATCGCAACGAATTTGGAATAA
* * *
1260170 ATCGCAACGCGAACTTCGACT--
1 ATCGCAA--CGAATTTGGAATAA
1260191 ATCGCAACGAATTTGG-A-AA
1 ATCGCAACGAATTTGGAATAA
* * *
1260210 ATCGCAAAGCGAACTTCGACT--
1 ATCGC-AA-CGAATTTGGAATAA
1260231 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAATTTGGAATAA
1260252 ATCGCAA
1 ATCGCAA
1260259 TGCAAACTTC
Statistics
Matches: 144, Mismatches: 28, Indels: 40
0.68 0.13 0.19
Matches are distributed among these distances:
19 44 0.31
20 4 0.03
21 78 0.54
23 18 0.12
ACGTcount: A:0.38, C:0.21, G:0.19, T:0.22
Consensus pattern (21 bp):
ATCGCAACGAATTTGGAATAA
Found at i:1260160 original size:42 final size:42
Alignment explanation
Indices: 1260109--1260321 Score: 285
Period size: 40 Copynumber: 5.2 Consensus size: 42
1260099 TTTGGAATAA
*
1260109 ATCGTAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
1 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
*
1260151 ATCGCAACGAATTTTG-A-AAATCGCAACGCGAACTTCGACT
1 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
*
1260191 ATCGCAACGAATTTGG-A-AAATCGCAAAGCGAACTTCGACT
1 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
* *
1260231 ATCGCAACGAATTTGGAATAAATCGCAATGCAAACTTCGACT
1 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
* * * *
1260273 ATCGCAACGCGAACTTCGACT--ATCGCAACGCGAACTTGGACT
1 ATCGCAA--CGAATTTGGAATAAATCGCAACGCGAACTTCGACT
1260315 ATCGCAA
1 ATCGCAA
1260322 TGCGAATATG
Statistics
Matches: 155, Mismatches: 12, Indels: 8
0.89 0.07 0.05
Matches are distributed among these distances:
40 77 0.50
41 2 0.01
42 67 0.43
44 9 0.06
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.22
Consensus pattern (42 bp):
ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
Found at i:1260276 original size:21 final size:21
Alignment explanation
Indices: 1260130--1260327 Score: 192
Period size: 21 Copynumber: 9.6 Consensus size: 21
1260120 TTTGGAATAA
1260130 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
* * **
1260151 ATCGCAA--CGAATTTTGAAA
1 ATCGCAACGCGAACTTCGACT
1260170 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
* * **
1260191 ATCGCAA--CGAATTTGGAAA
1 ATCGCAACGCGAACTTCGACT
*
1260210 ATCGCAAAGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
* * *
1260231 ATCGCAA--CGAATTTGGAAT
1 ATCGCAACGCGAACTTCGACT
* *
1260250 AAATCGCAATGCAAACTTCGACT
1 --ATCGCAACGCGAACTTCGACT
1260273 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
*
1260294 ATCGCAACGCGAACTTGGACT
1 ATCGCAACGCGAACTTCGACT
*
1260315 ATCGCAATGCGAA
1 ATCGCAACGCGAA
1260328 TATGTAAATC
Statistics
Matches: 142, Mismatches: 27, Indels: 16
0.77 0.15 0.09
Matches are distributed among these distances:
19 39 0.27
21 95 0.67
23 8 0.06
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.21
Consensus pattern (21 bp):
ATCGCAACGCGAACTTCGACT
Found at i:1260289 original size:63 final size:61
Alignment explanation
Indices: 1260042--1260302 Score: 260
Period size: 63 Copynumber: 4.2 Consensus size: 61
1260032 TGCGATTTTG
* * *
1260042 GACTATCGCAACGAATTTGGAATAAATCGGAACGCGAACTTCGACTATCGCAACGAATTTG
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTC
* * * *
1260103 GAATAAATCGTAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTT
1 GACT--ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTC
** * * * * * **
1260166 GAAAATCGCAACGCGAACTTCGACT--ATCGCAA--CGAATTTGGAAAATCGCAAAGCGAACTTC
1 GACTATCGCAA--CGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGC-AA-CGAACTTC
* *
1260227 GACTATCGCAACGAATTTGGAATAAATCGCAATGCAAACTTCGACTATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAA--CGAACTTC
1260290 GACTATCGCAACG
1 GACTATCGCAACG
1260303 CGAACTTGGA
Statistics
Matches: 164, Mismatches: 25, Indels: 20
0.78 0.12 0.10
Matches are distributed among these distances:
59 22 0.13
60 2 0.01
61 38 0.23
62 2 0.01
63 100 0.61
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.22
Consensus pattern (61 bp):
GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTC
Found at i:1260365 original size:21 final size:21
Alignment explanation
Indices: 1260336--1260388 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
1260326 AATATGTAAA
*
1260336 TCGCATTGCGATAGTCCAAGT
1 TCGCGTTGCGATAGTCCAAGT
*
1260357 TCGCGTTGCGATAGTCGAAGT
1 TCGCGTTGCGATAGTCCAAGT
*
1260378 TTGCGTTGCGA
1 TCGCGTTGCGA
1260389 ATCTGGAAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.19, C:0.21, G:0.30, T:0.30
Consensus pattern (21 bp):
TCGCGTTGCGATAGTCCAAGT
Found at i:1268655 original size:45 final size:46
Alignment explanation
Indices: 1268569--1268673 Score: 158
Period size: 45 Copynumber: 2.3 Consensus size: 46
1268559 TGCACTCTCC
* * *
1268569 ATGCATCGATGCACTCGGGTTTTAATGAAAACATCGAATGCATTTT
1 ATGCATCGATGCACTCAGGTCTTAATCAAAACATCGAATGCATTTT
* *
1268615 ATGCATCGATGCACTTAGG-CTTATTCAAAACATCGAATGCATTTT
1 ATGCATCGATGCACTCAGGTCTTAATCAAAACATCGAATGCATTTT
1268660 ATGCATCGATGCAC
1 ATGCATCGATGCAC
1268674 ACTTAGTGCA
Statistics
Matches: 54, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
45 37 0.69
46 17 0.31
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.31
Consensus pattern (46 bp):
ATGCATCGATGCACTCAGGTCTTAATCAAAACATCGAATGCATTTT
Found at i:1270490 original size:15 final size:15
Alignment explanation
Indices: 1270452--1270490 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
1270442 CTACATGGAG
1270452 CGATGAAGAAGGTTC
1 CGATGAAGAAGGTTC
*
1270467 CGATAAAGAAGGTTC
1 CGATGAAGAAGGTTC
*
1270482 TGATGAAGA
1 CGATGAAGA
1270491 GGAAAAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.38, C:0.10, G:0.31, T:0.21
Consensus pattern (15 bp):
CGATGAAGAAGGTTC
Found at i:1277197 original size:20 final size:20
Alignment explanation
Indices: 1277168--1277205 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1277158 TTTCAAATGG
1277168 ATGCACCGATGCACCAATCC
1 ATGCACCGATGCACCAATCC
*
1277188 ATGCATCGATGCACCAAT
1 ATGCACCGATGCACCAAT
1277206 GAATAAATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.34, G:0.16, T:0.18
Consensus pattern (20 bp):
ATGCACCGATGCACCAATCC
Found at i:1277364 original size:64 final size:66
Alignment explanation
Indices: 1277216--1277380 Score: 235
Period size: 64 Copynumber: 2.5 Consensus size: 66
1277206 GAATAAATTG
* * * * *
1277216 AACATCGAATGCAGTTTATGCATCGATGCACTCTCTCCATGCATCGATGCACTCTTGGTTTTAAT
1 AACATCGAATGCATTTTATGCATCGATGCA--CACACCATGCATCGATGCACTCTAGGTCTTAAT
*
1277281 GAA
64 CAA
*
1277284 AACATCGAATGCATTTTATGCATCGATGCACACACCATGCATCGATGCACT-TAGG-CTTATTCA
1 AACATCGAATGCATTTTATGCATCGATGCACACACCATGCATCGATGCACTCTAGGTCTTAATCA
1277347 A
66 A
1277348 AACATCGAATGCATTTTATGCATCGATGCACAC
1 AACATCGAATGCATTTTATGCATCGATGCACAC
1277381 TTAGTGCACC
Statistics
Matches: 90, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
64 39 0.43
65 3 0.03
66 19 0.21
68 29 0.32
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.30
Consensus pattern (66 bp):
AACATCGAATGCATTTTATGCATCGATGCACACACCATGCATCGATGCACTCTAGGTCTTAATCA
A
Found at i:1279898 original size:15 final size:14
Alignment explanation
Indices: 1279854--1279898 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 14
1279844 TAATGGTTAT
*
1279854 TTAATTCAAAATAA
1 TTAATTCAAATTAA
1279868 TTAAATTCAAATTTAA
1 TT-AATTCAAA-TTAA
1279884 TTAATTCAGAATTAA
1 TTAATTCA-AATTAA
1279899 AAACCCCAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
14 2 0.07
15 18 0.67
16 7 0.26
ACGTcount: A:0.51, C:0.07, G:0.02, T:0.40
Consensus pattern (14 bp):
TTAATTCAAATTAA
Found at i:1292979 original size:2 final size:2
Alignment explanation
Indices: 1292968--1293002 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
1292958 GCTCTTTGTT
1292968 TC TC -C TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1293003 GTCGATTGGA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
TC
Found at i:1294235 original size:2 final size:2
Alignment explanation
Indices: 1294228--1294260 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1294218 TTTAATCATT
1294228 TA TA TA 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 TA TA TA T
1294261 GTATTTACGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1294598 original size:10 final size:10
Alignment explanation
Indices: 1294572--1294605 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
1294562 TATATCAATT
1294572 TAAACTATAAA
1 TAAA-TATAAA
1294583 -AAATATAAA
1 TAAATATAAA
1294592 TAAATATAAA
1 TAAATATAAA
1294602 TAAA
1 TAAA
1294606 CAATAATTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 6 0.27
10 16 0.73
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (10 bp):
TAAATATAAA
Found at i:1294719 original size:17 final size:17
Alignment explanation
Indices: 1294697--1294744 Score: 60
Period size: 18 Copynumber: 2.8 Consensus size: 17
1294687 AATAATTAAA
1294697 ATAAATTATTAAAAGTT
1 ATAAATTATTAAAAGTT
* *
1294714 ATAAATTATTCGACAGTT
1 ATAAATTATT-AAAAGTT
*
1294732 TTAAATTATTAAA
1 ATAAATTATTAAA
1294745 GGGTAAATTA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
17 11 0.44
18 14 0.56
ACGTcount: A:0.48, C:0.04, G:0.06, T:0.42
Consensus pattern (17 bp):
ATAAATTATTAAAAGTT
Found at i:1295554 original size:15 final size:16
Alignment explanation
Indices: 1295521--1295558 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
1295511 CTCGTTTATC
* *
1295521 AAAATAAAATGAATTA
1 AAAATATAATGAATAA
1295537 AAAATATAAT-AATAA
1 AAAATATAATGAATAA
1295552 AAAATAT
1 AAAATAT
1295559 GTTTTTGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 11 0.55
16 9 0.45
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (16 bp):
AAAATATAATGAATAA
Found at i:1296985 original size:16 final size:18
Alignment explanation
Indices: 1296942--1296977 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1296932 TTAAATATGA
*
1296942 ATTATATTAAAAATTAAT
1 ATTATATAAAAAATTAAT
1296960 ATTATATAAAAAATTAAT
1 ATTATATAAAAAATTAAT
1296978 TTAGTAAATC
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:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
ATTATATAAAAAATTAAT
Found at i:1297116 original size:394 final size:395
Alignment explanation
Indices: 1296617--1297403 Score: 1522
Period size: 394 Copynumber: 2.0 Consensus size: 395
1296607 CTTTCTACAA
1296617 AGGGTGTTAGATCATGAAATATATCTGAATAGATTTCTAACAGGAAAATATATAACAAAAAGGTG
1 AGGGTGTTAGATCATGAAATATATCTGAATAGATTTCTAACAGGAAAATATATAACAAAAAGGTG
* *
1296682 ATTTTTGGGGAAAATCGCCCTAAATTGCATTCTCTATTTGTTATTAAATTACAAATTCATTTATG
66 AATTTTGGGGAAAATCGCCCTAAATTGCATGCTCTATTTGTTATTAAATTACAAATTCATTTATG
1296747 TATTGTATTTCATATTATTTCACACACATACATATATAATAAATTATTGAAATAAATATAATAAA
131 TATTGTATTTCATATTATTTCACACACATACATATATAATAAATTATTGAAATAAATATAATAAA
1296812 TAAATTACATTTCAAACATATATATATATTTTTAAATTATAGTTAATACAATATTT-AAAAAAAT
196 TAAATTACATTTCAAACATATATATATATTTTTAAATTATAGTTAATACAATATTTAAAAAAAAT
1296876 AAGTTTAATAATTTTATATTTTTTAAATTAAATTAATTTTCTATTGTTTTGAATAATTAAATATG
261 AAGTTTAATAATTTTATATTTTTTAAATTAAATTAATTTTCTATTGTTTTGAATAATTAAATATG
1296941 AATTATATTAAAAATTAATATTATATAAAAAATTAATTTAGTAAATCCAAAATTAGGGGTTGACA
326 AATTATATTAAAAATTAATATTATATAAAAAATTAATTTAGTAAATCCAAAATTAGGGGTTGACA
1297006 AAATT
391 AAATT
1297011 AGGGTGTTAGATCATGAAATATATCTGAATAGATTTCTAACAGGAAAATATATAACAAAAAGGTG
1 AGGGTGTTAGATCATGAAATATATCTGAATAGATTTCTAACAGGAAAATATATAACAAAAAGGTG
1297076 AATTTTGGGGAAAATCGCCCTAAATTGCATGCTCTATTTGTTATTAAATTACAAATTCATTTATG
66 AATTTTGGGGAAAATCGCCCTAAATTGCATGCTCTATTTGTTATTAAATTACAAATTCATTTATG
1297141 TATTGTATTTCATATTATTTCACACACATACATATATAATAAATTATTGAAATAAATATAATAAA
131 TATTGTATTTCATATTATTTCACACACATACATATATAATAAATTATTGAAATAAATATAATAAA
*
1297206 TAAATTACATTTCAAACATATCTATATATTTTTAAATTATAGTTAATACAATATTTAAAAAAAAT
196 TAAATTACATTTCAAACATATATATATATTTTTAAATTATAGTTAATACAATATTTAAAAAAAAT
*
1297271 AAGTTTAATAATTTTATATTTTTTAAATTAAATTAATTTTCTATTGTTTTGAATAATTATATATG
261 AAGTTTAATAATTTTATATTTTTTAAATTAAATTAATTTTCTATTGTTTTGAATAATTAAATATG
*
1297336 AATTATATTAAAAATTAATATTATATAAAAAATTCATTTAGTAAATCCAAAATTAGGGGTTGACA
326 AATTATATTAAAAATTAATATTATATAAAAAATTAATTTAGTAAATCCAAAATTAGGGGTTGACA
1297401 AAA
391 AAA
1297404 CTCGACTCGA
Statistics
Matches: 387, Mismatches: 5, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
394 248 0.64
395 139 0.36
ACGTcount: A:0.44, C:0.07, G:0.09, T:0.40
Consensus pattern (395 bp):
AGGGTGTTAGATCATGAAATATATCTGAATAGATTTCTAACAGGAAAATATATAACAAAAAGGTG
AATTTTGGGGAAAATCGCCCTAAATTGCATGCTCTATTTGTTATTAAATTACAAATTCATTTATG
TATTGTATTTCATATTATTTCACACACATACATATATAATAAATTATTGAAATAAATATAATAAA
TAAATTACATTTCAAACATATATATATATTTTTAAATTATAGTTAATACAATATTTAAAAAAAAT
AAGTTTAATAATTTTATATTTTTTAAATTAAATTAATTTTCTATTGTTTTGAATAATTAAATATG
AATTATATTAAAAATTAATATTATATAAAAAATTAATTTAGTAAATCCAAAATTAGGGGTTGACA
AAATT
Found at i:1297984 original size:14 final size:14
Alignment explanation
Indices: 1297965--1297991 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1297955 TTACAATCAT
1297965 TTAAAAAATAATTG
1 TTAAAAAATAATTG
1297979 TTAAAAAATAATT
1 TTAAAAAATAATT
1297992 TAATCTGATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (14 bp):
TTAAAAAATAATTG
Found at i:1306350 original size:105 final size:104
Alignment explanation
Indices: 1306163--1306377 Score: 358
Period size: 105 Copynumber: 2.1 Consensus size: 104
1306153 ATTTTGTTGC
* * * *
1306163 CCAAGAACCAAATAGGTATAGTTTGATAGAAGTAAGTCCCTTAAACTTCTCTTATTGTCAACAAA
1 CCAAGAACAAAATAGGTATAGTTTGATAAAAGTAAGTCCCTTAAACTTCTCTTAGTGTAAACAAA
1306228 AAATGGTTGCTTATGGTGTTGAATAATTATTTTCAATAAT
66 AAATGGTTGCTTATGGTGTTGAATAATTATTTTC-ATAAT
*
1306268 CCAAGAACAAAATAGGTATAGTTTGATAAAAGTAAGTCCTTTAAACTTCTCTTAGTGTAAACAAA
1 CCAAGAACAAAATAGGTATAGTTTGATAAAAGTAAGTCCCTTAAACTTCTCTTAGTGTAAACAAA
* *
1306333 AAATGGTTGCTTGTGGTGTTGAATAGTTATTTTCATAAT
66 AAATGGTTGCTTATGGTGTTGAATAATTATTTTCATAAT
1306372 CCAAGA
1 CCAAGA
1306378 TTAAAACATA
Statistics
Matches: 103, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
104 11 0.11
105 92 0.89
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.34
Consensus pattern (104 bp):
CCAAGAACAAAATAGGTATAGTTTGATAAAAGTAAGTCCCTTAAACTTCTCTTAGTGTAAACAAA
AAATGGTTGCTTATGGTGTTGAATAATTATTTTCATAAT
Found at i:1314496 original size:3 final size:3
Alignment explanation
Indices: 1314488--1314522 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
1314478 AGGTGATCTC
1314488 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1314523 TGACAAAAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1321012 original size:13 final size:13
Alignment explanation
Indices: 1320994--1321020 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1320984 AACTATATGT
1320994 ATATGTTTTCAAA
1 ATATGTTTTCAAA
1321007 ATATGTTTTCAAA
1 ATATGTTTTCAAA
1321020 A
1 A
1321021 CTATATTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.44
Consensus pattern (13 bp):
ATATGTTTTCAAA
Found at i:1321064 original size:111 final size:108
Alignment explanation
Indices: 1320949--1321172 Score: 285
Period size: 111 Copynumber: 2.0 Consensus size: 108
1320939 TCAAAAATTA
* *
1320949 TATATATTATATATGTTTTCAAAAACC-GTTTTAAAAACTATAT-GTATATGTTTTCAAAA-TAT
1 TATATA-T-TATATGTTTTCAAAAACCTCTTTTAAAAA-TATATAGTATATGTTTTCAAAACCAT
* *
1321011 GTTTTCAAAACTATAT-TATATACGTTTTCAAAAACCATTTTTTAAAAAC
63 -TTTTAAAAACTATATAT-TATACGTTTTCAAAAA--ATATTTTAAAAAC
*
1321060 TATATATTATATGTTTTCAAAAACCTTCTTTTAAAAATATATATTATATGTTTTCAAAACCATTT
1 TATATATTATATGTTTTCAAAAACC-TCTTTTAAAAATATATAGTATATGTTTTCAAAACCATTT
* *
1321125 TTAAAAACTATATATTATATGTTTTCAAAAAATATTTTCAAAAC
65 TTAAAAACTATATATTATACGTTTTCAAAAAATATTTTAAAAAC
1321169 TATA
1 TATA
1321173 CCATATATAT
Statistics
Matches: 101, Mismatches: 7, Indels: 12
0.84 0.06 0.10
Matches are distributed among these distances:
109 33 0.33
110 6 0.06
111 59 0.58
112 3 0.03
ACGTcount: A:0.42, C:0.10, G:0.04, T:0.44
Consensus pattern (108 bp):
TATATATTATATGTTTTCAAAAACCTCTTTTAAAAATATATAGTATATGTTTTCAAAACCATTTT
TAAAAACTATATATTATACGTTTTCAAAAAATATTTTAAAAAC
Found at i:1321131 original size:73 final size:73
Alignment explanation
Indices: 1320930--1321182 Score: 293
Period size: 73 Copynumber: 3.4 Consensus size: 73
1320920 AAAACAATAT
* *
1320930 AAAATGTTTTCAAAAATTATATATATTATATATGTTTTCAAAAACC-GTTTTAAAAACTATAT-G
1 AAAATGTTTTC-AAAA--ATATATA-TATATATGTTTTCAAAAACCATTTTTAAAAACTATATAT
1320993 TATATGTTTTCA
62 TATATGTTTTCA
* *
1321005 AAATATGTTTTCAAAACTATAT-TATATACGTTTTCAAAAACCATTTTTTAAAAACTATATATTA
1 AAA-ATGTTTTCAAAAATATATATATATATGTTTTCAAAAACCA-TTTTTAAAAACTATATATTA
1321069 TATGTTTTCA
64 TATGTTTTCA
*
1321079 AAAACCT-TCTTTTAAAAATATATAT-TATATGTTTTC-AAAACCATTTTTAAAAACTATATATT
1 AAAA--TGT-TTTCAAAAATATATATATATATGTTTTCAAAAACCATTTTTAAAAACTATATATT
1321141 ATATGTTTTCAA
63 ATATGTTTTC-A
* * *
1321153 AAAATATTTTCAAAACTATACCATATATAT
1 AAAATGTTTTCAAAAATATA-TATATATAT
1321183 CTTCAAAAAC
Statistics
Matches: 156, Mismatches: 10, Indels: 25
0.82 0.05 0.13
Matches are distributed among these distances:
71 19 0.12
72 12 0.08
73 53 0.34
74 33 0.21
75 30 0.19
76 9 0.06
ACGTcount: A:0.42, C:0.10, G:0.04, T:0.43
Consensus pattern (73 bp):
AAAATGTTTTCAAAAATATATATATATATGTTTTCAAAAACCATTTTTAAAAACTATATATTATA
TGTTTTCA
Found at i:1321137 original size:36 final size:38
Alignment explanation
Indices: 1320949--1321172 Score: 254
Period size: 36 Copynumber: 6.1 Consensus size: 38
1320939 TCAAAAATTA
*
1320949 TATATATTATATATGTTTTCAAAAACC--GTTTTAAAAAC
1 TATATA-T-TATATGTTTTCAAAAACCATATTTTAAAAAC
* * * *
1320987 TATAT-GTATATGTTTTC-AAAA-TATGTTTTCAAAAC
1 TATATATTATATGTTTTCAAAAACCATATTTTAAAAAC
* *
1321022 TATAT-TATATACGTTTTCAAAAACCATTTTTTAAAAAC
1 TATATAT-TATATGTTTTCAAAAACCATATTTTAAAAAC
* *
1321060 TATATATTATATGTTTTCAAAAACCTTCTTTTAAAAA-
1 TATATATTATATGTTTTCAAAAACCATATTTTAAAAAC
1321097 TATATATTATATGTTTTC-AAAACCAT-TTTTAAAAAC
1 TATATATTATATGTTTTCAAAAACCATATTTTAAAAAC
*
1321133 TATATATTATATGTTTTCAAAAA--ATATTTTCAAAAC
1 TATATATTATATGTTTTCAAAAACCATATTTTAAAAAC
1321169 TATA
1 TATA
1321173 CCATATATAT
Statistics
Matches: 164, Mismatches: 13, Indels: 20
0.83 0.07 0.10
Matches are distributed among these distances:
34 4 0.02
35 37 0.23
36 48 0.29
37 26 0.16
38 48 0.29
39 1 0.01
ACGTcount: A:0.42, C:0.10, G:0.04, T:0.44
Consensus pattern (38 bp):
TATATATTATATGTTTTCAAAAACCATATTTTAAAAAC
Found at i:1322849 original size:29 final size:29
Alignment explanation
Indices: 1322788--1322854 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 29
1322778 TTACTCTTTT
* * * * *
1322788 TTCTAATTTTAAGTTTATAATTATATTAT
1 TTCTTATTTTAAATTTAGAATTATAGTAA
*
1322817 TTCTTATTTTAAATTTAGAATTATGGTAA
1 TTCTTATTTTAAATTTAGAATTATAGTAA
1322846 TTCTTATTT
1 TTCTTATTT
1322855 ATATTATGAT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.31, C:0.04, G:0.06, T:0.58
Consensus pattern (29 bp):
TTCTTATTTTAAATTTAGAATTATAGTAA
Found at i:1323236 original size:45 final size:45
Alignment explanation
Indices: 1323172--1323262 Score: 173
Period size: 45 Copynumber: 2.0 Consensus size: 45
1323162 AGAGTGATTC
*
1323172 ATTAACTATTCGATTTCTTGTCAAGTTTCTTAACAAATGGAGTAA
1 ATTAACTATTCGATTTCTTGTCAAGTTTCTTAACAAATGAAGTAA
1323217 ATTAACTATTCGATTTCTTGTCAAGTTTCTTAACAAATGAAGTAA
1 ATTAACTATTCGATTTCTTGTCAAGTTTCTTAACAAATGAAGTAA
1323262 A
1 A
1323263 GTGAACAATT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (45 bp):
ATTAACTATTCGATTTCTTGTCAAGTTTCTTAACAAATGAAGTAA
Found at i:1324023 original size:24 final size:23
Alignment explanation
Indices: 1323977--1324028 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
1323967 TTAGTTCATG
*
1323977 TTTTATTTTAATATTTTTAAATA
1 TTTTAATTTAATATTTTTAAATA
* *
1324000 TTTTAATTTATTATTTGTTTAATA
1 TTTTAATTTAATATTT-TTAAATA
1324024 TTTTA
1 TTTTA
1324029 TATTGTCTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
23 14 0.56
24 11 0.44
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (23 bp):
TTTTAATTTAATATTTTTAAATA
Found at i:1327105 original size:58 final size:58
Alignment explanation
Indices: 1327043--1327158 Score: 205
Period size: 58 Copynumber: 2.0 Consensus size: 58
1327033 AATCATACAT
* *
1327043 CATTTGTGCACTTAATCATGCAATTATAAGGACCAAAAAGTCATGTACCAATAGCAAG
1 CATTTGCGCACTTAATCATGCAATTATAAGGACCAAAAAGTCAAGTACCAATAGCAAG
*
1327101 CATTTGCGCACTTAATCATGCAATTATAAGGACCAAAAAGTCAAGTTCCAATAGCAAG
1 CATTTGCGCACTTAATCATGCAATTATAAGGACCAAAAAGTCAAGTACCAATAGCAAG
1327159 TATACAATTG
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
58 55 1.00
ACGTcount: A:0.40, C:0.20, G:0.16, T:0.25
Consensus pattern (58 bp):
CATTTGCGCACTTAATCATGCAATTATAAGGACCAAAAAGTCAAGTACCAATAGCAAG
Found at i:1329561 original size:17 final size:17
Alignment explanation
Indices: 1329534--1329566 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1329524 TCCTCTTTAG
1329534 AAAAGATCAAT-ACATC
1 AAAAGATCAATCACATC
1329550 AAAAGCATCAATCACAT
1 AAAAG-ATCAATCACAT
1329567 AGATCATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 6 0.40
18 4 0.27
ACGTcount: A:0.55, C:0.21, G:0.06, T:0.18
Consensus pattern (17 bp):
AAAAGATCAATCACATC
Found at i:1329851 original size:73 final size:73
Alignment explanation
Indices: 1329770--1329923 Score: 290
Period size: 73 Copynumber: 2.1 Consensus size: 73
1329760 AAAGGAAATG
* *
1329770 AAGAGAAAGAAAAAGGTTTCATTCATGGGAGAAAGCTTAAGAGAATTTTGGGAGAAAAGATAGAA
1 AAGAGAAAGAAAAAAGTTTCAGTCATGGGAGAAAGCTTAAGAGAATTTTGGGAGAAAAGATAGAA
1329835 TTTGTGAA
66 TTTGTGAA
1329843 AAGAGAAAGAAAAAAGTTTCAGTCATGGGAGAAAGCTTAAGAGAATTTTGGGAGAAAAGATAGAA
1 AAGAGAAAGAAAAAAGTTTCAGTCATGGGAGAAAGCTTAAGAGAATTTTGGGAGAAAAGATAGAA
1329908 TTTGTGAA
66 TTTGTGAA
1329916 AAGAGAAA
1 AAGAGAAA
1329924 ATGAATGGTT
Statistics
Matches: 79, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
73 79 1.00
ACGTcount: A:0.47, C:0.04, G:0.27, T:0.21
Consensus pattern (73 bp):
AAGAGAAAGAAAAAAGTTTCAGTCATGGGAGAAAGCTTAAGAGAATTTTGGGAGAAAAGATAGAA
TTTGTGAA
Found at i:1342432 original size:15 final size:15
Alignment explanation
Indices: 1342412--1342442 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1342402 CACAGACTAC
1342412 TTCATTAATACAACA
1 TTCATTAATACAACA
1342427 TTCATTAATACAACA
1 TTCATTAATACAACA
1342442 T
1 T
1342443 GATAATTTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.45, C:0.19, G:0.00, T:0.35
Consensus pattern (15 bp):
TTCATTAATACAACA
Found at i:1343756 original size:17 final size:17
Alignment explanation
Indices: 1343734--1343770 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
1343724 AAATTGATTC
1343734 CACTATGTTTTTTAAAT
1 CACTATGTTTTTTAAAT
*
1343751 CACTATTTTTTTTAAAT
1 CACTATGTTTTTTAAAT
1343768 CAC
1 CAC
1343771 AAAATAACCG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.30, C:0.16, G:0.03, T:0.51
Consensus pattern (17 bp):
CACTATGTTTTTTAAAT
Found at i:1343792 original size:17 final size:17
Alignment explanation
Indices: 1343770--1343804 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1343760 TTTTAAATCA
*
1343770 CAAAATAACCGAAAGGC
1 CAAAATAAACGAAAGGC
*
1343787 CAAAATAAATGAAAGGC
1 CAAAATAAACGAAAGGC
1343804 C
1 C
1343805 CCTCTACCTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.54, C:0.20, G:0.17, T:0.09
Consensus pattern (17 bp):
CAAAATAAACGAAAGGC
Found at i:1347105 original size:37 final size:37
Alignment explanation
Indices: 1347015--1347119 Score: 158
Period size: 36 Copynumber: 2.9 Consensus size: 37
1347005 ATTAATCTTC
*
1347015 AATAAGAAATACTCAAATTTCTTATGAAACCTTTAAT
1 AATAAAAAATACTCAAATTTCTTATGAAACCTTTAAT
* * * *
1347052 AA-GAAAAATACCCAAATTTCTTATAAAACTTTTAAT
1 AATAAAAAATACTCAAATTTCTTATGAAACCTTTAAT
1347088 AATAAAAAATACTCAAATTTCTTATGAAACCT
1 AATAAAAAATACTCAAATTTCTTATGAAACCT
1347120 AAATTGGTGA
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
36 31 0.53
37 27 0.47
ACGTcount: A:0.49, C:0.14, G:0.04, T:0.33
Consensus pattern (37 bp):
AATAAAAAATACTCAAATTTCTTATGAAACCTTTAAT
Found at i:1349412 original size:16 final size:16
Alignment explanation
Indices: 1349393--1349423 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1349383 TCTTAATTAA
1349393 AGTTAATTTCAGTTTC
1 AGTTAATTTCAGTTTC
*
1349409 AGTTAATTTTAGTTT
1 AGTTAATTTCAGTTT
1349424 GGTTTGTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.26, C:0.06, G:0.13, T:0.55
Consensus pattern (16 bp):
AGTTAATTTCAGTTTC
Found at i:1349471 original size:16 final size:16
Alignment explanation
Indices: 1349452--1349493 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
1349442 ATTACTTTTG
1349452 GTTCAAGTTATTTTAA
1 GTTCAAGTTATTTTAA
* *
1349468 GTTCAAATTATTTTTA
1 GTTCAAGTTATTTTAA
1349484 GTTCAAGTTA
1 GTTCAAGTTA
1349494 CATTTGATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.31, C:0.07, G:0.12, T:0.50
Consensus pattern (16 bp):
GTTCAAGTTATTTTAA
Found at i:1351287 original size:23 final size:26
Alignment explanation
Indices: 1351243--1351292 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 26
1351233 TATTAATGAT
*
1351243 ATAAAATTCTTATATGGATAGATACAA
1 ATAAAATTCTTATA-GGATAGACACAA
1351270 ATAAAATT-TTATA-G-TAGACACAA
1 ATAAAATTCTTATAGGATAGACACAA
1351293 TTAGTAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
23 8 0.36
24 1 0.05
26 5 0.23
27 8 0.36
ACGTcount: A:0.50, C:0.08, G:0.10, T:0.32
Consensus pattern (26 bp):
ATAAAATTCTTATAGGATAGACACAA
Found at i:1351440 original size:23 final size:23
Alignment explanation
Indices: 1351414--1351525 Score: 125
Period size: 23 Copynumber: 4.8 Consensus size: 23
1351404 GGACAAATAT
* *
1351414 ATTTGGTGGATTGGTCAAACTAC
1 ATTTGGTTGATTGGTCAAGCTAC
* *
1351437 ATTTGGTTAATTTTGTCAAGCTAC
1 ATTTGGTTGA-TTGGTCAAGCTAC
*
1351461 ATTTGGTTGATTGGCCAAGCTAC
1 ATTTGGTTGATTGGTCAAGCTAC
* *
1351484 ATTTGGTCGATTGGTCAAGTTAC
1 ATTTGGTTGATTGGTCAAGCTAC
* **
1351507 ATTTGATCAATTGGTCAAG
1 ATTTGGTTGATTGGTCAAG
1351526 TTGTCCATCT
Statistics
Matches: 76, Mismatches: 12, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
23 56 0.74
24 20 0.26
ACGTcount: A:0.25, C:0.13, G:0.23, T:0.38
Consensus pattern (23 bp):
ATTTGGTTGATTGGTCAAGCTAC
Found at i:1357277 original size:11 final size:11
Alignment explanation
Indices: 1357258--1357293 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
1357248 GAAATCTAGA
*
1357258 ATCCTTTCTTC
1 ATCCCTTCTTC
1357269 ATCCCTTCTTC
1 ATCCCTTCTTC
*
1357280 ATCCCTCCTTC
1 ATCCCTTCTTC
1357291 ATC
1 ATC
1357294 TTCTCTACGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.11, C:0.44, G:0.00, T:0.44
Consensus pattern (11 bp):
ATCCCTTCTTC
Found at i:1358379 original size:40 final size:40
Alignment explanation
Indices: 1358335--1358428 Score: 179
Period size: 40 Copynumber: 2.4 Consensus size: 40
1358325 ATGATTCCAC
1358335 GAATACAAGCATATTGTTTATATGGTTTATATGTGTACAT
1 GAATACAAGCATATTGTTTATATGGTTTATATGTGTACAT
*
1358375 GAATACAAGCATATTGTTTATATGGTTTCTATGTGTACAT
1 GAATACAAGCATATTGTTTATATGGTTTATATGTGTACAT
1358415 GAATACAAGCATAT
1 GAATACAAGCATAT
1358429 GTCTACGTGT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 53 1.00
ACGTcount: A:0.34, C:0.10, G:0.17, T:0.39
Consensus pattern (40 bp):
GAATACAAGCATATTGTTTATATGGTTTATATGTGTACAT
Found at i:1358688 original size:23 final size:22
Alignment explanation
Indices: 1358652--1358725 Score: 94
Period size: 23 Copynumber: 3.2 Consensus size: 22
1358642 ATATCGAGGG
* *
1358652 TTCTACGTGGTCCTTCGGGACAA
1 TTCTACG-CGTCCTTCGGGACAT
1358675 TTCTACGCGATCCTTCGGGACAT
1 TTCTACGCG-TCCTTCGGGACAT
*
1358698 TTCTATGCCGTCCTTCGGGACAT
1 TTCTACG-CGTCCTTCGGGACAT
1358721 TTCTA
1 TTCTA
1358726 TGTAGAACTT
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
22 1 0.02
23 43 0.93
24 2 0.04
ACGTcount: A:0.16, C:0.28, G:0.22, T:0.34
Consensus pattern (22 bp):
TTCTACGCGTCCTTCGGGACAT
Found at i:1358726 original size:23 final size:22
Alignment explanation
Indices: 1358661--1358727 Score: 98
Period size: 23 Copynumber: 3.0 Consensus size: 22
1358651 GTTCTACGTG
* *
1358661 GTCCTTCGGGACAATTCTACGC
1 GTCCTTCGGGACATTTCTATGC
1358683 GATCCTTCGGGACATTTCTATGCC
1 G-TCCTTCGGGACATTTCTATG-C
1358707 GTCCTTCGGGACATTTCTATG
1 GTCCTTCGGGACATTTCTATG
1358728 TAGAACTTGG
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
22 1 0.02
23 38 0.93
24 2 0.05
ACGTcount: A:0.16, C:0.28, G:0.22, T:0.33
Consensus pattern (22 bp):
GTCCTTCGGGACATTTCTATGC
Found at i:1358904 original size:2 final size:2
Alignment explanation
Indices: 1358897--1358946 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
1358887 GTTGATAATG
1358897 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
1358939 AT AT AT AT
1 AT AT AT AT
1358947 GCTTTTGTTA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1366693 original size:131 final size:131
Alignment explanation
Indices: 1366459--1366753 Score: 432
Period size: 131 Copynumber: 2.3 Consensus size: 131
1366449 GAGAATAGTA
* * * *
1366459 ATATCTTTTCATTTCTGTTGGAGTAATAAATGATTGATTTAAGGCAGGAGATGTCATTTATTATC
1 ATATCTCTTCATTTCGGTTGGAGTAATAAATGATTGATTAAAGGCAGGAGAGGTCATTTATTATC
* *
1366524 GATTGAAAATAATTCAATACTATCATTTTCATTCGAATCAATATTGAATTTTAAGACGAAATAAT
66 GATCGAAAATAATTCAATACTATCATTTTCAATCGAATCAATATTGAATTTTAAGACGAAATAAT
1366589 G
131 G
* * * * *
1366590 ATATCTCTTCATTTCGGTTGAAGTAATAAAT-ATCTGCTTAAAGGTATGAGAGGTCATTTATTCT
1 ATATCTCTTCATTTCGGTTGGAGTAATAAATGAT-TGATTAAAGGCAGGAGAGGTCATTTATTAT
*
1366654 CGATCGAAAATAATT-AGATATTATCATTTTCAATCGAATCAATATTGAATTTTAAGACGAAATA
65 CGATCGAAAATAATTCA-ATACTATCATTTTCAATCGAATCAATATTGAATTTTAAGACGAAATA
*
1366718 GTG
129 ATG
*
1366721 ATATCTCTTCATTTCGATTGGAGTAATAAATGA
1 ATATCTCTTCATTTCGGTTGGAGTAATAAATGA
1366754 CTAAGGCTAT
Statistics
Matches: 146, Mismatches: 15, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
130 3 0.02
131 142 0.97
132 1 0.01
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.39
Consensus pattern (131 bp):
ATATCTCTTCATTTCGGTTGGAGTAATAAATGATTGATTAAAGGCAGGAGAGGTCATTTATTATC
GATCGAAAATAATTCAATACTATCATTTTCAATCGAATCAATATTGAATTTTAAGACGAAATAAT
G
Found at i:1372179 original size:36 final size:36
Alignment explanation
Indices: 1372139--1372212 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
1372129 ATAACACATT
1372139 TAGTCATGTTGTTTACATATTATCTTAATTTAGTCA
1 TAGTCATGTTGTTTACATATTATCTTAATTTAGTCA
1372175 TAGTCATGTTGTTTACATATTATCTTAATTTAGTCA
1 TAGTCATGTTGTTTACATATTATCTTAATTTAGTCA
1372211 TA
1 TA
1372213 CTTATAATAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.28, C:0.11, G:0.11, T:0.50
Consensus pattern (36 bp):
TAGTCATGTTGTTTACATATTATCTTAATTTAGTCA
Found at i:1372206 original size:17 final size:17
Alignment explanation
Indices: 1372150--1372206 Score: 53
Period size: 17 Copynumber: 3.2 Consensus size: 17
1372140 AGTCATGTTG
1372150 TTTACATATTATCTTAA
1 TTTACATATTATCTTAA
* * *
1372167 TTTAGTCATAGTCATGTT-G
1 TTTA--CATA-TTATCTTAA
1372186 TTTACATATTATCTTAA
1 TTTACATATTATCTTAA
1372203 TTTA
1 TTTA
1372207 GTCATACTTA
Statistics
Matches: 30, Mismatches: 6, Indels: 8
0.68 0.14 0.18
Matches are distributed among these distances:
16 5 0.17
17 12 0.40
19 8 0.27
20 5 0.17
ACGTcount: A:0.30, C:0.11, G:0.07, T:0.53
Consensus pattern (17 bp):
TTTACATATTATCTTAA
Found at i:1372482 original size:2 final size:2
Alignment explanation
Indices: 1372475--1372507 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1372465 ACTTATTTAT
1372475 TA TA TA 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 TA TA TA T
1372508 TTTATATTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1372632 original size:39 final size:38
Alignment explanation
Indices: 1372517--1372648 Score: 100
Period size: 39 Copynumber: 3.6 Consensus size: 38
1372507 TTTTATATTT
*
1372517 ATTTATAA-TTCTCAAAATATTTCAC--TAACATTCTAA
1 ATTTATAATTTCT-TAAATATTTCACATTAACATTCTAA
* ** * * *
1372553 AATCCTAATTTCTTAAAT-TTTGACATCATAACGTTATAA
1 ATTTATAATTTCTTAAATATTTCACAT--TAACATTCTAA
*
1372592 ATTTTTAATTTCTTAAATTATTTCACATTAACATTCTAA
1 ATTTATAATTTCTTAAA-TATTTCACATTAACATTCTAA
1372631 A--T-TAATTT-TTAAATATTT
1 ATTTATAATTTCTTAAATATTT
1372649 ATTTTAACTT
Statistics
Matches: 76, Mismatches: 13, Indels: 16
0.72 0.12 0.15
Matches are distributed among these distances:
34 5 0.07
35 10 0.13
36 15 0.20
37 5 0.07
39 33 0.43
40 1 0.01
41 7 0.09
ACGTcount: A:0.39, C:0.13, G:0.02, T:0.47
Consensus pattern (38 bp):
ATTTATAATTTCTTAAATATTTCACATTAACATTCTAA
Found at i:1372761 original size:2 final size:2
Alignment explanation
Indices: 1372754--1372809 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
1372744 ATGCATGGAT
1372754 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
1372796 TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA
1372810 CATACTTTAC
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1372956 original size:25 final size:24
Alignment explanation
Indices: 1372928--1373027 Score: 75
Period size: 27 Copynumber: 4.1 Consensus size: 24
1372918 ATATAACATA
1372928 ATTTTATATATATTAATTTAAAAAT
1 ATTTTAT-TATATTAATTTAAAAAT
*
1372953 A-TTT-TTATATTAACTTATTAAATAT
1 ATTTTATTATATTAA--T-TTAAAAAT
*
1372978 ATTTTATTATTAATTTAATTTTAAAAT
1 ATTTTATTA-T-A-TTAATTTAAAAAT
*
1373005 ATTTTA-T-T-TTCATTTAAAAAT
1 ATTTTATTATATTAATTTAAAAAT
1373026 AT
1 AT
1373028 ATAATTTGTT
Statistics
Matches: 62, Mismatches: 5, Indels: 20
0.71 0.06 0.23
Matches are distributed among these distances:
21 13 0.21
22 8 0.13
23 1 0.02
24 5 0.08
25 9 0.15
26 4 0.06
27 15 0.24
28 2 0.03
29 1 0.02
30 4 0.06
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (24 bp):
ATTTTATTATATTAATTTAAAAAT
Found at i:1372962 original size:22 final size:23
Alignment explanation
Indices: 1372936--1373029 Score: 84
Period size: 22 Copynumber: 3.9 Consensus size: 23
1372926 TAATTTTATA
1372936 TATATTAATTTAAAAATAT-TTT
1 TATATTAATTTAAAAATATATTT
* *
1372958 TATATTAACTTATTAAATATATTT
1 TATATTAATTTA-AAAATATATTT
1372982 TATTATTAATTTAATTTTAAA-ATATTT
1 TA-TATTAATTTAA----AAATATATTT
* *
1373009 TATTTTCATTTAAAAATATAT
1 TATATTAATTTAAAAATATAT
1373030 AATTTGTTTT
Statistics
Matches: 58, Mismatches: 6, Indels: 15
0.73 0.08 0.19
Matches are distributed among these distances:
22 14 0.24
23 10 0.17
24 5 0.09
25 9 0.16
26 9 0.16
27 8 0.14
28 3 0.05
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (23 bp):
TATATTAATTTAAAAATATATTT
Found at i:1373034 original size:21 final size:21
Alignment explanation
Indices: 1372995--1373034 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1372985 TATTAATTTA
* * *
1372995 ATTTTAAAATATTTTATTTTC
1 ATTTAAAAATATATAATTTTC
1373016 ATTTAAAAATATATAATTT
1 ATTTAAAAATATATAATTT
1373035 GTTTTAGTTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (21 bp):
ATTTAAAAATATATAATTTTC
Found at i:1373216 original size:87 final size:87
Alignment explanation
Indices: 1373096--1373257 Score: 245
Period size: 87 Copynumber: 1.9 Consensus size: 87
1373086 TGACCAAGTA
* *
1373096 TGTGATTATATCAAAATATTTAACTGATGTTAACAACAGTTAACTA-AGAGTGACTACATCTTAA
1 TGTGATTATATCAAAATATTTAACTGATATTAACAACAGTTAACTAGA-AGTGACCACATCTTAA
1373160 TTAAATAAAAATGAACTCAAATG
65 TTAAATAAAAATGAACTCAAATG
* * * * *
1373183 TGTGGTTATGTCAAAATATTTAACTGCTATTAACGACAGTTAACTCGAAGTGACCACATCTTAAT
1 TGTGATTATATCAAAATATTTAACTGATATTAACAACAGTTAACTAGAAGTGACCACATCTTAAT
1373248 TAAATAAAAA
66 TAAATAAAAA
1373258 CGAAAATGAC
Statistics
Matches: 67, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
87 66 0.99
88 1 0.01
ACGTcount: A:0.43, C:0.13, G:0.12, T:0.32
Consensus pattern (87 bp):
TGTGATTATATCAAAATATTTAACTGATATTAACAACAGTTAACTAGAAGTGACCACATCTTAAT
TAAATAAAAATGAACTCAAATG
Found at i:1382443 original size:31 final size:31
Alignment explanation
Indices: 1382401--1382459 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
1382391 AATTTAAAAG
* *
1382401 AGTTTTGCAATACTGAGATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
1382432 AGTTTTACAATACTGAAATTTAAATAAT
1 AGTTTTACAATACTGAAATTTAAATAAT
1382460 CCATACAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.42
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:1382551 original size:26 final size:26
Alignment explanation
Indices: 1382521--1382588 Score: 127
Period size: 26 Copynumber: 2.6 Consensus size: 26
1382511 AAGTATTTAA
*
1382521 AATAAATCAATTCATACAACTACAAT
1 AATAAATCAATCCATACAACTACAAT
1382547 AATAAATCAATCCATACAACTACAAT
1 AATAAATCAATCCATACAACTACAAT
1382573 AATAAATCAATCCATA
1 AATAAATCAATCCATA
1382589 TTTTAAAATA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 41 1.00
ACGTcount: A:0.54, C:0.21, G:0.00, T:0.25
Consensus pattern (26 bp):
AATAAATCAATCCATACAACTACAAT
Found at i:1382629 original size:14 final size:14
Alignment explanation
Indices: 1382612--1382665 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
1382602 CAATCTATAC
1382612 AAATAAATTATTTA
1 AAATAAATTATTTA
*
1382626 AAATAAATCAGTTCATA
1 AAATAAATTA-TT--TA
*
1382643 CTAATAAATTATTTA
1 -AAATAAATTATTTA
1382658 AAATAAAT
1 AAATAAAT
1382666 CAATCCATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
14 16 0.50
15 4 0.12
17 4 0.12
18 8 0.25
ACGTcount: A:0.56, C:0.06, G:0.02, T:0.37
Consensus pattern (14 bp):
AAATAAATTATTTA
Found at i:1382629 original size:32 final size:32
Alignment explanation
Indices: 1382590--1382674 Score: 109
Period size: 32 Copynumber: 2.7 Consensus size: 32
1382580 CAATCCATAT
*
1382590 TTTAAAATAAATCAA-TCTATACAAATAAATTA
1 TTTAAAATAAATCAATTC-ATACAAATAAAGTA
* * *
1382622 TTTAAAATAAATCAGTTCATACTAATAAATTA
1 TTTAAAATAAATCAATTCATACAAATAAAGTA
*
1382654 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATTCATA
1382675 TTTAAAATAA
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
32 46 0.96
33 2 0.04
ACGTcount: A:0.53, C:0.11, G:0.01, T:0.35
Consensus pattern (32 bp):
TTTAAAATAAATCAATTCATACAAATAAAGTA
Found at i:1382678 original size:21 final size:21
Alignment explanation
Indices: 1382652--1382691 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
1382642 ACTAATAAAT
1382652 TATTTAAAATAAATCAATCCA
1 TATTTAAAATAAATCAATCCA
1382673 TATTTAAAATAAATCAATC
1 TATTTAAAATAAATCAATC
1382692 TACTAATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (21 bp):
TATTTAAAATAAATCAATCCA
Found at i:1382764 original size:17 final size:16
Alignment explanation
Indices: 1382748--1382797 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 16
1382738 TAAATCAATC
1382748 CATATTTAAAATAAAT
1 CATATTTAAAATAAAT
*
1382764 CAATATATACAAATAAAT
1 C-ATATTTA-AAATAAAT
1382782 --TATTTAAAATAAAT
1 CATATTTAAAATAAAT
1382796 CA
1 CA
1382798 ATCCATACTA
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
14 8 0.29
15 5 0.18
16 1 0.04
17 6 0.21
18 8 0.29
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.34
Consensus pattern (16 bp):
CATATTTAAAATAAAT
Found at i:1382791 original size:32 final size:32
Alignment explanation
Indices: 1382750--1382989 Score: 161
Period size: 32 Copynumber: 7.4 Consensus size: 32
1382740 AATCAATCCA
*
1382750 TATTTAAAATAAATCAATATATACAAATAAAT
1 TATTTAAAATAAATCAATACATACAAATAAAT
* *
1382782 TATTTAAAATAAATCAATCCATACTAATAAAT
1 TATTTAAAATAAATCAATACATACAAATAAAT
* *
1382814 TATTTAAAATAAATC-ATCCATACAACTACAA-
1 TATTTAAAATAAATCAATACATACAAATA-AAT
* * * **
1382845 TA-AT-AAATCAATCTATATTTTA-AAA-AAAT
1 TATTTAAAATAAATCAATA-CATACAAATAAAT
* * * * * * * *
1382874 CAATCGATACTAATAAATTATTTA-AAATAAATCAAT
1 -TAT--TTA-AAATAAATCA-ATACATACAAATAAAT
*
1382910 CTATTTTAAAATAAATCAATACATACTAATAAAT
1 -TA-TTTAAAATAAATCAATACATACAAATAAAT
* *
1382944 TATTTAAAATAAATCAATCCATACTAATAAAT
1 TATTTAAAATAAATCAATACATACAAATAAAT
1382976 TATTTAAAATAAAT
1 TATTTAAAATAAAT
1382990 TATTTTAAAA
Statistics
Matches: 163, Mismatches: 30, Indels: 30
0.73 0.13 0.13
Matches are distributed among these distances:
28 2 0.01
29 9 0.06
30 6 0.04
31 15 0.09
32 89 0.55
33 6 0.04
34 17 0.10
35 11 0.07
36 7 0.04
37 1 0.01
ACGTcount: A:0.54, C:0.11, G:0.00, T:0.35
Consensus pattern (32 bp):
TATTTAAAATAAATCAATACATACAAATAAAT
Found at i:1382795 original size:162 final size:158
Alignment explanation
Indices: 1382547--1383012 Score: 594
Period size: 162 Copynumber: 2.9 Consensus size: 158
1382537 CAACTACAAT
* *
1382547 AATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATCTATAC
1 AATAAATCAATCCATACAACTACAATTATAAATCAATCCATATTTTAAAATAAATCAATATATAC
* *
1382612 AAATAAATTATTTAAAATAAATCAGTTCATACTAATAAATTATTTAAAATAAATCAATCCATATT
66 AAATAAATTATTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATC-ATCCATATT
1382677 TAAAATAAATCAATCTA-CTAATAAATTATTTAA
130 TAAAATAAATCAATCTATCT-AT--A-T-TTTAA
*
1382710 AATAAATCAATCTATACAACTACAATTATAAATCAATCCATA-TTTAAAATAAATCAATATATAC
1 AATAAATCAATCCATACAACTACAATTATAAATCAATCCATATTTTAAAATAAATCAATATATAC
*
1382774 AAATAAATTATTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCATCCATACAA
66 AAATAAATTATTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCATCCAT--AT
* * * *
1382839 CTACAAT-AATAAATCAATCTATATTTTAA
129 TTAAAATAAATCAATCTATCTATATTTTAA
* * *
1382868 AA-AAATCAATCGATACTAA-TA-AATTATTTAAAATAAATCAATCTATTTTAAAATAAATCAAT
1 AATAAATCAATCCATAC-AACTACAATTA--T-AAATCAATCCA--TATTTTAAAATAAATCAAT
* *
1382930 ACATACTAATAAATTATTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAAT--T--
60 ATATACAAATAAATTATTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCATCC
1382991 AT-TTTAAAATAAATCAATCTAT
125 ATATTTAAAATAAATCAATCTAT
1383013 TTTATAATAA
Statistics
Matches: 272, Mismatches: 20, Indels: 29
0.85 0.06 0.09
Matches are distributed among these distances:
155 5 0.02
156 14 0.05
157 15 0.06
158 12 0.04
159 10 0.04
160 2 0.01
161 8 0.03
162 158 0.58
163 48 0.18
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.34
Consensus pattern (158 bp):
AATAAATCAATCCATACAACTACAATTATAAATCAATCCATATTTTAAAATAAATCAATATATAC
AAATAAATTATTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCATCCATATTT
AAAATAAATCAATCTATCTATATTTTAA
Found at i:1382863 original size:110 final size:110
Alignment explanation
Indices: 1382673--1382910 Score: 383
Period size: 110 Copynumber: 2.2 Consensus size: 110
1382663 AATCAATCCA
* *
1382673 TATTTAAAATAAATCAAT-CTACTAATAAATTATTTAAAATAAATCAATCTATACAACTACAATT
1 TATTTAAAATAAATCAATCCTACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAATA
*
1382737 ATAAATCAATCCATA-TTTAAAATAAATCAATATATACAAATAAAT
66 ATAAATCAATCCATATTTTAAAA-AAATCAATAGATACAAATAAAT
1382782 TATTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATC-ATCCATACAACTACAAT
1 TATTTAAAATAAATCAATCC-TACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAAT
* * *
1382846 AATAAATCAATCTATATTTTAAAAAAATCAATCGATACTAATAAAT
65 AATAAATCAATCCATATTTTAAAAAAATCAATAGATACAAATAAAT
1382892 TATTTAAAATAAATCAATC
1 TATTTAAAATAAATCAATC
1382911 TATTTTAAAA
Statistics
Matches: 120, Mismatches: 6, Indels: 5
0.92 0.05 0.04
Matches are distributed among these distances:
109 18 0.15
110 69 0.57
111 33 0.28
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.34
Consensus pattern (110 bp):
TATTTAAAATAAATCAATCCTACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAATA
ATAAATCAATCCATATTTTAAAAAAATCAATAGATACAAATAAAT
Found at i:1382936 original size:52 final size:52
Alignment explanation
Indices: 1382846--1383022 Score: 199
Period size: 52 Copynumber: 3.5 Consensus size: 52
1382836 CAACTACAAT
1382846 AATAAATCAATCTATATTTTAAAA-AAATCAAT-CGATACTAATAAATTATTTAA
1 AATAAATCAATC--TATTTTAAAATAAATCAATAC-ATACTAATAAATTATTTAA
1382899 AATAAATCAATCTATTTTAAAATAAATCAATACATACTAATAAATTATTTAA
1 AATAAATCAATCTATTTTAAAATAAATCAATACATACTAATAAATTATTTAA
* ** ** *
1382951 AATAAATCAATCCATACT--AATAAAT---TATTTA-AAATAAATTATTTTAA
1 AATAAATCAATCTATTTTAAAATAAATCAATACATACTAATAAATTA-TTTAA
*
1382998 AATAAATCAATCTATTTTATAATAA
1 AATAAATCAATCTATTTTAAAATAA
1383023 TTATTTTATA
Statistics
Matches: 110, Mismatches: 9, Indels: 14
0.83 0.07 0.11
Matches are distributed among these distances:
46 9 0.08
47 24 0.22
49 5 0.05
50 7 0.06
51 10 0.09
52 42 0.38
53 13 0.12
ACGTcount: A:0.53, C:0.09, G:0.01, T:0.37
Consensus pattern (52 bp):
AATAAATCAATCTATTTTAAAATAAATCAATACATACTAATAAATTATTTAA
Found at i:1382998 original size:15 final size:15
Alignment explanation
Indices: 1382969--1383146 Score: 177
Period size: 15 Copynumber: 12.5 Consensus size: 15
1382959 AATCCATACT
1382969 AATAAATTA-TTTAA
1 AATAAATTATTTTAA
1382983 AATAAATTATTTTAA
1 AATAAATTATTTTAA
*
1382998 AATAAATCAATCTATTTTAT
1 AAT--A--AAT-TATTTTAA
*
1383018 AAT-AATTATTTTAT
1 AATAAATTATTTTAA
1383032 AATAAATTATTTT--
1 AATAAATTATTTTAA
1383045 AA-AAA--A--TTAA
1 AATAAATTATTTTAA
*
1383055 AATAAATTATTTTAT
1 AATAAATTATTTTAA
1383070 AATAAATTATTTTAA
1 AATAAATTATTTTAA
1383085 AA-AAA--A--TTAA
1 AATAAATTATTTTAA
*
1383095 AATAAATTATTTTAT
1 AATAAATTATTTTAA
1383110 AATAAATTATTTTAA
1 AATAAATTATTTTAA
1383125 AATAAATTATTTTAA
1 AATAAATTATTTTAA
1383140 AATAAAT
1 AATAAAT
1383147 AACCTTATTA
Statistics
Matches: 140, Mismatches: 5, Indels: 37
0.77 0.03 0.20
Matches are distributed among these distances:
8 2 0.01
10 9 0.06
11 6 0.04
12 4 0.03
13 4 0.03
14 23 0.16
15 78 0.56
17 1 0.01
19 3 0.02
20 10 0.07
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (15 bp):
AATAAATTATTTTAA
Found at i:1383051 original size:130 final size:128
Alignment explanation
Indices: 1382774--1383131 Score: 327
Period size: 130 Copynumber: 2.8 Consensus size: 128
1382764 CAATATATAC
*
1382774 AAATAAATTA-TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATC-ATCCATAC
1 AAATAAATTATTTTAAAATAAATCAATACATACTAATAAATTATTTAAAATAAATCAATCCATAC
* *
1382837 AACTACAA-TA-AT-AAATCAATCTATATTTTAAAA-AAATCAATCGATACTAATAAATTATTTA
66 AA-TA-AATTATTTAAAAT-AA-AT-TATTTTAAAATAAATCAATCGATACTAATAAATTATTT-
1382898 AAAT
125 AAAT
*
1382902 AAATCAATCTATTTTAAAATAAATCAATACATACTAATAAATTATTTAAAATAAATCAATCCATA
1 AAATAAAT-TATTTTAAAATAAATCAATACATACTAATAAATTATTTAAAATAAATCAATCCATA
*
1382967 CTAATAAATTATTTAAAATAAATTATTTTAAAATAAATCAATCTATTTTA-TAAT-AATTATTT-
65 C-AATAAATTATTTAAAATAAATTATTTTAAAATAAATCAATCGA---TACTAATAAATTATTTA
*
1383029 TAT
126 AAT
* ** *
1383032 -AATAAATTATTTTAAAAAATTAAAATAAATTATTTTA-TAATAAATTATTTTAAA-AAA--AAT
1 AAATAAATTATTTT--AAAA-T-AAATCAA-TA-CATACTAATAAATTATTTAAAATAAATCAAT
* *
1383092 ---TAAAATAAATTATTTTATAATAAATTATTTTAAAATAAAT
60 CCATACAATAAATTA-TTTAAAATAAATTATTTTAAAATAAAT
1383132 TATTTTAAAA
Statistics
Matches: 199, Mismatches: 13, Indels: 37
0.80 0.05 0.15
Matches are distributed among these distances:
126 9 0.05
127 28 0.14
128 13 0.07
129 8 0.04
130 65 0.33
131 24 0.12
132 22 0.11
133 26 0.13
134 4 0.02
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (128 bp):
AAATAAATTATTTTAAAATAAATCAATACATACTAATAAATTATTTAAAATAAATCAATCCATAC
AATAAATTATTTAAAATAAATTATTTTAAAATAAATCAATCGATACTAATAAATTATTTAAAT
Found at i:1383058 original size:23 final size:25
Alignment explanation
Indices: 1382979--1383078 Score: 81
Period size: 23 Copynumber: 4.1 Consensus size: 25
1382969 AATAAATTAT
1382979 TTAAAATAAATTA-TTT-T-A-AAA
1 TTAAAATAAATTATTTTATAATAAA
*
1383000 -T-AAATCAATCTATTTTATAATAATTA
1 TTAAAATAAAT-TATTTTATAATAA--A
*
1383026 TTTTATAATAAATTATTTTA-AA-AAA
1 --TTAAAATAAATTATTTTATAATAAA
1383051 TTAAAATAAATTATTTTATAATAAA
1 TTAAAATAAATTATTTTATAATAAA
1383076 TTA
1 TTA
1383079 TTTTAAAAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 22
0.70 0.05 0.25
Matches are distributed among these distances:
19 7 0.11
20 3 0.05
21 3 0.05
22 1 0.02
23 18 0.29
24 4 0.06
25 7 0.11
26 1 0.02
27 2 0.03
28 2 0.03
29 8 0.13
30 6 0.10
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (25 bp):
TTAAAATAAATTATTTTATAATAAA
Found at i:1383100 original size:40 final size:40
Alignment explanation
Indices: 1383021--1383133 Score: 203
Period size: 40 Copynumber: 2.9 Consensus size: 40
1383011 ATTTTATAAT
1383021 AATTATTTTATAATAAATTATTTT--AAAAAATTAAAATA
1 AATTATTTTATAATAAATTATTTTAAAAAAAATTAAAATA
1383059 AATTATTTTATAATAAATTATTTTAAAAAAAATTAAAATA
1 AATTATTTTATAATAAATTATTTTAAAAAAAATTAAAATA
*
1383099 AATTATTTTATAATAAATTATTTTAAAATAAATTA
1 AATTATTTTATAATAAATTATTTTAAAAAAAATTA
1383134 TTTTAAAATA
Statistics
Matches: 72, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
38 24 0.33
40 48 0.67
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (40 bp):
AATTATTTTATAATAAATTATTTTAAAAAAAATTAAAATA
Found at i:1383140 original size:25 final size:26
Alignment explanation
Indices: 1383057--1383140 Score: 64
Period size: 25 Copynumber: 3.2 Consensus size: 26
1383047 AAAATTAAAA
*
1383057 TAAATTATTTTATAATAAATTA-TTT
1 TAAATTATTTTAAAATAAATTACTTT
** ** *
1383082 TAAAAAAAATTAAAATAAATTATTTTAT
1 TAAATTATTTTAAAATAAATTA-CTT-T
1383110 AATAAATTATTTTAAAATAAATTA-TTT
1 --TAAATTATTTTAAAATAAATTACTTT
1383137 TAAA
1 TAAA
1383141 ATAAATAACC
Statistics
Matches: 45, Mismatches: 9, Indels: 10
0.70 0.14 0.16
Matches are distributed among these distances:
25 21 0.47
27 3 0.07
28 3 0.07
30 18 0.40
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (26 bp):
TAAATTATTTTAAAATAAATTACTTT
Found at i:1393604 original size:6 final size:6
Alignment explanation
Indices: 1393593--1393628 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
1393583 AACACTCGTA
1393593 CCTGAG CCTGAG CCTGAG CCTGAG CCTGAG CCTGAG
1 CCTGAG CCTGAG CCTGAG CCTGAG CCTGAG CCTGAG
1393629 AGCTAACTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.17, C:0.33, G:0.33, T:0.17
Consensus pattern (6 bp):
CCTGAG
Found at i:1408126 original size:3 final size:3
Alignment explanation
Indices: 1408118--1408183 Score: 132
Period size: 3 Copynumber: 22.0 Consensus size: 3
1408108 GTGTATGCAA
1408118 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1408166 AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT
1408184 CACTAAGAGA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 63 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1418830 original size:15 final size:15
Alignment explanation
Indices: 1418812--1418886 Score: 71
Period size: 15 Copynumber: 4.7 Consensus size: 15
1418802 AAAAAAGAAC
1418812 AAATAAAAAGATGAA
1 AAATAAAAAGATGAA
1418827 AAATGAAAAA-ATGAA
1 AAAT-AAAAAGATGAA
* *
1418842 AAAGAAAAAAATGAA
1 AAATAAAAAGATGAA
1418857 AAATGAAAAAAGAAATGAA
1 AAAT--AAAAAG--ATGAA
*
1418876 AAAAAAAAAGA
1 AAATAAAAAGA
1418887 AAATGAGGGT
Statistics
Matches: 50, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
14 5 0.10
15 21 0.42
16 5 0.10
17 11 0.22
19 8 0.16
ACGTcount: A:0.77, C:0.00, G:0.13, T:0.09
Consensus pattern (15 bp):
AAATAAAAAGATGAA
Found at i:1418834 original size:7 final size:7
Alignment explanation
Indices: 1418802--1418871 Score: 61
Period size: 7 Copynumber: 9.4 Consensus size: 7
1418792 TTGAAGAAAA
*
1418802 AAAAAAG
1 AAAAATG
*
1418809 AACAAATA
1 AA-AAATG
1418817 AAAAGATG
1 AAAA-ATG
1418825 AAAAATG
1 AAAAATG
1418832 AAAAAATG
1 -AAAAATG
1418840 AAAAA-G
1 AAAAATG
1418846 AAAAAAATG
1 --AAAAATG
1418855 AAAAATG
1 AAAAATG
*
1418862 AAAAAAG
1 AAAAATG
1418869 AAA
1 AAA
1418872 TGAAAAAAAA
Statistics
Matches: 53, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
6 1 0.02
7 28 0.53
8 23 0.43
9 1 0.02
ACGTcount: A:0.77, C:0.01, G:0.13, T:0.09
Consensus pattern (7 bp):
AAAAATG
Found at i:1418874 original size:12 final size:12
Alignment explanation
Indices: 1418832--1418889 Score: 57
Period size: 12 Copynumber: 5.0 Consensus size: 12
1418822 ATGAAAAATG
1418832 AAAAAATGAAAA
1 AAAAAATGAAAA
* *
1418844 AGAAAA--AAAT
1 AAAAAATGAAAA
*
1418854 GAAAAATGAAAA
1 AAAAAATGAAAA
*
1418866 AAGAAATGAAAA
1 AAAAAATGAAAA
*
1418878 AAAAAAAGAAAA
1 AAAAAATGAAAA
1418890 TGAGGGTTTG
Statistics
Matches: 35, Mismatches: 9, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
10 7 0.20
12 28 0.80
ACGTcount: A:0.81, C:0.00, G:0.12, T:0.07
Consensus pattern (12 bp):
AAAAAATGAAAA
Found at i:1418882 original size:30 final size:30
Alignment explanation
Indices: 1418801--1418880 Score: 101
Period size: 30 Copynumber: 2.7 Consensus size: 30
1418791 CTTGAAGAAA
* * *
1418801 AAAAAAAGAACAAATAAAAAGATGAAAAATG
1 AAAAAATGAA-AAAGAAAAAAATGAAAAATG
1418832 AAAAAATGAAAAAGAAAAAAATGAAAAATG
1 AAAAAATGAAAAAGAAAAAAATGAAAAATG
*
1418862 AAAAAA-G-AAATGAAAAAAA
1 AAAAAATGAAAAAGAAAAAAA
1418881 AAAAGAAAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
28 11 0.24
29 1 0.02
30 24 0.53
31 9 0.20
ACGTcount: A:0.78, C:0.01, G:0.12, T:0.09
Consensus pattern (30 bp):
AAAAAATGAAAAAGAAAAAAATGAAAAATG
Found at i:1418889 original size:23 final size:23
Alignment explanation
Indices: 1418799--1418889 Score: 60
Period size: 23 Copynumber: 3.7 Consensus size: 23
1418789 TGCTTGAAGA
* *
1418799 AAAAAAAAAGAACAAATAAAAAGATG
1 AAAAAAAAA-AAGAAA-AAGAA-ATG
1418825 AAAAATGAAAAAATGAAAAAGAAA--
1 AAAAA--AAAAAA-GAAAAAGAAATG
* *
1418849 AAAATGAAAAATGAAAAAAGAAATG
1 AAAA-AAAAAAAG-AAAAAGAAATG
1418874 AAAAAAAAAAAGAAAA
1 AAAAAAAAAAAGAAAA
1418890 TGAGGGTTTG
Statistics
Matches: 52, Mismatches: 6, Indels: 17
0.69 0.08 0.23
Matches are distributed among these distances:
22 1 0.02
23 18 0.35
24 10 0.19
25 4 0.08
26 6 0.12
27 6 0.12
28 7 0.13
ACGTcount: A:0.79, C:0.01, G:0.12, T:0.08
Consensus pattern (23 bp):
AAAAAAAAAAAGAAAAAGAAATG
Found at i:1420548 original size:3 final size:3
Alignment explanation
Indices: 1420533--1420578 Score: 76
Period size: 3 Copynumber: 15.7 Consensus size: 3
1420523 AGTTAAAAAA
*
1420533 TAT TAT TA- AAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1420579 AGTGTATTTA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
2 1 0.03
3 39 0.98
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:1440841 original size:33 final size:33
Alignment explanation
Indices: 1440799--1440861 Score: 126
Period size: 33 Copynumber: 1.9 Consensus size: 33
1440789 AAGTTGATAA
1440799 ATTGGAAATTTCATCTTGGTTGGTGGCCAACTT
1 ATTGGAAATTTCATCTTGGTTGGTGGCCAACTT
1440832 ATTGGAAATTTCATCTTGGTTGGTGGCCAA
1 ATTGGAAATTTCATCTTGGTTGGTGGCCAA
1440862 ACTTTGAACA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.22, C:0.14, G:0.25, T:0.38
Consensus pattern (33 bp):
ATTGGAAATTTCATCTTGGTTGGTGGCCAACTT
Found at i:1441786 original size:36 final size:37
Alignment explanation
Indices: 1441739--1441818 Score: 135
Period size: 37 Copynumber: 2.2 Consensus size: 37
1441729 TTCAAAAAAT
* *
1441739 TAATTTTTTTATTCGATTTG-AATTGATTTTGATTTA
1 TAATTTTTTTATTAGATTTGAAATTGATTTCGATTTA
1441775 TAATTTTTTTATTAGATTTGAAATTGATTTCGATTTA
1 TAATTTTTTTATTAGATTTGAAATTGATTTCGATTTA
1441812 TAATTTT
1 TAATTTT
1441819 ATAAACTCGA
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
36 19 0.46
37 22 0.54
ACGTcount: A:0.28, C:0.03, G:0.10, T:0.60
Consensus pattern (37 bp):
TAATTTTTTTATTAGATTTGAAATTGATTTCGATTTA
Found at i:1442466 original size:3 final size:3
Alignment explanation
Indices: 1442412--1442452 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
1442402 CTGAATGGCA
1442412 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1442453 AGAGAAGTAA
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1442682 original size:16 final size:17
Alignment explanation
Indices: 1442661--1442692 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
1442651 AAAATATATG
1442661 AAATTATTTAA-AAAAT
1 AAATTATTTAATAAAAT
1442677 AAATTATTTAATAAAA
1 AAATTATTTAATAAAA
1442693 CTAACAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
AAATTATTTAATAAAAT
Found at i:1442829 original size:2 final size:2
Alignment explanation
Indices: 1442822--1442934 Score: 184
Period size: 2 Copynumber: 59.5 Consensus size: 2
1442812 AACAATAATT
1442822 TA TA TA TA TA TA TA T- TA TA TA TA TA -A TA TA TA TA TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1442861 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1442901 TA TA TA TA TA T- 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 TA TA TA TA T
1442935 TATTAAATTA
Statistics
Matches: 105, Mismatches: 0, Indels: 12
0.90 0.00 0.10
Matches are distributed among these distances:
1 6 0.06
2 99 0.94
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1442879 original size:53 final size:51
Alignment explanation
Indices: 1442822--1442934 Score: 198
Period size: 51 Copynumber: 2.3 Consensus size: 51
1442812 AACAATAATT
1442822 TATATATATATATAT-TATATATAT-A-AT-ATATATATATATTATATATA
1 TATATATATATATATATATATATATAATATAATATATATATATTATATATA
1442869 TATATATATATATATATATATATATAATATAATATATATATATTATATATA
1 TATATATATATATATATATATATATAATATAATATATATATATTATATATA
1442920 TATATATATATATAT
1 TATATATATATATAT
1442935 TATTAAATTA
Statistics
Matches: 62, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
47 15 0.24
48 9 0.15
49 1 0.02
50 2 0.03
51 35 0.56
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (51 bp):
TATATATATATATATATATATATATAATATAATATATATATATTATATATA
Found at i:1445972 original size:18 final size:18
Alignment explanation
Indices: 1445930--1445974 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
1445920 ACACAGTTGA
*
1445930 AATTGAACCTCAAAATCT
1 AATTGAACCTCAAAATCC
* **
1445948 AACTGAACCTCAACCTCC
1 AATTGAACCTCAAAATCC
1445966 AATTGAACC
1 AATTGAACC
1445975 AAGTGTTGAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.40, C:0.31, G:0.07, T:0.22
Consensus pattern (18 bp):
AATTGAACCTCAAAATCC
Found at i:1445992 original size:36 final size:36
Alignment explanation
Indices: 1445951--1446195 Score: 233
Period size: 36 Copynumber: 6.6 Consensus size: 36
1445941 AAAATCTAAC
*
1445951 TGAACCTCAACCTCCAATTGAACCAAGTGTTGAAAT
1 TGAACCTCAACCTCCAAATGAACCAAGTGTTGAAAT
* * * * * *
1445987 CGAACCTCAACCTTCAACTGAGCCGATTGTTGAAAT
1 TGAACCTCAACCTCCAAATGAACCAAGTGTTGAAAT
* * *
1446023 TGAATCTCAACCTCCAAATGAACCAAGTATTAAAAT
1 TGAACCTCAACCTCCAAATGAACCAAGTGTTGAAAT
* * *
1446059 TGAATCTCAACCTCCAAATGAACCAACTGTTGAAAC
1 TGAACCTCAACCTCCAAATGAACCAAGTGTTGAAAT
* * *
1446095 TGAACCTCCTCAACCTCCAATTGAACCAACG-ATTAAAAT
1 TGAA---CCTCAACCTCCAAATGAACCAA-GTGTTGAAAT
* *
1446134 TGAACCTCAACCACCAAACGAA-CAAGTTGTTGAAAT
1 TGAACCTCAACCTCCAAATGAACCAAG-TGTTGAAAT
*
1446170 TGAACCTCCTCAACCTCCAACTGAAC
1 TGAA---CCTCAACCTCCAAATGAAC
1446196 TAACTAATGA
Statistics
Matches: 166, Mismatches: 33, Indels: 16
0.77 0.15 0.07
Matches are distributed among these distances:
34 1 0.01
35 3 0.02
36 118 0.71
39 44 0.27
ACGTcount: A:0.38, C:0.28, G:0.11, T:0.23
Consensus pattern (36 bp):
TGAACCTCAACCTCCAAATGAACCAAGTGTTGAAAT
Found at i:1446122 original size:75 final size:75
Alignment explanation
Indices: 1445955--1446195 Score: 303
Period size: 75 Copynumber: 3.3 Consensus size: 75
1445945 TCTAACTGAA
* * * * * * *
1445955 CCTCAACCTCCAATTGAACCAAGTGTTGAAATCGAACCTCAACCTTCAACTGAGCCGATTGTTGA
1 CCTCAACCTCCAATTGAACCAAGTATTAAAATTGAACCTCAACCTCCAAATGAACCAATTGTTGA
1446020 AATTGAA--T
66 AATTGAACCT
* * *
1446028 -CTCAACCTCCAAATGAACCAAGTATTAAAATTGAATCTCAACCTCCAAATGAACCAACTGTTGA
1 CCTCAACCTCCAATTGAACCAAGTATTAAAATTGAACCTCAACCTCCAAATGAACCAATTGTTGA
*
1446092 AACTGAACCT
66 AATTGAACCT
* *
1446102 CCTCAACCTCCAATTGAACCAACG-ATTAAAATTGAACCTCAACCACCAAACGAA-CAAGTTGTT
1 CCTCAACCTCCAATTGAACCAA-GTATTAAAATTGAACCTCAACCTCCAAATGAACCAA-TTGTT
1446165 GAAATTGAACCT
64 GAAATTGAACCT
*
1446177 CCTCAACCTCCAACTGAAC
1 CCTCAACCTCCAATTGAAC
1446196 TAACTAATGA
Statistics
Matches: 145, Mismatches: 18, Indels: 8
0.85 0.11 0.05
Matches are distributed among these distances:
72 60 0.41
74 4 0.03
75 80 0.55
76 1 0.01
ACGTcount: A:0.37, C:0.29, G:0.11, T:0.23
Consensus pattern (75 bp):
CCTCAACCTCCAATTGAACCAAGTATTAAAATTGAACCTCAACCTCCAAATGAACCAATTGTTGA
AATTGAACCT
Found at i:1449510 original size:22 final size:22
Alignment explanation
Indices: 1449482--1449531 Score: 100
Period size: 22 Copynumber: 2.3 Consensus size: 22
1449472 ACTAAAGTGG
1449482 GTATCGATACCATAGAAGGGAA
1 GTATCGATACCATAGAAGGGAA
1449504 GTATCGATACCATAGAAGGGAA
1 GTATCGATACCATAGAAGGGAA
1449526 GTATCG
1 GTATCG
1449532 GTACTGGGTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.38, C:0.14, G:0.28, T:0.20
Consensus pattern (22 bp):
GTATCGATACCATAGAAGGGAA
Found at i:1450143 original size:15 final size:15
Alignment explanation
Indices: 1450067--1450146 Score: 54
Period size: 15 Copynumber: 5.3 Consensus size: 15
1450057 TGTAATAGGA
* *
1450067 GAATATGTTATAAGT
1 GAATATGTTCTATGT
* * *
1450082 GAAAAATATTCTAAGT
1 G-AATATGTTCTATGT
* *
1450098 GAAAATG-TCTATAT
1 GAATATGTTCTATGT
* *
1450112 GAATATGTGCTAAGT
1 GAATATGTTCTATGT
*
1450127 GAATGTGTTCTATGT
1 GAATATGTTCTATGT
1450142 GAATA
1 GAATA
1450147 AATTATACTT
Statistics
Matches: 49, Mismatches: 14, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
14 11 0.22
15 26 0.53
16 12 0.24
ACGTcount: A:0.39, C:0.05, G:0.20, T:0.36
Consensus pattern (15 bp):
GAATATGTTCTATGT
Found at i:1450282 original size:24 final size:24
Alignment explanation
Indices: 1450255--1450351 Score: 119
Period size: 24 Copynumber: 4.1 Consensus size: 24
1450245 GGTTCTACGC
1450255 GGTCCTTCGGGACAAATTCTATGT
1 GGTCCTTCGGGACAAATTCTATGT
* * *
1450279 GGTCCTTCGAGACAAATTCTACGC
1 GGTCCTTCGGGACAAATTCTATGT
*
1450303 GGTCCTTCGGGATAAA-TCTATGT
1 GGTCCTTCGGGACAAATTCTATGT
1450326 GG-CACTTCGGTG-CAAATTCTATGT
1 GGTC-CTTCGG-GACAAATTCTATGT
1450350 GG
1 GG
1450352 CAGTGGTAAC
Statistics
Matches: 62, Mismatches: 8, Indels: 6
0.82 0.11 0.08
Matches are distributed among these distances:
22 1 0.02
23 16 0.26
24 45 0.73
ACGTcount: A:0.22, C:0.22, G:0.26, T:0.31
Consensus pattern (24 bp):
GGTCCTTCGGGACAAATTCTATGT
Found at i:1453352 original size:45 final size:45
Alignment explanation
Indices: 1453226--1453450 Score: 382
Period size: 45 Copynumber: 5.0 Consensus size: 45
1453216 GTAAGTATGC
*
1453226 AAATAAGCTTACGAGCTTATGGAAT-AATGGCAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
*
1453270 AAATAAGCTTACAAGCTT-TGGAATAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
1453314 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
*
1453359 AAATAAGCTTACGAGCTTATGGAATAAATGATAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
* *
1453404 AAATAAGCTTACGAGCTTATGAGATTAAATGGTTAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATG-GAATAAATGGTAAGTATATTGGTA
1453450 A
1 A
1453451 GAAATGTTAT
Statistics
Matches: 171, Mismatches: 7, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
43 6 0.04
44 52 0.30
45 91 0.53
46 22 0.13
ACGTcount: A:0.40, C:0.07, G:0.21, T:0.32
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
Found at i:1454106 original size:2 final size:2
Alignment explanation
Indices: 1454099--1454127 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1454089 ACATAAGAGT
1454099 TA 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 TA T
1454128 GTAAAATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1454381 original size:21 final size:21
Alignment explanation
Indices: 1454352--1454396 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
1454342 TGTAAAAAAA
* *
1454352 TGTAGCAGTGCATCGGTACAC
1 TGTAACAGTGCATCGATACAC
1454373 TGTAACAGTGCATCGATACAC
1 TGTAACAGTGCATCGATACAC
1454394 TGT
1 TGT
1454397 TCACGGCAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.27
Consensus pattern (21 bp):
TGTAACAGTGCATCGATACAC
Found at i:1457173 original size:21 final size:21
Alignment explanation
Indices: 1457135--1457178 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
1457125 AGTATAAATT
* * *
1457135 GTGTATCGATTCACTGCTGCA
1 GTGTACCGATGCACTGCTACA
*
1457156 GTGTACCGATGCATTGCTACA
1 GTGTACCGATGCACTGCTACA
1457177 GT
1 GT
1457179 AACTTCAGCT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.20, C:0.23, G:0.25, T:0.32
Consensus pattern (21 bp):
GTGTACCGATGCACTGCTACA
Done.