Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005680.1 Hibiscus syriacus cultivar Beakdansim tig00013285_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: 1821426
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
File 3 of 6
Found at i:528682 original size:41 final size:41
Alignment explanation
Indices: 528605--528682 Score: 102
Period size: 41 Copynumber: 1.9 Consensus size: 41
528595 GCGAATTGGG
* * **
528605 AAAATCGCAATGCGATACTGACTATCGCAATGCGATAATAA
1 AAAATCGCAACGAGATACTGACTATCGCAACACGATAATAA
* *
528646 AAAATCGCAACGAGATACTTACTTTCGCAACACGATA
1 AAAATCGCAACGAGATACTGACTATCGCAACACGATA
528683 CTGACTTTCG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 31 1.00
ACGTcount: A:0.41, C:0.22, G:0.15, T:0.22
Consensus pattern (41 bp):
AAAATCGCAACGAGATACTGACTATCGCAACACGATAATAA
Found at i:530557 original size:18 final size:18
Alignment explanation
Indices: 530531--530575 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
530521 TCCACTTCGG
*
530531 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
* *
530549 GAGCTATCACCTCACCTA
1 GAGCCATCACCTCACCCA
530567 GAGCCATCA
1 GAGCCATCA
530576 TCTGATCGAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.27, C:0.42, G:0.16, T:0.16
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:531071 original size:20 final size:20
Alignment explanation
Indices: 531046--531091 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
531036 TAGTTTACTT
531046 TCGCAACACAAAAATGACTA
1 TCGCAACACAAAAATGACTA
* ** *
531066 TCGCAACGCGGAAATGGCTA
1 TCGCAACACAAAAATGACTA
531086 TCGCAA
1 TCGCAA
531092 TGCGAAATGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.39, C:0.26, G:0.20, T:0.15
Consensus pattern (20 bp):
TCGCAACACAAAAATGACTA
Found at i:531100 original size:19 final size:20
Alignment explanation
Indices: 531057--531112 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
531047 CGCAACACAA
531057 AAATGACTATCGCAACGCGG
1 AAATGACTATCGCAACGCGG
* *
531077 AAATGGCTATCGCAATGC-G
1 AAATGACTATCGCAACGCGG
**
531096 AAATGAAAATCGCAACG
1 AAATGACTATCGCAACG
531113 ACAAAAGCGC
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.39, C:0.21, G:0.23, T:0.16
Consensus pattern (20 bp):
AAATGACTATCGCAACGCGG
Found at i:531123 original size:14 final size:14
Alignment explanation
Indices: 531101--531190 Score: 81
Period size: 14 Copynumber: 5.9 Consensus size: 14
531091 ATGCGAAATG
531101 AAAATCGCAACGAC
1 AAAATCGCAACGAC
* *
531115 AAAAGCGCAACGCGAA
1 AAAATCGCAA--CGAC
531131 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
*
531147 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
531163 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
531179 AAAATCGCAACG
1 AAAATCGCAACG
531191 CGAAACACAA
Statistics
Matches: 62, Mismatches: 6, Indels: 16
0.74 0.07 0.19
Matches are distributed among these distances:
14 29 0.47
16 16 0.26
18 17 0.27
ACGTcount: A:0.48, C:0.26, G:0.19, T:0.08
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:531143 original size:32 final size:32
Alignment explanation
Indices: 531085--531195 Score: 195
Period size: 32 Copynumber: 3.4 Consensus size: 32
531075 GGAAATGGCT
*
531085 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
*
531118 AGCGCAACGCGAAATGAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAATCGCAACGACAAA
531150 ATCGCAACGCGAAATGAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAATCGCAACGACAAA
531182 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
531196 CACAAATCGC
Statistics
Matches: 75, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
32 61 0.81
33 14 0.19
ACGTcount: A:0.47, C:0.24, G:0.20, T:0.09
Consensus pattern (32 bp):
ATCGCAACGCGAAATGAAATCGCAACGACAAA
Found at i:531224 original size:19 final size:19
Alignment explanation
Indices: 531202--531337 Score: 85
Period size: 19 Copynumber: 7.6 Consensus size: 19
531192 GAAACACAAA
*
531202 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
531221 TCGCGTTGCGA-TTT--TG
1 TCGCGTTGCGATTTTCATT
*
531237 T--CGTTGCGA-TTT--TG
1 TCGCGTTGCGATTTTCATT
531251 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* ***
531268 TCGCATTGCGATAGCCATT
1 TCGCGTTGCGATTTTCATT
**
531287 TCCGCGTTGCGATAGTCATT
1 T-CGCGTTGCGATTTTCATT
*
531307 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
531327 TCGTGTTGCGA
1 TCGCGTTGCGA
531338 AAGTAAACTA
Statistics
Matches: 97, Mismatches: 13, Indels: 13
0.79 0.11 0.11
Matches are distributed among these distances:
14 22 0.23
15 3 0.03
16 2 0.02
17 2 0.02
18 3 0.03
19 36 0.37
20 29 0.30
ACGTcount: A:0.13, C:0.20, G:0.24, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:531243 original size:14 final size:14
Alignment explanation
Indices: 531224--531263 Score: 80
Period size: 14 Copynumber: 2.9 Consensus size: 14
531214 TTTCATTTCG
531224 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
531238 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
531252 CGTTGCGATTTT
1 CGTTGCGATTTT
531264 CATTTCGCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.07, C:0.15, G:0.28, T:0.50
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:531298 original size:20 final size:19
Alignment explanation
Indices: 531264--531318 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 19
531254 TTGCGATTTT
*
531264 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
531283 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
531303 CATTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
531319 TTTAAGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 16 0.48
20 17 0.52
ACGTcount: A:0.16, C:0.25, G:0.24, T:0.35
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:533209 original size:14 final size:14
Alignment explanation
Indices: 533190--533225 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
533180 ATTGTTTAAT
533190 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
533204 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
533218 TGATTTGT
1 TGATTTGT
533226 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:533350 original size:14 final size:15
Alignment explanation
Indices: 533331--533398 Score: 50
Period size: 14 Copynumber: 4.2 Consensus size: 15
533321 CGAAATGGCT
533331 ATCGCAA-CGAGAAA
1 ATCGCAAGCGAGAAA
*
533345 ATCGCAATGCGAAATGAA
1 ATCGCAA-GCGAGA--AA
533363 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCG--A-GAAA
533382 ATCGCAA-CGAGAAA
1 ATCGCAAGCGAGAAA
533396 ATC
1 ATC
533399 ACAATGCGAT
Statistics
Matches: 45, Mismatches: 2, Indels: 14
0.74 0.03 0.23
Matches are distributed among these distances:
14 14 0.31
15 1 0.02
16 4 0.09
17 2 0.04
18 13 0.29
19 9 0.20
20 1 0.02
21 1 0.02
ACGTcount: A:0.47, C:0.19, G:0.21, T:0.13
Consensus pattern (15 bp):
ATCGCAAGCGAGAAA
Found at i:533395 original size:19 final size:19
Alignment explanation
Indices: 533341--533388 Score: 89
Period size: 18 Copynumber: 2.6 Consensus size: 19
533331 ATCGCAACGA
533341 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
533360 G-AAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
533378 GAAAATCGCAA
1 GAAAATCGCAA
533389 CGAGAAAATC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
18 18 0.64
19 10 0.36
ACGTcount: A:0.48, C:0.17, G:0.21, T:0.15
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:533972 original size:14 final size:15
Alignment explanation
Indices: 533953--534029 Score: 59
Period size: 14 Copynumber: 4.7 Consensus size: 15
533943 CGAAATGGCT
533953 ATCGCAA-CGAGAAA
1 ATCGCAAGCGAGAAA
*
533967 ATCGCAATGCGAAATGAA
1 ATCGCAA-GCGAGA--AA
533985 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCG--A-GAAA
534004 ATCGCAA-CGAGAAA
1 ATCGCAAGCGAGAAA
534018 ATCGCAATGCGA
1 ATCGCAA-GCGA
534030 TTTTCATTTC
Statistics
Matches: 52, Mismatches: 2, Indels: 16
0.74 0.03 0.23
Matches are distributed among these distances:
14 18 0.35
15 1 0.02
16 7 0.13
17 2 0.04
18 13 0.25
19 9 0.17
20 1 0.02
21 1 0.02
ACGTcount: A:0.45, C:0.19, G:0.22, T:0.13
Consensus pattern (15 bp):
ATCGCAAGCGAGAAA
Found at i:533985 original size:19 final size:19
Alignment explanation
Indices: 533963--534029 Score: 92
Period size: 18 Copynumber: 3.8 Consensus size: 19
533953 ATCGCAACGA
533963 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
533982 G-AAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
534000 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
534014 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
534030 TTTTCATTTC
Statistics
Matches: 44, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
14 11 0.25
15 1 0.02
16 2 0.05
17 2 0.05
18 18 0.41
19 10 0.23
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:534464 original size:14 final size:14
Alignment explanation
Indices: 534445--534480 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
534435 ATTGTTTAAT
534445 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
534459 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
534473 TGATTTGT
1 TGATTTGT
534481 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:534610 original size:14 final size:15
Alignment explanation
Indices: 534591--534667 Score: 59
Period size: 14 Copynumber: 4.7 Consensus size: 15
534581 GCGAATGGCT
534591 ATCGCAA-CGAGAAA
1 ATCGCAAGCGAGAAA
*
534605 ATCGCAATGCGAAATGAA
1 ATCGCAA-GCGAGA--AA
534623 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCG--A-GAAA
534642 ATCGCAA-CGAGAAA
1 ATCGCAAGCGAGAAA
534656 ATCGCAATGCGA
1 ATCGCAA-GCGA
534668 TTTTCATTTC
Statistics
Matches: 52, Mismatches: 2, Indels: 16
0.74 0.03 0.23
Matches are distributed among these distances:
14 18 0.35
15 1 0.02
16 7 0.13
17 2 0.04
18 13 0.25
19 9 0.17
20 1 0.02
21 1 0.02
ACGTcount: A:0.45, C:0.19, G:0.22, T:0.13
Consensus pattern (15 bp):
ATCGCAAGCGAGAAA
Found at i:534645 original size:19 final size:19
Alignment explanation
Indices: 534601--534667 Score: 92
Period size: 18 Copynumber: 3.8 Consensus size: 19
534591 ATCGCAACGA
534601 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
534620 G-AAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
534638 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
534652 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
534668 TTTTCATTTC
Statistics
Matches: 44, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
14 11 0.25
15 1 0.02
16 2 0.05
17 2 0.05
18 18 0.41
19 10 0.23
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:534801 original size:638 final size:639
Alignment explanation
Indices: 532940--534905 Score: 3719
Period size: 638 Copynumber: 3.1 Consensus size: 639
532930 TGGTAAGTCA
*
532940 AATGCAAGTTTTGTTAACATATATACTCCTTTTGGTTTGAAAATGTTTGGTTAAGTACATAGAAT
1 AATGCAAGTTTTGTTAACATATATACTCCTTTTGGTTTGAAAATGTTTGGTTAAGTACCTAGAAT
533005 TCAATAATTTGCTGTTTGTAGGTTTTAGATGTGTAGGAAGTCTTGTTTGAGCAAATGTTTGGTTT
66 TCAATAATTTGCTGTTTGTAGGTTTTAGATGTGTAGGAAGTCTTGTTTGAGCAAATGTTTGGTTT
533070 CTGCAGGTTAATCCTTAAGTGAGCTGCGTGAAATGGATGTACGGGGTCACAAAGTTGTTGATTCT
131 CTGCAGGTTAATCCTTAAGTGAGCTGCGTGAAATGGATGTACGGGGTCACAAAGTTGTTGATTCT
*
533135 TGATTCAATAATTGATGAAGAAATAAGAATTGTTATTATTTTTTGATTGTTTAATTGATTTGTAA
196 TGATTCAATAATTGATGAAGAAATAAGAATTATTATTATTTTTTGATTGTTTAATTGATTTGTAA
533200 AAGATGATTTGTAAATGTTGATTTGTTTAATTGATGTGTACATAA----T-TTGTGTTGAAATGT
261 AAGATGATTTGTAAATGTTGATTTGTTTAATTGATGTGTACATAATTTGTGTTGTGTTGAAATGT
533260 AATAGTTGATTTGTTGATTTTCAATCTGCTTTATGTTGAAGGC-AAACAGACTATCGCAACGCGA
326 AATAGTTGATTTGTTGATTTTCAATCTGCTTTATGTTGAAGGCAAAACAGACTATCGCAACGCGA
533324 AATGGCTATCGCAACGAGAAAATCGCAATGCGAAATGAAATCGCAATGCGAAATGAAAATCGCAA
391 AATGGCTATCGCAACGAGAAAATCGCAATGCGAAATGAAATCGCAATGCGAAATGAAAATCGCAA
*
533389 CGAGAAAATCACAATGCGATTTTCATTTCGCGTTGCGATATTCTCGTTGCGATAACCATTTTCGC
456 CGAGAAAATCGCAATGCGATTTTCATTTCGCGTTGCGATATTCTCGTTGCGATAACCATTTTCGC
533454 GTTGCGATAGTCAAATGAATTAAGTGATGACAACTGAACAGATCATAGCAATGTTC-AACTCAAG
521 GTTGCGATAGTCAAATGAATTAAGTGATGACAACTGAACAGATCATAGCAATGTTCAAACTCAAG
533518 TTACTAATACATGCCTAACTGAAAATGTTAAAAGTGCACACATAAAATACACAT
586 TTACTAATACATGCCTAACTGAAAATGTTAAAAGTGCACACATAAAATACACAT
533572 AATGCAAGTTTTGTTAACATATATACTCCTTTTGGTTTGAAAATGTTTGGTTAAGTACCTAGAAT
1 AATGCAAGTTTTGTTAACATATATACTCCTTTTGGTTTGAAAATGTTTGGTTAAGTACCTAGAAT
533637 TCAATAATTTGCTGTTTGTAGGTTTTAGATGTGTAGGAAGTCTTGTTTGAGCAAATGTTTGGTTT
66 TCAATAATTTGCTGTTTGTAGGTTTTAGATGTGTAGGAAGTCTTGTTTGAGCAAATGTTTGGTTT
533702 CTGCAGGTTAATCCTTAAGTGAGCTGCGTG-AATGGATGTACGGGGTCACAAAGTTGTTGATTCT
131 CTGCAGGTTAATCCTTAAGTGAGCTGCGTGAAATGGATGTACGGGGTCACAAAGTTGTTGATTCT
533766 TGATTCAATAATTGATGAAG-AATAAGAATTATTATTA-TTTTTGATTGTTTAATTGATTTGT--
196 TGATTCAATAATTGATGAAGAAATAAGAATTATTATTATTTTTTGATTGTTTAATTGATTTGTAA
533827 ----TGATTTGTAAATGTTGA-------AATTGATGTGTACATAATTTGTGTTGTGTTGAAATGT
261 AAGATGATTTGTAAATGTTGATTTGTTTAATTGATGTGTACATAATTTGTGTTGTGTTGAAATGT
533881 AATAGTTGATTTGTTGATTTTCAATCTGCTTTATGTTGAAGGCAAAACAGACTATCGCAACGCGA
326 AATAGTTGATTTGTTGATTTTCAATCTGCTTTATGTTGAAGGCAAAACAGACTATCGCAACGCGA
533946 AATGGCTATCGCAACGAGAAAATCGCAATGCGAAATGAAATCGCAATGCGAAATGAAAATCGCAA
391 AATGGCTATCGCAACGAGAAAATCGCAATGCGAAATGAAATCGCAATGCGAAATGAAAATCGCAA
534011 CGAGAAAATCGCAATGCGATTTTCATTTCGCGTTGCGATATTCTCGTTGCGATAACCATTTTCGC
456 CGAGAAAATCGCAATGCGATTTTCATTTCGCGTTGCGATATTCTCGTTGCGATAACCATTTTCGC
534076 GTTGCGATAGTCAAATGAATTAAGTGATGACAACTGAACAGATCATAGCAATGTTCAAACTCAAG
521 GTTGCGATAGTCAAATGAATTAAGTGATGACAACTGAACAGATCATAGCAATGTTCAAACTCAAG
534141 TTACTAATACATGCCTAACTGAAAATGTTAAAAGTGCACACATAAAATACACAT
586 TTACTAATACATGCCTAACTGAAAATGTTAAAAGTGCACACATAAAATACACAT
534195 AATGCAAGTTTTGTTAACATATATACTCCTTTTGGTTTGAAAATGTTTGGTTAAGTACCTAGAAT
1 AATGCAAGTTTTGTTAACATATATACTCCTTTTGGTTTGAAAATGTTTGGTTAAGTACCTAGAAT
534260 TCAATAATTTGCTGTTTGTAGGTTTTAGATGTGTAGGAAGTCTTGTTTGAGCAAATGTTTGGTTT
66 TCAATAATTTGCTGTTTGTAGGTTTTAGATGTGTAGGAAGTCTTGTTTGAGCAAATGTTTGGTTT
534325 CTGCAGGTTAATCCTTAAGTGAGCTGCGTGAAATGGATGTACGGGGTCACAAAGTTGTTGATTCT
131 CTGCAGGTTAATCCTTAAGTGAGCTGCGTGAAATGGATGTACGGGGTCACAAAGTTGTTGATTCT
534390 TGATTCAATAATTGATGAAGAAATAAGAATTATTATTATTTTTTGATTGTTTAATTGATTTGTAA
196 TGATTCAATAATTGATGAAGAAATAAGAATTATTATTATTTTTTGATTGTTTAATTGATTTGTAA
534455 AAGATGATTTGTAAATGTTGATTTGTTTAATTGATGTGTACATAATTTGTGTTGTGTTGAAATGT
261 AAGATGATTTGTAAATGTTGATTTGTTTAATTGATGTGTACATAATTTGTGTTGTGTTGAAATGT
534520 AATAGTTGATTTGTTGATTTTCAATCTGCTTTATGTTGAAGGCAAAACAGACTATCGCAACGCG-
326 AATAGTTGATTTGTTGATTTTCAATCTGCTTTATGTTGAAGGCAAAACAGACTATCGCAACGCGA
534584 AATGGCTATCGCAACGAGAAAATCGCAATGCGAAATGAAATCGCAATGCGAAATGAAAATCGCAA
391 AATGGCTATCGCAACGAGAAAATCGCAATGCGAAATGAAATCGCAATGCGAAATGAAAATCGCAA
534649 CGAGAAAATCGCAATGCGATTTTCATTTCGCGTTGCGATATTCTCGTTGCGATAACCATTTTCGC
456 CGAGAAAATCGCAATGCGATTTTCATTTCGCGTTGCGATATTCTCGTTGCGATAACCATTTTCGC
*
534714 GTTGCGATAGTCAAATGAATTAAGTGATGACAACTGAACAGATCATAACAATGTTCAAACTCAAG
521 GTTGCGATAGTCAAATGAATTAAGTGATGACAACTGAACAGATCATAGCAATGTTCAAACTCAAG
534779 TTACTAATACATGCCTAACTGAAAATGTTAAAAGTGCACACATAAAATACACAT
586 TTACTAATACATGCCTAACTGAAAATGTTAAAAGTGCACACATAAAATACACAT
*
534833 AATGCAAGTTTTGTTAACATATATACTCCTTTTGTTTTGAAAATGTTTGGTTAAGTACCTAGAAT
1 AATGCAAGTTTTGTTAACATATATACTCCTTTTGGTTTGAAAATGTTTGGTTAAGTACCTAGAAT
534898 TCAATAAT
66 TCAATAAT
534906 AATTGTTAAA
Statistics
Matches: 1306, Mismatches: 5, Indels: 40
0.97 0.00 0.03
Matches are distributed among these distances:
616 17 0.01
620 1 0.00
621 57 0.04
622 206 0.16
623 239 0.18
624 54 0.04
625 17 0.01
626 24 0.02
629 24 0.02
630 16 0.01
631 54 0.04
632 176 0.13
638 320 0.25
639 101 0.08
ACGTcount: A:0.32, C:0.13, G:0.20, T:0.35
Consensus pattern (639 bp):
AATGCAAGTTTTGTTAACATATATACTCCTTTTGGTTTGAAAATGTTTGGTTAAGTACCTAGAAT
TCAATAATTTGCTGTTTGTAGGTTTTAGATGTGTAGGAAGTCTTGTTTGAGCAAATGTTTGGTTT
CTGCAGGTTAATCCTTAAGTGAGCTGCGTGAAATGGATGTACGGGGTCACAAAGTTGTTGATTCT
TGATTCAATAATTGATGAAGAAATAAGAATTATTATTATTTTTTGATTGTTTAATTGATTTGTAA
AAGATGATTTGTAAATGTTGATTTGTTTAATTGATGTGTACATAATTTGTGTTGTGTTGAAATGT
AATAGTTGATTTGTTGATTTTCAATCTGCTTTATGTTGAAGGCAAAACAGACTATCGCAACGCGA
AATGGCTATCGCAACGAGAAAATCGCAATGCGAAATGAAATCGCAATGCGAAATGAAAATCGCAA
CGAGAAAATCGCAATGCGATTTTCATTTCGCGTTGCGATATTCTCGTTGCGATAACCATTTTCGC
GTTGCGATAGTCAAATGAATTAAGTGATGACAACTGAACAGATCATAGCAATGTTCAAACTCAAG
TTACTAATACATGCCTAACTGAAAATGTTAAAAGTGCACACATAAAATACACAT
Found at i:535665 original size:19 final size:19
Alignment explanation
Indices: 535643--535740 Score: 90
Period size: 19 Copynumber: 5.7 Consensus size: 19
535633 GGAAATTACT
535643 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
535662 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
535676 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
535695 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
535709 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
535728 ATCGCAACGCGAA
1 ATCGCAATGCGAA
535741 TTTAATTTCG
Statistics
Matches: 62, Mismatches: 7, Indels: 20
0.70 0.08 0.22
Matches are distributed among these distances:
14 19 0.31
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 31 0.50
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.12
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:535685 original size:33 final size:33
Alignment explanation
Indices: 535643--535736 Score: 179
Period size: 33 Copynumber: 2.8 Consensus size: 33
535633 GGAAATTACT
535643 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
535676 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
535709 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
535737 CGAATTTAAT
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 60 1.00
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:535758 original size:19 final size:20
Alignment explanation
Indices: 535736--535778 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
535726 AAATCGCAAC
535736 GCGAATTT-AATTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
* *
535755 GCGATTTTCATTTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
535775 GCGA
1 GCGA
535779 TTCTCTCGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.42
Consensus pattern (20 bp):
GCGAATTTCAATTTCGCGTT
Found at i:535763 original size:14 final size:14
Alignment explanation
Indices: 535764--535797 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
535754 TGCGATTTTC
535764 ATTTTCGCGTTGCG
1 ATTTTCGCGTTGCG
* *
535778 ATTCTCTCGTTGCG
1 ATTTTCGCGTTGCG
535792 ATTTTC
1 ATTTTC
535798 ATTTCGCATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.09, C:0.24, G:0.21, T:0.47
Consensus pattern (14 bp):
ATTTTCGCGTTGCG
Found at i:535938 original size:14 final size:14
Alignment explanation
Indices: 535919--535955 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
535909 CATCAATTAA
535919 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
535933 ACAAATCACCTTTT
1 ACAAATCAACTTTT
535947 ACAAATCAA
1 ACAAATCAA
535956 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:539529 original size:19 final size:19
Alignment explanation
Indices: 539412--539596 Score: 165
Period size: 19 Copynumber: 10.1 Consensus size: 19
539402 TCTTTTGGTT
*
539412 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
539431 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
539451 AGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
539469 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
539485 GAAATGACTATCGCGAC-C
1 GAAATGAAAATCGCAACGC
*
539503 ---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
539518 GAAATGAAAATCGCAACCGT
1 GAAATGAAAATCGCAA-CGC
*
539538 GAAATTAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
539557 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
539576 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
539595 GA
1 GA
539597 TTTTGGTTTC
Statistics
Matches: 136, Mismatches: 17, Indels: 26
0.76 0.09 0.15
Matches are distributed among these distances:
14 19 0.14
15 3 0.02
16 2 0.01
17 1 0.01
18 4 0.03
19 61 0.45
20 44 0.32
21 2 0.01
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:539561 original size:39 final size:38
Alignment explanation
Indices: 539412--539596 Score: 165
Period size: 33 Copynumber: 5.1 Consensus size: 38
539402 TCTTTTGGTT
* *
539412 GAAATGAAAATCGCAACGAGATAATGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGCGA-AATGAAAATCGCAACGC
** *
539451 AGAAATGACTATCGCAA--CG--A-GAGAATCGCAACGC
1 -GAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGC
** * *
539485 GAAATGACTATCGCGAC-C---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGC
* *
539518 GAAATGAAAATCGCAACCGTGAAATTAAAATCGCAACGC
1 GAAATGAAAATCGCAA-CGCGAAATGAAAATCGCAACGC
*
539557 GAAATGAAAATCGCAACGCGAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGC
539595 GA
1 GA
539597 TTTTGGTTTC
Statistics
Matches: 124, Mismatches: 14, Indels: 16
0.81 0.09 0.10
Matches are distributed among these distances:
33 42 0.34
34 16 0.13
35 1 0.01
38 23 0.19
39 28 0.23
40 14 0.11
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.13
Consensus pattern (38 bp):
GAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGC
Found at i:539625 original size:19 final size:19
Alignment explanation
Indices: 539592--539636 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
539582 AAAATCGCAA
*
539592 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGATTTCGCGT
*
539611 TGCGATTTTTATTTCGCGT
1 TGCGATTTTGATTTCGCGT
539630 TGCGATT
1 TGCGATT
539637 ATCTTGTTGC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.09, C:0.16, G:0.27, T:0.49
Consensus pattern (19 bp):
TGCGATTTTGATTTCGCGT
Found at i:540269 original size:20 final size:20
Alignment explanation
Indices: 540184--540277 Score: 80
Period size: 20 Copynumber: 4.7 Consensus size: 20
540174 CGCTAAGTAA
*
540184 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
* * *
540204 ATCGTGTTGCGAAAGTAAGT
1 ATCGCGTTGCGATAGTCAGT
* ** * *
540224 ATCTCGTTGCGATTTTTTATT
1 ATCGCGTTGCGA-TAGTCAGT
*
540245 ATCGCATTGCGATAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
*
540265 ATCGCATTGCGAT
1 ATCGCGTTGCGAT
540278 TTTCCCAATT
Statistics
Matches: 58, Mismatches: 15, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
20 45 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.17, G:0.24, T:0.35
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTCAGT
Found at i:540296 original size:41 final size:41
Alignment explanation
Indices: 540266--540361 Score: 147
Period size: 41 Copynumber: 2.3 Consensus size: 41
540256 ATAGTCAGTA
* * *
540266 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTCACGTAT
* *
540307 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTCACGTAT
540348 TCGCATTGCGAATT
1 TCGCATTGCGAATT
540362 GGGAAAATCG
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.19, C:0.24, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTCACGTAT
Found at i:540310 original size:20 final size:20
Alignment explanation
Indices: 540266--540358 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
540256 ATAGTCAGTA
* **
540266 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
*
540287 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
* **
540307 TCGCATTGCGAATTTCCCAAT
1 TCGCATTGCG-ATTTACTTAT
*
540328 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
540348 TCGCATTGCGA
1 TCGCATTGCGA
540359 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.18, C:0.25, G:0.18, T:0.39
Consensus pattern (20 bp):
TCGCATTGCGATTTACTTAT
Found at i:541721 original size:93 final size:93
Alignment explanation
Indices: 541547--541725 Score: 268
Period size: 93 Copynumber: 1.9 Consensus size: 93
541537 GACCAACCAG
* *
541547 TTCAGTAGGCTGTGGTGTGTTTGCCTGACATCTATCTTTAAGTGTTTTGCTTGTCGATGCTACCA
1 TTCAGTAGGCTGTGGTGTGTTCGCCTGACATCTATCTTTAAGTGTGTTGCTTGTCGATGCTACCA
* ** *
541612 TCTTACGGCTATGCTCTAGTACTCCCAA
66 TCCTACAACTACGCTCTAGTACTCCCAA
* * *
541640 TTCAGTAGGTTGTGGTGTGTTCGCCTGGCATCTATCTTTAAGTGTGTTGCTTGTCGATGCTGCCA
1 TTCAGTAGGCTGTGGTGTGTTCGCCTGACATCTATCTTTAAGTGTGTTGCTTGTCGATGCTACCA
*
541705 TCCTACAACTGCGCTCTAGTA
66 TCCTACAACTACGCTCTAGTA
541726 TTCTTGTGTT
Statistics
Matches: 76, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.16, C:0.22, G:0.23, T:0.38
Consensus pattern (93 bp):
TTCAGTAGGCTGTGGTGTGTTCGCCTGACATCTATCTTTAAGTGTGTTGCTTGTCGATGCTACCA
TCCTACAACTACGCTCTAGTACTCCCAA
Found at i:543251 original size:43 final size:43
Alignment explanation
Indices: 543204--543285 Score: 128
Period size: 43 Copynumber: 1.9 Consensus size: 43
543194 CAATAAGTCA
* * *
543204 AGATCTACAGCGGTGTTTTTGGAACAAACGCCGCAAAAGATAT
1 AGATCTACAGCGGCGTTTTTAGAACAAACACCGCAAAAGATAT
*
543247 AGATCTATAGCGGCGTTTTTAGAACAAACACCGCAAAAG
1 AGATCTACAGCGGCGTTTTTAGAACAAACACCGCAAAAG
543286 TTGATATCTG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 35 1.00
ACGTcount: A:0.37, C:0.20, G:0.22, T:0.22
Consensus pattern (43 bp):
AGATCTACAGCGGCGTTTTTAGAACAAACACCGCAAAAGATAT
Found at i:543317 original size:41 final size:43
Alignment explanation
Indices: 543204--543317 Score: 117
Period size: 43 Copynumber: 2.7 Consensus size: 43
543194 CAATAAGTCA
* * * *
543204 AGATCTACAGCGGTGTTTTTGGAACAAACGCCGCAAAAGATAT
1 AGATCTATAGCAGCGTTTTTGGAACAAACACCGCAAAAGATAT
* *
543247 AGATCTATAGCGGCGTTTTTAGAACAAACACCGCAAAAG-T-T
1 AGATCTATAGCAGCGTTTTTGGAACAAACACCGCAAAAGATAT
* * *
543288 GATATCTGTAG-ATCGTTTTTGGAACAAACA
1 -AGATCTATAGCAGCGTTTTTGGAACAAACA
543318 TTGAAATTAA
Statistics
Matches: 61, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
41 17 0.28
42 9 0.15
43 35 0.57
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.26
Consensus pattern (43 bp):
AGATCTATAGCAGCGTTTTTGGAACAAACACCGCAAAAGATAT
Found at i:550321 original size:2 final size:2
Alignment explanation
Indices: 550314--550342 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
550304 GGTCACGAAA
550314 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 A
550343 GTTAGAATTT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:554681 original size:8 final size:8
Alignment explanation
Indices: 554668--554692 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
554658 ACAAAACAGC
554668 CCCATGAA
1 CCCATGAA
554676 CCCATGAA
1 CCCATGAA
554684 CCCATGAA
1 CCCATGAA
554692 C
1 C
554693 GTGATCCCCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.36, C:0.40, G:0.12, T:0.12
Consensus pattern (8 bp):
CCCATGAA
Found at i:556543 original size:15 final size:15
Alignment explanation
Indices: 556523--556555 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
556513 TGAGACATTA
*
556523 CCCGCCCCGCATCCG
1 CCCGCCCCACATCCG
556538 CCCGCCCCACATCCG
1 CCCGCCCCACATCCG
556553 CCC
1 CCC
556556 ACTAAATATC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.09, C:0.70, G:0.15, T:0.06
Consensus pattern (15 bp):
CCCGCCCCACATCCG
Found at i:558338 original size:2 final size:2
Alignment explanation
Indices: 558331--558380 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
558321 TGGGCAAGAC
558331 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
558373 TA TA TA TA
1 TA TA TA TA
558381 AATTTTATTA
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):
TA
Found at i:558704 original size:20 final size:20
Alignment explanation
Indices: 558665--558705 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
558655 TGAGATAGTC
*
558665 TCTTAATATTTTTCTTTATA
1 TCTTAATATTTTTCTATATA
558685 TCTTAGATATTTTT-TATATA
1 TCTTA-ATATTTTTCTATATA
558705 T
1 T
558706 TTATATTGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.27, C:0.07, G:0.02, T:0.63
Consensus pattern (20 bp):
TCTTAATATTTTTCTATATA
Found at i:559341 original size:16 final size:16
Alignment explanation
Indices: 559320--559353 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
559310 TTTGGTTTGA
559320 AAAAAAACCGATTTTT
1 AAAAAAACCGATTTTT
* *
559336 AAAAAAATCGGTTTTT
1 AAAAAAACCGATTTTT
559352 AA
1 AA
559354 TCAAGTAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.09, G:0.09, T:0.32
Consensus pattern (16 bp):
AAAAAAACCGATTTTT
Found at i:559399 original size:19 final size:20
Alignment explanation
Indices: 559375--559423 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
559365 ATCCAGTCAT
559375 CCGGATTTTTAAA-CCCAAA
1 CCGGATTTTTAAACCCCAAA
*
559394 CCGGATTTTTAAACCCCATA
1 CCGGATTTTTAAACCCCAAA
559414 CCGGATTTTT
1 CCGGATTTTT
559424 TTCCGGATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
19 13 0.46
20 15 0.54
ACGTcount: A:0.29, C:0.27, G:0.12, T:0.33
Consensus pattern (20 bp):
CCGGATTTTTAAACCCCAAA
Found at i:568853 original size:17 final size:18
Alignment explanation
Indices: 568820--568853 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
568810 TCAATTCTGT
*
568820 CTTATTATTTAATTCCAA
1 CTTATCATTTAATTCCAA
568838 CTTATCATTT-ATTCCA
1 CTTATCATTTAATTCCA
568854 GACCTTTCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.29, C:0.21, G:0.00, T:0.50
Consensus pattern (18 bp):
CTTATCATTTAATTCCAA
Found at i:572583 original size:16 final size:17
Alignment explanation
Indices: 572556--572589 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
572546 TTTCACAGGG
*
572556 AAAAAGAGAGAAGAACA
1 AAAAAGAGAGAAAAACA
572573 AAAAAGA-AGAAAAACA
1 AAAAAGAGAGAAAAACA
572589 A
1 A
572590 TCACCCTTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.76, C:0.06, G:0.18, T:0.00
Consensus pattern (17 bp):
AAAAAGAGAGAAAAACA
Found at i:574086 original size:32 final size:34
Alignment explanation
Indices: 574014--574103 Score: 108
Period size: 38 Copynumber: 2.5 Consensus size: 34
574004 CTAGCCAGGT
574014 ATATATATATATATATATTTAAATTAAATATATAA
1 ATAT-TATATATATATATTTAAATTAAATATATAA
* * *
574049 ATATTATATATATTTTTTAATTTAAATTAAATTTATTA
1 ATATTATATATA---TAT-ATTTAAATTAAATATATAA
574087 ATATTATATATATATAT
1 ATATTATATATATATAT
574104 AATTATTATT
Statistics
Matches: 47, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
34 10 0.21
35 6 0.13
37 2 0.04
38 29 0.62
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (34 bp):
ATATTATATATATATATTTAAATTAAATATATAA
Found at i:574227 original size:6 final size:6
Alignment explanation
Indices: 574216--574240 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
574206 AAACGAATTT
574216 TCCCCG TCCCCG TCCCCG TCCCCG T
1 TCCCCG TCCCCG TCCCCG TCCCCG T
574241 TAAGCATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.64, G:0.16, T:0.20
Consensus pattern (6 bp):
TCCCCG
Found at i:584679 original size:401 final size:402
Alignment explanation
Indices: 583895--584699 Score: 1576
Period size: 401 Copynumber: 2.0 Consensus size: 402
583885 GGACATCTAT
*
583895 GGCCTTACAAAAGAAAACACATCTTGAGAAAAAAACATCACCTGTATAAGTAGCTCGGTCTTCAA
1 GGCCTTACAAAAGAAAAAACATCTTGAGAAAAAAACAT--CCTGTATAAGTAGCTCGGTCTTCAA
583960 TCGCCTACTTGCTTCATGCTCGCTGTTCCCTTCACCGCCACGCTGACTTATGATGGCATCAATTT
64 TCGCCTACTTGCTTCATGCTCGCTGTTCCCTTCACCGCCACGCTGACTTATGATGGCATCAATTT
584025 CATCAAGAAATATGGTAGACGGTGCATGGTGCCTAGCTAGGTCGAAAAGTACTTTTATTAGCTTC
129 CATCAAGAAATATGGTAGACGGTGCATGGTGCCTAGCTAGGTCGAAAAGTACTTTTATTAGCTTC
584090 TCAGAATCACCTGAAATGTTATAAACCCCGTTGTTAGATAACTGGGTGATATTTCTAAGAATCAC
194 TCAGAATCACCTGAAATGTTATAAACCCCGTTGTTAGATAACTGGGTGATATTTCTAAGAATCAC
584155 TATAGTGGTGTTCAGACAGGTCCTTCTATTCATATTGACATCATGATCTCCTTTTCTTAGTGGAT
259 TATAGTGGTGTTCAGACAGGTCCTTCTATTCATATTGACATCATGATCTCCTTTTCTTAGTGGAT
584220 TGATGTCGTGATCTTAAATAGCGTATCAAATAATTTGATCAATAATAATTTTTCTTCTGCTGCTA
324 TGATGTCGTGATCTTAAATAGCGTATCAAATAATTTGATCAATAATAATTTTTCTTCTGCTGCTA
584285 AGTAAGAAATTCGG
389 AGTAAGAAATTCGG
584299 GGCCTTACAAAAGAAAAAACATCTTGAGAAAAAAACAT-CTGTATAAGTAGCTCGGTCTTCAATC
1 GGCCTTACAAAAGAAAAAACATCTTGAGAAAAAAACATCCTGTATAAGTAGCTCGGTCTTCAATC
584363 GCCTACTTGCTTCATGCTCGCTGTTCCCTTCACCGCCACGCTGACTTATGATGGCATCAATTTCA
66 GCCTACTTGCTTCATGCTCGCTGTTCCCTTCACCGCCACGCTGACTTATGATGGCATCAATTTCA
584428 TCAAGAAATATGGTAGACGGTGCATGGTGCCTAGCTAGGTCGAAAAGTACTTTTATTAGCTTCTC
131 TCAAGAAATATGGTAGACGGTGCATGGTGCCTAGCTAGGTCGAAAAGTACTTTTATTAGCTTCTC
584493 AGAATCACCTGAAATGTTATAAACCCCGTTGTTAGATAACTGGGTGATATTTCTAAGAATCACTA
196 AGAATCACCTGAAATGTTATAAACCCCGTTGTTAGATAACTGGGTGATATTTCTAAGAATCACTA
584558 TAGTGGTGTTCAGACAGGTCCTTCTATTCATATTGACATCATGATCTCCTTTTCTTAGTGGATTG
261 TAGTGGTGTTCAGACAGGTCCTTCTATTCATATTGACATCATGATCTCCTTTTCTTAGTGGATTG
584623 ATGTCGTGATCTTAAATAGCGTATCAAATAATTTGATCAATAATAATTTTTCTTCTGCTGCTAAG
326 ATGTCGTGATCTTAAATAGCGTATCAAATAATTTGATCAATAATAATTTTTCTTCTGCTGCTAAG
584688 TAAGAAATTCGG
391 TAAGAAATTCGG
584700 ATGGAACAGA
Statistics
Matches: 400, Mismatches: 1, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
401 363 0.91
404 37 0.09
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (402 bp):
GGCCTTACAAAAGAAAAAACATCTTGAGAAAAAAACATCCTGTATAAGTAGCTCGGTCTTCAATC
GCCTACTTGCTTCATGCTCGCTGTTCCCTTCACCGCCACGCTGACTTATGATGGCATCAATTTCA
TCAAGAAATATGGTAGACGGTGCATGGTGCCTAGCTAGGTCGAAAAGTACTTTTATTAGCTTCTC
AGAATCACCTGAAATGTTATAAACCCCGTTGTTAGATAACTGGGTGATATTTCTAAGAATCACTA
TAGTGGTGTTCAGACAGGTCCTTCTATTCATATTGACATCATGATCTCCTTTTCTTAGTGGATTG
ATGTCGTGATCTTAAATAGCGTATCAAATAATTTGATCAATAATAATTTTTCTTCTGCTGCTAAG
TAAGAAATTCGG
Found at i:592105 original size:2 final size:2
Alignment explanation
Indices: 592098--592122 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
592088 ACTTATTCAG
592098 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 A
592123 CCTGCAAGGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:595352 original size:37 final size:37
Alignment explanation
Indices: 595276--595352 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 37
595266 TTTTTATATT
*
595276 TTTAATTTTGTAAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
* * *
595313 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTAT-CAA
595350 TTT
1 TTT
595353 GTAATATTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
36 13 0.37
37 22 0.63
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.47
Consensus pattern (37 bp):
TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
Found at i:595534 original size:20 final size:20
Alignment explanation
Indices: 595498--595535 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
595488 ATCTTATTCC
**
595498 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
595518 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
595536 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:596854 original size:33 final size:33
Alignment explanation
Indices: 596817--596880 Score: 119
Period size: 33 Copynumber: 1.9 Consensus size: 33
596807 AGGTCCCTGA
596817 GCCATGACAATAAGCTCAGATTTCATTCCACGT
1 GCCATGACAATAAGCTCAGATTTCATTCCACGT
*
596850 GCCATGACAATAAGCTCATATTTCATTCCAC
1 GCCATGACAATAAGCTCAGATTTCATTCCAC
596881 ACACACCCCA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.31, C:0.28, G:0.12, T:0.28
Consensus pattern (33 bp):
GCCATGACAATAAGCTCAGATTTCATTCCACGT
Found at i:601249 original size:26 final size:26
Alignment explanation
Indices: 601220--601272 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
601210 TAATATCAAA
601220 TATATTTTTATTTTATTAATTTAGGG
1 TATATTTTTATTTTATTAATTTAGGG
601246 TATATTTTTATTTTATTAATTTAGGG
1 TATATTTTTATTTTATTAATTTAGGG
601272 T
1 T
601273 GAAAATGATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.26, C:0.00, G:0.11, T:0.62
Consensus pattern (26 bp):
TATATTTTTATTTTATTAATTTAGGG
Found at i:601688 original size:17 final size:16
Alignment explanation
Indices: 601657--601687 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
601647 AATATTGAAA
*
601657 CTTGAATTCAAAAAAG
1 CTTGAACTCAAAAAAG
601673 CTTGAACTCAAAAAA
1 CTTGAACTCAAAAAA
601688 AAATTAGAAA
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:0.52, C:0.16, G:0.10, T:0.23
Consensus pattern (16 bp):
CTTGAACTCAAAAAAG
Found at i:602514 original size:16 final size:16
Alignment explanation
Indices: 602493--602525 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
602483 TAATAAATAA
602493 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
602509 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
602525 A
1 A
602526 AATTTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.24, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:602605 original size:10 final size:10
Alignment explanation
Indices: 602590--602664 Score: 52
Period size: 10 Copynumber: 7.7 Consensus size: 10
602580 CATTTAATAA
602590 ATAAACGAAC
1 ATAAACGAAC
602600 ATAAACGAAC
1 ATAAACGAAC
*
602610 ----ACGAAT
1 ATAAACGAAC
602616 ATAAACGAAC
1 ATAAACGAAC
** *
602626 ACGAAC-ATAA
1 ATAAACGA-AC
602636 ATGAACACGAAC
1 AT-AA-ACGAAC
602648 ATAAACGAAC
1 ATAAACGAAC
602658 ATAAACG
1 ATAAACG
602665 TTGGAGACCC
Statistics
Matches: 49, Mismatches: 8, Indels: 16
0.67 0.11 0.22
Matches are distributed among these distances:
6 5 0.10
9 1 0.02
10 34 0.69
11 3 0.06
12 5 0.10
13 1 0.02
ACGTcount: A:0.57, C:0.20, G:0.12, T:0.11
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:602619 original size:16 final size:16
Alignment explanation
Indices: 602594--602658 Score: 112
Period size: 16 Copynumber: 4.1 Consensus size: 16
602584 TAATAAATAA
602594 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
602610 ACGAATATAAACGAAC
1 ACGAACATAAACGAAC
*
602626 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
602642 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
602658 A
1 A
602659 TAAACGTTGG
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 45 1.00
ACGTcount: A:0.57, C:0.22, G:0.12, T:0.09
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:603424 original size:24 final size:24
Alignment explanation
Indices: 603388--603462 Score: 107
Period size: 24 Copynumber: 3.1 Consensus size: 24
603378 GATTGTGTTA
603388 AACATAAAT-GAACGAACATAAACG
1 AACAT-AATCGAACGAACATAAACG
603412 AACATAATCGAACGAACATAAACG
1 AACATAATCGAACGAACATAAACG
* * *
603436 AACATAACCAAACGAACATAACCG
1 AACATAATCGAACGAACATAAACG
603460 AAC
1 AAC
603463 GTTCACCAAC
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
23 3 0.06
24 44 0.94
ACGTcount: A:0.56, C:0.23, G:0.11, T:0.11
Consensus pattern (24 bp):
AACATAATCGAACGAACATAAACG
Found at i:603437 original size:14 final size:14
Alignment explanation
Indices: 603388--603438 Score: 56
Period size: 14 Copynumber: 3.9 Consensus size: 14
603378 GATTGTGTTA
*
603388 AACATAAATGAACG
1 AACATAAACGAACG
603402 AACAT--A--AACG
1 AACATAAACGAACG
*
603412 AACATAATCGAACG
1 AACATAAACGAACG
603426 AACATAAACGAAC
1 AACATAAACGAAC
603439 ATAACCAAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
10 9 0.29
12 1 0.03
14 21 0.68
ACGTcount: A:0.57, C:0.20, G:0.12, T:0.12
Consensus pattern (14 bp):
AACATAAACGAACG
Found at i:603448 original size:14 final size:14
Alignment explanation
Indices: 603407--603463 Score: 59
Period size: 14 Copynumber: 4.4 Consensus size: 14
603397 GAACGAACAT
*
603407 AAACGAACATAATC
1 AAACGAACATAACC
*
603421 GAACGAACAT----
1 AAACGAACATAACC
603431 AAACGAACATAACC
1 AAACGAACATAACC
603445 AAACGAACATAACC
1 AAACGAACATAACC
*
603459 GAACG
1 AAACG
603464 TTCACCAACG
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
10 9 0.25
14 27 0.75
ACGTcount: A:0.54, C:0.25, G:0.12, T:0.09
Consensus pattern (14 bp):
AAACGAACATAACC
Found at i:603461 original size:10 final size:10
Alignment explanation
Indices: 603398--603442 Score: 54
Period size: 10 Copynumber: 4.1 Consensus size: 10
603388 AACATAAATG
603398 AACGAACATA
1 AACGAACATA
603408 AACGAACATAA
1 AACGAACAT-A
603419 TCGAACGAACATA
1 ---AACGAACATA
603432 AACGAACATA
1 AACGAACATA
603442 A
1 A
603443 CCAAACGAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
10 20 0.65
11 1 0.03
13 1 0.03
14 9 0.29
ACGTcount: A:0.58, C:0.20, G:0.11, T:0.11
Consensus pattern (10 bp):
AACGAACATA
Found at i:604165 original size:29 final size:29
Alignment explanation
Indices: 604139--604200 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 29
604129 AAAATTTTGT
*
604139 TTTAATTATTAAAATTTT-AAATTTTTTAA
1 TTTAATCATT-AAATTTTCAAATTTTTTAA
604168 TTTAATCATTAAATTTTCAAATAATTTTTAA
1 TTTAATCATTAAATTTTCAAAT--TTTTTAA
604199 TT
1 TT
604201 CAGAATATCT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
28 7 0.24
29 13 0.45
31 9 0.31
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.56
Consensus pattern (29 bp):
TTTAATCATTAAATTTTCAAATTTTTTAA
Found at i:606327 original size:31 final size:31
Alignment explanation
Indices: 606292--606350 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
606282 GATGTATTGG
*
606292 AATTTGTTCCTTTCAAGTTGAAATTGCTAGA
1 AATTTGTTCCTTTCAAGTTGAAACTGCTAGA
*
606323 AATTTGTTCCTTTCGAGTTGAAACTGCT
1 AATTTGTTCCTTTCAAGTTGAAACTGCT
606351 TTAGATGATT
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:0.25, C:0.15, G:0.17, T:0.42
Consensus pattern (31 bp):
AATTTGTTCCTTTCAAGTTGAAACTGCTAGA
Found at i:615723 original size:14 final size:14
Alignment explanation
Indices: 615704--615733 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
615694 TGAGTAATTT
615704 AAATATTTTATTAA
1 AAATATTTTATTAA
615718 AAATATTTTATTAA
1 AAATATTTTATTAA
615732 AA
1 AA
615734 TTTATAAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
AAATATTTTATTAA
Found at i:616713 original size:10 final size:10
Alignment explanation
Indices: 616698--616750 Score: 60
Period size: 10 Copynumber: 5.7 Consensus size: 10
616688 ACACACACAC
616698 ATGTATGTAT
1 ATGTATGTAT
616708 ATGTATGTAT
1 ATGTATGTAT
616718 ATGTA--TAT
1 ATGTATGTAT
616726 ATGTA--TAT
1 ATGTATGTAT
*
616734 ATGTATATAT
1 ATGTATGTAT
*
616744 ATATATG
1 ATGTATG
616751 GGTGAAGAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
8 16 0.41
10 23 0.59
ACGTcount: A:0.36, C:0.00, G:0.15, T:0.49
Consensus pattern (10 bp):
ATGTATGTAT
Found at i:616717 original size:14 final size:14
Alignment explanation
Indices: 616698--616750 Score: 56
Period size: 14 Copynumber: 3.9 Consensus size: 14
616688 ACACACACAC
*
616698 ATGTATGTATATGT
1 ATGTATATATATGT
* *
616712 ATGTATATGTATAT
1 ATGTATATATATGT
616726 ATG--TATATATGT
1 ATGTATATATATGT
*
616738 ATATATATATATG
1 ATGTATATATATG
616751 GGTGAAGAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
12 9 0.29
14 22 0.71
ACGTcount: A:0.36, C:0.00, G:0.15, T:0.49
Consensus pattern (14 bp):
ATGTATATATATGT
Found at i:616728 original size:8 final size:8
Alignment explanation
Indices: 616705--616749 Score: 63
Period size: 8 Copynumber: 5.4 Consensus size: 8
616695 CACATGTATG
616705 TATATGTA
1 TATATGTA
616713 TGTATATGTA
1 --TATATGTA
616723 TATATGTA
1 TATATGTA
616731 TATATGTA
1 TATATGTA
*
616739 TATATATA
1 TATATGTA
616747 TAT
1 TAT
616750 GGGTGAAGAA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
8 26 0.76
10 8 0.24
ACGTcount: A:0.38, C:0.00, G:0.11, T:0.51
Consensus pattern (8 bp):
TATATGTA
Found at i:631372 original size:22 final size:23
Alignment explanation
Indices: 631347--631389 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
631337 AAAAAAGAAT
*
631347 GAGGTCTAATTA-AATTTTTTGA
1 GAGGTCTAATAAGAATTTTTTGA
*
631369 GAGGTTTAATAAGAATTTTTT
1 GAGGTCTAATAAGAATTTTTT
631390 AAAAATTTGC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.33, C:0.02, G:0.19, T:0.47
Consensus pattern (23 bp):
GAGGTCTAATAAGAATTTTTTGA
Found at i:641123 original size:19 final size:19
Alignment explanation
Indices: 641099--641136 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
641089 ATCACAATAG
641099 GAACGATTGGAGCTTCTGC
1 GAACGATTGGAGCTTCTGC
641118 GAACGATTGGAGCTTCTGC
1 GAACGATTGGAGCTTCTGC
641137 TCCACCCACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.21, G:0.32, T:0.26
Consensus pattern (19 bp):
GAACGATTGGAGCTTCTGC
Found at i:642423 original size:12 final size:12
Alignment explanation
Indices: 642406--642430 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
642396 TTAATGAAAT
642406 TAAAATAAAAAA
1 TAAAATAAAAAA
642418 TAAAATAAAAAA
1 TAAAATAAAAAA
642430 T
1 T
642431 TTATTTACCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (12 bp):
TAAAATAAAAAA
Found at i:644362 original size:35 final size:35
Alignment explanation
Indices: 644289--644362 Score: 103
Period size: 35 Copynumber: 2.1 Consensus size: 35
644279 AAAACAATCC
* * *
644289 TCAATTTTATTTTAAACCCCAAATTCCAGAATAAT
1 TCAATTATATTCTAAACCCCAAATTCCAAAATAAT
* *
644324 TCAATTATATTCTAAACCCCAAATTCTAAAATACT
1 TCAATTATATTCTAAACCCCAAATTCCAAAATAAT
644359 TCAA
1 TCAA
644363 AATAATATTG
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.42, C:0.22, G:0.01, T:0.35
Consensus pattern (35 bp):
TCAATTATATTCTAAACCCCAAATTCCAAAATAAT
Found at i:644908 original size:35 final size:36
Alignment explanation
Indices: 644861--644931 Score: 99
Period size: 35 Copynumber: 2.0 Consensus size: 36
644851 TATTATTTTG
* * *
644861 ATTATTTTTGGAATGTGGGGTTTAGAATGTAATTGA
1 ATTATTTTTGGAATGTGAGGTTTAAAATGAAATTGA
*
644897 ATTA-TTTTGGAATTTGAGGTTTAAAATGAAATTGA
1 ATTATTTTTGGAATGTGAGGTTTAAAATGAAATTGA
644932 TGACTATTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
35 27 0.87
36 4 0.13
ACGTcount: A:0.32, C:0.00, G:0.24, T:0.44
Consensus pattern (36 bp):
ATTATTTTTGGAATGTGAGGTTTAAAATGAAATTGA
Found at i:645956 original size:22 final size:22
Alignment explanation
Indices: 645931--645973 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
645921 TGAAAATTTT
* * *
645931 ATAAACTATATAATCTTTTAGA
1 ATAAAATAGATAATATTTTAGA
645953 ATAAAATAGATAATATTTTAG
1 ATAAAATAGATAATATTTTAG
645974 TTTGATATCG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.49, C:0.05, G:0.07, T:0.40
Consensus pattern (22 bp):
ATAAAATAGATAATATTTTAGA
Found at i:647650 original size:34 final size:35
Alignment explanation
Indices: 647606--647678 Score: 94
Period size: 34 Copynumber: 2.1 Consensus size: 35
647596 CAATATTATT
*
647606 TTGAAGTATTTTAGAATTT-GGATTTAGAATGTAA
1 TTGAAGTATTTTAGAATTTAGGATTTAGAATGAAA
* * * *
647640 TTGAATTATTTTGGAATTTAGGGTTTATAATGAAA
1 TTGAAGTATTTTAGAATTTAGGATTTAGAATGAAA
647675 TTGA
1 TTGA
647679 CGACTGTTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
34 17 0.52
35 16 0.48
ACGTcount: A:0.34, C:0.00, G:0.21, T:0.45
Consensus pattern (35 bp):
TTGAAGTATTTTAGAATTTAGGATTTAGAATGAAA
Found at i:650422 original size:20 final size:20
Alignment explanation
Indices: 650375--650430 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
650365 ATCATATTAC
* *
650375 CTGATAATCTTACATTCCCA
1 CTGATAATCTTATATTCCAA
*
650395 CT-AGTAATCTTATATTCTAA
1 CTGA-TAATCTTATATTCCAA
650415 CTGATAATCTTATATT
1 CTGATAATCTTATATT
650431 TCGTGAACCA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
19 1 0.03
20 29 0.94
21 1 0.03
ACGTcount: A:0.32, C:0.20, G:0.05, T:0.43
Consensus pattern (20 bp):
CTGATAATCTTATATTCCAA
Found at i:653850 original size:25 final size:25
Alignment explanation
Indices: 653816--653873 Score: 116
Period size: 25 Copynumber: 2.3 Consensus size: 25
653806 CGGATCAAAA
653816 GACTCCAACGAATGACCAGTTTATC
1 GACTCCAACGAATGACCAGTTTATC
653841 GACTCCAACGAATGACCAGTTTATC
1 GACTCCAACGAATGACCAGTTTATC
653866 GACTCCAA
1 GACTCCAA
653874 GACTATTAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.33, C:0.29, G:0.16, T:0.22
Consensus pattern (25 bp):
GACTCCAACGAATGACCAGTTTATC
Found at i:655078 original size:22 final size:21
Alignment explanation
Indices: 655042--655109 Score: 70
Period size: 22 Copynumber: 3.2 Consensus size: 21
655032 TATATATCTT
655042 ATTTAGAG-TTTAAGGTTTATA
1 ATTTA-AGTTTTAAGGTTTATA
655063 ATTTGAAGTTTTAAGGTTTATGA
1 ATTT-AAGTTTTAAGGTTTAT-A
*
655086 CTTTAAGTTTT-AGGATTTA-A
1 ATTTAAGTTTTAAGG-TTTATA
655106 ATTT
1 ATTT
655110 TATAATTTGG
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
20 4 0.10
21 9 0.22
22 24 0.59
23 4 0.10
ACGTcount: A:0.31, C:0.01, G:0.18, T:0.50
Consensus pattern (21 bp):
ATTTAAGTTTTAAGGTTTATA
Found at i:662135 original size:21 final size:21
Alignment explanation
Indices: 662109--662152 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
662099 CACAGGCATC
662109 GCGAGGTAGTCCTATATGATT
1 GCGAGGTAGTCCTATATGATT
662130 GCGAGGTAGTCCTATATGATT
1 GCGAGGTAGTCCTATATGATT
662151 GC
1 GC
662153 TCTTTCATAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.16, G:0.30, T:0.32
Consensus pattern (21 bp):
GCGAGGTAGTCCTATATGATT
Found at i:663911 original size:15 final size:15
Alignment explanation
Indices: 663887--663922 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
663877 ATACCATTAA
*
663887 ATTAATTTATAAAAC
1 ATTAAATTATAAAAC
*
663902 ATTAAATTATAAAAT
1 ATTAAATTATAAAAC
663917 ATTAAA
1 ATTAAA
663923 CGTAAAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (15 bp):
ATTAAATTATAAAAC
Found at i:665215 original size:2 final size:2
Alignment explanation
Indices: 665208--665232 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
665198 AATATTTGTG
665208 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
665233 CGTATTATTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:668656 original size:14 final size:14
Alignment explanation
Indices: 668619--668656 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
668609 ACTCGTTCGA
668619 ATGGCCTCGGTCGG
1 ATGGCCTCGGTCGG
*
668633 ATGCCCTCGGTCGG
1 ATGGCCTCGGTCGG
*
668647 ATGGCTTCGG
1 ATGGCCTCGG
668657 ATGCCCAATG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.08, C:0.29, G:0.39, T:0.24
Consensus pattern (14 bp):
ATGGCCTCGGTCGG
Found at i:669506 original size:20 final size:20
Alignment explanation
Indices: 669481--669538 Score: 107
Period size: 20 Copynumber: 2.9 Consensus size: 20
669471 GTAATTCGCG
669481 TTGCGATAGTACTGTTTACA
1 TTGCGATAGTACTGTTTACA
669501 TTGCGATAGTACTGTTTACA
1 TTGCGATAGTACTGTTTACA
*
669521 TTGCGATAGTATTGTTTA
1 TTGCGATAGTACTGTTTA
669539 TCTATATCGG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.24, C:0.12, G:0.21, T:0.43
Consensus pattern (20 bp):
TTGCGATAGTACTGTTTACA
Found at i:669544 original size:77 final size:75
Alignment explanation
Indices: 669448--669704 Score: 338
Period size: 77 Copynumber: 3.3 Consensus size: 75
669438 TTCGCGTTGT
* * * **
669448 GATAGT-TGTGTTTACCTATATCGGTAATTCGCGTTGCGATAGTACTG-TTTACATTGCGATAGT
1 GATAGTAT-TGTTTACCTATATCGGTAATTAGCGTTGCGA-A-T-TTGAATCGCATTGCGATAGT
669511 ACTGTTTACATTGC
62 ACTGTTTACATTGC
*
669525 GATAGTATTGTTTATCTATATCGGTAATTAGCGTTGCGAATTTGAAAATCGCATTGCGATAGTAC
1 GATAGTATTGTTTACCTATATCGGTAATTAGCGTTGCGAATTTG--AATCGCATTGCGATAGTAC
669590 TGTTTACATTGC
64 TGTTTACATTGC
* * *
669602 GATAGTGTTGTTTACCTATATCGGTAATTAACGTTGCGAATTTGAAAATCGCATTGCGATAATAC
1 GATAGTATTGTTTACCTATATCGGTAATTAGCGTTGCGAATTTG--AATCGCATTGCGATAGTAC
669667 TGTTTACATTGC
64 TGTTTACATTGC
*
669679 GATAGTACTGTTTACCTATATCGGTA
1 GATAGTATTGTTTACCTATATCGGTA
669705 TAAAGAAAAT
Statistics
Matches: 164, Mismatches: 12, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
74 2 0.01
75 1 0.01
76 1 0.01
77 159 0.97
78 1 0.01
ACGTcount: A:0.26, C:0.14, G:0.21, T:0.39
Consensus pattern (75 bp):
GATAGTATTGTTTACCTATATCGGTAATTAGCGTTGCGAATTTGAATCGCATTGCGATAGTACTG
TTTACATTGC
Found at i:669676 original size:20 final size:20
Alignment explanation
Indices: 669653--669693 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
669643 TTGAAAATCG
669653 CATTGCGATAATACTGTTTA
1 CATTGCGATAATACTGTTTA
*
669673 CATTGCGATAGTACTGTTTA
1 CATTGCGATAATACTGTTTA
669693 C
1 C
669694 CTATATCGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.27, C:0.17, G:0.17, T:0.39
Consensus pattern (20 bp):
CATTGCGATAATACTGTTTA
Found at i:675874 original size:17 final size:16
Alignment explanation
Indices: 675847--675880 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
675837 TTAAAATTTT
675847 TAAAAATTTTTATATA
1 TAAAAATTTTTATATA
*
675863 TAAAATATTTTTTTATA
1 TAAAA-ATTTTTATATA
675880 T
1 T
675881 TTTATATGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TAAAAATTTTTATATA
Found at i:677499 original size:13 final size:14
Alignment explanation
Indices: 677481--677518 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
677471 TTCATGTTCT
677481 TTTTCTTGTTAA-G
1 TTTTCTTGTTAAGG
*
677494 TTTTCTAGTTAAGG
1 TTTTCTTGTTAAGG
677508 TTTATCTTGTT
1 TTT-TCTTGTT
677519 GCATGGTGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 11 0.52
14 4 0.19
15 6 0.29
ACGTcount: A:0.16, C:0.08, G:0.16, T:0.61
Consensus pattern (14 bp):
TTTTCTTGTTAAGG
Found at i:684279 original size:51 final size:53
Alignment explanation
Indices: 684170--684279 Score: 170
Period size: 56 Copynumber: 2.1 Consensus size: 53
684160 GTTCCTCGAT
*
684170 CCATAGTCTTTCTGCAAGCTACAAAATGAGATAAGCCATTTTGGAAAACCTGTCAA
1 CCATAGTCTTTCTGCAAGCTACAAAAT-AG--AAGCCATCTTGGAAAACCTGTCAA
684226 CCATAGTCTTTCTGCAAGCTACAAAAT-G-AGCCATCTTGGAAAACCTGTCAA
1 CCATAGTCTTTCTGCAAGCTACAAAATAGAAGCCATCTTGGAAAACCTGTCAA
684277 CCA
1 CCA
684280 CAACAAAGAT
Statistics
Matches: 53, Mismatches: 1, Indels: 5
0.90 0.02 0.08
Matches are distributed among these distances:
51 25 0.47
54 1 0.02
56 27 0.51
ACGTcount: A:0.35, C:0.25, G:0.15, T:0.25
Consensus pattern (53 bp):
CCATAGTCTTTCTGCAAGCTACAAAATAGAAGCCATCTTGGAAAACCTGTCAA
Found at i:687517 original size:15 final size:15
Alignment explanation
Indices: 687499--687528 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
687489 CCACGGTGCT
687499 CCCGAAATCCTGCGC
1 CCCGAAATCCTGCGC
*
687514 CCCGAAATCTTGCGC
1 CCCGAAATCCTGCGC
687529 GATTGTGATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.43, G:0.20, T:0.17
Consensus pattern (15 bp):
CCCGAAATCCTGCGC
Found at i:688524 original size:133 final size:133
Alignment explanation
Indices: 688286--688550 Score: 521
Period size: 133 Copynumber: 2.0 Consensus size: 133
688276 AACATACTCA
688286 AAACGACCCCAATGAGGAACATGTCACAATCAATTCCCGCCTTTGCGCTGATCTGCCAACTCATG
1 AAACGACCCCAATGAGGAACATGTCACAATCAATTCCCGCCTTTGCGCTGATCTGCCAACTCATG
688351 GTATCTCAGCGCCATCAACGTGCAATCTGACAGCTCAGCATCATCTGTCTCGGATCCCCCTGCAT
66 GTATCTCAGCGCCATCAACGTGCAATCTGACAGCTCAGCATCATCTGTCTCGGATCCCCCTGCAT
688416 CAG
131 CAG
688419 AAACGACCCCAATGAGGAACATGTCACAATCAATTCCCGCCTTTGCGCTGATCTGCCAACTCATG
1 AAACGACCCCAATGAGGAACATGTCACAATCAATTCCCGCCTTTGCGCTGATCTGCCAACTCATG
*
688484 GTATCTCAGCGCCATCAACGTGCAATCTGACAGCTCAGCATCATCTGTCTCGGATTCCCCTGCAT
66 GTATCTCAGCGCCATCAACGTGCAATCTGACAGCTCAGCATCATCTGTCTCGGATCCCCCTGCAT
688549 CA
131 CA
688551 AGTCCTCAAT
Statistics
Matches: 131, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
133 131 1.00
ACGTcount: A:0.26, C:0.34, G:0.18, T:0.23
Consensus pattern (133 bp):
AAACGACCCCAATGAGGAACATGTCACAATCAATTCCCGCCTTTGCGCTGATCTGCCAACTCATG
GTATCTCAGCGCCATCAACGTGCAATCTGACAGCTCAGCATCATCTGTCTCGGATCCCCCTGCAT
CAG
Found at i:688732 original size:2 final size:2
Alignment explanation
Indices: 688725--688751 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
688715 TACAATACTC
688725 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 A
688752 AAAGAAAGAG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:689988 original size:2 final size:2
Alignment explanation
Indices: 689981--690023 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
689971 TTGTTTGAGC
689981 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
690023 T
1 T
690024 GATGACGAAG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:693097 original size:6 final size:6
Alignment explanation
Indices: 693058--693100 Score: 54
Period size: 6 Copynumber: 7.5 Consensus size: 6
693048 GTCCGTCTCG
* *
693058 GGTCG- GGTCG- GGTCGG GGTCGG GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
693101 AATGGCAATG
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
5 10 0.28
6 26 0.72
ACGTcount: A:0.00, C:0.16, G:0.58, T:0.26
Consensus pattern (6 bp):
GGTCGT
Found at i:693239 original size:21 final size:19
Alignment explanation
Indices: 693186--693242 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
693176 AATCTTTTTT
*
693186 TTTAAACTATCGCAACGAA
1 TTTAGACTATCGCAACGAA
* **
693205 TTTGGAAAATCGCAACGACA
1 TTTAGACTATCGCAACGA-A
693225 TTGTAGACTATCGCAACG
1 TT-TAGACTATCGCAACG
693243 CGAATTAGAT
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
19 14 0.48
20 3 0.10
21 12 0.41
ACGTcount: A:0.37, C:0.21, G:0.18, T:0.25
Consensus pattern (19 bp):
TTTAGACTATCGCAACGAA
Found at i:698345 original size:30 final size:31
Alignment explanation
Indices: 698309--698368 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
698299 AAAACATTTG
* *
698309 ACGTCTTTGAGA-AGATGCATGGAAGACAAC
1 ACGTCTTTGAGATAGAAGCAGGGAAGACAAC
*
698339 ACGTCTTTGGGATAGAAGCAGGGAAGACAA
1 ACGTCTTTGAGATAGAAGCAGGGAAGACAA
698369 AGTGTCTTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 11 0.42
31 15 0.58
ACGTcount: A:0.37, C:0.15, G:0.30, T:0.18
Consensus pattern (31 bp):
ACGTCTTTGAGATAGAAGCAGGGAAGACAAC
Found at i:698675 original size:7 final size:7
Alignment explanation
Indices: 698663--698696 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
698653 CTTTAATTGC
698663 AAAAATT
1 AAAAATT
698670 AAAAATT
1 AAAAATT
*
698677 -TAAATT
1 AAAAATT
698683 AAAAATT
1 AAAAATT
698690 AAAAATT
1 AAAAATT
698697 CGACCATGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
6 5 0.21
7 19 0.79
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (7 bp):
AAAAATT
Found at i:698681 original size:13 final size:13
Alignment explanation
Indices: 698665--698689 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
698655 TTAATTGCAA
698665 AAATTAAAAATTT
1 AAATTAAAAATTT
698678 AAATTAAAAATT
1 AAATTAAAAATT
698690 AAAAATTCGA
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:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
AAATTAAAAATTT
Found at i:701072 original size:165 final size:165
Alignment explanation
Indices: 700785--702529 Score: 1751
Period size: 165 Copynumber: 10.5 Consensus size: 165
700775 AAATCTGGTT
* * *
700785 TGCCTCTG-AGCTGAGTGTAATCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTT
1 TGCCT-TGAAGCTGAGCGTAGTCGAACTCGAAGGTCTTTT-G-G-CAGATAACCCTTCTAGACTT
* * *
700849 GAA-TTATGCTGCAAATGATATGCCCTCGAAGCTGAGCGTAATCGAACTCAAAGGTCTTTGGTTG
62 -AAGTTATGCTGCAAATGATATG-CCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTG
* * *
700913 GCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATA
125 GCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATG
* * * * * * *
700954 TGTCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTC-TTTGGCAGATAGCCCTTATCGACTTAAG
1 TG-CCTTGAAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGCAGATAACCCTTCTAGACTTAAG
* *
701018 CTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGCATA
65 TTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGCAGA
*
701083 TAACCCTTCTTGACTTAAGTTATGCTGCAAATGATG
130 TAACCCTTCTAGACTTAAGTTATGCTGCAAATGATG
* * * * * *
701119 TGCCCTCAGAGCTGAGTGTAATCGAACTCGAAGGTC-TTTGGCAGATAGCCCTTCTCGACTTAAG
1 TGCCTTGA-AGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGCAGATAACCCTTCTAGACTTAAG
* * *
701183 CTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGCAGA
65 TTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGCAGA
* * * *
701248 CAACCCTTTTAGACTTAAGTTGTGCTGCAAATGATA
130 TAACCCTTCTAGACTTAAGTTATGCTGCAAATGATG
* * * * *
701284 TGCCCTCGAAGCTGAGTGTAATCGAACTCGAAGGTC-TTTGGCAGATAGCCCTTCTATACTTAAG
1 TG-CCTTGAAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGCAGATAACCCTTCTAGACTTAAG
* * *
701348 TTATGCTGCAAATGATGTGCCTTGGAGCTGAGTGTAGTCGAACTCAAAGGTCTTTTGTTGGCA-A
65 TTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGCAGA
* *
701412 TCAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATA
130 T-AACCCTTCTAGACTTAAGTTATGCTGCAAATGATG
* *
701449 TGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGATGGCAGATAACCCTTCTCGACTTA
1 TGCCTTGAAGCTGAGCGTAGTCGAACTCGAAGGTCTTT---TGGCAGATAACCCTTCTAGACTTA
* * * * * ***
701514 AGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTC--T--TTGGC
63 AGTTATGCTGCAAATGATATG-CCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGC
* * *
701575 AGATAGCCCTTCTCGACTTAAGTTATACTGCAAATGATG
127 AGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATG
* * * * *
701614 TGCCTGGGAGCTGAGCGTAGTCGAACTCGAAGATCTTTTGGTCACAGATAACCCTTCTAGCCTTG
1 TGCCTTGAAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGG---CAGATAACCCTTCTAGACTTA
* * * * * * ***
701679 AGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTC--T--TTGGC
63 AGTTATGCTGCAAATGATATG-CCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGC
* * * * *
701740 AGATAGCCCTTCTCGACTTAAGCTATACTGTAAATGATG
127 AGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATG
* *
701779 TGCCGTTG-AGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGCAGACAACCCTTCTAGA-TT
1 TGCC-TTGAAGCTGAGCGTAGTCGAACTCGAAGGTC-TT--TTGGCAGATAACCCTTCTAGACTT
* * * *
701842 CAAGTTGTGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGATCTTTTGG-TC
62 -AAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTC-TTTGGTTG
* * * *
701906 ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATG
125 GCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATG
** * * ** ** * *
701947 TGCCCTCAAAGCTGAGTGTAATCGAACTCGGGGGTC-TTTGGCAGATAGTCATTCTCGACTTAAG
1 TG-CCTTGAAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGCAGATAACCCTTCTAGACTTAAG
* * * * *
702011 CTATACTGTAAATGATGTATTG--TT-GAGCTGAGCGTAGTCGAACTCAAACGTCTTTTGTTGGC
65 TTATGCTGCAAATGA--TA-TGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGC
* * *
702073 AGACAACCCTTCTAGACTTTAAGTTGTGCTGCAAATGATA
127 AGATAACCCTTCTAGAC-TTAAGTTATGCTGCAAATGATG
* * * *
702113 TGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGATCTTTTGGTCACAGATAACCCTTCTAGCCTTG
1 TGCCTTGAAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGG---CAGATAACCCTTCTAGACTTA
* * * * * * * ***
702178 AGTTATGATGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTC--T--TTGGC
63 AGTTATGCTGCAAATGATATG-CCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGC
* * * * *
702239 AGATAGCCCTTCTCGACTTAAGCTATACTGTAAATGATG
127 AGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATG
* *
702278 TGCCGTTG-AGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTT
1 TGCC-TTGAAGCTGAGCGTAGTCGAACTCGAAGGTC--TT-TTGGCAGATAACCCTTCTAGAC-T
* * *
702342 TAAGTTGTGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGCACTCGAAGGTCTTTGGTTGG
61 TAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGG
*
702407 CAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATG
126 CAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATG
* * * *
702447 TGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGATCTTTTGGTCACAGATAACCCTTCTAGCCTTG
1 TGCCTTGAAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGG---CAGATAACCCTTCTAGACTTA
*
702512 AGTTATGCTGTAAATGAT
63 AGTTATGCTGCAAATGAT
702530 TTGTTTAAAA
Statistics
Matches: 1344, Mismatches: 178, Indels: 109
0.82 0.11 0.07
Matches are distributed among these distances:
162 3 0.00
164 65 0.05
165 810 0.60
166 119 0.09
167 12 0.01
168 113 0.08
169 172 0.13
170 50 0.04
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.30
Consensus pattern (165 bp):
TGCCTTGAAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGCAGATAACCCTTCTAGACTTAAGT
TATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGCAGAT
AACCCTTCTAGACTTAAGTTATGCTGCAAATGATG
Found at i:701443 original size:249 final size:247
Alignment explanation
Indices: 700746--702529 Score: 1912
Period size: 249 Copynumber: 7.1 Consensus size: 247
700736 GTTTTGACGA
* * * * * *
700746 ATAGCCCTTCTTG-CATTGAGCTATGCTGTAAATCTGGTTTG-CCTCTGAGCTGAGTGTAATCGA
1 ATAGCCCTTCTCGAC-TTAAGCTATGCTGTAAA--TGATGTGCCCT-TGAGCTGAGCGTAGTCGA
* *
700809 ACTCGAAGGTCTT-TTGGTGACAGATAACCCTTCTAGCCTTGAA-TTATGCTGCAAATGATATGC
62 ACTCAAAGGTCTTGTT-G-G-CAGATAACCCTTCTAGACTT-AAGTTATGCTGCAAATGATATG-
* * * * * *
700872 CCTCGAAGCTGAGCGTAATCGAACTCAAAGGTCTTTGGTTGGCAGACAACCCTTCTAGACTTAAG
122 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGACTTAAG
* * *
700937 TTGTGCTGCAAATGATATGTCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAG
187 TTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAG
* * *
700998 ATAGCCCTTATCGACTTAAGCTATGCTGCAAATGATATG-CCTTGGAGCTGAGCGTAGTCGAACT
1 ATAGCCCTTCTCGACTTAAGCTATGCTGTAAATGATGTGCCCTT-GAGCTGAGCGTAGTCGAACT
* * * **
701062 CAAAGGTCTTTGGTTGGCATATAACCCTTCTTGACTTAAGTTATGCTGCAAATGATGTGCCCTCA
65 CAAAGGTC-TT-GTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATG-CCTTG
* * * * * *
701127 GAGCTGAGTGTAATCGAACTCGAAGGTC---T-TTGGCAGATAGCCCTTCTCGACTTAAGCTATA
127 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGACTTAAGTTATG
* * * * * *
701188 CTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGCAG
192 CTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTC--T--TTGGCAG
* * * * * * * * * * *
701247 ACAACCCTTTTAGACTTAAGTTGTGCTGCAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACT
1 ATAGCCCTTCTCGACTTAAGCTATGCTGTAAATGATGTGCCCTTG-AGCTGAGCGTAGTCGAACT
* * * *
701312 CGAAGGTC-T-TTGGCAGATAGCCCTTCTATACTTAAGTTATGCTGCAAATGATGTGCCTTGGAG
65 CAAAGGTCTTGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCTTGGAG
* * *
701375 CTGAGTGTAGTCGAACTCAAAGGTCTTTTGTTGGCA-ATCAACCCTTCTAGACTTAAGTTGTGCT
130 CTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGAT-AACCCTTCTAGACTTAAGTTATGCT
* * * * * *
701439 GCAAATGATATG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGATGGCAG
194 GCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTC-TT---TGGCAG
* * * * * *
701496 ATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACT
1 ATAGCCCTTCTCGACTTAAGCTATGCTGTAAATGATGTGCCCTTG-AGCTGAGCGTAGTCGAACT
*** * * * * *
701561 CGGGGGTC-T-TTGGCAGATAGCCCTTCTCGACTTAAGTTATACTGCAAATGATGTGCCTGGGAG
65 CAAAGGTCTTGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCTTGGAG
* * ** * *
701624 CTGAGCGTAGTCGAACTCGAAGATCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTG
130 CTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTG
* *
701689 TAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAG
195 CAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAG
* *
701742 ATAGCCCTTCTCGACTTAAGCTATACTGTAAATGATGTGCCGTTGAGCTGAGCGTAGTCGAACTC
1 ATAGCCCTTCTCGACTTAAGCTATGCTGTAAATGATGTGCCCTTGAGCTGAGCGTAGTCGAACTC
* *
701807 AAAGGTCTTTGGTTGGCAGACAACCCTTCTAGA-TTCAAGTTGTGCTGCAAATGATATGCCTTGG
66 AAAGGTC-TT-GTTGGCAGATAACCCTTCTAGACTT-AAGTTATGCTGCAAATGATATGCCTTGG
* * ** * *
701871 AGCTGAGCGTAGTCGAACTCGAAGATCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGC
128 AGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGACTTAAGTTATGC
* * *
701936 TGTAAATGATGTGCCCTCAAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAG
193 TGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAG
* * * ****
701991 ATAGTCATTCTCGACTTAAGCTATACTGTAAATGATGTATTGTTGAGCTGAGCGTAGTCGAACTC
1 ATAGCCCTTCTCGACTTAAGCTATGCTGTAAATGATGTGCCCTTGAGCTGAGCGTAGTCGAACTC
* * *
702056 AAACGTCTTTTGTTGGCAGACAACCCTTCTAGACTTTAAGTTGTGCTGCAAATGATATGCCTTGG
66 AAAGGTC--TTGTTGGCAGATAACCCTTCTAGAC-TTAAGTTATGCTGCAAATGATATGCCTTGG
* * ** * * *
702121 AGCTGAGCGTAGTCGAACTCGAAGATCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGA
128 AGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGACTTAAGTTATGC
* *
702186 TGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAG
193 TGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAG
* *
702241 ATAGCCCTTCTCGACTTAAGCTATACTGTAAATGATGTGCCGTTGAGCTGAGCGTAGTCGAACTC
1 ATAGCCCTTCTCGACTTAAGCTATGCTGTAAATGATGTGCCCTTGAGCTGAGCGTAGTCGAACTC
* *
702306 AAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTTAAGTTGTGCTGCAAATGATATGCCTTGG
66 AAAGGTC--TTGTTGGCAGATAACCCTTCTAGAC-TTAAGTTATGCTGCAAATGATATGCCTTGG
* * *
702371 AGCTGAGCGTAGTCGCACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGC
128 AGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGACTTAAGTTATGC
* * * * * *
702436 TGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGATCTTTTGGTCACAG
193 TGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTC-TTTGG---CAG
* * * * *
702494 ATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGAT
1 ATAGCCCTTCTCGACTTAAGCTATGCTGTAAATGAT
702530 TTGTTTAAAA
Statistics
Matches: 1357, Mismatches: 141, Indels: 67
0.87 0.09 0.04
Matches are distributed among these distances:
245 78 0.06
246 127 0.09
247 2 0.00
248 8 0.01
249 575 0.42
250 499 0.37
251 5 0.00
252 27 0.02
253 36 0.03
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.30
Consensus pattern (247 bp):
ATAGCCCTTCTCGACTTAAGCTATGCTGTAAATGATGTGCCCTTGAGCTGAGCGTAGTCGAACTC
AAAGGTCTTGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGC
TGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGC
AAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAG
Found at i:701571 original size:414 final size:412
Alignment explanation
Indices: 700792--702529 Score: 2138
Period size: 414 Copynumber: 4.2 Consensus size: 412
700782 GTTTGCCTCT
* *
700792 GAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAA-TTAT
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTT-AAGTTAT
* *
700856 GCTGCAAATGATATGCCCTCGAAGCTGAGCGTAATCGAACTCAAAGGTCTTTGGTTGGCAGACAA
65 GCTGCAAATGATATGCCCTCGAAGCTGAGCGTAATCGAACTCGAAGGTC-TT--TTGGCAGATAA
* * * * *
700921 CCCTTCTAGACTTAAGTTGTGCTGCAAATGATATGTCCTCGAAGCTGAGTGTAATCGAACTCGAG
127 CCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCAAA
* * *
700986 GGTCTTTGGCAGATAGCCCTTATCGACTTAAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGC
192 GGTCTTTGGCAGATAACCCTTCTAGACTTAAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGC
* *
701051 GTAGTCGAACTCAAAGGTCTTTGGTTGGCATATAACCCTTCTTGACTTAAGTTATGCTGCAAATG
257 GTAGTCGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATG
701116 ATGTGCCCTC-AGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCGACTT
322 ATGTGCCCTCGA-AGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCGACTT
701180 AAGCTATACTGCAAATGATGTGCCTTG
386 AAGCTATACTGCAAATGATGTGCCTTG
* * * * * *
701207 GAGCTGAGCGTAGTCGAACTCAAAGGTC-TTTGGTTGGCAGACAACCCTTTTAGACTTAAGTTGT
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGG-TGACAGATAACCCTTCTAGCCTTAAGTTAT
* *
701271 GCTGCAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGAAGGTC-TTTGGCAGATAGCCC
65 GCTGCAAATGATATGCCCTCGAAGCTGAGCGTAATCGAACTCGAAGGTCTTTTGGCAGATAACCC
* * * *
701335 TTCTATACTTAAGTTATGCTGCAAATGATGTG-CCTTGGAGCTGAGTGTAGTCGAACTCAAAGGT
130 TTCTAGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCAAAGGT
* *
701399 CTTTTGTTGGCA-ATCAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATATGCCTTGGAGCTGA
195 C---T-TTGGCAGAT-AACCCTTCTAGACTTAAGCTATGCTGCAAATGATATGCCTTGGAGCTGA
* * *
701463 GCGTAGTCGAACTCGAAGGTCTTTGGATGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAA
255 GCGTAGTCGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAA
**
701528 TGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACT
320 TGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCGACT
* *
701593 TAAGTTATACTGCAAATGATGTGCCTGG
385 TAAGCTATACTGCAAATGATGTGCCTTG
* * *
701621 GAGCTGAGCGTAGTCGAACTCGAAGATCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATG
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTAAGTTATG
* * * ** *
701686 CTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTC-TTTGGCAGATAGCCCT
66 CTGCAAATGATATGCCCTCGAAGCTGAGCGTAATCGAACTCGAAGGTCTTTTGGCAGATAACCCT
* * * * * * * *
701750 TCTCGACTTAAGCTATACTGTAAATGATGTGCCGTTG-AGCTGAGCGTAGTCGAACTCAAAGGTC
131 TCTAGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCAAAGGTC
* * *
701814 TTTGGTTGGCAGACAACCCTTCTAGA-TTCAAGTTGTGCTGCAAATGATATGCCTTGGAGCTGAG
196 --T--TTGGCAGATAACCCTTCTAGACTT-AAGCTATGCTGCAAATGATATGCCTTGGAGCTGAG
* * ** * * *
701878 CGTAGTCGAACTCGAAGATCTTTTGG-TCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAA
256 CGTAGTCGAACTCAAAGGTC-TTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAA
* ** * *
701942 TGATGTGCCCTCAAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGTCATTCTCGACT
320 TGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCGACT
* *
702007 TAAGCTATACTGTAAATGATGT--ATTG
385 TAAGCTATACTGCAAATGATGTGCCTTG
* * * * * *
702033 TTGAGCTGAGCGTAGTCGAACTCAAACGTCTTTTGTTGGCAGACAACCCTTCTAGACTTTAAGTT
1 --GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAG-CCTTAAGTT
* * * * *
702098 GTGCTGCAAATGATATG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGATCTTTTGGTCACAGAT
63 ATGCTGCAAATGATATGCCCTCGAAGCTGAGCGTAATCGAACTCGAAGGTCTTTTGG---CAGAT
* * * * *
702162 AACCCTTCTAGCCTTGAGTTATGATGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCG
125 AACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCA
** * * * * *
702227 GGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGTAAATGATGTGCCGTT-GAGCTG
190 AAGGTCTTTGGCAGATAACCCTTCTAGACTTAAGCTATGCTGCAAATGATATGCC-TTGGAGCTG
* * *
702291 AGCGTAGTCGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTTAAGTTGTGCTGCA
254 AGCGTAGTCGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTAGAC-TTAAGTTATGCTGCA
* * * * * * *
702356 AATGATATG-CCTTGGAGCTGAGCGTAGTCGCACTCGAAGGTCTTTGGTTGGCAGATAACCCTTC
318 AATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAAGGTC--T--TTGGCAGATAGCCCTTC
* *
702420 TCGACTTAAGTTATGCTGCAAATGATGTGCCTTG
379 TCGACTTAAGCTATACTGCAAATGATGTGCCTTG
* * *
702454 GAGCTGAGCGTAGTCGAACTCGAAGATCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATG
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTAAGTTATG
*
702519 CTGTAAATGAT
66 CTGCAAATGAT
702530 TTGTTTAAAA
Statistics
Matches: 1145, Mismatches: 146, Indels: 61
0.85 0.11 0.05
Matches are distributed among these distances:
410 28 0.02
411 41 0.04
412 2 0.00
413 9 0.01
414 630 0.55
415 241 0.21
416 24 0.02
417 2 0.00
418 58 0.05
419 107 0.09
421 3 0.00
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (412 bp):
GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTAAGTTATG
CTGCAAATGATATGCCCTCGAAGCTGAGCGTAATCGAACTCGAAGGTCTTTTGGCAGATAACCCT
TCTAGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCAAAGGTC
TTTGGCAGATAACCCTTCTAGACTTAAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAG
TCGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGT
GCCCTCGAAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCT
ATACTGCAAATGATGTGCCTTG
Found at i:705575 original size:17 final size:19
Alignment explanation
Indices: 705553--705596 Score: 74
Period size: 17 Copynumber: 2.4 Consensus size: 19
705543 AGTTAATGTG
705553 AATGCAAAG-AAATAAC-A
1 AATGCAAAGAAAATAACAA
705570 AATGCAAAGAAAATAACAA
1 AATGCAAAGAAAATAACAA
705589 AATGCAAA
1 AATGCAAA
705597 ATGTCTAATG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
17 9 0.36
18 7 0.28
19 9 0.36
ACGTcount: A:0.66, C:0.11, G:0.11, T:0.11
Consensus pattern (19 bp):
AATGCAAAGAAAATAACAA
Found at i:707090 original size:7 final size:7
Alignment explanation
Indices: 707078--707111 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
707068 CTTTAATTGC
707078 AAAAATT
1 AAAAATT
707085 AAAAATT
1 AAAAATT
*
707092 -TAAATT
1 AAAAATT
707098 AAAAATT
1 AAAAATT
707105 AAAAATT
1 AAAAATT
707112 CGACCATGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
6 5 0.21
7 19 0.79
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (7 bp):
AAAAATT
Found at i:707096 original size:13 final size:13
Alignment explanation
Indices: 707080--707104 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
707070 TTAATTGCAA
707080 AAATTAAAAATTT
1 AAATTAAAAATTT
707093 AAATTAAAAATT
1 AAATTAAAAATT
707105 AAAAATTCGA
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:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
AAATTAAAAATTT
Found at i:722262 original size:57 final size:57
Alignment explanation
Indices: 722193--722305 Score: 217
Period size: 57 Copynumber: 2.0 Consensus size: 57
722183 TTAGATCGAT
*
722193 TATGTTATATTATTTAACCAAAAATATTATAAAGTACAATAATATACTAAGTAGCGC
1 TATGTTATATTATTTAACCAAAAATATTATAAAGTACAATAACATACTAAGTAGCGC
722250 TATGTTATATTATTTAACCAAAAATATTATAAAGTACAATAACATACTAAGTAGCG
1 TATGTTATATTATTTAACCAAAAATATTATAAAGTACAATAACATACTAAGTAGCG
722306 TTTATATAAT
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 55 1.00
ACGTcount: A:0.46, C:0.11, G:0.09, T:0.35
Consensus pattern (57 bp):
TATGTTATATTATTTAACCAAAAATATTATAAAGTACAATAACATACTAAGTAGCGC
Found at i:722842 original size:23 final size:23
Alignment explanation
Indices: 722806--722878 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
722796 GATATTTACA
* *
722806 ATATAAGCACTACCTATTACATT
1 ATATAAACGCTACCTATTACATT
*
722829 ATATAAACGTTACCTATTACATT
1 ATATAAACGCTACCTATTACATT
* *
722852 ATATAAGCGCTACCTATTACATC
1 ATATAAACGCTACCTATTACATT
722875 ATAT
1 ATAT
722879 TTTTACCTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.36
Consensus pattern (23 bp):
ATATAAACGCTACCTATTACATT
Found at i:723278 original size:23 final size:23
Alignment explanation
Indices: 723243--723315 Score: 110
Period size: 23 Copynumber: 3.2 Consensus size: 23
723233 ATGTTTTACA
* *
723243 ATATAAGCACTACATATTACATT
1 ATATAAGCGCTACCTATTACATT
*
723266 ATATAAACGCTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
723289 ATATAAGCGCTACCTATTACATC
1 ATATAAGCGCTACCTATTACATT
723312 ATAT
1 ATAT
723316 TTTTACCTAT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 45 1.00
ACGTcount: A:0.40, C:0.21, G:0.05, T:0.34
Consensus pattern (23 bp):
ATATAAGCGCTACCTATTACATT
Found at i:723754 original size:23 final size:23
Alignment explanation
Indices: 723728--723800 Score: 128
Period size: 23 Copynumber: 3.2 Consensus size: 23
723718 ATATTTTACA
*
723728 ATATAAGCACTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
723751 ATATAAGCGCTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
723774 ATATAAGCGCTACCTATTACATC
1 ATATAAGCGCTACCTATTACATT
723797 ATAT
1 ATAT
723801 TTTTACCTAT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 48 1.00
ACGTcount: A:0.37, C:0.22, G:0.07, T:0.34
Consensus pattern (23 bp):
ATATAAGCGCTACCTATTACATT
Found at i:724253 original size:23 final size:23
Alignment explanation
Indices: 724218--724290 Score: 119
Period size: 23 Copynumber: 3.2 Consensus size: 23
724208 ATACTTTACA
*
724218 ATATAAGCACTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
724241 ATATAAACGCTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
724264 ATATAAGCGCTACCTATTACATC
1 ATATAAGCGCTACCTATTACATT
724287 ATAT
1 ATAT
724291 TTTTACCTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.38, C:0.22, G:0.05, T:0.34
Consensus pattern (23 bp):
ATATAAGCGCTACCTATTACATT
Found at i:724345 original size:490 final size:489
Alignment explanation
Indices: 723237--724644 Score: 2538
Period size: 490 Copynumber: 2.9 Consensus size: 489
723227 AAGTTAATGT
*
723237 TTTACAATATAAGCACTACATATTACATTATATAAACGCTACCTATTACATTATATAAGCGCTAC
1 TTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAAGCGCTAC
*
723302 CTATTACATCATATTTTTACCTATTATATTGAAAGTGTCCATACATTTTAT-AAAA-ATCGATAC
66 CTATTACATCATATTTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGATCGATAC
* *
723365 TTTTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTTAATAGTATTTCATATTTTCCACCTAC
131 TTTTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTAC
723430 AATATTAATTTAATAATTTCATTTGCACAAAAAATTATTTGATTATTTTGATATTTTATAAAATA
196 AATATTAATTTAATAATTTCATTTGCACAAAAAATTATTTGATTATTTTGATATTTTATAAAATA
723495 TTATTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATGTAATATATATGTTT
261 TTATTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATGTAATATATATGTTT
723560 ATTGTTTTTAATTTAATAATAATATATACCGTAACAT-AAAAA-AAATCATTAGATACATATAAT
326 ATTGTTTTTAATTTAATAATAATATATACCGTAACATAAAAAATAAATCATTAGATACATATAAT
*
723623 TACTAAATTGATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTTCACAGTGAAA
391 TACTAAATTGATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAA
* *
723688 AAAATATGGACACTTTTATAAAAATGATAGATAT
456 AAAATATGGACACTTTTATAAAAAGGATAGATAC
*
723722 TTTACAATATAAGCACTACCTATTACATTATATAAGCGCTACCTATTACATTATATAAGCGCTAC
1 TTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAAGCGCTAC
723787 CTATTACATCATATTTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAATGATCGATA
66 CTATTACATCATATTTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAA-GATCGATA
723852 CTTTTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTA
130 CTTTTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTA
*
723917 CAATATTAATTTAATAATTTCATTTACACAAAAAATTATTTGATTATTTTGATATTTTATAAAAT
195 CAATATTAATTTAATAATTTCATTTGCACAAAAAATTATTTGATTATTTTGATATTTTATAAAAT
* *
723982 ATTATTTAGTATTTAAATTTAACAATATTAACCAAATATAATAATAAATATGTAATATATATGTT
260 ATTATTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATGTAATATATATGTT
* *
724047 TATTGTTTTTAATTTAATAATAATATATACCGTAACGTAAAAAATAAATTATTAGATACATATAA
325 TATTGTTTTTAATTTAATAATAATATATACCGTAACATAAAAAATAAATCATTAGATACATATAA
*
724112 TTACTAAATTGATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACATTGAA
390 TTACTAAATTGATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAA
* *
724177 AAAAGTATTGACACTTTTATAAAAAGGATAGATAC
455 AAAAATATGGACACTTTTATAAAAAGGATAGATAC
724212 TTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAAGCGCTAC
1 TTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAAGCGCTAC
724277 CTATTACATCATATTTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATA
66 CTATTACATCATATTTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAA-GATCGATA
* * *
724342 CTTTTTTTTAAAGTTATGTAATTTATGTTTCAA-TTTTTTTAATTGTGTTTCAAGTTTTCCATCT
130 C-TTTTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCT
*
724406 ACAATATTAATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAA
194 ACAATATTAATTTAATAATTTCATTTGCACAAAAAATTATTTGATTATTTTGATATTTTATAAAA
* *
724471 TATTATTTAGAATTTAAATTTAATAATATTAATCAAAGATAATAATAAATATGTAATATATATGT
259 TATTATTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATGTAATATATATGT
* *
724536 TTATTGTTTTTAATTTAATGATAATATATACCGTAATATAAAAAATAAATCATTAGATACATATA
324 TTATTGTTTTTAATTTAATAATAATATATACCGTAACATAAAAAATAAATCATTAGATACATATA
724601 ATTACTAAATTGATATCTTAAAACTCACTCAAAAGATAACCTTA
389 ATTACTAAATTGATATCTTAAAACTCACTCAAAAGATAACCTTA
724645 CCTAAATATG
Statistics
Matches: 886, Mismatches: 31, Indels: 7
0.96 0.03 0.01
Matches are distributed among these distances:
485 113 0.13
486 4 0.00
488 234 0.26
489 5 0.01
490 499 0.56
491 31 0.03
ACGTcount: A:0.40, C:0.11, G:0.07, T:0.42
Consensus pattern (489 bp):
TTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAAGCGCTAC
CTATTACATCATATTTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGATCGATAC
TTTTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTAC
AATATTAATTTAATAATTTCATTTGCACAAAAAATTATTTGATTATTTTGATATTTTATAAAATA
TTATTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATGTAATATATATGTTT
ATTGTTTTTAATTTAATAATAATATATACCGTAACATAAAAAATAAATCATTAGATACATATAAT
TACTAAATTGATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAA
AAAATATGGACACTTTTATAAAAAGGATAGATAC
Found at i:727428 original size:183 final size:183
Alignment explanation
Indices: 727120--727875 Score: 1316
Period size: 183 Copynumber: 4.1 Consensus size: 183
727110 TACTTAAAAT
*
727120 TACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTTGCTCATAAAACCGGTATA
1 TACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATA
* *
727185 GTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
66 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGT
727250 CGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
131 CGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
727303 TACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATA
1 TACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATA
*
727368 TTTATACCGATTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGT
66 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGT
* * *
727433 CGACACTTTTTGACAAGATATCGACATATTTTTCTTCAAATCTGGACATAAAG
131 CGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
*
727486 TACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCACTCATAAAACCGGTATA
1 TACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATA
727551 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGT
66 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGT
* *
727616 CGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCAATCTGTACATAAAA
131 CGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
* * * *
727669 TACCGACACAATATTAAAATGTGTTGATATAGGTTGTAGACTTATTCTCTCATAAAACCGGTATA
1 TACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATA
*
727734 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCTGATGTGTAAATGT
66 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGT
* * * *
727799 TGACACTTTTTGA-AATAGTATCGACACATTTTTCTTCCATTCTAGACATAAAG
131 CGACACTTTTTGACAA-GGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
*
727852 TACAGACACAATATTAAAAAGTGT
1 TACCGACACAATATTAAAAAGTGT
727876 GAAAACTTTG
Statistics
Matches: 545, Mismatches: 27, Indels: 2
0.95 0.05 0.00
Matches are distributed among these distances:
182 2 0.00
183 543 1.00
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.35
Consensus pattern (183 bp):
TACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATA
TTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGT
CGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
Found at i:729099 original size:12 final size:12
Alignment explanation
Indices: 729083--729176 Score: 125
Period size: 12 Copynumber: 7.8 Consensus size: 12
729073 CTTGTTTGGA
* *
729083 TCATCATCATCA
1 TCATCGTCATCT
729095 TCATCGTCATCT
1 TCATCGTCATCT
729107 TCATCGTCATCT
1 TCATCGTCATCT
*
729119 TCATCGTCAGCT
1 TCATCGTCATCT
* *
729131 TCATCGTTATCA
1 TCATCGTCATCT
729143 TCATCGTCATCT
1 TCATCGTCATCT
*
729155 TCATCGTCAGCT
1 TCATCGTCATCT
*
729167 TCATCTTCAT
1 TCATCGTCAT
729177 TGACCGCTTG
Statistics
Matches: 71, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 71 1.00
ACGTcount: A:0.20, C:0.32, G:0.09, T:0.39
Consensus pattern (12 bp):
TCATCGTCATCT
Found at i:729174 original size:6 final size:6
Alignment explanation
Indices: 729083--729176 Score: 82
Period size: 6 Copynumber: 15.7 Consensus size: 6
729073 CTTGTTTGGA
* * * * * *
729083 TCATCA TCATCA TCATCG TCATCT TCATCG TCATCT TCATCG TCAGCT
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT
* * * *
729131 TCATCGT T-ATCA TCATCG TCATCT TCATCG TCAGCT TCATCT TCAT
1 TCATC-T TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCAT
729177 TGACCGCTTG
Statistics
Matches: 71, Mismatches: 15, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
5 1 0.01
6 68 0.96
7 2 0.03
ACGTcount: A:0.20, C:0.32, G:0.09, T:0.39
Consensus pattern (6 bp):
TCATCT
Found at i:730076 original size:20 final size:19
Alignment explanation
Indices: 730030--730076 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
730020 TCCGATATCG
730030 TTTTACCGATTTTATCATT
1 TTTTACCGATTTTATCATT
* *
730049 TTGATACCGGTTTTATCATAT
1 TT-TTACCGATTTTATCAT-T
730070 TTTTACC
1 TTTTACC
730077 TGTTATATCG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.21, C:0.17, G:0.09, T:0.53
Consensus pattern (19 bp):
TTTTACCGATTTTATCATT
Found at i:730257 original size:20 final size:19
Alignment explanation
Indices: 730211--730257 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
730201 TCCGGTAACG
730211 TTTTACCGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
730230 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
730251 TTTTACC
1 TTTTACC
730258 TGGTATATCG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.19, C:0.17, G:0.11, T:0.53
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:730301 original size:181 final size:181
Alignment explanation
Indices: 729997--730375 Score: 607
Period size: 181 Copynumber: 2.1 Consensus size: 181
729987 CGTACTTACG
*
729997 AAAGTATCGACATTTTCAATATATCCGATATCGTTTTACCGATTTTATCATTTTGATACCGGTTT
1 AAAGTATCGACATTTT-AATATATCCGATAACGTTTTACCGATTTTATCATTTTGATACCGGTTT
* * *
730062 TATCATATTTTTACCTGTTATATCGTTGTGGATCGATATATTTTTTTAAAGTATCGACACATTAT
65 TATCATATTTTTACCTGGTATATCGTTGTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
* *
730127 AGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATA-T
130 AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCATTATATT
* *
730178 AAAGTATCGACACTTTTAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
1 AAAGTATCGACA-TTTTAATATATCCGATAACGTTTTACCGATTTTATCATTTTGATACCGGTTT
* *
730243 TATCATATTTTTACCTGGTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACTTTAT
65 TATCATATTTTTACCTGGTATATCGTTGTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
** *
730308 AGGATTTAAAACTGCTTCTCTTTTAAATTCACGAAGTGTCGATCATTATATT
130 AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCATTATATT
*
730360 AAAGTACCGACATTTT
1 AAAGTATCGACATTTT
730376 TAATTTGGAT
Statistics
Matches: 182, Mismatches: 14, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
181 166 0.91
182 16 0.09
ACGTcount: A:0.28, C:0.16, G:0.13, T:0.42
Consensus pattern (181 bp):
AAAGTATCGACATTTTAATATATCCGATAACGTTTTACCGATTTTATCATTTTGATACCGGTTTT
ATCATATTTTTACCTGGTATATCGTTGTGGATCGATACATTTTTTAAAAGTATCGACACATTATA
GGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCATTATATT
Found at i:733048 original size:13 final size:13
Alignment explanation
Indices: 733030--733059 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
733020 TGGTGTACAA
733030 GTTCCATGACGAT
1 GTTCCATGACGAT
733043 GTTCCATGACGAT
1 GTTCCATGACGAT
733056 GTTC
1 GTTC
733060 ATGGCGAAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.20, C:0.23, G:0.23, T:0.33
Consensus pattern (13 bp):
GTTCCATGACGAT
Found at i:743150 original size:47 final size:45
Alignment explanation
Indices: 743062--743151 Score: 105
Period size: 47 Copynumber: 2.0 Consensus size: 45
743052 CTATGAAATT
*
743062 AATAAATAATATAAATTTTATTAATAGTTTATTATATATTATTAA
1 AATAAATAATATAAATTTTATTAATAGTTTATAATATATTATTAA
743107 AATAAA-AATATAATATCTTATATTAATA-TTATATAAT-TGATTATT
1 AATAAATAATATAA-AT-TT-TATTAATAGTT-TATAATAT-ATTATT
743152 TTATTGTAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
44 7 0.18
45 8 0.21
46 5 0.13
47 19 0.49
ACGTcount: A:0.49, C:0.01, G:0.02, T:0.48
Consensus pattern (45 bp):
AATAAATAATATAAATTTTATTAATAGTTTATAATATATTATTAA
Found at i:743178 original size:22 final size:23
Alignment explanation
Indices: 743153--743199 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
743143 TTGATTATTT
*
743153 TATTGTAATATTAAAAATA-TAA
1 TATTATAATATTAAAAATATTAA
* *
743175 TATTATATTATTAGAAATATTAA
1 TATTATAATATTAAAAATATTAA
743198 TA
1 TA
743200 AATATATTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (23 bp):
TATTATAATATTAAAAATATTAA
Found at i:743186 original size:30 final size:34
Alignment explanation
Indices: 743126--743205 Score: 96
Period size: 32 Copynumber: 2.4 Consensus size: 34
743116 ATAATATCTT
* * *
743126 ATATTAATATTATATAATTGATTATTTTATT-GTA
1 ATATTAATA-AATATAATTGATTATATTATTAGAA
743160 ATATTAA-AAATATAA-T-ATTATATTATTAGAA
1 ATATTAATAAATATAATTGATTATATTATTAGAA
743191 ATATTAATAAATATA
1 ATATTAATAAATATA
743206 TTTTAAATGT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
30 10 0.24
31 10 0.24
32 13 0.32
33 1 0.02
34 7 0.17
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (34 bp):
ATATTAATAAATATAATTGATTATATTATTAGAA
Found at i:743204 original size:22 final size:22
Alignment explanation
Indices: 743161--743204 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
743151 TTTATTGTAA
*
743161 TATTAAAAATATAATATTATAT
1 TATTAAAAATATAATATAATAT
*
743183 TATTAGAAATATTAATA-AATAT
1 TATTAAAAATA-TAATATAATAT
743205 ATTTTAAATG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (22 bp):
TATTAAAAATATAATATAATAT
Found at i:744503 original size:17 final size:17
Alignment explanation
Indices: 744416--744506 Score: 59
Period size: 17 Copynumber: 5.6 Consensus size: 17
744406 ACTAAGCCTA
744416 TAATTATAA-ATTAATT
1 TAATTATAATATTAATT
* *
744432 TAAATCTAA-ATGTAATT
1 TAATTATAATAT-TAATT
*
744449 TAATTAAAATA-TAATAT
1 TAATTATAATATTAAT-T
* * *
744466 TTA-TAAAATATTAGTT
1 TAATTATAATATTAATT
*
744482 T--TTATAATATTATTT
1 TAATTATAATATTAATT
744497 TAATTATAAT
1 TAATTATAAT
744507 TAAATCACAT
Statistics
Matches: 59, Mismatches: 9, Indels: 13
0.73 0.11 0.16
Matches are distributed among these distances:
15 12 0.20
16 22 0.37
17 24 0.41
18 1 0.02
ACGTcount: A:0.47, C:0.01, G:0.02, T:0.49
Consensus pattern (17 bp):
TAATTATAATATTAATT
Found at i:744920 original size:23 final size:23
Alignment explanation
Indices: 744892--744939 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
744882 AAATATTGTA
*
744892 TTTTAATTAAATTACATTTATAT
1 TTTTAATTAAATTACAATTATAT
*
744915 TTTTAATTAAATTATAATTATAT
1 TTTTAATTAAATTACAATTATAT
744938 TT
1 TT
744940 AGTACTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (23 bp):
TTTTAATTAAATTACAATTATAT
Found at i:771844 original size:13 final size:14
Alignment explanation
Indices: 771807--771845 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
771797 AAACAAGTAA
* *
771807 AATATTAATTCATT
1 AATATTCATTAATT
771821 AATATTCATTAATT
1 AATATTCATTAATT
771835 AATA-TCATTAA
1 AATATTCATTAA
771846 ACATTATTAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 7 0.30
14 16 0.70
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (14 bp):
AATATTCATTAATT
Found at i:771859 original size:19 final size:20
Alignment explanation
Indices: 771827--771864 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
771817 CATTAATATT
771827 CATTAATTAATATCATTAAA
1 CATTAATTAATATCATTAAA
*
771847 CATT-ATTAGTATCATTAA
1 CATTAATTAATATCATTAA
771865 TCAACTATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.45, C:0.11, G:0.03, T:0.42
Consensus pattern (20 bp):
CATTAATTAATATCATTAAA
Found at i:774037 original size:25 final size:27
Alignment explanation
Indices: 773991--774041 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
773981 TTTTTTTTGG
773991 TTTTTTTAAAATAATAATAATTTTAAGT
1 TTTTTTTAAAAT-ATAATAATTTTAAGT
*
774019 TTTTTTTTAAAT-TAA-AATTTTAA
1 TTTTTTTAAAATATAATAATTTTAA
774042 AAATTTATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 8 0.36
26 3 0.14
28 11 0.50
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (27 bp):
TTTTTTTAAAATATAATAATTTTAAGT
Done.