Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008702.1 Hibiscus syriacus cultivar Beakdansim tig00111741_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: 3201804
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 14
Found at i:1093008 original size:23 final size:24
Alignment explanation
Indices: 1092973--1093020 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 24
1092963 AAGCAAAGAA
1092973 AAATGAAAAAAAATTATAA-TAAAT
1 AAATGAAAAAAAA-TATAATTAAAT
*
1092997 AAAT-AAATAAAATATAATTAAAT
1 AAATGAAAAAAAATATAATTAAAT
1093020 A
1 A
1093021 TATACATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 5 0.23
23 13 0.59
24 4 0.18
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (24 bp):
AAATGAAAAAAAATATAATTAAAT
Found at i:1098572 original size:6 final size:5
Alignment explanation
Indices: 1098536--1098569 Score: 50
Period size: 5 Copynumber: 6.4 Consensus size: 5
1098526 CTAAAAGGGG
1098536 AAAAT AAAAT AAAAT AAAAT AATAAT AATAAT AA
1 AAAAT AAAAT AAAAT AAAAT AA-AAT AA-AAT AA
1098570 TAAGATTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 17 0.61
6 11 0.39
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (5 bp):
AAAAT
Found at i:1099765 original size:14 final size:14
Alignment explanation
Indices: 1099746--1099773 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1099736 AATTAAATTA
1099746 ATAAAAATAATAAT
1 ATAAAAATAATAAT
1099760 ATAAAAATAATAAT
1 ATAAAAATAATAAT
1099774 TATTATAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (14 bp):
ATAAAAATAATAAT
Found at i:1099790 original size:2 final size:2
Alignment explanation
Indices: 1099783--1099819 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1099773 TTATTATAAT
1099783 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1099820 TTAAGCCCGG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1100217 original size:84 final size:84
Alignment explanation
Indices: 1100053--1100229 Score: 210
Period size: 84 Copynumber: 2.1 Consensus size: 84
1100043 CGAACTCGTC
* * * *
1100053 AGGTCTTTGGTTGGCAGATAGCCCTTGTCGACTTAAGCTATACTGTAAATGATGTGCCTCGGAGC
1 AGGTCTTTGGTTGGCAAATAACCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTCGGAGC
* * *
1100118 TGAACGTAGTTGAACTAGA
66 TGAACATAATCGAACTAGA
* * * ** *
1100137 AGGTCTTTGGTTGGCAAATAACCCTTCTTGCCTTGAGCTATGTTGCAAATGATGTGCCTTGGAGC
1 AGGTCTTTGGTTGGCAAATAACCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTCGGAGC
** *
1100202 TGAGTATAATCGAACTCGA
66 TGAACATAATCGAACTAGA
1100221 AGGTCTTTG
1 AGGTCTTTG
1100230 TGTTTTAAGA
Statistics
Matches: 77, Mismatches: 16, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
84 77 1.00
ACGTcount: A:0.24, C:0.18, G:0.27, T:0.32
Consensus pattern (84 bp):
AGGTCTTTGGTTGGCAAATAACCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTCGGAGC
TGAACATAATCGAACTAGA
Found at i:1100326 original size:34 final size:33
Alignment explanation
Indices: 1100226--1100376 Score: 234
Period size: 33 Copynumber: 4.6 Consensus size: 33
1100216 CTCGAAGGTC
*
1100226 TTTGTGTTTTAAGAGAAAC-ATCTTCAAAGGTTT
1 TTTGTGTTTCAAGAGAAACGAT-TTCAAAGGTTT
*
1100259 TTTGTGTTTCAAGAGAAACAATTTCAAA-GTTT
1 TTTGTGTTTCAAGAGAAACGATTTCAAAGGTTT
*
1100291 TTTTTGTTTCAAGAGAAACGATTTCAAAGGTTTT
1 TTTGTGTTTCAAGAGAAACGATTTCAAAGG-TTT
*
1100325 TTTGTGTTTCAAGATAAACGATTTCAAAGGTTT
1 TTTGTGTTTCAAGAGAAACGATTTCAAAGGTTT
1100358 TTTGTGTTTCAAGAGAAAC
1 TTTGTGTTTCAAGAGAAAC
1100377 TGTCTCCAAG
Statistics
Matches: 109, Mismatches: 6, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
32 30 0.28
33 46 0.42
34 33 0.30
ACGTcount: A:0.31, C:0.09, G:0.18, T:0.42
Consensus pattern (33 bp):
TTTGTGTTTCAAGAGAAACGATTTCAAAGGTTT
Found at i:1100409 original size:37 final size:34
Alignment explanation
Indices: 1100362--1100527 Score: 128
Period size: 37 Copynumber: 4.8 Consensus size: 34
1100352 AGGTTTTTTG
1100362 TGTTTCAAGAGAAACTGTCTCCAAGGAGGCAGAATTT
1 TGTTTCAAGAGAAACTGTCT-CAA-GAGG-AGAATTT
* *
1100399 TGTTTCAAGAGAAACATAT-TC-A-A--AG-ATTGG
1 TGTTTCAAGAGAAAC-TGTCTCAAGAGGAGAATT-T
*
1100429 TGTTTCAAGAGAAACTGTCTCAAGAGAGAGAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAG-GAG-AATTT
* * *
1100465 TGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAG-G--AGAATTT
* *
1100502 TGTTTCAAGAGAAACTATCTAAAGAG
1 TGTTTCAAGAGAAACTGTCTCAAGAG
1100528 AGACAAAACA
Statistics
Matches: 106, Mismatches: 11, Indels: 24
0.75 0.08 0.17
Matches are distributed among these distances:
29 5 0.05
30 19 0.18
31 1 0.01
32 1 0.01
33 1 0.01
35 3 0.03
36 28 0.26
37 45 0.42
38 3 0.03
ACGTcount: A:0.39, C:0.13, G:0.21, T:0.27
Consensus pattern (34 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGGAGAATTT
Found at i:1100475 original size:17 final size:17
Alignment explanation
Indices: 1100455--1100515 Score: 54
Period size: 17 Copynumber: 3.4 Consensus size: 17
1100445 GTCTCAAGAG
1100455 AGAGAAAATTTGTTTCA
1 AGAGAAAATTTGTTTCA
*
1100472 AGAG-AAA-TTGTCTCAA
1 AGAGAAAATTTGTTTC-A
1100488 GAGAGACAAAACTTTGTTTCA
1 -AGAG--AAAA-TTTGTTTCA
1100509 AGAGAAA
1 AGAGAAA
1100516 CTATCTAAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 13
0.70 0.04 0.26
Matches are distributed among these distances:
15 6 0.17
16 4 0.11
17 8 0.23
18 3 0.09
20 7 0.20
21 1 0.03
22 6 0.17
ACGTcount: A:0.44, C:0.10, G:0.20, T:0.26
Consensus pattern (17 bp):
AGAGAAAATTTGTTTCA
Found at i:1100528 original size:37 final size:37
Alignment explanation
Indices: 1100429--1100536 Score: 173
Period size: 37 Copynumber: 2.9 Consensus size: 37
1100419 CAAAGATTGG
*
1100429 TGTTTCAAGAGAAACTGTCTCAAGAGAGAGAAAA-TT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
*
1100465 TGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
* *
1100502 TGTTTCAAGAGAAACTATCTAAAGAGAGACAAAAC
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAC
1100537 ATAGTTCTAA
Statistics
Matches: 66, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
36 32 0.48
37 34 0.52
ACGTcount: A:0.44, C:0.13, G:0.19, T:0.24
Consensus pattern (37 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
Found at i:1100578 original size:73 final size:73
Alignment explanation
Indices: 1100429--1100567 Score: 181
Period size: 73 Copynumber: 1.9 Consensus size: 73
1100419 CAAAGATTGG
* * * * * *
1100429 TGTTTCAAGAGAAACTGTCTCAAGAGAGAGAAAATTTGTTTCAAGAGAAATTGTCTCAAGAGAGA
1 TGTTTCAAGAGAAACTATCTAAAGAGAGACAAAAATAGTTTCAAAAGAAATTGTCTCAAGAGAGA
1100494 CAAAACTT
66 CAAAACTT
* *
1100502 TGTTTCAAGAGAAACTATCTAAAGAGAGACAAAACATAG-TTCTAAAAGAAGTTGTCTCAAGGGA
1 TGTTTCAAGAGAAACTATCTAAAGAGAGACAAAA-ATAGTTTC-AAAAGAAATTGTCTCAAGAGA
1100566 GA
64 GA
1100568 TGAAATTTGT
Statistics
Matches: 56, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
73 34 0.61
74 22 0.39
ACGTcount: A:0.42, C:0.12, G:0.21, T:0.24
Consensus pattern (73 bp):
TGTTTCAAGAGAAACTATCTAAAGAGAGACAAAAATAGTTTCAAAAGAAATTGTCTCAAGAGAGA
CAAAACTT
Found at i:1100629 original size:36 final size:36
Alignment explanation
Indices: 1100586--1100654 Score: 129
Period size: 36 Copynumber: 1.9 Consensus size: 36
1100576 GTTCAAAGAT
*
1100586 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAGAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAGAA
1100622 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACA
1100655 AAACTTTATT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.26
Consensus pattern (36 bp):
TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAGAA
Found at i:1105217 original size:22 final size:23
Alignment explanation
Indices: 1105192--1105234 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
1105182 TGTTAGATAA
1105192 GAAATAATA-AAT-AAATAAAAGG
1 GAAA-AATATAATAAAATAAAAGG
1105214 GAAAAATATAATAAAATAAAA
1 GAAAAATATAATAAAATAAAA
1105235 TAATAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 4 0.21
22 7 0.37
23 8 0.42
ACGTcount: A:0.72, C:0.00, G:0.09, T:0.19
Consensus pattern (23 bp):
GAAAAATATAATAAAATAAAAGG
Found at i:1105237 original size:13 final size:14
Alignment explanation
Indices: 1105221--1105249 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1105211 AGGGAAAAAT
1105221 ATAAT-AAAATAAA
1 ATAATAAAAATAAA
1105234 ATAATAAAAATAAA
1 ATAATAAAAATAAA
1105248 AT
1 AT
1105250 TTTAAGATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.33
14 10 0.67
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (14 bp):
ATAATAAAAATAAA
Found at i:1106441 original size:3 final size:3
Alignment explanation
Indices: 1106411--1106474 Score: 51
Period size: 3 Copynumber: 21.3 Consensus size: 3
1106401 TGGCCTGCAA
* *
1106411 AAT AATT AAT -AT AAT GAAT AAA AAT AAT AAT -AT AAA AAT AAT AAT
1 AAT AA-T AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * *
1106456 AAT TAT TAT AAT TAT AAT A
1 AAT AAT AAT AAT AAT AAT A
1106475 TATATATATT
Statistics
Matches: 49, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
2 4 0.08
3 39 0.80
4 6 0.12
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:1106447 original size:14 final size:14
Alignment explanation
Indices: 1106428--1106456 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1106418 AATATAATGA
1106428 ATAAAAATAATAAT
1 ATAAAAATAATAAT
1106442 ATAAAAATAATAAT
1 ATAAAAATAATAAT
1106456 A
1 A
1106457 ATTATTATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (14 bp):
ATAAAAATAATAAT
Found at i:1106870 original size:84 final size:84
Alignment explanation
Indices: 1106724--1106898 Score: 235
Period size: 84 Copynumber: 2.1 Consensus size: 84
1106714 AACTCGTCAT
* * *
1106724 GTCTTTGGTTGGCAGATATCCCTTCTCGACTTAAGTTATGCTTCAAATGATGTGCCTCGGAGCTG
1 GTCTTTGGTTGGCAAATAGCCCTTCTCGACTTAAGCTATGCTTCAAATGATGTGCCTCGGAGCTG
* *
1106789 AGCGTAGTCGAACTCGAAG
66 AGCGTAATCGAACTCAAAG
* * * * *
1106808 GTCTTTGGTTGGTAAATAGCCCTTCTTGCCTTGAGCTATG-TTGCAAATGATGTGCCTTGGAGCT
1 GTCTTTGGTTGGCAAATAGCCCTTCTCGACTTAAGCTATGCTT-CAAATGATGTGCCTCGGAGCT
*
1106872 GAGTGTAATCGAACTCAAAG
65 GAGCGTAATCGAACTCAAAG
1106892 GTCTTTG
1 GTCTTTG
1106899 TGTTTTAAGA
Statistics
Matches: 79, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
83 2 0.03
84 77 0.97
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.33
Consensus pattern (84 bp):
GTCTTTGGTTGGCAAATAGCCCTTCTCGACTTAAGCTATGCTTCAAATGATGTGCCTCGGAGCTG
AGCGTAATCGAACTCAAAG
Found at i:1106996 original size:34 final size:33
Alignment explanation
Indices: 1106886--1107046 Score: 218
Period size: 33 Copynumber: 4.9 Consensus size: 33
1106876 GTAATCGAAC
* *
1106886 TCAAAGG-TCTTTGTGTTTTAAGAGAAAC-ATCT
1 TCAAAGGTTTTTTGTGTTTCAAGAGAAACGAT-T
*
1106918 TCAATGGTTTTTTGTGTTTCAAGAGAAACGATT
1 TCAAAGGTTTTTTGTGTTTCAAGAGAAACGATT
* *
1106951 TCAAAGGTTTTTTTTATTTCAAGAGAAACGATT
1 TCAAAGGTTTTTTGTGTTTCAAGAGAAACGATT
* * *
1106984 TCAAAGGTTTTTTTGTGTTTAAAGATAAGCGATT
1 TCAAAGG-TTTTTTGTGTTTCAAGAGAAACGATT
1107018 TCAAAGGTTTTTTGTGTTTCAAGAGAAAC
1 TCAAAGGTTTTTTGTGTTTCAAGAGAAAC
1107047 TGTCTCCAAG
Statistics
Matches: 112, Mismatches: 14, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
32 6 0.05
33 76 0.68
34 30 0.27
ACGTcount: A:0.30, C:0.09, G:0.19, T:0.41
Consensus pattern (33 bp):
TCAAAGGTTTTTTGTGTTTCAAGAGAAACGATT
Found at i:1107022 original size:67 final size:66
Alignment explanation
Indices: 1106886--1107046 Score: 211
Period size: 67 Copynumber: 2.4 Consensus size: 66
1106876 GTAATCGAAC
* * *
1106886 TCAAAGGTCTTTGTGT-TTT-AAGAGAAACATCTTCAATGGTTTTTTGTGTTTCAAGAGAAACGA
1 TCAAAGGT-TTTTTGTATTTCAAGAGAAACATCTTCAAAGGTTTTTTGTGTTTAAAGAGAAACGA
1106949 TT
65 TT
* * *
1106951 TCAAAGGTTTTTTTTATTTCAAGAGAAACGAT-TTCAAAGGTTTTTTTGTGTTTAAAGATAAGCG
1 TCAAAGGTTTTTTGTATTTCAAGAGAAAC-ATCTTCAAAGG-TTTTTTGTGTTTAAAGAGAAACG
1107015 ATT
64 ATT
*
1107018 TCAAAGGTTTTTTGTGTTTCAAGAGAAAC
1 TCAAAGGTTTTTTGTATTTCAAGAGAAAC
1107047 TGTCTCCAAG
Statistics
Matches: 84, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
64 5 0.06
65 11 0.13
66 16 0.19
67 52 0.62
ACGTcount: A:0.30, C:0.09, G:0.19, T:0.41
Consensus pattern (66 bp):
TCAAAGGTTTTTTGTATTTCAAGAGAAACATCTTCAAAGGTTTTTTGTGTTTAAAGAGAAACGAT
T
Found at i:1107079 original size:37 final size:38
Alignment explanation
Indices: 1107032--1107198 Score: 155
Period size: 37 Copynumber: 4.7 Consensus size: 38
1107022 AGGTTTTTTG
*
1107032 TGTTTCAAGAGAAACTGTCTCCAAG-GAGGCAGAATTT
1 TGTTTCAAGAGAAACTGTCTCCAAGAGAGACAGAATTT
* *
1107069 TGTTTCAAGAGAAAC-ATATCC-----A-A-AG-ATTT
1 TGTTTCAAGAGAAACTGTCTCCAAGAGAGACAGAATTT
*
1107098 GTGTTTCAAGAGAAACTGTCT-CAAGAGAGACA-AAATT
1 -TGTTTCAAGAGAAACTGTCTCCAAGAGAGACAGAATTT
* * *
1107135 TGTTTCAAGAGAAATTGTCT-CAAGAGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCCAAGAGAGACAGAATTT
*
1107172 TGTTTCAAGAGAAACTATCT-CAAGAGA
1 TGTTTCAAGAGAAACTGTCTCCAAGAGA
1107199 AATAAAACTT
Statistics
Matches: 109, Mismatches: 10, Indels: 22
0.77 0.07 0.16
Matches are distributed among these distances:
29 4 0.04
30 18 0.17
31 2 0.02
32 1 0.01
35 1 0.01
36 35 0.32
37 48 0.44
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.27
Consensus pattern (38 bp):
TGTTTCAAGAGAAACTGTCTCCAAGAGAGACAGAATTT
Found at i:1107206 original size:37 final size:37
Alignment explanation
Indices: 1107099--1107236 Score: 181
Period size: 36 Copynumber: 3.8 Consensus size: 37
1107089 CAAAGATTTG
1107099 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
*
1107135 TGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
* * *
1107172 TGTTTCAAGAGAAACTATCTCAAGAGAAATAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
* * * * *
1107209 AGTCT-AAAAGAAATTGTCTCAAGGGAGA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGA
1107237 TGGAATTTGT
Statistics
Matches: 89, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
36 51 0.57
37 38 0.43
ACGTcount: A:0.43, C:0.13, G:0.19, T:0.25
Consensus pattern (37 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
Found at i:1107221 original size:73 final size:73
Alignment explanation
Indices: 1107099--1107236 Score: 197
Period size: 73 Copynumber: 1.9 Consensus size: 73
1107089 CAAAGATTTG
* * * * *
1107099 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAATTGTCTCAAGAGAGA
1 TGTTTCAAGAGAAACTATCTCAAGAGAAACAAAATTAGTCTCAAAAGAAATTGTCTCAAGAGAGA
1107164 CAAAACTT
66 CAAAACTT
* *
1107172 TGTTTCAAGAGAAACTATCTCAAGAGAAATAAAACTTAGTCT-AAAAGAAATTGTCTCAAGGGAG
1 TGTTTCAAGAGAAACTATCTCAAGAGAAACAAAA-TTAGTCTCAAAAGAAATTGTCTCAAGAGAG
1107236 A
65 A
1107237 TGGAATTTGT
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
73 52 0.91
74 5 0.09
ACGTcount: A:0.43, C:0.13, G:0.19, T:0.25
Consensus pattern (73 bp):
TGTTTCAAGAGAAACTATCTCAAGAGAAACAAAATTAGTCTCAAAAGAAATTGTCTCAAGAGAGA
CAAAACTT
Found at i:1107298 original size:36 final size:36
Alignment explanation
Indices: 1107255--1107323 Score: 129
Period size: 36 Copynumber: 1.9 Consensus size: 36
1107245 GTTCAAAGAT
*
1107255 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAGGA
1 TTTGTTTCAAGGGAAACTATCTCAAGAGAGACAGGA
1107291 TTTGTTTCAAGGGAAACTATCTCAAGAGAGACA
1 TTTGTTTCAAGGGAAACTATCTCAAGAGAGACA
1107324 AAACTTTGTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.35, C:0.14, G:0.25, T:0.26
Consensus pattern (36 bp):
TTTGTTTCAAGGGAAACTATCTCAAGAGAGACAGGA
Found at i:1107618 original size:124 final size:122
Alignment explanation
Indices: 1107417--1107891 Score: 379
Period size: 124 Copynumber: 3.8 Consensus size: 122
1107407 GCTGGTGGGT
* * * * * * *
1107417 ACGATTCCCTTTGTCATGAAGTTAAAACCATGAATGGCCCTTTCGTTGTGAAGTTGAGCCTTGAA
1 ACGATTCCCTTCGTCGTGAAGTTAAAACCATGGATGTCCCCTCCGTTGTGGAGTTGAGCCTTGAA
*
1107482 TTCGATATCCTTCATCGTGAAGTTGAAATCCAATATAAAGATGAATGCTGCTTGTGTGC
66 TTGGATATCCTTCATCGTGAAGTTGAAATCCAAT-TAAAGATG-ATGCTGCTTGTGTGC
* *
1107541 ACGATTCCCTTCGTCGTGAAGTTAAAACCATGGATGTCCCCTCCGTCGTGGAGTTGAGCGTTGAA
1 ACGATTCCCTTCGTCGTGAAGTTAAAACCATGGATGTCCCCTCCGTTGTGGAGTTGAGCCTTGAA
* * * * * * *
1107606 TTGGATATCCTTCGTCGTGAAGTTGAAATCCAATGAAAGTTG-TGTTGTTTTGAGTCC
66 TTGGATATCCTTCATCGTGAAGTTGAAATCCAATTAAAGATGATGCTG-CTTGTGTGC
* * * *** ** * **
1107663 A-G-TAT-CCTTCGTCGTGAAGTTGAAA--TTGGATCTGAAACTGGAAAGTTTATTGACAGACAC
1 ACGAT-TCCCTTCGTCGTGAAGTTAAAACCATGGATGT-CCCCT---CCG-TT-GTG---GA-GT
* * * * ** *
1107723 TCATTCTTTGAGTTGGATATCCTTCATCGTGAAGTTGAAATCCAAATCTGGAGATGGATGCTACT
55 TGA-GCCTTGAATTGGATATCCTTCATCGTGAAGTTGAAATCC-AAT-TAAAGAT-GATGCTGCT
1107788 TGTGTGC
116 TGTGTGC
* * *
1107795 ACGATTCCCTTCGTCGTGAAGTTGAAACCATGGATGACCCCTCCGTTGTGGATTTGAGCCTTGAA
1 ACGATTCCCTTCGTCGTGAAGTTAAAACCATGGATGTCCCCTCCGTTGTGGAGTTGAGCCTTGAA
* *
1107860 TTGGATATCCTT-TTCATGAAGTTGAAATCCAA
66 TTGGATATCCTTCATCGTGAAGTTGAAATCCAA
1107892 GTAAGTTGTA
Statistics
Matches: 269, Mismatches: 60, Indels: 45
0.72 0.16 0.12
Matches are distributed among these distances:
118 6 0.02
119 2 0.01
120 20 0.07
121 6 0.02
122 8 0.03
123 9 0.03
124 106 0.39
125 17 0.06
126 2 0.01
127 4 0.01
128 2 0.01
129 35 0.13
130 5 0.02
131 5 0.02
132 9 0.03
133 5 0.02
134 21 0.08
135 2 0.01
136 5 0.02
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (122 bp):
ACGATTCCCTTCGTCGTGAAGTTAAAACCATGGATGTCCCCTCCGTTGTGGAGTTGAGCCTTGAA
TTGGATATCCTTCATCGTGAAGTTGAAATCCAATTAAAGATGATGCTGCTTGTGTGC
Found at i:1114505 original size:25 final size:25
Alignment explanation
Indices: 1114458--1114505 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
1114448 AGGTTTATAT
*
1114458 TATAAAGTATATTTTTATCTAAATA
1 TATAAAGTATATTTTTATATAAATA
*
1114483 TATAAAGTAT-TTTCTTTTATAAA
1 TATAAAGTATATTT-TTATATAAA
1114506 ATAAATACTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 3 0.15
25 17 0.85
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.50
Consensus pattern (25 bp):
TATAAAGTATATTTTTATATAAATA
Found at i:1115208 original size:59 final size:59
Alignment explanation
Indices: 1115143--1115267 Score: 173
Period size: 59 Copynumber: 2.1 Consensus size: 59
1115133 TAGTCAGATG
* *
1115143 ATCATTTTATAACTTTTAATAGTCGAAT-GACTCAATAAAATAATA-TATCATAATAAAAA
1 ATCATTTTATAACTTTAAATAATC-AATCGACTCAATAAAATAATATTAT-ATAATAAAAA
* * *
1115202 ATCATTTTATAACTTTAAATAATCATTCGACTTAATAAAATAATATTATATAGTAAAAA
1 ATCATTTTATAACTTTAAATAATCAATCGACTCAATAAAATAATATTATATAATAAAAA
1115261 ATCATTT
1 ATCATTT
1115268 ATGTATTTTT
Statistics
Matches: 59, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
58 2 0.03
59 54 0.92
60 3 0.05
ACGTcount: A:0.48, C:0.10, G:0.04, T:0.38
Consensus pattern (59 bp):
ATCATTTTATAACTTTAAATAATCAATCGACTCAATAAAATAATATTATATAATAAAAA
Found at i:1117350 original size:19 final size:19
Alignment explanation
Indices: 1117309--1117365 Score: 55
Period size: 19 Copynumber: 3.0 Consensus size: 19
1117299 TAAAAGTAAA
* *
1117309 AAAAGAAATAAAATAAA-AT
1 AAAATAAAT-AAATAAATAG
*
1117328 AAAATACAA-ATATAAATAG
1 AAAATA-AATAAATAAATAG
1117347 AAAATAAATAAATAAATAG
1 AAAATAAATAAATAAATAG
1117366 TGAAAAAAGA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
18 8 0.26
19 21 0.68
20 2 0.06
ACGTcount: A:0.74, C:0.02, G:0.05, T:0.19
Consensus pattern (19 bp):
AAAATAAATAAATAAATAG
Found at i:1117351 original size:13 final size:11
Alignment explanation
Indices: 1117299--1117358 Score: 52
Period size: 11 Copynumber: 5.4 Consensus size: 11
1117289 AATTAATAAG
*
1117299 TAAAAGTAAAA
1 TAAAAATAAAA
*
1117310 AAAGAAATAAAA
1 TAA-AAATAAAA
1117322 T-AAAATAAAA
1 TAAAAATAAAA
*
1117332 TACAAATATAAA
1 TAAAAATA-AAA
1117344 TAGAAAAT-AAA
1 TA-AAAATAAAA
1117355 TAAA
1 TAAA
1117359 TAAATAGTGA
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
10 11 0.28
11 13 0.32
12 12 0.30
13 4 0.10
ACGTcount: A:0.75, C:0.02, G:0.05, T:0.18
Consensus pattern (11 bp):
TAAAAATAAAA
Found at i:1117460 original size:33 final size:33
Alignment explanation
Indices: 1117408--1117496 Score: 83
Period size: 33 Copynumber: 2.7 Consensus size: 33
1117398 ATAACGTATT
* **
1117408 AAAAATAAAAAAAGGAAAAAAATGATGAT-AAGA
1 AAAAATAAATAAACAAAAAAAATGA-GATAAAGA
* * *
1117441 AAAAA-AATATAAACAAAAAAAGTTAGGTAAAGA
1 AAAAATAA-ATAAACAAAAAAAATGAGATAAAGA
*
1117474 AAAAATAAATAAACAAAACAAAT
1 AAAAATAAATAAACAAAAAAAAT
1117497 AAAATAAAAG
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
32 4 0.09
33 39 0.87
34 2 0.04
ACGTcount: A:0.73, C:0.03, G:0.10, T:0.13
Consensus pattern (33 bp):
AAAAATAAATAAACAAAAAAAATGAGATAAAGA
Found at i:1120863 original size:81 final size:81
Alignment explanation
Indices: 1120755--1121042 Score: 375
Period size: 81 Copynumber: 3.6 Consensus size: 81
1120745 CTATGCTGTG
* * * *
1120755 AATGATGTG-CCTTG-AGCTGAATGGAATCGAACTCGAAGGTATTTGGCATATAACCCTTTTAGC
1 AATGATGTGCCCTTGAAGCTGAGTGGAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTAGC
* *
1120818 CTTGAGCTATCCTACA
66 CTTGAGTTATGCTACA
* * * *
1120834 AATGATAGTGTCTTTG-AGCTGAGTGGAATCAAACTCTAAGGTCTTTGGCAGATAACCCTTCTAG
1 AATGAT-GTGCCCTTGAAGCTGAGTGGAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTAG
* *
1120898 CCTTAAGTTATGCTGCA
65 CCTTGAGTTATGCTACA
* * * *
1120915 AATGATGTGCCCTTGAATCTGAGTGTAATTGAACTCGAGGGTCTTTGGCAGATAACCCTTCTAGC
1 AATGATGTGCCCTTGAAGCTGAGTGGAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTAGC
*
1120980 CTTGAGTTATGCTATA
66 CTTGAGTTATGCTACA
* *
1120996 AATGATGTGCCCTTGAAGCTGAGTGTAGTCGAACTCGAAGGTCTTTG
1 AATGATGTGCCCTTGAAGCTGAGTGGAATCGAACTCGAAGGTCTTTG
1121043 TGTTTCAAGA
Statistics
Matches: 180, Mismatches: 26, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
79 6 0.03
80 10 0.06
81 164 0.91
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.32
Consensus pattern (81 bp):
AATGATGTGCCCTTGAAGCTGAGTGGAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTAGC
CTTGAGTTATGCTACA
Found at i:1121279 original size:36 final size:36
Alignment explanation
Indices: 1121187--1121657 Score: 342
Period size: 36 Copynumber: 13.3 Consensus size: 36
1121177 CAAATATTGG
*
1121187 TGTTTCAAGAGAAACTGTCTCAAGAGAGATAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
* * * *
1121224 AGTTTTAAGGGAAATTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* * *
1121260 CGTTTTAAGAGAAACTGTCTC---A-A-ACAAAGCTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAA-ATT
* * *
1121292 AGTTTCAAAAGAAACTGTCTCAAGGGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* * *
1121328 TATTTCAAG-GAAAACATAT-TC-A-A-AG----ATTT
1 TGTTTCAAGAG-AAAC-TGTCTCAAGAGAGACAAAATT
* * * *
1121357 TGTTTCAAGGGAAACTATATCAAGAGAAACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
1121393 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTC-A-AGAG----AGACAAAATT
1121435 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
* * * *
1121472 AGTTCCAAAAGAAACTGTCTCAAGGGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* *
1121508 TGTTT-AATGTA-AAACATAT-TC-A-A-AG----ATTT
1 TGTTTCAA-G-AGAAAC-TGTCTCAAGAGAGACAAAATT
*
1121537 TGTTTCAAGGTAGAAACTATCTCAAGAGAGACAAAATT
1 TGTTTCAA-G-AGAAACTGTCTCAAGAGAGACAAAATT
* * *
1121575 GGTTTCAAGGGAAACTGTCTCAATAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* **
1121611 TGTTTTAAGAGACGCTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
1121648 TGTTTCAAGA
1 TGTTTCAAGA
1121658 CGACCCCTTA
Statistics
Matches: 346, Mismatches: 50, Indels: 76
0.73 0.11 0.16
Matches are distributed among these distances:
28 3 0.01
29 25 0.07
30 10 0.03
31 12 0.03
32 23 0.07
33 6 0.02
34 2 0.01
35 5 0.01
36 127 0.37
37 84 0.24
38 14 0.04
40 4 0.01
41 1 0.00
42 30 0.09
ACGTcount: A:0.42, C:0.13, G:0.18, T:0.27
Consensus pattern (36 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
Found at i:1121434 original size:42 final size:41
Alignment explanation
Indices: 1121383--1121505 Score: 173
Period size: 42 Copynumber: 3.1 Consensus size: 41
1121373 ATATCAAGAG
1121383 AAACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACA
1 AAACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACA
1121424 AAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACA
1 AA-ACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACA
* * * *
1121466 AAAC----TTAGTTCCAAAAGAAACTGTCTCAAGGGAGACA
1 AAACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACA
1121503 AAA
1 AAA
1121506 TTTGTTTAAT
Statistics
Matches: 77, Mismatches: 4, Indels: 6
0.89 0.05 0.07
Matches are distributed among these distances:
37 32 0.42
41 4 0.05
42 41 0.53
ACGTcount: A:0.46, C:0.15, G:0.18, T:0.20
Consensus pattern (41 bp):
AAACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACA
Found at i:1121496 original size:180 final size:173
Alignment explanation
Indices: 1121129--1121647 Score: 638
Period size: 180 Copynumber: 2.9 Consensus size: 173
1121119 GTGTTTCAAG
* * * *
1121129 AGAAATTGTCT-ACAGGGAGGCAAAATTTTGTTTTAA-GAGAAACATATTCAAATATTGGTGTTT
1 AGAAACTGTCTCA-AGGGAGACAAAA-TTTG-TTTAAGGA-AAACATATTCAAAGATT-TTGTTT
* * * * *
1121192 CAAGAGAAACTGTCTCAAGAGAGATAAAACTTAGTTTTAAGGGAAATTGTCTCAAGAGAGACAAA
61 CAAGGGAAACTATCTCAAGAGAGACAAAA-TTAGTTTCAAGGGAAACTGTCTCAAGAGAGACAAA
* * *
1121257 ATTCGTTTTAAGAGAAACTGTCTC---A-A-ACAAAGCTTAGTTTCAAA
125 ATTTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAA
*
1121301 AGAAACTGTCTCAAGGGAGACAAAATTTATTTCAAGGAAAACATATTCAAAGATTTTGTTTCAAG
1 AGAAACTGTCTCAAGGGAGACAAAATTTGTTT-AAGGAAAACATATTCAAAGATTTTGTTTCAAG
* * * *
1121366 GGAAACTATATCAAGAGAAACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAGACAA
65 GGAAACTATCTCAAGAGAGACAAAATTAGTTTCAAGGGAAACTGTCTC-A-AGAG----AGACAA
*
1121431 AATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAA
124 AATTTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAA
*
1121481 AGAAACTGTCTCAAGGGAGACAAAATTTGTTTAATGTAAAACATATTCAAAGATTTTGTTTCAAG
1 AGAAACTGTCTCAAGGGAGACAAAATTTGTTTAA-GGAAAACATATTCAAAGATTTTGTTTCAAG
* *
1121546 GTAGAAACTATCTCAAGAGAGACAAAATTGGTTTCAAGGGAAACTGTCTCAATAGAGACAAAATT
65 G--GAAACTATCTCAAGAGAGACAAAATTAGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
**
1121611 TGTTTTAAGAGACGCTGTCTCAAGAGAGACAAAACTT
128 TGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAACTT
1121648 TGTTTCAAGA
Statistics
Matches: 302, Mismatches: 28, Indels: 30
0.84 0.08 0.08
Matches are distributed among these distances:
169 19 0.06
170 33 0.11
171 25 0.08
172 23 0.08
173 1 0.00
175 29 0.10
176 44 0.15
178 1 0.00
179 3 0.01
180 80 0.26
181 1 0.00
182 43 0.14
ACGTcount: A:0.42, C:0.13, G:0.18, T:0.27
Consensus pattern (173 bp):
AGAAACTGTCTCAAGGGAGACAAAATTTGTTTAAGGAAAACATATTCAAAGATTTTGTTTCAAGG
GAAACTATCTCAAGAGAGACAAAATTAGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGT
TTTAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAA
Found at i:1123128 original size:95 final size:95
Alignment explanation
Indices: 1122959--1123141 Score: 264
Period size: 95 Copynumber: 1.9 Consensus size: 95
1122949 AATATGTAAA
* * *
1122959 CACCTTTATCAGGTTAGCTGAATCTTATCCATAAAGCCGGAGCGATTAACCAATTGCCTTAAAGG
1 CACCTTTATCAAGCTAGCTGAATATTATCCATAAAGCCGGAGCGATTAACCAATTGCCTTAAAGG
1123024 GAAAGCTCAAGCTTTATTGTATAGTATAAT
66 GAAAGCTCAAGCTTTATTGTATAGTATAAT
* **
1123054 CACCTTTATCAAGCTAGCTGAATATTATCCATAAAGCCGG-GACGTTTAACCAATTG-CTCTGGA
1 CACCTTTATCAAGCTAGCTGAATATTATCCATAAAGCCGGAG-CGATTAACCAATTGCCT-TAAA
1123117 GGGACAA-CTCAAGCTTTATTGTATA
64 GGGA-AAGCTCAAGCTTTATTGTATA
1123142 CATATAATAT
Statistics
Matches: 79, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
94 3 0.04
95 74 0.94
96 2 0.03
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (95 bp):
CACCTTTATCAAGCTAGCTGAATATTATCCATAAAGCCGGAGCGATTAACCAATTGCCTTAAAGG
GAAAGCTCAAGCTTTATTGTATAGTATAAT
Found at i:1124849 original size:11 final size:11
Alignment explanation
Indices: 1124810--1124858 Score: 61
Period size: 10 Copynumber: 4.8 Consensus size: 11
1124800 GAACGCTGGA
1124810 AACCGGTTTTG
1 AACCGGTTTTG
1124821 -ACCGG-TTT-
1 AACCGGTTTTG
*
1124829 AACTGGTTTTG
1 AACCGGTTTTG
1124840 AACCGGTTTTG
1 AACCGGTTTTG
1124851 -ACCGGTTT
1 AACCGGTTT
1124859 GACCGGTCAC
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
9 7 0.21
10 16 0.48
11 10 0.30
ACGTcount: A:0.16, C:0.18, G:0.27, T:0.39
Consensus pattern (11 bp):
AACCGGTTTTG
Found at i:1124861 original size:9 final size:10
Alignment explanation
Indices: 1124811--1124865 Score: 69
Period size: 9 Copynumber: 5.6 Consensus size: 10
1124801 AACGCTGGAA
1124811 ACCGGTTTTG
1 ACCGGTTTTG
*
1124821 ACCGG-TTTA
1 ACCGGTTTTG
*
1124830 ACTGGTTTTG
1 ACCGGTTTTG
1124840 AACCGGTTTTG
1 -ACCGGTTTTG
1124851 ACCGG-TTTG
1 ACCGGTTTTG
1124860 ACCGGT
1 ACCGGT
1124866 CACGACCCGT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
9 16 0.42
10 13 0.34
11 9 0.24
ACGTcount: A:0.15, C:0.20, G:0.29, T:0.36
Consensus pattern (10 bp):
ACCGGTTTTG
Found at i:1132039 original size:10 final size:10
Alignment explanation
Indices: 1132024--1132078 Score: 51
Period size: 9 Copynumber: 5.6 Consensus size: 10
1132014 AACGCTGGAA
1132024 ACCGGTTTTG
1 ACCGGTTTTG
* *
1132034 ACCGG-TCTA
1 ACCGGTTTTG
*
1132043 ACCGATTTTG
1 ACCGGTTTTG
1132053 AACCGGTTTTG
1 -ACCGGTTTTG
*
1132064 GCCGG-TTTG
1 ACCGGTTTTG
1132073 ACCGGT
1 ACCGGT
1132079 CACGACCCAT
Statistics
Matches: 34, Mismatches: 8, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
9 14 0.41
10 11 0.32
11 9 0.26
ACGTcount: A:0.15, C:0.24, G:0.29, T:0.33
Consensus pattern (10 bp):
ACCGGTTTTG
Found at i:1132114 original size:18 final size:18
Alignment explanation
Indices: 1132091--1132140 Score: 73
Period size: 18 Copynumber: 2.8 Consensus size: 18
1132081 CGACCCATTT
1132091 ACCCGACCCGTTGACCCG
1 ACCCGACCCGTTGACCCG
* *
1132109 ACCCGACCCATTGACTCG
1 ACCCGACCCGTTGACCCG
*
1132127 ACCCGTCCCGTTGA
1 ACCCGACCCGTTGA
1132141 TCGGTGCTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.18, C:0.46, G:0.20, T:0.16
Consensus pattern (18 bp):
ACCCGACCCGTTGACCCG
Found at i:1132204 original size:29 final size:29
Alignment explanation
Indices: 1132143--1132207 Score: 94
Period size: 29 Copynumber: 2.2 Consensus size: 29
1132133 CCCGTTGATC
*** *
1132143 GGTGCTATTCTGGGAATTAATTCGGTTTT
1 GGTGCTATTCTGGGAATTAATTCGAAATG
1132172 GGTGCTATTCTGGGAATTAATTCGAAATG
1 GGTGCTATTCTGGGAATTAATTCGAAATG
1132201 GGTGCTA
1 GGTGCTA
1132208 GTTTAGTAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.22, C:0.11, G:0.29, T:0.38
Consensus pattern (29 bp):
GGTGCTATTCTGGGAATTAATTCGAAATG
Found at i:1135360 original size:16 final size:16
Alignment explanation
Indices: 1135323--1135360 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
1135313 CCCAAAATAA
1135323 AAAAAATAAAATAAAT
1 AAAAAATAAAATAAAT
*
1135339 ACAAAATAAAA-AAAGT
1 AAAAAATAAAATAAA-T
1135355 AAAAAA
1 AAAAAA
1135361 CCAAATAAGG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
15 3 0.16
16 16 0.84
ACGTcount: A:0.82, C:0.03, G:0.03, T:0.13
Consensus pattern (16 bp):
AAAAAATAAAATAAAT
Found at i:1135456 original size:12 final size:12
Alignment explanation
Indices: 1135441--1135519 Score: 50
Period size: 12 Copynumber: 6.4 Consensus size: 12
1135431 CAAACAAAAC
1135441 AAAAAAATAATA
1 AAAAAAATAATA
*
1135453 AAAAATATACATA
1 AAAAAAATA-ATA
* * ***
1135466 TATAAAACGTTA
1 AAAAAAATAATA
*
1135478 AATAAAATAATA
1 AAAAAAATAATA
* *
1135490 ATAATAATAATA
1 AAAAAAATAATA
*
1135502 AGAAAAATAATTA
1 AAAAAAATAA-TA
1135515 AAAAA
1 AAAAA
1135520 GCATCTAATT
Statistics
Matches: 48, Mismatches: 17, Indels: 3
0.71 0.25 0.04
Matches are distributed among these distances:
12 35 0.73
13 13 0.27
ACGTcount: A:0.71, C:0.03, G:0.03, T:0.24
Consensus pattern (12 bp):
AAAAAAATAATA
Found at i:1135946 original size:2 final size:2
Alignment explanation
Indices: 1135939--1135963 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1135929 TAGATAAATA
1135939 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
1135964 CATAATTAAA
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:1141189 original size:34 final size:33
Alignment explanation
Indices: 1141125--1141194 Score: 88
Period size: 34 Copynumber: 2.1 Consensus size: 33
1141115 CTATTTGCAT
*
1141125 AAAAAAATTAGCTACAACGATAAGAAAATGACAA
1 AAAAAAATTAGCTACAACAATAAGAAAATGA-AA
**
1141159 AAAAAAAGTT-GCTACAACAATAAGCCAATGAAA
1 AAAAAAA-TTAGCTACAACAATAAGAAAATGAAA
1141192 AAA
1 AAA
1141195 TATGTTTATT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
33 5 0.16
34 25 0.78
35 2 0.06
ACGTcount: A:0.61, C:0.13, G:0.11, T:0.14
Consensus pattern (33 bp):
AAAAAAATTAGCTACAACAATAAGAAAATGAAA
Found at i:1158093 original size:22 final size:21
Alignment explanation
Indices: 1158050--1158089 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
1158040 AAGACTATTT
1158050 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTTGAAATA
1158071 TCATTTTT-ATATTTTGAAA
1 TCATTTTTCA-ATTTTGAAA
1158090 ATATAGTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.33, C:0.07, G:0.05, T:0.55
Consensus pattern (21 bp):
TCATTTTTCAATTTTGAAATA
Found at i:1158101 original size:21 final size:21
Alignment explanation
Indices: 1158060--1158102 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
1158050 TCATTTTTCA
* *
1158060 ATTTTGAAATATCATTTTTAT
1 ATTTTGAAATATCAGTCTTAT
1158081 ATTTTGAAAATAT-AGTCTTAT
1 ATTTTG-AAATATCAGTCTTAT
1158102 A
1 A
1158103 ATGCGAAGCC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.37, C:0.05, G:0.07, T:0.51
Consensus pattern (21 bp):
ATTTTGAAATATCAGTCTTAT
Found at i:1160083 original size:20 final size:21
Alignment explanation
Indices: 1160058--1160096 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1160048 ATCTTACATA
1160058 GGGGTATC-GGTACCCTCTTG
1 GGGGTATCGGGTACCCTCTTG
1160078 GGGGTATCGGGTACCCTCT
1 GGGGTATCGGGTACCCTCT
1160097 GGGCAATCTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.10, C:0.26, G:0.36, T:0.28
Consensus pattern (21 bp):
GGGGTATCGGGTACCCTCTTG
Found at i:1162739 original size:3 final size:3
Alignment explanation
Indices: 1162731--1162766 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
1162721 TTCACTATCA
1162731 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1162767 ATACAACAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1177667 original size:15 final size:15
Alignment explanation
Indices: 1177643--1177680 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
1177633 CCGCACCCCC
*
1177643 AACCCACATAATTAT
1 AACCCCCATAATTAT
*
1177658 AACCCCCATAATTGT
1 AACCCCCATAATTAT
1177673 AACCCCCA
1 AACCCCCA
1177681 CTACGAGACT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.39, C:0.37, G:0.03, T:0.21
Consensus pattern (15 bp):
AACCCCCATAATTAT
Found at i:1180437 original size:60 final size:60
Alignment explanation
Indices: 1180365--1180482 Score: 150
Period size: 60 Copynumber: 2.0 Consensus size: 60
1180355 GTCAGATGAT
* *
1180365 CATTTTATAACTTTTAATAGTCGAAT-GACTCAATAAAATAATA-TATCATAATAAAAAACC
1 CATTTTATAACTTTAAATAATC-AATCGACTCAATAAAATAATATTAT-ATAATAAAAAACC
* * * *
1180425 CATTTTGTAACTTTAAATAATCATTCGACTTAATAAAATAATATTATATAGTAAAAAA
1 CATTTTATAACTTTAAATAATCAATCGACTCAATAAAATAATATTATATAATAAAAAA
1180483 TCATTTATGT
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
59 2 0.04
60 45 0.90
61 3 0.06
ACGTcount: A:0.48, C:0.11, G:0.05, T:0.36
Consensus pattern (60 bp):
CATTTTATAACTTTAAATAATCAATCGACTCAATAAAATAATATTATATAATAAAAAACC
Found at i:1184997 original size:15 final size:15
Alignment explanation
Indices: 1184979--1185024 Score: 58
Period size: 15 Copynumber: 3.0 Consensus size: 15
1184969 ATCGTTTAAA
*
1184979 ATATAATAAATTATT
1 ATATAATATATTATT
1184994 ATATATATATATTATT
1 ATATA-ATATATTATT
1185010 AT-TAAATATATTATT
1 ATAT-AATATATTATT
1185025 TTAATTATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
15 16 0.57
16 12 0.43
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
ATATAATATATTATT
Found at i:1185018 original size:21 final size:21
Alignment explanation
Indices: 1184987--1185033 Score: 62
Period size: 19 Copynumber: 2.3 Consensus size: 21
1184977 AAATATAATA
*
1184987 AATTATTATATATA-TATATT
1 AATTATTAAATATATTATATT
*
1185007 -ATTATTAAATATATTATTTT
1 AATTATTAAATATATTATATT
1185027 AATTATT
1 AATTATT
1185034 TTAAAATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 12 0.52
20 5 0.22
21 6 0.26
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
AATTATTAAATATATTATATT
Found at i:1185040 original size:24 final size:25
Alignment explanation
Indices: 1185004--1185051 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
1184994 ATATATATAT
*
1185004 ATTATTATTAAAT-ATATTATTTTA
1 ATTATTATTAAATAATAATATTTTA
1185028 ATTATT-TTAAAATAATAATATTTT
1 ATTATTATT-AAATAATAATATTTT
1185052 CTAGATAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 2 0.10
24 10 0.48
25 9 0.43
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (25 bp):
ATTATTATTAAATAATAATATTTTA
Found at i:1186860 original size:3 final size:3
Alignment explanation
Indices: 1186852--1186889 Score: 67
Period size: 3 Copynumber: 12.3 Consensus size: 3
1186842 ACATAGGAAC
1186852 TAT TAT TAT TAT TAT TATT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT T
1186890 TGTACTTTAG
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 31 0.91
4 3 0.09
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:1186875 original size:16 final size:16
Alignment explanation
Indices: 1186854--1186886 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1186844 ATAGGAACTA
1186854 TTATTATTATTATTAT
1 TTATTATTATTATTAT
1186870 TTATTATTATTATTAT
1 TTATTATTATTATTAT
1186886 T
1 T
1186887 ATTTGTACTT
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:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
TTATTATTATTATTAT
Found at i:1186876 original size:19 final size:19
Alignment explanation
Indices: 1186852--1186890 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
1186842 ACATAGGAAC
1186852 TATTATTATTATTATTATT
1 TATTATTATTATTATTATT
1186871 TATTATTATTATTATTATT
1 TATTATTATTATTATTATT
1186890 T
1 T
1186891 GTACTTTAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (19 bp):
TATTATTATTATTATTATT
Found at i:1190100 original size:60 final size:60
Alignment explanation
Indices: 1189970--1190100 Score: 151
Period size: 60 Copynumber: 2.2 Consensus size: 60
1189960 GAATGATCAT
** * *
1189970 TTTGTA-ACTTTTAATAGTCGAGAGACTCAACAAAATAATACCCTATAGTTGAAGGACCA
1 TTTGTATACTTTTAATAACCGAGAGACTCAACAAAATAACACCCTATAATTGAAGGACCA
* * * *
1190029 CTT-TATAACTTTTAATAACCGATG-GACTCAATAAAGTAACACCCTATAATTGAGGGACCA
1 TTTGTAT-ACTTTTAATAACCGA-GAGACTCAACAAAATAACACCCTATAATTGAAGGACCA
1190089 TTTGTATACTTT
1 TTTGTATACTTT
1190101 ACCAAAACAG
Statistics
Matches: 59, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
58 2 0.03
59 2 0.03
60 51 0.86
61 4 0.07
ACGTcount: A:0.37, C:0.18, G:0.14, T:0.32
Consensus pattern (60 bp):
TTTGTATACTTTTAATAACCGAGAGACTCAACAAAATAACACCCTATAATTGAAGGACCA
Found at i:1192875 original size:25 final size:24
Alignment explanation
Indices: 1192847--1192893 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 24
1192837 AAGTAATAAT
1192847 TAAATA-AAAAGAAAATAATAAAAAG
1 TAAATAGAAAAG-AAATAA-AAAAAG
*
1192872 TAAATAGAAACGAAATAAAAAA
1 TAAATAGAAAAGAAATAAAAAA
1192894 TAAAAAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 4 0.20
25 12 0.60
26 4 0.20
ACGTcount: A:0.74, C:0.02, G:0.09, T:0.15
Consensus pattern (24 bp):
TAAATAGAAAAGAAATAAAAAAAG
Found at i:1192909 original size:23 final size:26
Alignment explanation
Indices: 1192873--1192927 Score: 71
Period size: 23 Copynumber: 2.2 Consensus size: 26
1192863 AATAAAAAGT
*
1192873 AAATAGAAACGAAATAAAAAAT-AAA
1 AAATAGAAACGAAACAAAAAATGAAA
1192898 AAATA-AAA-GAAACAAAAAATGAAA
1 AAATAGAAACGAAACAAAAAATGAAA
1192922 ATAATA
1 A-AATA
1192928 TACATATACA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
23 11 0.41
24 7 0.26
25 9 0.33
ACGTcount: A:0.76, C:0.04, G:0.07, T:0.13
Consensus pattern (26 bp):
AAATAGAAACGAAACAAAAAATGAAA
Found at i:1192922 original size:29 final size:29
Alignment explanation
Indices: 1192853--1192925 Score: 78
Period size: 29 Copynumber: 2.4 Consensus size: 29
1192843 TAATTAAATA
*
1192853 AAAAGAAAATAATAAAAAGTAAATAGAAACG
1 AAAA-AAAA-AATAAAAAATAAATAGAAACG
*
1192884 AAATAAAAAATAAAAAATAAA-AGAAAC-
1 AAAAAAAAAATAAAAAATAAATAGAAACG
1192911 AAAAAATGAAAATAA
1 AAAAAA--AAAATAA
1192926 TATACATATA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
27 5 0.14
28 6 0.16
29 19 0.51
30 4 0.11
31 3 0.08
ACGTcount: A:0.77, C:0.03, G:0.08, T:0.12
Consensus pattern (29 bp):
AAAAAAAAAATAAAAAATAAATAGAAACG
Found at i:1195037 original size:20 final size:20
Alignment explanation
Indices: 1195012--1195051 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
1195002 GAAGTTGAAA
1195012 TCCCATCTTGTAAATTGTTC
1 TCCCATCTTGTAAATTGTTC
1195032 TCCCATCTTGTAAATTGTTC
1 TCCCATCTTGTAAATTGTTC
1195052 ACTTCGAGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.20, C:0.25, G:0.10, T:0.45
Consensus pattern (20 bp):
TCCCATCTTGTAAATTGTTC
Found at i:1195066 original size:20 final size:22
Alignment explanation
Indices: 1195043--1195088 Score: 53
Period size: 20 Copynumber: 2.2 Consensus size: 22
1195033 CCCATCTTGT
1195043 AAATTG-TTCACTTCG-AGTTC
1 AAATTGCTTCACTTCGAAGTTC
* *
1195063 AAA-TGCTTCGCTTCGAAGTTG
1 AAATTGCTTCACTTCGAAGTTC
1195084 AAATT
1 AAATT
1195089 AACTCTAACA
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
19 2 0.10
20 11 0.52
21 7 0.33
22 1 0.05
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.37
Consensus pattern (22 bp):
AAATTGCTTCACTTCGAAGTTC
Found at i:1195896 original size:14 final size:15
Alignment explanation
Indices: 1195877--1195908 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1195867 ATTTCTTTTC
1195877 TTTTTC-TTTTTCAA
1 TTTTTCTTTTTTCAA
1195891 TTTTTCTTTTTTCAA
1 TTTTTCTTTTTTCAA
1195906 TTT
1 TTT
1195909 AGGGTGCCCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.75
Consensus pattern (15 bp):
TTTTTCTTTTTTCAA
Found at i:1196705 original size:12 final size:12
Alignment explanation
Indices: 1196688--1196769 Score: 56
Period size: 12 Copynumber: 6.8 Consensus size: 12
1196678 ACGGAGATAT
1196688 CAGAAATCAAAA
1 CAGAAATCAAAA
*
1196700 CAGAAATTCAGAA
1 CAGAAA-TCAAAA
* *
1196713 CAGATATCAGAA
1 CAGAAATCAAAA
** * *
1196725 CAGATTTCAGAT
1 CAGAAATCAAAA
**
1196737 CAGATGTCAAAA
1 CAGAAATCAAAA
* *
1196749 CAGAATTCAAAT
1 CAGAAATCAAAA
1196761 CAGAAATCA
1 CAGAAATCA
1196770 GATAAAATAT
Statistics
Matches: 58, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
12 48 0.83
13 10 0.17
ACGTcount: A:0.51, C:0.17, G:0.13, T:0.18
Consensus pattern (12 bp):
CAGAAATCAAAA
Found at i:1196740 original size:24 final size:24
Alignment explanation
Indices: 1196686--1196769 Score: 96
Period size: 24 Copynumber: 3.5 Consensus size: 24
1196676 AAACGGAGAT
1196686 ATCAGAAATCAAAACAGAAATTCAG
1 ATCAGAAATCAAAACAG-AATTCAG
* * * *
1196711 AACAGATATCAGAACAGATTTCAG
1 ATCAGAAATCAAAACAGAATTCAG
** *
1196735 ATCAGATGTCAAAACAGAATTCAA
1 ATCAGAAATCAAAACAGAATTCAG
1196759 ATCAGAAATCA
1 ATCAGAAATCA
1196770 GATAAAATAT
Statistics
Matches: 48, Mismatches: 11, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
24 34 0.71
25 14 0.29
ACGTcount: A:0.51, C:0.17, G:0.13, T:0.19
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATTCAG
Found at i:1199279 original size:15 final size:16
Alignment explanation
Indices: 1199249--1199282 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 16
1199239 GGTCAACATT
1199249 GGTCAACGTCGGTCAAC
1 GGTCAACG-CGGTCAAC
1199266 GGTCAACG-GGTCAAC
1 GGTCAACGCGGTCAAC
1199281 GG
1 GG
1199283 GTAGGGTCGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
17 8 0.47
ACGTcount: A:0.24, C:0.26, G:0.35, T:0.15
Consensus pattern (16 bp):
GGTCAACGCGGTCAAC
Found at i:1210546 original size:9 final size:8
Alignment explanation
Indices: 1210534--1210602 Score: 50
Period size: 8 Copynumber: 7.9 Consensus size: 8
1210524 TAATTGAAAT
1210534 AAATAAAA
1 AAATAAAA
1210542 CAAATTAAAA
1 -AAA-TAAAA
*
1210552 AAATAAAT
1 AAATAAAA
1210560 AAATAAAA
1 AAATAAAA
1210568 TAAA-ACAGTAA
1 -AAATA-A--AA
*
1210579 AATTAAAA
1 AAATAAAA
1210587 AAATAAAA
1 AAATAAAA
1210595 AAAGTAAA
1 AAA-TAAA
1210603 CACAAACGAA
Statistics
Matches: 49, Mismatches: 4, Indels: 14
0.73 0.06 0.21
Matches are distributed among these distances:
8 24 0.49
9 14 0.29
10 8 0.16
11 3 0.06
ACGTcount: A:0.77, C:0.03, G:0.03, T:0.17
Consensus pattern (8 bp):
AAATAAAA
Found at i:1210568 original size:13 final size:13
Alignment explanation
Indices: 1210530--1210594 Score: 62
Period size: 13 Copynumber: 4.9 Consensus size: 13
1210520 AGAATAATTG
*
1210530 AAATAAATAAAAC
1 AAATAAATAAAAT
1210543 AAATTAAA-AAAAT
1 AAA-TAAATAAAAT
1210556 AAATAAATAAAAT
1 AAATAAATAAAAT
*
1210569 AAA-ACAGTAAAATT
1 AAATA-AATAAAA-T
*
1210583 AAAAAAATAAAA
1 AAATAAATAAAA
1210595 AAAGTAAACA
Statistics
Matches: 44, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
12 5 0.11
13 24 0.55
14 14 0.32
15 1 0.02
ACGTcount: A:0.77, C:0.03, G:0.02, T:0.18
Consensus pattern (13 bp):
AAATAAATAAAAT
Found at i:1210568 original size:22 final size:20
Alignment explanation
Indices: 1210530--1210602 Score: 74
Period size: 22 Copynumber: 3.4 Consensus size: 20
1210520 AGAATAATTG
1210530 AAATAAATAAAACAAATTAAAA
1 AAATAAATAAAA-AAA-TAAAA
1210552 AAATAAATAAATAAAATAAAA
1 AAATAAATAAA-AAAATAAAA
* *
1210573 CAGTAAAATTAAAAAAATAAAA
1 AAAT-AAA-TAAAAAAATAAAA
1210595 AAAGTAAA
1 AAA-TAAA
1210603 CACAAACGAA
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
21 7 0.16
22 30 0.70
23 6 0.14
ACGTcount: A:0.77, C:0.03, G:0.03, T:0.18
Consensus pattern (20 bp):
AAATAAATAAAAAAATAAAA
Found at i:1210595 original size:23 final size:23
Alignment explanation
Indices: 1210547--1210602 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 23
1210537 TAAAACAAAT
*
1210547 TAAAAAAAT-AAA-TAAATAAAA
1 TAAAAAAGTAAAATTAAATAAAA
*
1210568 TAAAACAGTAAAATTAAA-AAAA
1 TAAAAAAGTAAAATTAAATAAAA
1210590 TAAAAAAAGTAAA
1 T-AAAAAAGTAAA
1210603 CACAAACGAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
21 7 0.24
22 8 0.28
23 14 0.48
ACGTcount: A:0.77, C:0.02, G:0.04, T:0.18
Consensus pattern (23 bp):
TAAAAAAGTAAAATTAAATAAAA
Found at i:1210642 original size:21 final size:21
Alignment explanation
Indices: 1210618--1210663 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
1210608 ACGAAAGTAG
1210618 AAAAA-AAAGAAATAAAAAATT
1 AAAAATAAA-AAATAAAAAATT
* *
1210639 AAAAATTAAAAATTAAAAATT
1 AAAAATAAAAAATAAAAAATT
1210660 AAAA
1 AAAA
1210664 TGAAAGTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 20 0.91
22 2 0.09
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (21 bp):
AAAAATAAAAAATAAAAAATT
Found at i:1210644 original size:14 final size:14
Alignment explanation
Indices: 1210627--1210663 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1210617 GAAAAAAAAG
1210627 AAATAAAAAATTAA
1 AAATAAAAAATTAA
*
1210641 AAATTAAAAATTAA
1 AAATAAAAAATTAA
1210655 AAATTAAAA
1 AAA-TAAAA
1210664 TGAAAGTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
14 16 0.80
15 4 0.20
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (14 bp):
AAATAAAAAATTAA
Found at i:1212991 original size:40 final size:39
Alignment explanation
Indices: 1212946--1213023 Score: 120
Period size: 40 Copynumber: 2.0 Consensus size: 39
1212936 GGGATTTCAA
* *
1212946 GAACAAGGTTTTATGTTTGTTTAATTAAATGAATAAACAT
1 GAACAAAGTTTTATGCTTGTTTAATTAAA-GAATAAACAT
*
1212986 GAACAAAGTTTTATGCTTGTTTAATTAAAGAATGAACA
1 GAACAAAGTTTTATGCTTGTTTAATTAAAGAATAAACA
1213024 CAAATAATTG
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
39 8 0.23
40 27 0.77
ACGTcount: A:0.41, C:0.06, G:0.15, T:0.37
Consensus pattern (39 bp):
GAACAAAGTTTTATGCTTGTTTAATTAAAGAATAAACAT
Found at i:1214453 original size:14 final size:13
Alignment explanation
Indices: 1214346--1214465 Score: 53
Period size: 15 Copynumber: 8.5 Consensus size: 13
1214336 ACGTTAGATT
*
1214346 ATAAAAAAAAAAA
1 ATAAAAAAAATAA
*
1214359 AT-AAACAAATAA
1 ATAAAAAAAATAA
**
1214371 ATATTAAGTAAATCAA
1 ATA--AAAAAAAT-AA
* *
1214387 AGAGAAAAAATAA
1 ATAAAAAAAATAA
1214400 ATAAAATAAAATAAA
1 ATAAAA-AAAAT-AA
1214415 ATAAAGAAAATATAA
1 ATAAA-AAAA-ATAA
* **
1214430 TTTTCAAAAAATAA
1 -ATAAAAAAAATAA
1214444 ATAAATAAAAAATAA
1 AT-AA-AAAAAATAA
1214459 ATTAAAA
1 A-TAAAA
1214466 GGATGCAAAT
Statistics
Matches: 79, Mismatches: 16, Indels: 23
0.67 0.14 0.19
Matches are distributed among these distances:
12 10 0.13
13 9 0.11
14 16 0.20
15 34 0.43
16 10 0.13
ACGTcount: A:0.73, C:0.03, G:0.03, T:0.21
Consensus pattern (13 bp):
ATAAAAAAAATAA
Found at i:1215850 original size:14 final size:13
Alignment explanation
Indices: 1215833--1215888 Score: 51
Period size: 14 Copynumber: 4.1 Consensus size: 13
1215823 ATCAAATGAA
1215833 ATAAATAATATAAT
1 ATAAAT-ATATAAT
*
1215847 ATAATATAAATAAT
1 ATAA-ATATATAAT
1215861 -TAAATATAATAAT
1 ATAAATAT-ATAAT
*
1215874 AAAAACTATATAAT
1 ATAAA-TATATAAT
1215888 A
1 A
1215889 CTATATTTCA
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
12 3 0.09
13 8 0.23
14 19 0.54
15 5 0.14
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (13 bp):
ATAAATATATAAT
Found at i:1215857 original size:19 final size:20
Alignment explanation
Indices: 1215832--1215876 Score: 67
Period size: 19 Copynumber: 2.3 Consensus size: 20
1215822 AATCAAATGA
1215832 AATAAATAA-TATAATATAAT
1 AATAAATAATTA-AATATAAT
1215852 -ATAAATAATTAAATATAAT
1 AATAAATAATTAAATATAAT
1215871 AATAAA
1 AATAAA
1215877 AACTATATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
AATAAATAATTAAATATAAT
Found at i:1215930 original size:22 final size:22
Alignment explanation
Indices: 1215902--1215945 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1215892 TATTTCAAAA
* *
1215902 ATATGTTTTCAAAAATTATTTT
1 ATATGTTCTCAAAAATCATTTT
1215924 ATATGTTCTCAAAAATCATTTT
1 ATATGTTCTCAAAAATCATTTT
1215946 TTAAAAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.36, C:0.09, G:0.05, T:0.50
Consensus pattern (22 bp):
ATATGTTCTCAAAAATCATTTT
Found at i:1216008 original size:35 final size:35
Alignment explanation
Indices: 1215944--1216145 Score: 225
Period size: 35 Copynumber: 5.9 Consensus size: 35
1215934 AAAAATCATT
* *
1215944 TTTTAAAAATATATATTATTATATGTTTTCAAAATTA
1 TTTTAAAAA-CTATA-TACTATATGTTTTCAAAATTA
* **
1215981 TTTTAAAAACTATATACCATATGTTTTCAAAATCG
1 TTTTAAAAACTATATACTATATGTTTTCAAAATTA
* **
1216016 TTTTAAAAACTTTATTTTATATGTTTTCAAAATTA
1 TTTTAAAAACTATATACTATATGTTTTCAAAATTA
*
1216051 TTTTAAAAACTATAT--TATACGTTTTCAAAATTA
1 TTTTAAAAACTATATACTATATGTTTTCAAAATTA
* **
1216084 -TTTAAAAA--ATATGCTATATGTTTTCAAAACCA
1 TTTTAAAAACTATATACTATATGTTTTCAAAATTA
* *
1216116 TTTTAAAAACAATATATTATATGTTTTCAA
1 TTTTAAAAACTATATACTATATGTTTTCAA
1216146 TACCGTTTTT
Statistics
Matches: 142, Mismatches: 18, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
30 4 0.03
32 23 0.16
33 25 0.18
35 77 0.54
36 4 0.03
37 9 0.06
ACGTcount: A:0.42, C:0.08, G:0.04, T:0.46
Consensus pattern (35 bp):
TTTTAAAAACTATATACTATATGTTTTCAAAATTA
Found at i:1216136 original size:100 final size:102
Alignment explanation
Indices: 1215960--1216145 Score: 277
Period size: 100 Copynumber: 1.8 Consensus size: 102
1215950 AAATATATAT
* * *
1215960 TATTATATGTTTTCAAAATTATTTTAAAAACTATATACCATATGTTTTCAAAATCGTTTTAAAAA
1 TATTATACGTTTTCAAAATTATTTTAAAAAC-ATATACCATATGTTTTCAAAACCATTTTAAAAA
** *
1216025 CTTTATTTTATATGTTTTCAAAATTATTTTAAAAACTA
65 CAATATATTATATGTTTTCAAAATTATTTTAAAAACTA
* *
1216063 TATTATACGTTTTCAAAATTA-TTTAAAAA-ATATGCTATATGTTTTCAAAACCATTTTAAAAAC
1 TATTATACGTTTTCAAAATTATTTTAAAAACATATACCATATGTTTTCAAAACCATTTTAAAAAC
1216126 AATATATTATATGTTTTCAA
66 AATATATTATATGTTTTCAA
1216146 TACCGTTTTT
Statistics
Matches: 75, Mismatches: 8, Indels: 3
0.87 0.09 0.03
Matches are distributed among these distances:
100 47 0.63
102 8 0.11
103 20 0.27
ACGTcount: A:0.41, C:0.09, G:0.04, T:0.46
Consensus pattern (102 bp):
TATTATACGTTTTCAAAATTATTTTAAAAACATATACCATATGTTTTCAAAACCATTTTAAAAAC
AATATATTATATGTTTTCAAAATTATTTTAAAAACTA
Found at i:1221832 original size:20 final size:20
Alignment explanation
Indices: 1221803--1221841 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1221793 AAAGCTCTTA
*
1221803 TAGGATCATATAGATGCATT
1 TAGGAGCATATAGATGCATT
*
1221823 TAGGAGCATATAGTTGCAT
1 TAGGAGCATATAGATGCAT
1221842 GTGGTGGAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.10, G:0.23, T:0.33
Consensus pattern (20 bp):
TAGGAGCATATAGATGCATT
Found at i:1235735 original size:35 final size:34
Alignment explanation
Indices: 1235670--1235753 Score: 82
Period size: 34 Copynumber: 2.4 Consensus size: 34
1235660 AAAAGAAGTT
*
1235670 AAAAATAAATAAATTAAGAAAATATTAATTTTAA
1 AAAAATAAATAAATAAAGAAAATATTAATTTTAA
* *
1235704 AAAAATGAAATAAA-AAAGGAAATGTTAAATTTTGAA
1 AAAAAT-AAATAAATAAAGAAAATATT-AATTTT-AA
**
1235740 TGAAATAAA-AAATA
1 AAAAATAAATAAATA
1235754 GAATAAAAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
34 18 0.44
35 17 0.41
36 6 0.15
ACGTcount: A:0.64, C:0.00, G:0.08, T:0.27
Consensus pattern (34 bp):
AAAAATAAATAAATAAAGAAAATATTAATTTTAA
Found at i:1236458 original size:4 final size:4
Alignment explanation
Indices: 1236432--1236479 Score: 53
Period size: 4 Copynumber: 11.2 Consensus size: 4
1236422 TTGGACTTGA
1236432 AAAT AAA- AAAT AAAAT GAAAT AAAT AAAAT AAAT AAAT AATAT AAAT
1 AAAT AAAT AAAT -AAAT -AAAT AAAT -AAAT AAAT AAAT AA-AT AAAT
1236479 A
1 A
1236480 CTAATATAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
3 3 0.08
4 20 0.51
5 16 0.41
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:1236467 original size:13 final size:13
Alignment explanation
Indices: 1236431--1236479 Score: 73
Period size: 13 Copynumber: 3.8 Consensus size: 13
1236421 TTTGGACTTG
1236431 AAAATAAA-AAAT
1 AAAATAAATAAAT
1236443 AAAATGAAATAAAT
1 AAAAT-AAATAAAT
1236457 AAAATAAATAAAT
1 AAAATAAATAAAT
*
1236470 AATATAAATA
1 AAAATAAATA
1236480 CTAATATAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
12 5 0.15
13 20 0.59
14 9 0.26
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (13 bp):
AAAATAAATAAAT
Found at i:1236537 original size:22 final size:22
Alignment explanation
Indices: 1236512--1236556 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1236502 ATTTTCAAAA
* *
1236512 ATATGTTTTCAATAATTAATTT
1 ATATGTTCTCAAAAATTAATTT
*
1236534 ATATGTTCTCAAAAATTATTTT
1 ATATGTTCTCAAAAATTAATTT
1236556 A
1 A
1236557 AAAACTATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.38, C:0.07, G:0.04, T:0.51
Consensus pattern (22 bp):
ATATGTTCTCAAAAATTAATTT
Found at i:1236628 original size:35 final size:35
Alignment explanation
Indices: 1236532--1236794 Score: 289
Period size: 35 Copynumber: 7.5 Consensus size: 35
1236522 AATAATTAAT
* *
1236532 TTATATGTTCTCAAAAATTATTTTAAAAACTAT-T-
1 TTATATGTTTTC-AAAATCATTTTAAAAACTATATA
* * *
1236566 TTATACGTTTTCAAAATTATTTAAAAAACTATATA
1 TTATATGTTTTCAAAATCATTTTAAAAACTATATA
* *
1236601 CTATATGTTTTCAAAAGCATTTTAAAAACTATATA
1 TTATATGTTTTCAAAATCATTTTAAAAACTATATA
*
1236636 TTATATGTTTTTAAAA-CTATTTTAAAAACTATATA
1 TTATATGTTTTCAAAATC-ATTTTAAAAACTATATA
* * * *
1236671 TTATACGTTTTCAAAATTATTTTGAAAACTATTTA
1 TTATATGTTTTCAAAATCATTTTAAAAACTATATA
* *
1236706 CTATATGTTTTCAAAACCATTTTAAAAACTATATA
1 TTATATGTTTTCAAAATCATTTTAAAAACTATATA
* * * *
1236741 TTATACGTTTTTAAAAATAAGTTTCCAAAAACTATATA
1 TTATATG-TTTTCAAAATCA-TTT-TAAAAACTATATA
*
1236779 TTATATATTTTCAAAA
1 TTATATGTTTTCAAAA
1236795 ACAATATTTG
Statistics
Matches: 192, Mismatches: 30, Indels: 11
0.82 0.13 0.05
Matches are distributed among these distances:
33 19 0.10
34 12 0.06
35 124 0.65
36 9 0.05
37 11 0.06
38 17 0.09
ACGTcount: A:0.43, C:0.10, G:0.04, T:0.44
Consensus pattern (35 bp):
TTATATGTTTTCAAAATCATTTTAAAAACTATATA
Found at i:1236683 original size:105 final size:105
Alignment explanation
Indices: 1236544--1236794 Score: 371
Period size: 105 Copynumber: 2.4 Consensus size: 105
1236534 ATATGTTCTC
1236544 AAAAATTATTTTAAAAACTAT-T-TTATACGTTTTCAAAATTATTTAAAAAACTATATACTATAT
1 AAAAA-TATTTTAAAAACTATATATTATACGTTTTCAAAATTATTTAAAAAACTATATACTATAT
* *
1236607 GTTTTCAAAAGCATTTTAAAAACTATATATTATATGTTTTT
65 GTTTTCAAAACCATTTTAAAAACTATATATTATACGTTTTT
* ** *
1236648 AAAACTATTTTAAAAACTATATATTATACGTTTTCAAAATTATTTTGAAAACTATTTACTATATG
1 AAAAATATTTTAAAAACTATATATTATACGTTTTCAAAATTATTTAAAAAACTATATACTATATG
1236713 TTTTCAAAACCATTTTAAAAACTATATATTATACGTTTTT
66 TTTTCAAAACCATTTTAAAAACTATATATTATACGTTTTT
* **
1236753 AAAAATAAGTTTCCAAAAACTATATATTATATATTTTCAAAA
1 AAAAAT-A-TTT-TAAAAACTATATATTATACGTTTTCAAAA
1236795 ACAATATTTG
Statistics
Matches: 132, Mismatches: 10, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
103 15 0.11
104 5 0.04
105 82 0.62
106 1 0.01
107 3 0.02
108 26 0.20
ACGTcount: A:0.44, C:0.09, G:0.04, T:0.43
Consensus pattern (105 bp):
AAAAATATTTTAAAAACTATATATTATACGTTTTCAAAATTATTTAAAAAACTATATACTATATG
TTTTCAAAACCATTTTAAAAACTATATATTATACGTTTTT
Found at i:1243456 original size:19 final size:18
Alignment explanation
Indices: 1243405--1243449 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
1243395 TTTATTTCTC
1243405 ATTTT-TTTCTC-TATTT-
1 ATTTTCTTTCTCAT-TTTA
1243421 ATTTTCTTTCTCATTTTA
1 ATTTTCTTTCTCATTTTA
*
1243439 ATTTTTTTTCT
1 ATTTTCTTTCT
1243450 TCGTTTTCGT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
16 5 0.20
17 9 0.36
18 11 0.44
ACGTcount: A:0.13, C:0.13, G:0.00, T:0.73
Consensus pattern (18 bp):
ATTTTCTTTCTCATTTTA
Found at i:1249603 original size:40 final size:41
Alignment explanation
Indices: 1249548--1249627 Score: 117
Period size: 40 Copynumber: 2.0 Consensus size: 41
1249538 CGGGAAATTC
* * *
1249548 ATGAACAAGGTTTTATATTTGTTT-AATTAAATGAATGAAT
1 ATGAACAAAGTTTTATACTCGTTTAAATTAAATGAATGAAT
*
1249588 ATGAACAAAGTTTTATGCTCGTTTAAATTAAATGAATGAA
1 ATGAACAAAGTTTTATACTCGTTTAAATTAAATGAATGAA
1249628 CACAAACAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
40 20 0.57
41 15 0.43
ACGTcount: A:0.41, C:0.05, G:0.15, T:0.39
Consensus pattern (41 bp):
ATGAACAAAGTTTTATACTCGTTTAAATTAAATGAATGAAT
Found at i:1252218 original size:268 final size:267
Alignment explanation
Indices: 1251697--1252235 Score: 819
Period size: 268 Copynumber: 2.0 Consensus size: 267
1251687 TCTCTGCGTT
* * *
1251697 TTTCTTCTCTGTTATGATGGTAAGAGGAAGTTAAATCATCCAATGCAGTGTGTATGTACTGATAT
1 TTTCTTCTATGTTATGATGGGAAGAGGAAGTTAAATCATCCAAAGCAGTGTGTATGTACTGATAT
*
1251762 ATTAATGCATTCAAATGCAGTGTTCTACAAACAAAGCACAACATCTATGGTTGTAAATTGACTAA
66 ATTAATGCATTCAAACGCAGTGTTCTACAAACAAAGCACAACATCTATGGTTGTAAATTGACTAA
* * *
1251827 TCACTAAATTGGAAGATGCAAAATGGAATCCATAATAATCGTGGGGTTTTAAACTTTTAAGTAAT
131 TCACTAAACTGGAAGATGCAAAATAGAATCCATAATAATCATGGGGTTTTAAACTTTTAAGTAAT
* * *
1251892 TTCAAATATTGGAAGTGCATGACCATTGTTATCTTTCTCATTGAGTTATTTGTGATTGCCCAATT
196 TTCAAATATTGGAAGTGCATGACCAATATTATCTTTCTCATTGAGTTATTTGTGATTGCCCAAAT
*
1251957 CCTACGA
261 CCTACAA
* *
1251964 TTTCTTCTATGTTATGATGGGAAGAGGTAGTTAAATGCATTCAAAGCAGTGTGTATGTACTGATA
1 TTTCTTCTATGTTATGATGGGAAGAGGAAGTTAAAT-CATCCAAAGCAGTGTGTATGTACTGATA
* * * * * * *
1252029 TATTAATGCATTCAAACGCAGTGTTCTATACACAAAGCATAACATTTATGGTTGTACATTATATT
65 TATTAATGCATTCAAACGCAGTGTTCTACAAACAAAGCACAACATCTATGGTTGTAAATT-GACT
* * * * *
1252094 GATCACTAAACTGGCAGATGCAAAATAGAATCCATAATAATCATGGGG-TTTATAGTTTTAATTA
129 AATCACTAAACTGGAAGATGCAAAATAGAATCCATAATAATCATGGGGTTTTAAACTTTTAAGTA
*
1252158 ATTTCAAATATTGGAAGTGCATGACCAATATTATCTTTCTCATTGTGTTATTTGTGATTGCCCAA
194 ATTTCAAATATTGGAAGTGCATGACCAATATTATCTTTCTCATTGAGTTATTTGTGATTGCCCAA
1252223 ATCCTACAA
259 ATCCTACAA
1252232 TTTC
1 TTTC
1252236 ATTATGATAT
Statistics
Matches: 244, Mismatches: 26, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
267 33 0.14
268 166 0.68
269 45 0.18
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (267 bp):
TTTCTTCTATGTTATGATGGGAAGAGGAAGTTAAATCATCCAAAGCAGTGTGTATGTACTGATAT
ATTAATGCATTCAAACGCAGTGTTCTACAAACAAAGCACAACATCTATGGTTGTAAATTGACTAA
TCACTAAACTGGAAGATGCAAAATAGAATCCATAATAATCATGGGGTTTTAAACTTTTAAGTAAT
TTCAAATATTGGAAGTGCATGACCAATATTATCTTTCTCATTGAGTTATTTGTGATTGCCCAAAT
CCTACAA
Found at i:1253381 original size:30 final size:31
Alignment explanation
Indices: 1253321--1253393 Score: 82
Period size: 30 Copynumber: 2.5 Consensus size: 31
1253311 AATGGATTTA
* **
1253321 TTTA-GTGACCAAATTATAAATTTGGTAAAG
1 TTTAGGTGACCAAAGTATAAATTTGAAAAAG
1253351 TTT-GGTGACCAAAGTATAAACTTT-AAAAAG
1 TTTAGGTGACCAAAGTATAAA-TTTGAAAAAG
1253381 TTTAGG-GACCAAA
1 TTTAGGTGACCAAA
1253394 ATGTAATTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
30 32 0.86
31 5 0.14
ACGTcount: A:0.41, C:0.10, G:0.18, T:0.32
Consensus pattern (31 bp):
TTTAGGTGACCAAAGTATAAATTTGAAAAAG
Found at i:1254600 original size:24 final size:24
Alignment explanation
Indices: 1254564--1254613 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
1254554 TACATGCATG
*
1254564 ATATTGTATATAGATGTTTTATAC
1 ATATTGTACATAGATGTTTTATAC
1254588 ATATTGTACATAGATGTTTTATAC
1 ATATTGTACATAGATGTTTTATAC
1254612 AT
1 AT
1254614 CATCTGGAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.34, C:0.06, G:0.12, T:0.48
Consensus pattern (24 bp):
ATATTGTACATAGATGTTTTATAC
Found at i:1262748 original size:15 final size:16
Alignment explanation
Indices: 1262717--1262749 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1262707 TAAAAGTGTT
*
1262717 TAAATTATAAGAATAA
1 TAAATAATAAGAATAA
1262733 TAAATAATAA-AATAA
1 TAAATAATAAGAATAA
1262748 TA
1 TA
1262750 TATCGAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (16 bp):
TAAATAATAAGAATAA
Found at i:1264996 original size:17 final size:15
Alignment explanation
Indices: 1264969--1265012 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 15
1264959 TTTAAAATAT
*
1264969 AATAAATTATTA-TA
1 AATATATTATTATTA
*
1264983 GATATATTATTATTA
1 AATATATTATTATTA
1264998 AATATATTATT-TTA
1 AATATATTATTATTA
1265012 A
1 A
1265013 TTATTTTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
14 14 0.54
15 12 0.46
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (15 bp):
AATATATTATTATTA
Found at i:1273911 original size:23 final size:23
Alignment explanation
Indices: 1273885--1273960 Score: 70
Period size: 23 Copynumber: 3.4 Consensus size: 23
1273875 TACAGAGTGT
1273885 ATCGATACACATTCAAGGAATGC
1 ATCGATACACATTCAAGGAATGC
* *
1273908 ATCGGTGCAC-TTACATA-G--TGC
1 ATCGATACACATT-CA-AGGAATGC
*
1273929 ATCGACACACATTCAAGGAATGC
1 ATCGATACACATTCAAGGAATGC
*
1273952 ATCGGTACA
1 ATCGATACA
1273961 ATTTGATAGT
Statistics
Matches: 40, Mismatches: 7, Indels: 12
0.68 0.12 0.20
Matches are distributed among these distances:
20 1 0.03
21 13 0.32
22 4 0.10
23 21 0.52
24 1 0.03
ACGTcount: A:0.34, C:0.24, G:0.20, T:0.22
Consensus pattern (23 bp):
ATCGATACACATTCAAGGAATGC
Found at i:1273970 original size:44 final size:44
Alignment explanation
Indices: 1273875--1273977 Score: 143
Period size: 44 Copynumber: 2.3 Consensus size: 44
1273865 ATTGGTACAG
* * * *
1273875 TACAGAGTGTATCGATACACATTCAAGGAATGCATCGGTGCACT
1 TACATAGTGTATCGACACACATTCAAGGAATGCATCGGTACAAT
*
1273919 TACATAGTGCATCGACACACATTCAAGGAATGCATCGGTACAAT
1 TACATAGTGTATCGACACACATTCAAGGAATGCATCGGTACAAT
**
1273963 TTGATAGTGTATCGA
1 TACATAGTGTATCGA
1273978 TCCACTTTGC
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
44 51 1.00
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.26
Consensus pattern (44 bp):
TACATAGTGTATCGACACACATTCAAGGAATGCATCGGTACAAT
Found at i:1284160 original size:2 final size:2
Alignment explanation
Indices: 1284153--1284191 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
1284143 AATTGAACCC
*
1284153 TA TA TA TA TA TA TA TA CA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1284192 GTGTGTGTGT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1285502 original size:15 final size:14
Alignment explanation
Indices: 1285481--1285536 Score: 76
Period size: 14 Copynumber: 3.9 Consensus size: 14
1285471 ATTGGTTTTT
*
1285481 TGGAAATTGAATTC
1 TGGAAAATGAATTC
*
1285495 TGGAAAATGAATTAA
1 TGGAAAATGAATT-C
*
1285510 TGGAAATTGAATTC
1 TGGAAAATGAATTC
1285524 TGGAAAATGAATT
1 TGGAAAATGAATT
1285537 ACATTTCTGG
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
14 24 0.67
15 12 0.33
ACGTcount: A:0.43, C:0.04, G:0.21, T:0.32
Consensus pattern (14 bp):
TGGAAAATGAATTC
Found at i:1285523 original size:29 final size:29
Alignment explanation
Indices: 1285481--1285537 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
1285471 ATTGGTTTTT
1285481 TGGAAATTGAATTCTGGAAAATGAATTAA
1 TGGAAATTGAATTCTGGAAAATGAATTAA
1285510 TGGAAATTGAATTCTGGAAAATGAATTA
1 TGGAAATTGAATTCTGGAAAATGAATTA
1285538 CATTTCTGGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.44, C:0.04, G:0.21, T:0.32
Consensus pattern (29 bp):
TGGAAATTGAATTCTGGAAAATGAATTAA
Found at i:1285755 original size:28 final size:27
Alignment explanation
Indices: 1285724--1285779 Score: 78
Period size: 27 Copynumber: 2.0 Consensus size: 27
1285714 CTTAATATTA
*
1285724 TTATTTTTAAAATATT-AATATACTTTAT
1 TTATTATT-AAATATTAAATAT-CTTTAT
1285752 TTATTATTAAATATTAAATATCTTTAT
1 TTATTATTAAATATTAAATATCTTTAT
1285779 T
1 T
1285780 AAAATATTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 14 0.54
28 12 0.46
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (27 bp):
TTATTATTAAATATTAAATATCTTTAT
Found at i:1285830 original size:51 final size:47
Alignment explanation
Indices: 1285725--1285830 Score: 113
Period size: 48 Copynumber: 2.1 Consensus size: 47
1285715 TTAATATTAT
* * *
1285725 TATTTTTAAAATATTAATATACTTTATTTATTATTAAATATTAAATA
1 TATTATTAAAATATTAATAGACTTTATTTAATATTAAATATTAAATA
* * *
1285772 TCTTTATTAAAATATTATTAGATTATTATATTAATATTAAATATATAAATAA
1 T-ATTATTAAAATATTAATAGACT-TTAT-TTAATATTAAATAT-TAAAT-A
1285824 TATTATT
1 TATTATT
1285831 CATTACTAAT
Statistics
Matches: 47, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
47 1 0.02
48 17 0.36
49 4 0.09
50 13 0.28
51 10 0.21
52 2 0.04
ACGTcount: A:0.45, C:0.02, G:0.01, T:0.52
Consensus pattern (47 bp):
TATTATTAAAATATTAATAGACTTTATTTAATATTAAATATTAAATA
Found at i:1285988 original size:22 final size:23
Alignment explanation
Indices: 1285960--1286006 Score: 78
Period size: 22 Copynumber: 2.1 Consensus size: 23
1285950 TTGATTATTT
1285960 TATTATAATATTAAAAATA-TAA
1 TATTATAATATTAAAAATATTAA
*
1285982 TATTATATTATTAAAAATATTAA
1 TATTATAATATTAAAAATATTAA
1286005 TA
1 TA
1286007 AATATATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
TATTATAATATTAAAAATATTAA
Found at i:1286014 original size:21 final size:22
Alignment explanation
Indices: 1285967--1286023 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
1285957 TTTTATTATA
*
1285967 ATATTAAAAATA-TAATATTAT
1 ATATTAAAAATATTAATATAAT
1285988 ATTATTAAAAATATTAATA-AAT
1 A-TATTAAAAATATTAATATAAT
**
1286010 ATATTTTAAATATT
1 ATATTAAAAATATT
1286024 TTGATTAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
21 12 0.39
22 14 0.45
23 5 0.16
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
ATATTAAAAATATTAATATAAT
Found at i:1291408 original size:9 final size:10
Alignment explanation
Indices: 1291370--1291424 Score: 51
Period size: 10 Copynumber: 5.7 Consensus size: 10
1291360 CGGCTTAACT
1291370 GGTCTGAATC
1 GGTCTGAATC
* *
1291380 GGTTTG-ACC
1 GGTCTGAATC
*
1291389 GGTTTGAATC
1 GGTCTGAATC
1291399 GGTCTG-ATC
1 GGTCTGAATC
* *
1291408 GGTCCGAACC
1 GGTCTGAATC
1291418 GGTCTGA
1 GGTCTGA
1291425 CCTGACCCGA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
9 16 0.44
10 20 0.56
ACGTcount: A:0.16, C:0.22, G:0.33, T:0.29
Consensus pattern (10 bp):
GGTCTGAATC
Found at i:1291410 original size:19 final size:19
Alignment explanation
Indices: 1291370--1291426 Score: 69
Period size: 19 Copynumber: 3.0 Consensus size: 19
1291360 CGGCTTAACT
*
1291370 GGTCTGAATCGGTTTGACC
1 GGTCTGAATCGGTCTGACC
* *
1291389 GGTTTGAATCGGTCTGATC
1 GGTCTGAATCGGTCTGACC
* *
1291408 GGTCCGAACCGGTCTGACC
1 GGTCTGAATCGGTCTGACC
1291427 TGACCCGACC
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.16, C:0.25, G:0.32, T:0.28
Consensus pattern (19 bp):
GGTCTGAATCGGTCTGACC
Found at i:1291495 original size:29 final size:29
Alignment explanation
Indices: 1291460--1291703 Score: 348
Period size: 29 Copynumber: 8.4 Consensus size: 29
1291450 CGACCCGACC
1291460 CGGTGATATTTTGGGAATTATTTTTAAAA
1 CGGTGATATTTTGGGAATTATTTTTAAAA
* **
1291489 CAGTGATATTTTGGTTATTATTTTTAAAA
1 CGGTGATATTTTGGGAATTATTTTTAAAA
* *
1291518 CGGTGATATTTTGGTAATTATTGTTAAAA
1 CGGTGATATTTTGGGAATTATTTTTAAAA
* *
1291547 CGGTGATATTTTAGTAATTATTTTTAAAA
1 CGGTGATATTTTGGGAATTATTTTTAAAA
*
1291576 CGGTGATATGTTGGGAATTATTTTTAAAA
1 CGGTGATATTTTGGGAATTATTTTTAAAA
** *
1291605 CAATGATATTTTAGGAATTATTTTTAAAA
1 CGGTGATATTTTGGGAATTATTTTTAAAA
1291634 CGGTGATATTTTGGGAATTATTTTTAAAGA
1 CGGTGATATTTTGGGAATTATTTTTAAA-A
1291664 -GGTGATATTTTGGGAATTATTTTTAAAGA
1 CGGTGATATTTTGGGAATTATTTTTAAA-A
*
1291693 -GGTGACATTTT
1 CGGTGATATTTT
1291704 AGTAAATACT
Statistics
Matches: 195, Mismatches: 19, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
29 194 0.99
30 1 0.01
ACGTcount: A:0.32, C:0.03, G:0.19, T:0.45
Consensus pattern (29 bp):
CGGTGATATTTTGGGAATTATTTTTAAAA
Found at i:1291716 original size:29 final size:29
Alignment explanation
Indices: 1291612--1291719 Score: 101
Period size: 29 Copynumber: 3.7 Consensus size: 29
1291602 AAACAATGAT
* * *
1291612 ATTTTAGGAATTATTTTTAAA-ACGGTGAT
1 ATTTTAGGAAATACTTTTAAAGA-GGTGAC
* * * *
1291641 ATTTTGGGAATTATTTTTAAAGAGGTGAT
1 ATTTTAGGAAATACTTTTAAAGAGGTGAC
* * *
1291670 ATTTTGGGAATTATTTTTAAAGAGGTGAC
1 ATTTTAGGAAATACTTTTAAAGAGGTGAC
*
1291699 ATTTTAGTAAATACTTTTAAA
1 ATTTTAGGAAATACTTTTAAA
1291720 AATAGTGTAA
Statistics
Matches: 72, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
29 71 0.99
30 1 0.01
ACGTcount: A:0.34, C:0.03, G:0.19, T:0.44
Consensus pattern (29 bp):
ATTTTAGGAAATACTTTTAAAGAGGTGAC
Found at i:1293219 original size:2 final size:2
Alignment explanation
Indices: 1293214--1293252 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1293204 TTTATATAGA
1293214 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1293253 ATGTAACCCC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1294060 original size:24 final size:24
Alignment explanation
Indices: 1294019--1294133 Score: 135
Period size: 24 Copynumber: 4.8 Consensus size: 24
1294009 ATAAATCAGT
* *
1294019 TCAAGTATCATATAAGAAAT-CAGG
1 TCAAGTATCAGATCAG-AATCCAGG
* *
1294043 TCAAGTAACAGATCAGAATCCAAG
1 TCAAGTATCAGATCAGAATCCAGG
*
1294067 TCAAGTATCAGATCAGAATCCATG
1 TCAAGTATCAGATCAGAATCCAGG
*
1294091 TC-AGATATCAGATCAGAATCCATG
1 TCAAG-TATCAGATCAGAATCCAGG
*
1294115 TCAAGTATCAAATCAGAAT
1 TCAAGTATCAGATCAGAAT
1294134 TTAAATCGAA
Statistics
Matches: 81, Mismatches: 7, Indels: 6
0.86 0.07 0.06
Matches are distributed among these distances:
23 5 0.06
24 74 0.91
25 2 0.02
ACGTcount: A:0.43, C:0.18, G:0.16, T:0.23
Consensus pattern (24 bp):
TCAAGTATCAGATCAGAATCCAGG
Found at i:1294149 original size:48 final size:48
Alignment explanation
Indices: 1294051--1294151 Score: 123
Period size: 48 Copynumber: 2.1 Consensus size: 48
1294041 GGTCAAGTAA
* ** *
1294051 CAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCCATGTCAGATAT
1 CAGATCAGAATCCAAGTCAAGTATCAAATCAGAATCCAAATCAGAAAT
* **
1294099 CAGATCAGAATCCATGTCAAGTATCAAATCAGAATTTAAATC-GAAAAT
1 CAGATCAGAATCCAAGTCAAGTATCAAATCAGAATCCAAATCAG-AAAT
1294147 CAGAT
1 CAGAT
1294152 AAAATATTCA
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
47 1 0.02
48 44 0.98
ACGTcount: A:0.43, C:0.19, G:0.15, T:0.24
Consensus pattern (48 bp):
CAGATCAGAATCCAAGTCAAGTATCAAATCAGAATCCAAATCAGAAAT
Found at i:1294365 original size:15 final size:15
Alignment explanation
Indices: 1294345--1294373 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1294335 ATCTTATTCG
1294345 GACAGTTTTCAGAAT
1 GACAGTTTTCAGAAT
1294360 GACAGTTTTCAGAA
1 GACAGTTTTCAGAA
1294374 GCTGTACGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.14, G:0.21, T:0.31
Consensus pattern (15 bp):
GACAGTTTTCAGAAT
Found at i:1296623 original size:13 final size:13
Alignment explanation
Indices: 1296605--1296642 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
1296595 GTCAACGGGT
1296605 CGGGTCGGGTCAA
1 CGGGTCGGGTCAA
* *
1296618 CGGGTCTGGTAAA
1 CGGGTCGGGTCAA
1296631 CGGGTCGGGTCA
1 CGGGTCGGGTCA
1296643 GGTCGGGTTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.16, C:0.21, G:0.45, T:0.18
Consensus pattern (13 bp):
CGGGTCGGGTCAA
Found at i:1303295 original size:29 final size:29
Alignment explanation
Indices: 1303250--1303373 Score: 176
Period size: 29 Copynumber: 4.3 Consensus size: 29
1303240 ACCCGACCCG
* *
1303250 GTGATATTTTGGGAATTATTTTTAAAATA
1 GTGATATTTTGGTAATTATTTTTAAAACA
* *
1303279 GTGATATTTTGGTAATTATTTTGAAAATA
1 GTGATATTTTGGTAATTATTTTTAAAACA
* *
1303308 GTGATATTTTGGTAATTATTGTTAAAACG
1 GTGATATTTTGGTAATTATTTTTAAAACA
* *
1303337 GTGATATTTTAGTAATTATTTTTAAAACG
1 GTGATATTTTGGTAATTATTTTTAAAACA
1303366 GTGATATT
1 GTGATATT
1303374 CAAGTATACC
Statistics
Matches: 87, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 87 1.00
ACGTcount: A:0.33, C:0.02, G:0.18, T:0.48
Consensus pattern (29 bp):
GTGATATTTTGGTAATTATTTTTAAAACA
Found at i:1304797 original size:2 final size:2
Alignment explanation
Indices: 1304792--1304844 Score: 97
Period size: 2 Copynumber: 26.5 Consensus size: 2
1304782 TTTATATAGA
1304792 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
1304834 AT AT AT TT AT A
1 AT AT AT AT AT A
1304845 ATTTCATAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1305346 original size:27 final size:25
Alignment explanation
Indices: 1305296--1305347 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 25
1305286 AGGTTTATAT
*
1305296 TATAAAGTATATTTTTATCCAAATA
1 TATAAAGTATATTTTTATCAAAATA
*
1305321 TATAAAGTATTTTCTTTTATCAAAATA
1 TATAAAGTA-TAT-TTTTATCAAAATA
1305348 AATACTTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 9 0.39
26 2 0.09
27 12 0.52
ACGTcount: A:0.42, C:0.08, G:0.04, T:0.46
Consensus pattern (25 bp):
TATAAAGTATATTTTTATCAAAATA
Found at i:1317972 original size:13 final size:13
Alignment explanation
Indices: 1317956--1317980 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1317946 TATATATATG
1317956 AAAAGAAGAAATA
1 AAAAGAAGAAATA
1317969 AAAAGAAGAAAT
1 AAAAGAAGAAAT
1317981 TTTTGTCGGA
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:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (13 bp):
AAAAGAAGAAATA
Found at i:1321004 original size:24 final size:24
Alignment explanation
Indices: 1320972--1321042 Score: 97
Period size: 24 Copynumber: 3.0 Consensus size: 24
1320962 GATACAAAAT
*
1320972 CTTGTGCTTTTGTAGTAGATGAGG
1 CTTGTGCTTTTGTAGCAGATGAGG
*
1320996 CTTGTGCTTTTGTAGCAGATGAAG
1 CTTGTGCTTTTGTAGCAGATGAGG
* * *
1321020 TTTGTGATTTTGCAGCAGATGAG
1 CTTGTGCTTTTGTAGCAGATGAG
1321043 TCCCCTTGAT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.20, C:0.10, G:0.31, T:0.39
Consensus pattern (24 bp):
CTTGTGCTTTTGTAGCAGATGAGG
Found at i:1324208 original size:45 final size:45
Alignment explanation
Indices: 1324159--1324330 Score: 236
Period size: 45 Copynumber: 3.8 Consensus size: 45
1324149 ACTCTAACAT
*
1324159 CTTTTCTGTTGATAATGCACCCATATGCATTTCAACTATAGTATA
1 CTTTTCTGTTGATAATGCACCCATATACATTTCAACTATAGTATA
* * * * *
1324204 CTTTTATGTTGATAATGTACCCATATACATCTCAACAATAGCATA
1 CTTTTCTGTTGATAATGCACCCATATACATTTCAACTATAGTATA
* * * *
1324249 TTTTTCTGTTGATAATGTACCCATATACATTTCAACTGTAATATA
1 CTTTTCTGTTGATAATGCACCCATATACATTTCAACTATAGTATA
* *
1324294 CTTTTCTATTGATAATGCACCCATATGCATTTCAACT
1 CTTTTCTGTTGATAATGCACCCATATACATTTCAACT
1324331 CTGGCATTCT
Statistics
Matches: 110, Mismatches: 17, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 110 1.00
ACGTcount: A:0.31, C:0.20, G:0.09, T:0.40
Consensus pattern (45 bp):
CTTTTCTGTTGATAATGCACCCATATACATTTCAACTATAGTATA
Found at i:1324354 original size:90 final size:90
Alignment explanation
Indices: 1324170--1324369 Score: 231
Period size: 90 Copynumber: 2.2 Consensus size: 90
1324160 TTTTCTGTTG
* * *
1324170 ATAATGCACCCATATGCATTTCAACTATAGTATACTTTTATGTTGATAATGTACCCATATACATC
1 ATAATGCACCCATATGCATTTCAACTATAATATACTTTTATATTGATAATGCACCCATATACATC
* ***
1324235 TCAACAATAGCATATTTTTCTGTTG
66 TCAACAATAGCATATCTTTCTGCCA
* * * * * *
1324260 ATAATGTACCCATATACATTTCAACTGTAATATACTTTTCTATTGATAATGCACCCATATGCATT
1 ATAATGCACCCATATGCATTTCAACTATAATATACTTTTATATTGATAATGCACCCATATACATC
** *
1324325 TCAACTCTGGCAT-TCTTTCATGCCA
66 TCAACAATAGCATATCTTTC-TGCCA
*
1324350 ATAATGCATCCATATGCATT
1 ATAATGCACCCATATGCATT
1324370 ATTCTGTTAT
Statistics
Matches: 90, Mismatches: 19, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
89 5 0.06
90 85 0.94
ACGTcount: A:0.32, C:0.21, G:0.10, T:0.38
Consensus pattern (90 bp):
ATAATGCACCCATATGCATTTCAACTATAATATACTTTTATATTGATAATGCACCCATATACATC
TCAACAATAGCATATCTTTCTGCCA
Found at i:1324435 original size:79 final size:79
Alignment explanation
Indices: 1324333--1324537 Score: 304
Period size: 79 Copynumber: 2.6 Consensus size: 79
1324323 TTTCAACTCT
* *
1324333 GGCATTCTTTCATGCCAATAATGCATCCATATGCATTATTCTGTTATGCCGATAATGTACCCATA
1 GGCATCCTTTCATGCCAATAATGCACCCATATGCATTATTCTGTTATGCCGATAATGTACCCATA
***
1324398 TACATATCCTCTAA
66 TACATATAAGCTAA
* * *
1324412 GGTATCCTTTCATGCCACTAATGCACCCATATGCATTATTATGTTATGCCGATAATGTACCCATA
1 GGCATCCTTTCATGCCAATAATGCACCCATATGCATTATTCTGTTATGCCGATAATGTACCCATA
1324477 TACATATAAGCTAA
66 TACATATAAGCTAA
* *
1324491 GGCATCCTTTCATGCCATTAATGCACCCATATG-AGTTATTCTTTTAT
1 GGCATCCTTTCATGCCAATAATGCACCCATATGCA-TTATTCTGTTAT
1324538 TCATTAGTTT
Statistics
Matches: 113, Mismatches: 12, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
78 1 0.01
79 112 0.99
ACGTcount: A:0.29, C:0.23, G:0.12, T:0.36
Consensus pattern (79 bp):
GGCATCCTTTCATGCCAATAATGCACCCATATGCATTATTCTGTTATGCCGATAATGTACCCATA
TACATATAAGCTAA
Found at i:1324855 original size:19 final size:21
Alignment explanation
Indices: 1324831--1324870 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
1324821 AACATTTCTA
1324831 ACCCTA-T-GGTATCGATACT
1 ACCCTATTAGGTATCGATACT
1324850 ACCCTATTAGGGTATCGATAC
1 ACCCTATTA-GGTATCGATAC
1324871 CCCCTTCATG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.33
20 1 0.06
22 11 0.61
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.30
Consensus pattern (21 bp):
ACCCTATTAGGTATCGATACT
Found at i:1328685 original size:2 final size:2
Alignment explanation
Indices: 1328678--1328704 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1328668 TTTTGTACAT
1328678 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1328705 CACCCCTTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1329262 original size:45 final size:45
Alignment explanation
Indices: 1329208--1329378 Score: 182
Period size: 45 Copynumber: 3.8 Consensus size: 45
1329198 CTCTAACAAC
* * *
1329208 TTTTCTGTTGATAATACGCCCATATGCATTTCAACTATAGTATAT
1 TTTTCTGTTGATAATGCACCCATATACATTTCAACTATAGTATAT
* * * * *
1329253 TTTTATGTTGATAATGTACCCATATACATCTCAACCATAGCATAT
1 TTTTCTGTTGATAATGCACCCATATACATTTCAACTATAGTATAT
* * * *
1329298 ATTTT-TGTTGATAATGTACCCATATACATTTAAACTCTAGTATAC
1 -TTTTCTGTTGATAATGCACCCATATACATTTCAACTATAGTATAT
* * * *
1329343 ATTTCTATTGATGATGCACCCATATGCATTTCAACT
1 TTTTCTGTTGATAATGCACCCATATACATTTCAACT
1329379 CTGGCATTTT
Statistics
Matches: 104, Mismatches: 20, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
44 3 0.03
45 97 0.93
46 4 0.04
ACGTcount: A:0.31, C:0.19, G:0.10, T:0.40
Consensus pattern (45 bp):
TTTTCTGTTGATAATGCACCCATATACATTTCAACTATAGTATAT
Done.