Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009235.1 Hibiscus syriacus cultivar Beakdansim tig00112857_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: 1478786
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 6
Found at i:1126687 original size:19 final size:19
Alignment explanation
Indices: 1126651--1126695 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
1126641 AAAATCGCAA
*
1126651 TGCGATTTTTGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
*
1126670 TGCGTTTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
1126689 TGCGATT
1 TGCGATT
1126696 CTCTCGTTGC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.07, C:0.16, G:0.24, T:0.53
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:1127252 original size:20 final size:20
Alignment explanation
Indices: 1127227--1127279 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
1127217 GCGCTATGTA
*
1127227 AATCGCGTTGCGAAAGTTAG
1 AATCGCGTTGCGAAAGTCAG
1127247 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
1127267 TATCTCGTTGCGA
1 AATCGCGTTGCGA
1127280 TTTTGTATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.26, C:0.19, G:0.28, T:0.26
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:1127313 original size:20 final size:20
Alignment explanation
Indices: 1127288--1127341 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
1127278 GATTTTGTAT
1127288 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
1127308 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
1127328 TATCGCATTGCGAT
1 TATCGCATTGCGAT
1127342 TTTCCCAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:1127326 original size:61 final size:61
Alignment explanation
Indices: 1127228--1127344 Score: 162
Period size: 61 Copynumber: 1.9 Consensus size: 61
1127218 CGCTATGTAA
* * * * *
1127228 ATCGCGTTGCGAAAGTTAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
* * *
1127289 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT
1127345 CCCAATTCGC
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 48 1.00
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.34
Consensus pattern (61 bp):
ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
Found at i:1127360 original size:61 final size:61
Alignment explanation
Indices: 1127228--1127362 Score: 155
Period size: 61 Copynumber: 2.2 Consensus size: 61
1127218 CGCTATGTAA
* * * * * ** *
1127228 ATCGCGTTGCGAAAGTTAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
* * *
1127289 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT-CCAAT
1127351 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
1127363 TTACTTATTC
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
61 59 0.97
62 2 0.03
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.33
Consensus pattern (61 bp):
ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
Found at i:1127452 original size:21 final size:21
Alignment explanation
Indices: 1127412--1127452 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1127402 ACTGTATACC
**
1127412 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
1127433 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
1127453 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:1135368 original size:60 final size:60
Alignment explanation
Indices: 1135300--1135419 Score: 231
Period size: 60 Copynumber: 2.0 Consensus size: 60
1135290 GACATTTTGA
*
1135300 GTTGAATGTTAACATGTTGATTGTGATATGATAAAATATGATCCTAAAATCTCAAACAAC
1 GTTGAATGTTAACATGCTGATTGTGATATGATAAAATATGATCCTAAAATCTCAAACAAC
1135360 GTTGAATGTTAACATGCTGATTGTGATATGATAAAATATGATCCTAAAATCTCAAACAAC
1 GTTGAATGTTAACATGCTGATTGTGATATGATAAAATATGATCCTAAAATCTCAAACAAC
1135420 TATCATATTT
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 59 1.00
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.33
Consensus pattern (60 bp):
GTTGAATGTTAACATGCTGATTGTGATATGATAAAATATGATCCTAAAATCTCAAACAAC
Found at i:1147504 original size:18 final size:18
Alignment explanation
Indices: 1147478--1147512 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1147468 TCGAAAGGAC
*
1147478 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
1147496 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
1147513 CCGGATGGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:1150730 original size:12 final size:12
Alignment explanation
Indices: 1150713--1150790 Score: 60
Period size: 12 Copynumber: 6.8 Consensus size: 12
1150703 CTATACGGTA
1150713 TGAACAGTACTG
1 TGAACAGTACTG
*
1150725 TGAACAGTA--A
1 TGAACAGTACTG
*
1150735 TGAACATTACTG
1 TGAACAGTACTG
**
1150747 TGAACA-TA-AA
1 TGAACAGTACTG
1150757 TGAACAAAGT-C-G
1 TGAAC--AGTACTG
1150769 TGAACAGTACTG
1 TGAACAGTACTG
1150781 TGAACAGTAC
1 TGAACAGTAC
1150791 CAAATGCTAA
Statistics
Matches: 52, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
10 16 0.31
11 3 0.06
12 32 0.62
13 1 0.02
ACGTcount: A:0.41, C:0.15, G:0.21, T:0.23
Consensus pattern (12 bp):
TGAACAGTACTG
Found at i:1150739 original size:22 final size:22
Alignment explanation
Indices: 1150712--1150762 Score: 77
Period size: 22 Copynumber: 2.3 Consensus size: 22
1150702 ACTATACGGT
1150712 ATGAACAGTACTGTGAACAGT-A
1 ATGAACAGTACTGTGAACA-TAA
*
1150734 ATGAACATTACTGTGAACATAA
1 ATGAACAGTACTGTGAACATAA
1150756 ATGAACA
1 ATGAACA
1150763 AAGTCGTGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 1 0.04
22 26 0.96
ACGTcount: A:0.45, C:0.14, G:0.18, T:0.24
Consensus pattern (22 bp):
ATGAACAGTACTGTGAACATAA
Found at i:1150849 original size:21 final size:22
Alignment explanation
Indices: 1150823--1150865 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
1150813 TGTTATATGG
*
1150823 GTATCGATACCC-TGCTACAGT
1 GTATCGATACCCTTCCTACAGT
1150844 GTATCGATACCCTTCCTACAGT
1 GTATCGATACCCTTCCTACAGT
1150866 AGTTTTGTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.23, C:0.30, G:0.16, T:0.30
Consensus pattern (22 bp):
GTATCGATACCCTTCCTACAGT
Found at i:1151433 original size:22 final size:22
Alignment explanation
Indices: 1151408--1151450 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
1151398 ATGTGAAATT
1151408 TATCCCGAAAGACCTCTGTATG
1 TATCCCGAAAGACCTCTGTATG
*
1151430 TATCCCGAAGGACCTCTGTAT
1 TATCCCGAAAGACCTCTGTAT
1151451 ATGTCCCAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.26, C:0.28, G:0.19, T:0.28
Consensus pattern (22 bp):
TATCCCGAAAGACCTCTGTATG
Found at i:1151457 original size:22 final size:22
Alignment explanation
Indices: 1151408--1151465 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
1151398 ATGTGAAATT
*
1151408 TATCCCGAAAGACCTCTGTATG
1 TATCCCGAAAGACCTCTGTATA
*
1151430 TATCCCGAAGGACCTCTGTATA
1 TATCCCGAAAGACCTCTGTATA
*
1151452 TGTCCC-AAATGACC
1 TATCCCGAAA-GACC
1151466 GCGTAGACCC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 2 0.06
22 29 0.94
ACGTcount: A:0.28, C:0.29, G:0.17, T:0.26
Consensus pattern (22 bp):
TATCCCGAAAGACCTCTGTATA
Found at i:1152574 original size:3 final size:3
Alignment explanation
Indices: 1152566--1152612 Score: 71
Period size: 3 Copynumber: 16.3 Consensus size: 3
1152556 TTGGGCACAC
*
1152566 AAG AAG AAG -AG ATG -AG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1152612 A
1 A
1152613 GAGTTTCCAG
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
2 3 0.08
3 37 0.93
ACGTcount: A:0.64, C:0.00, G:0.34, T:0.02
Consensus pattern (3 bp):
AAG
Found at i:1155867 original size:18 final size:18
Alignment explanation
Indices: 1155823--1155870 Score: 60
Period size: 20 Copynumber: 2.6 Consensus size: 18
1155813 TTGCCCCGTC
*
1155823 AGTATCGATAATGACCTT
1 AGTATCGATAATGACCCT
*
1155841 ATGGTATCGATATTGACCCT
1 A--GTATCGATAATGACCCT
1155861 AGTATCGATA
1 AGTATCGATA
1155871 CCAATTTCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
18 10 0.38
20 16 0.62
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (18 bp):
AGTATCGATAATGACCCT
Found at i:1162387 original size:22 final size:21
Alignment explanation
Indices: 1162353--1162428 Score: 53
Period size: 22 Copynumber: 3.4 Consensus size: 21
1162343 ACATGCTACT
1162353 TAATCATAGAAGTGCCTTAGCAC
1 TAAT-ATA-AAGTGCCTTAGCAC
* * *
1162376 TAATACTAAAGTGTCTCAGTAC
1 TAATA-TAAAGTGCCTTAGCAC
* * *
1162398 TAATAAAAAAGTGCATTCGCAC
1 TAAT-ATAAAGTGCCTTAGCAC
*
1162420 TGATATAAA
1 TAATATAAA
1162429 AGTTTCATAA
Statistics
Matches: 40, Mismatches: 11, Indels: 6
0.70 0.19 0.11
Matches are distributed among these distances:
21 4 0.10
22 29 0.73
23 7 0.17
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (21 bp):
TAATATAAAGTGCCTTAGCAC
Found at i:1162931 original size:20 final size:20
Alignment explanation
Indices: 1162906--1162956 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
1162896 AATTATCACC
1162906 AGTATCGATACCACCCTTTG
1 AGTATCGATACCACCCTTTG
1162926 AGTATCGATACCACCCTTTG
1 AGTATCGATACCACCCTTTG
1162946 AGTATCGATAC
1 AGTATCGATAC
1162957 TCCTTGAAGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.27, C:0.27, G:0.16, T:0.29
Consensus pattern (20 bp):
AGTATCGATACCACCCTTTG
Found at i:1164831 original size:3 final size:3
Alignment explanation
Indices: 1164823--1164864 Score: 59
Period size: 3 Copynumber: 14.0 Consensus size: 3
1164813 TTTTAATGGT
*
1164823 TTA TTA TTA TTA TTTA TTT TTA TTA TTA TTA TTA TTA -TA TTA
1 TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1164865 ATAATATTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
3 30 0.86
4 3 0.09
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1168099 original size:21 final size:21
Alignment explanation
Indices: 1168069--1168186 Score: 109
Period size: 21 Copynumber: 5.6 Consensus size: 21
1168059 GATTTACATA
*
1168069 TTCGCATTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCGAAG
* * *
1168090 TTCGCGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCGAAG
*
1168113 TT--CGTTGCAATAGTCGAAG
1 TTCGCGTTGCGATAGTCGAAG
* *
1168132 TTCGCGTTGCGATTTATTCCAAG
1 TTCGCGTTGCGA--TAGTCGAAG
1168155 TT--CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCGAAG
1168174 TTCGCGTTGCGAT
1 TTCGCGTTGCGAT
1168187 TTATACCAAG
Statistics
Matches: 76, Mismatches: 13, Indels: 16
0.72 0.12 0.15
Matches are distributed among these distances:
19 17 0.22
21 42 0.55
23 17 0.22
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.35
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTCGAAG
Found at i:1168131 original size:42 final size:42
Alignment explanation
Indices: 1168075--1168201 Score: 227
Period size: 42 Copynumber: 3.0 Consensus size: 42
1168065 CATATTCGCA
*
1168075 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCG
*
1168117 TTGCAATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCG
*
1168159 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATACCAAGTTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCG
1168201 T
1 T
1168202 GTTGCGATTT
Statistics
Matches: 81, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 81 1.00
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.35
Consensus pattern (42 bp):
TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCG
Found at i:1168157 original size:23 final size:23
Alignment explanation
Indices: 1168087--1168224 Score: 130
Period size: 23 Copynumber: 6.3 Consensus size: 23
1168077 GCGATAGTCG
1168087 AAGTTCGCGTTGCGATTTATTCC
1 AAGTTCGCGTTGCGATTTATTCC
* * * *
1168110 AAATT--CGTTGC-A-ATAGTCG
1 AAGTTCGCGTTGCGATTTATTCC
1168129 AAGTTCGCGTTGCGATTTATTCC
1 AAGTTCGCGTTGCGATTTATTCC
* *
1168152 AAGTT--CGTTGCGA--TAGTCG
1 AAGTTCGCGTTGCGATTTATTCC
*
1168171 AAGTTCGCGTTGCGATTTATACC
1 AAGTTCGCGTTGCGATTTATTCC
* *
1168194 AAGTTCGTGTTGCGATTTATTTC
1 AAGTTCGCGTTGCGATTTATTCC
*
1168217 AAATTCGC
1 AAGTTCGC
1168225 AACGACTGGT
Statistics
Matches: 89, Mismatches: 18, Indels: 16
0.72 0.15 0.13
Matches are distributed among these distances:
19 17 0.19
20 1 0.01
21 28 0.31
22 1 0.01
23 42 0.47
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.37
Consensus pattern (23 bp):
AAGTTCGCGTTGCGATTTATTCC
Found at i:1177086 original size:18 final size:17
Alignment explanation
Indices: 1177053--1177086 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
1177043 GAATAATTAA
1177053 ATAAAATATCAAAATAT
1 ATAAAATATCAAAATAT
*
1177070 ATAAAATCATTAAAATA
1 ATAAAAT-ATCAAAATA
1177087 ATACAGACTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (17 bp):
ATAAAATATCAAAATAT
Found at i:1185310 original size:17 final size:19
Alignment explanation
Indices: 1185288--1185326 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 19
1185278 GAATAATTAA
1185288 ATAAAAT-ATCAAAAT-AT
1 ATAAAATCATCAAAATAAT
*
1185305 ATAAAATCATTAAAATAAT
1 ATAAAATCATCAAAATAAT
1185324 ATA
1 ATA
1185327 GACTGAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 7 0.37
18 7 0.37
19 5 0.26
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (19 bp):
ATAAAATCATCAAAATAAT
Found at i:1193547 original size:18 final size:17
Alignment explanation
Indices: 1193514--1193547 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
1193504 GAATAATTAA
1193514 ATAAAATATCAAAATAT
1 ATAAAATATCAAAATAT
*
1193531 ATAAAATCATTAAAATA
1 ATAAAAT-ATCAAAATA
1193548 ATACAGACTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (17 bp):
ATAAAATATCAAAATAT
Found at i:1197228 original size:42 final size:42
Alignment explanation
Indices: 1197164--1197450 Score: 479
Period size: 42 Copynumber: 6.9 Consensus size: 42
1197154 GCGATTTTGA
* *
1197164 ACTATCGCAACGAACTTTGAATAAATCGCAACACGAACTTCG
1 ACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCG
* *
1197206 ACTAACGCAACGAACTTGGAATAAATCGCAATGCGAACTTCG
1 ACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCG
* *
1197248 ACTATCGCAACGAACTTGGAATAAATCGCAATGTGAACTTCG
1 ACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCG
1197290 ACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCG
1 ACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCG
* *
1197332 ACTATCGCAACGAACTTGGAATAAATCGCAACGCAAACTTCA
1 ACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCG
1197374 ACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCG
1 ACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCG
*
1197416 ACTATCGCAACGAACTTGGACT--ATCGCAACGCGAA
1 ACTATCGCAACGAACTTGGAATAAATCGCAACGCGAA
1197451 TTTGGAATAA
Statistics
Matches: 232, Mismatches: 13, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
40 13 0.06
42 219 0.94
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (42 bp):
ACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCG
Found at i:1197465 original size:42 final size:41
Alignment explanation
Indices: 1197164--1197490 Score: 433
Period size: 42 Copynumber: 7.8 Consensus size: 41
1197154 GCGATTTTGA
* *
1197164 ACTATCGCAACGAACTTTGAATAAATCGCAACACGAACTTCG
1 ACTATCGCAACGAACTTGGAAT-AATCGCAACGCGAACTTCG
* *
1197206 ACTAACGCAACGAACTTGGAATAAATCGCAATGCGAACTTCG
1 ACTATCGCAACGAACTTGGAAT-AATCGCAACGCGAACTTCG
* *
1197248 ACTATCGCAACGAACTTGGAATAAATCGCAATGTGAACTTCG
1 ACTATCGCAACGAACTTGGAAT-AATCGCAACGCGAACTTCG
1197290 ACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCG
1 ACTATCGCAACGAACTTGGAAT-AATCGCAACGCGAACTTCG
* *
1197332 ACTATCGCAACGAACTTGGAATAAATCGCAACGCAAACTTCA
1 ACTATCGCAACGAACTTGGAAT-AATCGCAACGCGAACTTCG
1197374 ACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCG
1 ACTATCGCAACGAACTTGGAAT-AATCGCAACGCGAACTTCG
* * *
1197416 ACTATCGCAACGAACTTGGACT-ATCGCAACGCGAATTTGG
1 ACTATCGCAACGAACTTGGAATAATCGCAACGCGAACTTCG
* *
1197456 AATAAATCGCAACGCGAACTTGGACT-ATCGCAACG
1 ACT--ATCGCAA--CGAACTTGGAATAATCGCAACG
1197491 AATTTAGAAA
Statistics
Matches: 265, Mismatches: 16, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
40 18 0.07
42 226 0.85
44 21 0.08
ACGTcount: A:0.36, C:0.25, G:0.18, T:0.20
Consensus pattern (41 bp):
ACTATCGCAACGAACTTGGAATAATCGCAACGCGAACTTCG
Found at i:1197505 original size:63 final size:61
Alignment explanation
Indices: 1197164--1197506 Score: 245
Period size: 63 Copynumber: 5.5 Consensus size: 61
1197154 GCGATTTTGA
* * * *
1197164 ACTATCGCAACGAACTTTGAATAAATCGCAACACGAACTTCGACT-AA-CGCAA--CGAACTTGG
1 ACTATCGCAACGAACTTAG-A-AAATCGC-A-ACGAACTTGGAATAAATCGCAACGCGAACTTCG
* * ** * *
1197225 AATAAATCGCAATGCGAACTTCGACTATCGCAACGAACTTGGAATAAATCGCAATGTGAACTTCG
1 ACT--ATCGCAA--CGAACTTAGAAAATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCG
* * * *
1197290 ACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACT--ATCGCAA--CGAACTTGG
1 ACTATCGCAACGAACTTAG-A-AAATCGCAA--CGAACTTGGAATAAATCGCAACGCGAACTTCG
* **
1197351 AATAAATCGCAACGCAAACTTCA-ACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
1 ACT--ATCGCAACG--AACTT-AGAAAATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
1197415 G
61 G
* ** * *
1197416 ACTATCGCAACGAACTTGGACTATCGCAACGCGAATTTGGAATAAATCGCAACGCGAACTTGG
1 ACTATCGCAACGAACTTAGAAAATCGCAA--CGAACTTGGAATAAATCGCAACGCGAACTTCG
*
1197479 ACTATCGCAACGAATTTAGAAAATCGCA
1 ACTATCGCAACGAACTTAGAAAATCGCA
1197507 TTGCGATAGT
Statistics
Matches: 227, Mismatches: 31, Indels: 46
0.75 0.10 0.15
Matches are distributed among these distances:
61 55 0.24
62 4 0.02
63 124 0.55
64 2 0.01
65 42 0.19
ACGTcount: A:0.37, C:0.24, G:0.18, T:0.20
Consensus pattern (61 bp):
ACTATCGCAACGAACTTAGAAAATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCG
Found at i:1197531 original size:21 final size:21
Alignment explanation
Indices: 1197502--1197554 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
1197492 ATTTAGAAAA
*
1197502 TCGCATTGCGATAGTCGAAGT
1 TCGCGTTGCGATAGTCGAAGT
*
1197523 TCGCGTTGCGATAGTCGATGT
1 TCGCGTTGCGATAGTCGAAGT
1197544 TCGCGTTGCGA
1 TCGCGTTGCGA
1197555 ATTTGGAAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.17, C:0.21, G:0.32, T:0.30
Consensus pattern (21 bp):
TCGCGTTGCGATAGTCGAAGT
Found at i:1212586 original size:30 final size:30
Alignment explanation
Indices: 1212550--1212610 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
1212540 AAGGATGCAC
1212550 GCACCGAATATGCATAATTTCAATGGGTTG
1 GCACCGAATATGCATAATTTCAATGGGTTG
*
1212580 GCACCGAATGTGCATAATTTCAATGGGTTG
1 GCACCGAATATGCATAATTTCAATGGGTTG
1212610 G
1 G
1212611 TAATTGTTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (30 bp):
GCACCGAATATGCATAATTTCAATGGGTTG
Found at i:1216839 original size:30 final size:30
Alignment explanation
Indices: 1216795--1216857 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
1216785 AAGGATGCAT
*
1216795 GCACCAAATATGCATAATTTCAATGGGTTG
1 GCACCAAATATGCATAATTTCAATGGGCTG
* *
1216825 GCACCGAATGTGCATAATTTCAATGGGCTG
1 GCACCAAATATGCATAATTTCAATGGGCTG
1216855 GCA
1 GCA
1216858 ATTATTTATT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.27
Consensus pattern (30 bp):
GCACCAAATATGCATAATTTCAATGGGCTG
Found at i:1223219 original size:16 final size:16
Alignment explanation
Indices: 1223198--1223235 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
1223188 TGAGGAACGG
1223198 ATGAAAAGGTCGTTGA
1 ATGAAAAGGTCGTTGA
1223214 ATGAAAAGGTCGTTGA
1 ATGAAAAGGTCGTTGA
1223230 ATGAAA
1 ATGAAA
1223236 GAGCCAGATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.42, C:0.05, G:0.29, T:0.24
Consensus pattern (16 bp):
ATGAAAAGGTCGTTGA
Found at i:1229970 original size:12 final size:12
Alignment explanation
Indices: 1229953--1229983 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
1229943 ATTTTCAAGA
1229953 GCTTCCTTAGAG
1 GCTTCCTTAGAG
1229965 GCTTCCTTAGAG
1 GCTTCCTTAGAG
1229977 GCTTCCT
1 GCTTCCT
1229984 CATCTTTCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.13, C:0.29, G:0.23, T:0.35
Consensus pattern (12 bp):
GCTTCCTTAGAG
Found at i:1231702 original size:2 final size:2
Alignment explanation
Indices: 1231695--1231721 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1231685 GCGGCTTCAA
1231695 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
1231722 AAGGGAGAGC
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:1234910 original size:11 final size:11
Alignment explanation
Indices: 1234894--1234923 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
1234884 GGGATAAGAA
1234894 AATGCAAGTAT
1 AATGCAAGTAT
1234905 AATGCAAGTAT
1 AATGCAAGTAT
*
1234916 GATGCAAG
1 AATGCAAG
1234924 AATACATGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.43, C:0.10, G:0.23, T:0.23
Consensus pattern (11 bp):
AATGCAAGTAT
Found at i:1239069 original size:20 final size:22
Alignment explanation
Indices: 1239041--1239086 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
1239031 ACATAAATTA
1239041 TAAATTAATCATTAAA-TTTAT
1 TAAATTAATCATTAAATTTTAT
*
1239062 TAAA-TAATTATTAAATTTTAT
1 TAAATTAATCATTAAATTTTAT
1239083 TAAA
1 TAAA
1239087 CTGTACCAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 10 0.43
21 13 0.57
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (22 bp):
TAAATTAATCATTAAATTTTAT
Found at i:1245711 original size:37 final size:37
Alignment explanation
Indices: 1245637--1245711 Score: 89
Period size: 38 Copynumber: 2.0 Consensus size: 37
1245627 TTTGGAAAAT
* * *
1245637 ATTTCTATATTTTATTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTATTTAAAAAATTAAAAATCATAAA
* *
1245674 ATTTATATAATTTTTTTTACAAAATTAAAAAT-ATAAA
1 ATTTATAT-ATTTTATTTAAAAAATTAAAAATCATAAA
1245711 A
1 A
1245712 AGGTTTAATG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
37 13 0.41
38 19 0.59
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (37 bp):
ATTTATATATTTTATTTAAAAAATTAAAAATCATAAA
Found at i:1245810 original size:24 final size:25
Alignment explanation
Indices: 1245765--1245814 Score: 93
Period size: 24 Copynumber: 2.0 Consensus size: 25
1245755 CATATAAAAT
1245765 TTTAATTATAGATTTTTTTTGTAAA
1 TTTAATTATAGATTTTTTTTGTAAA
1245790 TTTAATTATAGA-TTTTTTTGTAAA
1 TTTAATTATAGATTTTTTTTGTAAA
1245814 T
1 T
1245815 CTAAAATAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 13 0.52
25 12 0.48
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.60
Consensus pattern (25 bp):
TTTAATTATAGATTTTTTTTGTAAA
Found at i:1247934 original size:27 final size:27
Alignment explanation
Indices: 1247904--1247966 Score: 90
Period size: 27 Copynumber: 2.3 Consensus size: 27
1247894 TTTAATATTT
*
1247904 TCGGTAAAATGTCAAACAATAATAAAA
1 TCGGTAAAACGTCAAACAATAATAAAA
* * *
1247931 TCGGTAAAGCGTCCAATAATAATAAAA
1 TCGGTAAAACGTCAAACAATAATAAAA
1247958 TCGGTAAAA
1 TCGGTAAAA
1247967 AAAAATAATA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.51, C:0.13, G:0.14, T:0.22
Consensus pattern (27 bp):
TCGGTAAAACGTCAAACAATAATAAAA
Found at i:1273617 original size:3 final size:3
Alignment explanation
Indices: 1273611--1273674 Score: 85
Period size: 3 Copynumber: 21.0 Consensus size: 3
1273601 CCCATTTTTT
1273611 TTA TTA TTGA -TA TTA TTA TTA TTA TTA TTA TTA TTTA TTA TTA TTA
1 TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA
**
1273657 TTA TTA AAA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA
1273675 CAAACATGCC
Statistics
Matches: 54, Mismatches: 4, Indels: 6
0.84 0.06 0.09
Matches are distributed among these distances:
2 1 0.02
3 49 0.91
4 4 0.07
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:1274115 original size:15 final size:15
Alignment explanation
Indices: 1274083--1274127 Score: 63
Period size: 17 Copynumber: 2.8 Consensus size: 15
1274073 AGCGAGAGCG
1274083 ACAGAGAGAGATACAC
1 ACAGAGAGAGA-ACAC
1274099 ACAGCAGAGGAGAACAC
1 ACAG-AGA-GAGAACAC
1274116 ACAGAGAGAGAA
1 ACAGAGAGAGAA
1274128 AAGAAAGCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
15 5 0.19
16 7 0.26
17 11 0.41
18 4 0.15
ACGTcount: A:0.51, C:0.18, G:0.29, T:0.02
Consensus pattern (15 bp):
ACAGAGAGAGAACAC
Found at i:1275474 original size:11 final size:13
Alignment explanation
Indices: 1275437--1275476 Score: 50
Period size: 11 Copynumber: 3.3 Consensus size: 13
1275427 TGTTTAATAA
1275437 AATATA-TATATT
1 AATATATTATATT
*
1275449 AATATATTATCTT
1 AATATATTATATT
1275462 AA-A-ATTATATT
1 AATATATTATATT
1275473 AATA
1 AATA
1275477 AACTTAACAG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
11 9 0.38
12 8 0.33
13 7 0.29
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (13 bp):
AATATATTATATT
Found at i:1277504 original size:8 final size:7
Alignment explanation
Indices: 1277480--1277521 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
1277470 TTTTCATACA
1277480 TGCA-TT
1 TGCATTT
1277486 TGCATTT
1 TGCATTT
1277493 TGCATCTT
1 TGCAT-TT
1277501 TGCATTT
1 TGCATTT
* *
1277508 TTCATTG
1 TGCATTT
1277515 TGCATTT
1 TGCATTT
1277522 ATACTTTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
6 4 0.13
7 19 0.63
8 7 0.23
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.55
Consensus pattern (7 bp):
TGCATTT
Found at i:1277504 original size:15 final size:14
Alignment explanation
Indices: 1277480--1277521 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 14
1277470 TTTTCATACA
1277480 TGCA-TTTGCATTT
1 TGCATTTTGCATTT
1277493 TGCATCTTTGCATTT
1 TGCAT-TTTGCATTT
* *
1277508 TTCATTGTGCATTT
1 TGCATTTTGCATTT
1277522 ATACTTTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 4 0.16
14 8 0.32
15 13 0.52
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.55
Consensus pattern (14 bp):
TGCATTTTGCATTT
Found at i:1280140 original size:9 final size:9
Alignment explanation
Indices: 1280126--1280170 Score: 63
Period size: 9 Copynumber: 4.9 Consensus size: 9
1280116 TATTATACTT
1280126 GAAAAAAAG
1 GAAAAAAAG
*
1280135 GAAAAAAGG
1 GAAAAAAAG
1280144 AGAAAAAAAG
1 -GAAAAAAAG
*
1280154 GAAAAAATG
1 GAAAAAAAG
1280163 GAAAAAAA
1 GAAAAAAA
1280171 ATTGAACAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
9 23 0.74
10 8 0.26
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (9 bp):
GAAAAAAAG
Found at i:1280150 original size:19 final size:20
Alignment explanation
Indices: 1280126--1280171 Score: 78
Period size: 19 Copynumber: 2.4 Consensus size: 20
1280116 TATTATACTT
1280126 GAAAAAAAGGAAAAAA-GGA
1 GAAAAAAAGGAAAAAATGGA
1280145 GAAAAAAAGGAAAAAATGGA
1 GAAAAAAAGGAAAAAATGGA
1280165 -AAAAAAA
1 GAAAAAAA
1280172 TTGAACAAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 23 0.88
20 3 0.12
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (20 bp):
GAAAAAAAGGAAAAAATGGA
Found at i:1280172 original size:11 final size:10
Alignment explanation
Indices: 1280127--1280171 Score: 51
Period size: 8 Copynumber: 4.7 Consensus size: 10
1280117 ATTATACTTG
1280127 AAAAAAAGG-
1 AAAAAAAGGA
1280136 -AAAAAAGGA
1 AAAAAAAGGA
1280145 GAAAAAAAGG-
1 -AAAAAAAGGA
*
1280155 AAAAAATGGA
1 AAAAAAAGGA
1280165 AAAAAAA
1 AAAAAAA
1280172 TTGAACAAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
8 8 0.27
9 8 0.27
10 6 0.20
11 8 0.27
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (10 bp):
AAAAAAAGGA
Found at i:1280690 original size:32 final size:32
Alignment explanation
Indices: 1280654--1280716 Score: 101
Period size: 32 Copynumber: 2.0 Consensus size: 32
1280644 GTTAGACACA
*
1280654 AGAAGTATCTCTATC-AGATTAGCATAACAATG
1 AGAAGTATCTCTA-CAAGATGAGCATAACAATG
1280686 AGAAGTATCTCTACAAGATGAGCATAACAAT
1 AGAAGTATCTCTACAAGATGAGCATAACAAT
1280717 CATTTCTTCA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 1 0.03
32 28 0.97
ACGTcount: A:0.43, C:0.16, G:0.16, T:0.25
Consensus pattern (32 bp):
AGAAGTATCTCTACAAGATGAGCATAACAATG
Found at i:1282442 original size:114 final size:114
Alignment explanation
Indices: 1282237--1282464 Score: 366
Period size: 114 Copynumber: 2.0 Consensus size: 114
1282227 GTGCCACGTT
* *
1282237 CTCATAATAGAAATAAGGAGACCCAATAACATCTTTTGGAAGTGTTCTTTGAGTTATCTGATCTG
1 CTCATAATAGAAATAAAGAGACCCAATAACATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
* * * * *
1282302 GTTTGGTATGAACCCTAAAACTAATCATTGGATTTAAAAGATGAATTTG
66 GTTCGGTATAAACCCCAAAACCAATCATTGGATTTAAAAGATAAATTTG
* *
1282351 CTCATAGTAGAAATAAAGAGACCCAATAACATCTTCTGGAAGTGTTCTTTGAGTTATCTGATTTG
1 CTCATAATAGAAATAAAGAGACCCAATAACATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
*
1282416 GTTCGGTATAAACCCCAAAACCAATCATTGGATTTGAAAGATAAATTTG
66 GTTCGGTATAAACCCCAAAACCAATCATTGGATTTAAAAGATAAATTTG
1282465 ATGATAGTCT
Statistics
Matches: 104, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
114 104 1.00
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (114 bp):
CTCATAATAGAAATAAAGAGACCCAATAACATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
GTTCGGTATAAACCCCAAAACCAATCATTGGATTTAAAAGATAAATTTG
Found at i:1283751 original size:75 final size:75
Alignment explanation
Indices: 1283477--1283806 Score: 399
Period size: 76 Copynumber: 4.4 Consensus size: 75
1283467 ATTAACAAGA
* * *
1283477 AGCAAATGTTGGGGCATGCTGAAAACCCTTTTCAATCAGAATCAGGAATGTTGATGTATCCTGAA
1 AGCAAATGCTGGGGCATGCTGAAAACCCCTTTCAATCAGAATCAAGAATGTTGATGTATCCTGAA
* *
1283542 TGTTTATATC
66 CGTTCATATC
* *
1283552 AGCAAAATGCTGGGGCATGCTGAAAACCCCTTTCAATCAGAATGAGGAATGTTGATGTATCCTGA
1 AGC-AAATGCTGGGGCATGCTGAAAACCCCTTTCAATCAGAATCAAGAATGTTGATGTATCCTGA
* *
1283617 ATGTTTATATC
65 ACGTTCATATC
* * * **
1283628 AGCAAAATGCTGGGGCATGCTGAAAGCCCCTTTTAATCAGAATGAAGAATGTTGATGTATTTTGA
1 AGC-AAATGCTGGGGCATGCTGAAAACCCCTTTCAATCAGAATCAAGAATGTTGATGTATCCTGA
*
1283693 ACGTTCGTATC
65 ACGTTCATATC
* * * ** **
1283704 AGCAATTGATGGGGCATGCTGAAATCCTATTTCAATCAGAATCAAGAATGTTGATGTATTTTGAA
1 AGCAAATGCTGGGGCATGCTGAAAACCCCTTTCAATCAGAATCAAGAATGTTGATGTATCCTGAA
*
1283769 CGTTCGTATC
66 CGTTCATATC
* * * *
1283779 AACAATTGTTGGGGCATGCTGAAGACCC
1 AGCAAATGCTGGGGCATGCTGAAAACCC
1283807 ATATCATCCT
Statistics
Matches: 231, Mismatches: 23, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
75 91 0.39
76 140 0.61
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Consensus pattern (75 bp):
AGCAAATGCTGGGGCATGCTGAAAACCCCTTTCAATCAGAATCAAGAATGTTGATGTATCCTGAA
CGTTCATATC
Found at i:1283779 original size:151 final size:151
Alignment explanation
Indices: 1283479--1283806 Score: 408
Period size: 151 Copynumber: 2.2 Consensus size: 151
1283469 TAACAAGAAG
* *
1283479 CAAATGTTGGGGCATGCTGAAAACCCTTTTCAATCAGAATCAGGAATGTTGATGTATCCTGAATG
1 CAAATGTTGGGGCATGCTGAAAACCCTTTTCAATCAGAATCAAGAATGTTGATGTATCCTGAACG
* * * * *
1283544 TTTATATCAGCAAAATGCTGGGGCATGCTGAAAACCCCTTTCAATCAGAATGAGGAATGTTGATG
66 TTCATATCAGCAAAATGATGGGGCATGCTGAAAACCCATTTCAATCAGAATCAAGAATGTTGATG
* * *
1283609 TATCCTGAATGTTTATATCAG
131 TATCCTGAACGTTCATATCAA
* * * **
1283630 CAAAATGCTGGGGCATGCTGAAAGCCCCTTTT-AATCAGAATGAAGAATGTTGATGTATTTTGAA
1 C-AAATGTTGGGGCATGCTGAAA-ACCCTTTTCAATCAGAATCAAGAATGTTGATGTATCCTGAA
* * * *
1283694 CGTTCGTATCAGC-AATTGATGGGGCATGCTGAAATCCTATTTCAATCAGAATCAAGAATGTTGA
64 CGTTCATATCAGCAAAATGATGGGGCATGCTGAAAACCCATTTCAATCAGAATCAAGAATGTTGA
** *
1283758 TGTATTTTGAACGTTCGTATCAA
129 TGTATCCTGAACGTTCATATCAA
* *
1283781 CAATTGTTGGGGCATGCTGAAGACCC
1 CAAATGTTGGGGCATGCTGAAAACCC
1283807 ATATCATCCT
Statistics
Matches: 149, Mismatches: 26, Indels: 6
0.82 0.14 0.03
Matches are distributed among these distances:
149 3 0.02
150 18 0.12
151 63 0.42
152 58 0.39
153 7 0.05
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.30
Consensus pattern (151 bp):
CAAATGTTGGGGCATGCTGAAAACCCTTTTCAATCAGAATCAAGAATGTTGATGTATCCTGAACG
TTCATATCAGCAAAATGATGGGGCATGCTGAAAACCCATTTCAATCAGAATCAAGAATGTTGATG
TATCCTGAACGTTCATATCAA
Found at i:1285605 original size:113 final size:113
Alignment explanation
Indices: 1285401--1286180 Score: 897
Period size: 113 Copynumber: 6.8 Consensus size: 113
1285391 ATCCACCACA
* *
1285401 ATGGATCAACATTTCCAGA-AGGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAATAAGAAG
1 ATGGATCAACATTTCCAGAGA-AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAG
* * *
1285465 TTCATAATGAGAAGAGA-TTGTTTAACCTTTTGCTTAAATCCATCATTTG
65 TTCATAATGAGAAGA-ATTTGTTCAACCTTTTGCTTAAATTCATCACTTG
* *
1285514 ATGGATCATCATTTCTAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
1 ATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
* * * *
1285579 TCATAATGAGAAGAATTTATTCAACCTTTTGTTTGAATTCATCATTTG
66 TCATAATGAGAAGAATTTGTTCAACCTTTTGCTTAAATTCATCACTTG
* * * * *
1285627 AAGGATCAATATTTCTA-AAAAGAGTTTATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAG
1 ATGGATCAACATTTCCAGAGAA-AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAG
** * *
1285691 TTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTCAAATCCATCACTTG
65 TTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTAAATTCATCACTTG
* *
1285740 ATGGATCAGCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAATAAGAAGT
1 ATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
* * ** *
1285805 TCATAATGAGAAGAACTTGTTCAACCTTTTTCTCGAATTCATCACTCG
66 TCATAATGAGAAGAATTTGTTCAACCTTTTGCTTAAATTCATCACTTG
* * * * ** * * * *
1285853 GTGGATCAGCAGTGCCAGTTAGAGTTCATAATGAGAAGAACTCATATGAAGAAGGAATAAGAAAT
1 ATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
1285918 TCATAATGAGAAGAATTTGTTCAACCTTTTGCTTAAATTCATCACTTG
66 TCATAATGAGAAGAATTTGTTCAACCTTTTGCTTAAATTCATCACTTG
* *
1285966 ATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGC
1 ATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
** * * * * * **
1286031 TCATAATGAGAAGAGCTTGTTCGACCTTTTACATGACTTTGTCACAGAAGGAGATAT-
66 TCATAATGAGAAGAATTTGTTCAACCTTTTGCTTAAATTCATCAC---------T-TG
** ** * *
1286088 ATCATCATCAACATTTCCAGA-AGTGTTCATAATAAGAAGAACTCATTTGAAG-AGGAAGAAGAA
1 AT--GGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAA
1286151 GTTCATAATGAGAAGAATTTGTTCAACCTT
64 GTTCATAATGAGAAGAATTTGTTCAACCTT
1286181 ACCATAATTC
Statistics
Matches: 572, Mismatches: 79, Indels: 23
0.85 0.12 0.03
Matches are distributed among these distances:
112 4 0.01
113 482 0.84
114 4 0.01
122 40 0.07
123 28 0.05
124 14 0.02
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.28
Consensus pattern (113 bp):
ATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
TCATAATGAGAAGAATTTGTTCAACCTTTTGCTTAAATTCATCACTTG
Found at i:1286042 original size:24 final size:23
Alignment explanation
Indices: 1285999--1286043 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
1285989 GTTCATAATG
*
1285999 AGAAGAACTCATCTGAAGAAGGA
1 AGAAGAACTCATATGAAGAAGGA
1286022 AGAAGAAGCTCATAATG-AGAAG
1 AGAAGAA-CTCAT-ATGAAGAAG
1286044 AGCTTGTTCG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 7 0.37
24 10 0.53
25 2 0.11
ACGTcount: A:0.49, C:0.11, G:0.27, T:0.13
Consensus pattern (23 bp):
AGAAGAACTCATATGAAGAAGGA
Found at i:1286449 original size:119 final size:119
Alignment explanation
Indices: 1286230--1286459 Score: 365
Period size: 119 Copynumber: 1.9 Consensus size: 119
1286220 TCTTTTAAAG
*
1286230 ATCAACATTTCCAGAAGGAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGTTCATAATG
1 ATCAACATTTCCAGAAGGAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGTTCACAATG
* **
1286295 AGAAGAACTTGTTCAACCTTTATTTAATTCTATCACAGAAGAAGATCGGTCAAT
66 AGAAGAACATGTTCAACCTTTAGCTAATTCTATCACAGAAGAAGATCGGTCAAT
*
1286349 ATCAGCATTTCCAGAAGGAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGTTCACAATG
1 ATCAACATTTCCAGAAGGAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGTTCACAATG
* *
1286414 AGAAGAGCATGTTCAACCTTT-GCTAGATTAC-ATCACAGAAGGAGAT
66 AGAAGAACATGTTCAACCTTTAGCTA-ATT-CTATCACAGAAGAAGAT
1286460 AAATTGTCAT
Statistics
Matches: 102, Mismatches: 7, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
118 2 0.02
119 99 0.97
120 1 0.01
ACGTcount: A:0.40, C:0.16, G:0.20, T:0.25
Consensus pattern (119 bp):
ATCAACATTTCCAGAAGGAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGTTCACAATG
AGAAGAACATGTTCAACCTTTAGCTAATTCTATCACAGAAGAAGATCGGTCAAT
Found at i:1286663 original size:3 final size:3
Alignment explanation
Indices: 1286657--1286716 Score: 70
Period size: 3 Copynumber: 20.0 Consensus size: 3
1286647 ACCCATTTTT
1286657 TTA TTA TTGA -TA TTA TTA TTA TTA TT- TTA TTTA TTA TTA TTA TTA
1 TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA
**
1286702 TTA AAA TTA TTA TTA
1 TTA TTA TTA TTA TTA
1286717 CAAACATGCC
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
2 3 0.06
3 42 0.86
4 4 0.08
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:1287157 original size:17 final size:19
Alignment explanation
Indices: 1287126--1287166 Score: 61
Period size: 17 Copynumber: 2.3 Consensus size: 19
1287116 GTGAGAGCGA
1287126 CAGAGAGAGATACACACAG
1 CAGAGAGAGATACACACAG
1287145 CAGAG-GAGA-ACACACAG
1 CAGAGAGAGATACACACAG
1287162 -AGAGA
1 CAGAGA
1287167 AAAGAAAGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
16 4 0.19
17 8 0.38
18 4 0.19
19 5 0.24
ACGTcount: A:0.49, C:0.20, G:0.29, T:0.02
Consensus pattern (19 bp):
CAGAGAGAGATACACACAG
Found at i:1288409 original size:26 final size:28
Alignment explanation
Indices: 1288344--1288411 Score: 81
Period size: 26 Copynumber: 2.5 Consensus size: 28
1288334 AAAAAATAAA
1288344 TATTTTAATATATAAATATGTTTTTATAT
1 TATTTTAATAT-TAAATATGTTTTTATAT
*
1288373 TATTTT-CTATTAAA-AT-TTATTTAT-T
1 TATTTTAATATTAAATATGTT-TTTATAT
1288398 TATTTTAATATTAA
1 TATTTTAATATTAA
1288412 GAAATGAGCT
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
25 9 0.26
26 13 0.37
27 4 0.11
28 3 0.09
29 6 0.17
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.60
Consensus pattern (28 bp):
TATTTTAATATTAAATATGTTTTTATAT
Found at i:1288522 original size:11 final size:13
Alignment explanation
Indices: 1288482--1288524 Score: 54
Period size: 11 Copynumber: 3.4 Consensus size: 13
1288472 TATTGTTTAA
1288482 TAATATATATATAT
1 TAATATAT-TATAT
*
1288496 TAATATATTATCT
1 TAATATATTATAT
1288509 TAA-A-ATTATAT
1 TAATATATTATAT
1288520 TAATA
1 TAATA
1288525 AACTTAACAG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
11 9 0.35
12 2 0.08
13 7 0.27
14 8 0.31
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (13 bp):
TAATATATTATAT
Found at i:1289765 original size:20 final size:20
Alignment explanation
Indices: 1289737--1289802 Score: 55
Period size: 20 Copynumber: 3.2 Consensus size: 20
1289727 ACAAAGTTCG
*
1289737 CGTTACGATTCATTCCAAAT
1 CGTTGCGATTCATTCCAAAT
* * *
1289757 CGTTGCGA-T-AGTCGAAGTT
1 CGTTGCGATTCATTCCAA-AT
1289776 CGCGTTGCGATTCATTCCAAAT
1 --CGTTGCGATTCATTCCAAAT
1289798 CGTTG
1 CGTTG
1289803 TGATAGGCGA
Statistics
Matches: 34, Mismatches: 7, Indels: 10
0.67 0.14 0.20
Matches are distributed among these distances:
18 5 0.15
19 2 0.06
20 12 0.35
21 8 0.24
22 2 0.06
23 5 0.15
ACGTcount: A:0.23, C:0.23, G:0.21, T:0.33
Consensus pattern (20 bp):
CGTTGCGATTCATTCCAAAT
Found at i:1289775 original size:41 final size:41
Alignment explanation
Indices: 1289678--1289934 Score: 372
Period size: 41 Copynumber: 6.2 Consensus size: 41
1289668 GATTCGCAAC
* *
1289678 GCGATAGTCGAAGTTCGCATTGCGATTTATTCCAAATTCGTT
1 GCGATAGTCGAAGTTCGCGTTGCGATTCATTCCAAA-TCGTT
* * *
1289720 GCGATAGACAAAGTTCGCGTTACGATTCATTCCAAATCGTT
1 GCGATAGTCGAAGTTCGCGTTGCGATTCATTCCAAATCGTT
1289761 GCGATAGTCGAAGTTCGCGTTGCGATTCATTCCAAATCGTT
1 GCGATAGTCGAAGTTCGCGTTGCGATTCATTCCAAATCGTT
* * *
1289802 GTGATAGGCGAAGTTCGCGTTGCGATTCATTCCAATTCGTT
1 GCGATAGTCGAAGTTCGCGTTGCGATTCATTCCAAATCGTT
* * *
1289843 GCGATAAG-AGAAGTTCGTGTTGCGATTCATTCCAATTCGTT
1 GCGAT-AGTCGAAGTTCGCGTTGCGATTCATTCCAAATCGTT
*
1289884 GCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAAATTCGTT
1 GCGATAGTCGAAGTTCGCGTTGCGATTCATTCCAAA-TCGTT
1289926 GCGATAGTC
1 GCGATAGTC
1289935 CAAATATTGC
Statistics
Matches: 194, Mismatches: 18, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
40 2 0.01
41 146 0.75
42 46 0.24
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.32
Consensus pattern (41 bp):
GCGATAGTCGAAGTTCGCGTTGCGATTCATTCCAAATCGTT
Found at i:1289938 original size:19 final size:19
Alignment explanation
Indices: 1289876--1289939 Score: 56
Period size: 21 Copynumber: 3.2 Consensus size: 19
1289866 GATTCATTCC
* *
1289876 AATTCGTTGCGATAGGCGA
1 AATTCGTTGCGATAGTCCA
* *
1289895 AGTTCGCGTTGCGATTCATTCCA
1 AATT--CGTTGCGA-T-AGTCCA
1289918 AATTCGTTGCGATAGTCCA
1 AATTCGTTGCGATAGTCCA
1289937 AAT
1 AAT
1289940 ATTGCATTTG
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
19 11 0.31
20 1 0.03
21 16 0.46
22 1 0.03
23 6 0.17
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.31
Consensus pattern (19 bp):
AATTCGTTGCGATAGTCCA
Found at i:1301763 original size:53 final size:53
Alignment explanation
Indices: 1301683--1301787 Score: 183
Period size: 53 Copynumber: 2.0 Consensus size: 53
1301673 CGGGGGCATG
1301683 ATAAGGATATAAAATCAAATTGAGAAAGTCAAAGGAGAAAATCAAGGGATTTA
1 ATAAGGATATAAAATCAAATTGAGAAAGTCAAAGGAGAAAATCAAGGGATTTA
* * *
1301736 ATAAGGATATACAATCGAGTTGAGAAAGTCAAAGGAGAAAATCAAGGGATTT
1 ATAAGGATATAAAATCAAATTGAGAAAGTCAAAGGAGAAAATCAAGGGATTT
1301788 TCACCTTTGA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
53 49 1.00
ACGTcount: A:0.50, C:0.07, G:0.23, T:0.21
Consensus pattern (53 bp):
ATAAGGATATAAAATCAAATTGAGAAAGTCAAAGGAGAAAATCAAGGGATTTA
Found at i:1308149 original size:798 final size:799
Alignment explanation
Indices: 1306581--1308181 Score: 2988
Period size: 798 Copynumber: 2.0 Consensus size: 799
1306571 TTAGTCACTT
*
1306581 TTTTTATTTTCTCTAAACTCTAAAATCGTCATTTTTTATTTCATTTTGTTTGATATGCGGCGACA
1 TTTTTATTTTCTCTAAACTCTAAAATCATCATTTTTTATTTCATTTTGTTTGATATGCGGCGACA
1306646 TTAATTTTAGTATTGTTCGTGAATCACATTTTTTCTTTATTTCTCATTTACTTTCTTATGTCGTA
66 TTAATTTTAGTATTGTTCGTGAATCACATTTTTTCTTTATTTCTCATTTACTTTCTTATGTCGTA
1306711 TATTTACTTTTCTTTTGTTTTTTTAGTTTTTAATAATTACAGTTATGGTACATTTTCTTCTTATT
131 TATTTACTTTTCTTTTGTTTTTTTAGTTTTTAATAATTACAGTTATGGTACATTTTCTTCTTATT
* *
1306776 CTTCTTTTGGATAAGAAAATTTTATTCCAAATCCAAAAAGGATGCATCAAAGCTACAATAAATAA
196 CTTCATTTGGATAAGAAAATTTCATTCCAAATCCAAAAAGGATGCATCAAAGCTACAATAAATAA
*
1306841 ACCAGTAAAACAAAAACAAAAAAACACCACACCCACATCAAGAGCCTACAACAACCTAACTCAAA
261 ACCAGTAAAACAAAAACAAAAAAACACCACACCCACACCAAGAGCCTACAACAACCTAACTCAAA
1306906 CAAAAACAACAAACACTAGACCAAAGAAAAAGGGGAAAAACAATCACACCCAACACAAACACCCA
326 CAAAAACAACAAACACTAGACCAAAGAAAAAGGGGAAAAACAATCACACCCAACACAAACACCCA
*
1306971 TTAACAAGTCAAGCATCAGAGAATCCCACAGACATTACAAATCTACAGATTCCTATCGTCCTTAT
391 TTAACAAGTCAAGCATCAGAGAATCCCACAGACATTACAAATCTACAGATTCCTATCATCCTTAT
*
1307036 TGAAACAACAACCATGAAGCTTATAGCTAATAGCCTCTTGGATTACCTAACACAAGACCTCAGGG
456 TGAAACAACAACCATGAAGCTTATAGCTAATAGCCTATTGGATTACCTAACACAAGACCTCAGGG
*
1307101 GGTGCCTGATACCCTTGAATAGCCTGTGATTATGTTCTTCCCAAATATAATAAAGGTAACCAGTC
521 GGTGCCTGACACCCTTGAATAGCCTGTGATTATGTTCTTCCCAAATATAATAAAGGTAACCAGTC
* *
1307166 TAAGTCAGCTTCAAAATACCTACAATCAAAGATTTACCTTTAAACCTGCCAATCACCCAATCCAA
586 TAAGCCAGCTTCAAAATACCTACAATCAAAGATTTACCTTTAAACCTACCAATCACCCAATCCAA
1307231 AAGCTCAGCTCAGTCTCCCCAAGGAAAACCACAAATTTGCAAAACACGACCCCAAACAATGCAAG
651 AAGCTCAGCTCAGTCTCCCCAAGGAAAACCACAAATTTGCAAAACACGACCCCAAACAATGCAAG
*
1307296 TGTAAAGGCAATCGCCAATGATATGACTTCTACTTTCCTCACCAGCCTCACACAGCCTGCAATCA
716 TGTAAAGGCAATCGCCAATGATATGACTTCTACTCTCCTCACCAGCCTCACACAGCCTGCAATCA
*
1307361 CCATCAATAACTAAACATA
781 CCAACAATAACTAAACATA
*
1307380 TTTTTGTTTTCTCTAAACTCTAAAATCATCA-TTTTTATTTCATTTTGTTTGATATGCGGCGACA
1 TTTTTATTTTCTCTAAACTCTAAAATCATCATTTTTTATTTCATTTTGTTTGATATGCGGCGACA
1307444 TTAATTTTAGTATTGTTCGTGAATCACATTTTTTCTTTATTTCTCATTTACTTTCTTATGTCGTA
66 TTAATTTTAGTATTGTTCGTGAATCACATTTTTTCTTTATTTCTCATTTACTTTCTTATGTCGTA
* *
1307509 TATTTACTTTTCTTTTGTTTTTTTAGTTTTTAATAATTATAGTTATGGTACATTTTCTTTTTATT
131 TATTTACTTTTCTTTTGTTTTTTTAGTTTTTAATAATTACAGTTATGGTACATTTTCTTCTTATT
1307574 CTTCATTTGGATAAGAAAATTTCATTCCAAATCCAAAAAGGATGCATCAAAGCTACAATAAATAA
196 CTTCATTTGGATAAGAAAATTTCATTCCAAATCCAAAAAGGATGCATCAAAGCTACAATAAATAA
* *
1307639 ACCAGTCAAACAAAAACAGAAAAACACCACACCCACACCAAGAGCCTACAACAACCTAACTCAAA
261 ACCAGTAAAACAAAAACAAAAAAACACCACACCCACACCAAGAGCCTACAACAACCTAACTCAAA
*
1307704 CAAAAGCAACAAACACTAGACCAAAGAAAAAGGGGAAAAACAATCACACCCAACACAAACACCCA
326 CAAAAACAACAAACACTAGACCAAAGAAAAAGGGGAAAAACAATCACACCCAACACAAACACCCA
*
1307769 TTAACAAGTCAAGCATCAGAGAATCCTACAGACATTACAAATCTACAGATTCCTATCATCCTTAT
391 TTAACAAGTCAAGCATCAGAGAATCCCACAGACATTACAAATCTACAGATTCCTATCATCCTTAT
*
1307834 TGAAACAACAACTATGAAGCTTATAGCTAATAGCCTATTGGATTACCTAACACAAGACCTCAGGG
456 TGAAACAACAACCATGAAGCTTATAGCTAATAGCCTATTGGATTACCTAACACAAGACCTCAGGG
1307899 GGTGCCTGACACCCTTGAATAGCCTGTGATTATGTTCTTCCCAAATATAATAAAGGTAACCAGTC
521 GGTGCCTGACACCCTTGAATAGCCTGTGATTATGTTCTTCCCAAATATAATAAAGGTAACCAGTC
1307964 TAAGCCAGCTTCAAAATACCTACAATCAAAGATTTACCTTTAAACCTACCAATCACCCAATCCAA
586 TAAGCCAGCTTCAAAATACCTACAATCAAAGATTTACCTTTAAACCTACCAATCACCCAATCCAA
* *
1308029 AAGCTCAGCTCAGTCTCCCCAAGGAAAACCATAATTTTGCAAAACACGACCCCAAACAATGCAAG
651 AAGCTCAGCTCAGTCTCCCCAAGGAAAACCACAAATTTGCAAAACACGACCCCAAACAATGCAAG
* *
1308094 TGTAAGGGCAATCGCCAATGATATGACTTCTACTCTCCTCACCAGCCTCACACAGCCTGTAATCA
716 TGTAAAGGCAATCGCCAATGATATGACTTCTACTCTCCTCACCAGCCTCACACAGCCTGCAATCA
1308159 CCAACAATAACTAAACATA
781 CCAACAATAACTAAACATA
1308178 TTTT
1 TTTT
1308182 AGTAAGGTTG
Statistics
Matches: 779, Mismatches: 23, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
798 750 0.96
799 29 0.04
ACGTcount: A:0.37, C:0.23, G:0.11, T:0.29
Consensus pattern (799 bp):
TTTTTATTTTCTCTAAACTCTAAAATCATCATTTTTTATTTCATTTTGTTTGATATGCGGCGACA
TTAATTTTAGTATTGTTCGTGAATCACATTTTTTCTTTATTTCTCATTTACTTTCTTATGTCGTA
TATTTACTTTTCTTTTGTTTTTTTAGTTTTTAATAATTACAGTTATGGTACATTTTCTTCTTATT
CTTCATTTGGATAAGAAAATTTCATTCCAAATCCAAAAAGGATGCATCAAAGCTACAATAAATAA
ACCAGTAAAACAAAAACAAAAAAACACCACACCCACACCAAGAGCCTACAACAACCTAACTCAAA
CAAAAACAACAAACACTAGACCAAAGAAAAAGGGGAAAAACAATCACACCCAACACAAACACCCA
TTAACAAGTCAAGCATCAGAGAATCCCACAGACATTACAAATCTACAGATTCCTATCATCCTTAT
TGAAACAACAACCATGAAGCTTATAGCTAATAGCCTATTGGATTACCTAACACAAGACCTCAGGG
GGTGCCTGACACCCTTGAATAGCCTGTGATTATGTTCTTCCCAAATATAATAAAGGTAACCAGTC
TAAGCCAGCTTCAAAATACCTACAATCAAAGATTTACCTTTAAACCTACCAATCACCCAATCCAA
AAGCTCAGCTCAGTCTCCCCAAGGAAAACCACAAATTTGCAAAACACGACCCCAAACAATGCAAG
TGTAAAGGCAATCGCCAATGATATGACTTCTACTCTCCTCACCAGCCTCACACAGCCTGCAATCA
CCAACAATAACTAAACATA
Found at i:1310028 original size:14 final size:14
Alignment explanation
Indices: 1310009--1310035 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1309999 TCTCTTTTTA
1310009 ATAAAATGATAATG
1 ATAAAATGATAATG
1310023 ATAAAATGATAAT
1 ATAAAATGATAAT
1310036 AAGGTTGAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.00, G:0.11, T:0.30
Consensus pattern (14 bp):
ATAAAATGATAATG
Found at i:1310700 original size:36 final size:35
Alignment explanation
Indices: 1310619--1310758 Score: 192
Period size: 36 Copynumber: 3.9 Consensus size: 35
1310609 AGATAAACAA
* *
1310619 TTGAATAGAAAGTGCAGATGCTTCCTTCCGTTCAC
1 TTGAATCGAAAGTGCAGATGCTTCCTTTCGTTCAC
* *
1310654 TTGAATCGAAAGTGTC-GATGCTTCCTTTTGTTCTTC
1 TTGAATCGAAAGTG-CAGATGCTTCCTTTCGTTC-AC
*
1310690 TTGAATCGAAAGTGCCGATGCTTCCTTTCGTTCAC
1 TTGAATCGAAAGTGCAGATGCTTCCTTTCGTTCAC
*
1310725 TTTGAATCGAAAGTGCTGATGCTTCCTTTCGTTC
1 -TTGAATCGAAAGTGCAGATGCTTCCTTTCGTTC
1310759 TTCTTATTCA
Statistics
Matches: 94, Mismatches: 7, Indels: 7
0.87 0.06 0.06
Matches are distributed among these distances:
35 30 0.32
36 64 0.68
ACGTcount: A:0.20, C:0.22, G:0.20, T:0.38
Consensus pattern (35 bp):
TTGAATCGAAAGTGCAGATGCTTCCTTTCGTTCAC
Found at i:1310762 original size:72 final size:71
Alignment explanation
Indices: 1310619--1310763 Score: 229
Period size: 72 Copynumber: 2.0 Consensus size: 71
1310609 AGATAAACAA
*
1310619 TTGAATAGAAAGTGCAGATGCTTCCTTCCGTTCACTTGAATCGAAAGTGTCGATGCTTCCTTTTG
1 TTGAATAGAAAGTGCAGATGCTTCCTTCCGTTCACTTGAATCGAAAGTGTCGATGCTTCCTTTCG
1310684 TTCTTC
66 TTCTTC
* * *
1310690 TTGAATCGAAAGTGCCGATGCTTCCTTTCGTTCACTTTGAATCGAAAGTG-CTGATGCTTCCTTT
1 TTGAATAGAAAGTGCAGATGCTTCCTTCCGTTCAC-TTGAATCGAAAGTGTC-GATGCTTCCTTT
1310754 CGTTCTTC
64 CGTTCTTC
1310762 TT
1 TT
1310764 ATTCACCTTC
Statistics
Matches: 68, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
71 33 0.49
72 35 0.51
ACGTcount: A:0.19, C:0.22, G:0.19, T:0.39
Consensus pattern (71 bp):
TTGAATAGAAAGTGCAGATGCTTCCTTCCGTTCACTTGAATCGAAAGTGTCGATGCTTCCTTTCG
TTCTTC
Found at i:1311197 original size:15 final size:15
Alignment explanation
Indices: 1311177--1311206 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1311167 ACACGATGCA
1311177 TCCATAAATGGATTC
1 TCCATAAATGGATTC
*
1311192 TCCATAAATTGATTC
1 TCCATAAATGGATTC
1311207 ATCATGTTCA
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:0.33, C:0.20, G:0.10, T:0.37
Consensus pattern (15 bp):
TCCATAAATGGATTC
Found at i:1313528 original size:129 final size:129
Alignment explanation
Indices: 1313298--1313557 Score: 511
Period size: 129 Copynumber: 2.0 Consensus size: 129
1313288 TAACTTTTAA
1313298 TAGTCGATAAACTCAACAAAACAACACTATATAGTCAAAGGACTTAATACATCAATATCATATAG
1 TAGTCGATAAACTCAACAAAACAACACTATATAGTCAAAGGACTTAATACATCAATATCATATAG
1313363 TCGGGGGACCATTTGCGTTCTTTACCCAATTATTTATTGTCCACATTAATGATTCTTTATCCAT
66 TCGGGGGACCATTTGCGTTCTTTACCCAATTATTTATTGTCCACATTAATGATTCTTTATCCAT
1313427 TAGTCGATAAACTCAACAAAACAACACTATATAGTCAAAGGACTTAATACATCAATATCATATAG
1 TAGTCGATAAACTCAACAAAACAACACTATATAGTCAAAGGACTTAATACATCAATATCATATAG
*
1313492 TCGGGGGATCATTTGCGTTCTTTACCCAATTATTTATTGTCCACATTAATGATTCTTTATCCAT
66 TCGGGGGACCATTTGCGTTCTTTACCCAATTATTTATTGTCCACATTAATGATTCTTTATCCAT
1313556 TA
1 TA
1313558 TAGTGAATTG
Statistics
Matches: 130, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
129 130 1.00
ACGTcount: A:0.35, C:0.20, G:0.12, T:0.34
Consensus pattern (129 bp):
TAGTCGATAAACTCAACAAAACAACACTATATAGTCAAAGGACTTAATACATCAATATCATATAG
TCGGGGGACCATTTGCGTTCTTTACCCAATTATTTATTGTCCACATTAATGATTCTTTATCCAT
Found at i:1313784 original size:19 final size:20
Alignment explanation
Indices: 1313760--1313812 Score: 54
Period size: 19 Copynumber: 2.6 Consensus size: 20
1313750 TTGTTTATTG
*
1313760 TTAATTTTAATTT-ATAAAA
1 TTAATTTTAATTTCAAAAAA
* *
1313779 TTAATTATCATTTCAAAAAA
1 TTAATTTTAATTTCAAAAAA
*
1313799 TAATATTTTAATTT
1 TTA-ATTTTAATTT
1313813 TATCAATTTA
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
19 11 0.42
20 7 0.27
21 8 0.31
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (20 bp):
TTAATTTTAATTTCAAAAAA
Found at i:1315871 original size:34 final size:34
Alignment explanation
Indices: 1315833--1315898 Score: 123
Period size: 34 Copynumber: 1.9 Consensus size: 34
1315823 ATTAATCGTT
1315833 GGTATCTGATCTATTAGCCGACTAATCCAAATCG
1 GGTATCTGATCTATTAGCCGACTAATCCAAATCG
*
1315867 GGTATCTGATCTATTGGCCGACTAATCCAAAT
1 GGTATCTGATCTATTAGCCGACTAATCCAAAT
1315899 GGCTACATAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30
Consensus pattern (34 bp):
GGTATCTGATCTATTAGCCGACTAATCCAAATCG
Found at i:1316464 original size:2 final size:2
Alignment explanation
Indices: 1316457--1316501 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1316447 CTAAACTTTA
1316457 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
1316499 AT A
1 AT A
1316502 ATTTCTATGT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1319568 original size:21 final size:20
Alignment explanation
Indices: 1319544--1319613 Score: 59
Period size: 21 Copynumber: 3.4 Consensus size: 20
1319534 TATTTTTATA
1319544 AAAAGGTTAAGCTATTTCATC
1 AAAAGGTTAAGCT-TTTCATC
* * *
1319565 AAAAGGATAAACCTTTTAATC
1 AAAAGG-TTAAGCTTTTCATC
* *
1319586 TAAAGGTTAAGTTCTTTCATC
1 AAAAGGTTAAGCT-TTTCATC
*
1319607 GAAAGGT
1 AAAAGGT
1319614 CTTAACATTT
Statistics
Matches: 38, Mismatches: 9, Indels: 4
0.75 0.18 0.08
Matches are distributed among these distances:
20 4 0.11
21 29 0.76
22 5 0.13
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.33
Consensus pattern (20 bp):
AAAAGGTTAAGCTTTTCATC
Found at i:1323121 original size:21 final size:21
Alignment explanation
Indices: 1323097--1323146 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
1323087 AGATTAAGCC
1323097 TTTTCATCAAAAGGAGAAGTA
1 TTTTCATCAAAAGGAGAAGTA
* **
1323118 TTTTAATCAAAAGGTTAAGTA
1 TTTTCATCAAAAGGAGAAGTA
*
1323139 CTTTCATC
1 TTTTCATC
1323147 GAAATGTCTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (21 bp):
TTTTCATCAAAAGGAGAAGTA
Found at i:1324207 original size:20 final size:20
Alignment explanation
Indices: 1324184--1324240 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
1324174 TTGTTTATTG
1324184 TTAATTTTAATTTTATAAAA
1 TTAATTTTAATTTTATAAAA
* * * *
1324204 TTAATTATCATTTCAAAAAA
1 TTAATTTTAATTTTATAAAA
*
1324224 TAATATTTTAATTTTAT
1 TTA-ATTTTAATTTTAT
1324241 CAATTGAATC
Statistics
Matches: 27, Mismatches: 9, Indels: 1
0.73 0.24 0.03
Matches are distributed among these distances:
20 18 0.67
21 9 0.33
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.53
Consensus pattern (20 bp):
TTAATTTTAATTTTATAAAA
Found at i:1329756 original size:227 final size:227
Alignment explanation
Indices: 1329361--1329814 Score: 908
Period size: 227 Copynumber: 2.0 Consensus size: 227
1329351 GGTGAGTTTT
1329361 CTGATTTGTTAGTTATTTGTTAAATTAAAGGTTAGGTTTTGATCATTAGATGATAACTAAGCTTA
1 CTGATTTGTTAGTTATTTGTTAAATTAAAGGTTAGGTTTTGATCATTAGATGATAACTAAGCTTA
1329426 AGTTGTCTTATGATCAAAAGATGAAGAAGTTATAAAAGATTAAAAGAAACGGGATTTTATATGAA
66 AGTTGTCTTATGATCAAAAGATGAAGAAGTTATAAAAGATTAAAAGAAACGGGATTTTATATGAA
1329491 ATTATGGAAAATAGTTGATAAGTTGAATTTGAAGTTAAATTTGACTTGTCATCATGTTAATTAAG
131 ATTATGGAAAATAGTTGATAAGTTGAATTTGAAGTTAAATTTGACTTGTCATCATGTTAATTAAG
1329556 GAATATGAAGTGTTAGAATTGTATTTAGAATA
196 GAATATGAAGTGTTAGAATTGTATTTAGAATA
1329588 CTGATTTGTTAGTTATTTGTTAAATTAAAGGTTAGGTTTTGATCATTAGATGATAACTAAGCTTA
1 CTGATTTGTTAGTTATTTGTTAAATTAAAGGTTAGGTTTTGATCATTAGATGATAACTAAGCTTA
1329653 AGTTGTCTTATGATCAAAAGATGAAGAAGTTATAAAAGATTAAAAGAAACGGGATTTTATATGAA
66 AGTTGTCTTATGATCAAAAGATGAAGAAGTTATAAAAGATTAAAAGAAACGGGATTTTATATGAA
1329718 ATTATGGAAAATAGTTGATAAGTTGAATTTGAAGTTAAATTTGACTTGTCATCATGTTAATTAAG
131 ATTATGGAAAATAGTTGATAAGTTGAATTTGAAGTTAAATTTGACTTGTCATCATGTTAATTAAG
1329783 GAATATGAAGTGTTAGAATTGTATTTAGAATA
196 GAATATGAAGTGTTAGAATTGTATTTAGAATA
1329815 TATTGAAATT
Statistics
Matches: 227, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
227 227 1.00
ACGTcount: A:0.38, C:0.04, G:0.19, T:0.38
Consensus pattern (227 bp):
CTGATTTGTTAGTTATTTGTTAAATTAAAGGTTAGGTTTTGATCATTAGATGATAACTAAGCTTA
AGTTGTCTTATGATCAAAAGATGAAGAAGTTATAAAAGATTAAAAGAAACGGGATTTTATATGAA
ATTATGGAAAATAGTTGATAAGTTGAATTTGAAGTTAAATTTGACTTGTCATCATGTTAATTAAG
GAATATGAAGTGTTAGAATTGTATTTAGAATA
Found at i:1345513 original size:16 final size:15
Alignment explanation
Indices: 1345468--1345512 Score: 58
Period size: 14 Copynumber: 3.0 Consensus size: 15
1345458 ATATAGAATC
1345468 AAAATTGATAATATATA
1 AAAATT-AT-ATATATA
1345485 AAAATTAT-TATATA
1 AAAATTATATATATA
1345499 AAAA-TATATATATA
1 AAAATTATATATATA
1345513 TTTTTAATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
13 3 0.11
14 16 0.59
16 2 0.07
17 6 0.22
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (15 bp):
AAAATTATATATATA
Found at i:1347084 original size:21 final size:21
Alignment explanation
Indices: 1347058--1347109 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
1347048 ACCCAGGGTA
1347058 GAGTATCGATGCTCCCCATAG
1 GAGTATCGATGCTCCCCATAG
*
1347079 GAGTATCGATGCTCCTCATAG
1 GAGTATCGATGCTCCCCATAG
*
1347100 GAGGATCGAT
1 GAGTATCGAT
1347110 ACCAAGGCAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (21 bp):
GAGTATCGATGCTCCCCATAG
Found at i:1347172 original size:18 final size:19
Alignment explanation
Indices: 1347149--1347192 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
1347139 ATTTTTGGCG
* *
1347149 TCGATACTCAA-GTGAGTA
1 TCGATACCCAAGGTCAGTA
1347167 TCGATACCCAAGGGTCAGTA
1 TCGATACCCAA-GGTCAGTA
1347187 TCGATA
1 TCGATA
1347193 TTGTGCCAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 10 0.45
20 12 0.55
ACGTcount: A:0.32, C:0.20, G:0.23, T:0.25
Consensus pattern (19 bp):
TCGATACCCAAGGTCAGTA
Found at i:1348967 original size:21 final size:22
Alignment explanation
Indices: 1348918--1348970 Score: 63
Period size: 21 Copynumber: 2.4 Consensus size: 22
1348908 ACGTATAATT
*
1348918 ATAAATTAGTTGAAAATTTAAAG
1 ATAAATTA-TTGAAAATTAAAAG
* *
1348941 AAAAATTATTTAAAA-TAAAAG
1 ATAAATTATTGAAAATTAAAAG
1348962 ATAAATTAT
1 ATAAATTAT
1348971 ACTAGTGACC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 13 0.50
22 6 0.23
23 7 0.27
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.34
Consensus pattern (22 bp):
ATAAATTATTGAAAATTAAAAG
Found at i:1350073 original size:21 final size:22
Alignment explanation
Indices: 1350047--1350098 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 22
1350037 GGTCATTAGT
1350047 ATAATTTACCATTT-ATTTT-AA
1 ATAATTTA-CATTTAATTTTCAA
*
1350068 ATAATTTACTTTTAAATTTTCAA
1 ATAATTTACATTT-AATTTTCAA
1350091 ATAATTTA
1 ATAATTTA
1350099 TAATTATACA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
20 4 0.15
21 8 0.30
22 5 0.19
23 10 0.37
ACGTcount: A:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (22 bp):
ATAATTTACATTTAATTTTCAA
Found at i:1350168 original size:16 final size:16
Alignment explanation
Indices: 1350147--1350178 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1350137 ATAAATTACA
*
1350147 TTAATGGTGTTCATCG
1 TTAATGGTGCTCATCG
1350163 TTAATGGTGCTCATCG
1 TTAATGGTGCTCATCG
1350179 GTACCCATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.19, C:0.16, G:0.25, T:0.41
Consensus pattern (16 bp):
TTAATGGTGCTCATCG
Found at i:1351138 original size:2 final size:2
Alignment explanation
Indices: 1351131--1351157 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1351121 AAAATAAAAT
1351131 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
1351158 GTCATATCAA
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:1353275 original size:2 final size:2
Alignment explanation
Indices: 1353270--1353325 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
1353260 AGATTAAAAA
1353270 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
1353312 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
1353326 TAAAAAATAT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1353479 original size:19 final size:19
Alignment explanation
Indices: 1353455--1353513 Score: 60
Period size: 19 Copynumber: 3.5 Consensus size: 19
1353445 ATGGTAAAAG
1353455 AATATGAAATTTAGTTTAA
1 AATATGAAATTTAGTTTAA
*
1353474 AATATGAAA---A---T-C
1 AATATGAAATTTAGTTTAA
1353486 AATATGAAATTTAGTTTAA
1 AATATGAAATTTAGTTTAA
1353505 AATATGAAA
1 AATATGAAA
1353514 ATCTTACATT
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
12 9 0.29
13 1 0.03
15 1 0.03
16 1 0.03
18 1 0.03
19 18 0.58
ACGTcount: A:0.53, C:0.02, G:0.10, T:0.36
Consensus pattern (19 bp):
AATATGAAATTTAGTTTAA
Found at i:1353490 original size:31 final size:31
Alignment explanation
Indices: 1353455--1353516 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
1353445 ATGGTAAAAG
1353455 AATATGAAATTTAGTTTAAAATATGAAAATC
1 AATATGAAATTTAGTTTAAAATATGAAAATC
1353486 AATATGAAATTTAGTTTAAAATATGAAAATC
1 AATATGAAATTTAGTTTAAAATATGAAAATC
1353517 TTACATTGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.52, C:0.03, G:0.10, T:0.35
Consensus pattern (31 bp):
AATATGAAATTTAGTTTAAAATATGAAAATC
Found at i:1355267 original size:31 final size:31
Alignment explanation
Indices: 1355229--1355328 Score: 85
Period size: 31 Copynumber: 3.2 Consensus size: 31
1355219 TTACGGTCTA
*
1355229 TTACAAAATGATCATTAAATTTATCAAACTC
1 TTACAAAATAATCATTAAATTTATCAAACTC
* * * * * *
1355260 TTACAAAACAGTAATCAAATTTTATCAAAATG
1 TTACAAAATAATCATTAAA-TTTATCAAACTC
* * *
1355292 TTATAAAATAATCATT-AATTTCGTCAAACTT
1 TTACAAAATAATCATTAAATTT-ATCAAACTC
1355323 TTACAA
1 TTACAA
1355329 TTTATTATAA
Statistics
Matches: 51, Mismatches: 16, Indels: 4
0.72 0.23 0.06
Matches are distributed among these distances:
30 3 0.06
31 27 0.53
32 21 0.41
ACGTcount: A:0.46, C:0.14, G:0.04, T:0.36
Consensus pattern (31 bp):
TTACAAAATAATCATTAAATTTATCAAACTC
Found at i:1358282 original size:18 final size:19
Alignment explanation
Indices: 1358242--1358282 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
1358232 TTTTTGTTTA
*
1358242 TTTATAATTTATACTAATT
1 TTTATAATTTATACTAATG
*
1358261 TTTATAATTTA-ATTAATG
1 TTTATAATTTATACTAATG
1358279 TTTA
1 TTTA
1358283 CAGTTTTGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (19 bp):
TTTATAATTTATACTAATG
Found at i:1359205 original size:15 final size:14
Alignment explanation
Indices: 1359187--1359232 Score: 51
Period size: 15 Copynumber: 3.3 Consensus size: 14
1359177 AAAAATTATT
1359187 ATTAATTTGTAAGAA
1 ATTAATTTGTAA-AA
*
1359202 ATTAGTTTGTAATAA
1 ATTAATTTGTAA-AA
1359217 ATT-ATTT-TAAAA
1 ATTAATTTGTAAAA
1359229 ATTA
1 ATTA
1359233 GTTATTTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
12 5 0.19
13 3 0.11
14 3 0.11
15 16 0.59
ACGTcount: A:0.46, C:0.00, G:0.09, T:0.46
Consensus pattern (14 bp):
ATTAATTTGTAAAA
Found at i:1361599 original size:18 final size:19
Alignment explanation
Indices: 1361559--1361599 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
1361549 TTTTTGTTTA
*
1361559 TTTATAATTTATACTAATT
1 TTTATAATTTATACTAATG
*
1361578 TTTATAATTTA-ATTAATG
1 TTTATAATTTATACTAATG
1361596 TTTA
1 TTTA
1361600 CAGTTTTGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (19 bp):
TTTATAATTTATACTAATG
Found at i:1362522 original size:15 final size:14
Alignment explanation
Indices: 1362504--1362549 Score: 51
Period size: 15 Copynumber: 3.3 Consensus size: 14
1362494 AAAAATTATT
1362504 ATTAATTTGTAAGAA
1 ATTAATTTGTAA-AA
*
1362519 ATTAGTTTGTAATAA
1 ATTAATTTGTAA-AA
1362534 ATT-ATTT-TAAAA
1 ATTAATTTGTAAAA
1362546 ATTA
1 ATTA
1362550 GTTATTTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
12 5 0.19
13 3 0.11
14 3 0.11
15 16 0.59
ACGTcount: A:0.46, C:0.00, G:0.09, T:0.46
Consensus pattern (14 bp):
ATTAATTTGTAAAA
Found at i:1368537 original size:3 final size:3
Alignment explanation
Indices: 1368529--1368597 Score: 75
Period size: 3 Copynumber: 23.0 Consensus size: 3
1368519 ACTTGTTTGG
* * * *
1368529 ATC ATC ATC ATC ATC ATC ATC ATC ATC GTC GTC ATC ATC TTC ATC GTC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
* * *
1368577 ATC TTC ATC GTC ATC TTC ATC
1 ATC ATC ATC ATC ATC ATC ATC
1368598 GTCAGCTTCA
Statistics
Matches: 54, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.23, C:0.33, G:0.06, T:0.38
Consensus pattern (3 bp):
ATC
Found at i:1368546 original size:12 final size:12
Alignment explanation
Indices: 1368533--1368614 Score: 92
Period size: 12 Copynumber: 6.8 Consensus size: 12
1368523 GTTTGGATCA
*
1368533 TCATCATCATCA
1 TCATCATCATCT
*
1368545 TCATCATCATCG
1 TCATCATCATCT
*
1368557 TCGTCATCATCT
1 TCATCATCATCT
*
1368569 TCATCGTCATCT
1 TCATCATCATCT
*
1368581 TCATCGTCATCT
1 TCATCATCATCT
* *
1368593 TCATCGTCAGCT
1 TCATCATCATCT
*
1368605 TCATCTTCAT
1 TCATCATCAT
1368615 TGACCACTCG
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 62 1.00
ACGTcount: A:0.21, C:0.33, G:0.07, T:0.39
Consensus pattern (12 bp):
TCATCATCATCT
Found at i:1368612 original size:6 final size:6
Alignment explanation
Indices: 1368533--1368614 Score: 74
Period size: 6 Copynumber: 13.7 Consensus size: 6
1368523 GTTTGGATCA
* * * * * * *
1368533 TCATCA TCATCA TCATCA TCATCG TCGTCA TCATCT TCATCG TCATCT
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT
* * *
1368581 TCATCG TCATCT TCATCG TCAGCT TCATCT TCAT
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCAT
1368615 TGACCACTCG
Statistics
Matches: 63, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
6 63 1.00
ACGTcount: A:0.21, C:0.33, G:0.07, T:0.39
Consensus pattern (6 bp):
TCATCT
Found at i:1369428 original size:2 final size:2
Alignment explanation
Indices: 1369421--1369464 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
1369411 GTTTCAGGAG
1369421 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
1369463 AT
1 AT
1369465 CCTTCCTCAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1370587 original size:200 final size:200
Alignment explanation
Indices: 1370244--1370878 Score: 1121
Period size: 200 Copynumber: 3.2 Consensus size: 200
1370234 GATGTTTATG
1370244 GGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAAC
1 GGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAAC
1370309 TACAAAAGTGTCGACACATTATTAAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTA
66 TACAAAAGTGTCGACACATTATTAAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTA
*
1370374 GATTGAAAAATTACTTATTACATTATATTTTTGGTTTTCGATGTTTATGGGATCGACACTTTTTA
131 GATTGAAAAATTACATATTACATTATATTTTTGGTTTTCGATGTTTATGGGATCGACACTTTTTA
1370439 TATAT
196 TATAT
*
1370444 GGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACCAAAAATATCGACACAAAC
1 GGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAAC
* *
1370509 TACAAAAGTGTCGGCACATTATTAAGACCTATTCTCTCATAAAATCGGTATACTTGTACCGGTTA
66 TACAAAAGTGTCGACACATTATTAAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTA
*
1370574 GATTGAAAAATTACATATTACATTAT-TCTTTTGGTTTTCGATGCTTATGGGATCGACACTTTTT
131 GATTGAAAAATTACATATTACATTATAT-TTTTGGTTTTCGATGTTTATGGGATCGACACTTTTT
1370638 ATATAT
195 ATATAT
*
1370644 GGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAGAAATATCGACACAAAC
1 GGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAAC
* * * *
1370709 TACAAAAGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGCACCGATTA
66 TACAAAAGTGTCGACACATTATTAAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTA
* *
1370774 GATTGAAAAATTACCTATTACATTATACTTTTTGG-TTTCGATGTTTTTGGGATCGACACTTTTT
131 GATTGAAAAATTACATATTACATTATA-TTTTTGGTTTTCGATGTTTATGGGATCGACACTTTTT
1370838 ATATAT
195 ATATAT
*
1370844 GGAACGACACTTTATGGTTGCACCCTGTTTGCCAT
1 GGATCGACACTTTATGGTTGCACCCTGTTTGCCAT
1370879 ATTGTAAATT
Statistics
Matches: 415, Mismatches: 17, Indels: 6
0.95 0.04 0.01
Matches are distributed among these distances:
199 1 0.00
200 407 0.98
201 6 0.01
202 1 0.00
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.36
Consensus pattern (200 bp):
GGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAAC
TACAAAAGTGTCGACACATTATTAAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTA
GATTGAAAAATTACATATTACATTATATTTTTGGTTTTCGATGTTTATGGGATCGACACTTTTTA
TATAT
Found at i:1372849 original size:33 final size:33
Alignment explanation
Indices: 1372812--1372877 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
1372802 CATCTTAATA
*
1372812 TCACCCCTTAACACCCCAACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
* *
1372845 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
1372878 CTATCTATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.23, C:0.48, G:0.00, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCCCAACTTCTTTCACCACT
Found at i:1372936 original size:21 final size:21
Alignment explanation
Indices: 1372911--1372975 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
1372901 CCCCTTATGC
* *
1372911 CTCTCAAGTGTATCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
1372932 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
*
1372953 CTATCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
1372974 CT
1 CT
1372976 TGATTGTCTT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.17, C:0.31, G:0.11, T:0.42
Consensus pattern (21 bp):
CTCTCAAGTTTCTCTTCGACT
Found at i:1375412 original size:20 final size:20
Alignment explanation
Indices: 1375385--1375431 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
1375375 TCCGGTAACG
1375385 TTTTACCGGTTTTATCAT-T
1 TTTTACCGGTTTTATCATAT
1375404 TTGTTACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCATAT
1375425 TTTTACC
1 TTTTACC
1375432 TGGTATATCG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.55
Consensus pattern (20 bp):
TTTTACCGGTTTTATCATAT
Found at i:1375614 original size:183 final size:181
Alignment explanation
Indices: 1375171--1375644 Score: 689
Period size: 181 Copynumber: 2.6 Consensus size: 181
1375161 CGTACTTACG
* * *
1375171 AAAGTATCGACACTTTCAATATATCCGGTATCATTTTACCGGTTTTATCATTTTGATACTGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* * *
1375236 TATCATATTTTTACATGTTATATCGTTGTGGATCGATATATTTTTTTAAAGTATCGACACATTAT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTTAAAGTATCGACACATTAT
1375301 AGACGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATAT
131 AGACGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATAT
*
1375352 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGTTACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* *
1375417 TATCATATTTTTACCTGGTATATCGTTTTGGATCGATACATTTTTTTAAAAGTATCGACACTTTA
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTT-AAAGTATCGACACATTA
** * *
1375482 TAGGA-TTTAAAATTGCTTCTCTTTTAAATTCACGAAGTGTCGATCCTTATATT
130 TA-GACGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATA-T
* * * * * * **
1375535 AAAGTACCGACACTTTAAATGTATCTGGTAGCGCTTTACCGGTTTTATCATTTCAATACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* * * *
1375600 TGTCATAGTTTTACCTGTTATATCATTTTGGATCGACACATTTTT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTT
1375645 AATTTGGATC
Statistics
Matches: 263, Mismatches: 27, Indels: 4
0.89 0.09 0.01
Matches are distributed among these distances:
181 104 0.40
182 60 0.23
183 99 0.38
ACGTcount: A:0.27, C:0.16, G:0.14, T:0.43
Consensus pattern (181 bp):
AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTTAAAGTATCGACACATTAT
AGACGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATAT
Found at i:1376888 original size:24 final size:23
Alignment explanation
Indices: 1376861--1376996 Score: 80
Period size: 24 Copynumber: 5.7 Consensus size: 23
1376851 CTAAAAATAA
1376861 TATATGGTTTTTGAAAATATGTAG
1 TATAT-GTTTTTGAAAATATGTAG
* * * *
1376885 TATA-GTTTTTAAAAACATATAA
1 TATATGTTTTTGAAAATATGTAG
**
1376907 TATATAACTTTTGAAAATATGTAG
1 TATAT-GTTTTTGAAAATATGTAG
* *
1376931 TATA-GTTTTTAAAAACATATAATA-
1 TATATGTTTTT-GAAA-ATAT-GTAG
* *
1376955 TATATAGTTTTTTAAAACATATGTAA
1 TATAT-G-TTTTTGAAA-ATATGTAG
*
1376981 TATATATTTTTGAAAA
1 TATATGTTTTTGAAAA
1376997 CATAATATGG
Statistics
Matches: 86, Mismatches: 17, Indels: 19
0.70 0.14 0.16
Matches are distributed among these distances:
22 22 0.26
23 4 0.05
24 36 0.42
25 4 0.05
26 15 0.17
27 5 0.06
ACGTcount: A:0.43, C:0.03, G:0.10, T:0.44
Consensus pattern (23 bp):
TATATGTTTTTGAAAATATGTAG
Found at i:1376899 original size:22 final size:22
Alignment explanation
Indices: 1376867--1376945 Score: 79
Period size: 22 Copynumber: 3.5 Consensus size: 22
1376857 ATAATATATG
*
1376867 GTTTTTGAAAATATGTAGTATA
1 GTTTTTAAAAATATGTAGTATA
*
1376889 GTTTTTAAAAACATATAATA-TATA
1 GTTTTT-AAAA-ATAT-GTAGTATA
** *
1376913 ACTTTTGAAAATATGTAGTATA
1 GTTTTTAAAAATATGTAGTATA
1376935 GTTTTTAAAAA
1 GTTTTTAAAAA
1376946 CATATAATAT
Statistics
Matches: 44, Mismatches: 9, Indels: 8
0.72 0.15 0.13
Matches are distributed among these distances:
21 2 0.05
22 22 0.50
23 6 0.14
24 12 0.27
25 2 0.05
ACGTcount: A:0.43, C:0.03, G:0.11, T:0.43
Consensus pattern (22 bp):
GTTTTTAAAAATATGTAGTATA
Found at i:1376908 original size:46 final size:46
Alignment explanation
Indices: 1376869--1376958 Score: 180
Period size: 46 Copynumber: 2.0 Consensus size: 46
1376859 AATATATGGT
1376869 TTTTGAAAATATGTAGTATAGTTTTTAAAAACATATAATATATAAC
1 TTTTGAAAATATGTAGTATAGTTTTTAAAAACATATAATATATAAC
1376915 TTTTGAAAATATGTAGTATAGTTTTTAAAAACATATAATATATA
1 TTTTGAAAATATGTAGTATAGTTTTTAAAAACATATAATATATA
1376959 TAGTTTTTTA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.46, C:0.03, G:0.09, T:0.42
Consensus pattern (46 bp):
TTTTGAAAATATGTAGTATAGTTTTTAAAAACATATAATATATAAC
Found at i:1376956 original size:22 final size:22
Alignment explanation
Indices: 1376857--1376956 Score: 76
Period size: 22 Copynumber: 4.4 Consensus size: 22
1376847 TTGTCTAAAA
* *
1376857 ATAATATATGGTTTTTGAAAATAT
1 ATAATATA--GTTTTTAAAAACAT
* *
1376881 GTAGTATAGTTTTTAAAAACAT
1 ATAATATAGTTTTTAAAAACAT
* *
1376903 ATAATATA-TAACTTTTGAAAATAT
1 ATAATATAGT---TTTTAAAAACAT
* *
1376927 GTAGTATAGTTTTTAAAAACAT
1 ATAATATAGTTTTTAAAAACAT
1376949 ATAATATA
1 ATAATATA
1376957 TATAGTTTTT
Statistics
Matches: 58, Mismatches: 14, Indels: 10
0.71 0.17 0.12
Matches are distributed among these distances:
21 1 0.02
22 34 0.59
24 22 0.38
25 1 0.02
ACGTcount: A:0.45, C:0.03, G:0.10, T:0.42
Consensus pattern (22 bp):
ATAATATAGTTTTTAAAAACAT
Found at i:1376964 original size:26 final size:25
Alignment explanation
Indices: 1376885--1377004 Score: 108
Period size: 26 Copynumber: 5.0 Consensus size: 25
1376875 AAATATGTAG
1376885 TATAGTTTTTAAAAACATATA-ATA
1 TATAGTTTTTAAAAACATATATATA
** * * *
1376909 TATAACTTTT-GAAA-ATATGTA-G
1 TATAGTTTTTAAAAACATATATATA
1376931 TATAGTTTTTAAAAACATATAATATA
1 TATAGTTTTTAAAAACATAT-ATATA
* *
1376957 TATAGTTTTTTAAAACATATGTAATA
1 TATAGTTTTTAAAAACATATAT-ATA
*
1376983 TATA-TTTTTGAAAACATA-ATAT
1 TATAGTTTTTAAAAACATATATAT
1377005 GGTTTTGAAA
Statistics
Matches: 76, Mismatches: 14, Indels: 13
0.74 0.14 0.13
Matches are distributed among these distances:
22 12 0.16
23 9 0.12
24 13 0.17
25 16 0.21
26 26 0.34
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.43
Consensus pattern (25 bp):
TATAGTTTTTAAAAACATATATATA
Found at i:1379170 original size:60 final size:60
Alignment explanation
Indices: 1379096--1379212 Score: 173
Period size: 60 Copynumber: 1.9 Consensus size: 60
1379086 ATGGATTTGA
* * * *
1379096 GATAAAATTTGAATATTCAAAAGTTTAGGGA-TCAATTTAGAAAAAGAGTCATAGTTTGGG
1 GATAAAATTAGAATATTCAAAAGTTTAGAGACT-AATTTAGAAAAAGAATAATAGTTTGGG
*
1379156 GATAAAATTAGAATATTCAAAAGTTTAGAGACTAATTTAGAAAGAGAATAATAGTTT
1 GATAAAATTAGAATATTCAAAAGTTTAGAGACTAATTTAGAAAAAGAATAATAGTTT
1379213 AAGAACATAT
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
60 50 0.98
61 1 0.02
ACGTcount: A:0.45, C:0.04, G:0.19, T:0.32
Consensus pattern (60 bp):
GATAAAATTAGAATATTCAAAAGTTTAGAGACTAATTTAGAAAAAGAATAATAGTTTGGG
Found at i:1380434 original size:18 final size:18
Alignment explanation
Indices: 1380411--1380448 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
1380401 AATATCACTA
*
1380411 TACTTTTATAAATTAAAT
1 TACTTTTATAAACTAAAT
1380429 TACTTTTATAAACTAAAT
1 TACTTTTATAAACTAAAT
1380447 TA
1 TA
1380449 AAAATAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.45, C:0.08, G:0.00, T:0.47
Consensus pattern (18 bp):
TACTTTTATAAACTAAAT
Found at i:1382406 original size:13 final size:14
Alignment explanation
Indices: 1382383--1382427 Score: 58
Period size: 13 Copynumber: 3.4 Consensus size: 14
1382373 AATAATATAA
1382383 AAAT-ATATATTTT
1 AAATAATATATTTT
*
1382396 AAATACT-TATTTT
1 AAATAATATATTTT
*
1382409 AAAAAATATATTTT
1 AAATAATATATTTT
1382423 AAATA
1 AAATA
1382428 TCTAATTTGA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
13 15 0.58
14 11 0.42
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (14 bp):
AAATAATATATTTT
Found at i:1383278 original size:59 final size:60
Alignment explanation
Indices: 1383196--1383345 Score: 153
Period size: 59 Copynumber: 2.5 Consensus size: 60
1383186 GAACATATGA
* *
1383196 ATAGTTGAGTGATCATTTTGTAACTTTTAATAATTGAGGGACTCAACAAAGCAATGCC-CT
1 ATAGTTGAGTGATCATCTTGTAACTTTTAATAATTGAGAGACTCAACAAAGCAAT-CCTCT
* * * *
1383256 ATAGTTAGAG-GA-CATCTTGTAACTTTTAATAGTTGATAGATTCAACAAAGTAATCCTCT
1 ATAGTT-GAGTGATCATCTTGTAACTTTTAATAATTGAGAGACTCAACAAAGCAATCCTCT
** * *
1383315 ATAGACGAGGGATACATTTTGTAACATTTTA
1 ATAGTTGAGTGAT-CATCTTGTAAC-TTTTA
1383346 TTCATGTTTC
Statistics
Matches: 75, Mismatches: 9, Indels: 10
0.80 0.10 0.11
Matches are distributed among these distances:
58 5 0.07
59 44 0.59
60 8 0.11
61 13 0.17
62 5 0.07
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (60 bp):
ATAGTTGAGTGATCATCTTGTAACTTTTAATAATTGAGAGACTCAACAAAGCAATCCTCT
Found at i:1385240 original size:19 final size:19
Alignment explanation
Indices: 1385216--1385255 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
1385206 GATCACTCGT
1385216 CTGTCGTTGAAGCTCGAAA
1 CTGTCGTTGAAGCTCGAAA
1385235 CTGTCGTTGAAGCTCGAAA
1 CTGTCGTTGAAGCTCGAAA
1385254 CT
1 CT
1385256 CTTCGACACG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.25, C:0.23, G:0.25, T:0.28
Consensus pattern (19 bp):
CTGTCGTTGAAGCTCGAAA
Found at i:1394938 original size:17 final size:17
Alignment explanation
Indices: 1394916--1394950 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
1394906 GACCATTTTT
1394916 ATTGACTATATAAACCA
1 ATTGACTATATAAACCA
1394933 ATTGACTATATAAACCA
1 ATTGACTATATAAACCA
1394950 A
1 A
1394951 CTGGTGAAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.49, C:0.17, G:0.06, T:0.29
Consensus pattern (17 bp):
ATTGACTATATAAACCA
Found at i:1396105 original size:24 final size:23
Alignment explanation
Indices: 1396049--1396106 Score: 57
Period size: 24 Copynumber: 2.5 Consensus size: 23
1396039 ACATTAGATA
1396049 TAAT-TTTAAAAAAATTAAAATT
1 TAATATTTAAAAAAATTAAAATT
* *
1396071 TTATATATTAAAATATATTAAAA-T
1 TAATAT-TTAAAA-AAATTAAAATT
1396095 TAATAGTTTAAA
1 TAATA-TTTAAA
1396107 TATTAAATAC
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
22 3 0.10
23 1 0.03
24 16 0.55
25 9 0.31
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (23 bp):
TAATATTTAAAAAAATTAAAATT
Found at i:1398699 original size:21 final size:21
Alignment explanation
Indices: 1398671--1398789 Score: 125
Period size: 21 Copynumber: 5.8 Consensus size: 21
1398661 CCACTATCGC
1398671 AAATTCGCGTTGCGATAGTTG
1 AAATTCGCGTTGCGATAGTTG
* * *
1398692 AAAATCGCGTTGCGAT-TTTC
1 AAATTCGCGTTGCGATAGTTG
* *
1398712 CATTTCGCGTTGCGATAGTTG
1 AAATTCGCGTTGCGATAGTTG
* * * *
1398733 AAAATCACGTTGCGAT-TTTC
1 AAATTCGCGTTGCGATAGTTG
* *
1398753 CATTTCGCGTTGCGATAGTTG
1 AAATTCGCGTTGCGATAGTTG
1398774 AAATTCGCGTTGCGAT
1 AAATTCGCGTTGCGAT
1398790 TTTCCATTTC
Statistics
Matches: 74, Mismatches: 22, Indels: 4
0.74 0.22 0.04
Matches are distributed among these distances:
20 29 0.39
21 45 0.61
ACGTcount: A:0.22, C:0.18, G:0.24, T:0.35
Consensus pattern (21 bp):
AAATTCGCGTTGCGATAGTTG
Found at i:1398721 original size:20 final size:20
Alignment explanation
Indices: 1398696--1398809 Score: 120
Period size: 20 Copynumber: 5.6 Consensus size: 20
1398686 TAGTTGAAAA
1398696 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
* ** **
1398716 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGAT-TTTCCATT
*
1398737 TCACGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
* ** *
1398757 TCGCGTTGCGATAGTTGAAAT
1 TCGCGTTGCGAT-TTTCCATT
1398778 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
1398798 TCGCGTTGCGAT
1 TCGCGTTGCGAT
1398810 GGTCTACAGT
Statistics
Matches: 72, Mismatches: 20, Indels: 4
0.75 0.21 0.04
Matches are distributed among these distances:
20 42 0.58
21 30 0.42
ACGTcount: A:0.17, C:0.21, G:0.24, T:0.39
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCATT
Found at i:1398731 original size:41 final size:41
Alignment explanation
Indices: 1398674--1398809 Score: 254
Period size: 41 Copynumber: 3.3 Consensus size: 41
1398664 CTATCGCAAA
1398674 TTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAT
1 TTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAT
*
1398715 TTCGCGTTGCGATAGTTGAAAATCACGTTGCGATTTTCCAT
1 TTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAT
*
1398756 TTCGCGTTGCGATAGTTGAAATTCGCGTTGCGATTTTCCAT
1 TTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAT
1398797 TTCGCGTTGCGAT
1 TTCGCGTTGCGAT
1398810 GGTCTACAGT
Statistics
Matches: 92, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 92 1.00
ACGTcount: A:0.18, C:0.20, G:0.24, T:0.38
Consensus pattern (41 bp):
TTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAT
Found at i:1398829 original size:22 final size:21
Alignment explanation
Indices: 1398801--1398872 Score: 76
Period size: 22 Copynumber: 3.4 Consensus size: 21
1398791 TTCCATTTCG
1398801 CGTTGCGATGGTCTACAGTTGT
1 CGTTGCGAT-GTCTACAGTTGT
* * **
1398823 CGTTGCGAT-TTTCCAAAT-T
1 CGTTGCGATGTCTACAGTTGT
1398842 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGAT-GTCTACAGTTGT
1398864 CGTTGCGAT
1 CGTTGCGAT
1398873 TTTCCAAATT
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
19 10 0.26
20 5 0.13
21 5 0.13
22 19 0.49
ACGTcount: A:0.17, C:0.19, G:0.26, T:0.38
Consensus pattern (21 bp):
CGTTGCGATGTCTACAGTTGT
Found at i:1398846 original size:19 final size:19
Alignment explanation
Indices: 1398822--1398887 Score: 69
Period size: 19 Copynumber: 3.3 Consensus size: 19
1398812 TCTACAGTTG
1398822 TCGTTGCGATTTTCCAAAT
1 TCGTTGCGATTTTCCAAAT
* * **
1398841 TCGTTGCGATAGTCTACAGTT
1 TCGTTGCGAT--TTTCCAAAT
1398862 GTCGTTGCGATTTTCCAAAT
1 -TCGTTGCGATTTTCCAAAT
1398882 TCGTTG
1 TCGTTG
1398888 TGATAGTTAA
Statistics
Matches: 36, Mismatches: 8, Indels: 6
0.72 0.16 0.12
Matches are distributed among these distances:
19 16 0.44
20 5 0.14
21 5 0.14
22 10 0.28
ACGTcount: A:0.18, C:0.20, G:0.21, T:0.41
Consensus pattern (19 bp):
TCGTTGCGATTTTCCAAAT
Found at i:1398846 original size:41 final size:41
Alignment explanation
Indices: 1398740--1398894 Score: 176
Period size: 41 Copynumber: 3.8 Consensus size: 41
1398730 TTGAAAATCA
* *
1398740 CGTTGCGATTTTCC-ATTTCGCGTTGCGATAGT-TGA-AATTCG-
1 CGTTGCGATTTTCCAAATT--CGTTGCGATAGTCT-ACAGTT-GT
* *
1398781 CGTTGCGATTTTCC-ATTTCGCGTTGCGATGGTCTACAGTTGT
1 CGTTGCGATTTTCCAAATT--CGTTGCGATAGTCTACAGTTGT
1398823 CGTTGCGATTTTCCAAATTCGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATTTTCCAAATTCGTTGCGATAGTCTACAGTTGT
*
1398864 CGTTGCGATTTTCCAAATTCGTTGTGATAGT
1 CGTTGCGATTTTCCAAATTCGTTGCGATAGT
1398895 TAAAAAAAAA
Statistics
Matches: 105, Mismatches: 5, Indels: 8
0.89 0.04 0.07
Matches are distributed among these distances:
41 84 0.80
42 18 0.17
43 3 0.03
ACGTcount: A:0.17, C:0.19, G:0.24, T:0.40
Consensus pattern (41 bp):
CGTTGCGATTTTCCAAATTCGTTGCGATAGTCTACAGTTGT
Found at i:1398846 original size:82 final size:81
Alignment explanation
Indices: 1398672--1398878 Score: 242
Period size: 82 Copynumber: 2.5 Consensus size: 81
1398662 CACTATCGCA
*
1398672 AATTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAA
1 AATTC-CGTTGCGATAGTTGAAATTCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAA
1398737 TCACGTTGCGATTTTCC
65 TCACGTTGCGATTTTCC
* *
1398754 ATTTCGCGTTGCGATAGTTGAAATTCGCGTTGCGATTTTCCATTTCGCGTTGCGATGGTCT-ACA
1 AATTC-CGTTGCGATAGTTGAAATTCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGT-TGA-A
** **
1398818 GTTGTCGTTGCGATTTTCC
63 AATCACGTTGCGATTTTCC
*
1398837 AAATT-CGTTGCGATAGTCT-ACAGTT-GTCGTTGCGATTTTCCA
1 -AATTCCGTTGCGATAGT-TGA-AATTCG-CGTTGCGATTTTCCA
1398879 AATTCGTTGT
Statistics
Matches: 110, Mismatches: 9, Indels: 11
0.85 0.07 0.08
Matches are distributed among these distances:
82 71 0.65
83 36 0.33
84 3 0.03
ACGTcount: A:0.19, C:0.20, G:0.24, T:0.38
Consensus pattern (81 bp):
AATTCCGTTGCGATAGTTGAAATTCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAAT
CACGTTGCGATTTTCC
Found at i:1398983 original size:6 final size:6
Alignment explanation
Indices: 1398972--1399003 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
1398962 GACATGTATT
1398972 ACCACG ACCACG ACCACG ACCACG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1399004 CGAGACGAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.31, C:0.53, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:1399660 original size:20 final size:20
Alignment explanation
Indices: 1399635--1399707 Score: 65
Period size: 20 Copynumber: 3.6 Consensus size: 20
1399625 ATTGTAGACT
1399635 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
** ** *
1399655 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGGAA-A
*
1399676 ATCGCAACGCAAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
* *
1399696 ACCACAACGCGA
1 ATCGCAACGCGA
1399708 TTTTCAACTA
Statistics
Matches: 38, Mismatches: 14, Indels: 2
0.70 0.26 0.04
Matches are distributed among these distances:
20 24 0.63
21 14 0.37
ACGTcount: A:0.41, C:0.26, G:0.19, T:0.14
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:1399677 original size:41 final size:41
Alignment explanation
Indices: 1399607--1399732 Score: 173
Period size: 41 Copynumber: 3.0 Consensus size: 41
1399597 TCAACGAATT
* *
1399607 TGGAAAATCGCAACGACAATTGT-AGACTATCGCAACGCGAAA
1 TGGAAAATCGCAACG-CGATTTTCA-ACTATCGCAACGCGAAA
*
1399649 TGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCAAAA
1 TGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAA
* * *
1399690 TGGAAAACCACAACGCGATTTTCAACTATCGTAACGCGAAA
1 TGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAA
1399731 TG
1 TG
1399733 CAACGCGAAT
Statistics
Matches: 76, Mismatches: 7, Indels: 3
0.88 0.08 0.03
Matches are distributed among these distances:
41 60 0.79
42 16 0.21
ACGTcount: A:0.39, C:0.23, G:0.19, T:0.19
Consensus pattern (41 bp):
TGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAA
Done.