Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008087.1 Hibiscus syriacus cultivar Beakdansim tig00110597_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: 8279816
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 22 of 37
Found at i:4937817 original size:24 final size:23
Alignment explanation
Indices: 4937782--4937826 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 23
4937772 TGAACAAGCT
4937782 CTTCTCATTATGAACTTCTTCTTC
1 CTTCTCATTATG-ACTTCTTCTTC
*
4937806 CTTCTTCA-TATGAGTTCTTCT
1 CTTC-TCATTATGACTTCTTCT
4937827 CATTATGAGC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 8 0.42
24 8 0.42
25 3 0.16
ACGTcount: A:0.16, C:0.27, G:0.07, T:0.51
Consensus pattern (23 bp):
CTTCTCATTATGACTTCTTCTTC
Found at i:4937958 original size:112 final size:112
Alignment explanation
Indices: 4937766--4938637 Score: 1372
Period size: 112 Copynumber: 7.8 Consensus size: 112
4937756 AGCATCAAAC
* * *
4937766 AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCATATGAGTTCTTCTCATT
1 AAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * * * *
4937831 ATGAGCTTTCTCTGGAAAAGTTAATCCATCAAGTGATGAATTC-AGGCA
66 ATGAACTCT-TCTGGAAATGTTGATCCATCAAGTGATGGATTCGA-GCA
* * * *
4937879 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCC-TCTTCAGATAAGTTCTTCTCATT
1 AAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* *
4937943 ATGAACTTTCTCTGGAAATGTTGATCCATCAAGTGATGAATTCGAGCA
66 ATGAACTCT-TCTGGAAATGTTGATCCATCAAGTGATGGATTCGAGCA
*
4937991 AAAGGTTAAACAAGTTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
*
4938056 ATGAA-TACTTCTGGAAATGTTGATCCATCAAGTGATGGATTCGAACA
66 ATGAACT-CTTCTGGAAATGTTGATCCATCAAGTGATGGATTCGAGCA
*
4938103 AAAGGTTAAACAAGTTCTTCTCATTATGAACTTCCTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* *
4938168 ATGAACACTTCTGGAAATGTTGATCCATCAAGTGATGGATTCAAGCA
66 ATGAACTCTTCTGGAAATGTTGATCCATCAAGTGATGGATTCGAGCA
*
4938215 AAAGGTTAAACAAGTTCTTCTCATTATGAACTTCCTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
*
4938280 ATGAACACTTCTGGAAATGTTGATCCATCAAGTGATGGATTCGAGCA
66 ATGAACTCTTCTGGAAATGTTGATCCATCAAGTGATGGATTCGAGCA
* *
4938327 AAAGGTTAAACAAGTTCTTCTCATTATGAACTTCCTATTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* *
4938392 ATGAACACTTCTGGAAATATTGATCCATCAAGTGATGGATTCGAGCA
66 ATGAACTCTTCTGGAAATGTTGATCCATCAAGTGATGGATTCGAGCA
* *
4938439 AAAGGTTGAACAAGTTCTTATCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * *
4938504 ATGAACTCTTCTGGAAATGTTGATCCATCAAATGATGAATTCAAGCA
66 ATGAACTCTTCTGGAAATGTTGATCCATCAAGTGATGGATTCGAGCA
* * *
4938551 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGGTGAGTTCTTCTCATT
1 AAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
*
4938616 ATGAACTCTACTTGGAAATGTT
66 ATGAACTCTTC-TGGAAATGTT
4938638 TTAAGAAAAA
Statistics
Matches: 717, Mismatches: 37, Indels: 10
0.94 0.05 0.01
Matches are distributed among these distances:
112 640 0.89
113 77 0.11
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.37
Consensus pattern (112 bp):
AAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
ATGAACTCTTCTGGAAATGTTGATCCATCAAGTGATGGATTCGAGCA
Found at i:4938773 original size:76 final size:76
Alignment explanation
Indices: 4938647--4938828 Score: 303
Period size: 76 Copynumber: 2.4 Consensus size: 76
4938637 TTTAAGAAAA
* * *
4938647 AAACATTC-TGCACTGTAGGGCTTACAGCTGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCG
1 AAACA-TCATGCACTGTAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCG
4938711 AAGGCTTTTTGG
65 AAGGCTTTTTGG
*
4938723 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
4938788 AGGCTTTTTGG
66 AGGCTTTTTGG
*
4938799 AAACATCATGCATTGTAGGACTTACAGATG
1 AAACATCATGCACTGTAGGACTTACAGATG
4938829 TGAGAAATAG
Statistics
Matches: 100, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
75 2 0.02
76 98 0.98
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.25
Consensus pattern (76 bp):
AAACATCATGCACTGTAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGG
Found at i:4939516 original size:22 final size:22
Alignment explanation
Indices: 4939491--4939613 Score: 219
Period size: 22 Copynumber: 5.6 Consensus size: 22
4939481 AATAAAGCTT
*
4939491 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAGAGAGAATCTA
* *
4939513 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAGAGAGAATCTA
4939535 TCATCTTTGAAGAGAGAATCTA
1 TCATCTTTGAAGAGAGAATCTA
4939557 TCATCTTTGAAGAGAGAATCTA
1 TCATCTTTGAAGAGAGAATCTA
4939579 TCATCTTTGAAGAGAGAATCTA
1 TCATCTTTGAAGAGAGAATCTA
4939601 TCATCTTTGAAGA
1 TCATCTTTGAAGA
4939614 ATGTAGATGT
Statistics
Matches: 98, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 98 1.00
ACGTcount: A:0.38, C:0.14, G:0.15, T:0.33
Consensus pattern (22 bp):
TCATCTTTGAAGAGAGAATCTA
Found at i:4940049 original size:54 final size:54
Alignment explanation
Indices: 4939985--4940092 Score: 144
Period size: 54 Copynumber: 2.0 Consensus size: 54
4939975 TGACTGGTTC
* * * *
4939985 GTAAAACATTTGTCAATACATTCATCATCTCATGTGGTTTATGCTCAGATGCTA
1 GTAAAACATTTGACAACACATTCATCATCTCATGTGGCTTATGCACAGATGCTA
* * * *
4940039 GTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCACAGATGCTA
1 GTAAAACATTTGACAACACATTCATCATCTCATGTGGCTTATGCACAGATGCTA
4940093 TTTGACAACA
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
54 46 1.00
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.34
Consensus pattern (54 bp):
GTAAAACATTTGACAACACATTCATCATCTCATGTGGCTTATGCACAGATGCTA
Found at i:4942061 original size:31 final size:31
Alignment explanation
Indices: 4942026--4942088 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
4942016 AGAGATGTGG
4942026 TCTGAATTCATCAATTGCAGAGTTGACAGAT
1 TCTGAATTCATCAATTGCAGAGTTGACAGAT
4942057 TCTGAATTCATCAATTGCAGAGTTGACAGAT
1 TCTGAATTCATCAATTGCAGAGTTGACAGAT
4942088 T
1 T
4942089 TTATATGTGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Consensus pattern (31 bp):
TCTGAATTCATCAATTGCAGAGTTGACAGAT
Found at i:4942466 original size:114 final size:114
Alignment explanation
Indices: 4942266--4942485 Score: 341
Period size: 114 Copynumber: 1.9 Consensus size: 114
4942256 GATCATGCAG
* * * *
4942266 TTCATCTTTCAATTCCAATAATTGGTTCTGGGGTTCTTACCGAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATAATTAGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
*
4942331 ACACTTCCAGAAGATGCTATTGGGTCTCTTTATTTCTACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
* * * * *
4942380 TTCATCTTTTAAATCCAATGATTAGTTTTGGGGTTCATACCAAATCATATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATAATTAGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
*
4942445 ACATTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTA
66 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTA
4942486 AGAGAACGTG
Statistics
Matches: 95, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
114 95 1.00
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.35
Consensus pattern (114 bp):
TTCATCTTTCAAATCCAATAATTAGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
Found at i:4944692 original size:17 final size:17
Alignment explanation
Indices: 4944670--4944706 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
4944660 ATTTCTCCTT
* *
4944670 TTTTTCTTTCTTTTTTC
1 TTTTTCCTTCTTCTTTC
4944687 TTTTTCCTTCTTCTTTC
1 TTTTTCCTTCTTCTTTC
4944704 TTT
1 TTT
4944707 GTTGGATGAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTTTCCTTCTTCTTTC
Found at i:4947017 original size:20 final size:20
Alignment explanation
Indices: 4946994--4947032 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
4946984 CAAACGTAAA
*
4946994 AATGCAAATATAAAAATGTG
1 AATGCAAACATAAAAATGTG
* *
4947014 AATGTAACCATAAAAATGT
1 AATGCAAACATAAAAATGT
4947033 AAATTGTGCA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.54, C:0.08, G:0.13, T:0.26
Consensus pattern (20 bp):
AATGCAAACATAAAAATGTG
Found at i:4950992 original size:3 final size:3
Alignment explanation
Indices: 4950984--4951055 Score: 105
Period size: 3 Copynumber: 24.7 Consensus size: 3
4950974 TAAAATTATT
*
4950984 TAA TAA TAA TAA T-A TAA TTA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
4951031 TAA TAA TAA TAA -AA T-A TAAA TAA TA
1 TAA TAA TAA TAA TAA TAA T-AA TAA TA
4951056 TTCAAATGAA
Statistics
Matches: 63, Mismatches: 2, Indels: 8
0.86 0.03 0.11
Matches are distributed among these distances:
2 6 0.10
3 55 0.87
4 2 0.03
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:4955426 original size:20 final size:20
Alignment explanation
Indices: 4955401--4955440 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
4955391 TAAAACACGA
*
4955401 TTATTCAAGGCTATAATATG
1 TTATTCAAGACTATAATATG
4955421 TTATTCAAGACTATAATATG
1 TTATTCAAGACTATAATATG
4955441 AAGACACAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.10, G:0.12, T:0.40
Consensus pattern (20 bp):
TTATTCAAGACTATAATATG
Found at i:4957863 original size:22 final size:22
Alignment explanation
Indices: 4957837--4957879 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
4957827 TTTAACTATC
*
4957837 ACAACTGTAGACTTTCGCAACA
1 ACAACTGTAGACTATCGCAACA
4957859 ACAACTGTAGACTATCGCAAC
1 ACAACTGTAGACTATCGCAAC
4957880 GCGAAATGGA
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:0.37, C:0.28, G:0.14, T:0.21
Consensus pattern (22 bp):
ACAACTGTAGACTATCGCAACA
Found at i:4957922 original size:21 final size:21
Alignment explanation
Indices: 4957896--4958047 Score: 121
Period size: 21 Copynumber: 7.4 Consensus size: 21
4957886 TGGAAAATCA
4957896 CAACGCGATTTTCAACTATCG
1 CAACGCGATTTTCAACTATCG
** ** * *
4957917 CAACGCGAAATGGAA-AATCA
1 CAACGCGATTTTCAACTATCG
*
4957937 CAACGCGATTTTCAACTACCG
1 CAACGCGATTTTCAACTATCG
** ** * *
4957958 CAACGCGAAATAGAA-AATTG
1 CAACGCGATTTTCAACTATCG
4957978 CAACGCGATTTTCAACTATCG
1 CAACGCGATTTTCAACTATCG
** ** *
4957999 CAACGCGAAATGGAA-AATCG
1 CAACGCGATTTTCAACTATCG
4958019 CAACGCGATTTTCAACTATCG
1 CAACGCGATTTTCAACTATCG
4958040 CAACGCGA
1 CAACGCGA
4958048 AATGCAACGC
Statistics
Matches: 92, Mismatches: 36, Indels: 6
0.69 0.27 0.04
Matches are distributed among these distances:
20 42 0.46
21 50 0.54
ACGTcount: A:0.37, C:0.26, G:0.18, T:0.20
Consensus pattern (21 bp):
CAACGCGATTTTCAACTATCG
Found at i:4957982 original size:20 final size:20
Alignment explanation
Indices: 4957872--4958026 Score: 85
Period size: 20 Copynumber: 7.6 Consensus size: 20
4957862 ACTGTAGACT
*
4957872 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATAGAAA
* ** ** *
4957892 ATCACAACGCGATTTTCAACT
1 ATCGCAACGCGAAATAGAA-A
*
4957913 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATAGAAA
* ** ** *
4957933 ATCACAACGCGATTTTCAACT
1 ATCGCAACGCGAAATAGAA-A
*
4957954 ACCGCAACGCGAAATAGAAA
1 ATCGCAACGCGAAATAGAAA
* ** ** *
4957974 ATTGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATAGAA-A
*
4957995 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATAGAAA
4958015 ATCGCAACGCGA
1 ATCGCAACGCGA
4958027 TTTTCAACTA
Statistics
Matches: 94, Mismatches: 38, Indels: 6
0.68 0.28 0.04
Matches are distributed among these distances:
20 53 0.56
21 41 0.44
ACGTcount: A:0.39, C:0.25, G:0.19, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCGAAATAGAAA
Found at i:4958068 original size:41 final size:41
Alignment explanation
Indices: 4957869--4958051 Score: 321
Period size: 41 Copynumber: 4.5 Consensus size: 41
4957859 ACAACTGTAG
*
4957869 ACTATCGCAACGCGAAATGGAAAATCACAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
*
4957910 ACTATCGCAACGCGAAATGGAAAATCACAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
* * *
4957951 ACTACCGCAACGCGAAATAGAAAATTGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
4957992 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
4958033 ACTATCGCAACGCGAAATG
1 ACTATCGCAACGCGAAATG
4958052 CAACGCAAAT
Statistics
Matches: 135, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 135 1.00
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.19
Consensus pattern (41 bp):
ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
Found at i:4966316 original size:28 final size:29
Alignment explanation
Indices: 4966269--4966323 Score: 78
Period size: 28 Copynumber: 1.9 Consensus size: 29
4966259 AAATTACTCA
*
4966269 TTTAGTCACTCACTTCTTATTT-TTTTGT
1 TTTAGTCACTCACTTATTATTTATTTTGT
4966297 TTTAGTCACTCAAC-TATTATTTATTTT
1 TTTAGTCACTC-ACTTATTATTTATTTT
4966324 AAATCATACC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 18 0.75
29 6 0.25
ACGTcount: A:0.20, C:0.16, G:0.05, T:0.58
Consensus pattern (29 bp):
TTTAGTCACTCACTTATTATTTATTTTGT
Found at i:4968064 original size:48 final size:48
Alignment explanation
Indices: 4968012--4968103 Score: 157
Period size: 48 Copynumber: 1.9 Consensus size: 48
4968002 CTCTATATGG
*
4968012 TTGAGCATTACCAACAAAAAAATATTTTCTCCCTCTACATATATAAGA
1 TTGAGCATTACCAACAAAAAAATATTCTCTCCCTCTACATATATAAGA
**
4968060 TTGAGCATTACCAACAAAAAGTTATTCTCTCCCTCTACATATAT
1 TTGAGCATTACCAACAAAAAAATATTCTCTCCCTCTACATATAT
4968104 GGGGATTGTC
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
48 41 1.00
ACGTcount: A:0.38, C:0.23, G:0.07, T:0.33
Consensus pattern (48 bp):
TTGAGCATTACCAACAAAAAAATATTCTCTCCCTCTACATATATAAGA
Found at i:4970776 original size:66 final size:66
Alignment explanation
Indices: 4970670--4970797 Score: 256
Period size: 66 Copynumber: 1.9 Consensus size: 66
4970660 AAGTTTGTTT
4970670 AAGCGATATCAAGCTACTTATCACTTGAACCAACTATTGTTGGTAATAAATATATTTCAATTTGA
1 AAGCGATATCAAGCTACTTATCACTTGAACCAACTATTGTTGGTAATAAATATATTTCAATTTGA
4970735 C
66 C
4970736 AAGCGATATCAAGCTACTTATCACTTGAACCAACTATTGTTGGTAATAAATATATTTCAATT
1 AAGCGATATCAAGCTACTTATCACTTGAACCAACTATTGTTGGTAATAAATATATTTCAATT
4970798 ACTATAAATT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 62 1.00
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (66 bp):
AAGCGATATCAAGCTACTTATCACTTGAACCAACTATTGTTGGTAATAAATATATTTCAATTTGA
C
Found at i:4972388 original size:12 final size:12
Alignment explanation
Indices: 4972371--4972396 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
4972361 TATATTACCT
4972371 CTGTCAGTGCCC
1 CTGTCAGTGCCC
4972383 CTGTCAGTGCCC
1 CTGTCAGTGCCC
4972395 CT
1 CT
4972397 TGAGACGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.42, G:0.23, T:0.27
Consensus pattern (12 bp):
CTGTCAGTGCCC
Found at i:4983718 original size:120 final size:120
Alignment explanation
Indices: 4983547--4983764 Score: 346
Period size: 120 Copynumber: 1.8 Consensus size: 120
4983537 CATTGTATTC
* * **
4983547 TTGTGCAGACCCGACATTGTTCACTTCAAAAGGATCAACAATGTATTCTTCTACCGGATCAAAAT
1 TTGTGCAGACCCGACATTGTGCACTTCAAAAGGATAAACAATGTATTCTTCTACAAGATCAAAAT
*
4983612 TGTCTTCATATGTAGGATTCACAGGATTGATATATAATCCTTCTGTAAGATTATA
66 TGTCTTCATATGTAGGATTCACAGGATCGATATATAATCCTTCTGTAAGATTATA
* * * *
4983667 TTGTGCAGACTCGACGTTGTGCACTTCGAAAGGATAAACAATGTATTCTTCTACAAGATCAACAT
1 TTGTGCAGACCCGACATTGTGCACTTCAAAAGGATAAACAATGTATTCTTCTACAAGATCAAAAT
*
4983732 TGTCTTCATTTGTAGGATTCACAGGATCGATAT
66 TGTCTTCATATGTAGGATTCACAGGATCGATAT
4983765 TGTATTCTTC
Statistics
Matches: 88, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
120 88 1.00
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.33
Consensus pattern (120 bp):
TTGTGCAGACCCGACATTGTGCACTTCAAAAGGATAAACAATGTATTCTTCTACAAGATCAAAAT
TGTCTTCATATGTAGGATTCACAGGATCGATATATAATCCTTCTGTAAGATTATA
Found at i:4985404 original size:35 final size:35
Alignment explanation
Indices: 4985353--4985431 Score: 104
Period size: 35 Copynumber: 2.3 Consensus size: 35
4985343 AGAAATAGTG
* * * **
4985353 AACTAATTATTGAAATACGAAGAACCGTTGAAGTT
1 AACTAATTTTTAAAATACGAAAAACCGTCAAAGTT
*
4985388 AACTAATTTTTAAAATACTAAAAACCGTCAAAGTT
1 AACTAATTTTTAAAATACGAAAAACCGTCAAAGTT
4985423 AACTAATTT
1 AACTAATTT
4985432 GTTCCTTCAT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.46, C:0.13, G:0.10, T:0.32
Consensus pattern (35 bp):
AACTAATTTTTAAAATACGAAAAACCGTCAAAGTT
Found at i:4985813 original size:23 final size:24
Alignment explanation
Indices: 4985787--4985831 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
4985777 ACCTGTAAAA
4985787 TTCA-CAAGATGGATATTGTATTC
1 TTCAGCAAGATGGATATTGTATTC
* *
4985810 TTCAGCAGGATTGATATTGTAT
1 TTCAGCAAGATGGATATTGTAT
4985832 CCTGGTGTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.29, C:0.11, G:0.20, T:0.40
Consensus pattern (24 bp):
TTCAGCAAGATGGATATTGTATTC
Found at i:4987451 original size:2 final size:2
Alignment explanation
Indices: 4987444--4987473 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
4987434 TCTTTCAGGA
4987444 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
4987474 CAATTATTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4990004 original size:77 final size:78
Alignment explanation
Indices: 4989895--4990048 Score: 256
Period size: 77 Copynumber: 2.0 Consensus size: 78
4989885 AGTCCCAAAT
*
4989895 ATATCATAAGGAAAACCATTTGCAGTAAACTGAATTGCTAGATATAATTAAAAAAATAAAAGCAA
1 ATATCATAAGGAAAACCATTTGCAGTAAACTGAATTGATAGATATAATTAAAAAAATAAAAGCAA
4989960 AAGACCCAAAAAC
66 AAGACCCAAAAAC
* * * *
4989973 ATATCATAAGGAAAA-CATTTGCGGTAAACTGAATTGATTGATATAATTAAAGAAGTAAAAGCAA
1 ATATCATAAGGAAAACCATTTGCAGTAAACTGAATTGATAGATATAATTAAAAAAATAAAAGCAA
4990037 AAGACCCAAAAA
66 AAGACCCAAAAA
4990049 GAGACTGTAA
Statistics
Matches: 71, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
77 56 0.79
78 15 0.21
ACGTcount: A:0.53, C:0.12, G:0.14, T:0.21
Consensus pattern (78 bp):
ATATCATAAGGAAAACCATTTGCAGTAAACTGAATTGATAGATATAATTAAAAAAATAAAAGCAA
AAGACCCAAAAAC
Found at i:4991792 original size:15 final size:15
Alignment explanation
Indices: 4991745--4991792 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
4991735 GTTCAAATTG
*
4991745 TTAGGAATTTAGGGT
1 TTAGGAATTTAGGAT
4991760 TTAGGAATTTATGGAT
1 TTAGGAATTTA-GGAT
* *
4991776 TTATGAGTTTAGGAT
1 TTAGGAATTTAGGAT
4991791 TT
1 TT
4991793 TGGGATAATG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
15 17 0.59
16 12 0.41
ACGTcount: A:0.27, C:0.00, G:0.27, T:0.46
Consensus pattern (15 bp):
TTAGGAATTTAGGAT
Found at i:4995054 original size:2 final size:2
Alignment explanation
Indices: 4995047--4995080 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
4995037 TGGATGTTTC
4995047 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
4995081 CGTATTGGAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5000907 original size:55 final size:55
Alignment explanation
Indices: 5000849--5001359 Score: 479
Period size: 51 Copynumber: 9.6 Consensus size: 55
5000839 TGACGAGCCT
* **
5000849 GCTCCCTATTCCTTCAG-GAAGTATAAGACTCGAACAATCTTC-ATAAAAAGTGTAT
1 GCTCCCTATTCCTTCAGAG-AGTATAAGACTCGAACAATCTTCAAT-AAACGTGTCC
* * * * *
5000904 GCTCTCTATTCATTCAGAGAGTATAAGACTTGAACAATCTTTAATAAAACGGGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAAT-AAACGTGTCC
* * * *
5000960 GCTCTCTCTTTCTTCAGAGAGTAT-AGAACTCGAACAATCTTCAATAAACTTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAG-ACTCGAACAATCTTCAATAAACGTGTCC
* * ** *
5001015 GCTCCCTATTCATTCAGAGAGTATAGGACT----CAATCTTCAACGAACTTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAATAAACGTGTCC
* * * *
5001066 GCTCCCTATTCCTTCAGAGAGTATAGGACTCGAGCAATCTTC-ATAAAACGGGTTC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAAT-AAACGTGTCC
* * *
5001121 GCTCTCTATTCCTTCAGAGAGTAT-AGAACTCGAACAATCTTCAATGAACTTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAG-ACTCGAACAATCTTCAATAAACGTGTCC
* ** *
5001176 GCTCCCTATTCCTTCAGAGAGTATAGGACT----CAATCTTCAACGAACTTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAATAAACGTGTCC
* * ** *
5001227 GCTCCCTATTCATTCAGAGAGTATAGGACT----CAATCTTCAACGAACTTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAATAAACGTGTCC
* ** *
5001278 GCTCCCTATTCCTTCAGAGAGTATAGGACT----CAATCTTCAACGAACTTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAATAAACGTGTCC
*
5001329 GCTCCCTATTCCTTCAGAGAGTATAGGACTC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTC
5001360 AATCTTCAAC
Statistics
Matches: 403, Mismatches: 40, Indels: 29
0.85 0.08 0.06
Matches are distributed among these distances:
51 198 0.49
54 2 0.00
55 152 0.38
56 51 0.13
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.30
Consensus pattern (55 bp):
GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAATAAACGTGTCC
Found at i:5001068 original size:51 final size:51
Alignment explanation
Indices: 5000956--5001369 Score: 569
Period size: 51 Copynumber: 7.9 Consensus size: 51
5000946 AATAAAACGG
* * * * **
5000956 GTCCGCTCTCTCTTTCTTCAGAGAGTATAGAACTCGAACAATCTTCAATAAACTT
1 GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACT----CAATCTTCAACGAACTT
*
5001011 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
1 GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
* **
5001062 GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCGAGCAATCTTCATA-AAACGG
1 GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACT----CAATCTTCA-ACGAACTT
* * * *
5001117 GTTCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAATGAACTT
1 GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACT----CAATCTTCAACGAACTT
5001172 GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
1 GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
*
5001223 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
1 GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
5001274 GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
1 GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
5001325 GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAAC
1 GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAAC
5001370 AAACGAATTT
Statistics
Matches: 329, Mismatches: 24, Indels: 16
0.89 0.07 0.04
Matches are distributed among these distances:
51 209 0.64
54 1 0.00
55 118 0.36
56 1 0.00
ACGTcount: A:0.27, C:0.28, G:0.16, T:0.30
Consensus pattern (51 bp):
GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
Found at i:5001141 original size:161 final size:159
Alignment explanation
Indices: 5000904--5001369 Score: 694
Period size: 161 Copynumber: 2.9 Consensus size: 159
5000894 AAAAGTGTAT
* * * *
5000904 GCTCTCTATTCATTCAGAGAGTATAAGACTTGAACAATCTTTAATAAAACGGGTCCGCTCTCTCT
1 GCTCCCTATTCATTCAGAGAGTATAGGAC-TG-ACAATC-TTCATAAAACGGGTCCGCTCTCTAT
* * *
5000969 TTCTTCAGAGAGTATAGAACTCGAACAATCTTCAATAAACTTGTCCGCTCCCTATTCATTCAGAG
63 TCCTTCAGAGAGTATAGAACTCGAACAATCTTCAATGAACTTGTCCGCTCCCTATTCCTTCAGAG
5001034 AGTATAGGACTCAATCTTCAACGAACTTGTCC
128 AGTATAGGACTCAATCTTCAACGAACTTGTCC
* *
5001066 GCTCCCTATTCCTTCAGAGAGTATAGGACTCGAGCAATCTTCATAAAACGGGTTCGCTCTCTATT
1 GCTCCCTATTCATTCAGAGAGTATAGGACT-GA-CAATCTTCATAAAACGGGTCCGCTCTCTATT
5001131 CCTTCAGAGAGTATAGAACTCGAACAATCTTCAATGAACTTGTCCGCTCCCTATTCCTTCAGAGA
64 CCTTCAGAGAGTATAGAACTCGAACAATCTTCAATGAACTTGTCCGCTCCCTATTCCTTCAGAGA
5001196 GTATAGGACTCAATCTTCAACGAACTTGTCC
129 GTATAGGACTCAATCTTCAACGAACTTGTCC
* ** *
5001227 GCTCCCTATTCATTCAGAGAGTATAGGACT--CAATCTTCA-ACGAACTTGTCCGCTCCCTATTC
1 GCTCCCTATTCATTCAGAGAGTATAGGACTGACAATCTTCATA-AAACGGGTCCGCTCTCTATTC
* *
5001289 CTTCAGAGAGTATAGGACT----CAATCTTCAACGAACTTGTCCGCTCCCTATTCCTTCAGAGAG
65 CTTCAGAGAGTATAGAACTCGAACAATCTTCAATGAACTTGTCCGCTCCCTATTCCTTCAGAGAG
5001350 TATAGGACTCAATCTTCAAC
130 TATAGGACTCAATCTTCAAC
5001370 AAACGAATTT
Statistics
Matches: 284, Mismatches: 17, Indels: 15
0.90 0.05 0.05
Matches are distributed among these distances:
153 61 0.21
156 1 0.00
157 43 0.15
161 147 0.52
162 32 0.11
ACGTcount: A:0.28, C:0.26, G:0.16, T:0.30
Consensus pattern (159 bp):
GCTCCCTATTCATTCAGAGAGTATAGGACTGACAATCTTCATAAAACGGGTCCGCTCTCTATTCC
TTCAGAGAGTATAGAACTCGAACAATCTTCAATGAACTTGTCCGCTCCCTATTCCTTCAGAGAGT
ATAGGACTCAATCTTCAACGAACTTGTCC
Found at i:5001291 original size:102 final size:103
Alignment explanation
Indices: 5000849--5001369 Score: 575
Period size: 106 Copynumber: 4.9 Consensus size: 103
5000839 TGACGAGCCT
* ** ** *
5000849 GCTCCCTATTCCTTCAG-GAAGTATAAGACTCGAACAATCTTCATA-AAAAGTGTATGCTCTCTA
1 GCTCCCTATTCCTTCAGAG-AGTATAGGACT---ACAATCTTCA-ACAAACTTGTCCGCTCCCTA
* * ** **
5000912 TTCATTCAGAGAGTATAAGACTTGAACAATCTTTAATAAAACGGGTCC
61 TTCATTCAGAGAGTATAGGAC-T---CAATCTTCAA-CGAACTTGTCC
* * * * *
5000960 GCTCTCTCTTTCTTCAGAGAGTATAGAACTCGAACAATCTTCAATAAACTTGTCCGCTCCCTATT
1 GCTCCCTATTCCTTCAGAGAGTATAGGACT---ACAATCTTCAACAAACTTGTCCGCTCCCTATT
5001025 CATTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCC
63 CATTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCC
** * *
5001066 GCTCCCTATTCCTTCAGAGAGTATAGGACTCGAGCAATCTTCATA-AAACGGGTTCGCTCTCTAT
1 GCTCCCTATTCCTTCAGAGAGTATAGGACT--A-CAATCTTCA-ACAAACTTGTCCGCTCCCTAT
* * *
5001130 TCCTTCAGAGAGTATAGAACTCGAACAATCTTCAATGAACTTGTCC
62 TCATTCAGAGAGTATAGGACT----CAATCTTCAACGAACTTGTCC
*
5001176 GCTCCCTATTCCTTCAGAGAGTATAGGACT-CAATCTTCAACGAACTTGTCCGCTCCCTATTCAT
1 GCTCCCTATTCCTTCAGAGAGTATAGGACTACAATCTTCAACAAACTTGTCCGCTCCCTATTCAT
5001240 TCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCC
66 TCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCC
* *
5001278 GCTCCCTATTCCTTCAGAGAGTATAGGACT-CAATCTTCAACGAACTTGTCCGCTCCCTATTCCT
1 GCTCCCTATTCCTTCAGAGAGTATAGGACTACAATCTTCAACAAACTTGTCCGCTCCCTATTCAT
5001342 TCAGAGAGTATAGGACTCAATCTTCAAC
66 TCAGAGAGTATAGGACTCAATCTTCAAC
5001370 AAACGAATTT
Statistics
Matches: 363, Mismatches: 38, Indels: 27
0.85 0.09 0.06
Matches are distributed among these distances:
102 111 0.31
105 2 0.01
106 118 0.33
107 10 0.03
110 52 0.14
111 69 0.19
112 1 0.00
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.30
Consensus pattern (103 bp):
GCTCCCTATTCCTTCAGAGAGTATAGGACTACAATCTTCAACAAACTTGTCCGCTCCCTATTCAT
TCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCC
Found at i:5002726 original size:21 final size:19
Alignment explanation
Indices: 5002698--5002752 Score: 69
Period size: 21 Copynumber: 2.8 Consensus size: 19
5002688 TTTTTTTTTC
5002698 TTTTTCTTCCTTTTTCCAT
1 TTTTTCTTCCTTTTTCCAT
5002717 TTGTTCTCTTCCCTTTTT-CAT
1 TT-TT-TCTT-CCTTTTTCCAT
5002738 TTTTTCTT-CTTTTTC
1 TTTTTCTTCCTTTTTC
5002753 TTTCTTTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
17 6 0.19
19 6 0.19
20 4 0.12
21 9 0.28
22 7 0.22
ACGTcount: A:0.04, C:0.25, G:0.02, T:0.69
Consensus pattern (19 bp):
TTTTTCTTCCTTTTTCCAT
Found at i:5002776 original size:25 final size:24
Alignment explanation
Indices: 5002737--5002813 Score: 70
Period size: 24 Copynumber: 3.3 Consensus size: 24
5002727 CCCTTTTTCA
* *
5002737 TTTTTTCTTCTTTTTCTTTCTTTT
1 TTTTTTCCTCATTTTCTTTCTTTT
*
5002761 TTTTTTCCATCATTTTCTTT-TTCT
1 TTTTTTCC-TCATTTTCTTTCTTTT
* *
5002785 TATTTT-CTCATTTT-TTTCTCTT
1 TTTTTTCCTCATTTTCTTTCTTTT
*
5002807 TTATTTC
1 TTTTTTC
5002814 TTCTTCAAGC
Statistics
Matches: 42, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
21 3 0.07
22 13 0.31
23 1 0.02
24 15 0.36
25 10 0.24
ACGTcount: A:0.06, C:0.18, G:0.00, T:0.75
Consensus pattern (24 bp):
TTTTTTCCTCATTTTCTTTCTTTT
Found at i:5002782 original size:22 final size:21
Alignment explanation
Indices: 5002753--5002806 Score: 51
Period size: 22 Copynumber: 2.5 Consensus size: 21
5002743 CTTCTTTTTC
5002753 TTTCTTTT-TT-TTTTCCATCAT
1 TTTCTTTTCTTATTTT-C-TCAT
5002774 TTTCTTTTTCTTATTTTCTCAT
1 TTTC-TTTTCTTATTTTCTCAT
5002796 TTT-TTTCTCTT
1 TTTCTTT-TCTT
5002807 TTATTTCTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
20 3 0.10
21 8 0.28
22 11 0.38
23 3 0.10
24 4 0.14
ACGTcount: A:0.07, C:0.19, G:0.00, T:0.74
Consensus pattern (21 bp):
TTTCTTTTCTTATTTTCTCAT
Found at i:5017629 original size:28 final size:28
Alignment explanation
Indices: 5017592--5017658 Score: 116
Period size: 28 Copynumber: 2.4 Consensus size: 28
5017582 CAATACCTCT
*
5017592 TCTCCACCGTCCAACCAACCCAACCCAA
1 TCTCCGCCGTCCAACCAACCCAACCCAA
*
5017620 TCTCCGCCGTCCAATCAACCCAACCCAA
1 TCTCCGCCGTCCAACCAACCCAACCCAA
5017648 TCTCCGCCGTC
1 TCTCCGCCGTC
5017659 ACTGCCATCT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.25, C:0.52, G:0.07, T:0.15
Consensus pattern (28 bp):
TCTCCGCCGTCCAACCAACCCAACCCAA
Found at i:5024384 original size:23 final size:22
Alignment explanation
Indices: 5024340--5024392 Score: 56
Period size: 24 Copynumber: 2.4 Consensus size: 22
5024330 TAAAACTTAA
5024340 ATTTAGAAAAAAATCAATAAAT
1 ATTTAGAAAAAAATCAATAAAT
* *
5024362 CATTTATGAAAAATATGAA-AAAT
1 -ATTTA-GAAAAAAATCAATAAAT
5024385 ATTT-GAAA
1 ATTTAGAAA
5024393 CCATTGAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
20 4 0.15
22 4 0.15
23 9 0.33
24 10 0.37
ACGTcount: A:0.58, C:0.04, G:0.08, T:0.30
Consensus pattern (22 bp):
ATTTAGAAAAAAATCAATAAAT
Found at i:5025853 original size:2 final size:2
Alignment explanation
Indices: 5025846--5025876 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
5025836 CCTCCATCCA
5025846 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5025877 TATTTTAGCA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5026893 original size:3 final size:3
Alignment explanation
Indices: 5026885--5026910 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
5026875 TTAAATAAAA
5026885 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
5026911 ATTCTAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:5027657 original size:37 final size:37
Alignment explanation
Indices: 5027614--5027687 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
5027604 ACCACAGATT
5027614 CTAAGGTAATAACAGGATTATTACTAGAGAACAGACC
1 CTAAGGTAATAACAGGATTATTACTAGAGAACAGACC
5027651 CTAAGGTAATAACAGGATTATTACTAGAGAACAGACC
1 CTAAGGTAATAACAGGATTATTACTAGAGAACAGACC
5027688 AAATGCTTCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.43, C:0.16, G:0.19, T:0.22
Consensus pattern (37 bp):
CTAAGGTAATAACAGGATTATTACTAGAGAACAGACC
Found at i:5063214 original size:16 final size:15
Alignment explanation
Indices: 5063193--5063222 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
5063183 TTTATTTTAT
5063193 TTATAATATTTAATTA
1 TTATAATA-TTAATTA
5063209 TTATAATATTAATT
1 TTATAATATTAATT
5063223 TTAAAAATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TTATAATATTAATTA
Found at i:5063243 original size:27 final size:32
Alignment explanation
Indices: 5063213--5063273 Score: 87
Period size: 32 Copynumber: 2.1 Consensus size: 32
5063203 TAATTATTAT
5063213 AATAT-TA-ATTT-TAA-AAATAT-AAAATAA
1 AATATATATATTTCTAATAAATATCAAAATAA
5063240 AATATATATATTTCTAATAAATATCAAAATAA
1 AATATATATATTTCTAATAAATATCAAAATAA
5063272 AA
1 AA
5063274 AACATAAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
27 5 0.17
28 2 0.07
29 4 0.14
30 3 0.10
31 6 0.21
32 9 0.31
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (32 bp):
AATATATATATTTCTAATAAATATCAAAATAA
Found at i:5063329 original size:20 final size:20
Alignment explanation
Indices: 5063292--5063328 Score: 51
Period size: 18 Copynumber: 1.9 Consensus size: 20
5063282 TAAAATATTC
*
5063292 ATAAATAATAATACAAAAAT
1 ATAAATAATAATAAAAAAAT
5063312 ATAAAT-A-AATAAAAAAA
1 ATAAATAATAATAAAAAAA
5063329 ATTACATTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 9 0.56
19 1 0.06
20 6 0.38
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.22
Consensus pattern (20 bp):
ATAAATAATAATAAAAAAAT
Found at i:5063939 original size:10 final size:10
Alignment explanation
Indices: 5063924--5063995 Score: 78
Period size: 10 Copynumber: 7.4 Consensus size: 10
5063914 TGAATTTAAA
5063924 AAAAAATCAG
1 AAAAAATCAG
5063934 AAAAAAT-ATG
1 AAAAAATCA-G
5063944 AAAAAATCAG
1 AAAAAATCAG
* *
5063954 AAAAAATAAA
1 AAAAAATCAG
*
5063964 AAAAAAT-AC
1 AAAAAATCAG
5063973 AAAAAATCA-
1 AAAAAATCAG
*
5063982 AAAAAATCAT
1 AAAAAATCAG
5063992 AAAA
1 AAAA
5063996 CAATTAGTAT
Statistics
Matches: 55, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
9 18 0.33
10 36 0.65
11 1 0.02
ACGTcount: A:0.76, C:0.07, G:0.04, T:0.12
Consensus pattern (10 bp):
AAAAAATCAG
Found at i:5063949 original size:20 final size:20
Alignment explanation
Indices: 5063920--5063987 Score: 93
Period size: 20 Copynumber: 3.4 Consensus size: 20
5063910 TACTTGAATT
5063920 TAAAAAAAAATCAGAAAAAA
1 TAAAAAAAAATCAGAAAAAA
**
5063940 TATGAAAAAATCAGAAAAAA
1 TAAAAAAAAATCAGAAAAAA
*
5063960 TAAAAAAAAAT-ACAAAAAA
1 TAAAAAAAAATCAGAAAAAA
5063979 TCAAAAAAA
1 T-AAAAAAA
5063988 TCATAAAACA
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
19 8 0.19
20 34 0.81
ACGTcount: A:0.78, C:0.06, G:0.04, T:0.12
Consensus pattern (20 bp):
TAAAAAAAAATCAGAAAAAA
Found at i:5065062 original size:2 final size:2
Alignment explanation
Indices: 5065055--5065103 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
5065045 GGATGATAAT
5065055 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5065097 TA TA TA T
1 TA TA TA T
5065104 TGAGATGCAG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5065515 original size:3 final size:3
Alignment explanation
Indices: 5065507--5065539 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
5065497 AAATTTACAA
5065507 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
5065540 GCCACAACTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:5071039 original size:19 final size:18
Alignment explanation
Indices: 5071015--5071054 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
5071005 TTTAAAAATC
5071015 TTATATATTAATCTTTAAA
1 TTATATATTAAT-TTTAAA
* *
5071034 TTATATTTTTATTTTAAA
1 TTATATATTAATTTTAAA
5071052 TTA
1 TTA
5071055 ATTTTATAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (18 bp):
TTATATATTAATTTTAAA
Found at i:5078753 original size:2 final size:2
Alignment explanation
Indices: 5078706--5078739 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
5078696 ACTTTGAATG
*
5078706 AT AT AC 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
5078740 TAAGAAATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:5088265 original size:20 final size:21
Alignment explanation
Indices: 5088240--5088298 Score: 86
Period size: 20 Copynumber: 2.9 Consensus size: 21
5088230 GGCTGCTAGA
5088240 AACCGGTT-TAACCGGTTTTC
1 AACCGGTTCTAACCGGTTTTC
*
5088260 AACCGGTTCTGACCGG-TTTC
1 AACCGGTTCTAACCGGTTTTC
*
5088280 AACCGGTTCGAACCGGTTT
1 AACCGGTTCTAACCGGTTT
5088299 GACCGGTCTG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 26 0.76
21 8 0.24
ACGTcount: A:0.19, C:0.27, G:0.24, T:0.31
Consensus pattern (21 bp):
AACCGGTTCTAACCGGTTTTC
Found at i:5088276 original size:10 final size:10
Alignment explanation
Indices: 5088261--5088330 Score: 53
Period size: 10 Copynumber: 7.3 Consensus size: 10
5088251 CCGGTTTTCA
5088261 ACCGGTTCTG
1 ACCGGTTCTG
*
5088271 ACCGGTT-TCA
1 ACCGGTTCT-G
5088281 ACCGGTTC-G
1 ACCGGTTCTG
5088290 AACCGGTT-TG
1 -ACCGGTTCTG
5088300 ACCGG-TCTG
1 ACCGGTTCTG
*
5088309 AATCGGTT-TG
1 -ACCGGTTCTG
5088319 ACCGG-TCTG
1 ACCGGTTCTG
5088328 ACC
1 ACC
5088331 CGACCCGACC
Statistics
Matches: 48, Mismatches: 4, Indels: 17
0.70 0.06 0.25
Matches are distributed among these distances:
8 2 0.04
9 17 0.35
10 28 0.58
11 1 0.02
ACGTcount: A:0.16, C:0.29, G:0.29, T:0.27
Consensus pattern (10 bp):
ACCGGTTCTG
Found at i:5088277 original size:30 final size:29
Alignment explanation
Indices: 5088241--5088305 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 29
5088231 GCTGCTAGAA
5088241 ACCGGTTT-AACCGGTTTTC-AACCGGTTCTG
1 ACCGGTTTCAACCGG--TTCGAACCGGTT-TG
5088271 ACCGGTTTCAACCGGTTCGAACCGGTTTG
1 ACCGGTTTCAACCGGTTCGAACCGGTTTG
5088300 ACCGGT
1 ACCGGT
5088306 CTGAATCGGT
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
29 11 0.33
30 16 0.48
31 6 0.18
ACGTcount: A:0.17, C:0.28, G:0.26, T:0.29
Consensus pattern (29 bp):
ACCGGTTTCAACCGGTTCGAACCGGTTTG
Found at i:5088305 original size:19 final size:20
Alignment explanation
Indices: 5088261--5088328 Score: 81
Period size: 19 Copynumber: 3.5 Consensus size: 20
5088251 CCGGTTTTCA
*
5088261 ACCGGTTCTG-ACCGGTTTCA
1 ACCGGTTCTGAACCGGTTT-G
5088281 ACCGGTTC-GAACCGGTTTG
1 ACCGGTTCTGAACCGGTTTG
*
5088300 ACCGG-TCTGAATCGGTTTG
1 ACCGGTTCTGAACCGGTTTG
5088319 ACCGG-TCTGA
1 ACCGGTTCTGA
5088329 CCCGACCCGA
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
18 2 0.05
19 26 0.59
20 16 0.36
ACGTcount: A:0.16, C:0.26, G:0.29, T:0.28
Consensus pattern (20 bp):
ACCGGTTCTGAACCGGTTTG
Found at i:5088337 original size:5 final size:5
Alignment explanation
Indices: 5088327--5088384 Score: 62
Period size: 5 Copynumber: 10.8 Consensus size: 5
5088317 TGACCGGTCT
* *
5088327 GACCC GACCC GACCGTT GACCC GACCC GACCC GACCGTT GACCC GACCC
1 GACCC GACCC GACC--C GACCC GACCC GACCC GACC--C GACCC GACCC
5088376 GACCC GACC
1 GACCC GACC
5088385 GTTGACCGTT
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
5 37 0.82
7 8 0.18
ACGTcount: A:0.19, C:0.52, G:0.22, T:0.07
Consensus pattern (5 bp):
GACCC
Found at i:5088353 original size:22 final size:22
Alignment explanation
Indices: 5088327--5088391 Score: 130
Period size: 22 Copynumber: 3.0 Consensus size: 22
5088317 TGACCGGTCT
5088327 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
5088349 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
5088371 GACCCGACCCGACCGTTGACC
1 GACCCGACCCGACCGTTGACC
5088392 GTTGACCATT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.18, C:0.49, G:0.23, T:0.09
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCC
Found at i:5095591 original size:10 final size:9
Alignment explanation
Indices: 5095556--5095653 Score: 70
Period size: 10 Copynumber: 10.2 Consensus size: 9
5095546 GCTGCTGGAA
*
5095556 ACCGGTTTA
1 ACCGGTTTG
*
5095565 ACCGGTTTTCA
1 ACCGG-TTT-G
5095576 ACCGGTTCTG
1 ACCGGTT-TG
5095586 ACCGGTTTG
1 ACCGGTTTG
*
5095595 ACCGGTTTCA
1 ACCGGTTT-G
*
5095605 ACCGGTTCG
1 ACCGGTTTG
5095614 AACCGGTTTG
1 -ACCGGTTTG
* *
5095624 ACCGATCTG
1 ACCGGTTTG
*
5095633 AATCGGTTTG
1 -ACCGGTTTG
*
5095643 ACCGGTCTG
1 ACCGGTTTG
5095652 AC
1 AC
5095654 TCGACCCGAT
Statistics
Matches: 71, Mismatches: 12, Indels: 12
0.75 0.13 0.13
Matches are distributed among these distances:
9 31 0.44
10 33 0.46
11 7 0.10
ACGTcount: A:0.17, C:0.27, G:0.27, T:0.30
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:5095600 original size:19 final size:19
Alignment explanation
Indices: 5095557--5095653 Score: 67
Period size: 19 Copynumber: 5.1 Consensus size: 19
5095547 CTGCTGGAAA
* * *
5095557 CCGGTTTAACCGGTTTTCAA
1 CCGGTTTGACCGGTTCT-GA
5095577 CCGGTTCTGACCGGTT-TGA
1 CCGGTT-TGACCGGTTCTGA
*
5095596 CCGGTTTCAACCGGTTC-GAA
1 CCGGTTT-GACCGGTTCTG-A
*
5095616 CCGGTTTGACC-GATCTGAA
1 CCGGTTTGACCGGTTCTG-A
*
5095635 TCGGTTTGACCGG-TCTGA
1 CCGGTTTGACCGGTTCTGA
5095653 C
1 C
5095654 TCGACCCGAT
Statistics
Matches: 64, Mismatches: 7, Indels: 14
0.75 0.08 0.16
Matches are distributed among these distances:
18 5 0.08
19 35 0.55
20 16 0.25
21 8 0.12
ACGTcount: A:0.16, C:0.27, G:0.27, T:0.30
Consensus pattern (19 bp):
CCGGTTTGACCGGTTCTGA
Found at i:5095618 original size:29 final size:31
Alignment explanation
Indices: 5095555--5095627 Score: 116
Period size: 29 Copynumber: 2.5 Consensus size: 31
5095545 GGCTGCTGGA
*
5095555 AACCGGTTTAACCGGTTTTCAACCGGTTCTG
1 AACCGGTTTGACCGGTTTTCAACCGGTTCTG
5095586 -ACCGGTTTGACCGG-TTTCAACCGGTTC-G
1 AACCGGTTTGACCGGTTTTCAACCGGTTCTG
5095614 AACCGGTTTGACCG
1 AACCGGTTTGACCG
5095628 ATCTGAATCG
Statistics
Matches: 40, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
28 1 0.03
29 26 0.65
30 13 0.32
ACGTcount: A:0.18, C:0.27, G:0.26, T:0.29
Consensus pattern (31 bp):
AACCGGTTTGACCGGTTTTCAACCGGTTCTG
Found at i:5095639 original size:29 final size:28
Alignment explanation
Indices: 5095573--5095653 Score: 90
Period size: 29 Copynumber: 2.8 Consensus size: 28
5095563 TAACCGGTTT
* *
5095573 TCAACCGGTTCTGACCGGTTTGACCGGTT
1 TCAACCGGTTC-GACCGGTTTGACCGATC
5095602 TCAACCGGTTCGAACCGGTTTGACCGATC
1 TCAACCGGTTCG-ACCGGTTTGACCGATC
* * * *
5095631 TGAATCGGTTTGACCGGTCTGAC
1 TCAACCGGTTCGACCGGTTTGAC
5095654 TCGACCCGAT
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
28 11 0.24
29 34 0.76
ACGTcount: A:0.17, C:0.27, G:0.27, T:0.28
Consensus pattern (28 bp):
TCAACCGGTTCGACCGGTTTGACCGATC
Found at i:5095678 original size:5 final size:5
Alignment explanation
Indices: 5095668--5095730 Score: 72
Period size: 5 Copynumber: 11.8 Consensus size: 5
5095658 CCCGATCGTT
* *
5095668 GACCC GACCC GACCC GACCGTT GACCC GACCC GACCC GACCGTT GACCC
1 GACCC GACCC GACCC GACC--C GACCC GACCC GACCC GACC--C GACCC
5095717 GACCC GACCC GACC
1 GACCC GACCC GACC
5095731 GTTGACCATT
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
5 42 0.84
7 8 0.16
ACGTcount: A:0.19, C:0.52, G:0.22, T:0.06
Consensus pattern (5 bp):
GACCC
Found at i:5095698 original size:27 final size:22
Alignment explanation
Indices: 5095655--5095737 Score: 157
Period size: 22 Copynumber: 3.8 Consensus size: 22
5095645 CGGTCTGACT
*
5095655 CGACCCGATCGTTGACCCGACC
1 CGACCCGACCGTTGACCCGACC
5095677 CGACCCGACCGTTGACCCGACC
1 CGACCCGACCGTTGACCCGACC
5095699 CGACCCGACCGTTGACCCGACC
1 CGACCCGACCGTTGACCCGACC
5095721 CGACCCGACCGTTGACC
1 CGACCCGACCGTTGACC
5095738 ATTGACTTTC
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 60 1.00
ACGTcount: A:0.18, C:0.48, G:0.23, T:0.11
Consensus pattern (22 bp):
CGACCCGACCGTTGACCCGACC
Found at i:5098144 original size:14 final size:13
Alignment explanation
Indices: 5098125--5098220 Score: 70
Period size: 13 Copynumber: 7.3 Consensus size: 13
5098115 GGGGCAGTTT
5098125 GACCCGTTTGACCC
1 GACCCG-TTGACCC
5098139 GACCCGGTTGACCC
1 GACCC-GTTGACCC
* *
5098153 GACCTGTTGTCCC
1 GACCCGTTGACCC
* *
5098166 GACTCGTTGACTC
1 GACCCGTTGACCC
*
5098179 GACCTGTT-ATCCC
1 GACCCGTTGA-CCC
**
5098192 GACTTGTTGACCC
1 GACCCGTTGACCC
* *
5098205 AACCCGTAGA-CC
1 GACCCGTTGACCC
5098217 GACC
1 GACC
5098221 ATTGTCCGTT
Statistics
Matches: 64, Mismatches: 15, Indels: 8
0.74 0.17 0.09
Matches are distributed among these distances:
12 6 0.09
13 40 0.62
14 17 0.27
15 1 0.02
ACGTcount: A:0.17, C:0.39, G:0.22, T:0.23
Consensus pattern (13 bp):
GACCCGTTGACCC
Found at i:5098176 original size:26 final size:26
Alignment explanation
Indices: 5098136--5098204 Score: 93
Period size: 26 Copynumber: 2.6 Consensus size: 26
5098126 ACCCGTTTGA
* *
5098136 CCCGACCCGGTTGACCCGACCTGTTGT
1 CCCGACTC-GTTGACCCGACCTGTTAT
*
5098163 CCCGACTCGTTGACTCGACCTGTTAT
1 CCCGACTCGTTGACCCGACCTGTTAT
*
5098189 CCCGACTTGTTGACCC
1 CCCGACTCGTTGACCC
5098205 AACCCGTAGA
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
26 30 0.81
27 7 0.19
ACGTcount: A:0.13, C:0.39, G:0.22, T:0.26
Consensus pattern (26 bp):
CCCGACTCGTTGACCCGACCTGTTAT
Found at i:5098277 original size:17 final size:17
Alignment explanation
Indices: 5098253--5098294 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
5098243 TGACTTTGAC
5098253 CAAAAAGTTAAATTTTT
1 CAAAAAGTTAAATTTTT
* *
5098270 CGAAAAGTTCAATTTTT
1 CAAAAAGTTAAATTTTT
5098287 CAAAAAGT
1 CAAAAAGT
5098295 CATATTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.45, C:0.10, G:0.10, T:0.36
Consensus pattern (17 bp):
CAAAAAGTTAAATTTTT
Found at i:5098301 original size:17 final size:16
Alignment explanation
Indices: 5098253--5098302 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 16
5098243 TGACTTTGAC
*
5098253 CAAAAAGTTAAATTTTT
1 CAAAAAG-TCAATTTTT
*
5098270 CGAAAAGTTCAATTTTT
1 CAAAAAG-TCAATTTTT
5098287 CAAAAAGTCATATTTT
1 CAAAAAGTCA-ATTTT
5098303 ATGTTTTTCG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
16 3 0.10
17 26 0.90
ACGTcount: A:0.42, C:0.10, G:0.08, T:0.40
Consensus pattern (16 bp):
CAAAAAGTCAATTTTT
Found at i:5100900 original size:43 final size:43
Alignment explanation
Indices: 5100847--5101180 Score: 425
Period size: 43 Copynumber: 7.7 Consensus size: 43
5100837 CGTATGCTCA
*
5100847 TTTGCTGTGTGCAAGGGTAAGCCTTATAGTTTCCCCATGTTCC
1 TTTGCTGTGTGCAAGGGTAAGCCTTATAGTTTCCCCAGGTTCC
*
5100890 TTTGTTGTGTGCAAGGGTAAGCCTTATAGTTTCCCCAGGTTCC
1 TTTGCTGTGTGCAAGGGTAAGCCTTATAGTTTCCCCAGGTTCC
* * *
5100933 TTTGCTGTGTGCAAAGATAAGCCTTACAGTTTCCCCAGGTTCC
1 TTTGCTGTGTGCAAGGGTAAGCCTTATAGTTTCCCCAGGTTCC
** * *
5100976 TTTATTATGTGCAAGGGTAAGCCTTATAGTTTCTCCAGGTTCC
1 TTTGCTGTGTGCAAGGGTAAGCCTTATAGTTTCCCCAGGTTCC
* * * *
5101019 TTTGTTGTGTGCAAAGGTAAGCCTTACAGTTTCCCTAGGTTCC
1 TTTGCTGTGTGCAAGGGTAAGCCTTATAGTTTCCCCAGGTTCC
* * * ** * * *
5101062 TTTGATTTGTGCAAGGGTAAGCCTTACAGTTTCCATATGCTCT
1 TTTGCTGTGTGCAAGGGTAAGCCTTATAGTTTCCCCAGGTTCC
* * *
5101105 TTTGCTATGTGCAAGGGTAAGCCTTATAGTTTCCCCATGTTCT
1 TTTGCTGTGTGCAAGGGTAAGCCTTATAGTTTCCCCAGGTTCC
* *
5101148 TTTGCTATGTGCAAGGGTAAGACCTTATCGTTT
1 TTTGCTGTGTGCAAGGGTAAG-CCTTATAGTTT
5101181 TTGCATGCTC
Statistics
Matches: 257, Mismatches: 33, Indels: 1
0.88 0.11 0.00
Matches are distributed among these distances:
43 247 0.96
44 10 0.04
ACGTcount: A:0.19, C:0.21, G:0.22, T:0.38
Consensus pattern (43 bp):
TTTGCTGTGTGCAAGGGTAAGCCTTATAGTTTCCCCAGGTTCC
Found at i:5101846 original size:26 final size:26
Alignment explanation
Indices: 5101810--5101860 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
5101800 CGGTCTGAGG
*
5101810 GGGTTATAAATTTTAATAGTTAAAGA
1 GGGTTACAAATTTTAATAGTTAAAGA
5101836 GGGTTACAAATTTTAATAGTTAAAG
1 GGGTTACAAATTTTAATAGTTAAAG
5101861 GGGGCGTTCT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.41, C:0.02, G:0.20, T:0.37
Consensus pattern (26 bp):
GGGTTACAAATTTTAATAGTTAAAGA
Found at i:5103351 original size:23 final size:22
Alignment explanation
Indices: 5103325--5103403 Score: 77
Period size: 23 Copynumber: 3.4 Consensus size: 22
5103315 CACCACAGCT
*
5103325 CATATAAATGCACCGAAGTGCCA
1 CATA-AAATGCACCGTAGTGCCA
* *
5103348 CATAGAATTGCACCGTAGTGCCG
1 CATA-AAATGCACCGTAGTGCCA
*
5103371 CGTAAAATTGCACCGTAGTGCCA
1 CATAAAA-TGCACCGTAGTGCCA
*
5103394 TATAATAATG
1 CATAA-AATG
5103404 TCCATAATGA
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
22 2 0.04
23 41 0.91
24 2 0.04
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.23
Consensus pattern (22 bp):
CATAAAATGCACCGTAGTGCCA
Found at i:5103582 original size:103 final size:103
Alignment explanation
Indices: 5103412--5103729 Score: 609
Period size: 103 Copynumber: 3.1 Consensus size: 103
5103402 TGTCCATAAT
5103412 GACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCAGAC
1 GACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCAGAC
5103477 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAG
66 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAG
* *
5103515 GACCACATATCATTCCTTAAGAATCATATACATATACGAGGGATCAAGTATGTGTCTCACCATAC
1 GACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCAGAC
5103580 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAG
66 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAG
5103618 GACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCAGAC
1 GACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCAGAC
*
5103683 TTCACACATGTTCCAAAGAATACATATATGTCCTGAAG
66 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAG
5103721 GACCACATA
1 GACCACATA
5103730 GACCCTCGAC
Statistics
Matches: 210, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
103 210 1.00
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.27
Consensus pattern (103 bp):
GACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCAGAC
TTCACACATGTTCCAAAGAATACATATATGTCCCGAAG
Found at i:5106212 original size:2 final size:2
Alignment explanation
Indices: 5106205--5106231 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5106195 TCACATATGA
5106205 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
5106232 GTTGTAAGTA
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:5106273 original size:12 final size:12
Alignment explanation
Indices: 5106212--5106296 Score: 52
Period size: 12 Copynumber: 7.2 Consensus size: 12
5106202 TGAATATATA
* *
5106212 TATATATATATA
1 TATATATGTATG
5106224 TATATATAGT-TG
1 TATATAT-GTATG
5106236 TA-AGTATGTATG
1 TATA-TATGTATG
* **
5106248 TATATA--CACA
1 TATATATGTATG
5106258 TATATATGTATG
1 TATATATGTATG
* *
5106270 TATATTTGTTTG
1 TATATATGTATG
*
5106282 TATGTATGTATG
1 TATATATGTATG
5106294 TAT
1 TAT
5106297 GTATATCATA
Statistics
Matches: 54, Mismatches: 13, Indels: 12
0.68 0.16 0.15
Matches are distributed among these distances:
10 7 0.13
11 3 0.06
12 42 0.78
13 2 0.04
ACGTcount: A:0.34, C:0.02, G:0.14, T:0.49
Consensus pattern (12 bp):
TATATATGTATG
Found at i:5106287 original size:4 final size:4
Alignment explanation
Indices: 5106262--5106300 Score: 51
Period size: 4 Copynumber: 9.8 Consensus size: 4
5106252 TACACATATA
* * *
5106262 TATG TATG TATA TTTG TTTG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
5106301 ATCATATATA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.23, C:0.00, G:0.21, T:0.56
Consensus pattern (4 bp):
TATG
Found at i:5106862 original size:21 final size:21
Alignment explanation
Indices: 5106821--5106862 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
5106811 TTCAAGAAAA
*
5106821 AAAATAAGTGGGCAGCTTATT
1 AAAATAAGTGGGCACCTTATT
*
5106842 AAAATAAG-GGGTACCTATATT
1 AAAATAAGTGGGCACCT-TATT
5106863 GACAGCAATC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.40, C:0.10, G:0.21, T:0.29
Consensus pattern (21 bp):
AAAATAAGTGGGCACCTTATT
Found at i:5122377 original size:29 final size:28
Alignment explanation
Indices: 5122353--5122409 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 28
5122343 TGTGTTTTCC
*
5122353 TGATTTT-GACACTTTAGTTTCTGTTATT
1 TGATTTTAGACACTTAAGTTTCTGTT-TT
* *
5122381 TTATTTTAGTCACTTAAGTTTCTGTTTT
1 TGATTTTAGACACTTAAGTTTCTGTTTT
5122409 T
1 T
5122410 ACTATTTATG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 9 0.36
29 16 0.64
ACGTcount: A:0.18, C:0.11, G:0.12, T:0.60
Consensus pattern (28 bp):
TGATTTTAGACACTTAAGTTTCTGTTTT
Found at i:5122437 original size:30 final size:30
Alignment explanation
Indices: 5122368--5122500 Score: 121
Period size: 30 Copynumber: 4.4 Consensus size: 30
5122358 TTGACACTTT
**
5122368 AGTTTCTGTTATTT--TATTTTAGTCACTTA
1 AGTTTCTGTT-TTTACTATTTTAGTCTTTTA
5122397 AGTTTCTGTTTTTACTA-TTTATGTCTTTTA
1 AGTTTCTGTTTTTACTATTTTA-GTCTTTTA
* * *
5122427 AATTTATGTTTTAACTATTTTAGTCTTTTA
1 AGTTTCTGTTTTTACTATTTTAGTCTTTTA
* * * *
5122457 AGTTTCTGTTCTTACCATTTTTAATCCTTTA
1 AGTTTCTGTTTTTACTA-TTTTAGTCTTTTA
5122488 AG-TTCATGTTTTT
1 AGTTTC-TGTTTTT
5122501 GCTAGATCTA
Statistics
Matches: 85, Mismatches: 13, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
28 3 0.04
29 14 0.16
30 45 0.53
31 23 0.27
ACGTcount: A:0.20, C:0.11, G:0.09, T:0.59
Consensus pattern (30 bp):
AGTTTCTGTTTTTACTATTTTAGTCTTTTA
Found at i:5122741 original size:34 final size:30
Alignment explanation
Indices: 5122703--5122771 Score: 95
Period size: 30 Copynumber: 2.2 Consensus size: 30
5122693 TTGATATAAC
5122703 AATTTAAGGCAAAATGGTTTTTGGACTTGAATTG
1 AATTTAA--CAAAAT-GTTTTTGGACTT-AATTG
5122737 AATTT-ACAAAATGTTTTTGGACTTAATTG
1 AATTTAACAAAATGTTTTTGGACTTAATTG
5122766 AATTTA
1 AATTTA
5122772 TTCAAAGTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
29 10 0.29
30 12 0.35
31 6 0.18
33 1 0.03
34 5 0.15
ACGTcount: A:0.35, C:0.06, G:0.17, T:0.42
Consensus pattern (30 bp):
AATTTAACAAAATGTTTTTGGACTTAATTG
Found at i:5122782 original size:29 final size:30
Alignment explanation
Indices: 5122712--5122771 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
5122702 CAATTTAAGG
5122712 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTGAATTTA
5122743 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
5122772 TTCAAAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 12 0.41
31 6 0.21
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:5122946 original size:15 final size:15
Alignment explanation
Indices: 5122926--5122955 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5122916 ATACCCCCAG
*
5122926 GGGTATCCATACCCC
1 GGGTATCAATACCCC
5122941 GGGTATCAATACCCC
1 GGGTATCAATACCCC
5122956 CAAAGTATCT
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:0.23, C:0.37, G:0.20, T:0.20
Consensus pattern (15 bp):
GGGTATCAATACCCC
Found at i:5125249 original size:12 final size:12
Alignment explanation
Indices: 5125232--5125257 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
5125222 GGGGGAGCTT
5125232 TGATTTTTAAAA
1 TGATTTTTAAAA
5125244 TGATTTTTAAAA
1 TGATTTTTAAAA
5125256 TG
1 TG
5125258 CCAAATTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (12 bp):
TGATTTTTAAAA
Found at i:5125610 original size:34 final size:30
Alignment explanation
Indices: 5125571--5125639 Score: 86
Period size: 30 Copynumber: 2.2 Consensus size: 30
5125561 TTGATATAAC
5125571 AATTTAAGGCAAAATAGTTTTTGAACTTGAATTG
1 AATTTAA--CAAAAT-GTTTTTGAACTT-AATTG
*
5125605 AATTT-ACAAAATGTTTTTGGACTTAATTG
1 AATTTAACAAAATGTTTTTGAACTTAATTG
5125634 AATTTA
1 AATTTA
5125640 TTCAAAGTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
29 10 0.30
30 11 0.33
31 6 0.18
33 1 0.03
34 5 0.15
ACGTcount: A:0.38, C:0.06, G:0.14, T:0.42
Consensus pattern (30 bp):
AATTTAACAAAATGTTTTTGAACTTAATTG
Found at i:5125621 original size:30 final size:30
Alignment explanation
Indices: 5125580--5125639 Score: 95
Period size: 29 Copynumber: 2.0 Consensus size: 30
5125570 CAATTTAAGG
5125580 CAAAATAGTTTTTGAACTTGAATTGAATTTA
1 CAAAATAGTTTTTGAACTT-AATTGAATTTA
*
5125611 CAAAAT-GTTTTTGGACTTAATTGAATTTA
1 CAAAATAGTTTTTGAACTTAATTGAATTTA
5125640 TTCAAAGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.37, C:0.07, G:0.13, T:0.43
Consensus pattern (30 bp):
CAAAATAGTTTTTGAACTTAATTGAATTTA
Found at i:5126201 original size:34 final size:32
Alignment explanation
Indices: 5126163--5126232 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 32
5126153 TTTTGAAAAG
*
5126163 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
* * *
5126197 GGGAAATGTTTTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
5126229 GGGA
1 GGGA
5126233 GTTTGTAAGG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 11 0.34
33 1 0.03
34 20 0.62
ACGTcount: A:0.31, C:0.14, G:0.30, T:0.24
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:5131004 original size:61 final size:61
Alignment explanation
Indices: 5130928--5131099 Score: 227
Period size: 61 Copynumber: 2.8 Consensus size: 61
5130918 TAATTTTTTG
* * * *
5130928 CAGCTTTCAAAGCCAATTTCAACTTCACATCGAATGATATTGGACTCAACAAATAACTTTC
1 CAGCTTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAACAAACAACTTTC
* **
5130989 CAGCTTTCAGAGCCAATTTCAACTTTACAACGAAGGATATTATACTCAACAAACAACTTTC
1 CAGCTTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAACAAACAACTTTC
* * *
5131050 CAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTC
1 CAG---CTTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
5131100 GAATCAACAC
Statistics
Matches: 95, Mismatches: 13, Indels: 3
0.86 0.12 0.03
Matches are distributed among these distances:
61 57 0.60
64 38 0.40
ACGTcount: A:0.35, C:0.24, G:0.12, T:0.29
Consensus pattern (61 bp):
CAGCTTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAACAAACAACTTTC
Found at i:5131551 original size:39 final size:38
Alignment explanation
Indices: 5131491--5131635 Score: 141
Period size: 38 Copynumber: 3.8 Consensus size: 38
5131481 TTGTTTTTAA
* *
5131491 AGAAGATTTTGTCT-TGCTTGAGATAGTTTCCCTCGAAAC
1 AGAA-ATTTTGTCTCT-CTTGAGACAATTTCCCTCGAAAC
5131530 AGAAAGTTTTGTCTCTCTTGAGACAATTTCCCTCGAAAC
1 AGAAA-TTTTGTCTCTCTTGAGACAATTTCCCTCGAAAC
* * * * *
5131569 ATAAACTTTGTCTC-CTTTGAGACAATTTCTCTTGAAAT
1 AGAAATTTTGTCTCTC-TTGAGACAATTTCCCTCGAAAC
* * * *
5131607 ATAAACTTAGTCTCCCTTGAGACAATTTC
1 AGAAATTTTGTCTCTCTTGAGACAATTTC
5131636 TTTTGAAACA
Statistics
Matches: 94, Mismatches: 8, Indels: 9
0.85 0.07 0.08
Matches are distributed among these distances:
37 1 0.01
38 54 0.57
39 38 0.40
40 1 0.01
ACGTcount: A:0.28, C:0.21, G:0.14, T:0.37
Consensus pattern (38 bp):
AGAAATTTTGTCTCTCTTGAGACAATTTCCCTCGAAAC
Found at i:5131589 original size:38 final size:38
Alignment explanation
Indices: 5131508--5131654 Score: 161
Period size: 38 Copynumber: 3.8 Consensus size: 38
5131498 TTTGTCTTGC
* * * *
5131508 TTGAGATAGTTTCCCTCGAAACAGAAAGTTTTGTCT-CT
1 TTGAGACAATTTCCCTCGAAACATAAA-CTTTGTCTCCT
5131546 CTTGAGACAATTTCCCTCGAAACATAAACTTTGTCTCCT
1 -TTGAGACAATTTCCCTCGAAACATAAACTTTGTCTCCT
* * * * *
5131585 TTGAGACAATTTCTCTTGAAATATAAACTTAGTCTCCC
1 TTGAGACAATTTCCCTCGAAACATAAACTTTGTCTCCT
** *
5131623 TTGAGACAATTTCTTTTGAAACATAAACTTTG
1 TTGAGACAATTTCCCTCGAAACATAAACTTTG
5131655 AAAACATTTC
Statistics
Matches: 95, Mismatches: 12, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
38 69 0.73
39 26 0.27
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (38 bp):
TTGAGACAATTTCCCTCGAAACATAAACTTTGTCTCCT
Found at i:5131713 original size:35 final size:35
Alignment explanation
Indices: 5131667--5131735 Score: 120
Period size: 35 Copynumber: 2.0 Consensus size: 35
5131657 AACATTTCCC
*
5131667 TTGAAACGAATTTTGTCTTTCTTGAGATAGTTTCG
1 TTGAAACGAATTTTGTCTCTCTTGAGATAGTTTCG
*
5131702 TTGAAACGAATTTTGTCTCTCTTGAGATATTTTC
1 TTGAAACGAATTTTGTCTCTCTTGAGATAGTTTC
5131736 CCTTGAAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.23, C:0.13, G:0.17, T:0.46
Consensus pattern (35 bp):
TTGAAACGAATTTTGTCTCTCTTGAGATAGTTTCG
Found at i:5131750 original size:36 final size:36
Alignment explanation
Indices: 5131660--5131780 Score: 138
Period size: 36 Copynumber: 3.4 Consensus size: 36
5131650 CTTTGAAAAC
*
5131660 ATTTCCCTTGAAACGAATTTTGTCTTTCTTGAGATA
1 ATTTCCCTTGAAACGAATTTTGTCTCTCTTGAGATA
* *
5131696 GTTT-CGTTGAAACGAATTTTGTCTCTCTTGAGATA
1 ATTTCCCTTGAAACGAATTTTGTCTCTCTTGAGATA
* ** * *
5131731 TTTTCCCTTGAAATAAATTTTATCTC-CATTGAGACA
1 ATTTCCCTTGAAACGAATTTTGTCTCTC-TTGAGATA
*
5131767 ATTTCTCTTGAAAC
1 ATTTCCCTTGAAAC
5131781 ATAAACTTTG
Statistics
Matches: 71, Mismatches: 12, Indels: 4
0.82 0.14 0.05
Matches are distributed among these distances:
35 33 0.46
36 38 0.54
ACGTcount: A:0.26, C:0.17, G:0.13, T:0.43
Consensus pattern (36 bp):
ATTTCCCTTGAAACGAATTTTGTCTCTCTTGAGATA
Found at i:5131771 original size:136 final size:138
Alignment explanation
Indices: 5131575--5131836 Score: 377
Period size: 136 Copynumber: 1.9 Consensus size: 138
5131565 AAACATAAAC
* * *
5131575 TTTGTCTCCTTTGAGACAATTTCTCTTGAAATATAAACTTAGTCTCCCTTGAGACAATTTCTTTT
1 TTTGTCTCCTTTGAGACAATTTCCCTTGAAATATAAACTTAGTCTCCATTGAGACAATTTCTCTT
* * *
5131640 GAAACATAAACTTTGAAAACATTTCCCTTGAAACGAATTTTGTCTTTCTTGAGATAGTTTCGTTG
66 GAAACATAAACTTTGAAAACATTTCCCTTGAAACGAATTTTATCTCTCTTGAGACAGTTTCGTTG
5131705 AAACGAAT
131 AAACGAAT
* * **
5131713 TTTGTCT-CTCTTGAGATATTTTCCCTTGAAATA-AATTTTA-TCTCCATTGAGACAATTTCTCT
1 TTTGTCTCCT-TTGAGACAATTTCCCTTGAAATATAAACTTAGTCTCCATTGAGACAATTTCTCT
** *
5131775 TGAAACATAAACTTTGAAAATGTTTCCCTTGAAACGAGTTTTATCTCTCTTGAGACAGTTTC
65 TGAAACATAAACTTTGAAAACATTTCCCTTGAAACGAATTTTATCTCTCTTGAGACAGTTTC
5131837 CCTTCAAACA
Statistics
Matches: 110, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
136 76 0.69
137 7 0.06
138 27 0.25
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.41
Consensus pattern (138 bp):
TTTGTCTCCTTTGAGACAATTTCCCTTGAAATATAAACTTAGTCTCCATTGAGACAATTTCTCTT
GAAACATAAACTTTGAAAACATTTCCCTTGAAACGAATTTTATCTCTCTTGAGACAGTTTCGTTG
AAACGAAT
Found at i:5132024 original size:69 final size:69
Alignment explanation
Indices: 5131912--5132083 Score: 224
Period size: 69 Copynumber: 2.5 Consensus size: 69
5131902 CTTATGAAAC
* * ** * *
5131912 ACCAAACTTTGATATTGTTTCCCTTGAAACAAGTTTTAGTTTCTTTGAGATCTTTTCTCATGAAA
1 ACCAAACTTTGAGATTGTTTCCCTTGAAACAAATCGTAGTTTCTTTGAGATCGTTTATCATGAAA
5131977 CAACA
66 CAA-A
* *
5131982 ACCAAACTTTGAGA-TGTTTCTCTTGAAACAAATCGTATTTTCTTTGAGATCGTTTATCATGAAA
1 ACCAAACTTTGAGATTGTTTCCCTTGAAACAAATCGTAGTTTCTTTGAGATCGTTTATCATGAAA
5132046 CAAA
66 CAAA
5132050 A--AATATCTTTGAGATTGTTTCCCTTGAAACAAAT
1 ACCAA-A-CTTTGAGATTGTTTCCCTTGAAACAAAT
5132084 TTTATCTCTT
Statistics
Matches: 90, Mismatches: 9, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
66 2 0.02
67 1 0.01
68 10 0.11
69 64 0.71
70 13 0.14
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.38
Consensus pattern (69 bp):
ACCAAACTTTGAGATTGTTTCCCTTGAAACAAATCGTAGTTTCTTTGAGATCGTTTATCATGAAA
CAAA
Found at i:5132090 original size:33 final size:33
Alignment explanation
Indices: 5131918--5132090 Score: 107
Period size: 33 Copynumber: 5.1 Consensus size: 33
5131908 AAACACCAAA
* * *
5131918 CTTTGATATTGTTTCCCTTGAAACAAGTTTTAGTTT
1 CTTTGAGATTGTTTCTCTTGAAACAAATTTTA---T
* **** *
5131954 CTTTGAGATCT-TTTCTCATGAAACAACAACCAAA
1 CTTTGAGAT-TGTTTCTCTTGAAACAA-ATTTTAT
*
5131988 CTTTGAGA-TGTTTCTCTTGAAACAAATCGTATTTT
1 CTTTGAGATTGTTTCTCTTGAAACAAAT--T-TTAT
* * * ***
5132023 CTTTGAGATCGTTTATCATGAAACAAAAAATAT
1 CTTTGAGATTGTTTCTCTTGAAACAAATTTTAT
*
5132056 CTTTGAGATTGTTTCCCTTGAAACAAATTTTAT
1 CTTTGAGATTGTTTCTCTTGAAACAAATTTTAT
5132089 CT
1 CT
5132091 CTTTTGAGAA
Statistics
Matches: 100, Mismatches: 30, Indels: 17
0.68 0.20 0.12
Matches are distributed among these distances:
32 2 0.02
33 44 0.44
34 8 0.08
35 8 0.08
36 36 0.36
37 2 0.02
ACGTcount: A:0.31, C:0.16, G:0.12, T:0.41
Consensus pattern (33 bp):
CTTTGAGATTGTTTCTCTTGAAACAAATTTTAT
Found at i:5132272 original size:43 final size:41
Alignment explanation
Indices: 5132174--5132537 Score: 173
Period size: 43 Copynumber: 8.6 Consensus size: 41
5132164 TGGCCTGTCG
*
5132174 TCCTCATCACGTAGGAACAGTGTCATTACCC-G--ACCTA-ATC-
1 TCCTCATCACGTAGGAACCGTGTCA--ACCCAGATACC-AGA-CA
* *
5132214 TCCTCATCACTTAGGAGCCGTGTCAACCACAGATAACCAGACA
1 TCCTCATCACGTAGGAACCGTGTCAACC-CAGAT-ACCAGACA
* ** *
5132257 TCCTCATCACGTAGGAACCGTGTTATCACCCTTAGATGGCATGTCA
1 TCCTCATCACGTAGGAACCGTGTCA--ACCC--AGATACCA-GACA
* *
5132303 TCCTCATCACGTAGGAACCGTGTCATCAACC-G--ACCTGATC-
1 TCCTCATCACGTAGGAACCGTGTCA--ACCCAGATACCAGA-CA
* *
5132343 TCTTCATCACGTAGGAGCCGTGTCAACCCCAGATAACCAG-CAA
1 TCCTCATCACGTAGGAACCGTGTCAA-CCCAGAT-ACCAGAC-A
* ** * *
5132386 TCCTCATCACGTAGGAACCGTGTTATTACCCTTAGATGACTTGTCG
1 TCCTCATCACGTAGGAACCGTGTCA--ACCC--AGAT-ACCAGACA
* *
5132432 TCCTCATCACGTAGGAACCATGTCATCACCC-G--ACCTGATC-
1 TCCTCATCACGTAGGAACCGTGTCA--ACCCAGATACCAGA-CA
* * *
5132472 TCCTCATCACGTAGGAGCTGTGTCAACCCCAGATAACCA-ACCG
1 TCCTCATCACGTAGGAACCGTGTCAA-CCCAGAT-ACCAGA-CA
*
5132515 TCCTCATCACGTAGGAATCGTGT
1 TCCTCATCACGTAGGAACCGTGT
5132538 TATCACTCTT
Statistics
Matches: 253, Mismatches: 39, Indels: 61
0.72 0.11 0.17
Matches are distributed among these distances:
38 5 0.02
39 6 0.02
40 75 0.30
41 4 0.02
42 4 0.02
43 77 0.30
44 4 0.02
45 6 0.02
46 71 0.28
47 1 0.00
ACGTcount: A:0.26, C:0.32, G:0.18, T:0.24
Consensus pattern (41 bp):
TCCTCATCACGTAGGAACCGTGTCAACCCAGATACCAGACA
Found at i:5132311 original size:46 final size:44
Alignment explanation
Indices: 5132255--5132590 Score: 195
Period size: 46 Copynumber: 7.8 Consensus size: 44
5132245 GATAACCAGA
*
5132255 CATCCTCATCACGTAGGAACCGTGTTATCACCCTTAGATGGCATGT
1 CATCCTCATCACGTAGGAACCGTGTCATCACCC-TAGAT-GCATGT
* *
5132301 CATCCTCATCACGTAGGAACCGTGTCATCAACC--GA--CCTGAT
1 CATCCTCATCACGTAGGAACCGTGTCATCACCCTAGATGCATG-T
* * * *
5132342 C-TCTTCATCACGTAGGAGCCGTGTCA--ACCCCAGATAACCA-G-
1 CATCCTCATCACGTAGGAACCGTGTCATCACCCTAGAT--GCATGT
* * *
5132383 CAATCCTCATCACGTAGGAACCGTGTTATTACCCTTAGATGACTTGT
1 C-ATCCTCATCACGTAGGAACCGTGTCATCACCC-TAGATG-CATGT
* * *
5132430 CGTCCTCATCACGTAGGAACCATGTCATCACCC--GA--CCTGAT
1 CATCCTCATCACGTAGGAACCGTGTCATCACCCTAGATGCATG-T
* * * * **
5132471 C-TCCTCATCACGTAGGAGCTGTGTCA--ACCCCAGATAACCA-AC
1 CATCCTCATCACGTAGGAACCGTGTCATCACCCTAGAT--GCATGT
* * * * *
5132513 CGTCCTCATCACGTAGGAATCGTGTTATCACTCTTAGATGACCTG-
1 CATCCTCATCACGTAGGAACCGTGTCATCAC-CCTAGATG-CATGT
* *
5132558 CGTCCTCATCACGTAGGAACTGTGTCATCACCC
1 CATCCTCATCACGTAGGAACCGTGTCATCACCC
5132591 GACCTGATAT
Statistics
Matches: 225, Mismatches: 37, Indels: 58
0.70 0.12 0.18
Matches are distributed among these distances:
38 7 0.03
40 55 0.24
41 5 0.02
42 1 0.00
43 48 0.21
44 3 0.01
45 36 0.16
46 69 0.31
47 1 0.00
ACGTcount: A:0.25, C:0.32, G:0.18, T:0.25
Consensus pattern (44 bp):
CATCCTCATCACGTAGGAACCGTGTCATCACCCTAGATGCATGT
Found at i:5132392 original size:129 final size:129
Alignment explanation
Indices: 5132144--5132626 Score: 700
Period size: 129 Copynumber: 3.7 Consensus size: 129
5132134 CTCTTAAAAT
* * * *
5132144 CGTGTTATCATCCCTAATGATGGCCTGTCGTCCTCATCACGTAGGAACAGTGTCATTACCCGACC
1 CGTGTTATCA-CCCTTA-GATGACCTGTCGTCCTCATCACGTAGGAACCGTGTCATCACCCGACC
* * *
5132209 TAATCTCCTCATCACTTAGGAGCCGTGTCAACCACAGATAACCAG-ACATCCTCATCACGTAGGA
64 TGATCTCCTCATCACGTAGGAGCCGTGTCAACCCCAGATAACCAGCA-ATCCTCATCACGTAGGA
5132273 AC
128 AC
* * * *
5132275 CGTGTTATCACCCTTAGATGGCATGTCATCCTCATCACGTAGGAACCGTGTCATCAACCGACCTG
1 CGTGTTATCACCCTTAGATGACCTGTCGTCCTCATCACGTAGGAACCGTGTCATCACCCGACCTG
*
5132340 ATCTCTTCATCACGTAGGAGCCGTGTCAACCCCAGATAACCAGCAATCCTCATCACGTAGGAAC
66 ATCTCCTCATCACGTAGGAGCCGTGTCAACCCCAGATAACCAGCAATCCTCATCACGTAGGAAC
* * *
5132404 CGTGTTATTACCCTTAGATGACTTGTCGTCCTCATCACGTAGGAACCATGTCATCACCCGACCTG
1 CGTGTTATCACCCTTAGATGACCTGTCGTCCTCATCACGTAGGAACCGTGTCATCACCCGACCTG
* * ** *
5132469 ATCTCCTCATCACGTAGGAGCTGTGTCAACCCCAGATAACCAACCGTCCTCATCACGTAGGAAT
66 ATCTCCTCATCACGTAGGAGCCGTGTCAACCCCAGATAACCAGCAATCCTCATCACGTAGGAAC
* *
5132533 CGTGTTATCACTCTTAGATGACCTG-CGTCCTCATCACGTAGGAACTGTGTCATCACCCGACCTG
1 CGTGTTATCACCCTTAGATGACCTGTCGTCCTCATCACGTAGGAACCGTGTCATCACCCGACCTG
* * *
5132597 ATATCTTCATCACGTAGGAGTCGTGTCAAC
66 ATCTCCTCATCACGTAGGAGCCGTGTCAAC
5132627 TGTTAGATGA
Statistics
Matches: 320, Mismatches: 31, Indels: 5
0.90 0.09 0.01
Matches are distributed among these distances:
128 63 0.20
129 241 0.75
130 6 0.02
131 10 0.03
ACGTcount: A:0.25, C:0.31, G:0.18, T:0.25
Consensus pattern (129 bp):
CGTGTTATCACCCTTAGATGACCTGTCGTCCTCATCACGTAGGAACCGTGTCATCACCCGACCTG
ATCTCCTCATCACGTAGGAGCCGTGTCAACCCCAGATAACCAGCAATCCTCATCACGTAGGAAC
Found at i:5133050 original size:17 final size:17
Alignment explanation
Indices: 5133012--5133051 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
5133002 ATTGAAAAAT
*
5133012 GAGA-AGCCATACGTGG
1 GAGAGAGCCATACGTGA
*
5133028 GGGAGAGCCATACGTGA
1 GAGAGAGCCATACGTGA
5133045 GAGAGAG
1 GAGAGAG
5133052 ATAAGAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 3 0.15
17 17 0.85
ACGTcount: A:0.33, C:0.15, G:0.42, T:0.10
Consensus pattern (17 bp):
GAGAGAGCCATACGTGA
Found at i:5133606 original size:30 final size:31
Alignment explanation
Indices: 5133563--5133637 Score: 73
Period size: 31 Copynumber: 2.4 Consensus size: 31
5133553 GTTTTTACTA
*
5133563 TTTATGTCCTTTAAATTTCCGTT-TTAAC-TGT
1 TTTA-GTCTTTTAAATTTCCGTTCTTAACAT-T
* * *
5133594 TTTAGTCTTTTAAGTTTCTGTTCTTACCATT
1 TTTAGTCTTTTAAATTTCCGTTCTTAACATT
*
5133625 TTTAATCTTTTAA
1 TTTAGTCTTTTAA
5133638 GTTCATGTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
30 15 0.41
31 21 0.57
32 1 0.03
ACGTcount: A:0.20, C:0.15, G:0.08, T:0.57
Consensus pattern (31 bp):
TTTAGTCTTTTAAATTTCCGTTCTTAACATT
Found at i:5133628 original size:31 final size:30
Alignment explanation
Indices: 5133533--5133648 Score: 94
Period size: 30 Copynumber: 3.8 Consensus size: 30
5133523 TGTTATTTTA
** *
5133533 TTTTAGTCACTTAAGTTTCTGTTTTTACTAT
1 TTTTAGTCTTTTAAGTTTCTG-TTTTACCAT
* * * * *
5133564 TTAT-GTCCTTTAAATTTCCGTTTTAAC-T
1 TTTTAGTCTTTTAAGTTTCTGTTTTACCAT
5133592 GTTTTAGTCTTTTAAGTTTCTGTTCTTACCAT
1 -TTTTAGTCTTTTAAGTTTCTGTT-TTACCAT
*
5133624 TTTTAATCTTTTAAG-TTCATGTTTT
1 TTTTAGTCTTTTAAGTTTC-TGTTTT
5133649 TGCTAGATCT
Statistics
Matches: 67, Mismatches: 13, Indels: 11
0.74 0.14 0.12
Matches are distributed among these distances:
28 1 0.01
29 8 0.12
30 32 0.48
31 25 0.37
32 1 0.01
ACGTcount: A:0.19, C:0.14, G:0.09, T:0.58
Consensus pattern (30 bp):
TTTTAGTCTTTTAAGTTTCTGTTTTACCAT
Found at i:5141683 original size:23 final size:23
Alignment explanation
Indices: 5141625--5141686 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 23
5141615 ACAACCTTAT
* *
5141625 ATGGCACTTCGGTGCATTTCTAT
1 ATGGCACTTCGGTGCAATTCTAC
** * *
5141648 GCGGTACTACGGTGCAATTCTAC
1 ATGGCACTTCGGTGCAATTCTAC
5141671 ATGGCACTTCGGTGCA
1 ATGGCACTTCGGTGCA
5141687 TTTATACGAG
Statistics
Matches: 29, Mismatches: 10, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.19, C:0.24, G:0.26, T:0.31
Consensus pattern (23 bp):
ATGGCACTTCGGTGCAATTCTAC
Found at i:5147327 original size:8 final size:9
Alignment explanation
Indices: 5147306--5147332 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
5147296 ATAAGCACTC
5147306 AAAAAATTT
1 AAAAAATTT
5147315 AAAAAATTT
1 AAAAAATTT
5147324 AAAAAATTT
1 AAAAAATTT
5147333 TAAACCTTCG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (9 bp):
AAAAAATTT
Found at i:5148292 original size:224 final size:219
Alignment explanation
Indices: 5147889--5148438 Score: 718
Period size: 224 Copynumber: 2.5 Consensus size: 219
5147879 CTTATTCATA
* *
5147889 TATTGAAT-AAAATTATTTTTTTATTATTTCGGGTCGGGTTTCTAATTTATATATTCGGGTCGGG
1 TATTGAATAAAAATAATTTTTTTATTATTTCGGGTCGGGTTTCTAATTCATATATTCGGGTCGGG
* ** * ** * * * *
5147953 TCGGTTTTTTTAAGTGTGATATTCGGGTCGGGTCGAGTTCGGGTTTAGGGTGAAAAATACTGACC
66 TCGG---GTGAAACT-T--TATTTTGGTAGGGTCGGGTTCGGGTTTAAGGTGAAAAATACCGACC
* * *
5148018 CGAAAATATATATAATTTTACTTTATATATTTAGGAATAATTACAATAATACCCCTCTATATATA
125 CGAAAAAATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATACCCCTATATATATA
*
5148083 -AT-T-T-TTTTCAATTAAGTCAATGTTTT
190 TATATATATTTCCAATTAAGTCAATGTTTT
5148109 TATTGAA-AAATAATAA-TTTTTTATTATTTCGGGTCGGGTCGGATTTCTAATTCATATATTCGG
1 TATTGAATAAA-AATAATTTTTTTATTATTTCGGGTC--G--GG-TTTCTAATTCATATATTCGG
5148172 GTCGGGTCGGGTGAAACTTTATTTTGGTAGGGTCGGGTTCGGGTTTAAGGTGAAAAATACCCGAC
60 GTCGGGTCGGGTGAAACTTTATTTTGGTAGGGTCGGGTTCGGGTTTAAGGTGAAAAATA-CCGAC
*
5148237 CCGACCCAAAAAATATATAATTTTACCTTATATATTTAGGAATAATTATAATAATACCCCTATAT
124 CCG----AAAAAATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATACCCCTATAT
*
5148302 ATATATATATATATTTCCAATTAAGTCACTGTTTT
185 ATATATATATATATTTCCAATTAAGTCAATGTTTT
5148337 TATTGAATAAAAATAATTTTTTTATTATTTCGGGTCGGGTTTCTAATTCATATATTCGGGTCGGG
1 TATTGAATAAAAATAATTTTTTTATTATTTCGGGTCGGGTTTCTAATTCATATATTCGGGTCGGG
*
5148402 TCGGGTGAAACTTTATTTTGGTCGGGTCGGGTCTCGG
66 TCGGGTGAAACTTTATTTTGGTAGGGTCGGGT-TCGG
5148439 ATGGAGGTTC
Statistics
Matches: 292, Mismatches: 19, Indels: 33
0.85 0.06 0.10
Matches are distributed among these distances:
219 35 0.12
220 35 0.12
221 5 0.02
222 5 0.02
224 118 0.40
225 37 0.13
226 1 0.00
227 2 0.01
228 32 0.11
229 22 0.08
ACGTcount: A:0.28, C:0.12, G:0.19, T:0.41
Consensus pattern (219 bp):
TATTGAATAAAAATAATTTTTTTATTATTTCGGGTCGGGTTTCTAATTCATATATTCGGGTCGGG
TCGGGTGAAACTTTATTTTGGTAGGGTCGGGTTCGGGTTTAAGGTGAAAAATACCGACCCGAAAA
AATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATACCCCTATATATATATATATA
TATTTCCAATTAAGTCAATGTTTT
Found at i:5149029 original size:18 final size:18
Alignment explanation
Indices: 5148985--5149031 Score: 67
Period size: 19 Copynumber: 2.6 Consensus size: 18
5148975 ATAGCGTCAC
*
5148985 AAGTTTATAAATATAAAA
1 AAGTTTAAAAATATAAAA
*
5149003 AATTCTTAAAAATATAAAA
1 AAGT-TTAAAAATATAAAA
5149022 AAGTTTAAAA
1 AAGTTTAAAA
5149032 TATTATGTGG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 9 0.36
19 16 0.64
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (18 bp):
AAGTTTAAAAATATAAAA
Found at i:5154218 original size:34 final size:34
Alignment explanation
Indices: 5154175--5154250 Score: 143
Period size: 34 Copynumber: 2.2 Consensus size: 34
5154165 GAAAAGAATG
5154175 AATTACAGTACAATTGCTTAATGATTATAAGGGA
1 AATTACAGTACAATTGCTTAATGATTATAAGGGA
5154209 AATTACAGTACAATTGCTTAATGATTATAAGGGA
1 AATTACAGTACAATTGCTTAATGATTATAAGGGA
*
5154243 AATCACAG
1 AATTACAG
5154251 CCATTGCTGA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 41 1.00
ACGTcount: A:0.42, C:0.11, G:0.17, T:0.30
Consensus pattern (34 bp):
AATTACAGTACAATTGCTTAATGATTATAAGGGA
Found at i:5157282 original size:37 final size:35
Alignment explanation
Indices: 5157230--5157301 Score: 117
Period size: 37 Copynumber: 2.0 Consensus size: 35
5157220 TGGCAACCAA
5157230 CTTTGAAAAATGTTTTTCAAAATTTGGTAAATGTTT
1 CTTTGAAAAATGTTTTTCAAAATTTGGTAAA-GTTT
*
5157266 CTTTGAAAAAATGTTTTTCAAAGTTTGGTAAAGTTT
1 CTTTG-AAAAATGTTTTTCAAAATTTGGTAAAGTTT
5157302 GGTAGATGGT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
36 9 0.26
37 25 0.74
ACGTcount: A:0.33, C:0.06, G:0.15, T:0.46
Consensus pattern (35 bp):
CTTTGAAAAATGTTTTTCAAAATTTGGTAAAGTTT
Found at i:5161786 original size:37 final size:37
Alignment explanation
Indices: 5161733--5161813 Score: 130
Period size: 37 Copynumber: 2.2 Consensus size: 37
5161723 TGGCAACCAA
5161733 CTTTG-AAAAATGTTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAAATGTTTTTCAAAGTTTGGTAAATGTTT
*
5161769 CTTTGAAAAAATGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAAATGTTTTTCAAAGTTTGGTAAATGTTT
*
5161806 -GTTGAAAA
1 CTTTGAAAA
5161814 TAGGAATGGG
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
36 12 0.29
37 30 0.71
ACGTcount: A:0.32, C:0.05, G:0.19, T:0.44
Consensus pattern (37 bp):
CTTTGAAAAAATGTTTTTCAAAGTTTGGTAAATGTTT
Found at i:5162897 original size:42 final size:40
Alignment explanation
Indices: 5162819--5162897 Score: 97
Period size: 42 Copynumber: 1.9 Consensus size: 40
5162809 ATATTCCGAT
* *
5162819 GTTTTTTTGATGTCAAATGACATAAAATTATGTTTTAAGA
1 GTTTTTTTGATGTCAAATAACAGAAAATTATGTTTTAAGA
*
5162859 GTTTATTTTGATGTTTAAATAACAGAAAATTTAT-TTTTA
1 GTTT-TTTTGATG-TCAAATAACAGAAAA-TTATGTTTTA
5162898 TACATTTTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 4 0.12
41 8 0.24
42 17 0.52
43 4 0.12
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.48
Consensus pattern (40 bp):
GTTTTTTTGATGTCAAATAACAGAAAATTATGTTTTAAGA
Found at i:5165480 original size:7 final size:7
Alignment explanation
Indices: 5165468--5165494 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
5165458 TTTAATTATA
5165468 CATTGGC
1 CATTGGC
5165475 CATTGGC
1 CATTGGC
5165482 CATTGGC
1 CATTGGC
5165489 CATTGG
1 CATTGG
5165495 GCTTCGGCCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.15, C:0.26, G:0.30, T:0.30
Consensus pattern (7 bp):
CATTGGC
Found at i:5165773 original size:6 final size:6
Alignment explanation
Indices: 5165764--5165792 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
5165754 TAAAAAGAAA
5165764 AATTAT AATTAT AATTAT AATTAT AATTA
1 AATTAT AATTAT AATTAT AATTAT AATTA
5165793 AAAGATACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
AATTAT
Found at i:5167171 original size:21 final size:22
Alignment explanation
Indices: 5167142--5167184 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
5167132 AATAGTCTAA
*
5167142 AACAGATAAG-ATCATCATAAT
1 AACAAATAAGTATCATCATAAT
*
5167163 AACAAATAAGTATCATCTTAAT
1 AACAAATAAGTATCATCATAAT
5167185 TAGTCACGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.51, C:0.14, G:0.07, T:0.28
Consensus pattern (22 bp):
AACAAATAAGTATCATCATAAT
Found at i:5173169 original size:15 final size:15
Alignment explanation
Indices: 5173149--5173179 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
5173139 CAACAAATAA
5173149 AATTTTTATATAAAT
1 AATTTTTATATAAAT
*
5173164 AATTTTTATTTAAAT
1 AATTTTTATATAAAT
5173179 A
1 A
5173180 TTTAGAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AATTTTTATATAAAT
Found at i:5174861 original size:23 final size:23
Alignment explanation
Indices: 5174831--5174917 Score: 122
Period size: 23 Copynumber: 3.8 Consensus size: 23
5174821 CAACTCATAT
5174831 AATTGCACCTAAGTGCCACGTAG
1 AATTGCACCTAAGTGCCACGTAG
*
5174854 AATTGCACCTAAGTGTCACGTAG
1 AATTGCACCTAAGTGCCACGTAG
** *
5174877 AATTGCACCGGAGTGCCGCGTAG
1 AATTGCACCTAAGTGCCACGTAG
5174900 AATTGCACCGT-AGTGCCA
1 AATTGCACC-TAAGTGCCA
5174918 TATAATAATA
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
23 56 1.00
ACGTcount: A:0.28, C:0.25, G:0.25, T:0.22
Consensus pattern (23 bp):
AATTGCACCTAAGTGCCACGTAG
Found at i:5175666 original size:19 final size:20
Alignment explanation
Indices: 5175629--5175666 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
5175619 TTTTTCATTA
*
5175629 TGGGGGAATCGGTTCCCCCC
1 TGGGGGAATCGATTCCCCCC
*
5175649 TGGGGGTATCGATTCCCC
1 TGGGGGAATCGATTCCCC
5175667 TCTAGCATTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.11, C:0.32, G:0.34, T:0.24
Consensus pattern (20 bp):
TGGGGGAATCGATTCCCCCC
Found at i:5175718 original size:21 final size:21
Alignment explanation
Indices: 5175694--5175736 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
5175684 TCATATTCGT
* *
5175694 TTGAGGGGGGATCGATTCCCC
1 TTGAAGGGGGACCGATTCCCC
* *
5175715 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGGACCGATTCCCC
5175736 T
1 T
5175737 AGCCTAGAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.16, C:0.26, G:0.30, T:0.28
Consensus pattern (21 bp):
TTGAAGGGGGACCGATTCCCC
Found at i:5181799 original size:23 final size:22
Alignment explanation
Indices: 5181773--5181836 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 22
5181763 CAGCTCATAT
5181773 AATTGCACCTAAGTGCCACGTAG
1 AATTGCACCT-AGTGCCACGTAG
* *
5181796 AATTGCACCGGAGTGCTACGTAG
1 AATTGCACC-TAGTGCCACGTAG
5181819 AATTGCACCGTAGTGCCA
1 AATTGCACC-TAGTGCCA
5181837 TATAATAATA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.28, C:0.25, G:0.25, T:0.22
Consensus pattern (22 bp):
AATTGCACCTAGTGCCACGTAG
Found at i:5182583 original size:19 final size:20
Alignment explanation
Indices: 5182546--5182583 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
5182536 TTTTTCATTA
*
5182546 TGGGGGAATCGGTTCCCCCC
1 TGGGGGAATCGATTCCCCCC
*
5182566 TGGGGGCATCGATTCCCC
1 TGGGGGAATCGATTCCCC
5182584 TCTAGCATTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.11, C:0.34, G:0.34, T:0.21
Consensus pattern (20 bp):
TGGGGGAATCGATTCCCCCC
Found at i:5182635 original size:21 final size:21
Alignment explanation
Indices: 5182611--5182653 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
5182601 TCATATTCGT
* *
5182611 TTGAGGGGGGATCGATTCCCC
1 TTGAAGGGGGACCGATTCCCC
* *
5182632 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGGACCGATTCCCC
5182653 T
1 T
5182654 AGCCCAGAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.16, C:0.26, G:0.30, T:0.28
Consensus pattern (21 bp):
TTGAAGGGGGACCGATTCCCC
Found at i:5183929 original size:2 final size:2
Alignment explanation
Indices: 5183887--5183919 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
5183877 ATAAACAAAT
5183887 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5183920 TAAAATATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5208235 original size:25 final size:25
Alignment explanation
Indices: 5208206--5208255 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
5208196 GATATAATAG
5208206 TAAGATTATTTCTCAATGTTCCATT
1 TAAGATTATTTCTCAATGTTCCATT
5208231 TAAGATTATTTCTCAATGTTCCATT
1 TAAGATTATTTCTCAATGTTCCATT
5208256 GATTCTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.28, C:0.16, G:0.08, T:0.48
Consensus pattern (25 bp):
TAAGATTATTTCTCAATGTTCCATT
Found at i:5219056 original size:2 final size:2
Alignment explanation
Indices: 5219049--5219075 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5219039 TCTATCAAAA
5219049 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
5219076 AACCTACCGC
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:5220860 original size:30 final size:31
Alignment explanation
Indices: 5220825--5220900 Score: 118
Period size: 31 Copynumber: 2.5 Consensus size: 31
5220815 AAAAGAATAA
* *
5220825 AGTTTAGGTACTAAAATAG-ATAAAAGTGAT
1 AGTTTAAGTACTAAAATAGAATAAAAATGAT
*
5220855 AGTTTAAGTACTAAAATGGAATAAAAATGAT
1 AGTTTAAGTACTAAAATAGAATAAAAATGAT
5220886 AGTTTAAGTACTAAA
1 AGTTTAAGTACTAAA
5220901 CATATAGTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
30 17 0.40
31 25 0.60
ACGTcount: A:0.49, C:0.04, G:0.17, T:0.30
Consensus pattern (31 bp):
AGTTTAAGTACTAAAATAGAATAAAAATGAT
Found at i:5221133 original size:29 final size:29
Alignment explanation
Indices: 5221101--5221157 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
5221091 TATGATTTTG
*
5221101 AATAAAAATAA-AATTTAGCTACTAAATGA
1 AATAAAAA-AATAATTTAGATACTAAATGA
*
5221130 AATAAAAAAATAATTTATATACTAAATG
1 AATAAAAAAATAATTTAGATACTAAATG
5221158 TGTAATTTAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 2 0.08
29 23 0.92
ACGTcount: A:0.60, C:0.05, G:0.05, T:0.30
Consensus pattern (29 bp):
AATAAAAAAATAATTTAGATACTAAATGA
Found at i:5221573 original size:21 final size:20
Alignment explanation
Indices: 5221487--5221644 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
5221477 AAATGACCAA
**
5221487 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
5221506 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
5221526 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
5221546 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
5221567 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
5221588 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
5221608 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
5221629 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
5221645 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:5221847 original size:20 final size:20
Alignment explanation
Indices: 5221611--5221860 Score: 234
Period size: 20 Copynumber: 12.5 Consensus size: 20
5221601 CGATTTTCCA
* ** *
5221611 AAATCGCAACGCGAATATGA
1 AAATCGCAACGAGAATCCGT
* *
5221631 AAATCGCAACGCGAA-CACAT
1 AAATCGCAACGAGAATC-CGT
* *
5221651 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGAGAATCCGT
* *
5221671 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGAGAATCCGT
* **
5221691 AAATCGCAACGCA-TATGGGT
1 AAATCGCAACG-AGAATCCGT
* * *
5221711 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGAGAATCCGT
* * * *
5221731 ATATCGCAATGCGTATCCGT
1 AAATCGCAACGAGAATCCGT
*
5221751 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGAGAATCCGT
*
5221771 AAATCGCAACGATAATCCGT
1 AAATCGCAACGAGAATCCGT
*
5221791 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGAGAATCCGT
*
5221811 AAATCGCAACGATAATCCGT
1 AAATCGCAACGAGAATCCGT
*
5221831 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGAGAATCCGT
*
5221851 AAATCACAAC
1 AAATCGCAAC
5221861 ACTGAAATTT
Statistics
Matches: 198, Mismatches: 28, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
20 197 0.99
21 1 0.01
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGAGAATCCGT
Found at i:5222582 original size:24 final size:24
Alignment explanation
Indices: 5222543--5222589 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
5222533 AAATTTGGTC
5222543 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
5222567 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
5222590 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Done.