Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008342.1 Hibiscus syriacus cultivar Beakdansim tig00111069_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: 1228932
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 6
Found at i:1172506 original size:14 final size:14
Alignment explanation
Indices: 1172487--1172516 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
1172477 AGCGTTTCTA
1172487 AAGTCTGATAGATC
1 AAGTCTGATAGATC
1172501 AAGTCTGATAGATC
1 AAGTCTGATAGATC
1172515 AA
1 AA
1172517 TAGGAACAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.27
Consensus pattern (14 bp):
AAGTCTGATAGATC
Found at i:1182218 original size:2 final size:2
Alignment explanation
Indices: 1182155--1182206 Score: 95
Period size: 2 Copynumber: 26.0 Consensus size: 2
1182145 ATTAGATTCA
*
1182155 AT AT AA 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
1182197 AT AT AT AT AT
1 AT AT AT AT AT
1182207 TCTAAAATAT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1182306 original size:27 final size:26
Alignment explanation
Indices: 1182276--1182346 Score: 72
Period size: 27 Copynumber: 2.7 Consensus size: 26
1182266 CTAGTAGAAG
* *
1182276 TTGAAAATTTTAAACTC-AAGTCGAGC
1 TTGATAATTTTAAACTCGAA-TCGAAC
**
1182302 TTTGATTTTTTTAAACTCGAATCGAAC
1 -TTGATAATTTTAAACTCGAATCGAAC
*
1182329 TTCATAATTTTAAACTCG
1 TTGATAATTTTAAACTCG
1182347 TAAATTTTTG
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
26 15 0.42
27 19 0.53
28 2 0.06
ACGTcount: A:0.34, C:0.15, G:0.11, T:0.39
Consensus pattern (26 bp):
TTGATAATTTTAAACTCGAATCGAAC
Found at i:1182535 original size:388 final size:389
Alignment explanation
Indices: 1181819--1184090 Score: 4040
Period size: 388 Copynumber: 5.9 Consensus size: 389
1181809 TTGAACTAAG
1181819 TCTAAAATATATCAAGTTTAAGGTTTTTGGACATCGAGTCAAGTTTTAATTTTTAATTTCTAGTA
1 TCTAAAATATATCAAGTTTAAGGTTTTTGGACATCGAGTCAAGTTTTAATTTTTAATTTCTAGTA
* *
1181884 GAAGTTGAAAATTTTAAACTCAAGTCGAGCTTTGATTTTTTTTTAAACTTGAATCGAACTTCATA
66 GAAGTTGAAAATTTTAAACTCAAGTCAAGCTTTGA-TTTTTTTTAAACTCGAATCGAACTTCATA
*
1181949 ATTTTAAGCTCGTAAATTTTTGAGTTGAATCAAAATCAACAAAATTCGAACCGGGTTCGTTTACA
130 ATTTTAAACTCGTAAATTTTTGAGTTGAATCAAAATCAACAAAATTCGAACCGGGTTCGTTTACA
1182014 ATCCTAATAAAAACCAATGTTATTAATATTATTTACTTTTCTCTGTCAAATTTCTTTGAAGATAT
195 ATCCTAATAAAAACCAATGTTATTAATATTATTTACTTTTCTCTGTCAAATTTCTTTGAAGATAT
*
1182079 AATTATAATCTACACAAACATACATATATACTGC--ATAAAATCAACCACCAATATAATAAATGT
260 AATTATAATCTACACACACATACATATATACTGCATATAAAATCAACCACCAATATAATAAATGT
1182142 AAAATTAGATTCAATATAAATATATATATATATATATATATATATATATATATATATATATATAT
325 AAAATTAGATTCAATATAAATATATATATATATATATATATATATATATATATATATATATATAT
1182207 TCTAAAATATATCAAGTTTAAGGTTTTTGGACATCGAGTCAAGTTTTAATTTTTAATTTCTAGTA
1 TCTAAAATATATCAAGTTTAAGGTTTTTGGACATCGAGTCAAGTTTTAATTTTTAATTTCTAGTA
*
1182272 GAAGTTGAAAATTTTAAACTCAAGTCGAGCTTTGA-TTTTTTTAAACTCGAATCGAACTTCATAA
66 GAAGTTGAAAATTTTAAACTCAAGTCAAGCTTTGATTTTTTTTAAACTCGAATCGAACTTCATAA
1182336 TTTTAAACTCGTAAATTTTTGAGTTGAATCAAAATCAACAAAATTCGAACCGGGTTCGTTTACAA
131 TTTTAAACTCGTAAATTTTTGAGTTGAATCAAAATCAACAAAATTCGAACCGGGTTCGTTTACAA
1182401 TCCTAATAAAAACCAATGTTATTAATATTATTTACTTTTCTCTGTCAAATTTCTTTGAAGATATA
196 TCCTAATAAAAACCAATGTTATTAATATTATTTACTTTTCTCTGTCAAATTTCTTTGAAGATATA
1182466 ATTATAATCTACACACACATACATATATACTGCATATAAAATCAACCACCAATATAATAAATGTA
261 ATTATAATCTACACACACATACATATATACTGCATATAAAATCAACCACCAATATAATAAATGTA
1182531 AAATTAGATTCAATATAAATATATATATATATATATATATATATATATATATATATATATAT-T
326 AAATTAGATTCAATATAAATATATATATATATATATATATATATATATATATATATATATATAT
1182594 TCTAAAATATATCAAGTTTAAGGTTTTTGGACATCGAGTCAAGTTTTAATTTTTAATTTCTAGTA
1 TCTAAAATATATCAAGTTTAAGGTTTTTGGACATCGAGTCAAGTTTTAATTTTTAATTTCTAGTA
*
1182659 GAAGTTGAAAATTTTAAGCTCAAGTCAAGCTTTGATTTTTTTTTTAAACTCGAATCGAACTTCAT
66 GAAGTTGAAAATTTTAAACTCAAGTCAAGCTTTGA--TTTTTTTTAAACTCGAATCGAACTTCAT
1182724 AATTTTAAACTCGTAAATTTTTGAGTTGAATCAAAATCAACAAAATTCGAACCGGGTTCGTTTAC
129 AATTTTAAACTCGTAAATTTTTGAGTTGAATCAAAATCAACAAAATTCGAACCGGGTTCGTTTAC
1182789 AATCCTAATAAAAACCAATGTTATTAATATTATTTACTTTTCTCTGTC-AA----TTTGAAGATA
194 AATCCTAATAAAAACCAATGTTATTAATATTATTTACTTTTCTCTGTCAAATTTCTTTGAAGATA
1182849 TAATTATAATCTACACACACATACATATATACTGCATATAAAATCAACCACCAATATAATAAATG
259 TAATTATAATCTACACACACATACATATATACTGCATATAAAATCAACCACCAATATAATAAATG
1182914 TAAAATTAGATTC-------------------A-ATATA-ATATATATATATATATATATATATA
324 TAAAATTAGATTCAATATAAATATATATATATATATATATATATATATATATATATATATATATA
1182958 T
389 T
1182959 TCTAAAATATATCAAGTTTAAGGTTTTT-GACATCGAGTCAAGTTTTAATTTTTAATTTCTAGTA
1 TCTAAAATATATCAAGTTTAAGGTTTTTGGACATCGAGTCAAGTTTTAATTTTTAATTTCTAGTA
*
1183023 GAAGTTGAAAATTTTAAGCTCAAGTCAAGCTTTGATTTTTTTTAAACTCGAATCGAACTTCATAA
66 GAAGTTGAAAATTTTAAACTCAAGTCAAGCTTTGATTTTTTTTAAACTCGAATCGAACTTCATAA
1183088 TTTTAAACTCGTAAATTTTTGAGTTGAATCAAAATCAACAAAATTCGAACCGGGTTCGTTTACAA
131 TTTTAAACTCGTAAATTTTTGAGTTGAATCAAAATCAACAAAATTCGAACCGGGTTCGTTTACAA
1183153 TCCTAATAAAAACCAATGTTATTAATATTATTTACTTTTCTCTGTCAAATTTCTTTGAAGATATA
196 TCCTAATAAAAACCAATGTTATTAATATTATTTACTTTTCTCTGTCAAATTTCTTTGAAGATATA
1183218 ATTATAATCTACACACACATAC--ATATACTGCATATAAAATCAACCACCAATATAATAAATGTA
261 ATTATAATCTACACACACATACATATATACTGCATATAAAATCAACCACCAATATAATAAATGTA
1183281 AAATTAGATTC------AATATATATATATATATATATATATATATATATATATATATATAT-T
326 AAATTAGATTCAATATAAATATATATATATATATATATATATATATATATATATATATATATAT
1183338 TCTAAAATATATCAAGTTTAAGGTTTTTGGACATCGAGTCAAGTTTTAATTTTTAATTTCTAGTA
1 TCTAAAATATATCAAGTTTAAGGTTTTTGGACATCGAGTCAAGTTTTAATTTTTAATTTCTAGTA
*
1183403 GAAGTTGAAAATTTTAAGCTCAAGTCAAGCTTTGATTTTTTTTTAAACTCGAATCGAACTTCATA
66 GAAGTTGAAAATTTTAAACTCAAGTCAAGCTTTGA-TTTTTTTTAAACTCGAATCGAACTTCATA
1183468 ATTTTAAACTCGTAAATTTTTGAGTTGAATCAAAATCAACAAAATTCGAACCGGGTTCGTTTACA
130 ATTTTAAACTCGTAAATTTTTGAGTTGAATCAAAATCAACAAAATTCGAACCGGGTTCGTTTACA
1183533 ATCCTAATAAAAACCAATGTTATTAATATTATTTACTTTTCTCTGTC-AA----TTTGAAGATAT
195 ATCCTAATAAAAACCAATGTTATTAATATTATTTACTTTTCTCTGTCAAATTTCTTTGAAGATAT
1183593 AATTATAATCTACACACACATACATATATACTGCATATAAAATCAACCACCAATATAATAAATGT
260 AATTATAATCTACACACACATACATATATACTGCATATAAAATCAACCACCAATATAATAAATGT
1183658 AAAATTAGATTCAATATAATATATATATATATATATATATATATATATATATATATATATATATA
325 AAAATTAGATTCAATATAA-ATATATATATATATATATATATATATATATATATATATATATATA
1183723 TT
389 -T
1183725 TCTAAAATATATCAAGTTTAAGGTTTTTGGACATCGAGTCAAGTTTTAATTTTTAATTTCTAGTA
1 TCTAAAATATATCAAGTTTAAGGTTTTTGGACATCGAGTCAAGTTTTAATTTTTAATTTCTAGTA
* *
1183790 GAAGTTGAAAATTTTAAACTCAAGTCGAGCTTTGATTTTTTTTTTAAACTTGAATCGAACTTCAT
66 GAAGTTGAAAATTTTAAACTCAAGTCAAGCTTTGA--TTTTTTTTAAACTCGAATCGAACTTCAT
* *
1183855 AATTTTAAGCTCGTAAATTTTTGAGTTGAATCAAAATCAACAAAATTCGAACCGGGTTCATTTAC
129 AATTTTAAACTCGTAAATTTTTGAGTTGAATCAAAATCAACAAAATTCGAACCGGGTTCGTTTAC
1183920 AATCCTAATAAAAACCAATGTTATTAATATTATTTACTTTTCTCTGTCAAATTTCTTTGAAGATA
194 AATCCTAATAAAAACCAATGTTATTAATATTATTTACTTTTCTCTGTCAAATTTCTTTGAAGATA
*
1183985 TAATTATAATCTACACAAACATACATATATACTGCATATAAAATCAACCACCAATATAATAAATG
259 TAATTATAATCTACACACACATACATATATACTGCATATAAAATCAACCACCAATATAATAAATG
1184050 TAAAATTAGATTCAATATAAATATATATATATATATATATA
324 TAAAATTAGATTCAATATAAATATATATATATATATATATA
1184091 ATGTAAAAAA
Statistics
Matches: 1828, Mismatches: 11, Indels: 86
0.95 0.01 0.04
Matches are distributed among these distances:
362 141 0.08
363 2 0.00
364 95 0.05
365 86 0.05
366 1 0.00
367 34 0.02
376 34 0.02
378 53 0.03
379 34 0.02
380 97 0.05
381 141 0.08
384 1 0.00
385 132 0.07
386 189 0.10
387 198 0.11
388 331 0.18
389 4 0.00
390 140 0.08
392 21 0.01
393 94 0.05
ACGTcount: A:0.40, C:0.12, G:0.09, T:0.39
Consensus pattern (389 bp):
TCTAAAATATATCAAGTTTAAGGTTTTTGGACATCGAGTCAAGTTTTAATTTTTAATTTCTAGTA
GAAGTTGAAAATTTTAAACTCAAGTCAAGCTTTGATTTTTTTTAAACTCGAATCGAACTTCATAA
TTTTAAACTCGTAAATTTTTGAGTTGAATCAAAATCAACAAAATTCGAACCGGGTTCGTTTACAA
TCCTAATAAAAACCAATGTTATTAATATTATTTACTTTTCTCTGTCAAATTTCTTTGAAGATATA
ATTATAATCTACACACACATACATATATACTGCATATAAAATCAACCACCAATATAATAAATGTA
AAATTAGATTCAATATAAATATATATATATATATATATATATATATATATATATATATATATAT
Found at i:1182605 original size:2 final size:2
Alignment explanation
Indices: 1182543--1182592 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
1182533 ATTAGATTCA
*
1182543 AT AT AA 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
1182585 AT AT AT AT
1 AT AT AT AT
1182593 TTCTAAAATA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1182970 original size:2 final size:2
Alignment explanation
Indices: 1182928--1182958 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1182918 ATTAGATTCA
1182928 AT AT A- 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
1182959 TCTAAAATAT
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:1183349 original size:2 final size:2
Alignment explanation
Indices: 1183293--1183336 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
1183283 ATTAGATTCA
1183293 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
1183335 AT
1 AT
1183337 TTCTAAAATA
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:1183736 original size:2 final size:2
Alignment explanation
Indices: 1183671--1183723 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
1183661 ATTAGATTCA
1183671 AT AT A- 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
1183712 AT AT AT AT AT AT
1 AT AT AT AT AT AT
1183724 TTCTAAAATA
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 49 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1185813 original size:12 final size:12
Alignment explanation
Indices: 1185796--1185826 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
1185786 ATTGAATTTA
1185796 CTTCTTTTAAAT
1 CTTCTTTTAAAT
*
1185808 CTTCTTCTAAAT
1 CTTCTTTTAAAT
1185820 CTTCTTT
1 CTTCTTT
1185827 ACTTTTTAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.19, C:0.23, G:0.00, T:0.58
Consensus pattern (12 bp):
CTTCTTTTAAAT
Found at i:1187944 original size:24 final size:24
Alignment explanation
Indices: 1187917--1187965 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
1187907 TGTGATCTTA
*
1187917 ATGGTGTTAATGGTGGGGCC-GTTG
1 ATGGTGATAATGGT-GGGCCAGTTG
*
1187941 ATGGTGATGATGGTGGGCCAGTTG
1 ATGGTGATAATGGTGGGCCAGTTG
1187965 A
1 A
1187966 AAGTATGACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 5 0.23
24 17 0.77
ACGTcount: A:0.16, C:0.08, G:0.45, T:0.31
Consensus pattern (24 bp):
ATGGTGATAATGGTGGGCCAGTTG
Found at i:1189394 original size:21 final size:21
Alignment explanation
Indices: 1189339--1189397 Score: 75
Period size: 21 Copynumber: 2.8 Consensus size: 21
1189329 CAACAGCATG
*
1189339 CAACAACTTCATCTCAGACTA
1 CAACAACTTTATCTCAGACTA
* *
1189360 CAAC-AGTTTCATCTCAGTCTA
1 CAACAACTTT-ATCTCAGACTA
1189381 CAACAACTTTATCTCAG
1 CAACAACTTTATCTCAG
1189398 CCAGTAACAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
20 3 0.09
21 25 0.78
22 4 0.12
ACGTcount: A:0.34, C:0.31, G:0.07, T:0.29
Consensus pattern (21 bp):
CAACAACTTTATCTCAGACTA
Found at i:1189416 original size:42 final size:42
Alignment explanation
Indices: 1189339--1189418 Score: 99
Period size: 42 Copynumber: 1.9 Consensus size: 42
1189329 CAACAGCATG
* * *
1189339 CAACAACTTCATCTCAGACTACAACAGTTTCATCTCAGTCTA
1 CAACAACTTCATCTCAGACCACAACAATTTAATCTCAGTCTA
* *
1189381 CAACAACTTTATCTCAG-CCAGTAACAATTTAATCTCAG
1 CAACAACTTCATCTCAGACCA-CAACAATTTAATCTCAG
1189419 CCTCTAGGAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
41 2 0.06
42 30 0.94
ACGTcount: A:0.35, C:0.29, G:0.07, T:0.29
Consensus pattern (42 bp):
CAACAACTTCATCTCAGACCACAACAATTTAATCTCAGTCTA
Found at i:1189705 original size:12 final size:12
Alignment explanation
Indices: 1189688--1189712 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1189678 TAATGTATTT
1189688 CATGTGGTGAAA
1 CATGTGGTGAAA
1189700 CATGTGGTGAAA
1 CATGTGGTGAAA
1189712 C
1 C
1189713 TAAAGTATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.12, G:0.32, T:0.24
Consensus pattern (12 bp):
CATGTGGTGAAA
Found at i:1193388 original size:18 final size:18
Alignment explanation
Indices: 1193365--1193431 Score: 116
Period size: 18 Copynumber: 3.7 Consensus size: 18
1193355 ATAACTCTTT
1193365 GATGACGGTGGTGGTGTC
1 GATGACGGTGGTGGTGTC
1193383 GATGACGGTGGTGGTGTC
1 GATGACGGTGGTGGTGTC
1193401 GATGACGGTGGTGGTGTC
1 GATGACGGTGGTGGTGTC
* *
1193419 GTTGAAGGTGGTG
1 GATGACGGTGGTG
1193432 TCGTTGACGT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 47 1.00
ACGTcount: A:0.12, C:0.09, G:0.51, T:0.28
Consensus pattern (18 bp):
GATGACGGTGGTGGTGTC
Found at i:1193394 original size:15 final size:16
Alignment explanation
Indices: 1193374--1193440 Score: 64
Period size: 18 Copynumber: 4.0 Consensus size: 16
1193364 TGATGACGGT
1193374 GGTGGTGTCGATGACGG
1 GGTGGTGTCGATGAC-G
1193391 TGGTGGTGTCGATGACGG
1 -GGTGGTGTCGATGAC-G
* *
1193409 TGGTGGTGTCGTTGA-A
1 -GGTGGTGTCGATGACG
*
1193425 GGTGGTGTCGTTGACG
1 GGTGGTGTCGATGACG
1193441 TGACTTGGAA
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
15 14 0.31
18 31 0.69
ACGTcount: A:0.10, C:0.10, G:0.49, T:0.30
Consensus pattern (16 bp):
GGTGGTGTCGATGACG
Found at i:1197694 original size:64 final size:63
Alignment explanation
Indices: 1197605--1197755 Score: 178
Period size: 64 Copynumber: 2.3 Consensus size: 63
1197595 ATGCACATTC
* * * *
1197605 ATAAGTGCATCGATGCATTCC-TTTAAAAGAAGAACATCGAATGCCTTTGATACATCGATGCATA
1 ATAA-TGCATCGATGCA-TCCTTTTAAAAGAAAAACATCGAATGCATTTGATACACCGATGCACA
* * *
1197669 GATAATGCATCGATGCATCCTTTTAAAATAAAAACATCGAATGCATTTTATGCACCGATGCACA
1 -ATAATGCATCGATGCATCCTTTTAAAAGAAAAACATCGAATGCATTTGATACACCGATGCACA
*
1197733 AGTAGTGCATCGATGCATACCTT
1 A-TAATGCATCGATGCAT-CCTT
1197756 CATTGAAAGA
Statistics
Matches: 75, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
63 4 0.05
64 63 0.84
65 8 0.11
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (63 bp):
ATAATGCATCGATGCATCCTTTTAAAAGAAAAACATCGAATGCATTTGATACACCGATGCACA
Found at i:1198261 original size:17 final size:19
Alignment explanation
Indices: 1198239--1198274 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
1198229 GATTTACATG
1198239 AATACATGT-ATAT-ATAT
1 AATACATGTGATATGATAT
1198256 AATACATGTGATATGATAT
1 AATACATGTGATATGATAT
1198275 GAGATATATG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
18 4 0.24
19 4 0.24
ACGTcount: A:0.44, C:0.06, G:0.11, T:0.39
Consensus pattern (19 bp):
AATACATGTGATATGATAT
Found at i:1198464 original size:31 final size:31
Alignment explanation
Indices: 1198406--1198470 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 31
1198396 AGAGTCGAGG
* *
1198406 GTTTACCTATGTTCTAAGGAACATATGGATA
1 GTTTACCTAGGTTCTAAGGAACATATGGACA
** * *
1198437 GTTTACCTAGGTTCTTCGGGACCTATGGACA
1 GTTTACCTAGGTTCTAAGGAACATATGGACA
1198468 GTT
1 GTT
1198471 ACCGAGGATC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.25, C:0.17, G:0.23, T:0.35
Consensus pattern (31 bp):
GTTTACCTAGGTTCTAAGGAACATATGGACA
Found at i:1198521 original size:29 final size:30
Alignment explanation
Indices: 1198456--1198527 Score: 92
Period size: 29 Copynumber: 2.4 Consensus size: 30
1198446 GGTTCTTCGG
* * *
1198456 GACCTATGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTGTAT
* *
1198486 GACCTCTGGATAGTTACCG-GGGTCTGTGT
1 GACCTCTGGATAGTTACCGAGGATCTGTAT
1198515 GACCTCTGGATAG
1 GACCTCTGGATAG
1198528 GTCCTTCGGG
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
29 20 0.54
30 17 0.46
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGGATCTGTAT
Found at i:1201892 original size:63 final size:64
Alignment explanation
Indices: 1201759--1201905 Score: 192
Period size: 64 Copynumber: 2.3 Consensus size: 64
1201749 CACATTCATA
* * * *
1201759 AGTGCATCGATGCATTCC-TTTAAAAGAAGAACATCGAATGCCTTTGATGCATCGATGCATAGAT
1 AGTGCATCGATGCA-TCCTTTTAAAAGAAAAACATCGAATGCATTTGATGCACCGATGCAAAGAT
* *
1201823 AATGCATCGATGCATCCTTTTAAAATAAAAACATCGAATGCATTT-ATGCACCGATGCACAAG-T
1 AGTGCATCGATGCATCCTTTTAAAAGAAAAACATCGAATGCATTTGATGCACCGATGCA-AAGAT
1201886 AGTGCATCGATGCATACCTT
1 AGTGCATCGATGCAT-CCTT
1201906 CATTGAAAGA
Statistics
Matches: 73, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
63 30 0.41
64 43 0.59
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.28
Consensus pattern (64 bp):
AGTGCATCGATGCATCCTTTTAAAAGAAAAACATCGAATGCATTTGATGCACCGATGCAAAGAT
Found at i:1202596 original size:31 final size:31
Alignment explanation
Indices: 1202558--1202622 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
1202548 AGAGTCGAGG
*
1202558 GTTTACCTATGTTCTAAGGAACATATGGACA
1 GTTTACCTAGGTTCTAAGGAACATATGGACA
** * *
1202589 GTTTACCTAGGTTCTTCGGGACCTATGGACA
1 GTTTACCTAGGTTCTAAGGAACATATGGACA
1202620 GTT
1 GTT
1202623 ACCGAGGATC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.34
Consensus pattern (31 bp):
GTTTACCTAGGTTCTAAGGAACATATGGACA
Found at i:1202642 original size:30 final size:30
Alignment explanation
Indices: 1202581--1202656 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 30
1202571 CTAAGGAACA
* * *
1202581 TATGGACAGTTTACCTAGGTTCTTCGGGACC
1 TATGGACAG-TTACCGAGGATCTTCAGGACC
* *
1202612 TATGGACAGTTACCGAGGATCTTTATGACC
1 TATGGACAGTTACCGAGGATCTTCAGGACC
* *
1202642 TCTGGATAGTTACCG
1 TATGGACAGTTACCG
1202657 GGGTCTGTGT
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
30 29 0.76
31 9 0.24
ACGTcount: A:0.22, C:0.21, G:0.25, T:0.32
Consensus pattern (30 bp):
TATGGACAGTTACCGAGGATCTTCAGGACC
Found at i:1202673 original size:29 final size:30
Alignment explanation
Indices: 1202608--1202679 Score: 92
Period size: 29 Copynumber: 2.4 Consensus size: 30
1202598 GGTTCTTCGG
* * *
1202608 GACCTATGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTGTAT
* *
1202638 GACCTCTGGATAGTTACCG-GGGTCTGTGT
1 GACCTCTGGATAGTTACCGAGGATCTGTAT
1202667 GACCTCTGGATAG
1 GACCTCTGGATAG
1202680 GTCCTTCGGG
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
29 20 0.54
30 17 0.46
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGGATCTGTAT
Found at i:1204845 original size:27 final size:27
Alignment explanation
Indices: 1204810--1204874 Score: 121
Period size: 27 Copynumber: 2.4 Consensus size: 27
1204800 ATACCCAAGC
*
1204810 CATTGTGGCTTCAAAACCATCTCAAAT
1 CATTCTGGCTTCAAAACCATCTCAAAT
1204837 CATTCTGGCTTCAAAACCATCTCAAAT
1 CATTCTGGCTTCAAAACCATCTCAAAT
1204864 CATTCTGGCTT
1 CATTCTGGCTT
1204875 TCTCTCAATA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.29, C:0.28, G:0.11, T:0.32
Consensus pattern (27 bp):
CATTCTGGCTTCAAAACCATCTCAAAT
Found at i:1208117 original size:21 final size:20
Alignment explanation
Indices: 1208090--1208153 Score: 59
Period size: 20 Copynumber: 3.4 Consensus size: 20
1208080 TTTTTCAAAG
1208090 AAACATTTACCAAACTTTGA
1 AAACATTTACCAAACTTTGA
*
1208110 AAACCATTT-TCAAA----G-
1 AAA-CATTTACCAAACTTTGA
1208125 AAACATTTACCAAACTTTGA
1 AAACATTTACCAAACTTTGA
1208145 AAATCATTT
1 AAA-CATTT
1208154 TTCAAAGTTG
Statistics
Matches: 34, Mismatches: 2, Indels: 15
0.67 0.04 0.29
Matches are distributed among these distances:
14 5 0.15
15 7 0.21
16 1 0.03
19 1 0.03
20 10 0.29
21 10 0.29
ACGTcount: A:0.45, C:0.19, G:0.05, T:0.31
Consensus pattern (20 bp):
AAACATTTACCAAACTTTGA
Found at i:1208127 original size:35 final size:36
Alignment explanation
Indices: 1208045--1208160 Score: 173
Period size: 35 Copynumber: 3.2 Consensus size: 36
1208035 CCCATTCCTA
* * *
1208045 TTTTC-AACAAACATCTACCAAACTTTGAAAAACTAT
1 TTTTCAAAGAAACATTTACCAAACTTTG-AAAACCAT
1208081 TTTTCAAAGAAACATTTACCAAACTTTGAAAACCA-
1 TTTTCAAAGAAACATTTACCAAACTTTGAAAACCAT
*
1208116 TTTTCAAAGAAACATTTACCAAACTTTGAAAATCAT
1 TTTTCAAAGAAACATTTACCAAACTTTGAAAACCAT
1208152 TTTTCAAAG
1 TTTTCAAAG
1208161 TTGGTTACCA
Statistics
Matches: 74, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
35 34 0.46
36 20 0.27
37 20 0.27
ACGTcount: A:0.44, C:0.19, G:0.05, T:0.32
Consensus pattern (36 bp):
TTTTCAAAGAAACATTTACCAAACTTTGAAAACCAT
Found at i:1212707 original size:34 final size:36
Alignment explanation
Indices: 1212627--1212717 Score: 125
Period size: 34 Copynumber: 2.6 Consensus size: 36
1212617 ACCCATTCCT
* * *
1212627 ATTTTC-AACAAACATCTACCAAACTTTGAAAATCT
1 ATTTTCAAAGAAACATTTACCAAACTTTGAAAATCC
1212662 ATTTTTCAAAGAAACATTTACCAAACTTTG-AAA-CC
1 A-TTTTCAAAGAAACATTTACCAAACTTTGAAAATCC
1212697 ATTTTCAAAGAAACATTTACC
1 ATTTTCAAAGAAACATTTACC
1212718 TGAAAACCAT
Statistics
Matches: 51, Mismatches: 3, Indels: 5
0.86 0.05 0.08
Matches are distributed among these distances:
34 20 0.39
35 3 0.06
36 8 0.16
37 20 0.39
ACGTcount: A:0.43, C:0.21, G:0.04, T:0.32
Consensus pattern (36 bp):
ATTTTCAAAGAAACATTTACCAAACTTTGAAAATCC
Found at i:1216779 original size:16 final size:17
Alignment explanation
Indices: 1216752--1216784 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
1216742 GTATTGTCGG
1216752 CAAAATTTTACTATTCA
1 CAAAATTTTACTATTCA
1216769 CAAAA-TTTACTATTCA
1 CAAAATTTTACTATTCA
1216785 TATGAATAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.42, C:0.18, G:0.00, T:0.39
Consensus pattern (17 bp):
CAAAATTTTACTATTCA
Found at i:1217223 original size:26 final size:27
Alignment explanation
Indices: 1217191--1217241 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
1217181 CCCATTCCTA
*
1217191 TTTTC-AACAAACATCTATCAAACTAT
1 TTTTCAAACAAACATCTACCAAACTAT
* *
1217217 TTTTCAAAGAAACATTTACCAAACT
1 TTTTCAAACAAACATCTACCAAACT
1217242 TTGAAAACCA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 5 0.24
27 16 0.76
ACGTcount: A:0.43, C:0.22, G:0.02, T:0.33
Consensus pattern (27 bp):
TTTTCAAACAAACATCTACCAAACTAT
Found at i:1217256 original size:35 final size:37
Alignment explanation
Indices: 1217215--1217297 Score: 152
Period size: 35 Copynumber: 2.3 Consensus size: 37
1217205 CTATCAAACT
1217215 ATTTTTCAAAGAAACATTTACCAAACTTTGAAAACC-
1 ATTTTTCAAAGAAACATTTACCAAACTTTGAAAACCA
1217251 A-TTTTCAAAGAAACATTTACCAAACTTTGAAAACCA
1 ATTTTTCAAAGAAACATTTACCAAACTTTGAAAACCA
1217287 ATTTTTCAAAG
1 ATTTTTCAAAG
1217298 TTGGTTACCA
Statistics
Matches: 45, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
35 34 0.76
36 2 0.04
37 9 0.20
ACGTcount: A:0.45, C:0.18, G:0.06, T:0.31
Consensus pattern (37 bp):
ATTTTTCAAAGAAACATTTACCAAACTTTGAAAACCA
Found at i:1217306 original size:35 final size:35
Alignment explanation
Indices: 1217210--1217324 Score: 128
Period size: 35 Copynumber: 3.3 Consensus size: 35
1217200 AACATCTATC
* *
1217210 AAACTATTTTTCAAAGAAACATTTACCAAACTTTGA
1 AAACCATTTTTCAAAG-AACAGTTACCAAACTTTGA
*
1217246 AAACCA-TTTTCAAAGAAACATTTACCAAACTTTGA
1 AAACCATTTTTCAAAG-AACAGTTACCAAACTTTGA
***
1217281 AAACCAATTTTTCAAAG-TTGGTTACCAAAC-TTGA
1 AAACC-ATTTTTCAAAGAACAGTTACCAAACTTTGA
1217315 AAACCATTTT
1 AAACCATTTT
1217325 AATACTTTCA
Statistics
Matches: 72, Mismatches: 5, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
33 5 0.07
34 9 0.12
35 43 0.60
36 6 0.08
37 9 0.12
ACGTcount: A:0.43, C:0.18, G:0.07, T:0.32
Consensus pattern (35 bp):
AAACCATTTTTCAAAGAACAGTTACCAAACTTTGA
Found at i:1219914 original size:13 final size:13
Alignment explanation
Indices: 1219896--1219921 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1219886 GTCCGATTTA
1219896 CCATTCATCAAAC
1 CCATTCATCAAAC
1219909 CCATTCATCAAAC
1 CCATTCATCAAAC
1219922 ATGTATAAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.38, G:0.00, T:0.23
Consensus pattern (13 bp):
CCATTCATCAAAC
Found at i:1222777 original size:6 final size:6
Alignment explanation
Indices: 1222766--1222792 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
1222756 CGGCTACGAG
1222766 TTCCGA TTCCGA TTCCGA TTCCGA TTC
1 TTCCGA TTCCGA TTCCGA TTCCGA TTC
1222793 GGCAGTGGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.33, G:0.15, T:0.37
Consensus pattern (6 bp):
TTCCGA
Found at i:1226078 original size:228 final size:226
Alignment explanation
Indices: 1225500--1226151 Score: 957
Period size: 228 Copynumber: 2.9 Consensus size: 226
1225490 AACCAAATGA
* * *
1225500 AGGGTCGACTCCTT-TGGATGTTGTAATCGGCCAAGGTACGACCGTCCTCGAGCTGTTTTCCGGC
1 AGGGTCGACTCCTTCTGGATGTTGTAGTCGGCCAAGGTACGGCCGTCCTCGAGCTGCTTTCCGGC
* * * *
1225564 GAAGATGAGACGTTGCTGGTCCGGTGGGATCCCTTCCTTGTCTTGGATCTTGGCCTTGACGTTGT
66 GAAGATAAGACGCTGCTGGTCCGGAGGGATTCCTTCCTTGTCTTGGATCTTGGCCTTGACGTTGT
* *
1225629 CGATGGTGTCGGAGCTCTCGACTTCCAAGGTGATTGTCTTGCCCGTCAGGGTTTTCACGAAGA-T
131 CGATGGTGTCGGAGCTCTCGACCTCCAAGGTGATTGTCTTGCCGGTCAGGGTTTTCACGAAGATT
*
1225693 CGCATGCCCCACGAAGACGGAGGACAGGTGG
196 TGCATGCCCCACGAAGACGGAGGACAGGTGG
* * * *
1225724 AGGGTCGACTCCTTCTGGATGTTATAGTCCGCCAAGGTACGGCCGTCCTCGAGTTGCTTCCCGGC
1 AGGGTCGACTCCTTCTGGATGTTGTAGTCGGCCAAGGTACGGCCGTCCTCGAGCTGCTTTCCGGC
* * * * *
1225789 GAAGATCAGCCTCTGCTGGTCTGGGGGGATTCCTTCCTTGTCTTGGATCTTGGCCTTGACGTTGT
66 GAAGATAAGACGCTGCTGGTCCGGAGGGATTCCTTCCTTGTCTTGGATCTTGGCCTTGACGTTGT
* * *
1225854 CGATGGTGTCGGAGCTCTCGACCTCCAAGGTGATGGTTTTGCCGGTAAGGGTTTTCACGAAGATT
131 CGATGGTGTCGGAGCTCTCGACCTCCAAGGTGATTGTCTTGCCGGTCAGGGTTTTCACGAAGATT
1225919 TGCATGCCTCCACGAAGACGGAGGACGAGGTGG
196 TGCATGCC-CCACGAAGACGGAGGAC-AGGTGG
*
1225952 AGGGTTGACTCCTTCTGGATGTTGTAGTCGGCCAAGGTACGGCCGTCCTCGAGCTGCTTTCCGGC
1 AGGGTCGACTCCTTCTGGATGTTGTAGTCGGCCAAGGTACGGCCGTCCTCGAGCTGCTTTCCGGC
* * * * *
1226017 AAAGATAAGACGCTGTTGGTCCGGAGGAATTCCTTCCTTGTCTTGGATCTTCGCCTTGACGTTAT
66 GAAGATAAGACGCTGCTGGTCCGGAGGGATTCCTTCCTTGTCTTGGATCTTGGCCTTGACGTTGT
* * * * * * *
1226082 CAATGGTGTCGGAGCTCTCAACCTCGAGGGTGATTGTCTTGCCGGTCAGGGTCTTAACGAAGATC
131 CGATGGTGTCGGAGCTCTCGACCTCCAAGGTGATTGTCTTGCCGGTCAGGGTTTTCACGAAGATT
1226147 TGCAT
196 TGCAT
1226152 CTTGTTTGGT
Statistics
Matches: 379, Mismatches: 45, Indels: 4
0.89 0.11 0.01
Matches are distributed among these distances:
224 14 0.04
225 159 0.42
226 8 0.02
227 17 0.04
228 181 0.48
ACGTcount: A:0.17, C:0.24, G:0.31, T:0.28
Consensus pattern (226 bp):
AGGGTCGACTCCTTCTGGATGTTGTAGTCGGCCAAGGTACGGCCGTCCTCGAGCTGCTTTCCGGC
GAAGATAAGACGCTGCTGGTCCGGAGGGATTCCTTCCTTGTCTTGGATCTTGGCCTTGACGTTGT
CGATGGTGTCGGAGCTCTCGACCTCCAAGGTGATTGTCTTGCCGGTCAGGGTTTTCACGAAGATT
TGCATGCCCCACGAAGACGGAGGACAGGTGG
Found at i:1226094 original size:453 final size:452
Alignment explanation
Indices: 1225330--1226151 Score: 1101
Period size: 453 Copynumber: 1.8 Consensus size: 452
1225320 TTCCAATTGT
*
1225330 TTCCCAGCGAAAATCAACCTCTGCTGGTCTGGGGAATCCCTTCTTTGTCCTGAATCTTCGCCTTG
1 TTCCCAGCGAAAATCAACCTCTGCTGGTCTGGGGAATCCCTTCCTTGTCCTGAATCTTCGCCTTG
*
1225395 ACATTATCAATCGTATCAGAACTCTCCACCTCCAGAGTAATGGTTTTCCCGGTCAAAGTTTTGAC
66 ACATTATCAATCGTATCAGAACTCTCCACCTCCAGAGTAATGGTTTTCCCGGTCAAAGTTTTCAC
* *
1225460 GAAGATCTGCATCCCGCCACGAAGCCTCAAAACCAAATGAAGGGTCGACTCCTTTGGATGTTGTA
131 GAAGATCTGCATCCCGCCACGAAGACGCAAAACCAAATGAAGGGTCGACTCCTTTGGATGTTGTA
* * * * *
1225525 ATCGGCCAAGGTACGACCGTCCTCGAGCTGTTTTCCGGCGAAGATGAGACGTTGCTGGTCCGGTG
196 ATCGGCCAAGGTACGACCGTCCTCGAGCTGCTTTCCGGCAAAGATAAGACGCTGCTGGTCCGGAG
* * * * * *
1225590 GGATCCCTTCCTTGTCTTGGATCTTGGCCTTGACGTTGTCGATGGTGTCGGAGCTCTCGACTTCC
261 GAATCCCTTCCTTGTCTTGGATCTTCGCCTTGACGTTATCAATGGTGTCGGAGCTCTCAACCTCC
* *
1225655 AAGGTGATTGTCTTGCCCGTCAGGGTTTTCACGAAGATC-GCATGCCCCACGAAGACGGAGGACA
326 AAGGTGATTGTCTTGCCCGTCAGGGTCTTAACGAAGATCTGCATGCCCCACGAAGACGGAGGACA
1225719 GGTGGAGGGTCGACTCCTTCTGGATGTTATAGTCCGCCAAGGTACGGCCGTCCTCGAGTTGC
391 GGTGGAGGGTCGACTCCTTCTGGATGTTATAGTCCGCCAAGGTACGGCCGTCCTCGAGTTGC
* * * * * * * *
1225781 TTCCCGGCGAAGATCAGCCTCTGCTGGTCTGGGGGGATTCCTTCCTTGTCTTGGATCTTGGCCTT
1 TTCCCAGCGAAAATCAACCTCTGCTGGTCT-GGGGAATCCCTTCCTTGTCCTGAATCTTCGCCTT
* * * * * * * * * * *
1225846 GACGTTGTCGATGGTGTCGGAGCTCTCGACCTCCA-AGGTGATGGTTTTGCCGGT-AAGGGTTTT
65 GACATTATCAATCGTATCAGAACTCTCCACCTCCAGA-GTAATGGTTTTCCCGGTCAA-AGTTTT
* * * * ** * ** * *
1225909 CACGAAGATTTGCATGCCTCCACGAAGACGGAGGACGAGGTGGAGGGTTGACTCCTTCTGGATGT
128 CACGAAGATCTGCATCCCGCCACGAAGACGCAAAACCAAATGAAGGGTCGACTCCTT-TGGATGT
* * *
1225974 TGTAGTCGGCCAAGGTACGGCCGTCCTCGAGCTGCTTTCCGGCAAAGATAAGACGCTGTTGGTCC
192 TGTAATCGGCCAAGGTACGACCGTCCTCGAGCTGCTTTCCGGCAAAGATAAGACGCTGCTGGTCC
*
1226039 GGAGGAATTCCTTCCTTGTCTTGGATCTTCGCCTTGACGTTATCAATGGTGTCGGAGCTCTCAAC
257 GGAGGAATCCCTTCCTTGTCTTGGATCTTCGCCTTGACGTTATCAATGGTGTCGGAGCTCTCAAC
* * *
1226104 CTCGAGGGTGATTGTCTTGCCGGTCAGGGTCTTAACGAAGATCTGCAT
322 CTCCAAGGTGATTGTCTTGCCCGTCAGGGTCTTAACGAAGATCTGCAT
1226152 CTTGTTTGGT
Statistics
Matches: 312, Mismatches: 54, Indels: 7
0.84 0.14 0.02
Matches are distributed among these distances:
451 30 0.10
452 118 0.38
453 160 0.51
454 4 0.01
ACGTcount: A:0.18, C:0.25, G:0.28, T:0.28
Consensus pattern (452 bp):
TTCCCAGCGAAAATCAACCTCTGCTGGTCTGGGGAATCCCTTCCTTGTCCTGAATCTTCGCCTTG
ACATTATCAATCGTATCAGAACTCTCCACCTCCAGAGTAATGGTTTTCCCGGTCAAAGTTTTCAC
GAAGATCTGCATCCCGCCACGAAGACGCAAAACCAAATGAAGGGTCGACTCCTTTGGATGTTGTA
ATCGGCCAAGGTACGACCGTCCTCGAGCTGCTTTCCGGCAAAGATAAGACGCTGCTGGTCCGGAG
GAATCCCTTCCTTGTCTTGGATCTTCGCCTTGACGTTATCAATGGTGTCGGAGCTCTCAACCTCC
AAGGTGATTGTCTTGCCCGTCAGGGTCTTAACGAAGATCTGCATGCCCCACGAAGACGGAGGACA
GGTGGAGGGTCGACTCCTTCTGGATGTTATAGTCCGCCAAGGTACGGCCGTCCTCGAGTTGC
Found at i:1227174 original size:27 final size:24
Alignment explanation
Indices: 1227115--1227175 Score: 63
Period size: 23 Copynumber: 2.5 Consensus size: 24
1227105 TCAGTATTAA
1227115 TAAA-ATTTATTTACTAAATTTAT
1 TAAATATTTATTTACTAAATTTAT
* *
1227138 TAGATA-TTATTTATCTGAAATATTTT
1 TAAATATTTATTTA-CT-AAAT-TTAT
1227164 TAAATATTTATT
1 TAAATATTTATT
1227176 ATTGAACAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
23 10 0.33
24 3 0.10
25 4 0.13
26 8 0.27
27 5 0.17
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.54
Consensus pattern (24 bp):
TAAATATTTATTTACTAAATTTAT
Done.