Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000686.1 Hibiscus syriacus cultivar Beakdansim tig00001340_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: 1443669
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 6
Found at i:1257032 original size:81 final size:81
Alignment explanation
Indices: 1256944--1257361 Score: 547
Period size: 81 Copynumber: 5.2 Consensus size: 81
1256934 ATTTAGCCTC
** * * * *
1256944 TCATCTAACTTTCATGATTTACACTTTTCTGCCAAATGCAAAGCTAGGCCATTAATCTTTTACTC
1 TCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCAAAGCTAGGCCATTAATATTTTACTC
*
1257009 AACGGTACTTAACCGT
66 AACGGTACTTAACCAT
* * *
1257025 TCATCTAACTGGCATTATTGACACCTTTCTGCCAAATGCACAA-CAAGGCCATTAATTTTTTACT
1 TCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCA-AAGCTAGGCCATTAATATTTTACT
* * *
1257089 CAACGATACTTAATCGT
65 CAACGGTACTTAACCAT
* *
1257106 TCATCTAACTGGCATAATTGACACCTTTCAT-CCAAATGCACAGCTAGGCCATTAATATTCTA-T
1 TCATCTAACTGGCATAATTGACACCTTTC-TGCCAAATGCAAAGCTAGGCCATTAATATTTTACT
1257169 GCAACGGTACTTAACCAT
65 -CAACGGTACTTAACCAT
* * *
1257187 TCATCTAACTAGCCTAATTGACACCTTTCTACCAAATGCACAA-CTAGGCCATTAATATTTTACT
1 TCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCA-AAGCTAGGCCATTAATATTTTACT
*
1257251 CAACGGTACTTAACCTT
65 CAACGGTACTTAACCAT
* * ** *
1257268 TCATCTAACTGGCATAATTGACACCTTTCTGTCAAATACGCAGCTAGGCCATTAATCTTTTACTC
1 TCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCAAAGCTAGGCCATTAATATTTTACTC
*
1257333 AACGGTACTTAACTAT
66 AACGGTACTTAACCAT
1257349 TCATCTAACTGGC
1 TCATCTAACTGGC
1257362 TGCATAGCTA
Statistics
Matches: 297, Mismatches: 32, Indels: 16
0.86 0.09 0.05
Matches are distributed among these distances:
80 4 0.01
81 288 0.97
82 5 0.02
ACGTcount: A:0.30, C:0.26, G:0.11, T:0.33
Consensus pattern (81 bp):
TCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCAAAGCTAGGCCATTAATATTTTACTC
AACGGTACTTAACCAT
Found at i:1257176 original size:162 final size:162
Alignment explanation
Indices: 1256944--1257361 Score: 606
Period size: 162 Copynumber: 2.6 Consensus size: 162
1256934 ATTTAGCCTC
** * * * *
1256944 TCATCTAACTTTCATGATTTACACTTTTCTGCCAAATGCAAAGCTAGGCCATTAATCTTTTACTC
1 TCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACTC
* * *
1257009 AACGGTACTTAACCGTTCATCTAACTGGCATTATTGACACCTTTCTGCCAAATGCACAACAAGGC
66 AACGGTACTTAACCATTCATCTAACTGGCATAATTGACACCTTTCTACCAAATGCACAACAAGGC
* *
1257074 CATTAATTTTTTACTCAACGATACTTAATCGT
131 CATTAATATTTTACTCAACGATACTTAACCGT
* *
1257106 TCATCTAACTGGCATAATTGACACCTTTCAT-CCAAATGCACAGCTAGGCCATTAATATTCTA-T
1 TCATCTAACTGGCATAATTGACACCTTTC-TGCCAAATGCACAGCTAGGCCATTAATCTTTTACT
* * *
1257169 GCAACGGTACTTAACCATTCATCTAACTAGCCTAATTGACACCTTTCTACCAAATGCACAACTAG
65 -CAACGGTACTTAACCATTCATCTAACTGGCATAATTGACACCTTTCTACCAAATGCACAACAAG
* *
1257234 GCCATTAATATTTTACTCAACGGTACTTAACCTT
129 GCCATTAATATTTTACTCAACGATACTTAACCGT
* * *
1257268 TCATCTAACTGGCATAATTGACACCTTTCTGTCAAATACGCAGCTAGGCCATTAATCTTTTACTC
1 TCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACTC
*
1257333 AACGGTACTTAACTATTCATCTAACTGGC
66 AACGGTACTTAACCATTCATCTAACTGGC
1257362 TGCATAGCTA
Statistics
Matches: 227, Mismatches: 25, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
161 2 0.01
162 223 0.98
163 2 0.01
ACGTcount: A:0.30, C:0.26, G:0.11, T:0.33
Consensus pattern (162 bp):
TCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACTC
AACGGTACTTAACCATTCATCTAACTGGCATAATTGACACCTTTCTACCAAATGCACAACAAGGC
CATTAATATTTTACTCAACGATACTTAACCGT
Found at i:1257480 original size:139 final size:139
Alignment explanation
Indices: 1257230--1257491 Score: 436
Period size: 139 Copynumber: 1.9 Consensus size: 139
1257220 AAATGCACAA
* * *
1257230 CTAGGCCATTAATATTTTACTCAACGGTACTTAACCTTTCATCTAACTGGCATAATTGACACCTT
1 CTAGGCCAATAATATTTTACTCAACGGTACTTAACCGTTCATCTAACTGACATAATTGACACCTT
* * *
1257295 TCTGTCAAATACGCAGCTAGGCCATTAATCTTTTACTCAACGGTACTTAACTATTCATCTAACTG
66 TCTGTCAAATACACAGCTAGGCCATTAATCTTGTACTCAACGGTACTTAACCATTCATCTAACTG
1257360 GCTGCATAG
131 GCTGCATAG
*
1257369 CTAGGCCAATAATCTTTTACTCAACGGTACTTAACCGTTCATCTAACTGACATAATTGACACCTT
1 CTAGGCCAATAATATTTTACTCAACGGTACTTAACCGTTCATCTAACTGACATAATTGACACCTT
*
1257434 TCT-TCCAAATGCACAGCTAGGCCATTAATCTTGTACTCAACGGTACTTAACCATTCAT
66 TCTGT-CAAATACACAGCTAGGCCATTAATCTTGTACTCAACGGTACTTAACCATTCAT
1257492 ATAATTGGAA
Statistics
Matches: 114, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
138 1 0.01
139 113 0.99
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (139 bp):
CTAGGCCAATAATATTTTACTCAACGGTACTTAACCGTTCATCTAACTGACATAATTGACACCTT
TCTGTCAAATACACAGCTAGGCCATTAATCTTGTACTCAACGGTACTTAACCATTCATCTAACTG
GCTGCATAG
Found at i:1257505 original size:81 final size:81
Alignment explanation
Indices: 1257362--1257711 Score: 481
Period size: 81 Copynumber: 4.3 Consensus size: 81
1257352 TCTAACTGGC
* * * *
1257362 TGCATAGCTAGGCCAATAATCTTTTACTCAACGGTACTTAACCGTTCATCTAACTGACATAATTG
1 TGCACAGCTAGGCCATTAATCTTTTACTCAACGATACTTAACCATTCATCTAACTGACATAATTG
*
1257427 ACACCTTTCTTCCAAA
66 ACACATTTCTTCCAAA
* * * *
1257443 TGCACAGCTAGGCCATTAATCTTGTACTCAACGGTACTTAACCATTCATATAATTGGA-ATAATT
1 TGCACAGCTAGGCCATTAATCTTTTACTCAACGATACTTAACCATTCATCTAACT-GACATAATT
*
1257507 GACACATTTCTTCAAAA
65 GACACATTTCTTCCAAA
*
1257524 TGCACAGCTAGGCCATTAATATTTTACTCAACGATACTTAACCATTCATCTAACTGACATAATTG
1 TGCACAGCTAGGCCATTAATCTTTTACTCAACGATACTTAACCATTCATCTAACTGACATAATTG
* *
1257589 ATATC-TTTCTGCCAAA
66 ACA-CATTTCTTCCAAA
* * * * *
1257605 TGCACAGCTAGGCCATTAATCTTTTACTCAACGATACTTAATCGTTTATCTAACTGACTTAGTTG
1 TGCACAGCTAGGCCATTAATCTTTTACTCAACGATACTTAACCATTCATCTAACTGACATAATTG
1257670 ACACATTTCTGT-CAAA
66 ACACATTTCT-TCCAAA
*
1257686 TGCAAAGCTAGGCCATTAATCTTTTA
1 TGCACAGCTAGGCCATTAATCTTTTA
1257712 TTTTACAACA
Statistics
Matches: 239, Mismatches: 25, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
80 3 0.01
81 233 0.97
82 3 0.01
ACGTcount: A:0.32, C:0.23, G:0.12, T:0.33
Consensus pattern (81 bp):
TGCACAGCTAGGCCATTAATCTTTTACTCAACGATACTTAACCATTCATCTAACTGACATAATTG
ACACATTTCTTCCAAA
Found at i:1257534 original size:220 final size:220
Alignment explanation
Indices: 1257142--1257579 Score: 648
Period size: 220 Copynumber: 2.0 Consensus size: 220
1257132 TTCATCCAAA
* *
1257142 TGCACAGCTAGGCCATTAATATTCTATGCAACGGTACTTAACCATTCATCTAACTAGCCTAATTG
1 TGCACAGCTAGGCCAATAATATTCTATGCAACGGTACTTAACCATTCATCTAACTAGCATAATTG
* *
1257207 ACACCTTTCTACCAAATGCACAACTAGGCCATTAATATTTTACTCAACGGTACTTAACCTTTCAT
66 ACACCTTTCTACCAAATGCACAACTAGGCCATTAATATTGTACTCAACGGTACTTAACCATTCAT
* * * * *
1257272 CTAACTGGCATAATTGACACCTTTCTGTCAAATACGCAGCTAGGCCATTAATCTTTTACTCAACG
131 ATAACTGGAATAATTGACACATTTCTGTCAAATACACAGCTAGGCCATTAATATTTTACTCAACG
* *
1257337 GTACTTAACTATTCATCTAACTGGC
196 ATACTTAACCATTCATCTAACTGGC
* * * *
1257362 TGCATAGCTAGGCCAATAATCTTTTACT-CAACGGTACTTAACCGTTCATCTAACT-GACATAAT
1 TGCACAGCTAGGCCAATAATATTCTA-TGCAACGGTACTTAACCATTCATCTAACTAG-CATAAT
* * *
1257425 TGACACCTTTCTTCCAAATGCACAGCTAGGCCATTAATCTTGTACTCAACGGTACTTAACCATTC
64 TGACACCTTTCTACCAAATGCACAACTAGGCCATTAATATTGTACTCAACGGTACTTAACCATTC
* *
1257490 ATATAATTGGAATAATTGACACATTTCT-TCAAAATGCACAGCTAGGCCATTAATATTTTACTCA
129 ATATAACTGGAATAATTGACACATTTCTGTC-AAATACACAGCTAGGCCATTAATATTTTACTCA
1257554 ACGATACTTAACCATTCATCTAACTG
193 ACGATACTTAACCATTCATCTAACTG
1257580 ACATAATTGA
Statistics
Matches: 195, Mismatches: 20, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
219 3 0.02
220 191 0.98
221 1 0.01
ACGTcount: A:0.32, C:0.25, G:0.12, T:0.32
Consensus pattern (220 bp):
TGCACAGCTAGGCCAATAATATTCTATGCAACGGTACTTAACCATTCATCTAACTAGCATAATTG
ACACCTTTCTACCAAATGCACAACTAGGCCATTAATATTGTACTCAACGGTACTTAACCATTCAT
ATAACTGGAATAATTGACACATTTCTGTCAAATACACAGCTAGGCCATTAATATTTTACTCAACG
ATACTTAACCATTCATCTAACTGGC
Found at i:1257660 original size:301 final size:301
Alignment explanation
Indices: 1257070--1257645 Score: 902
Period size: 301 Copynumber: 1.9 Consensus size: 301
1257060 ATGCACAACA
* * * *
1257070 AGGCCATTAATTTTTTACTCAACGATACTTAATCGTTCATCTAACTGGCATAATTGACACCTTTC
1 AGGCCAATAATCTTTTACTCAACGATACTTAACCGTTCATCTAACTGACATAATTGACACCTTTC
* *
1257135 ATCCAAATGCACAGCTAGGCCATTAATATTCTATGCAACGGTACTTAACCATTCATCTAACTAGC
66 ATCCAAATGCACAGCTAGGCCATTAATATTCTATGCAACGGTACTTAACCATTCATATAACTAGA
* * * *
1257200 CTAATTGACACCTTTCTACCAAATGCACAACTAGGCCATTAATATTTTACTCAACGGTACTTAAC
131 ATAATTGACACATTTCTACAAAATGCACAACTAGGCCATTAATATTTTACTCAACGATACTTAAC
* * * *
1257265 CTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATACGCAGCTAGGCCATTAATCTTTTA
196 CATTCATCTAACTGACATAATTGACACCTTTCTGCCAAATACACAGCTAGGCCATTAATCTTTTA
*
1257330 CTCAACGGTACTTAACTATTCATCTAACTGGCTGCATAGCT
261 CTCAACGATACTTAACTATTCATCTAACTGGCTGCATAGCT
*
1257371 AGGCCAATAATCTTTTACTCAACGGTACTTAACCGTTCATCTAACTGACATAATTGACACCTTTC
1 AGGCCAATAATCTTTTACTCAACGATACTTAACCGTTCATCTAACTGACATAATTGACACCTTTC
* * * * *
1257436 TTCCAAATGCACAGCTAGGCCATTAATCTTGTACT-CAACGGTACTTAACCATTCATATAATTGG
66 ATCCAAATGCACAGCTAGGCCATTAATATTCTA-TGCAACGGTACTTAACCATTCATATAACTAG
* *
1257500 AATAATTGACACATTTCTTCAAAATGCACAGCTAGGCCATTAATATTTTACTCAACGATACTTAA
130 AATAATTGACACATTTCTACAAAATGCACAACTAGGCCATTAATATTTTACTCAACGATACTTAA
* * *
1257565 CCATTCATCTAACTGACATAATTGATATCTTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTT
195 CCATTCATCTAACTGACATAATTGACACCTTTCTGCCAAATACACAGCTAGGCCATTAATCTTTT
1257630 ACTCAACGATACTTAA
260 ACTCAACGATACTTAA
1257646 TCGTTTATCT
Statistics
Matches: 248, Mismatches: 26, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
301 247 1.00
302 1 0.00
ACGTcount: A:0.32, C:0.24, G:0.11, T:0.32
Consensus pattern (301 bp):
AGGCCAATAATCTTTTACTCAACGATACTTAACCGTTCATCTAACTGACATAATTGACACCTTTC
ATCCAAATGCACAGCTAGGCCATTAATATTCTATGCAACGGTACTTAACCATTCATATAACTAGA
ATAATTGACACATTTCTACAAAATGCACAACTAGGCCATTAATATTTTACTCAACGATACTTAAC
CATTCATCTAACTGACATAATTGACACCTTTCTGCCAAATACACAGCTAGGCCATTAATCTTTTA
CTCAACGATACTTAACTATTCATCTAACTGGCTGCATAGCT
Found at i:1257697 original size:382 final size:382
Alignment explanation
Indices: 1256980--1257711 Score: 1101
Period size: 382 Copynumber: 1.9 Consensus size: 382
1256970 TTCTGCCAAA
* * *
1256980 TGCAAAGCTAGGCCATTAATCTTTTACTCAACGGTACTTAACCGTTCATCTAACTGGCATTATTG
1 TGCAAAGCTAGGCCAATAATCTTTTACTCAACGGTACTTAACCGTTCATCTAACTGACATAATTG
* * * *
1257045 ACACCTTTCTGCCAAATGCACAACAAGGCCATTAATTTTTTACTCAACGATACTTAATCGTTCAT
66 ACACCTTTCTGCCAAATGCACAACAAGGCCATTAATCTTGTACTCAACGATACTTAACCATTCAT
* * * *
1257110 CTAACTGGCATAATTGACACCTTTCATCCAAATGCACAGCTAGGCCATTAATATTCTATGCAACG
131 ATAACTGGAATAATTGACACATTTCATCAAAATGCACAGCTAGGCCATTAATATTCTATGCAACG
* *
1257175 GTACTTAACCATTCATCTAACTAGCCTAATTGACACCTTTCTACCAAATGCACAACTAGGCCATT
196 ATACTTAACCATTCATCTAACTAGCATAATTGACACCTTTCTACCAAATGCACAACTAGGCCATT
* * *
1257240 AATATTTTACTCAACGGTACTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAAT
261 AATATTTTACTCAACGATACTTAACCTTTCATCTAACTGACATAATTGACACATTTCTGTCAAAT
**
1257305 ACGCAGCTAGGCCATTAATCTTTTACTCAACGGTACTTAACTATTCATCTAACTGGC
326 ACAAAGCTAGGCCATTAATCTTTTACTCAACGGTACTTAACTATTCATCTAACTGGC
*
1257362 TGCATAGCTAGGCCAATAATCTTTTACTCAACGGTACTTAACCGTTCATCTAACTGACATAATTG
1 TGCAAAGCTAGGCCAATAATCTTTTACTCAACGGTACTTAACCGTTCATCTAACTGACATAATTG
* * * *
1257427 ACACCTTTCTTCCAAATGCACAGCTAGGCCATTAATCTTGTACTCAACGGTACTTAACCATTCAT
66 ACACCTTTCTGCCAAATGCACAACAAGGCCATTAATCTTGTACTCAACGATACTTAACCATTCAT
* * *
1257492 ATAATTGGAATAATTGACACATTTCTTCAAAATGCACAGCTAGGCCATTAATATTTTACT-CAAC
131 ATAACTGGAATAATTGACACATTTCATCAAAATGCACAGCTAGGCCATTAATATTCTA-TGCAAC
* * * *
1257556 GATACTTAACCATTCATCTAACT-GACATAATTGATATCTTTCTGCCAAATGCACAGCTAGGCCA
195 GATACTTAACCATTCATCTAACTAG-CATAATTGACACCTTTCTACCAAATGCACAACTAGGCCA
* * * *
1257620 TTAATCTTTTACTCAACGATACTTAATCGTTT-ATCTAACTGACTTAGTTGACACATTTCTGTCA
259 TTAATATTTTACTCAACGATACTTAA-CCTTTCATCTAACTGACATAATTGACACATTTCTGTCA
*
1257684 AATGCAAAGCTAGGCCATTAATCTTTTA
323 AATACAAAGCTAGGCCATTAATCTTTTA
1257712 TTTTACAACA
Statistics
Matches: 312, Mismatches: 35, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
381 1 0.00
382 306 0.98
383 5 0.02
ACGTcount: A:0.31, C:0.24, G:0.12, T:0.33
Consensus pattern (382 bp):
TGCAAAGCTAGGCCAATAATCTTTTACTCAACGGTACTTAACCGTTCATCTAACTGACATAATTG
ACACCTTTCTGCCAAATGCACAACAAGGCCATTAATCTTGTACTCAACGATACTTAACCATTCAT
ATAACTGGAATAATTGACACATTTCATCAAAATGCACAGCTAGGCCATTAATATTCTATGCAACG
ATACTTAACCATTCATCTAACTAGCATAATTGACACCTTTCTACCAAATGCACAACTAGGCCATT
AATATTTTACTCAACGATACTTAACCTTTCATCTAACTGACATAATTGACACATTTCTGTCAAAT
ACAAAGCTAGGCCATTAATCTTTTACTCAACGGTACTTAACTATTCATCTAACTGGC
Found at i:1258394 original size:19 final size:19
Alignment explanation
Indices: 1258370--1258417 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
1258360 TCAATGTTAT
*
1258370 TGATACCATCCTCATGGTA
1 TGATACCACCCTCATGGTA
*
1258389 TGATACTC-CCCTCTTGGTA
1 TGATAC-CACCCTCATGGTA
1258408 TCGATACCAC
1 T-GATACCAC
1258418 TTGAATCGGT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
19 17 0.71
20 7 0.29
ACGTcount: A:0.23, C:0.31, G:0.15, T:0.31
Consensus pattern (19 bp):
TGATACCACCCTCATGGTA
Found at i:1258433 original size:15 final size:15
Alignment explanation
Indices: 1258407--1258445 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
1258397 CCCTCTTGGT
*
1258407 ATCGATACCACTTGA
1 ATCGATATCACTTGA
*
1258422 ATCGGTATCACTTGA
1 ATCGATATCACTTGA
1258437 ATCGATATC
1 ATCGATATC
1258446 GATACTACTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (15 bp):
ATCGATATCACTTGA
Found at i:1267215 original size:22 final size:22
Alignment explanation
Indices: 1267176--1267222 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 22
1267166 TTAAAAATGT
1267176 AACCATTGGAATAAGGTTTTAGA
1 AACCATTGGAATAAGG-TTTAGA
* *
1267199 AACCA-TGTAATAGGGTTTAGA
1 AACCATTGGAATAAGGTTTAGA
1267220 AAC
1 AAC
1267223 TAGTGGTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 9 0.41
22 8 0.36
23 5 0.23
ACGTcount: A:0.40, C:0.11, G:0.21, T:0.28
Consensus pattern (22 bp):
AACCATTGGAATAAGGTTTAGA
Found at i:1267259 original size:20 final size:20
Alignment explanation
Indices: 1267234--1267274 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
1267224 AGTGGTTTTA
1267234 AAACCAGTCAAGGGGTCTTG
1 AAACCAGTCAAGGGGTCTTG
*
1267254 AAACCAGTCAAGGGGTTTTG
1 AAACCAGTCAAGGGGTCTTG
1267274 A
1 A
1267275 GTTTCTAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.32, C:0.17, G:0.29, T:0.22
Consensus pattern (20 bp):
AAACCAGTCAAGGGGTCTTG
Found at i:1270608 original size:20 final size:20
Alignment explanation
Indices: 1270570--1270609 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
1270560 GCTTAAAATC
***
1270570 ATTTTTCAAAATTTTATTTT
1 ATTTTTCAAAATCAAATTTT
1270590 ATTTTTCAAAATCAAATTTT
1 ATTTTTCAAAATCAAATTTT
1270610 GCTTTCAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.35, C:0.07, G:0.00, T:0.57
Consensus pattern (20 bp):
ATTTTTCAAAATCAAATTTT
Found at i:1282985 original size:11 final size:12
Alignment explanation
Indices: 1282964--1283035 Score: 64
Period size: 11 Copynumber: 6.2 Consensus size: 12
1282954 TTTATAAGTT
*
1282964 GGTGATAATATA
1 GGTGATGATATA
1282976 GGT-ATGATAT-
1 GGTGATGATATA
1282986 GGTGATGATATA
1 GGTGATGATATA
*
1282998 GGCG-TGATA-A
1 GGTGATGATATA
1283008 TGGTGATGGACTAT-
1 -GGTGAT-GA-TATA
1283022 GGTGATGATATA
1 GGTGATGATATA
1283034 GG
1 GG
1283036 CGTGATAATG
Statistics
Matches: 49, Mismatches: 3, Indels: 16
0.72 0.04 0.24
Matches are distributed among these distances:
10 4 0.08
11 24 0.49
12 11 0.22
13 8 0.16
14 2 0.04
ACGTcount: A:0.31, C:0.03, G:0.35, T:0.32
Consensus pattern (12 bp):
GGTGATGATATA
Found at i:1283005 original size:36 final size:38
Alignment explanation
Indices: 1282965--1283054 Score: 122
Period size: 36 Copynumber: 2.5 Consensus size: 38
1282955 TTATAAGTTG
1282965 GTGATAATATAGGT-AT-GA-TATGGTGATGATATAGGC
1 GTGATAATAT-GGTGATGGACTATGGTGATGATATAGGC
1283001 GTGAT-A-ATGGTGATGGACTATGGTGATGATATAGGC
1 GTGATAATATGGTGATGGACTATGGTGATGATATAGGC
1283037 GTGAT-A-ATGGTGATGGAC
1 GTGATAATATGGTGATGGAC
1283055 AGATTGTATC
Statistics
Matches: 51, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
33 3 0.06
34 4 0.08
35 3 0.06
36 41 0.80
ACGTcount: A:0.30, C:0.04, G:0.34, T:0.31
Consensus pattern (38 bp):
GTGATAATATGGTGATGGACTATGGTGATGATATAGGC
Found at i:1286678 original size:21 final size:20
Alignment explanation
Indices: 1286648--1286691 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
1286638 ATGTAGGAAT
*
1286648 CTTTTTC-T-TTTCTTTTTG
1 CTTTTTCTTCTTTCTTGTTG
*
1286666 TTTTTTCTTCTTTCTTGTTG
1 CTTTTTCTTCTTTCTTGTTG
1286686 CTTTTT
1 CTTTTT
1286692 GTTTTAGAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 6 0.29
19 1 0.05
20 14 0.67
ACGTcount: A:0.00, C:0.16, G:0.07, T:0.77
Consensus pattern (20 bp):
CTTTTTCTTCTTTCTTGTTG
Found at i:1286689 original size:27 final size:24
Alignment explanation
Indices: 1286647--1286696 Score: 73
Period size: 27 Copynumber: 2.0 Consensus size: 24
1286637 GATGTAGGAA
1286647 TCTTTTTCTTTTCTTTTTGTTTTT
1 TCTTTTTCTTTTCTTTTTGTTTTT
1286671 TCTTCTTTCTTGTTGCTTTTTGTTTT
1 TCTT-TTTCTT-TT-CTTTTTGTTTT
1286697 AGAACTTTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 4 0.17
25 6 0.26
26 2 0.09
27 11 0.48
ACGTcount: A:0.00, C:0.14, G:0.08, T:0.78
Consensus pattern (24 bp):
TCTTTTTCTTTTCTTTTTGTTTTT
Found at i:1287134 original size:36 final size:36
Alignment explanation
Indices: 1287061--1287165 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
1287051 ATTTATAAGT
*
1287061 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATAATATAGGCGTGATAATGGTGATGGACTA
*
1287096 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATAATATAGGCGTGATAATGGTGATGGACTA
*
1287132 TGGTGATAATATAGGCGTGATAATGGTAATGGAC
1 TGGTGATAATATAGGCGTGATAATGGTGATGGAC
1287166 AGATTGTATC
Statistics
Matches: 65, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
35 20 0.31
36 45 0.69
ACGTcount: A:0.30, C:0.05, G:0.34, T:0.30
Consensus pattern (36 bp):
TGGTGATAATATAGGCGTGATAATGGTGATGGACTA
Found at i:1287136 original size:13 final size:11
Alignment explanation
Indices: 1287078--1287143 Score: 53
Period size: 13 Copynumber: 5.5 Consensus size: 11
1287068 AATATAGGCG
1287078 TGATATGGTGA
1 TGATATGGTGA
1287089 TGGAATATGGTGA
1 T-G-ATATGGTGA
*
1287102 TGATATAGGCG-
1 TGATAT-GGTGA
1287113 TGATAATGGTGA
1 TGAT-ATGGTGA
1287125 TGGACTATGGTGA
1 T-GA-TATGGTGA
*
1287138 TAATAT
1 TGATAT
1287144 AGGCGTGATA
Statistics
Matches: 45, Mismatches: 3, Indels: 14
0.73 0.05 0.23
Matches are distributed among these distances:
11 15 0.33
12 9 0.20
13 20 0.44
14 1 0.02
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.33
Consensus pattern (11 bp):
TGATATGGTGA
Found at i:1291007 original size:15 final size:12
Alignment explanation
Indices: 1290973--1291004 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
1290963 ATTATACTAT
1290973 TGTTGTTGGTAG
1 TGTTGTTGGTAG
1290985 TGTTGTTGGTAG
1 TGTTGTTGGTAG
*
1290997 TGATGTTG
1 TGTTGTTG
1291005 TTGAAGATTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.09, C:0.00, G:0.41, T:0.50
Consensus pattern (12 bp):
TGTTGTTGGTAG
Found at i:1297385 original size:2 final size:2
Alignment explanation
Indices: 1297378--1297412 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1297368 AAAACAATTC
1297378 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1297413 ATTTTCTTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1300353 original size:29 final size:29
Alignment explanation
Indices: 1300289--1300344 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
1300279 CAATAGACTG
*
1300289 AAATAAATACAACATATAAATTAGAAACC
1 AAATAAATACAACATACAAATTAGAAACC
*
1300318 AAATAAATACAAGATACAAATTAGAAA
1 AAATAAATACAACATACAAATTAGAAA
1300345 TCGATTAAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.64, C:0.11, G:0.05, T:0.20
Consensus pattern (29 bp):
AAATAAATACAACATACAAATTAGAAACC
Found at i:1301602 original size:19 final size:19
Alignment explanation
Indices: 1301578--1301615 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
1301568 CCATTAAAAT
1301578 TGATTACAAAAGCTACTAC
1 TGATTACAAAAGCTACTAC
1301597 TGATTACAAAAGCTACTAC
1 TGATTACAAAAGCTACTAC
1301616 CATGAGTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.21, G:0.11, T:0.26
Consensus pattern (19 bp):
TGATTACAAAAGCTACTAC
Found at i:1301829 original size:32 final size:32
Alignment explanation
Indices: 1301774--1301853 Score: 81
Period size: 32 Copynumber: 2.5 Consensus size: 32
1301764 CGAAACTCGA
* * * *
1301774 AAGGGGAAAATCGGTCGTAGAAGTCACTAGGG
1 AAGGGGAAGATCGGCCGGAGAAGTCACAAGGG
* **
1301806 AAGGGGAAGATCGGCCGGCGAAGTGGCAAGGG
1 AAGGGGAAGATCGGCCGGAGAAGTCACAAGGG
*
1301838 AA-AGGAAGATCGGCCG
1 AAGGGGAAGATCGGCCG
1301854 AGGAAGTGAA
Statistics
Matches: 40, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
31 13 0.32
32 27 0.68
ACGTcount: A:0.33, C:0.15, G:0.42, T:0.10
Consensus pattern (32 bp):
AAGGGGAAGATCGGCCGGAGAAGTCACAAGGG
Found at i:1302019 original size:2 final size:2
Alignment explanation
Indices: 1302012--1302036 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1302002 AAATTTATTA
1302012 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1302037 ATTATTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1302506 original size:2 final size:2
Alignment explanation
Indices: 1302499--1302527 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1302489 AATTGATAGA
1302499 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
1302528 TGATATAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1306714 original size:123 final size:123
Alignment explanation
Indices: 1306559--1306809 Score: 484
Period size: 123 Copynumber: 2.0 Consensus size: 123
1306549 ACGAGCCAGC
1306559 TCTTCAACTCGTTTGAGATCATTTATGCATGCTTTGTTTCTGAGAAAATGCATCTTAGAACTCTT
1 TCTTCAACTCGTTTGAGATCATTTATGCATGCTTTGTTTCTGAGAAAATGCATCTTAGAACTCTT
1306624 TCAATATTTCTTATATTAGCATTACTCAAATGGTCTGCCATTAAGATTGAAGAAAGCT
66 TCAATATTTCTTATATTAGCATTACTCAAATGGTCTGCCATTAAGATTGAAGAAAGCT
1306682 TCTTCAACTCGTTTGAGATCATTTATGCATGCTTTGTTTCTGAGAAAATGCATCTTAGAACTCTT
1 TCTTCAACTCGTTTGAGATCATTTATGCATGCTTTGTTTCTGAGAAAATGCATCTTAGAACTCTT
* *
1306747 TCAATATTTCTTATATTAGCATTACTCAAATGGTCTGCCTTTAAGATTGAAGAATGCT
66 TCAATATTTCTTATATTAGCATTACTCAAATGGTCTGCCATTAAGATTGAAGAAAGCT
1306805 TCTTC
1 TCTTC
1306810 TTTTTACTGA
Statistics
Matches: 126, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
123 126 1.00
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.40
Consensus pattern (123 bp):
TCTTCAACTCGTTTGAGATCATTTATGCATGCTTTGTTTCTGAGAAAATGCATCTTAGAACTCTT
TCAATATTTCTTATATTAGCATTACTCAAATGGTCTGCCATTAAGATTGAAGAAAGCT
Found at i:1311409 original size:2 final size:2
Alignment explanation
Indices: 1311404--1311446 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
1311394 TGTGCGTGTG
* *
1311404 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1311446 T
1 T
1311447 GGATTCTGTT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1312812 original size:82 final size:82
Alignment explanation
Indices: 1312698--1312870 Score: 294
Period size: 82 Copynumber: 2.1 Consensus size: 82
1312688 CCGGAAAAAG
*
1312698 ATTATAAAAATAATGCAATTAATATTTTATTTTAAACAATTTACTT-TTAAATCTTTAATTAATT
1 ATTATAAAAATAATGCAATTAATATTTTATTTTAAACAATTTACTTATAAAAT-TTTAATTAATT
*
1312762 TTTAATTATACGTTAATT
65 TATAATTATACGTTAATT
*
1312780 ATTATAAAAATAATGTAATTAATATTTTATTTTAAACAATTTACTTATAAAATTTTAATTAATTT
1 ATTATAAAAATAATGCAATTAATATTTTATTTTAAACAATTTACTTATAAAATTTTAATTAATTT
1312845 ATAATTATACGTTAATT
66 ATAATTATACGTTAATT
*
1312862 ATTTTAAAA
1 ATTATAAAA
1312871 TTTTAAATTT
Statistics
Matches: 86, Mismatches: 4, Indels: 2
0.93 0.04 0.02
Matches are distributed among these distances:
82 81 0.94
83 5 0.06
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.49
Consensus pattern (82 bp):
ATTATAAAAATAATGCAATTAATATTTTATTTTAAACAATTTACTTATAAAATTTTAATTAATTT
ATAATTATACGTTAATT
Found at i:1317956 original size:21 final size:21
Alignment explanation
Indices: 1317932--1317993 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 21
1317922 TGTAGTTAGT
*
1317932 AAAGCTGTTAGGCTATTAAGC
1 AAAGCTGTTAGGCAATTAAGC
* *
1317953 AAAGTTGTTAGAGCAATTATGC
1 AAAGCTGTTAG-GCAATTAAGC
*
1317975 -AGGCTGTTAGGCAATTAAG
1 AAAGCTGTTAGGCAATTAAG
1317994 AGCTTGGTGC
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
20 8 0.24
21 18 0.53
22 8 0.24
ACGTcount: A:0.34, C:0.11, G:0.26, T:0.29
Consensus pattern (21 bp):
AAAGCTGTTAGGCAATTAAGC
Found at i:1327283 original size:237 final size:237
Alignment explanation
Indices: 1326846--1327491 Score: 931
Period size: 237 Copynumber: 2.7 Consensus size: 237
1326836 AGTGATTTTC
** *
1326846 GAAAAATGAGAAAATGA-TTTCGAAAGTTTATCATTTAATTGTTTTTTGAAAATGAAATTTTTGA
1 GAAAAATGAGAAAGCGATTTTC-AAAGTTTCTCATTTAA-TGTTTTTTGAAAATGAAATTTTTGA
* *
1326910 AAAGTAAGAAAGCAATTTCCAAAGTTTCTTACTTAGTAAGTCCTTCGGGCCATCAGTAAGTCTTT
64 AAAGTAAGAAAGCAATTTCCAAAGTTTCTTACTTAGTAAGACCTTCGGGCCATCAATAAGTCTTT
** * *
1326975 CGAGCATGATGATTAAATAATTCGGGTCATCTATAAGTCTTTCGAGAAAGATGATAAGTCCATTG
129 CGAGCATGATGATTAAATCCTTCGGGTTATCTGTAAGTCTTTCGAGAAAGATGATAAGTCCATTG
* * *
1327040 GGCCATCCATAAGACCTTCGGGTAGGATGTTTTCATATGAATTT
194 GGCCATCCATAAGACCTTAGGGCAGGATGTTTTCAAATGAATTT
* *
1327084 G-AAAATTAGAAAGCGATTTTCAAAGTTTCTCATTTAATGTTTTTTGAAAAAAT-AAATATTTGA
1 GAAAAATGAGAAAGCGATTTTCAAAGTTTCTCATTTAATGTTTTTTG--AAAATGAAATTTTTGA
* * * *
1327147 AAAGTAAGAAAACAATTTCCAAAGGTTCTTACTTGGTAAGACCTTCGGGCTATCAATAAGTCTTT
64 AAAGTAAGAAAGCAATTTCCAAAGTTTCTTACTTAGTAAGACCTTCGGGCCATCAATAAGTCTTT
* * *
1327212 CGAGCATGATAATTGAATCCTTCGGGTTATCTGTAAGTCTTTCGAGCAAGATGATAAGT-CATTC
129 CGAGCATGATGATTAAATCCTTCGGGTTATCTGTAAGTCTTTCGAGAAAGATGATAAGTCCATT-
*
1327276 GGGCCATCCATAAGACCTTATGGCAGGATGTTTTCAAATGAATTT
193 GGGCCATCCATAAGACCTTAGGGCAGGATGTTTTCAAATGAATTT
** * *
1327321 GAAAAATGAGAAATTGATTTTCAAAGTTTCTCATTTAATGTTTTTTTAAGATGAAATTTTTGAAA
1 GAAAAATGAGAAAGCGATTTTCAAAGTTTCTCATTTAATGTTTTTTGAAAATGAAATTTTTGAAA
** * *
1327386 AGTAAGAAAGTGATTTCCAAAGTTTCTTACTTAGTAAGACTTTCAGGCCATCAATAAGTCTTTCG
66 AGTAAGAAAGCAATTTCCAAAGTTTCTTACTTAGTAAGACCTTCGGGCCATCAATAAGTCTTTCG
* *
1327451 AGCATGATGATTAAATCCTTCGGGTTATCTGTTAGCCTTTC
131 AGCATGATGATTAAATCCTTCGGGTTATCTGTAAGTCTTTC
1327492 AAACATGATG
Statistics
Matches: 362, Mismatches: 40, Indels: 13
0.87 0.10 0.03
Matches are distributed among these distances:
236 17 0.05
237 294 0.81
238 51 0.14
ACGTcount: A:0.33, C:0.13, G:0.18, T:0.35
Consensus pattern (237 bp):
GAAAAATGAGAAAGCGATTTTCAAAGTTTCTCATTTAATGTTTTTTGAAAATGAAATTTTTGAAA
AGTAAGAAAGCAATTTCCAAAGTTTCTTACTTAGTAAGACCTTCGGGCCATCAATAAGTCTTTCG
AGCATGATGATTAAATCCTTCGGGTTATCTGTAAGTCTTTCGAGAAAGATGATAAGTCCATTGGG
CCATCCATAAGACCTTAGGGCAGGATGTTTTCAAATGAATTT
Found at i:1327508 original size:42 final size:42
Alignment explanation
Indices: 1327453--1327571 Score: 145
Period size: 42 Copynumber: 2.9 Consensus size: 42
1327443 GTCTTTCGAG
* *
1327453 CATGATGATTAAATCCTTCGGGTTATCTGTTAGCCTTTCAAA
1 CATGATGAGTAAATCCTTCGGGTTATCTGTAAGCCTTTCAAA
* *
1327495 CATGATGAGTAAATCCTTCGGGTTATCTGTAAGCCTTTCGAG
1 CATGATGAGTAAATCCTTCGGGTTATCTGTAAGCCTTTCAAA
* * *
1327537 CAAGATGA-TAAGTTC-TCTGGGTTATCT-TAAGCCTT
1 CATGATGAGTAAATCCTTC-GGGTTATCTGTAAGCCTT
1327572 CACGGAAGAG
Statistics
Matches: 69, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
40 10 0.14
41 14 0.20
42 45 0.65
ACGTcount: A:0.25, C:0.18, G:0.20, T:0.36
Consensus pattern (42 bp):
CATGATGAGTAAATCCTTCGGGTTATCTGTAAGCCTTTCAAA
Found at i:1327607 original size:37 final size:37
Alignment explanation
Indices: 1327563--1327671 Score: 173
Period size: 37 Copynumber: 2.9 Consensus size: 37
1327553 CTGGGTTATC
1327563 TTAAGCCTTCACGGAAGAGTAGTGAAGCAAATCAATT
1 TTAAGCCTTCACGGAAGAGTAGTGAAGCAAATCAATT
* * * *
1327600 TTAAGCCTTCACGAAACAGCAGTGAAGCAAATAAATT
1 TTAAGCCTTCACGGAAGAGTAGTGAAGCAAATCAATT
*
1327637 TTAAGCCTTCACAGAAGAGTAGTGAAGCAAATCAA
1 TTAAGCCTTCACGGAAGAGTAGTGAAGCAAATCAA
1327672 GATCGAGTAT
Statistics
Matches: 63, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 63 1.00
ACGTcount: A:0.41, C:0.17, G:0.19, T:0.22
Consensus pattern (37 bp):
TTAAGCCTTCACGGAAGAGTAGTGAAGCAAATCAATT
Found at i:1331119 original size:17 final size:16
Alignment explanation
Indices: 1331076--1331119 Score: 52
Period size: 18 Copynumber: 2.6 Consensus size: 16
1331066 TCATAATTAA
1331076 CTCTTTAATTTCCTTT
1 CTCTTTAATTTCCTTT
*
1331092 TTCCGTTTAATTTCCTTAT
1 CT-C-TTTAATTTCCTT-T
1331111 CTCTTTAAT
1 CTCTTTAAT
1331120 CCACCATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
16 1 0.04
17 7 0.30
18 13 0.57
19 2 0.09
ACGTcount: A:0.16, C:0.23, G:0.02, T:0.59
Consensus pattern (16 bp):
CTCTTTAATTTCCTTT
Found at i:1333120 original size:18 final size:17
Alignment explanation
Indices: 1333097--1333135 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 17
1333087 TATATATATT
*
1333097 ATTATCCTCTTCCTTATC
1 ATTATCCTCTT-ATTATC
1333115 ATTATCCTCTTATTATC
1 ATTATCCTCTTATTATC
1333132 ATTA
1 ATTA
1333136 ATACCTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.23, C:0.26, G:0.00, T:0.51
Consensus pattern (17 bp):
ATTATCCTCTTATTATC
Found at i:1333497 original size:31 final size:31
Alignment explanation
Indices: 1333449--1333573 Score: 169
Period size: 31 Copynumber: 4.0 Consensus size: 31
1333439 CCCGAAGGAC
* * * *
1333449 CAGTCCATAGGTTCCGAAGAACCTAGGTAAT
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
* *
1333480 TAGTCCATGTGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1333511 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
* * *
1333542 CATTACATATGTCCCGAAGAATATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1333573 C
1 C
1333574 CCTCGACCCT
Statistics
Matches: 83, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 83 1.00
ACGTcount: A:0.37, C:0.21, G:0.20, T:0.22
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:1342723 original size:39 final size:39
Alignment explanation
Indices: 1342664--1342741 Score: 120
Period size: 39 Copynumber: 2.0 Consensus size: 39
1342654 AGATGCAAGA
* *
1342664 GAAGTTTTGCCAGAGAAACAAGTAGAACAAGTGGAAAAT
1 GAAGTTTTGCAAGAGAAACAAGTAGAACAAGAGGAAAAT
* *
1342703 GAAGTTTTGCAAGAGCAACAAGTAGAGCAAGAGGAAAAT
1 GAAGTTTTGCAAGAGAAACAAGTAGAACAAGAGGAAAAT
1342742 CATATTGATA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.46, C:0.10, G:0.27, T:0.17
Consensus pattern (39 bp):
GAAGTTTTGCAAGAGAAACAAGTAGAACAAGAGGAAAAT
Found at i:1343020 original size:24 final size:22
Alignment explanation
Indices: 1342988--1343033 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
1342978 TGAAGTTCGA
*
1342988 AAGAATGTGCCATTTGGAGATCC
1 AAGAATGTG-AATTTGGAGATCC
*
1343011 AAGAACTGTGAATTTTGAGATCC
1 AAGAA-TGTGAATTTGGAGATCC
1343034 CAAGTTCAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 16 0.80
24 4 0.20
ACGTcount: A:0.33, C:0.15, G:0.24, T:0.28
Consensus pattern (22 bp):
AAGAATGTGAATTTGGAGATCC
Found at i:1346211 original size:23 final size:22
Alignment explanation
Indices: 1346168--1346219 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
1346158 TTTATAGGAG
* *
1346168 TTAAATTATAAACTAAAAAAAT
1 TTAAATTAAAAACTAAAAAAAC
**
1346190 TTAAATTACAAAACTAGTAAAAC
1 TTAAATTA-AAAACTAAAAAAAC
1346213 TTAAATT
1 TTAAATT
1346220 TTGATATTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
22 8 0.32
23 17 0.68
ACGTcount: A:0.58, C:0.08, G:0.02, T:0.33
Consensus pattern (22 bp):
TTAAATTAAAAACTAAAAAAAC
Found at i:1347304 original size:24 final size:22
Alignment explanation
Indices: 1347277--1347324 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
1347267 TAGTTTCAAA
1347277 AATATATAACATATATAGTTTTTG
1 AATATAT-ACA-ATATAGTTTTTG
*
1347301 AATATATATAATATAGTTTTTG
1 AATATATACAATATAGTTTTTG
1347323 AA
1 AA
1347325 AACACGATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 14 0.61
23 2 0.09
24 7 0.30
ACGTcount: A:0.44, C:0.02, G:0.08, T:0.46
Consensus pattern (22 bp):
AATATATACAATATAGTTTTTG
Found at i:1347418 original size:90 final size:89
Alignment explanation
Indices: 1347302--1347464 Score: 247
Period size: 90 Copynumber: 1.8 Consensus size: 89
1347292 TAGTTTTTGA
* * *
1347302 ATATATATAATATAGTTTTTGAAAACACGA-TTTTGAAAACGTATAATATATAGTTTTCTTAAAA
1 ATATATATAATAAAGTATTTGAAAACA-GATTTTTGAAAACATATAATATATAGTTTT-TTAAAA
*
1347366 AATTGTTTTTTTGAAAATGTATATAT
64 AATGGTTTTTTTGAAAATGTATATAT
* *
1347392 ATATTTATAATAAAGTATTTGAAAACATATTTTTGAAAACATATAATATATAGTTTTTTAAAAAA
1 ATATATATAATAAAGTATTTGAAAACAGATTTTTGAAAACATATAATATATAGTTTTTTAAAAAA
1347457 TGGTTTTT
66 TGGTTTTT
1347465 AAAAACGATA
Statistics
Matches: 66, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
89 16 0.24
90 50 0.76
ACGTcount: A:0.42, C:0.04, G:0.09, T:0.45
Consensus pattern (89 bp):
ATATATATAATAAAGTATTTGAAAACAGATTTTTGAAAACATATAATATATAGTTTTTTAAAAAA
TGGTTTTTTTGAAAATGTATATAT
Found at i:1347426 original size:14 final size:14
Alignment explanation
Indices: 1347409--1347435 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1347399 TAATAAAGTA
1347409 TTTGAAAACATATT
1 TTTGAAAACATATT
1347423 TTTGAAAACATAT
1 TTTGAAAACATAT
1347436 AATATATAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.41
Consensus pattern (14 bp):
TTTGAAAACATATT
Found at i:1347481 original size:38 final size:37
Alignment explanation
Indices: 1347422--1347529 Score: 123
Period size: 38 Copynumber: 2.9 Consensus size: 37
1347412 GAAAACATAT
*
1347422 TTTTGAAAACATATAATATATAGTTTTTTAAAAAATGG
1 TTTTGAAAA-ACATAATATATAGTTTTTTAAAAAATGG
* *
1347460 TTTTTAAAAACGATAATATATAGTTTTTT--TAAATGG
1 TTTTGAAAAAC-ATAATATATAGTTTTTTAAAAAATGG
*
1347496 TTTTGGAAAACATATATAATATAG-TTTTTAAAAA
1 TTTTGAAAAACATA-AT-ATATAGTTTTTTAAAAA
1347530 CATATTGTTA
Statistics
Matches: 59, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
35 3 0.05
36 22 0.37
37 7 0.12
38 27 0.46
ACGTcount: A:0.44, C:0.03, G:0.10, T:0.44
Consensus pattern (37 bp):
TTTTGAAAAACATAATATATAGTTTTTTAAAAAATGG
Found at i:1347529 original size:24 final size:24
Alignment explanation
Indices: 1347502--1347585 Score: 89
Period size: 24 Copynumber: 3.4 Consensus size: 24
1347492 ATGGTTTTGG
1347502 AAAACATATATAATATAGTTTTTA
1 AAAACATATATAATATAGTTTTTA
* * * *
1347526 AAAACATATTGTTATATA-ATTTTG
1 AAAACATA-TATAATATAGTTTTTA
1347550 AAAACATATAATATATATAGTTTTTGA
1 AAAACATAT-ATA-ATATAGTTTTT-A
1347577 AAAACATAT
1 AAAACATAT
1347586 GTTATATATA
Statistics
Matches: 47, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
23 1 0.02
24 21 0.45
25 12 0.26
26 4 0.09
27 9 0.19
ACGTcount: A:0.49, C:0.05, G:0.06, T:0.40
Consensus pattern (24 bp):
AAAACATATATAATATAGTTTTTA
Found at i:1347542 original size:25 final size:25
Alignment explanation
Indices: 1347514--1347593 Score: 92
Period size: 25 Copynumber: 3.2 Consensus size: 25
1347504 AACATATATA
1347514 ATATAGTTTTTAAAAACATATTGTT
1 ATATAGTTTTTAAAAACATATTGTT
* * **
1347539 ATATA-ATTTTGAAAACATATAATAT
1 ATATAGTTTTTAAAAACATATTGT-T
1347564 ATATAGTTTTTGAAAAACATA-TGTT
1 ATATAGTTTTT-AAAAACATATTGTT
1347589 ATATA
1 ATATA
1347594 TATATATATA
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
24 14 0.32
25 17 0.39
26 5 0.11
27 8 0.18
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.44
Consensus pattern (25 bp):
ATATAGTTTTTAAAAACATATTGTT
Found at i:1347589 original size:50 final size:49
Alignment explanation
Indices: 1347496--1347593 Score: 155
Period size: 50 Copynumber: 2.0 Consensus size: 49
1347486 TTTTAAATGG
1347496 TTTTGGAAAACATATATAATATAGTTTTTAAAAACATATTGTTATATAA
1 TTTTGGAAAACATATATAATATAGTTTTTAAAAACATATTGTTATATAA
1347545 TTTT-GAAAACATATAATATATATAGTTTTTGAAAAACATA-TGTTATATA
1 TTTTGGAAAACATAT-ATA-ATATAGTTTTT-AAAAACATATTGTTATATA
1347594 TATATATATA
Statistics
Matches: 46, Mismatches: 0, Indels: 5
0.90 0.00 0.10
Matches are distributed among these distances:
48 10 0.22
49 7 0.15
50 20 0.43
51 9 0.20
ACGTcount: A:0.45, C:0.04, G:0.08, T:0.43
Consensus pattern (49 bp):
TTTTGGAAAACATATATAATATAGTTTTTAAAAACATATTGTTATATAA
Found at i:1347595 original size:2 final size:2
Alignment explanation
Indices: 1347588--1347612 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1347578 AAACATATGT
1347588 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1347613 TGAAAACATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1347623 original size:19 final size:21
Alignment explanation
Indices: 1347599--1347668 Score: 83
Period size: 19 Copynumber: 3.4 Consensus size: 21
1347589 ATATATATAT
*
1347599 ATATATATAT-ATATTGAAAAC
1 ATAT-TATATGATTTTGAAAAC
1347620 ATATTATATGATTTTG--AAC
1 ATATTATATGATTTTGAAAAC
*
1347639 ATATTATATGATTTTGAAAAT
1 ATATTATATGATTTTGAAAAC
*
1347660 ATAATATAT
1 ATATTATAT
1347669 TATATAGTTT
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
19 19 0.44
20 5 0.12
21 19 0.44
ACGTcount: A:0.46, C:0.03, G:0.07, T:0.44
Consensus pattern (21 bp):
ATATTATATGATTTTGAAAAC
Found at i:1347623 original size:21 final size:21
Alignment explanation
Indices: 1347599--1347673 Score: 75
Period size: 21 Copynumber: 3.7 Consensus size: 21
1347589 ATATATATAT
1347599 ATATATATAT-ATATTGAAAAC
1 ATAT-TATATGATATTGAAAAC
*
1347620 ATATTATATGATTTTG--AAC
1 ATATTATATGATATTGAAAAC
* *
1347639 ATATTATATGATTTTGAAAAT
1 ATATTATATGATATTGAAAAC
* *
1347660 ATAATATATTATAT
1 ATATTATATGATAT
1347674 AGTTTTTTAT
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
19 19 0.41
20 5 0.11
21 22 0.48
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.45
Consensus pattern (21 bp):
ATATTATATGATATTGAAAAC
Found at i:1347695 original size:3 final size:3
Alignment explanation
Indices: 1347687--1347733 Score: 69
Period size: 3 Copynumber: 15.7 Consensus size: 3
1347677 TTTTTATCTT
*
1347687 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTTA TTT TTA TT- TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA
1347732 TT
1 TT
1347734 TCAGTTTTCC
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
2 2 0.05
3 35 0.88
4 3 0.08
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (3 bp):
TTA
Found at i:1368902 original size:15 final size:15
Alignment explanation
Indices: 1368882--1368914 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
1368872 AGAGAATGCC
1368882 TAAACTAAAATTTGA
1 TAAACTAAAATTTGA
1368897 TAAACTAAAATTTGA
1 TAAACTAAAATTTGA
1368912 TAA
1 TAA
1368915 TGAAAAAATC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.55, C:0.06, G:0.06, T:0.33
Consensus pattern (15 bp):
TAAACTAAAATTTGA
Found at i:1371781 original size:22 final size:22
Alignment explanation
Indices: 1371755--1371834 Score: 85
Period size: 23 Copynumber: 3.7 Consensus size: 22
1371745 ATAGGGCAGA
*
1371755 GGGAATCGATACCCCCTTGAAG
1 GGGAACCGATACCCCCTTGAAG
*
1371777 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATACCCCC-TTGAAG
* *
1371800 GGGAACCAATTCCCCC-T--AG
1 GGGAACCGATACCCCCTTGAAG
*
1371819 GGGAATCGATACCCCC
1 GGGAACCGATACCCCC
1371835 ATGGGGTTCT
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
19 15 0.29
21 1 0.02
22 14 0.27
23 21 0.41
ACGTcount: A:0.25, C:0.33, G:0.25, T:0.17
Consensus pattern (22 bp):
GGGAACCGATACCCCCTTGAAG
Found at i:1371797 original size:23 final size:23
Alignment explanation
Indices: 1371755--1371816 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
1371745 ATAGGGCAGA
* *
1371755 GGGAATCGATACCCCC-TTGAAG
1 GGGAACCGATTCCCCCTTTGAAG
1371777 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCCTTTGAAG
*
1371800 GGGAACCAATTCCCCCT
1 GGGAACCGATTCCCCCT
1371817 AGGGGAATCG
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
22 14 0.39
23 22 0.61
ACGTcount: A:0.24, C:0.32, G:0.24, T:0.19
Consensus pattern (23 bp):
GGGAACCGATTCCCCCTTTGAAG
Found at i:1373890 original size:21 final size:21
Alignment explanation
Indices: 1373820--1373887 Score: 91
Period size: 21 Copynumber: 3.2 Consensus size: 21
1373810 GCTTTGGAAA
* *
1373820 TTTTCCTGGGATGCAATTAGC
1 TTTTCCTGGGATGTAATCAGC
*
1373841 TTTTCCTGGGAAGTAATCAGC
1 TTTTCCTGGGATGTAATCAGC
* *
1373862 TTTTCTTGGGATGTAACCAGC
1 TTTTCCTGGGATGTAATCAGC
1373883 TTTTC
1 TTTTC
1373888 TTGTGAAATT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.19, C:0.19, G:0.22, T:0.40
Consensus pattern (21 bp):
TTTTCCTGGGATGTAATCAGC
Found at i:1375077 original size:20 final size:20
Alignment explanation
Indices: 1375054--1375111 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
1375044 AAAAGATATA
1375054 ATAAAATAAAGTAAATAATT
1 ATAAAATAAAGTAAATAATT
* * *
1375074 ATAAAA-AATGAAAAATAATA
1 ATAAAATAAAG-TAAATAATT
1375094 ATAAAAT-AA-TAAATAATT
1 ATAAAATAAAGTAAATAATT
1375112 TTTAAGACAA
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
18 7 0.23
19 3 0.10
20 20 0.67
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (20 bp):
ATAAAATAAAGTAAATAATT
Found at i:1376071 original size:25 final size:24
Alignment explanation
Indices: 1376034--1376095 Score: 61
Period size: 25 Copynumber: 2.5 Consensus size: 24
1376024 TTTAGGATAA
* * *
1376034 TGTTTTAAATATTATATTTTATATT
1 TGTTTT-AGTATTATAGTTTAAATT
*
1376059 TGTTTTAGGTATTTTAGTTTAAATT
1 TGTTTTA-GTATTATAGTTTAAATT
*
1376084 GGTTTTAGTATT
1 TGTTTTAGTATT
1376096 TTAATTAGGA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
24 6 0.19
25 25 0.81
ACGTcount: A:0.26, C:0.00, G:0.13, T:0.61
Consensus pattern (24 bp):
TGTTTTAGTATTATAGTTTAAATT
Found at i:1376164 original size:85 final size:82
Alignment explanation
Indices: 1376024--1376207 Score: 271
Period size: 85 Copynumber: 2.2 Consensus size: 82
1376014 AAACTAAAGT
* *
1376024 TTTAGGATAATGTTTTAAATATTATATTTTATATTTGTTTTAGGTATTTTAGTTTAAATTGGTTT
1 TTTAGGATAATATTTTAAATATTATATTTTATATTTGTTTTAGGTATTTTAGTTTAAA-TAGTTT
1376089 T-AGTATTTTAATTAGGA
65 TAAGTATTTTAATTAGGA
*
1376106 TTTAGGATAATATTTTAAATATTATTTTATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGT
1 TTTAGGATAATATTTTAAATATTA---TATTTTATATTTGTTTTAGGTATTTTAGTTTAAATAGT
*
1376171 TTTAAGTGTTTTAATTAGGA
63 TTTAAGTATTTTAATTAGGA
* *
1376191 TTTAAGATATTATTTTA
1 TTTAGGATAATATTTTA
1376208 GGAATTAAAT
Statistics
Matches: 92, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
82 23 0.25
84 6 0.07
85 63 0.68
ACGTcount: A:0.30, C:0.01, G:0.13, T:0.57
Consensus pattern (82 bp):
TTTAGGATAATATTTTAAATATTATATTTTATATTTGTTTTAGGTATTTTAGTTTAAATAGTTTT
AAGTATTTTAATTAGGA
Found at i:1377116 original size:39 final size:37
Alignment explanation
Indices: 1377017--1377116 Score: 107
Period size: 39 Copynumber: 2.7 Consensus size: 37
1377007 AAAAAACCCC
* *
1377017 TTTTATCT-TTATTATT-ATCTTTAAAATTATTTATTA
1 TTTTAT-TATTATTTTTCATCTTTATAATTATTTATTA
* *
1377053 TTTTATTATTATTTTTCCTTTTTATAATTATTTACTTTA
1 TTTTATTATTATTTTTCATCTTTATAATTATTTA--TTA
1377092 TTTTATTA-TATCTTTTCATCTTTAT
1 TTTTATTATTAT-TTTTCATCTTTAT
1377117 CTGGGATTCT
Statistics
Matches: 53, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
35 1 0.02
36 13 0.25
37 14 0.26
38 3 0.06
39 22 0.42
ACGTcount: A:0.25, C:0.08, G:0.00, T:0.67
Consensus pattern (37 bp):
TTTTATTATTATTTTTCATCTTTATAATTATTTATTA
Found at i:1381836 original size:80 final size:81
Alignment explanation
Indices: 1381614--1381862 Score: 340
Period size: 81 Copynumber: 3.1 Consensus size: 81
1381604 AAGCATTTAG
* * * * * *
1381614 TCTTTTACCCAAAAGCATTTAGCCTTTCATCTAACTTGCATGATTGACACCTTTCTACCAAATGC
1 TCTTTTACTCAAAGGCATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTATCAAATGC
* * * *
1381679 ATATCTAAGCATTTAA
66 ACAGCTAGGCAATTAA
* *
1381695 TCTTTAACTCAAAGGCATTTATCCTTTCATCTAACTGGCATAATTGACACCTTTC-AGTCAAATG
1 TCTTTTACTCAAAGGCATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTA-TCAAATG
1381759 CACAGCTAGGCAATTAA
65 CACAGCTAGGCAATTAA
* *
1381776 TCTTTTACTCAAAGG-TTTTAACCTTTCATCTAACTGGCATAATTGACACTTTTCTATCAAATGC
1 TCTTTTACTCAAAGGCATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTATCAAATGC
*
1381840 ACAGCTAGGCTATTAA
66 ACAGCTAGGCAATTAA
1381856 TCTTTTA
1 TCTTTTA
1381863 TTTAAAACAA
Statistics
Matches: 150, Mismatches: 16, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
80 67 0.45
81 83 0.55
ACGTcount: A:0.31, C:0.23, G:0.10, T:0.36
Consensus pattern (81 bp):
TCTTTTACTCAAAGGCATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTATCAAATGC
ACAGCTAGGCAATTAA
Found at i:1382280 original size:22 final size:22
Alignment explanation
Indices: 1382252--1382308 Score: 96
Period size: 22 Copynumber: 2.6 Consensus size: 22
1382242 ACCCCTACCA
*
1382252 TGGTATCGATACTTCAATACTT
1 TGGTATCGATACTTCAATACTG
*
1382274 TGGTATCGATACTTCTATACTG
1 TGGTATCGATACTTCAATACTG
1382296 TGGTATCGATACT
1 TGGTATCGATACT
1382309 CCCTTTCAGT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.25, C:0.18, G:0.18, T:0.40
Consensus pattern (22 bp):
TGGTATCGATACTTCAATACTG
Found at i:1382375 original size:20 final size:20
Alignment explanation
Indices: 1382350--1382401 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
1382340 TGGATTCATG
*
1382350 GTATCGATACTTTCCTTCTA
1 GTATCGATACTTTCCTTATA
1382370 GTATCGATACTTTCCTTATA
1 GTATCGATACTTTCCTTATA
*
1382390 GTACCGATACTT
1 GTATCGATACTT
1382402 CTATACTATG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.23, C:0.23, G:0.12, T:0.42
Consensus pattern (20 bp):
GTATCGATACTTTCCTTATA
Found at i:1382666 original size:80 final size:81
Alignment explanation
Indices: 1382466--1382692 Score: 276
Period size: 80 Copynumber: 2.8 Consensus size: 81
1382456 GAATCCATGG
* * * * * * * * * *
1382466 CCTTTTATCTAACTTGTATGATTGACACCATTATACCAAATGCACATCTAGGCATTTAATCTTTA
1 CCTTTCATCTAACTGGCATAATTGACACCTTTCTATCAAATGCACAACTAGGCAATTAATCTTTT
*
1382531 ACTCAAAGGCATTTAT
66 ACTCAAAGGCATTTAA
* * *
1382547 CCTTTCATCTAACTGACAAAATTGACACCTTTCTATCAAATGCACAGCTAGGCAATTAATCTTTT
1 CCTTTCATCTAACTGGCATAATTGACACCTTTCTATCAAATGCACAACTAGGCAATTAATCTTTT
*
1382612 ACTCAAAGG-TTTTAA
66 ACTCAAAGGCATTTAA
* * * *
1382627 CCTTTCATCTAACTGGCATAATTGACACTTTTCTATCAAATGCGCAACTAAGCTATTAATCTTTT
1 CCTTTCATCTAACTGGCATAATTGACACCTTTCTATCAAATGCACAACTAGGCAATTAATCTTTT
1382692 A
66 A
1382693 TTTAAAACAA
Statistics
Matches: 125, Mismatches: 21, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
80 63 0.50
81 62 0.50
ACGTcount: A:0.32, C:0.22, G:0.10, T:0.36
Consensus pattern (81 bp):
CCTTTCATCTAACTGGCATAATTGACACCTTTCTATCAAATGCACAACTAGGCAATTAATCTTTT
ACTCAAAGGCATTTAA
Found at i:1383241 original size:94 final size:95
Alignment explanation
Indices: 1383096--1383277 Score: 249
Period size: 94 Copynumber: 1.9 Consensus size: 95
1383086 ACCATGGTAT
* * * * * * *
1383096 CGATACTTCTATATTATGGTATCGATACTCCCTTTTAGTATTGATACCATTTCTATATTCT-GGA
1 CGATAATTCTATACTATGGTACCGATACTCCCTTTCAGTATTAATACCATTTCTACATTCTAGAA
1383160 TCCATAGTATCGATACTTTCCTTCTAGTAC
66 TCCATAGTATCGATACTTTCCTTCTAGTAC
* * * *
1383190 CGATAATTCTATACTATGGTACCGATACTCCCTTTCAGTTTTAATATCATTTTTGCATTCTAGAA
1 CGATAATTCTATACTATGGTACCGATACTCCCTTTCAGTATTAATACCATTTCTACATTCTAGAA
*
1383255 TCCATGGTATCGATACTTTCCTT
66 TCCATAGTATCGATACTTTCCTT
1383278 TTTGGTATCG
Statistics
Matches: 75, Mismatches: 12, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
94 51 0.68
95 24 0.32
ACGTcount: A:0.25, C:0.21, G:0.12, T:0.42
Consensus pattern (95 bp):
CGATAATTCTATACTATGGTACCGATACTCCCTTTCAGTATTAATACCATTTCTACATTCTAGAA
TCCATAGTATCGATACTTTCCTTCTAGTAC
Found at i:1384278 original size:24 final size:24
Alignment explanation
Indices: 1384246--1384292 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
1384236 CTTGAATAAG
1384246 TTGATATGTGATATCACAAATTAA
1 TTGATATGTGATATCACAAATTAA
1384270 TTGATATGTGATATCACAAATTA
1 TTGATATGTGATATCACAAATTA
1384293 TTCGTTAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.40, C:0.09, G:0.13, T:0.38
Consensus pattern (24 bp):
TTGATATGTGATATCACAAATTAA
Found at i:1391693 original size:25 final size:24
Alignment explanation
Indices: 1391665--1391721 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 24
1391655 TCTTTAATGT
1391665 ATATTTAATTTGAATTAATT-AAATA
1 ATATTTAATTT--ATTAATTAAAATA
*
1391690 ATATTTTATTTATTAATTCAAAATA
1 ATATTTAATTTATTAATT-AAAATA
1391715 A-ATTTAA
1 ATATTTAA
1391722 AAACCCTAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
23 7 0.25
24 5 0.18
25 16 0.57
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (24 bp):
ATATTTAATTTATTAATTAAAATA
Found at i:1392521 original size:2 final size:2
Alignment explanation
Indices: 1392514--1392568 Score: 64
Period size: 2 Copynumber: 29.0 Consensus size: 2
1392504 GGGGTACTAC
*
1392514 AT AT AT AT -T AT AT -T AT AT AT AT AT AT AT AT AT GT AT -T AGT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T
1392554 AT AT AT -T AT AT AT AT
1 AT AT AT AT AT AT AT AT
1392569 TATTAAAATT
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
1 4 0.09
2 40 0.87
3 2 0.04
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.53
Consensus pattern (2 bp):
AT
Found at i:1393146 original size:35 final size:37
Alignment explanation
Indices: 1393075--1393147 Score: 89
Period size: 35 Copynumber: 2.0 Consensus size: 37
1393065 GTTGAAAAAT
* *
1393075 ATTTATATATTTTCTTTAAAAAAATTAAATTCATAAA
1 ATTTATATAATTTCTTTAAAAAAATTAAAATCATAAA
*
1393112 ATTTATATAATTT-TTT-ACAAAATTGAAAAT-ATAAA
1 ATTTATATAATTTCTTTAAAAAAATT-AAAATCATAAA
1393147 A
1 A
1393148 AAAGTTTAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
35 13 0.41
36 7 0.22
37 12 0.38
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.44
Consensus pattern (37 bp):
ATTTATATAATTTCTTTAAAAAAATTAAAATCATAAA
Found at i:1397486 original size:32 final size:32
Alignment explanation
Indices: 1397445--1397523 Score: 140
Period size: 32 Copynumber: 2.5 Consensus size: 32
1397435 ACCATCATTT
1397445 TGTCATTTTGTCAAAGTAGCAATATTAGGTTA
1 TGTCATTTTGTCAAAGTAGCAATATTAGGTTA
* *
1397477 TGTCATTTTGTCAAGGTAGCAATTTTAGGTTA
1 TGTCATTTTGTCAAAGTAGCAATATTAGGTTA
1397509 TGTCATTTTGTCAAA
1 TGTCATTTTGTCAAA
1397524 TGTTAGCTTA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 44 1.00
ACGTcount: A:0.28, C:0.10, G:0.19, T:0.43
Consensus pattern (32 bp):
TGTCATTTTGTCAAAGTAGCAATATTAGGTTA
Found at i:1402087 original size:19 final size:20
Alignment explanation
Indices: 1402060--1402098 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
1402050 TATATAATTT
1402060 TTATCAAAA-TAATAATCTAA
1 TTATCAAAACT-ATAATCTAA
1402080 TTAT-AAAACTATAATCTAA
1 TTATCAAAACTATAATCTAA
1402099 AATCGATCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.54, C:0.10, G:0.00, T:0.36
Consensus pattern (20 bp):
TTATCAAAACTATAATCTAA
Found at i:1403162 original size:111 final size:111
Alignment explanation
Indices: 1403020--1403241 Score: 390
Period size: 111 Copynumber: 2.0 Consensus size: 111
1403010 ATTACAAAAA
** *
1403020 TTAATTCTTAATCTAATAATTGTACATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATACATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
*
1403085 AATTAAAACGTTAAAATGTTACCGTATCAACAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAACAAAGTGTAGAGATAT
*
1403131 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATACATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
*
1403196 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAACAAAGTGTAGAGATAT
1403242 ATGATTTCCA
Statistics
Matches: 105, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
111 105 1.00
ACGTcount: A:0.45, C:0.11, G:0.08, T:0.36
Consensus pattern (111 bp):
TTAATTCTTAATCTAATAATCATACATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
AATTAAAACGTTAAAATGTTACCGTATCAACAAAGTGTAGAGATAT
Found at i:1403346 original size:17 final size:18
Alignment explanation
Indices: 1403303--1403337 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
1403293 GAATTATATT
1403303 AGTTAAATA-TTAAATAA
1 AGTTAAATACTTAAATAA
1403320 AGTTAAATACTTAAATAA
1 AGTTAAATACTTAAATAA
1403338 TTTATATACA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.57, C:0.03, G:0.06, T:0.34
Consensus pattern (18 bp):
AGTTAAATACTTAAATAA
Found at i:1403400 original size:12 final size:10
Alignment explanation
Indices: 1403385--1403424 Score: 55
Period size: 10 Copynumber: 4.0 Consensus size: 10
1403375 TTTAAAAAGG
*
1403385 GAGAGTATTT
1 GAGAGAATTT
1403395 GAGAGAAATTT
1 GAGAG-AATTT
1403406 -AGAGAATTT
1 GAGAGAATTT
1403415 GAGAGAATTT
1 GAGAGAATTT
1403425 AGTGTGATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
9 5 0.19
10 18 0.67
11 4 0.15
ACGTcount: A:0.40, C:0.00, G:0.28, T:0.33
Consensus pattern (10 bp):
GAGAGAATTT
Found at i:1403414 original size:20 final size:19
Alignment explanation
Indices: 1403386--1403426 Score: 64
Period size: 20 Copynumber: 2.1 Consensus size: 19
1403376 TTAAAAAGGG
*
1403386 AGAGTATTTGAGAGAAATTT
1 AGAGAATTTGAGAG-AATTT
1403406 AGAGAATTTGAGAGAATTT
1 AGAGAATTTGAGAGAATTT
1403425 AG
1 AG
1403427 TGTGATAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.41, C:0.00, G:0.27, T:0.32
Consensus pattern (19 bp):
AGAGAATTTGAGAGAATTT
Found at i:1403599 original size:50 final size:49
Alignment explanation
Indices: 1403545--1403670 Score: 128
Period size: 50 Copynumber: 2.5 Consensus size: 49
1403535 AGATACCTAG
* * *
1403545 GTATAGCGTGGATCAGGGGACACGCTATACCCACGTGGCGCCAAATCACC
1 GTATAGCG-GGATCAGGGGACGCGCTATACCCACATGGCACCAAATCACC
** * *
1403595 GTATATCGCGGGAGAAGGGG-CGCGCTATACCCACATGGCACTAAATCAGC
1 GTATA--GCGGGATCAGGGGACGCGCTATACCCACATGGCACCAAATCACC
* *
1403645 GTATAGAGCGGTTCAGGGGACGCGCT
1 GTATAGCG-GGATCAGGGGACGCGCT
1403671 TTACTGCTAC
Statistics
Matches: 61, Mismatches: 11, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
48 2 0.03
49 7 0.11
50 41 0.67
51 8 0.13
52 3 0.05
ACGTcount: A:0.25, C:0.26, G:0.32, T:0.17
Consensus pattern (49 bp):
GTATAGCGGGATCAGGGGACGCGCTATACCCACATGGCACCAAATCACC
Found at i:1403726 original size:29 final size:29
Alignment explanation
Indices: 1403682--1403760 Score: 140
Period size: 29 Copynumber: 2.7 Consensus size: 29
1403672 TACTGCTACG
1403682 GGTGTTAGATCGAAAAATATAATCTGACC
1 GGTGTTAGATCGAAAAATATAATCTGACC
*
1403711 GGTGTTAGATCAAAAAATATAATCTGACC
1 GGTGTTAGATCGAAAAATATAATCTGACC
*
1403740 GGTGTTAGATCGATAAATATA
1 GGTGTTAGATCGAAAAATATA
1403761 CCGATCACCG
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 47 1.00
ACGTcount: A:0.39, C:0.11, G:0.20, T:0.29
Consensus pattern (29 bp):
GGTGTTAGATCGAAAAATATAATCTGACC
Found at i:1408147 original size:34 final size:34
Alignment explanation
Indices: 1408087--1408151 Score: 94
Period size: 34 Copynumber: 1.9 Consensus size: 34
1408077 CACATAACTT
*** *
1408087 ACATAATTTTATATTTGGAGAGAATTTATAATTC
1 ACATAATTTTATATTAAAAGAAAATTTATAATTC
1408121 ACATAATTTTATATTAAAAGAAAATTTATAA
1 ACATAATTTTATATTAAAAGAAAATTTATAA
1408152 AATTTTAAAG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 27 1.00
ACGTcount: A:0.46, C:0.05, G:0.08, T:0.42
Consensus pattern (34 bp):
ACATAATTTTATATTAAAAGAAAATTTATAATTC
Found at i:1408187 original size:15 final size:16
Alignment explanation
Indices: 1408167--1408213 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
1408157 TAAAGGAAGT
1408167 AAAAATATAAT-TTTA
1 AAAAATATAATATTTA
*
1408182 AAAAATAAAAATATTTA
1 AAAAAT-ATAATATTTA
* *
1408199 AAATATATAAAATTT
1 AAAAATATAATATTT
1408214 TAAAGAGAGC
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
15 6 0.23
16 11 0.42
17 9 0.35
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
AAAAATATAATATTTA
Found at i:1408192 original size:21 final size:22
Alignment explanation
Indices: 1408152--1408195 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
1408142 AAATTTATAA
*
1408152 AATTTTAAAGGAAGTAAAAATAT
1 AATTTTAAA-GAAATAAAAATAT
1408175 AATTTTAAA-AAATAAAAATAT
1 AATTTTAAAGAAATAAAAATAT
1408196 TTAAAATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 11 0.55
23 9 0.45
ACGTcount: A:0.61, C:0.00, G:0.07, T:0.32
Consensus pattern (22 bp):
AATTTTAAAGAAATAAAAATAT
Found at i:1408200 original size:17 final size:17
Alignment explanation
Indices: 1408167--1408217 Score: 63
Period size: 17 Copynumber: 3.1 Consensus size: 17
1408157 TAAAGGAAGT
1408167 AAAAATAT--AATTTTA
1 AAAAATATAAAATTTTA
1408182 AAAAATA-AAAATATTTA
1 AAAAATATAAAAT-TTTA
*
1408199 AAATATATAAAATTTTA
1 AAAAATATAAAATTTTA
1408216 AA
1 AA
1408218 GAGAGCTGCC
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
15 7 0.23
16 3 0.10
17 16 0.52
18 5 0.16
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
AAAAATATAAAATTTTA
Found at i:1409364 original size:24 final size:25
Alignment explanation
Indices: 1409337--1409383 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
1409327 TAAAATTTCA
*
1409337 TATTAAAATTATTAATT-TTTTATT
1 TATTAAAAGTATTAATTATTTTATT
*
1409361 TATTAAAAGTATTAGTTATTTTA
1 TATTAAAAGTATTAATTATTTTA
1409384 AATATATAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.57
Consensus pattern (25 bp):
TATTAAAAGTATTAATTATTTTATT
Found at i:1409465 original size:18 final size:18
Alignment explanation
Indices: 1409439--1409475 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1409429 GATTAATTTT
1409439 TTAAAATAAAAAATTAAA
1 TTAAAATAAAAAATTAAA
* *
1409457 TTAATATAAAAATTTAAA
1 TTAAAATAAAAAATTAAA
1409475 T
1 T
1409476 CAAATTGAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
TTAAAATAAAAAATTAAA
Found at i:1412167 original size:22 final size:19
Alignment explanation
Indices: 1412117--1412186 Score: 77
Period size: 22 Copynumber: 3.5 Consensus size: 19
1412107 GCAAAATTGA
1412117 TATCGATACCATAATAGGG
1 TATCGATACCATAATAGGG
*
1412136 TATCGGTACCATAATATGGTAG
1 TATCGATACCATAATA-GG--G
**
1412158 TATCGATACCATGGTAGGGG
1 TATCGATACCATAATA-GGG
1412178 TATCGATAC
1 TATCGATAC
1412187 TGAGGAGTAA
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
19 15 0.35
20 12 0.28
22 16 0.37
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.29
Consensus pattern (19 bp):
TATCGATACCATAATAGGG
Found at i:1412576 original size:55 final size:55
Alignment explanation
Indices: 1412517--1412683 Score: 298
Period size: 55 Copynumber: 3.0 Consensus size: 55
1412507 AATGAACTAA
* * *
1412517 GTGTGCCAAACTAAGAAATTAATACTAAGTGTATGAATATCCGTATGGGCACTTT
1 GTGTGCAAAACTAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGGCACTTT
*
1412572 GTGTGCAAAACTAAGAAATTCATACTAAGTGTATAAATTTCCGTATGGGCACTTT
1 GTGTGCAAAACTAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGGCACTTT
1412627 GTGTGCAAAACTAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGGCACTTT
1 GTGTGCAAAACTAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGGCACTTT
1412682 GT
1 GT
1412684 ATGAGCACTA
Statistics
Matches: 107, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 107 1.00
ACGTcount: A:0.34, C:0.14, G:0.20, T:0.32
Consensus pattern (55 bp):
GTGTGCAAAACTAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGGCACTTT
Found at i:1413078 original size:68 final size:68
Alignment explanation
Indices: 1412950--1413272 Score: 517
Period size: 68 Copynumber: 4.8 Consensus size: 68
1412940 TAAAAGATTA
* *
1412950 GAGGCATAACTGTGCATTTGACAGAAA-GATG-CAATTATG-CAGTTAGATGAAAGGCTAAGTGC
1 GAGGCCTAATTGTGCATTTGACAGAAATG-TGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGC
1413012 CTTT
65 CTTT
* *
1413016 GAGGCCTAATTGTGCATTTGACAGAAATGTGTCAAGTATACCAGTTAGATGAAAGGCTAAGTGCC
1 GAGGCCTAATTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCC
1413081 TTT
66 TTT
* * *
1413084 GAGGCCTAATTGTGCATTTGACAGAAAGGTGTCAATTATGCCAATTAGATGAAAGGCTAAGTTCC
1 GAGGCCTAATTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCC
1413149 TTT
66 TTT
* *
1413152 GAGGCCTAACTGTGCATTTGATAGAAATGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCC
1 GAGGCCTAATTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCC
1413217 TTT
66 TTT
**
1413220 GAGGCCTAATTGCACATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAA
1 GAGGCCTAATTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAA
1413273 CGATTAAATA
Statistics
Matches: 236, Mismatches: 18, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
66 27 0.11
67 7 0.03
68 202 0.86
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.29
Consensus pattern (68 bp):
GAGGCCTAATTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCC
TTT
Found at i:1413375 original size:81 final size:81
Alignment explanation
Indices: 1413234--1413621 Score: 456
Period size: 81 Copynumber: 4.8 Consensus size: 81
1413224 CCTAATTGCA
* * * *
1413234 CATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAACGATTAAATACCGCTGAGTAAAAGAT
1 CATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAATACCGTTGAGTAAAAGAT
*
1413299 GAATAGCCAAGCTATG
66 GAATAGCCTAGCTATG
* * * *
1413315 CATTTGGCAGAAAGGTGTCTATTATGCCAGTTAGATGAACAGTTAAATATCGTTGTGTAAAAGAT
1 CATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAATACCGTTGAGTAAAAGAT
*
1413380 GAATAGCCTAGCCATG
66 GAATAGCCTAGCTATG
* *
1413396 CATTTGGCAGAAAGGTGTCAATTATGTCAGTTAGATGAACGGTTAAATACCGTAGAGTAAAAGAT
1 CATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAATACCGTTGAGTAAAAGAT
*
1413461 GAAT-GACCTAGCTGTG
66 GAATAG-CCTAGCTATG
* * * *
1413477 CATTTGGCAGAAAGGTGTCAATTGTGCCAGTTAGGTGAACGGTTAAACACTGTTGAGTAAAAGAA
1 CATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAATACCGTTGAGTAAAAG-A
* * * *
1413542 T-AATGGACTAGCTGTA
65 TGAATAGCCTAGCTATG
* * * * * * * * ** *
1413558 CATTTGTCAGAAAAGTATCAAATATGCAATTTAGATGAAAGGCTAAATACATTTGGGTAAAAGA
1 CATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAATACCGTTGAGTAAAAGA
1413622 AGCAACGAAT
Statistics
Matches: 264, Mismatches: 40, Indels: 7
0.85 0.13 0.02
Matches are distributed among these distances:
80 2 0.01
81 259 0.98
82 3 0.01
ACGTcount: A:0.36, C:0.13, G:0.23, T:0.28
Consensus pattern (81 bp):
CATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAATACCGTTGAGTAAAAGAT
GAATAGCCTAGCTATG
Found at i:1415376 original size:3 final size:3
Alignment explanation
Indices: 1415368--1415453 Score: 79
Period size: 3 Copynumber: 29.0 Consensus size: 3
1415358 TTTTTAATTG
* *
1415368 TTA TTA TTA TT- TTA TTTA TCA CTA TTA TTA TTA TT- TTA TTA TTA
1 TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * *
1415412 TTA TTA TTA -TA TTT TTA TTA TTAA TAA TAA ATA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA
1415454 CATATTACAG
Statistics
Matches: 68, Mismatches: 10, Indels: 10
0.77 0.11 0.11
Matches are distributed among these distances:
2 6 0.09
3 57 0.84
4 5 0.07
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:1415413 original size:20 final size:20
Alignment explanation
Indices: 1415368--1415434 Score: 86
Period size: 20 Copynumber: 3.5 Consensus size: 20
1415358 TTTTTAATTG
1415368 TTATTATTATT-TTA-TTTA
1 TTATTATTATTATTATTTTA
* *
1415386 TCACTATTATTATTATTTTA
1 TTATTATTATTATTATTTTA
1415406 TTATTATTATTATTATATTT-
1 TTATTATTATTATTAT-TTTA
1415426 TTATTATTA
1 TTATTATTA
1415435 ATAATAAATA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
18 9 0.21
19 3 0.07
20 27 0.64
21 3 0.07
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (20 bp):
TTATTATTATTATTATTTTA
Found at i:1416888 original size:23 final size:22
Alignment explanation
Indices: 1416849--1416901 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 22
1416839 TATTTTAGTC
1416849 ATTGTTTATTTATATTTATATT-TT
1 ATTGTTTA--TATATTTA-ATTATT
1416873 ATATGTTTATATATTTAATTATT
1 AT-TGTTTATATATTTAATTATT
1416896 ATTGTT
1 ATTGTT
1416902 ATAATTATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
22 7 0.26
23 12 0.44
24 2 0.07
25 6 0.22
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.66
Consensus pattern (22 bp):
ATTGTTTATATATTTAATTATT
Found at i:1417125 original size:142 final size:144
Alignment explanation
Indices: 1416970--1417235 Score: 334
Period size: 146 Copynumber: 1.8 Consensus size: 144
1416960 TTATATATAT
1416970 TAAATAAAAATCCTA-TTTATAAA-T-T-TA-A-T-TTTATATAAATTACTTTTAAGAAAAATAA
1 TAAATAAAAATCCTATTTTATAAATTATATATATTATTTATATAAATTA-TTTTAAGAAAAAT--
1417028 TAATATT-TTAATATTTATTTA-TTTTTAATATTAAGAAATGGGATGTCTTAAAGCACCTAGAAG
63 T--T-TTATTAATATTTATTTATTTTTTAATATTAAGAAAT-GGATGTCTTAAAGCACCTAGAAG
1417091 TACTTTTTTTATATTCTTAAA
124 TACTTTTTTTATATTCTTAAA
* * * * *
1417112 TAAATAAATATCCTATTTTTATAAATTATATATATTAATTTATTTTAATTATTTTTAGAGAAATT
1 TAAATAAAAATCCTA-TTTTATAAATTATATATATT-ATTTATATAAATTATTTTAAGAAAAATT
*
1417177 TTTATTAATATTTATTTATTTTTTAATATTAAGAAATGGCTGTCTTAAAGCACCTAGAA
64 TTTATTAATATTTATTTATTTTTTAATATTAAGAAATGGATGTCTTAAAGCACCTAGAA
1417236 TTCATTTTCT
Statistics
Matches: 107, Mismatches: 6, Indels: 18
0.82 0.05 0.14
Matches are distributed among these distances:
142 14 0.13
144 8 0.07
145 3 0.03
146 37 0.35
147 20 0.19
148 2 0.02
149 1 0.01
150 11 0.10
151 11 0.10
ACGTcount: A:0.41, C:0.06, G:0.06, T:0.47
Consensus pattern (144 bp):
TAAATAAAAATCCTATTTTATAAATTATATATATTATTTATATAAATTATTTTAAGAAAAATTTT
TATTAATATTTATTTATTTTTTAATATTAAGAAATGGATGTCTTAAAGCACCTAGAAGTACTTTT
TTTATATTCTTAAA
Found at i:1417309 original size:146 final size:145
Alignment explanation
Indices: 1417035--1417303 Score: 363
Period size: 146 Copynumber: 1.9 Consensus size: 145
1417025 TAATAATATT
*
1417035 TTAATATTTATTTATTTTTAATATTAAGAAATGGGATGTCTTAAAGCACCTAGAAGTACTTTTTT
1 TTAATATTTATTTATTTTTAATATTAAGAAATGGGATGTCTTAAAGCACCTAGAAGTACTTTTCT
* * *
1417100 TATATTCTTAAATAAATAAATATCCTATTTTTATAAATTATATATATTAATTTATTTTAATTATT
66 AATATTCTTAAATAAATAAATAT-CTATTTTTACAAATTATATATATTAATATATTTTAATTATT
1417165 TTTAGAGAAATTTTTA
130 TTTAGAGAAATTTTTA
* *
1417181 TTAATATTTATTTATTTTTTAATATTAAGAAAT-GGCTGTCTTAAAGCACCTAGAA-TTCATTTT
1 TTAATATTTATTTA-TTTTTAATATTAAGAAATGGGATGTCTTAAAGCACCTAGAAGTAC-TTTT
*
1417244 CTAATATT-TCTAAGTAAATAAATAT-T-TTATTTACAAA-TATATATA-TATATATATTCTTAA
64 CTAATATTCT-TAAATAAATAAATATCTATT-TTTACAAATTATATATATTA-ATATATT-TTAA
1417304 AATTATATTA
Statistics
Matches: 110, Mismatches: 7, Indels: 14
0.84 0.05 0.11
Matches are distributed among these distances:
142 2 0.02
143 16 0.15
144 12 0.11
145 3 0.03
146 59 0.54
147 18 0.16
ACGTcount: A:0.38, C:0.07, G:0.06, T:0.49
Consensus pattern (145 bp):
TTAATATTTATTTATTTTTAATATTAAGAAATGGGATGTCTTAAAGCACCTAGAAGTACTTTTCT
AATATTCTTAAATAAATAAATATCTATTTTTACAAATTATATATATTAATATATTTTAATTATTT
TTAGAGAAATTTTTA
Found at i:1425489 original size:75 final size:75
Alignment explanation
Indices: 1425352--1425524 Score: 213
Period size: 75 Copynumber: 2.3 Consensus size: 75
1425342 ATTAACAAGA
* * * * *
1425352 AGCAAATGATAGAGCATGCCGAAAGCCCATTTCAATCATAATCAGGAATATTGACACTTTTTGAA
1 AGCAAATGATGGGGCATGCTGAAAGCCCATTTCAATCAGAATCAAGAATATTGACACTTTTTGAA
1425417 CATTTGTATT
66 CATTTGTATT
* * * **
1425427 AGCCAATGCTGGGGCATGCTGAAAGCCCCTTTCAATCAGAATCAAGAATATTGA-TGTATTTTGA
1 AGCAAATGATGGGGCATGCTGAAAGCCCATTTCAATCAGAATCAAGAATATTGACACT-TTTTGA
**
1425491 ATGTTTGTATT
65 ACATTTGTATT
*
1425502 AGCAAATGATGGGGCATGATGAA
1 AGCAAATGATGGGGCATGCTGAA
1425525 GATCCATATC
Statistics
Matches: 82, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
74 1 0.01
75 81 0.99
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.30
Consensus pattern (75 bp):
AGCAAATGATGGGGCATGCTGAAAGCCCATTTCAATCAGAATCAAGAATATTGACACTTTTTGAA
CATTTGTATT
Found at i:1426460 original size:52 final size:53
Alignment explanation
Indices: 1426400--1426546 Score: 154
Period size: 54 Copynumber: 2.8 Consensus size: 53
1426390 TTGACTAGAA
* *
1426400 ATCTGTGCAGAAGCCACA-G-ATGGATGAATGTATTGTCAAAAATTTTACATAC
1 ATCTGTGCAGAAGCCACAGGAAT-GATGAATGTGTTGTCAAAAATTTTACAAAC
* * * * * **
1426452 ATCTGTGCAGAGGCCACATGAAAAGATGAATATGTTATCAAATGTTTTACAAAC
1 ATCTGTGCAGAAGCCACA-GGAATGATGAATGTGTTGTCAAAAATTTTACAAAC
* *
1426506 ATCTGGGCAGAAACCACAGGAAATGATGAATGTGTTGTCAA
1 ATCTGTGCAGAAGCCACAGG-AATGATGAATGTGTTGTCAA
1426547 GTGTTTTACG
Statistics
Matches: 75, Mismatches: 16, Indels: 6
0.77 0.16 0.06
Matches are distributed among these distances:
52 17 0.23
53 1 0.01
54 56 0.75
55 1 0.01
ACGTcount: A:0.37, C:0.15, G:0.21, T:0.27
Consensus pattern (53 bp):
ATCTGTGCAGAAGCCACAGGAATGATGAATGTGTTGTCAAAAATTTTACAAAC
Found at i:1428182 original size:17 final size:17
Alignment explanation
Indices: 1428162--1428221 Score: 59
Period size: 17 Copynumber: 3.4 Consensus size: 17
1428152 CAGCAATTCC
1428162 AGAAGAAGTTCATAATG
1 AGAAGAAGTTCATAATG
* **
1428179 AGAAGAA-CTCATCTGAAAA
1 AGAAGAAGTTCA--T-AATG
1428198 AGAAGAAGTTCATAATG
1 AGAAGAAGTTCATAATG
1428215 AGAAGAA
1 AGAAGAA
1428222 TTTGTTAACT
Statistics
Matches: 33, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
16 3 0.09
17 16 0.48
18 2 0.06
19 9 0.27
20 3 0.09
ACGTcount: A:0.52, C:0.08, G:0.22, T:0.18
Consensus pattern (17 bp):
AGAAGAAGTTCATAATG
Found at i:1428476 original size:3 final size:3
Alignment explanation
Indices: 1428464--1428554 Score: 98
Period size: 3 Copynumber: 30.7 Consensus size: 3
1428454 TTCCATTTTT
* * *
1428464 TTA TTG TTA TTA TTA TT- TTA TTTA TCA CTA TTA TTA TTA TT- TTA
1 TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA
* *
1428508 TTA TTA TTA TTA -TA TTA TTA TTA TTA TTA TTAA TAA ATA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA
1428553 TT
1 TT
1428555 GCATATTACA
Statistics
Matches: 73, Mismatches: 10, Indels: 10
0.78 0.11 0.11
Matches are distributed among these distances:
2 6 0.08
3 62 0.85
4 5 0.07
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:1428484 original size:17 final size:17
Alignment explanation
Indices: 1428464--1428538 Score: 98
Period size: 17 Copynumber: 4.3 Consensus size: 17
1428454 TTCCATTTTT
1428464 TTATTGTTATTATTATT-
1 TTATT-TTATTATTATTA
*
1428481 TTATTTATCACTATTATTA
1 TTATTT-T-ATTATTATTA
1428500 TTATTTTATTATTATTA
1 TTATTTTATTATTATTA
*
1428517 TTATATTATTATTATTA
1 TTATTTTATTATTATTA
1428534 TTATT
1 TTATT
1428539 AATAAATATT
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
16 1 0.02
17 35 0.69
18 9 0.18
19 6 0.12
ACGTcount: A:0.29, C:0.03, G:0.01, T:0.67
Consensus pattern (17 bp):
TTATTTTATTATTATTA
Found at i:1428511 original size:14 final size:14
Alignment explanation
Indices: 1428492--1428539 Score: 78
Period size: 14 Copynumber: 3.4 Consensus size: 14
1428482 TATTTATCAC
1428492 TATTATTATTATTT
1 TATTATTATTATTT
*
1428506 TATTATTATTATTA
1 TATTATTATTATTT
1428520 TATTATTATTATTAT
1 TATTATTATTATT-T
1428535 TATTA
1 TATTA
1428540 ATAAATATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
14 26 0.84
15 5 0.16
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TATTATTATTATTT
Found at i:1441261 original size:23 final size:23
Alignment explanation
Indices: 1441197--1441261 Score: 103
Period size: 23 Copynumber: 2.8 Consensus size: 23
1441187 TCGATTCCCT
* * *
1441197 AAAGAGGGAATCAGTTCCCATTC
1 AAAGGGGGAATCGGTTCCTATTC
1441220 AAAGGGGGAATCGGTTCCTATTC
1 AAAGGGGGAATCGGTTCCTATTC
1441243 AAAGGGGGAATCGGTTCCT
1 AAAGGGGGAATCGGTTCCT
1441262 CCTACACTAA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.29, C:0.18, G:0.29, T:0.23
Consensus pattern (23 bp):
AAAGGGGGAATCGGTTCCTATTC
Done.