Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002126.1 Hibiscus syriacus cultivar Beakdansim tig00004355_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: 1482737
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 8
Found at i:222976 original size:18 final size:15
Alignment explanation
Indices: 222936--222980 Score: 54
Period size: 18 Copynumber: 2.7 Consensus size: 15
222926 ATTAATCGAT
222936 TTTAAGGTTTTGTTG
1 TTTAAGGTTTTGTTG
222951 TGTTAAGGTTTTGTCTTG
1 T-TTAAGGTTTTG--TTG
222969 ATTTAAGGTTTT
1 -TTTAAGGTTTT
222981 AAGGTCGTGG
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
15 1 0.04
16 11 0.42
18 13 0.50
19 1 0.04
ACGTcount: A:0.16, C:0.02, G:0.24, T:0.58
Consensus pattern (15 bp):
TTTAAGGTTTTGTTG
Found at i:223792 original size:30 final size:30
Alignment explanation
Indices: 223756--223819 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
223746 GTTGCAAGAG
**
223756 AAAAACAGAAACTTAATGGATTAAAACAGC
1 AAAAACAGAAACTTAAAAGATTAAAACAGC
*
223786 AAAAACAGAAATTTAAAAGATTAAAACAGC
1 AAAAACAGAAACTTAAAAGATTAAAACAGC
223816 AAAA
1 AAAA
223820 TAAGAAGTCA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.62, C:0.11, G:0.11, T:0.16
Consensus pattern (30 bp):
AAAAACAGAAACTTAAAAGATTAAAACAGC
Found at i:224957 original size:2 final size:2
Alignment explanation
Indices: 224950--225013 Score: 91
Period size: 2 Copynumber: 34.0 Consensus size: 2
224940 TAATTGTACA
224950 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
224990 A- AT AT A- AT AT AT AA AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
225014 TTATTTCGGT
Statistics
Matches: 56, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
1 4 0.07
2 52 0.93
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:225547 original size:68 final size:67
Alignment explanation
Indices: 225433--225613 Score: 186
Period size: 67 Copynumber: 2.7 Consensus size: 67
225423 ACATAATTCA
* * * * * *
225433 TTTCAAGGGAAACGATCTCAGAGATATTTGTTATTTCATGAGAAACTATCTCTAGGGAAACAAAA
1 TTTCAAGGGAAACAATGTCAAAGAT-TTTG-TGTTTCAAGAGAAACTATCTCCAGGGAAACAAAA
225498 TTTTG
64 -TTTG
* * * * * *
225503 TTTTAAGAGAGATA-AAT-TCAAAGATTTTGTGTTTCAAGAAAAACTGTCTCCAGTGAGACAAAA
1 TTTCAAG-G-GAAACAATGTCAAAGATTTTGTGTTTCAAGAGAAACTATCTCCAGGGAAACAAAA
225566 TTTG
64 TTTG
*
225570 TTTCAAGGGAAACAATGTCAAAGGTTTTGTGTTTCAAGAGAAAC
1 TTTCAAGGGAAACAATGTCAAAGATTTTGTGTTTCAAGAGAAAC
225614 ATTTTCAAAG
Statistics
Matches: 92, Mismatches: 15, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
65 3 0.03
66 4 0.04
67 35 0.38
68 27 0.29
69 4 0.04
70 13 0.14
71 3 0.03
72 3 0.03
ACGTcount: A:0.37, C:0.12, G:0.19, T:0.32
Consensus pattern (67 bp):
TTTCAAGGGAAACAATGTCAAAGATTTTGTGTTTCAAGAGAAACTATCTCCAGGGAAACAAAATT
TG
Found at i:225599 original size:67 final size:66
Alignment explanation
Indices: 225395--225613 Score: 179
Period size: 67 Copynumber: 3.2 Consensus size: 66
225385 GTTCATATGA
** * * ** * *
225395 TGTTTCAAGAAAAGTTGTCTCAAAAGAGACATAATTCATTTCAAGGGAAACGATCTCAGAGATAT
1 TGTTTCAAGAAAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAAT-TCAAAGAT-T
225460 TTG
64 TTG
* * * * * * * * *
225463 TTATTTCATGAGAAACTATCTCTAGGGAAACAAAATTTTGTTTTAAGAGAGATA-AATTCAAAGA
1 -TGTTTCAAGAAAAACTGTCTCAAGAGAGACAAAA-TTTGTTTCAAG-G-GAAACAATTCAAAGA
225527 TTTTG
62 TTTTG
* * *
225532 TGTTTCAAGAAAAACTGTCTCCAGTGAGACAAAATTTGTTTCAAGGGAAACAATGTCAAAGGTTT
1 TGTTTCAAGAAAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAAT-TCAAAGATTT
225597 TG
65 TG
*
225599 TGTTTCAAGAGAAAC
1 TGTTTCAAGAAAAAC
225614 ATTTTCAAAG
Statistics
Matches: 117, Mismatches: 28, Indels: 12
0.75 0.18 0.08
Matches are distributed among these distances:
65 3 0.03
66 4 0.03
67 35 0.30
68 27 0.23
69 27 0.23
70 15 0.13
71 3 0.03
72 3 0.03
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.32
Consensus pattern (66 bp):
TGTTTCAAGAAAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAATTCAAAGATTTT
G
Found at i:225634 original size:26 final size:27
Alignment explanation
Indices: 225579--225657 Score: 88
Period size: 26 Copynumber: 2.8 Consensus size: 27
225569 GTTTCAAGGG
* *
225579 AAACAATGTCAAAGGTTTTGTGTTTCAAGAG
1 AAACAATTTCAAAGG-TTT-T-TTT-AAGAA
*
225610 AAACATTTTCAAA-GTTTTTTTAAGAA
1 AAACAATTTCAAAGGTTTTTTTAAGAA
225636 AAACAATTTCAAAGGTTTTTTT
1 AAACAATTTCAAAGGTTTTTTT
225658 GTGTTTCAAG
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
26 16 0.37
27 11 0.26
28 1 0.02
29 3 0.07
30 1 0.02
31 11 0.26
ACGTcount: A:0.38, C:0.09, G:0.14, T:0.39
Consensus pattern (27 bp):
AAACAATTTCAAAGGTTTTTTTAAGAA
Found at i:225671 original size:60 final size:63
Alignment explanation
Indices: 225570--225769 Score: 223
Period size: 66 Copynumber: 3.2 Consensus size: 63
225560 ACAAAATTTG
** *
225570 TTTCAAGGGAAACAATGTCAAAGG--TTTTGTGTTTCAAGAGAAACATTTTCAAAG-TTT-T-
1 TTTCAAGAAAAACAATTTCAAAGGTTTTTTGTGTTTCAAGAGAAACATTTTCAAAGTTTTGTA
225628 TTT-AAGAAAAACAATTTCAAAGGTTTTTTTGTGTTTCAAGAGAAACATTTTCAAAGGTTTTTTG
1 TTTCAAGAAAAACAATTTCAAAGG-TTTTTTGTGTTTCAAGAGAAACATTTTCAAA-G--TTTTG
225692 TA
62 TA
* * ** * * *
225694 TTTCAAGAGAAGCAATTTCAAAGGTTTTTTGTGTTTCAAGAGAAACAAATTCAAAGATTGGTG
1 TTTCAAGAAAAACAATTTCAAAGGTTTTTTGTGTTTCAAGAGAAACATTTTCAAAGTTTTGTA
*
225757 TTTCAAGAGAAAC
1 TTTCAAGAAAAAC
225770 TGTCTCAAGA
Statistics
Matches: 121, Mismatches: 11, Indels: 15
0.82 0.07 0.10
Matches are distributed among these distances:
57 17 0.14
58 3 0.02
60 29 0.24
61 1 0.01
63 16 0.13
64 3 0.02
65 2 0.02
66 32 0.26
67 18 0.15
ACGTcount: A:0.36, C:0.10, G:0.18, T:0.36
Consensus pattern (63 bp):
TTTCAAGAAAAACAATTTCAAAGGTTTTTTGTGTTTCAAGAGAAACATTTTCAAAGTTTTGTA
Found at i:225698 original size:33 final size:33
Alignment explanation
Indices: 225631--225769 Score: 185
Period size: 33 Copynumber: 4.3 Consensus size: 33
225621 AAGTTTTTTT
*
225631 AAGAAAAACAATTTCAAAGGTTTTTTTGTGTTTC
1 AAGAGAAACAATTTCAAAGG-TTTTTTGTGTTTC
* *
225665 AAGAGAAACATTTTCAAAGGTTTTTTGTATTTC
1 AAGAGAAACAATTTCAAAGGTTTTTTGTGTTTC
*
225698 AAGAGAAGCAATTTCAAAGGTTTTTTGTGTTTC
1 AAGAGAAACAATTTCAAAGGTTTTTTGTGTTTC
* * *
225731 AAGAGAAACAAATTCAAA-G--ATTGGTGTTTC
1 AAGAGAAACAATTTCAAAGGTTTTTTGTGTTTC
225761 AAGAGAAAC
1 AAGAGAAAC
225770 TGTCTCAAGA
Statistics
Matches: 95, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
30 18 0.19
32 1 0.01
33 58 0.61
34 18 0.19
ACGTcount: A:0.37, C:0.09, G:0.18, T:0.35
Consensus pattern (33 bp):
AAGAGAAACAATTTCAAAGGTTTTTTGTGTTTC
Found at i:225827 original size:36 final size:37
Alignment explanation
Indices: 225755--225845 Score: 166
Period size: 38 Copynumber: 2.5 Consensus size: 37
225745 CAAAGATTGG
225755 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAAATT
225793 TGTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAATT
225829 TGTTTCAAGAGAAACTG
1 TGTTTCAAGAGAAACTG
225846 ATTCAAACAT
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
36 23 0.43
38 30 0.57
ACGTcount: A:0.42, C:0.13, G:0.20, T:0.25
Consensus pattern (37 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAATT
Found at i:226529 original size:23 final size:23
Alignment explanation
Indices: 226511--226569 Score: 102
Period size: 22 Copynumber: 2.6 Consensus size: 23
226501 CTCGTATAAA
226511 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTGCCCCGTAGAAT
226534 TGCACCGAAGTG-CCCGTAGAAT
1 TGCACCGAAGTGCCCCGTAGAAT
*
226556 TGCACCGTAGTGCC
1 TGCACCGAAGTGCC
226570 ATATAATGAT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
22 21 0.62
23 13 0.38
ACGTcount: A:0.24, C:0.31, G:0.27, T:0.19
Consensus pattern (23 bp):
TGCACCGAAGTGCCCCGTAGAAT
Found at i:227352 original size:67 final size:67
Alignment explanation
Indices: 227179--227330 Score: 225
Period size: 67 Copynumber: 2.3 Consensus size: 67
227169 TTTTTCTCAT
* *
227179 GGGGGAATCGGTTCCCCCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAATTTCATATACG
1 GGGGGTATCGGTT--CCCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAAATTCATATACG
227244 ATGA
64 ATGA
* * * *
227248 GGGGGTATCGGTTCCCCCCTGGGGGTATCGATTCCCCTCTAGCATTCTGGAAATTCAT-TTCGTT
1 GGGGGTATCGGTTCCCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAAATTCATATACGAT
227312 GA
66 GA
227314 GGGGGTATCGGTTCCCC
1 GGGGGTATCGGTTCCCC
227331 TTGAATGGGT
Statistics
Matches: 77, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
66 23 0.30
67 42 0.55
69 12 0.16
ACGTcount: A:0.17, C:0.27, G:0.28, T:0.28
Consensus pattern (67 bp):
GGGGGTATCGGTTCCCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAAATTCATATACGAT
GA
Found at i:227835 original size:17 final size:19
Alignment explanation
Indices: 227813--227847 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
227803 ACGTTGAGAG
227813 AAGGAAG-A-GAAGAAAAT
1 AAGGAAGAAGGAAGAAAAT
227830 AAGGAAGAAGGAAGAAAA
1 AAGGAAGAAGGAAGAAAA
227848 AATGGGAGGG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 1 0.06
19 8 0.50
ACGTcount: A:0.66, C:0.00, G:0.31, T:0.03
Consensus pattern (19 bp):
AAGGAAGAAGGAAGAAAAT
Found at i:233406 original size:23 final size:23
Alignment explanation
Indices: 233388--233446 Score: 102
Period size: 22 Copynumber: 2.6 Consensus size: 23
233378 CTCGTATAAA
233388 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTGCCCCGTAGAAT
233411 TGCACCGAAGTG-CCCGTAGAAT
1 TGCACCGAAGTGCCCCGTAGAAT
*
233433 TGCACCGTAGTGCC
1 TGCACCGAAGTGCC
233447 ATATAATGAT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
22 21 0.62
23 13 0.38
ACGTcount: A:0.24, C:0.31, G:0.27, T:0.19
Consensus pattern (23 bp):
TGCACCGAAGTGCCCCGTAGAAT
Found at i:234230 original size:67 final size:67
Alignment explanation
Indices: 234058--234208 Score: 232
Period size: 67 Copynumber: 2.3 Consensus size: 67
234048 TTTTTCTCAT
* *
234058 GGGGGAATCGGTTCCCCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAATTTCATATACGA
1 GGGGGTATCGGTT-CCCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAAATTCATATACGA
234123 TGA
65 TGA
* * * *
234126 GGGGGTATCGGTTCCCCCCTGGGGGTATCGATTCCCCTCTAGCATTCTGGAAATTCAT-TTCGTT
1 GGGGGTATCGGTTCCCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAAATTCATATACGAT
234190 GA
66 GA
234192 GGGGGTATCGGTTCCCC
1 GGGGGTATCGGTTCCCC
234209 TTGAATGGGT
Statistics
Matches: 77, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
66 23 0.30
67 42 0.55
68 12 0.16
ACGTcount: A:0.17, C:0.26, G:0.28, T:0.28
Consensus pattern (67 bp):
GGGGGTATCGGTTCCCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAAATTCATATACGAT
GA
Found at i:235019 original size:15 final size:15
Alignment explanation
Indices: 235001--235038 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
234991 TGTTTATGTT
*
235001 TCAAGAGAAATTGTC
1 TCAAGAGAAACTGTC
235016 TCAATG-GAAACTGTC
1 TCAA-GAGAAACTGTC
235031 TCAAGAGA
1 TCAAGAGA
235039 GACAATGGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
14 1 0.05
15 18 0.90
16 1 0.05
ACGTcount: A:0.39, C:0.16, G:0.21, T:0.24
Consensus pattern (15 bp):
TCAAGAGAAACTGTC
Found at i:236243 original size:17 final size:17
Alignment explanation
Indices: 236221--236256 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
236211 AAGAGTTTCG
236221 AAAAAATGTTTAATCAA
1 AAAAAATGTTTAATCAA
236238 AAAAAATGTTTAATCAA
1 AAAAAATGTTTAATCAA
236255 AA
1 AA
236257 GTTTTGAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.61, C:0.06, G:0.06, T:0.28
Consensus pattern (17 bp):
AAAAAATGTTTAATCAA
Found at i:237165 original size:26 final size:24
Alignment explanation
Indices: 237134--237190 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 24
237124 TCCCTTGTCC
*
237134 CTTTTTCTTTTTGATTTTTGTTCTTT
1 CTTTTTCCTTTT-ATTTTTGTTC-TT
*
237160 CTTTTTTCCTTTTCTTTTTGTTCTT
1 C-TTTTTCCTTTTATTTTTGTTCTT
237185 CTTTTT
1 CTTTTT
237191 TTTGTTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
24 5 0.18
25 3 0.11
26 10 0.36
27 10 0.36
ACGTcount: A:0.02, C:0.16, G:0.05, T:0.77
Consensus pattern (24 bp):
CTTTTTCCTTTTATTTTTGTTCTT
Found at i:237199 original size:34 final size:33
Alignment explanation
Indices: 237136--237216 Score: 94
Period size: 34 Copynumber: 2.4 Consensus size: 33
237126 CCTTGTCCCT
237136 TTTTCTTTTTGATTTTTGTTCTTTCTTTTTTCC
1 TTTTCTTTTTGATTTTTGTTCTTTCTTTTTTCC
* * *
237169 TTTTCTTTTTG-TTCTTCTTTTTTTTGTTTTTTCC
1 TTTTCTTTTTGATT-TT-TGTTCTTTCTTTTTTCC
237203 TTTT-TGTTTTGATT
1 TTTTCT-TTTTGATT
237217 GAATCTTCGC
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
32 2 0.05
33 14 0.34
34 23 0.56
35 2 0.05
ACGTcount: A:0.02, C:0.12, G:0.07, T:0.78
Consensus pattern (33 bp):
TTTTCTTTTTGATTTTTGTTCTTTCTTTTTTCC
Found at i:240340 original size:24 final size:24
Alignment explanation
Indices: 240312--240360 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
240302 AACATAAAAT
* *
240312 AATTGGATGAAACAAAAAAAATGA
1 AATTGAATAAAACAAAAAAAATGA
* *
240336 AATTGAATAAAATAAAATAAATGA
1 AATTGAATAAAACAAAAAAAATGA
240360 A
1 A
240361 GATAAAATAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.65, C:0.02, G:0.12, T:0.20
Consensus pattern (24 bp):
AATTGAATAAAACAAAAAAAATGA
Found at i:240470 original size:22 final size:21
Alignment explanation
Indices: 240440--240573 Score: 89
Period size: 21 Copynumber: 6.2 Consensus size: 21
240430 GCAAAGAAAC
240440 TAAA-AATATAATGAAAATAAA
1 TAAATAATATAAT-AAAATAAA
240461 TAAATAATATAAATAAAAT-AA
1 TAAATAATAT-AATAAAATAAA
* *
240482 TAAATATATATATATATATATATA
1 TAAATA-ATATA-ATA-AAATAAA
* **
240506 TATATAA-AT-ATAAAAATGTA
1 TAAATAATATAAT-AAAATAAA
**
240526 TGTATAATATAATAAAAT-AA
1 TAAATAATATAATAAAATAAA
*
240546 TAAATAGTAATAATAATAATAAA
1 TAAATAAT-ATAATAA-AATAAA
240569 TAAAT
1 TAAAT
240574 GAAAAATAAA
Statistics
Matches: 91, Mismatches: 10, Indels: 22
0.74 0.08 0.18
Matches are distributed among these distances:
20 19 0.21
21 28 0.31
22 24 0.26
23 14 0.15
24 6 0.07
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (21 bp):
TAAATAATATAATAAAATAAA
Found at i:240481 original size:14 final size:13
Alignment explanation
Indices: 240456--240515 Score: 52
Period size: 14 Copynumber: 4.5 Consensus size: 13
240446 TATAATGAAA
240456 ATAAATAAATAAT
1 ATAAATAAATAAT
240469 ATAAAT-AA-AAT
1 ATAAATAAATAAT
*
240480 AATAAATATATATAT
1 -ATAAATAAATA-AT
* *
240495 ATATATATATATAT
1 ATAAATAAATA-AT
240509 ATAAATA
1 ATAAATA
240516 TAAAAATGTA
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
11 3 0.08
12 8 0.20
13 7 0.17
14 20 0.50
15 2 0.05
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (13 bp):
ATAAATAAATAAT
Found at i:240492 original size:2 final size:2
Alignment explanation
Indices: 240485--240517 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
240475 AAAATAATAA
*
240485 AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
240518 AAAATGTATG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:240518 original size:6 final size:6
Alignment explanation
Indices: 240456--240519 Score: 53
Period size: 6 Copynumber: 10.8 Consensus size: 6
240446 TATAATGAAA
* * *
240456 ATAAAT AAATAAT ATAAAT A-AAAT AATAAAT AT--AT ATATAT ATATAT
1 ATAAAT ATA-AAT ATAAAT ATAAAT -ATAAAT ATAAAT ATAAAT ATAAAT
*
240503 ATATAT ATAAAT ATAAA
1 ATAAAT ATAAAT ATAAA
240520 AATGTATGTA
Statistics
Matches: 50, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
4 4 0.08
5 4 0.08
6 33 0.66
7 9 0.18
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (6 bp):
ATAAAT
Found at i:240653 original size:2 final size:2
Alignment explanation
Indices: 240646--240672 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
240636 TGAAGTAAGA
240646 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
240673 ACGTTAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:241350 original size:37 final size:36
Alignment explanation
Indices: 241297--241398 Score: 136
Period size: 34 Copynumber: 2.9 Consensus size: 36
241287 ATGCTTATGG
* * *
241297 ATCCTATCTTTGGGAGTTTGAATCATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTA-AACTCT
*
241334 ATCCTATTTTTAGGAGTTTGAATCCTA--AAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAACTCT
*
241368 ATCTTATTTTTAGGAGTTTGAATCCTAGTAA
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAA
241399 GATGAAAAGA
Statistics
Matches: 58, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
34 31 0.53
35 1 0.02
36 2 0.03
37 24 0.41
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (36 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAAACTCT
Found at i:241888 original size:24 final size:24
Alignment explanation
Indices: 241856--241902 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
241846 CATGCATTAT
241856 ACATGTATCATCCTTACACGTATG
1 ACATGTATCATCCTTACACGTATG
* * *
241880 ACATTTATCATCTTTACTCGTAT
1 ACATGTATCATCCTTACACGTAT
241903 CTTTTCTTCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.28, C:0.23, G:0.09, T:0.40
Consensus pattern (24 bp):
ACATGTATCATCCTTACACGTATG
Found at i:242056 original size:25 final size:22
Alignment explanation
Indices: 242026--242074 Score: 62
Period size: 25 Copynumber: 2.1 Consensus size: 22
242016 AATTTTTTTG
242026 TGTTGCGAGAGTTTGAAAAACGTGT
1 TGTTGCGAGAG--TGAAAAA-GTGT
*
242051 TGTTGCGATAGTGAAAAAGTGT
1 TGTTGCGAGAGTGAAAAAGTGT
242073 TG
1 TG
242075 CGATAGTGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 6 0.26
23 7 0.30
25 10 0.43
ACGTcount: A:0.29, C:0.06, G:0.33, T:0.33
Consensus pattern (22 bp):
TGTTGCGAGAGTGAAAAAGTGT
Found at i:242075 original size:19 final size:19
Alignment explanation
Indices: 242051--242087 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
242041 AAAAACGTGT
242051 TGTTGCGATAGTGAAAAAG
1 TGTTGCGATAGTGAAAAAG
242070 TGTTGCGATAGTGAAAAA
1 TGTTGCGATAGTGAAAAA
242088 TCTAAAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.38, C:0.05, G:0.30, T:0.27
Consensus pattern (19 bp):
TGTTGCGATAGTGAAAAAG
Found at i:242597 original size:21 final size:20
Alignment explanation
Indices: 242573--242631 Score: 64
Period size: 21 Copynumber: 2.9 Consensus size: 20
242563 TATTCGCATT
242573 GCGATTTTTTAAAATCGCAAC
1 GCGA-TTTTTAAAATCGCAAC
** *
242594 GCGAATTTGGAAAATCGCAAT
1 GCG-ATTTTTAAAATCGCAAC
*
242615 GCGATATTTAAAATCGC
1 GCGATTTTTAAAATCGC
242632 GTTGCGAATT
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
20 11 0.35
21 19 0.61
22 1 0.03
ACGTcount: A:0.36, C:0.17, G:0.19, T:0.29
Consensus pattern (20 bp):
GCGATTTTTAAAATCGCAAC
Found at i:242637 original size:20 final size:19
Alignment explanation
Indices: 242522--242642 Score: 73
Period size: 20 Copynumber: 6.0 Consensus size: 19
242512 ACGAATTTGG
* *
242522 AAAATCGCATTGCGATAGTC
1 AAAATCGCATTGCGA-ATTT
* *
242542 AGAATCGCGTTGCG-ATTT
1 AAAATCGCATTGCGAATTT
* *
242560 ACATATTCGCATTGCGATTTTTT
1 A-A-AATCGCATTGCGA--ATTT
**
242583 AAAATCGCAACGCGAATTT
1 AAAATCGCATTGCGAATTT
*
242602 GGAAAATCGCAATGCGATATTT
1 --AAAATCGCATTGCGA-ATTT
*
242624 AAAATCGCGTTGCGAATTT
1 AAAATCGCATTGCGAATTT
242643 GGAAACTGAT
Statistics
Matches: 78, Mismatches: 15, Indels: 17
0.71 0.14 0.15
Matches are distributed among these distances:
18 3 0.04
19 7 0.09
20 35 0.45
21 24 0.31
22 5 0.06
23 4 0.05
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.31
Consensus pattern (19 bp):
AAAATCGCATTGCGAATTT
Found at i:242671 original size:40 final size:41
Alignment explanation
Indices: 242594--242799 Score: 129
Period size: 40 Copynumber: 5.1 Consensus size: 41
242584 AAATCGCAAC
* * * *
242594 GCGAATTTGGAAAATCGCA-ATGCGATATTTAAAATCGCGTT
1 GCGAATTTGGAAACTCG-ATTTGCGATACTGAAAATCGCGTT
* *
242635 GCGAATTTGGAAACT-GATTTGCGATACTGGAGATCGCGTT
1 GCGAATTTGGAAACTCGATTTGCGATACTGAAAATCGCGTT
* * ** * * ***
242675 GCG-ATTTAGAGA-TCGCGTTGTGATTTTCT-AAAATCGCAAC
1 GCGAATTTGGAAACTCGATTTGCGA--TACTGAAAATCGCGTT
* * * *
242715 GCGAATTTGGAAAATCGCA-ATGCGATAGTCAAAATCGCGTT
1 GCGAATTTGGAAACTCG-ATTTGCGATACTGAAAATCGCGTT
* * *
242756 GCGAATCTGGAAACT-GATTTGCGATACTGGAGATCGCGTT
1 GCGAATTTGGAAACTCGATTTGCGATACTGAAAATCGCGTT
242796 GCGA
1 GCGA
242800 TTTAGAGATC
Statistics
Matches: 122, Mismatches: 34, Indels: 19
0.70 0.19 0.11
Matches are distributed among these distances:
38 1 0.01
39 15 0.12
40 54 0.44
41 45 0.37
42 7 0.06
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.28
Consensus pattern (41 bp):
GCGAATTTGGAAACTCGATTTGCGATACTGAAAATCGCGTT
Found at i:242676 original size:20 final size:19
Alignment explanation
Indices: 242653--242694 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
242643 GGAAACTGAT
*
242653 TTGCGATACTGGAGATCGCG
1 TTGCGAT-CTAGAGATCGCG
*
242673 TTGCGATTTAGAGATCGCG
1 TTGCGATCTAGAGATCGCG
242692 TTG
1 TTG
242695 TGATTTTCTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.19, C:0.17, G:0.33, T:0.31
Consensus pattern (19 bp):
TTGCGATCTAGAGATCGCG
Found at i:242688 original size:19 final size:19
Alignment explanation
Indices: 242664--242700 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
242654 TGCGATACTG
242664 GAGATCGCGTTGCGATTTA
1 GAGATCGCGTTGCGATTTA
*
242683 GAGATCGCGTTGTGATTT
1 GAGATCGCGTTGCGATTT
242701 TCTAAAATCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.19, C:0.14, G:0.32, T:0.35
Consensus pattern (19 bp):
GAGATCGCGTTGCGATTTA
Found at i:242729 original size:121 final size:121
Alignment explanation
Indices: 242545--242822 Score: 475
Period size: 121 Copynumber: 2.3 Consensus size: 121
242535 GATAGTCAGA
* * *
242545 ATCGCGTTGCGATTTACATATTCGCATTGCGATTTTTTAAAATCGCAACGCGAATTTGGAAAATC
1 ATCGCGTTGCGATTTAGAGA-TCGCATTGCGATTTTCTAAAATCGCAACGCGAATTTGGAAAATC
* * *
242610 GCAATGCGATATTTAAAATCGCGTTGCGAATTTGGAAACTGATTTGCGATACTGGAG
65 GCAATGCGATAGTCAAAATCGCGTTGCGAATCTGGAAACTGATTTGCGATACTGGAG
* *
242667 ATCGCGTTGCGATTTAGAGATCGCGTTGTGATTTTCTAAAATCGCAACGCGAATTTGGAAAATCG
1 ATCGCGTTGCGATTTAGAGATCGCATTGCGATTTTCTAAAATCGCAACGCGAATTTGGAAAATCG
242732 CAATGCGATAGTCAAAATCGCGTTGCGAATCTGGAAACTGATTTGCGATACTGGAG
66 CAATGCGATAGTCAAAATCGCGTTGCGAATCTGGAAACTGATTTGCGATACTGGAG
242788 ATCGCGTTGCGATTTAGAGATCGCATTGCGATTTT
1 ATCGCGTTGCGATTTAGAGATCGCATTGCGATTTT
242823 GTTTGTCATT
Statistics
Matches: 146, Mismatches: 10, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
121 128 0.88
122 18 0.12
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.31
Consensus pattern (121 bp):
ATCGCGTTGCGATTTAGAGATCGCATTGCGATTTTCTAAAATCGCAACGCGAATTTGGAAAATCG
CAATGCGATAGTCAAAATCGCGTTGCGAATCTGGAAACTGATTTGCGATACTGGAG
Found at i:242797 original size:20 final size:19
Alignment explanation
Indices: 242774--242819 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
242764 GGAAACTGAT
* *
242774 TTGCGATACTGGAGATCGCG
1 TTGCGAT-CTAGAGATCGCA
*
242794 TTGCGATTTAGAGATCGCA
1 TTGCGATCTAGAGATCGCA
242813 TTGCGAT
1 TTGCGAT
242820 TTTGTTTGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.30
Consensus pattern (19 bp):
TTGCGATCTAGAGATCGCA
Found at i:242809 original size:19 final size:19
Alignment explanation
Indices: 242785--242821 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
242775 TGCGATACTG
*
242785 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTGCGATTTA
242804 GAGATCGCATTGCGATTT
1 GAGATCGCATTGCGATTT
242822 TGTTTGTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:244468 original size:221 final size:218
Alignment explanation
Indices: 244076--244502 Score: 728
Period size: 221 Copynumber: 1.9 Consensus size: 218
244066 CTGACCCGAA
* *
244076 ATATTTATCATCCACCTGACTCCGATCCAACCTAAATTTTTAAAGTATAAAGCTGATCTGACTCG
1 ATATATATCATCCACCTGACTCCGATCCAACCTAAATTTTTAAAGTATAAAGCTGATCTGACCCG
244141 ACTCGATAAAAAAATAAGGATTTAATTAAAAAACTAATAAATTTTTTAAGAACATCACATTATTA
66 ACTCGATAAAAAAATAAGGATTTAATTAAAAAACTAATAAATTTTTTAAGAACATCACATTATTA
* *
244206 TCATCGGGTCAGAGTTTTTCACCCTTCACCCGAACTGACCCGATCTAACCTTATCCCTTAAAACT
131 TCATCGGGTCAAAGTTTTTCACCCTTCACCCGAACTGACCCGACCTAACCTTATCCCTTAAAACT
*
244271 TTGACCCGACCCAAAATATATAT
196 TCGACCCGACCCAAAATATATAT
* * *
244294 ATATATATCATCCACCTGACTCCGATCCAACCTAAATTTTTAGAGTATAAATCTGATTTGACCCG
1 ATATATATCATCCACCTGACTCCGATCCAACCTAAATTTTTAAAGTATAAAGCTGATCTGACCCG
244359 ACTCGATAAAAAAATAAGGAATATTTAATTAAAAAACTAATAAATTTTTTAAGAACATCACATTA
66 ACTCGATAAAAAAATAAGG---ATTTAATTAAAAAACTAATAAATTTTTTAAGAACATCACATTA
* *
244424 TTATCATCGGGTCAAAGTTTTTCACCCTTCACCCGAATTGACCCGACCTAACCTTATCTCTTAAA
128 TTATCATCGGGTCAAAGTTTTTCACCCTTCACCCGAACTGACCCGACCTAACCTTATCCCTTAAA
*
244489 ACTTCGACCTGACC
193 ACTTCGACCCGACC
244503 TGATTTAAAA
Statistics
Matches: 195, Mismatches: 11, Indels: 3
0.93 0.05 0.01
Matches are distributed among these distances:
218 79 0.41
221 116 0.59
ACGTcount: A:0.37, C:0.23, G:0.10, T:0.31
Consensus pattern (218 bp):
ATATATATCATCCACCTGACTCCGATCCAACCTAAATTTTTAAAGTATAAAGCTGATCTGACCCG
ACTCGATAAAAAAATAAGGATTTAATTAAAAAACTAATAAATTTTTTAAGAACATCACATTATTA
TCATCGGGTCAAAGTTTTTCACCCTTCACCCGAACTGACCCGACCTAACCTTATCCCTTAAAACT
TCGACCCGACCCAAAATATATAT
Found at i:247191 original size:3 final size:3
Alignment explanation
Indices: 247185--247254 Score: 88
Period size: 3 Copynumber: 23.3 Consensus size: 3
247175 TTAAATAATA
*
247185 TAT TAT TAT TAT TAT TAT TAT TAT TAT AAT TACT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT
* * *
247231 TA- TAT TAA TAC TAT TAA TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
247255 TTGCAGGCTC
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
2 2 0.03
3 53 0.91
4 3 0.05
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:252736 original size:106 final size:106
Alignment explanation
Indices: 252519--253325 Score: 1272
Period size: 106 Copynumber: 7.6 Consensus size: 106
252509 ATATCATGCC
* * * ** * * *
252519 ACTCGAGACAACACAAGTTCAACTTCACGAAGAAGGGACTACTGGTTGTCAAAAAAAAATAACTG
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTC---AACAAACAACTT
252584 CCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
63 CCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
252628 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
252693 AATTTTAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
252734 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
252799 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
252840 ACTCCAGACAACGTATGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
252905 AATATCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
252946 ACTCCAGACAACGTATGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
253011 AATATCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
253052 ACTCTAGACAACGCAAGTTCAACTTCATGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
253117 AATTTCAGAGCCAATTTCAACTTCACAGCAAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
253158 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * * *
253223 AATTTCAGAGTCAATTTCAACTTCATAGCAAAGGATATTGA
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
253264 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTT
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTT
253326 TCAACTTCAC
Statistics
Matches: 658, Mismatches: 40, Indels: 3
0.94 0.06 0.00
Matches are distributed among these distances:
106 613 0.93
109 45 0.07
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.22
Consensus pattern (106 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:253523 original size:84 final size:84
Alignment explanation
Indices: 253381--253641 Score: 362
Period size: 84 Copynumber: 3.1 Consensus size: 84
253371 AAAGACCCCC
* * * *
253381 GAGTTCGATTACGCTCAGCTCTAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTAT
1 GAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTAT
253446 CTTCCAACCAAAGACCTTT
66 CTTCCAACCAAAGACCTTT
* * * * *
253465 GAGTTCGACTACGCTCAGCTCCAAGGTACATCATTTGCAACATAGCTCAAGGCAAGAAGGGCTAT
1 GAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTAT
*
253530 -TTGCCAACCAAAGACCTTC
66 CTT-CCAACCAAAGACCTTT
* * *
253549 GAGTTTGACTACGCTCAGCTCCGAGGCACATCATTTGCAGCATAGCTTAAGTTGAGAAGGGCTAT
1 GAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTAT
* *
253614 CTGCCAACCAAAGACCTGAT
66 CTTCCAACCAAAGACCT-TT
253634 GAGTTCGA
1 GAGTTCGA
253642 TTTCATTCAG
Statistics
Matches: 152, Mismatches: 22, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
83 2 0.01
84 142 0.93
85 8 0.05
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.24
Consensus pattern (84 bp):
GAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTAT
CTTCCAACCAAAGACCTTT
Found at i:253881 original size:3 final size:3
Alignment explanation
Indices: 253870--253946 Score: 113
Period size: 3 Copynumber: 26.3 Consensus size: 3
253860 TTAAATAATA
253870 TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
253917 TAT TA- TAT TAT TAA TAC TAT TAA TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
253947 TTTGCAGGCT
Statistics
Matches: 67, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
2 4 0.06
3 63 0.94
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:260298 original size:244 final size:243
Alignment explanation
Indices: 259624--260490 Score: 1184
Period size: 244 Copynumber: 3.6 Consensus size: 243
259614 CTTTGTCCAC
* * * *
259624 ATTATGTTTTTTTGTTCTCTTCTTCACTGAATGAGGAAGGCTGTTCATTCTGTGGCAAATATTAC
1 ATTATG-TTTTTTGTTCTCCTCTTCACTGAATGAGGAAGACTATTCATTCTTTGGCAAATATTAC
* * *
259689 ACACCTATTTACCTTTATGCCTGCCTGTGTTCATAACAGTTTTGGTTTGTGGTCATTGATATGCT
65 ATACCTATTTACCTTTATACCTGTCTGTGTTCATAACAGTTTTGGTTTGTGGTCATTGATATGCT
* *
259754 TACACTCATCATCATGCATGTTCCTTGTTATTAATGTGCTTATGGACGGTCTTGTGCTGATTAGA
130 TACACTCATCATCTTGCATGTTCCTTGTTATTAATGTGCTTATGGACGGTCCTGTGCTGATTAGA
* * *
259819 TTGTTTTCCTTCAGCACATAACATATTCATAAGCTACATGTATGGCCGT
195 TTGTTCTCCATCAGCACATAACATATTCATAAGCTACATGTATGGCCAT
* * * *
259868 TTTATGTTCTTTTGTTTTCCTCTTCACTGAATGAGGAACACTATCCATT-TTGTGGCAAATATTA
1 ATTATGTT-TTTTGTTCTCCTCTTCACTGAATGAGGAAGACTATTCATTCTT-TGGCAAATATTA
* *
259932 CATACCTATTTACCTTTATGCCGTCTTCCTGTGTTCATAACAGTTTTGGTTTGTGGTCATTGATA
64 CATACCTATTTACCTTTATACC-T-GT-CTGTGTTCATAACAGTTTTGGTTTGTGGTCATTGATA
* *
259997 TGCTTACACACATCATCTTGCATGTTCTTTGTTATTAATGTGCTTATGGACGGTCCTGTGCTGAT
126 TGCTTACACTCATCATCTTGCATGTTCCTTGTTATTAATGTGCTTATGGACGGTCCTGTGCTGAT
*
260062 TAGATTGTTCTCCATCAGCACATAACATATTCATAAGCTACACGTATGGCCAT
191 TAGATTGTTCTCCATCAGCACATAACATATTCATAAGCTACATGTATGGCCAT
*
260115 ATTATGTTTTTTGTTCTCCTCTTAACTGAATGAGGAAGACTATTCATTCTTTGGCAAATATTACA
1 ATTATGTTTTTTGTTCTCCTCTTCACTGAATGAGGAAGACTATTCATTCTTTGGCAAATATTACA
* * * * *
260180 TACCTGTTTACCTTTACACCTGTCTGTTTTCCATAGCAGTTTT-GTTTGGTGGTCATTGATGTGC
66 TACCTATTTACCTTTATACCTGTCTGTGTT-CATAACAGTTTTGGTTT-GTGGTCATTGATATGC
* *
260244 TTACACTCATCATCTTGTATGTTCCTTGTTCTTAATGTGCTTATGGACGGTCCTGTGCTGATTAG
129 TTACACTCATCATCTTGCATGTTCCTTGTTATTAATGTGCTTATGGACGGTCCTGTGCTGATTAG
* *
260309 ATTGTTCTCCGTCAGCACATAACATATTCATAAGCTACATATATGGCCAT
194 ATTGTTCTCCATCAGCACATAACATATTCATAAGCTACATGTATGGCCAT
* *
260359 ATCCCATATTTTTTTTGTTCTCCTC--CACTGAATGAGGAAGA-TCATTCATTCTTTGGCAAAAA
1 AT----TATGTTTTTTGTTCTCCTCTTCACTGAATGAGGAAGACT-ATTCATTCTTTGGCAAATA
* * *
260421 TTCCATACC----TA--TTTATACCTGTCTGT-TTCCATAGCAGTTTT-GTTTGGTGGTCATTAA
61 TTACATACCTATTTACCTTTATACCTGTCTGTGTT-CATAACAGTTTTGGTTT-GTGGTCATTGA
260478 TATGCTTACACTC
124 TATGCTTACACTC
260491 TTTCTCTGAT
Statistics
Matches: 565, Mismatches: 45, Indels: 31
0.88 0.07 0.05
Matches are distributed among these distances:
239 42 0.07
240 14 0.02
242 2 0.00
243 13 0.02
244 209 0.37
245 3 0.01
246 108 0.19
247 156 0.28
248 18 0.03
ACGTcount: A:0.22, C:0.20, G:0.16, T:0.41
Consensus pattern (243 bp):
ATTATGTTTTTTGTTCTCCTCTTCACTGAATGAGGAAGACTATTCATTCTTTGGCAAATATTACA
TACCTATTTACCTTTATACCTGTCTGTGTTCATAACAGTTTTGGTTTGTGGTCATTGATATGCTT
ACACTCATCATCTTGCATGTTCCTTGTTATTAATGTGCTTATGGACGGTCCTGTGCTGATTAGAT
TGTTCTCCATCAGCACATAACATATTCATAAGCTACATGTATGGCCAT
Found at i:262321 original size:12 final size:12
Alignment explanation
Indices: 262304--262369 Score: 89
Period size: 12 Copynumber: 5.6 Consensus size: 12
262294 TTAGCATAAA
262304 CGGGTATTGGGC
1 CGGGTATTGGGC
*
262316 CGGGTATTGGGT
1 CGGGTATTGGGC
*
262328 CGGGTATTGGGT
1 CGGGTATTGGGC
262340 C-GGTATTGGGC
1 CGGGTATTGGGC
* *
262351 CGGGAATCGGGC
1 CGGGTATTGGGC
262363 CGGGTAT
1 CGGGTAT
262370 ATATATATAT
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
11 10 0.21
12 38 0.79
ACGTcount: A:0.11, C:0.15, G:0.48, T:0.26
Consensus pattern (12 bp):
CGGGTATTGGGC
Found at i:262336 original size:24 final size:24
Alignment explanation
Indices: 262304--262369 Score: 89
Period size: 23 Copynumber: 2.8 Consensus size: 24
262294 TTAGCATAAA
*
262304 CGGGTATTGGGCCGGGTATTGGGT
1 CGGGTATTGGGCCGGGTATTGGGC
*
262328 CGGGTATTGGGTC-GGTATTGGGC
1 CGGGTATTGGGCCGGGTATTGGGC
* *
262351 CGGGAATCGGGCCGGGTAT
1 CGGGTATTGGGCCGGGTAT
262370 ATATATATAT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
23 19 0.53
24 17 0.47
ACGTcount: A:0.11, C:0.15, G:0.48, T:0.26
Consensus pattern (24 bp):
CGGGTATTGGGCCGGGTATTGGGC
Found at i:262496 original size:13 final size:12
Alignment explanation
Indices: 262465--262501 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
262455 TTTTAATATT
*
262465 TATCGGGTCGGG
1 TATCGGGGCGGG
262477 TATCGGGGCGGG
1 TATCGGGGCGGG
262489 TAATCGGGGCGGG
1 T-ATCGGGGCGGG
262502 GATTACCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 12 0.52
13 11 0.48
ACGTcount: A:0.11, C:0.16, G:0.54, T:0.19
Consensus pattern (12 bp):
TATCGGGGCGGG
Found at i:264885 original size:11 final size:12
Alignment explanation
Indices: 264855--264908 Score: 74
Period size: 12 Copynumber: 4.6 Consensus size: 12
264845 TTAGTATAAA
264855 CGGGTATTGGGC
1 CGGGTATTGGGC
*
264867 CGGGTATTGGGT
1 CGGGTATTGGGC
264879 C-GGTATTGGGC
1 CGGGTATTGGGC
* *
264890 CGGGAATCGGGC
1 CGGGTATTGGGC
264902 CGGGTAT
1 CGGGTAT
264909 ATATATATAT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
11 10 0.28
12 26 0.72
ACGTcount: A:0.11, C:0.17, G:0.48, T:0.24
Consensus pattern (12 bp):
CGGGTATTGGGC
Found at i:264913 original size:2 final size:2
Alignment explanation
Indices: 264906--264988 Score: 50
Period size: 2 Copynumber: 44.0 Consensus size: 2
264896 TCGGGCCGGG
* * * * * *
264906 TA TA TA TA TA TA TA TT TA AA T- TA AA TA TA TA TT TT TA TT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
264947 AA T- TA AA TT TA T- TA -A TA T- TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
264985 TA TA
1 TA TA
264989 AATAATTATT
Statistics
Matches: 60, Mismatches: 16, Indels: 10
0.70 0.19 0.12
Matches are distributed among these distances:
1 5 0.08
2 55 0.92
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:265025 original size:12 final size:12
Alignment explanation
Indices: 265008--265046 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
264998 TTTTAATATT
*
265008 TATCGGGTCGGG
1 TATCGGGGCGGG
265020 TATCGGGGCGGG
1 TATCGGGGCGGG
*
265032 TAATCGGGGTGGG
1 T-ATCGGGGCGGG
265045 TA
1 TA
265047 ATCAGGTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
12 13 0.54
13 11 0.46
ACGTcount: A:0.13, C:0.13, G:0.51, T:0.23
Consensus pattern (12 bp):
TATCGGGGCGGG
Found at i:265039 original size:13 final size:13
Alignment explanation
Indices: 265009--265049 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
264999 TTTAATATTT
*
265009 ATCGGGTCGGGT-
1 ATCGGGGCGGGTA
265021 ATCGGGGCGGGTA
1 ATCGGGGCGGGTA
*
265034 ATCGGGGTGGGTA
1 ATCGGGGCGGGTA
265047 ATC
1 ATC
265050 AGGTAATCGG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
12 11 0.42
13 15 0.58
ACGTcount: A:0.15, C:0.15, G:0.49, T:0.22
Consensus pattern (13 bp):
ATCGGGGCGGGTA
Found at i:265850 original size:14 final size:14
Alignment explanation
Indices: 265832--265890 Score: 61
Period size: 14 Copynumber: 4.4 Consensus size: 14
265822 TAAAGGGCTC
*
265832 GTTCGTTCATTTAC
1 GTTCGTTCATTTAT
265846 GTTCG---ATTATAT
1 GTTCGTTCATT-TAT
265858 GTTCGTTCATTTAT
1 GTTCGTTCATTTAT
* *
265872 GATCGTTTATTTAT
1 GTTCGTTCATTTAT
265886 GTTCG
1 GTTCG
265891 AACAGAGGGC
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
11 3 0.08
12 7 0.19
14 24 0.65
15 3 0.08
ACGTcount: A:0.17, C:0.14, G:0.17, T:0.53
Consensus pattern (14 bp):
GTTCGTTCATTTAT
Found at i:265881 original size:26 final size:27
Alignment explanation
Indices: 265832--265890 Score: 75
Period size: 26 Copynumber: 2.2 Consensus size: 27
265822 TAAAGGGCTC
*
265832 GTTCGTTCATTTACGTTCGATTA-TAT
1 GTTCGTTCATTTACGATCGATTATTAT
* *
265858 GTTCGTTCATTTATGATCGTTTATTTAT
1 GTTCGTTCATTTACGATCGATTA-TTAT
265886 GTTCG
1 GTTCG
265891 AACAGAGGGC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 20 0.71
28 8 0.29
ACGTcount: A:0.17, C:0.14, G:0.17, T:0.53
Consensus pattern (27 bp):
GTTCGTTCATTTACGATCGATTATTAT
Found at i:266127 original size:10 final size:10
Alignment explanation
Indices: 266112--266152 Score: 55
Period size: 10 Copynumber: 3.8 Consensus size: 10
266102 GTGTTTGCGT
266112 TGTTCGTTTA
1 TGTTCGTTTA
266122 TGTTCGTTTA
1 TGTTCGTTTA
266132 TTGTGTTCGTTTA
1 ---TGTTCGTTTA
266145 TGTTCGTT
1 TGTTCGTT
266153 CATTCGTGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
10 18 0.64
13 10 0.36
ACGTcount: A:0.07, C:0.10, G:0.22, T:0.61
Consensus pattern (10 bp):
TGTTCGTTTA
Found at i:266138 original size:23 final size:24
Alignment explanation
Indices: 266112--266169 Score: 91
Period size: 23 Copynumber: 2.5 Consensus size: 24
266102 GTGTTTGCGT
*
266112 TGTTCGTTTATGTTCGTTTATT-G
1 TGTTCGTTTATGTTCGTTCATTCG
266135 TGTTCGTTTATGTTCGTTCATTCG
1 TGTTCGTTTATGTTCGTTCATTCG
*
266159 TGTTTGTTTAT
1 TGTTCGTTTAT
266170 TTATTAAATG
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
23 21 0.66
24 11 0.34
ACGTcount: A:0.09, C:0.10, G:0.21, T:0.60
Consensus pattern (24 bp):
TGTTCGTTTATGTTCGTTCATTCG
Found at i:270468 original size:15 final size:15
Alignment explanation
Indices: 270427--270462 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
270417 ACTTCTCTTT
270427 ACAACCCAAAACCCA
1 ACAACCCAAAACCCA
*
270442 ACAACCCAAAACCTA
1 ACAACCCAAAACCCA
270457 ACAACC
1 ACAACC
270463 ATAAACGACT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.53, C:0.44, G:0.00, T:0.03
Consensus pattern (15 bp):
ACAACCCAAAACCCA
Found at i:272241 original size:29 final size:30
Alignment explanation
Indices: 272178--272246 Score: 77
Period size: 31 Copynumber: 2.3 Consensus size: 30
272168 TTATATGAAT
* *
272178 TATGGGATAAAGGTATGGAAAATGAAATGTT
1 TATGCGATAAAGGTATGG-AAATGAAATGTC
* **
272209 TATGTGATAAAGGTATGG-AATGTTATGTC
1 TATGCGATAAAGGTATGGAAATGAAATGTC
272238 TATGCGATA
1 TATGCGATA
272247 TAAATTATGT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
29 16 0.48
31 17 0.52
ACGTcount: A:0.36, C:0.03, G:0.28, T:0.33
Consensus pattern (30 bp):
TATGCGATAAAGGTATGGAAATGAAATGTC
Found at i:272462 original size:24 final size:25
Alignment explanation
Indices: 272435--272484 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 25
272425 ATTTATATGT
* *
272435 GGTCCTTCGGGATAAAT-TCTACGC
1 GGTCCTCCGGGACAAATCTCTACGC
272459 GGTCCTCCGGGACAAATCTCTACGC
1 GGTCCTCCGGGACAAATCTCTACGC
272484 G
1 G
272485 ACACTTAGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 15 0.65
25 8 0.35
ACGTcount: A:0.20, C:0.30, G:0.26, T:0.24
Consensus pattern (25 bp):
GGTCCTCCGGGACAAATCTCTACGC
Found at i:273137 original size:24 final size:23
Alignment explanation
Indices: 273099--273143 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
273089 CATGTTTATG
*
273099 AACACGTTCATGAACATATAAACA
1 AACACGTTCACGAACAT-TAAACA
*
273123 AACACGTTCGCGAACATTAAA
1 AACACGTTCACGAACATTAAA
273144 TGAACATATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.47, C:0.22, G:0.11, T:0.20
Consensus pattern (23 bp):
AACACGTTCACGAACATTAAACA
Found at i:273149 original size:23 final size:23
Alignment explanation
Indices: 273096--273167 Score: 72
Period size: 23 Copynumber: 3.1 Consensus size: 23
273086 GAACATGTTT
*
273096 ATGAACACGTTCATGAACATATAA
1 ATGAACACGTTCGTGAACAT-TAA
** *
273120 ACAAACACGTTCGCGAACATTAA
1 ATGAACACGTTCGTGAACATTAA
** *
273143 ATGAACATATTCGTGAACAATAA
1 ATGAACACGTTCGTGAACATTAA
273166 AT
1 AT
273168 AAACGAAAAT
Statistics
Matches: 38, Mismatches: 10, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
23 22 0.58
24 16 0.42
ACGTcount: A:0.46, C:0.18, G:0.12, T:0.24
Consensus pattern (23 bp):
ATGAACACGTTCGTGAACATTAA
Found at i:274969 original size:1 final size:1
Alignment explanation
Indices: 274965--274991 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
274955 GTAGTGCTAC
274965 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
274992 CCTCAGCCCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:281452 original size:27 final size:27
Alignment explanation
Indices: 281414--281465 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
281404 AGCTAGAGTG
281414 TGATAATACAGCAAGCAAAAAGAAGGA
1 TGATAATACAGCAAGCAAAAAGAAGGA
*
281441 TGATAATTCAGCAAGCAAAAAGAAG
1 TGATAATACAGCAAGCAAAAAGAAG
281466 TTAAAGTCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.54, C:0.12, G:0.21, T:0.13
Consensus pattern (27 bp):
TGATAATACAGCAAGCAAAAAGAAGGA
Found at i:283397 original size:21 final size:21
Alignment explanation
Indices: 283373--283421 Score: 62
Period size: 22 Copynumber: 2.3 Consensus size: 21
283363 TACCTTTTTT
* *
283373 TTATTTTTAAAAAATTTAATA
1 TTATTTTAAAAAAATTTAAAA
*
283394 TTATAATTAAAAAAATTTAAAA
1 TTAT-TTTAAAAAAATTTAAAA
283416 TTATTT
1 TTATTT
283422 CCTCCATCGC
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 5 0.22
22 18 0.78
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
TTATTTTAAAAAAATTTAAAA
Found at i:289111 original size:15 final size:15
Alignment explanation
Indices: 289091--289123 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
289081 GTGGAGGAAG
289091 AAAGATGAA-AAATGA
1 AAAGATGAAGAAAT-A
289106 AAAGATGAAGAAATA
1 AAAGATGAAGAAATA
289121 AAA
1 AAA
289124 AATGCAGGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.70, C:0.00, G:0.18, T:0.12
Consensus pattern (15 bp):
AAAGATGAAGAAATA
Found at i:291030 original size:198 final size:197
Alignment explanation
Indices: 290694--291089 Score: 758
Period size: 198 Copynumber: 2.0 Consensus size: 197
290684 ATGAAAAATC
290694 ATTACTTTAATATGAATAACTAAAAATCTTGTTTTCATAAATTTAAACCCCATGAGTGCACACAA
1 ATTACTTTAATATGAATAACTAAAAATCTTGTTTTCATAAATTTAAACCCCATGAGTGCACACAA
290759 GGCTCATACACTACAACAAGCAAAAAACTACACATGCTAACTTACAAGTAGTAAAATAAGGTTAG
66 GGCTCATACACTACAACAAGCAAAAAACTACACATGCTAACTTACAAGTAGTAAAATAAGGTTAG
290824 AAGTGTTACTTTACACCTAAAAGCT-AGAAATAGCCCAAGATTCACCCAATCATCTTATTCTCCT
131 AAGTGTTACTTTACACCTAAAAGCTAAGAAATAGCCCAAGATTCACCCAATCATCTTATTCTCCT
290888 TG
196 TG
290890 ATTACTTTAATATGAATAACTAAAAATCTTGTTTTCATAAATTTAAACCCCATGAGTGCACACAA
1 ATTACTTTAATATGAATAACTAAAAATCTTGTTTTCATAAATTTAAACCCCATGAGTGCACAC-A
290955 AGGCTCATACAACTACAACAAGCAAAAAACTACACATGCTAACTTACAAGTAGTAAAATAAGGTT
65 AGGCTCATAC-ACTACAACAAGCAAAAAACTACACATGCTAACTTACAAGTAGTAAAATAAGGTT
291020 AGAAGTGTTACTTTACACCTAAAAGCTAGAGAAATAGCCCAAGATTCACCCAATCATCTTATTCT
129 AGAAGTGTTACTTTACACCTAAAAGCTA-AGAAATAGCCCAAGATTCACCCAATCATCTTATTCT
291085 CCTTG
193 CCTTG
291090 TCCTTCCTCT
Statistics
Matches: 196, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
196 63 0.32
197 11 0.06
198 81 0.41
200 41 0.21
ACGTcount: A:0.41, C:0.21, G:0.11, T:0.28
Consensus pattern (197 bp):
ATTACTTTAATATGAATAACTAAAAATCTTGTTTTCATAAATTTAAACCCCATGAGTGCACACAA
GGCTCATACACTACAACAAGCAAAAAACTACACATGCTAACTTACAAGTAGTAAAATAAGGTTAG
AAGTGTTACTTTACACCTAAAAGCTAAGAAATAGCCCAAGATTCACCCAATCATCTTATTCTCCT
TG
Found at i:305527 original size:22 final size:22
Alignment explanation
Indices: 305502--305543 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
305492 TAAATAACAT
305502 AAAATAAAATACAGAAATGACC
1 AAAATAAAATACAGAAATGACC
305524 AAAATAAAATACAGAAATGA
1 AAAATAAAATACAGAAATGA
305544 TATGGAGCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.67, C:0.10, G:0.10, T:0.14
Consensus pattern (22 bp):
AAAATAAAATACAGAAATGACC
Found at i:306700 original size:3 final size:3
Alignment explanation
Indices: 306689--306738 Score: 64
Period size: 3 Copynumber: 16.7 Consensus size: 3
306679 ATACTTAAAC
* * * *
306689 AAT AGT AAT AAT AAT AAT AAT AAT ATT AAT ATT AAT AAT AAT TAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
306737 AA
1 AA
306739 CATATTAAAA
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (3 bp):
AAT
Found at i:307511 original size:9 final size:9
Alignment explanation
Indices: 307497--307522 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
307487 GGATGCTTAT
307497 CTTCTTCTC
1 CTTCTTCTC
307506 CTTCTTCTC
1 CTTCTTCTC
307515 CTTCTTCT
1 CTTCTTCT
307523 TCTCCCCGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.00, C:0.42, G:0.00, T:0.58
Consensus pattern (9 bp):
CTTCTTCTC
Found at i:314157 original size:139 final size:139
Alignment explanation
Indices: 313845--314137 Score: 442
Period size: 139 Copynumber: 2.1 Consensus size: 139
313835 CTCCCAATGA
* * * * *
313845 AAATGTTGATCCCTCGAGTGAGGTGTTGCTGATTCGACTCCATATGCGATGAATCGAGTTAAGAT
1 AAATATTGATCCCTCAAGTGAGGTGTTGCTGATTCAACTCCATATACGATGAATCGAGCTAAGAT
*
313910 TGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTAATCGAATGAGTTCTTCTCATTATGAACT
66 TGAACAAATTCTTCTCATTATGAACTTCTTCTCCCTAATCGAATGAGTTCTTCTCATTATGAACT
313975 CTCTACTGG
131 CTCTACTGG
* * * *
313984 AAATATTGATCCCTCAAGTGAGGTATTGTTGATTCAACTCCATATATGATGAATCGAGCTAAGGT
1 AAATATTGATCCCTCAAGTGAGGTGTTGCTGATTCAACTCCATATACGATGAATCGAGCTAAGAT
** * *
314049 TGAACAAATTCTTCTCATTATGAACTTCTTCTCCCTCGTCGGATGAGTTCTTCTCATTATGAATT
66 TGAACAAATTCTTCTCATTATGAACTTCTTCTCCCTAATCGAATGAGTTCTTCTCATTATGAACT
* *
314114 CTCTATTTG
131 CTCTACTGG
314123 AAATATTGATCCCTC
1 AAATATTGATCCCTC
314138 CATCGAGGCG
Statistics
Matches: 138, Mismatches: 16, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
139 138 1.00
ACGTcount: A:0.26, C:0.20, G:0.17, T:0.37
Consensus pattern (139 bp):
AAATATTGATCCCTCAAGTGAGGTGTTGCTGATTCAACTCCATATACGATGAATCGAGCTAAGAT
TGAACAAATTCTTCTCATTATGAACTTCTTCTCCCTAATCGAATGAGTTCTTCTCATTATGAACT
CTCTACTGG
Found at i:314373 original size:41 final size:43
Alignment explanation
Indices: 314316--314415 Score: 143
Period size: 42 Copynumber: 2.4 Consensus size: 43
314306 AGGTCTCATG
* *
314316 GATGGCCCAAAGGACTTA-TCATCTTGCTCGAAAGACTT-ATA
1 GATGGCCCAAAGGACTTACACATCATGCTCGAAAGACTTAATA
*
314357 GATGGCCCAAAGGACTTACACATCATGCTCGAAATACTTAATA
1 GATGGCCCAAAGGACTTACACATCATGCTCGAAAGACTTAATA
*
314400 -ATGGCCCGAAGGACTT
1 GATGGCCCAAAGGACTT
314416 TAGCTGATTC
Statistics
Matches: 53, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
41 18 0.34
42 32 0.60
43 3 0.06
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.24
Consensus pattern (43 bp):
GATGGCCCAAAGGACTTACACATCATGCTCGAAAGACTTAATA
Found at i:314374 original size:20 final size:21
Alignment explanation
Indices: 314316--314374 Score: 59
Period size: 20 Copynumber: 2.9 Consensus size: 21
314306 AGGTCTCATG
314316 GATGGCCCAAAGGACTTATCA
1 GATGGCCCAAAGGACTTATCA
** * *
314337 TCTTGCTCGAAA-GACTTAT-A
1 GATGGC-CCAAAGGACTTATCA
314357 GATGGCCCAAAGGACTTA
1 GATGGCCCAAAGGACTTA
314375 CACATCATGC
Statistics
Matches: 28, Mismatches: 8, Indels: 5
0.68 0.20 0.12
Matches are distributed among these distances:
19 4 0.14
20 10 0.36
21 10 0.36
22 4 0.14
ACGTcount: A:0.32, C:0.22, G:0.22, T:0.24
Consensus pattern (21 bp):
GATGGCCCAAAGGACTTATCA
Found at i:314492 original size:60 final size:58
Alignment explanation
Indices: 314418--314531 Score: 165
Period size: 60 Copynumber: 1.9 Consensus size: 58
314408 AAGGACTTTA
* * * *
314418 GCTGATTCGAAGTGTTATGAATCGAGCAATATGAAATGTTAACCCCTCTGGTGGGGCGTT
1 GCTGATTCAAAGTGTTATGAATCAAGCAA-AGGAAATGTTAACCCAT-TGGTGGGGCGTT
*
314478 GCTGATTCAAAGTGTTGTGAATCAAGCAAAGGAAATGTTAACCCATTGGTGGGG
1 GCTGATTCAAAGTGTTATGAATCAAGCAAAGGAAATGTTAACCCATTGGTGGGG
314532 TGATCGCTTG
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
58 8 0.16
59 15 0.31
60 26 0.53
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.28
Consensus pattern (58 bp):
GCTGATTCAAAGTGTTATGAATCAAGCAAAGGAAATGTTAACCCATTGGTGGGGCGTT
Found at i:327463 original size:21 final size:21
Alignment explanation
Indices: 327438--327485 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
327428 CCTCTAGTAC
327438 TGGTGGTACTTGTGTTGCTAG
1 TGGTGGTACTTGTGTTGCTAG
327459 TGGTGGTACTTGTGTTGCTAG
1 TGGTGGTACTTGTGTTGCTAG
327480 TGGTGG
1 TGGTGG
327486 CACATAAACG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.08, C:0.08, G:0.42, T:0.42
Consensus pattern (21 bp):
TGGTGGTACTTGTGTTGCTAG
Found at i:328726 original size:84 final size:84
Alignment explanation
Indices: 328579--328784 Score: 279
Period size: 84 Copynumber: 2.4 Consensus size: 84
328569 TGGGGCGTTA
* * * *
328579 CTGATTCGAAGTGTTGTGAATCGAGTAAAGTAAATGTTGAGAACATACCGCCCGAAGGTCTTATG
1 CTGATTCGAAGTG-TGTGAATCGAGAAAAGGAAATATTGAAAACATACCGCCCGAAGGTCTTATG
*
328644 GATGGCCCGAATAACTTAAG
65 GATAGCCCGAATAACTTAAG
* * * * *
328664 TTGATTTGAAGTGTGTGAATCAAGAAAAGGAAATATTGAAAACA-CCCTGCCTGAAGGTCTTATG
1 CTGATTCGAAGTGTGTGAATCGAGAAAAGGAAATATTGAAAACATACC-GCCCGAAGGTCTTATG
*
328728 GATAGCCCGAATGACTTAAG
65 GATAGCCCGAATAACTTAAG
*
328748 CTGATTCGAAGTGTGTGAATCGAGCAAAGGAAATATT
1 CTGATTCGAAGTGTGTGAATCGAGAAAAGGAAATATT
328785 ACCTCCTCTG
Statistics
Matches: 105, Mismatches: 15, Indels: 3
0.85 0.12 0.02
Matches are distributed among these distances:
83 2 0.02
84 92 0.88
85 11 0.10
ACGTcount: A:0.34, C:0.15, G:0.25, T:0.26
Consensus pattern (84 bp):
CTGATTCGAAGTGTGTGAATCGAGAAAAGGAAATATTGAAAACATACCGCCCGAAGGTCTTATGG
ATAGCCCGAATAACTTAAG
Found at i:329052 original size:36 final size:37
Alignment explanation
Indices: 329011--329084 Score: 123
Period size: 36 Copynumber: 2.0 Consensus size: 37
329001 GCTCCTTTCA
*
329011 AATTCATTTAAAAACATCGATAAACCCCT-AAAAATC
1 AATTCATTTAAAAACATCGAGAAACCCCTGAAAAATC
*
329047 AATTCATTTGAAAACATCGAGAAACCCCTGAAAAATC
1 AATTCATTTAAAAACATCGAGAAACCCCTGAAAAATC
329084 A
1 A
329085 GGCTTTGATT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
36 27 0.77
37 8 0.23
ACGTcount: A:0.49, C:0.22, G:0.07, T:0.23
Consensus pattern (37 bp):
AATTCATTTAAAAACATCGAGAAACCCCTGAAAAATC
Found at i:329157 original size:53 final size:52
Alignment explanation
Indices: 329047--329326 Score: 254
Period size: 53 Copynumber: 5.3 Consensus size: 52
329037 CCTAAAAATC
* * *
329047 AATTCATTTGAAAACATCGAGAAACCCCTGAAAAATCAGGCTTTGATTCTTTAA
1 AATTCATTTAAAAACATCGAGAAACCCCT-AAAAATCAGGC-TTAATTCTTTCA
** *
329101 AATTCATTTAAAAACATCGAGAAACCCCTAAAAATTGGGCTTAATTGCTATCA
1 AATTCATTTAAAAACATCGAGAAACCCCTAAAAATCAGGCTTAATT-CTTTCA
* * * *
329154 AATTCATTTGAAAACATCGAGAAACCCCTAAAAATCAGGATTAGTTTTTTCA
1 AATTCATTTAAAAACATCGAGAAACCCCTAAAAATCAGGCTTAATTCTTTCA
* * * ** * *
329206 AACTCATTTTAAAACATCAAGAAACCTTTAAAAATTAGGCTTAATTTCTTTGA
1 AATTCATTTAAAAACATCGAGAAACCCCTAAAAATCAGGCTTAA-TTCTTTCA
* * ** * ** * * *
329259 AAGTTCTTTTAAAAATCATCAAGAAACTTCTGAAAATCAAACTTAGTTTTTTTA
1 AA-TTCATTTAAAAA-CATCGAGAAACCCCTAAAAATCAGGCTTAATTCTTTCA
*
329313 AACTCATTTAAAAA
1 AATTCATTTAAAAA
329327 TCTTCAAGAA
Statistics
Matches: 185, Mismatches: 37, Indels: 9
0.80 0.16 0.04
Matches are distributed among these distances:
52 45 0.24
53 72 0.39
54 45 0.24
55 23 0.12
ACGTcount: A:0.41, C:0.16, G:0.10, T:0.33
Consensus pattern (52 bp):
AATTCATTTAAAAACATCGAGAAACCCCTAAAAATCAGGCTTAATTCTTTCA
Found at i:329320 original size:107 final size:105
Alignment explanation
Indices: 329047--329346 Score: 307
Period size: 107 Copynumber: 2.8 Consensus size: 105
329037 CCTAAAAATC
* * ** * * * *
329047 AATTCATTTGAAAACATCGAGAAACCCCTGAAAAATCAGGCTTTGATTCTTTAAAATTCATTTAA
1 AATTCATTTAAAAACATCAAGAAACCCCT-AAAAATCAGAATTAG-TTTTTTCAAACTCATTTAA
* ** *
329112 AAACATCGAGAAACCCCTAAAAATTGGGCTTAATTGCTATCA
64 AAACATCAAGAAACCTTTAAAAATTAGGCTTAATTGCTATCA
* * * *
329154 AATTCATTTGAAAACATCGAGAAACCCCTAAAAATCAGGATTAGTTTTTTCAAACTCATTTTAAA
1 AATTCATTTAAAAACATCAAGAAACCCCTAAAAATCAGAATTAGTTTTTTCAAACTCATTTAAAA
* * *
329219 ACATCAAGAAACCTTTAAAAATTAGGCTTAATTTCTTTGA
66 ACATCAAGAAACCTTTAAAAATTAGGCTTAATTGCTATCA
* ** * *
329259 AAGTTCTTTTAAAAATCATCAAGAAACTTCTGAAAATCA-AACTTAGTTTTTTTAAACTCATTTA
1 AA-TTCATTTAAAAA-CATCAAGAAACCCCTAAAAATCAGAA-TTAGTTTTTTCAAACTCATTTA
*
329323 AAAATCTTCAAGAAA-CTTTAAAAA
63 AAAA-CATCAAGAAACCTTTAAAAA
329347 AAAAATAGAC
Statistics
Matches: 166, Mismatches: 23, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
105 52 0.31
106 24 0.14
107 81 0.49
108 9 0.05
ACGTcount: A:0.42, C:0.16, G:0.09, T:0.32
Consensus pattern (105 bp):
AATTCATTTAAAAACATCAAGAAACCCCTAAAAATCAGAATTAGTTTTTTCAAACTCATTTAAAA
ACATCAAGAAACCTTTAAAAATTAGGCTTAATTGCTATCA
Found at i:329335 original size:53 final size:52
Alignment explanation
Indices: 329151--329346 Score: 164
Period size: 52 Copynumber: 3.7 Consensus size: 52
329141 TTAATTGCTA
* * * ** *
329151 TCAAATTCATTTGAAAA-CATCGAGAAACCCCTAAAAATCAGGA-TTAGTTTTT
1 TCAAACTCATTTAAAAATCATCAAGAAA-CTTTAAAAATCA-AACTTAGTTTTT
* * ** *
329203 TCAAACTCATTTTAAAA-CATCAAGAAACCTTTAAAAATTAGGCTTAATTTCTT
1 TCAAACTCATTTAAAAATCATCAAGAAA-CTTTAAAAATCAAACTTAGTTT-TT
* * * *
329256 TGAAAGTTCTTTTAAAAATCATCAAGAAACTTCTGAAAATCAAACTTAGTTTTT
1 TCAAA-CTCATTTAAAAATCATCAAGAAACTT-TAAAAATCAAACTTAGTTTTT
* *
329310 TTAAACTCATTTAAAAATCTTCAAGAAACTTTAAAAA
1 TCAAACTCATTTAAAAATCATCAAGAAACTTTAAAAA
329347 AAAAATAGAC
Statistics
Matches: 117, Mismatches: 22, Indels: 10
0.79 0.15 0.07
Matches are distributed among these distances:
51 1 0.01
52 45 0.38
53 29 0.25
54 18 0.15
55 24 0.21
ACGTcount: A:0.43, C:0.15, G:0.08, T:0.34
Consensus pattern (52 bp):
TCAAACTCATTTAAAAATCATCAAGAAACTTTAAAAATCAAACTTAGTTTTT
Found at i:331307 original size:11 final size:11
Alignment explanation
Indices: 331291--331322 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
331281 TTTGATCGGT
331291 TTTCTTTCTTC
1 TTTCTTTCTTC
*
331302 TTTCTTTCTTT
1 TTTCTTTCTTC
331313 TTTCTTTCTT
1 TTTCTTTCTT
331323 TTCTTTTTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (11 bp):
TTTCTTTCTTC
Found at i:331311 original size:15 final size:16
Alignment explanation
Indices: 331290--331328 Score: 62
Period size: 15 Copynumber: 2.5 Consensus size: 16
331280 ATTTGATCGG
331290 TTTTCTTTCTTCTTTC
1 TTTTCTTTCTTCTTTC
*
331306 -TTTCTTTTTTCTTTC
1 TTTTCTTTCTTCTTTC
331321 TTTTCTTT
1 TTTTCTTT
331329 TTGTCATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 14 0.67
16 7 0.33
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTTCTTTCTTCTTTC
Found at i:331312 original size:8 final size:8
Alignment explanation
Indices: 331291--331397 Score: 55
Period size: 8 Copynumber: 13.4 Consensus size: 8
331281 TTTGATCGGT
331291 TTTCTTTC
1 TTTCTTTC
331299 -TTCTTTC
1 TTTCTTTC
331306 TTTCTTT-
1 TTTCTTTC
331313 TTTCTTTC
1 TTTCTTTC
331321 TTTTCTTT-
1 -TTTCTTTC
331329 TTGTCATTT-
1 TT-TC-TTTC
*
331338 TCTCTTT-
1 TTTCTTTC
* *
331345 TTTTTTTA
1 TTTCTTTC
*
331353 TGTT-TTTA
1 T-TTCTTTC
*
331361 TGTTTTTTC
1 T-TTCTTTC
*
331370 TTTTCTTTT
1 -TTTCTTTC
*
331379 TTTCTTTT
1 TTTCTTTC
331387 TTTCTTTC
1 TTTCTTTC
331395 TTT
1 TTT
331398 TTGTGTGTTT
Statistics
Matches: 83, Mismatches: 7, Indels: 18
0.77 0.06 0.17
Matches are distributed among these distances:
7 24 0.29
8 37 0.45
9 21 0.25
10 1 0.01
ACGTcount: A:0.03, C:0.15, G:0.03, T:0.79
Consensus pattern (8 bp):
TTTCTTTC
Found at i:331325 original size:20 final size:19
Alignment explanation
Indices: 331291--331427 Score: 82
Period size: 21 Copynumber: 6.8 Consensus size: 19
331281 TTTGATCGGT
* *
331291 TTTCTTTCTTCTTTCTTTC
1 TTTCTTTTTTCTTTTTTTC
331310 TTT-TTTCTTTCTTTTCTTT-
1 TTTCTTT-TTTCTTTT-TTTC
*
331329 TTGTCATTTTCTCTTTTTTT-
1 TT-TC-TTTTTTCTTTTTTTC
* *
331349 TTTATGTTTTTATGTTTTTTC
1 TTTCT-TTTTTCT-TTTTTTC
331370 TTTTCTTTTTTTCTTTTTTTC
1 -TTTC-TTTTTTCTTTTTTTC
*
331391 TTTCTTTTTGTGTGTTTTTTC
1 TTTCTTTTT-TCT-TTTTTTC
* * *
331412 TATATCTTTTCTTTTT
1 TTTCTTTTTTCTTTTT
331428 CTCTCTGTGT
Statistics
Matches: 93, Mismatches: 13, Indels: 24
0.72 0.10 0.18
Matches are distributed among these distances:
18 4 0.04
19 26 0.28
20 23 0.25
21 27 0.29
22 12 0.13
23 1 0.01
ACGTcount: A:0.04, C:0.14, G:0.04, T:0.78
Consensus pattern (19 bp):
TTTCTTTTTTCTTTTTTTC
Found at i:331373 original size:7 final size:7
Alignment explanation
Indices: 331290--331393 Score: 77
Period size: 7 Copynumber: 14.1 Consensus size: 7
331280 ATTTGATCGG
331290 TTTTCTT
1 TTTTCTT
*
331297 TCTTCTT
1 TTTTCTT
331304 TCTTTCTT
1 T-TTTCTT
331312 TTTTCTTT
1 TTTTC-TT
331320 CTTTTCTT
1 -TTTTCTT
331328 TTTGTCATT
1 TTT-TC-TT
*
331337 TTCTCTT
1 TTTTCTT
331344 TTTT-TT
1 TTTTCTT
* *
331350 TTATGTT
1 TTTTCTT
*
331357 TTTATGTT
1 TTT-TCTT
331365 TTTTCTT
1 TTTTCTT
*
331372 TTCT-TT
1 TTTTCTT
331378 TTTTCTTT
1 TTTTC-TT
331386 TTTTCTT
1 TTTTCTT
331393 T
1 T
331394 CTTTTTGTGT
Statistics
Matches: 79, Mismatches: 9, Indels: 18
0.75 0.08 0.17
Matches are distributed among these distances:
6 10 0.13
7 32 0.41
8 28 0.35
9 9 0.11
ACGTcount: A:0.03, C:0.14, G:0.03, T:0.80
Consensus pattern (7 bp):
TTTTCTT
Found at i:331399 original size:21 final size:20
Alignment explanation
Indices: 331290--331399 Score: 80
Period size: 20 Copynumber: 5.5 Consensus size: 20
331280 ATTTGATCGG
* *
331290 TTTTC-TTTCTTCTTTCTTT
1 TTTTCTTTTTTTCTTTTTTT
* *
331309 CTTT-TTTCTTTCTTTTCTTT
1 TTTTCTTTTTTTCTTTT-TTT
* * *
331329 TTGTCATTTTCTCTTTTTTT
1 TTTTCTTTTTTTCTTTTTTT
* * * *
331349 TTTATGTTTTTATGTTTTTTC
1 TTT-TCTTTTTTTCTTTTTTT
331370 TTTTCTTTTTTTCTTTTTTT
1 TTTTCTTTTTTTCTTTTTTT
*
331390 CTTTCTTTTT
1 TTTTCTTTTT
331400 GTGTGTTTTT
Statistics
Matches: 67, Mismatches: 20, Indels: 7
0.71 0.21 0.07
Matches are distributed among these distances:
19 11 0.16
20 32 0.48
21 24 0.36
ACGTcount: A:0.03, C:0.15, G:0.03, T:0.80
Consensus pattern (20 bp):
TTTTCTTTTTTTCTTTTTTT
Found at i:331664 original size:2 final size:2
Alignment explanation
Indices: 331657--331706 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
331647 ATAACAAGGG
331657 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
331699 AT AT AT AT
1 AT AT AT AT
331707 TGAAAGAATA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:332750 original size:13 final size:13
Alignment explanation
Indices: 332734--332765 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
332724 AAAAACAAAG
332734 ATGCAAAATGGAA
1 ATGCAAAATGGAA
*
332747 ATGCAAAATGTAA
1 ATGCAAAATGGAA
332760 ATGCAA
1 ATGCAA
332766 CAAAGGAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.53, C:0.09, G:0.19, T:0.19
Consensus pattern (13 bp):
ATGCAAAATGGAA
Found at i:342106 original size:3 final size:3
Alignment explanation
Indices: 342098--342132 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
342088 ACTCCCTTAA
342098 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
342133 AGTTAATAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:363045 original size:38 final size:39
Alignment explanation
Indices: 362994--363075 Score: 130
Period size: 40 Copynumber: 2.1 Consensus size: 39
362984 TTCGAGTAAT
*
362994 ATATGCACCGTAGTGC-TACACATAAGGTCGTGCCCACC
1 ATATGCACCGTAGTACATACACATAAGGTCGTGCCCACC
*
363032 ATATGTACCGTAGTACATTACACATAAGGTCGTGCCCACC
1 ATATGCACCGTAGTACA-TACACATAAGGTCGTGCCCACC
363072 ATAT
1 ATAT
363076 ACACTTAGTG
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
38 14 0.35
40 26 0.65
ACGTcount: A:0.29, C:0.28, G:0.18, T:0.24
Consensus pattern (39 bp):
ATATGCACCGTAGTACATACACATAAGGTCGTGCCCACC
Found at i:363764 original size:65 final size:64
Alignment explanation
Indices: 363695--363854 Score: 248
Period size: 65 Copynumber: 2.5 Consensus size: 64
363685 GATTTAATTG
* *
363695 AACATCGAATGCATTTTATGCATCGATGCACATACCATGCATCGATGCACTCAGGGTTTTATAAA
1 AACATCGAATGCATTTTATGCATCGATGCACAAACCATGCATCGATGCACTCAGGCTTTT-TAAA
* ** * *
363760 AACATCGAATGTATTTGGTGCATCGATGCACAAACCATGCATCGATGCACTTAGGCTTTTTTAA
1 AACATCGAATGCATTTTATGCATCGATGCACAAACCATGCATCGATGCACTCAGGCTTTTTAAA
363824 AACATCGAATGCATTTTATGCATCGATGCAC
1 AACATCGAATGCATTTTATGCATCGATGCAC
363855 TCTTAGTGCA
Statistics
Matches: 85, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
64 31 0.36
65 54 0.64
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.30
Consensus pattern (64 bp):
AACATCGAATGCATTTTATGCATCGATGCACAAACCATGCATCGATGCACTCAGGCTTTTTAAA
Found at i:365819 original size:21 final size:21
Alignment explanation
Indices: 365794--365833 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
365784 GAGAAATTGT
365794 TTTCAAAATAT-AAAAATGATG
1 TTTCAAAAT-TGAAAAATGATG
365815 TTTCAAAATTGAAAAATGA
1 TTTCAAAATTGAAAAATGA
365834 AAATAAACTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.53, C:0.05, G:0.10, T:0.33
Consensus pattern (21 bp):
TTTCAAAATTGAAAAATGATG
Found at i:371991 original size:7 final size:7
Alignment explanation
Indices: 371979--372026 Score: 53
Period size: 7 Copynumber: 6.6 Consensus size: 7
371969 GGGGGAGAAA
371979 TGTTAAG
1 TGTTAAG
371986 TGTTAAG
1 TGTTAAG
371993 TGTTGATA-
1 TGTT-A-AG
*
372001 TGTTTAAA
1 TG-TTAAG
372009 TGTTAAG
1 TGTTAAG
372016 TGTTAAG
1 TGTTAAG
372023 TGTT
1 TGTT
372027 GATATATTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
7 27 0.75
8 6 0.17
9 3 0.08
ACGTcount: A:0.27, C:0.00, G:0.25, T:0.48
Consensus pattern (7 bp):
TGTTAAG
Found at i:374466 original size:5 final size:5
Alignment explanation
Indices: 374456--374481 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
374446 ATTCATATAT
374456 TCGGG TCGGG TCGGG TCGGG TCGGG T
1 TCGGG TCGGG TCGGG TCGGG TCGGG T
374482 GAAACTTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.19, G:0.58, T:0.23
Consensus pattern (5 bp):
TCGGG
Found at i:374745 original size:27 final size:28
Alignment explanation
Indices: 374710--374772 Score: 103
Period size: 28 Copynumber: 2.3 Consensus size: 28
374700 TGTTCGGGTT
374710 GGGTC-GGTTTTTT-AAGTATGATATTC
1 GGGTCGGGTTTTTTAAAGTATGATATTC
*
374736 GGGTCGGGTTTTTTAAAGTGTGATATTC
1 GGGTCGGGTTTTTTAAAGTATGATATTC
374764 GGGTCGGGT
1 GGGTCGGGT
374773 CAGGTCGAGT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
26 5 0.15
27 8 0.24
28 21 0.62
ACGTcount: A:0.16, C:0.08, G:0.35, T:0.41
Consensus pattern (28 bp):
GGGTCGGGTTTTTTAAAGTATGATATTC
Found at i:374997 original size:32 final size:34
Alignment explanation
Indices: 374927--375005 Score: 108
Period size: 37 Copynumber: 2.3 Consensus size: 34
374917 TATTTTGTTT
374927 GGGTCGGGTTTTTTAAGTGTGATATTCGGGCCAAGTC
1 GGGTCGGGTTTTTTAAGTGTGATATTCGGG---AGTC
*
374964 GGGTCGGGTTTTTTAAGTGTGATATT-TGG-GTC
1 GGGTCGGGTTTTTTAAGTGTGATATTCGGGAGTC
374996 GGGTCGGGTT
1 GGGTCGGGTT
375006 CGAGTTTAGG
Statistics
Matches: 41, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
32 13 0.32
36 2 0.05
37 26 0.63
ACGTcount: A:0.13, C:0.10, G:0.39, T:0.38
Consensus pattern (34 bp):
GGGTCGGGTTTTTTAAGTGTGATATTCGGGAGTC
Found at i:375189 original size:222 final size:220
Alignment explanation
Indices: 374734--375282 Score: 543
Period size: 222 Copynumber: 2.4 Consensus size: 220
374724 AGTATGATAT
374734 TCGGGTCGGGTTTTTTAAAGTGTGATATTCGGGTCGGGTCAGGTCGAGTTC-AGGTTTAGGGTGA
1 TCGGGTCGGGTTTTTT-AAGTGTGATATTCGGGTCGGGTC--G--G-GTTCGA-GTTTAGGGTGA
* *
374798 AAAAAAACGGACCGACCCGAAAATATATATAATTTGGGTCGGGTCGGATTAAGTCATTGTTTTTA
59 AAAAAAACGGACCGACCCGAAAATATATATAATTTGGGTCGGATCGGATTAAGTCACTGTTTTTA
* * * ** * *
374863 TTAAATAAAAATAATTTTTTATTATTTCAGGTCGGGTCGGGTCGAATGAAACTTTATTTTGTTTG
124 TTAAATAAAAATAATTTTTTATTATTTCAGGTCGGGT--GGTCGAATCAAACTTGAGTCAGGTCG
*** *
374928 GGTCGGGTTTTTTAAGTGTGATATTCGGGCCAAG
187 GGTCGGGAACTTTAAGTGTGATATTCGGACCAAG
* *
374962 TCGGGTCGGGTTTTTTAAGTGTGATATTTGGGTCGGGTCGGGTTCGAGTTTAGGGTGAAAAAAAC
1 TCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTCGGGTCGGGTTCGAGTTTAGGGTGAAAAAAAA
* * *
375027 CAGACCGATCCGAAAATATATATAATTTGGTTCGGATCGGATTAAGTCACTGTTTTTATTAAATA
66 CGGACCGACCCGAAAATATATATAATTTGGGTCGGATCGGATTAAGTCACTGTTTTTATTAAATA
* * * *
375092 AAAATATTTTTTTTATTATTTCGGGTCGGGT-TTCTAATTCATATA-TTCGAGTCAGGTCGGGTC
131 AAAATA-ATTTTTTATTATTTCAGGTCGGGTGGTCGAA-TCA-A-ACTT-GAGTCAGGTCGGGTC
** * ** **
375155 GGATGAAACTTTATTTTGTTCG-GATT-GGGTCGGG
191 GG--G-AACTTTA-AGTG-T-GATATTCGGACCAAG
* * * *
375189 TCGGGTTGGGTTTCTTTAAGTGTGATATTCGGGTCAGGTCGGGTT-GGGGTTAGGGTGAAAAAAA
1 TCGGGTCGGGTTT-TTTAAGTGTGATATTCGGGTCGGGTCGGGTTCGAGTTTAGGGTGAAAAAAA
* *
375253 TCGGACCGACCCGAAAAAAATATATAATTT
65 ACGGACCGACCCG-AAAATATATATAATTT
375283 TACCTTATAT
Statistics
Matches: 271, Mismatches: 36, Indels: 28
0.81 0.11 0.08
Matches are distributed among these distances:
220 4 0.01
221 2 0.01
222 90 0.33
223 36 0.13
225 2 0.01
226 4 0.01
227 68 0.25
228 64 0.24
229 1 0.00
ACGTcount: A:0.25, C:0.11, G:0.28, T:0.36
Consensus pattern (220 bp):
TCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTCGGGTCGGGTTCGAGTTTAGGGTGAAAAAAAA
CGGACCGACCCGAAAATATATATAATTTGGGTCGGATCGGATTAAGTCACTGTTTTTATTAAATA
AAAATAATTTTTTATTATTTCAGGTCGGGTGGTCGAATCAAACTTGAGTCAGGTCGGGTCGGGAA
CTTTAAGTGTGATATTCGGACCAAG
Found at i:375833 original size:16 final size:18
Alignment explanation
Indices: 375812--375857 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
375802 TATGAAATTG
375812 GATTCCAATTCC-T-ACA
1 GATTCCAATTCCTTCACA
375828 GATTCCAATTCCTTCACA
1 GATTCCAATTCCTTCACA
375846 GATTCCAATTCC
1 GATTCCAATTCC
375858 CTCATAAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
16 12 0.43
17 1 0.04
18 15 0.54
ACGTcount: A:0.28, C:0.33, G:0.07, T:0.33
Consensus pattern (18 bp):
GATTCCAATTCCTTCACA
Found at i:378292 original size:29 final size:29
Alignment explanation
Indices: 378241--378298 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
378231 GTGTTGATCG
*
378241 TAGGTCGCCATGTCATCCGGGCGACCTAC
1 TAGGTCGCCATGTCATCCCGGCGACCTAC
* * * *
378270 TAGGTCGTCATTTCTTCCCGGCGAGCTAC
1 TAGGTCGCCATGTCATCCCGGCGACCTAC
378299 AAGAGATTTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.16, C:0.33, G:0.26, T:0.26
Consensus pattern (29 bp):
TAGGTCGCCATGTCATCCCGGCGACCTAC
Found at i:378369 original size:24 final size:24
Alignment explanation
Indices: 378337--378385 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 24
378327 CCAACACGTT
378337 GGGCATCCGAG-GCCATCCGAACGA
1 GGGCATCCGAGCG-CATCCGAACGA
*
378361 GGGCATCCGAGCGCATCCGACCGA
1 GGGCATCCGAGCGCATCCGAACGA
378385 G
1 G
378386 CTATGCGAGG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 22 0.96
25 1 0.04
ACGTcount: A:0.22, C:0.35, G:0.35, T:0.08
Consensus pattern (24 bp):
GGGCATCCGAGCGCATCCGAACGA
Found at i:378371 original size:10 final size:10
Alignment explanation
Indices: 378358--378413 Score: 51
Period size: 10 Copynumber: 5.4 Consensus size: 10
378348 GCCATCCGAA
378358 CGAGGGCATC
1 CGAGGGCATC
*
378368 CGAGCGCATC
1 CGAGGGCATC
* *
378378 CGACCGAGCTATG
1 CGA--GGGC-ATC
378391 CGA-GGCATC
1 CGAGGGCATC
378400 CGAGGGCATC
1 CGAGGGCATC
378410 CGAG
1 CGAG
378414 CAAGGGTAGG
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
9 5 0.14
10 24 0.65
12 3 0.08
13 5 0.14
ACGTcount: A:0.21, C:0.32, G:0.36, T:0.11
Consensus pattern (10 bp):
CGAGGGCATC
Found at i:378490 original size:29 final size:29
Alignment explanation
Indices: 378418--378491 Score: 94
Period size: 29 Copynumber: 2.6 Consensus size: 29
378408 TCCGAGCAAG
*
378418 GGTAGGTCGCCATGCACGCTAGGCGACAT
1 GGTAGGTCGCCATGCACGCCAGGCGACAT
* * *
378447 TGTAGGTCACCATGCACGCCAGGTGACAT
1 GGTAGGTCGCCATGCACGCCAGGCGACAT
* *
378476 GGTAGGTTGCAATGCA
1 GGTAGGTCGCCATGCA
378492 TGCTGGGCGA
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.23, C:0.24, G:0.32, T:0.20
Consensus pattern (29 bp):
GGTAGGTCGCCATGCACGCCAGGCGACAT
Found at i:378540 original size:22 final size:22
Alignment explanation
Indices: 378515--378573 Score: 91
Period size: 22 Copynumber: 2.7 Consensus size: 22
378505 TGTCCTACAC
* *
378515 CCTGCTCCTCGCTGCATGCTCG
1 CCTGCTCCCCACTGCATGCTCG
378537 CCTGCTCCCCACTGCATGCTCG
1 CCTGCTCCCCACTGCATGCTCG
*
378559 CCTTCTCCCCACTGC
1 CCTGCTCCCCACTGC
378574 TCCATGCACC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.07, C:0.51, G:0.17, T:0.25
Consensus pattern (22 bp):
CCTGCTCCCCACTGCATGCTCG
Found at i:378903 original size:17 final size:17
Alignment explanation
Indices: 378881--378916 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
378871 TTATTAGTTT
378881 GTTAGTTTAGGGTTAGG
1 GTTAGTTTAGGGTTAGG
378898 GTTAGTTTAGGGTTAGG
1 GTTAGTTTAGGGTTAGG
378915 GT
1 GT
378917 AAAAAATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.17, C:0.00, G:0.42, T:0.42
Consensus pattern (17 bp):
GTTAGTTTAGGGTTAGG
Found at i:379091 original size:29 final size:29
Alignment explanation
Indices: 379049--379149 Score: 105
Period size: 30 Copynumber: 3.3 Consensus size: 29
379039 ATTAGTTAAT
379049 TAGTTT-TTAGTAGTAAATTATAATTAAAAAA
1 TAGTTTATTAGT--TAAATTAT-ATTAAAAAA
* *
379080 TCGTTTATTAGTTTAAGTTATATTAAAAAA
1 TAGTTTATTAG-TTAAATTATATTAAAAAA
* * *
379110 TAGTTTATTAATTGAAGTTATATTAAAGAA
1 TAGTTTATTAGTT-AAATTATATTAAAAAA
379140 TAGTTTATTA
1 TAGTTTATTA
379150 ATTGTTTAAG
Statistics
Matches: 62, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
29 2 0.03
30 43 0.69
31 12 0.19
32 4 0.06
33 1 0.02
ACGTcount: A:0.43, C:0.01, G:0.11, T:0.46
Consensus pattern (29 bp):
TAGTTTATTAGTTAAATTATATTAAAAAA
Found at i:379107 original size:30 final size:30
Alignment explanation
Indices: 379066--379153 Score: 131
Period size: 30 Copynumber: 2.9 Consensus size: 30
379056 TAGTAGTAAA
* * *
379066 TTATAATTAAAAAATCGTTTATTAGTTTAAG
1 TTAT-ATTAAAAAATAGTTTATTAATTGAAG
379097 TTATATTAAAAAATAGTTTATTAATTGAAG
1 TTATATTAAAAAATAGTTTATTAATTGAAG
*
379127 TTATATTAAAGAATAGTTTATTAATTG
1 TTATATTAAAAAATAGTTTATTAATTG
379154 TTTAAGGGAA
Statistics
Matches: 53, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
30 49 0.92
31 4 0.08
ACGTcount: A:0.43, C:0.01, G:0.10, T:0.45
Consensus pattern (30 bp):
TTATATTAAAAAATAGTTTATTAATTGAAG
Found at i:379118 original size:15 final size:16
Alignment explanation
Indices: 379095--379150 Score: 55
Period size: 15 Copynumber: 3.7 Consensus size: 16
379085 TATTAGTTTA
379095 AGTTATATTAAAAAAT
1 AGTTATATTAAAAAAT
***
379111 AGTT-TATTAATTGA-
1 AGTTATATTAAAAAAT
*
379125 AGTTATATTAAAGAAT
1 AGTTATATTAAAAAAT
379141 AGTT-TATTAA
1 AGTTATATTAA
379151 TTGTTTAAGG
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
14 4 0.12
15 20 0.62
16 8 0.25
ACGTcount: A:0.46, C:0.00, G:0.11, T:0.43
Consensus pattern (16 bp):
AGTTATATTAAAAAAT
Found at i:379235 original size:15 final size:16
Alignment explanation
Indices: 379207--379240 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
379197 GTTTGTTACT
379207 TTATAAGTTTATTATA
1 TTATAAGTTTATTATA
379223 TTATAAG-TTATTATA
1 TTATAAGTTTATTATA
379238 TTA
1 TTA
379241 AATTTTTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 11 0.61
16 7 0.39
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (16 bp):
TTATAAGTTTATTATA
Found at i:381462 original size:11 final size:11
Alignment explanation
Indices: 381442--381513 Score: 51
Period size: 11 Copynumber: 6.5 Consensus size: 11
381432 ATTTCATTAC
381442 TAGT-AATCAT
1 TAGTAAATCAT
381452 TAGTAAATCAT
1 TAGTAAATCAT
*
381463 TAGTATCAAATAAT
1 TAG--T-AAATCAT
* *
381477 TA--AATATTAA
1 TAGTAA-ATCAT
*
381487 TAATAAATCAT
1 TAGTAAATCAT
381498 TAGTAAATCAT
1 TAGTAAATCAT
381509 TAGTA
1 TAGTA
381514 TCAAATCTTT
Statistics
Matches: 49, Mismatches: 6, Indels: 13
0.72 0.09 0.19
Matches are distributed among these distances:
9 2 0.04
10 9 0.18
11 27 0.55
12 2 0.04
13 1 0.02
14 8 0.16
ACGTcount: A:0.49, C:0.07, G:0.07, T:0.38
Consensus pattern (11 bp):
TAGTAAATCAT
Found at i:381498 original size:46 final size:43
Alignment explanation
Indices: 381446--381548 Score: 152
Period size: 46 Copynumber: 2.3 Consensus size: 43
381436 CATTACTAGT
381446 AATCATTAGTAAATCATTAGTATCAAATAATTAAATATTAATAATA
1 AATCATTAGTAAATCATTAGTATCAAATAATTAAATATT--TAA-A
**
381492 AATCATTAGTAAATCATTAGTATCAAATCTTTAAATATTTAAA
1 AATCATTAGTAAATCATTAGTATCAAATAATTAAATATTTAAA
*
381535 AATCATTAATAAAT
1 AATCATTAGTAAAT
381549 TCGACTATGT
Statistics
Matches: 54, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
43 14 0.26
44 3 0.06
46 37 0.69
ACGTcount: A:0.50, C:0.08, G:0.04, T:0.38
Consensus pattern (43 bp):
AATCATTAGTAAATCATTAGTATCAAATAATTAAATATTTAAA
Found at i:381648 original size:14 final size:14
Alignment explanation
Indices: 381627--381936 Score: 153
Period size: 14 Copynumber: 22.9 Consensus size: 14
381617 ATTAGTAATA
381627 ATTATTAAATCATT
1 ATTATTAAATCATT
*
381641 AGTATTAAATCATT
1 ATTATTAAATCATT
*
381655 ATTA-TAAA--ATC
1 ATTATTAAATCATT
*
381666 ATTACTAAATCATT
1 ATTATTAAATCATT
*
381680 ACTATTAAATCATT
1 ATTATTAAATCATT
**
381694 ATTA-T-AATGGTT
1 ATTATTAAATCATT
381706 ATTATTAAATC---
1 ATTATTAAATCATT
381717 ATTATT--ATCATT
1 ATTATTAAATCATT
381729 ATTATTAAATCATT
1 ATTATTAAATCATT
* *
381743 TTTA-T-AATAATT
1 ATTATTAAATCATT
*
381755 ATTATCAAATCATT
1 ATTATTAAATCATT
*
381769 ACTAAATCATCAAATCATT
1 A-T---T-ATTAAATCATT
* *
381788 AAATATTAAA--ATC
1 -ATTATTAAATCATT
*
381801 ATTATTAAATAATT
1 ATTATTAAATCATT
* *
381815 ATT-GT-AATGATT
1 ATTATTAAATCATT
*
381827 ATTACTAAATCATT
1 ATTATTAAATCATT
*
381841 ATTA-T-AATGATT
1 ATTATTAAATCATT
*
381853 ATTATCAAATCATT
1 ATTATTAAATCATT
*
381867 ACTAAATCATCAAATCATT
1 A-T---T-ATTAAATCATT
* *
381886 AAATATTAAA--ATC
1 -ATTATTAAATCATT
381899 ATTATTAAATCATT
1 ATTATTAAATCATT
381913 A-TATTAAA--ATT
1 ATTATTAAATCATT
*
381924 ATTACTAAATCAT
1 ATTATTAAATCAT
381937 CAAATCATTA
Statistics
Matches: 228, Mismatches: 33, Indels: 70
0.69 0.10 0.21
Matches are distributed among these distances:
9 3 0.01
11 16 0.07
12 69 0.30
13 21 0.09
14 79 0.35
15 12 0.05
16 2 0.01
18 2 0.01
19 22 0.10
20 2 0.01
ACGTcount: A:0.45, C:0.09, G:0.02, T:0.44
Consensus pattern (14 bp):
ATTATTAAATCATT
Found at i:381711 original size:26 final size:26
Alignment explanation
Indices: 381627--381876 Score: 202
Period size: 26 Copynumber: 10.0 Consensus size: 26
381617 ATTAGTAATA
*
381627 ATTATTAAATCATTAGTATTAAATCATT
1 ATTATTAAATCATTATTA-T-AATCATT
* *
381655 ATTATAAAATCATTACTA-AATCATT
1 ATTATTAAATCATTATTATAATCATT
* **
381680 ACTATTAAATCATTATTATAATGGTT
1 ATTATTAAATCATTATTATAATCATT
381706 ATTATTAAATCATTA-T-T-ATCATT
1 ATTATTAAATCATTATTATAATCATT
* *
381729 ATTATTAAATCATTTTTATAATAATT
1 ATTATTAAATCATTATTATAATCATT
* * *
381755 ATTATCAAATCATTACTA-AATCATCAA
1 ATTATTAAATCATTATTATAATCAT--T
*
381782 ATCATTAAAT-ATTA--A-AATC---
1 ATTATTAAATCATTATTATAATCATT
* * *
381801 ATTATTAAATAATTATTGTAATGATT
1 ATTATTAAATCATTATTATAATCATT
* *
381827 ATTACTAAATCATTATTATAATGATT
1 ATTATTAAATCATTATTATAATCATT
* *
381853 ATTATCAAATCATTACTA-AATCAT
1 ATTATTAAATCATTATTATAATCAT
381877 CAAATCATTA
Statistics
Matches: 180, Mismatches: 29, Indels: 29
0.76 0.12 0.12
Matches are distributed among these distances:
19 9 0.05
20 4 0.02
23 21 0.12
24 7 0.04
25 34 0.19
26 81 0.45
27 8 0.04
28 16 0.09
ACGTcount: A:0.44, C:0.09, G:0.02, T:0.44
Consensus pattern (26 bp):
ATTATTAAATCATTATTATAATCATT
Found at i:381720 original size:23 final size:23
Alignment explanation
Indices: 381644--381996 Score: 148
Period size: 26 Copynumber: 14.6 Consensus size: 23
381634 AATCATTAGT
*
381644 ATTA-AATCATTATTATAAAATC
1 ATTATAATCATTATTATTAAATC
*
381666 ATTACTAAATCATTACTATTAAATC
1 ATTA-T-AATCATTATTATTAAATC
**
381691 ATTATTATAATGGTTATTATTAAATC
1 ---ATTATAATCATTATTATTAAATC
*
381717 ATTATTATCATTATTATTAAATC
1 ATTATAATCATTATTATTAAATC
* *
381740 ATTTTTATAATAATTATTATCAAATC
1 A---TTATAATCATTATTATTAAATC
* *
381766 ATTACTAAATCATCAAATCATTAAAT-
1 ATTA-T-AATCAT--TATTATTAAATC
* * *
381792 ATTAAAATCATTATTA-AATAATT
1 ATTATAATCATTATTATTA-AATC
* * *
381815 ATTGTAATGATTATTACTAAATC
1 ATTATAATCATTATTATTAAATC
* *
381838 ATTATTATAATGATTATTATCAAATC
1 ---ATTATAATCATTATTATTAAATC
* *
381864 ATTACTAAATCATCAAATCATTAAAT-
1 ATTA-T-AATCAT--TATTATTAAATC
*
381890 ATTA-AA--ATCATTATTAAATC
1 ATTATAATCATTATTATTAAATC
** *
381910 ATTATATTAAAATTATTACTAAATC
1 ATTATA--ATCATTATTATTAAATC
* *
381935 ATCA-AATCATTAAATATTAAAATC
1 ATTATAATCATT-ATTATT-AAATC
* *
381959 ATTACTAATCATCAAATCATTAAAT-
1 ATTA-TAATCAT--TATTATTAAATC
*
381984 ATTAAAATCATTA
1 ATTATAATCATTA
381997 CTAATCATCA
Statistics
Matches: 250, Mismatches: 46, Indels: 70
0.68 0.13 0.19
Matches are distributed among these distances:
19 9 0.04
20 4 0.02
21 4 0.02
22 15 0.06
23 51 0.20
24 24 0.10
25 45 0.18
26 73 0.29
27 21 0.08
28 4 0.02
ACGTcount: A:0.46, C:0.10, G:0.01, T:0.42
Consensus pattern (23 bp):
ATTATAATCATTATTATTAAATC
Found at i:381810 original size:35 final size:35
Alignment explanation
Indices: 381761--382108 Score: 384
Period size: 34 Copynumber: 10.5 Consensus size: 35
381751 AATTATTATC
381761 AAATCATTACTAAATCATCAAATCATTAAATATTA
1 AAATCATTACTAAATCATCAAATCATTAAATATTA
* * * * * *
381796 AAATCATTATTAAATAATTATTGTAATGATT-ATTACT-
1 AAATCATTACTAAATCATCA----AATCATTAAATATTA
* * *
381833 AAATCATTA-T---T-AT--AATGATT-ATTA-TC
1 AAATCATTACTAAATCATCAAATCATTAAATATTA
381859 AAATCATTACTAAATCATCAAATCATTAAATATTA
1 AAATCATTACTAAATCATCAAATCATTAAATATTA
381894 AAATCA-T--T--AT--T-AAATCATT--ATATTA
1 AAATCATTACTAAATCATCAAATCATTAAATATTA
*
381919 AAATTATTACTAAATCATCAAATCATTAAATATTA
1 AAATCATTACTAAATCATCAAATCATTAAATATTA
381954 AAATCATTACT-AATCATCAAATCATTAAATATTA
1 AAATCATTACTAAATCATCAAATCATTAAATATTA
381988 AAATCATTACT-AATCATCAAATCATTAAATATTA
1 AAATCATTACTAAATCATCAAATCATTAAATATTA
382022 AAATCATTACT-AATCATCAAATCATTAAATATTA
1 AAATCATTACTAAATCATCAAATCATTAAATATTA
*
382056 AAATCATGACTAAATCATCAAATCATTAAATATTA
1 AAATCATTACTAAATCATCAAATCATTAAATATTA
*
382091 AAATCATTATTAAATCAT
1 AAATCATTACTAAATCAT
382109 TTTTATGGTT
Statistics
Matches: 274, Mismatches: 14, Indels: 50
0.81 0.04 0.15
Matches are distributed among these distances:
25 12 0.04
26 21 0.08
27 9 0.03
28 2 0.01
30 5 0.02
31 2 0.01
32 4 0.01
33 15 0.05
34 105 0.38
35 79 0.29
36 1 0.00
37 9 0.03
38 4 0.01
39 6 0.02
ACGTcount: A:0.49, C:0.12, G:0.01, T:0.38
Consensus pattern (35 bp):
AAATCATTACTAAATCATCAAATCATTAAATATTA
Found at i:381842 original size:37 final size:37
Alignment explanation
Indices: 381796--381936 Score: 109
Period size: 37 Copynumber: 3.9 Consensus size: 37
381786 TTAAATATTA
* *
381796 AAATCATTATTA-AATAATTATTGT-AATGATTATTACT
1 AAATCATTATTATAATAATTATTATCAA--ATCATTACT
*
381833 AAATCATTATTATAATGATTATTATCAAATCATTACT
1 AAATCATTATTATAATAATTATTATCAAATCATTACT
* * * * *
381870 AAATCATCA-AATCATTAAATATTA--AAATCATTATT
1 AAATCATTATTAT-AATAATTATTATCAAATCATTACT
381905 AAATCATTA-TATTAA-AATTATTA-CTAAATCAT
1 AAATCATTATTA-TAATAATTATTATC-AAATCAT
381937 CAAATCATTA
Statistics
Matches: 85, Mismatches: 13, Indels: 13
0.77 0.12 0.12
Matches are distributed among these distances:
34 7 0.08
35 20 0.24
36 10 0.12
37 36 0.42
38 10 0.12
39 2 0.02
ACGTcount: A:0.47, C:0.09, G:0.02, T:0.42
Consensus pattern (37 bp):
AAATCATTATTATAATAATTATTATCAAATCATTACT
Found at i:381888 original size:16 final size:16
Alignment explanation
Indices: 381878--382099 Score: 153
Period size: 16 Copynumber: 13.6 Consensus size: 16
381868 CTAAATCATC
381878 AAATCATTAAATATTA
1 AAATCATTAAATATTA
381894 AAATCA-T---TATT-
1 AAATCATTAAATATTA
381905 AAATCATT--ATATTA
1 AAATCATTAAATATTA
* *
381919 AAATTATTACTAA-ATCATC
1 AAATCATTA--AATAT--TA
381938 AAATCATTAAATATTA
1 AAATCATTAAATATTA
*
381954 AAATCATTACTAATCA-TC
1 AAATCATTA--AAT-ATTA
381972 AAATCATTAAATATTA
1 AAATCATTAAATATTA
*
381988 AAATCATTACTAATCA-TC
1 AAATCATTA--AAT-ATTA
382006 AAATCATTAAATATTA
1 AAATCATTAAATATTA
*
382022 AAATCATTACTAATCA-TC
1 AAATCATTA--AAT-ATTA
382040 AAATCATTAAATATTA
1 AAATCATTAAATATTA
*
382056 AAATCATGACTAAATCA-TC
1 AAATCAT---TAAAT-ATTA
382075 AAATCATTAAATATTA
1 AAATCATTAAATATTA
382091 AAATCATTA
1 AAATCATTA
382100 TTAAATCATT
Statistics
Matches: 167, Mismatches: 12, Indels: 54
0.72 0.05 0.23
Matches are distributed among these distances:
11 6 0.04
12 5 0.03
13 4 0.02
14 7 0.04
15 5 0.03
16 68 0.41
17 4 0.02
18 42 0.25
19 25 0.15
20 1 0.01
ACGTcount: A:0.51, C:0.13, G:0.00, T:0.36
Consensus pattern (16 bp):
AAATCATTAAATATTA
Found at i:381897 original size:8 final size:9
Alignment explanation
Indices: 381859--382109 Score: 132
Period size: 8 Copynumber: 28.9 Consensus size: 9
381849 GATTATTATC
381859 AAATCATTA
1 AAATCATTA
*
381868 CTAAATCA-TC
1 --AAATCATTA
381878 AAATCATT-
1 AAATCATTA
381886 AAAT-ATTA
1 AAATCATTA
381894 AAATCATTA
1 AAATCATTA
381903 TTAAATCATT-
1 --AAATCATTA
381913 --AT-ATTA
1 AAATCATTA
*
381919 AAATTATTA
1 AAATCATTA
*
381928 CTAAATCA-TC
1 --AAATCATTA
381938 AAATCATT-
1 AAATCATTA
381946 AAAT-ATTA
1 AAATCATTA
381954 AAATCATTA
1 AAATCATTA
* *
381963 CTAATCA-TC
1 -AAATCATTA
381972 AAATCATT-
1 AAATCATTA
381980 AAAT-ATTA
1 AAATCATTA
381988 AAATCATTA
1 AAATCATTA
* *
381997 CTAATCA-TC
1 -AAATCATTA
382006 AAATCATT-
1 AAATCATTA
382014 AAAT-ATTA
1 AAATCATTA
382022 AAATCATTA
1 AAATCATTA
* *
382031 CTAATCA-TC
1 -AAATCATTA
382040 AAATCATT-
1 AAATCATTA
382048 AAAT-ATTA
1 AAATCATTA
*
382056 AAATCATGA
1 AAATCATTA
*
382065 CTAAATCA-TC
1 --AAATCATTA
382075 AAATCATT-
1 AAATCATTA
382083 AAAT-ATTA
1 AAATCATTA
382091 AAATCATTA
1 AAATCATTA
382100 TTAAATCATT
1 --AAATCATT
382110 TTTATGGTTA
Statistics
Matches: 192, Mismatches: 15, Indels: 66
0.70 0.05 0.24
Matches are distributed among these distances:
5 3 0.02
6 2 0.01
7 18 0.09
8 83 0.43
9 36 0.19
10 17 0.09
11 33 0.17
ACGTcount: A:0.50, C:0.13, G:0.00, T:0.36
Consensus pattern (9 bp):
AAATCATTA
Found at i:382379 original size:49 final size:49
Alignment explanation
Indices: 382316--382640 Score: 453
Period size: 49 Copynumber: 6.6 Consensus size: 49
382306 AATACTAATA
*
382316 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATT
1 ATTACT-AATCATTACTACCAAATCATTAAATATTAATAATAATTTCATT
382366 ATTACTAATCATTACTACCAAATCATTAAATATTAATAATAATTTCATT
1 ATTACTAATCATTACTACCAAATCATTAAATATTAATAATAATTTCATT
382415 ATTACTAATCATT-CTACCAAATCATTAAATATTAATAATAATTTCATT
1 ATTACTAATCATTACTACCAAATCATTAAATATTAATAATAATTTCATT
382463 ATTACTAATCATTACTACCAAATCATTCATTAAATATTAATAATAATTTCATT
1 ATTACTAATCATTACTACC-AA--A-TCATTAAATATTAATAATAATTTCATT
* *
382516 ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAATTTAATT
1 ATTACTAATCATTACTACCAAATCATTAAATATTAATAATAATTTCATT
* * * *
382565 ATTACTAATCATTACTA-AATAATTATTATAATTTTAA-ATATAAATTCATT
1 ATTACTAATCATTACTACCA-AATCATTA-AATATTAATA-ATAATTTCATT
* * *
382615 ATTA--AATCATGATTAGCAAATCATTA
1 ATTACTAATCATTACTACCAAATCATTA
382641 CTAAATCAAA
Statistics
Matches: 254, Mismatches: 12, Indels: 20
0.89 0.04 0.07
Matches are distributed among these distances:
48 65 0.26
49 112 0.44
50 29 0.11
52 3 0.01
53 45 0.18
ACGTcount: A:0.45, C:0.12, G:0.01, T:0.42
Consensus pattern (49 bp):
ATTACTAATCATTACTACCAAATCATTAAATATTAATAATAATTTCATT
Found at i:382623 original size:150 final size:148
Alignment explanation
Indices: 382316--382639 Score: 453
Period size: 150 Copynumber: 2.2 Consensus size: 148
382306 AATACTAATA
* *
382316 ATTACTAAATCATTACTATC-AA--A-TCATTAAATATTAATAATAATTTCATTATTACTAATCA
1 ATTATTAAATCATTACTACCAAATCATTCATTAAATATTAATAATAATTTCATTATTACTAATCA
* *
382377 TTACTACCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTCTACCAAATCATTA
66 TTACTACCAAATCATTAAATATTAATAATAATTTAATTATTACTAATCATTCTACAAAATCATTA
*
382442 AATATTAATAATAATTTC
131 AATATTAATAATAAATTC
382460 ATTATTACTAATCATTACTACCAAATCATTCATTAAATATTAATAATAATTTCATTATTACTAAT
1 ATTATTA--AATCATTACTACCAAATCATTCATTAAATATTAATAATAATTTCATTATTACTAAT
* *
382525 CATTACTATCAAATCATTAAATATTAATAATAATTTAATTATTACTAATCATTACTA-AATAATT
64 CATTACTACCAAATCATTAAATATTAATAATAATTTAATTATTACTAATCATT-CTACAA-AATC
*
382589 ATTATAATTTTAA-ATATAAATTC
127 ATTA-AATATTAATA-ATAAATTC
* * *
382612 ATTATTAAATCATGATTAGCAAATCATT
1 ATTATTAAATCATTACTACCAAATCATT
382640 ACTAAATCAA
Statistics
Matches: 159, Mismatches: 11, Indels: 14
0.86 0.06 0.08
Matches are distributed among these distances:
144 6 0.04
146 12 0.08
147 2 0.01
149 1 0.01
150 106 0.67
151 11 0.07
152 21 0.13
ACGTcount: A:0.45, C:0.12, G:0.01, T:0.42
Consensus pattern (148 bp):
ATTATTAAATCATTACTACCAAATCATTCATTAAATATTAATAATAATTTCATTATTACTAATCA
TTACTACCAAATCATTAAATATTAATAATAATTTAATTATTACTAATCATTCTACAAAATCATTA
AATATTAATAATAAATTC
Found at i:385808 original size:83 final size:82
Alignment explanation
Indices: 385670--385838 Score: 293
Period size: 83 Copynumber: 2.0 Consensus size: 82
385660 AATATTTTTT
*
385670 TAAAAAAACACTAAATATTTCTAAACACAATATTTTTTTAAACTGGAATAAATTAAACAAATTAA
1 TAAAAAAACACTAAATATTTCTAAACACAATATTTTTTTAAACGGGAATAAATTAAACAAATTAA
385735 TTTTATATAATCTAATA
66 TTTTATATAATCTAATA
* *
385752 TAAAATAAACACTGAATATTTTTAAACACAATATTTTTTTAAACGGGAATAAATTAAACAAATTA
1 TAAAA-AAACACTAAATATTTCTAAACACAATATTTTTTTAAACGGGAATAAATTAAACAAATTA
*
385817 ATTTTATATACTCTAATA
65 ATTTTATATAATCTAATA
385835 TAAA
1 TAAA
385839 CTAACTAACT
Statistics
Matches: 82, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
82 5 0.06
83 77 0.94
ACGTcount: A:0.50, C:0.09, G:0.04, T:0.37
Consensus pattern (82 bp):
TAAAAAAACACTAAATATTTCTAAACACAATATTTTTTTAAACGGGAATAAATTAAACAAATTAA
TTTTATATAATCTAATA
Found at i:385887 original size:14 final size:14
Alignment explanation
Indices: 385868--385894 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
385858 ACACATACAC
385868 AACAACAAAAAATG
1 AACAACAAAAAATG
385882 AACAACAAAAAAT
1 AACAACAAAAAAT
385895 AATAAATTAC
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:0.74, C:0.15, G:0.04, T:0.07
Consensus pattern (14 bp):
AACAACAAAAAATG
Found at i:386323 original size:28 final size:28
Alignment explanation
Indices: 386292--386345 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
386282 ATAATCTAAT
*
386292 ATATAACTTAAACTAACAAATTAATATA
1 ATATAACTTAAACTAACAAACTAATATA
386320 ATATAACTTAAACTAACAAACTAATA
1 ATATAACTTAAACTAACAAACTAATA
386346 ATTTATACTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (28 bp):
ATATAACTTAAACTAACAAACTAATATA
Found at i:386352 original size:28 final size:28
Alignment explanation
Indices: 386288--386352 Score: 96
Period size: 28 Copynumber: 2.3 Consensus size: 28
386278 TTATATAATC
*
386288 TAATATATAACTTAAACTAACAAATTAA
1 TAATATATAACTTAAACTAACAAACTAA
386316 T-ATAATATAACTTAAACTAACAAACTAA
1 TAAT-ATATAACTTAAACTAACAAACTAA
*
386344 TAATTTATA
1 TAATATATA
386353 CTAACAAACT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 2 0.06
28 29 0.88
29 2 0.06
ACGTcount: A:0.55, C:0.11, G:0.00, T:0.34
Consensus pattern (28 bp):
TAATATATAACTTAAACTAACAAACTAA
Found at i:386355 original size:21 final size:21
Alignment explanation
Indices: 386322--386370 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
386312 TTAATATAAT
386322 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
* *
386343 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
386364 ATTAACT
1 A-TAACT
386371 AAATTTCTGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Done.