Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008662.1 Hibiscus syriacus cultivar Beakdansim tig00111662_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: 1703488
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 8
Found at i:1116018 original size:63 final size:63
Alignment explanation
Indices: 1115885--1116203 Score: 453
Period size: 63 Copynumber: 5.0 Consensus size: 63
1115875 GGGATAATGG
* * * **
1115885 TTTCAAAAGAAACCGTCTCAAGAGAGACAAAAC-ATGTTTCAAGGGAAA-AAATCTCAAAGGTT
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACAAA-CTCAAATATT
*
1115947 TTTCAAGAGAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACAAACTCAAATATT
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACAAACTCAAATATT
* *
1116010 TTTTAAGAGAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACAAACTCAAATATT
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACAAACTCAAATATT
*
1116073 TTTCAAGAGAAACTGTCTTAAGAGAGACAAAACTTTGTTTCAAGGGAAACAAACTCAAATATTT
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACAAACTCAAATA-TT
* * * * * * *
1116137 ATTTTAAGAGAAACTGTATCAAAAGAGACAAAACTTTTTTTCAAAGGAAACAAACACAAAGATT
1 -TTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACAAACTCAAATATT
1116201 TTT
1 TTT
1116204 GATTTTGTTT
Statistics
Matches: 235, Mismatches: 18, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
62 30 0.13
63 145 0.62
64 7 0.03
65 53 0.23
ACGTcount: A:0.44, C:0.14, G:0.15, T:0.27
Consensus pattern (63 bp):
TTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACAAACTCAAATATT
Found at i:1116342 original size:37 final size:37
Alignment explanation
Indices: 1116235--1116361 Score: 123
Period size: 36 Copynumber: 3.5 Consensus size: 37
1116225 ATTTTAGAAT
* * * * **
1116235 TTTGTTTTAAAGAAAAAACTGTCTCCAGCGAGATGAAA
1 TTTGTTTT-TAGAGAAAACTATCTCAAGCGAGACAAAA
* * * *
1116273 TTTGTTTTGAGA-AAAATTGTTTCAAGCGAGACAAAA
1 TTTGTTTTTAGAGAAAACTATCTCAAGCGAGACAAAA
* *
1116309 TTTGTTTTTAGAGAAAACTATCTCAAGTGAGACAACA
1 TTTGTTTTTAGAGAAAACTATCTCAAGCGAGACAAAA
1116346 TTTGTTTTTA-AGAAAA
1 TTTGTTTTTAGAGAAAA
1116362 AATTTCTCTA
Statistics
Matches: 76, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
36 36 0.47
37 32 0.42
38 8 0.11
ACGTcount: A:0.39, C:0.10, G:0.17, T:0.34
Consensus pattern (37 bp):
TTTGTTTTTAGAGAAAACTATCTCAAGCGAGACAAAA
Found at i:1122294 original size:21 final size:21
Alignment explanation
Indices: 1122268--1122389 Score: 120
Period size: 21 Copynumber: 5.8 Consensus size: 21
1122258 ATAGAATTTG
1122268 TCCCGAAGGACCACATATATA
1 TCCCGAAGGACCACATATATA
*
1122289 TCCCGAAGGATCACATATATA
1 TCCCGAAGGACCACATATATA
* * * *
1122310 TTCCAAAGGACCAAATATGTA
1 TCCCGAAGGACCACATATATA
* *
1122331 TCCCGAAGAACCGA-ATATATG
1 TCCCGAAGGACC-ACATATATA
* * **
1122352 TTCCAAAGGATTACATATATA
1 TCCCGAAGGACCACATATATA
*
1122373 TTCCGAAGGACCACATA
1 TCCCGAAGGACCACATA
1122390 GAACCCTCGA
Statistics
Matches: 79, Mismatches: 20, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
20 1 0.01
21 77 0.97
22 1 0.01
ACGTcount: A:0.39, C:0.23, G:0.15, T:0.23
Consensus pattern (21 bp):
TCCCGAAGGACCACATATATA
Found at i:1122320 original size:42 final size:42
Alignment explanation
Indices: 1122273--1122389 Score: 146
Period size: 42 Copynumber: 2.8 Consensus size: 42
1122263 ATTTGTCCCG
*
1122273 AAGGACCACATATATATCCCGAAGGATCACATATATATTCCA
1 AAGGACCACATATATATCCCGAAGGACCACATATATATTCCA
* * * *
1122315 AAGGACCAAATATGTATCCCGAAGAACCGA-ATATATGTTCCA
1 AAGGACCACATATATATCCCGAAGGACC-ACATATATATTCCA
** *
1122357 AAGGATTACATATATATTCCGAAGGACCACATA
1 AAGGACCACATATATATCCCGAAGGACCACATA
1122390 GAACCCTCGA
Statistics
Matches: 62, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 1 0.02
42 60 0.97
43 1 0.02
ACGTcount: A:0.41, C:0.21, G:0.15, T:0.23
Consensus pattern (42 bp):
AAGGACCACATATATATCCCGAAGGACCACATATATATTCCA
Found at i:1123130 original size:20 final size:19
Alignment explanation
Indices: 1123065--1123130 Score: 61
Period size: 20 Copynumber: 3.6 Consensus size: 19
1123055 AATTCAAAAT
1123065 GGTATCGATAC-ACACCTTA
1 GGTATCGATACTAC-CCTTA
1123084 TGGTATCG--A-TACCCTTA
1 -GGTATCGATACTACCCTTA
*
1123101 -GTATCAATACTACCCTTTA
1 GGTATCGATACTACCC-TTA
1123120 GGTATCGATAC
1 GGTATCGATAC
1123131 CCATTGCATA
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
15 5 0.13
17 6 0.16
18 8 0.21
19 3 0.08
20 16 0.42
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.32
Consensus pattern (19 bp):
GGTATCGATACTACCCTTA
Found at i:1129353 original size:42 final size:42
Alignment explanation
Indices: 1129277--1129365 Score: 106
Period size: 42 Copynumber: 2.1 Consensus size: 42
1129267 CTTAAGGATC
* *
1129277 ACATATATATTCCAAAGGACCAAATATGTGTCCCGAAGAACA
1 ACATATATATTCCAAAGGACCAAATATATATCCCGAAGAACA
* ** * * *
1129319 ACATATATGTTCCAAAGGATTACATATATATCCCGAAGGACC
1 ACATATATATTCCAAAGGACCAAATATATATCCCGAAGAACA
1129361 ACATA
1 ACATA
1129366 GAACCCTCGA
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.42, C:0.21, G:0.13, T:0.24
Consensus pattern (42 bp):
ACATATATATTCCAAAGGACCAAATATATATCCCGAAGAACA
Found at i:1129364 original size:21 final size:21
Alignment explanation
Indices: 1129270--1129365 Score: 75
Period size: 21 Copynumber: 4.6 Consensus size: 21
1129260 ACCACTCCTT
* *
1129270 AAGGATCACATATATATTCCA
1 AAGGACCACATATATATCCCA
* * * *
1129291 AAGGACCAAATATGTGTCCCG
1 AAGGACCACATATATATCCCA
* * * *
1129312 AAGAACAACATATATGTTCCA
1 AAGGACCACATATATATCCCA
** *
1129333 AAGGATTACATATATATCCCG
1 AAGGACCACATATATATCCCA
1129354 AAGGACCACATA
1 AAGGACCACATA
1129366 GAACCCTCGA
Statistics
Matches: 55, Mismatches: 20, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
21 55 1.00
ACGTcount: A:0.42, C:0.21, G:0.15, T:0.23
Consensus pattern (21 bp):
AAGGACCACATATATATCCCA
Found at i:1130085 original size:35 final size:35
Alignment explanation
Indices: 1130039--1130107 Score: 97
Period size: 35 Copynumber: 2.0 Consensus size: 35
1130029 TAATTCAAAA
1130039 TGGTATCGATACATA-CCTTATA-GTATCCATACCCT
1 TGGTATCGATAC-TACCCTT-TAGGTATCCATACCCT
*
1130074 TGGTATCGATACTACCCTTTAGGTATCGATACCC
1 TGGTATCGATACTACCCTTTAGGTATCCATACCC
1130108 CTTGCATAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
34 4 0.13
35 27 0.87
ACGTcount: A:0.26, C:0.26, G:0.14, T:0.33
Consensus pattern (35 bp):
TGGTATCGATACTACCCTTTAGGTATCCATACCCT
Found at i:1136197 original size:85 final size:82
Alignment explanation
Indices: 1136047--1136219 Score: 215
Period size: 85 Copynumber: 2.1 Consensus size: 82
1136037 ATTATGCTGC
* * *
1136047 TTGTTTCCCCACTTGTTTCCTTAATTTAAGCTATAGTGGTTTAGTTTTTATTGATTATAATATAT
1 TTGTTTCCCCACTTGTTTCCCTAATTTAAGCTATAGTGGTTTAATTTTTATTAATTATAATATAT
1136112 ATAGAATAATTATAATA
66 ATAGAATAATTATAATA
**
1136129 TTTGTTTCTTCACTTGTTTCCCTAATTTAA-CTACGTACG-GTGTTTAATTTTTATTAATTATAA
1 -TTGTTTCCCCACTTGTTTCCCTAATTTAAGCTA--TA-GTG-GTTTAATTTTTATTAATTATAA
* * *
1136192 TATATATGGAATTATTATACTA
61 TATATATAGAATAATTATAATA
1136214 TTGTTT
1 TTGTTT
1136220 TTTTATGTTC
Statistics
Matches: 78, Mismatches: 8, Indels: 7
0.84 0.09 0.08
Matches are distributed among these distances:
82 3 0.04
83 26 0.33
84 9 0.12
85 40 0.51
ACGTcount: A:0.28, C:0.10, G:0.10, T:0.51
Consensus pattern (82 bp):
TTGTTTCCCCACTTGTTTCCCTAATTTAAGCTATAGTGGTTTAATTTTTATTAATTATAATATAT
ATAGAATAATTATAATA
Found at i:1146355 original size:21 final size:22
Alignment explanation
Indices: 1146331--1146374 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1146321 TGTAGCAGCA
*
1146331 CTGTAGCA-AGGTATCGGTTCC
1 CTGTAGCAGAGGAATCGGTTCC
*
1146352 CTGTAGCAGGGGAATCGGTTCC
1 CTGTAGCAGAGGAATCGGTTCC
1146374 C
1 C
1146375 CTCTGACAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.18, C:0.25, G:0.32, T:0.25
Consensus pattern (22 bp):
CTGTAGCAGAGGAATCGGTTCC
Found at i:1149600 original size:111 final size:112
Alignment explanation
Indices: 1149193--1149620 Score: 637
Period size: 112 Copynumber: 3.8 Consensus size: 112
1149183 CCCACAAATA
* ** * * *
1149193 TGATATTCCATTTCAAAGAAGCATAACATATCTATCTCTTCCAAGATTTGATATTCTCTGAGTGA
1 TGATATTCCCTTTCAAAGAAGCGGAACAGATCTCTCTCTTCCAAGATTTGATATTCCCTGAGTGA
1149258 CAGCGGAACAAGTCTACCTCGATTCAATGGATCAATTTTTCCAGATC
66 CAGCGGAACAAGTCTACCTCGATTCAATGGATCAATTTTTCCAGATC
*
1149305 TGATATTCCCTTTCAAAGAAGCGGAACATATCTCTCTCTTCCAAGATTTGATATTCCCTGAGTGA
1 TGATATTCCCTTTCAAAGAAGCGGAACAGATCTCTCTCTTCCAAGATTTGATATTCCCTGAGTGA
1149370 CAGCGGAACAAGTCTACCTCGATTCAATGGATCAATTTTTCCAGATC
66 CAGCGGAACAAGTCTACCTCGATTCAATGGATCAATTTTTCCAGATC
1149417 TGATATTCCCTTTCAAAGAAGCGGAACAGATCTCTCTCTTCCAAGATTTGATATTCCCTGAGTGA
1 TGATATTCCCTTTCAAAGAAGCGGAACAGATCTCTCTCTTCCAAGATTTGATATTCCCTGAGTGA
* * * * *
1149482 CAGTGGAACAAGTCTATCC-CGATTCAATGTATCAACTTTCCCATATC
66 CAGCGGAACAAGTCTA-CCTCGATTCAATGGATCAATTTTTCCAGATC
* * * *
1149529 TGATATTCCC-TT-AGAAGAAGCGGAAAAGATCTCTCTCTTTCAAGATTTGATATTCCATAAGTG
1 TGATATTCCCTTTCA-AAGAAGCGGAACAGATCTCTCTCTTCCAAGATTTGATATTCCCTGAGTG
** **
1149592 ACAATGGAACAAGTCTGTCTCGATTCAAT
65 ACAGCGGAACAAGTCTACCTCGATTCAAT
1149621 ATTTCCTGGT
Statistics
Matches: 295, Mismatches: 18, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
110 2 0.01
111 71 0.24
112 220 0.75
113 2 0.01
ACGTcount: A:0.30, C:0.22, G:0.16, T:0.32
Consensus pattern (112 bp):
TGATATTCCCTTTCAAAGAAGCGGAACAGATCTCTCTCTTCCAAGATTTGATATTCCCTGAGTGA
CAGCGGAACAAGTCTACCTCGATTCAATGGATCAATTTTTCCAGATC
Found at i:1150609 original size:83 final size:82
Alignment explanation
Indices: 1150408--1150684 Score: 357
Period size: 80 Copynumber: 3.3 Consensus size: 82
1150398 TCTTTTTTAA
* *
1150408 ATATATGGAATCATTATATTGTTTGTTTCACCACTTGTTTCCTTAATTTAAGCTATAATGGTTTA
1 ATATATGGAATCATTATAATATTTGTTTCACCACTTGTTTCCTTAATTTAAGCTAT-ATGGTTTA
1150473 G-TTTT-TT-ATTATAAT
65 GTTTTTATTGATTATAAT
* *
1150488 ATATATGGAATCATTATAATATTTGTTTCCCCTCTTGTTTCCTTAATTTAAGCTATAGTGGTTTA
1 ATATATGGAATCATTATAATATTTGTTTCACCACTTGTTTCCTTAATTTAAGCTATA-TGGTTTA
*
1150553 GTTTTTATTGATTATAGT
65 GTTTTTATTGATTATAAT
* * *
1150571 ATATATGAAATAATTATAATATTTGTTTCTCCACTTGTTTCCCTT-ATTTAAGCTACGTATGGTG
1 ATATATGGAATCATTATAATATTTGTTTCACCACTTGTTT-CCTTAATTTAAGCTA--TAT-G-G
*
1150635 TTTAATTTTTTATTGATTATAAT
61 TTT-AGTTTTTATTGATTATAAT
*
1150658 ATATATGGAATCATTATACTA-TTGTTT
1 ATATATGGAATCATTATAATATTTGTTT
1150685 TTTTATGTTC
Statistics
Matches: 173, Mismatches: 14, Indels: 14
0.86 0.07 0.07
Matches are distributed among these distances:
79 1 0.01
80 60 0.35
81 4 0.02
82 2 0.01
83 53 0.31
84 5 0.03
85 3 0.02
86 10 0.06
87 35 0.20
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.51
Consensus pattern (82 bp):
ATATATGGAATCATTATAATATTTGTTTCACCACTTGTTTCCTTAATTTAAGCTATATGGTTTAG
TTTTTATTGATTATAAT
Found at i:1153955 original size:19 final size:19
Alignment explanation
Indices: 1153922--1153960 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
1153912 ATGCATAGAT
1153922 ACTAATAAAACTAAACTAA
1 ACTAATAAAACTAAACTAA
1153941 ACTAAGTAAAA-TAAACTAA
1 ACTAA-TAAAACTAAACTAA
1153960 A
1 A
1153961 ATAGTTCTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.64, C:0.13, G:0.03, T:0.21
Consensus pattern (19 bp):
ACTAATAAAACTAAACTAA
Found at i:1154569 original size:36 final size:36
Alignment explanation
Indices: 1154525--1154663 Score: 233
Period size: 36 Copynumber: 3.9 Consensus size: 36
1154515 ACGATGCTGG
1154525 ACATTGATACACGAATGTACCAAAGCTGATATGATA
1 ACATTGATACACGAATGTACCAAAGCTGATATGATA
*
1154561 ACACTGATACACGAATGTACCAAAGCTGATATGATA
1 ACATTGATACACGAATGTACCAAAGCTGATATGATA
* *
1154597 ACATTGATACACGAATGTATCAAAGCTGACATGATA
1 ACATTGATACACGAATGTACCAAAGCTGATATGATA
* *
1154633 ACATTGATACACAAATGTATCAAAGCTGATA
1 ACATTGATACACGAATGTACCAAAGCTGATA
1154664 ATGGATAAAT
Statistics
Matches: 97, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 97 1.00
ACGTcount: A:0.42, C:0.17, G:0.16, T:0.24
Consensus pattern (36 bp):
ACATTGATACACGAATGTACCAAAGCTGATATGATA
Found at i:1161682 original size:66 final size:66
Alignment explanation
Indices: 1161606--1161737 Score: 264
Period size: 66 Copynumber: 2.0 Consensus size: 66
1161596 CTGAGACATA
1161606 GAATAATCTCTTGTCGTAGCAAATCCAAACCACGTGCTCAGTTAGAAGCTTGATTGTGAGAGGTT
1 GAATAATCTCTTGTCGTAGCAAATCCAAACCACGTGCTCAGTTAGAAGCTTGATTGTGAGAGGTT
1161671 T
66 T
1161672 GAATAATCTCTTGTCGTAGCAAATCCAAACCACGTGCTCAGTTAGAAGCTTGATTGTGAGAGGTT
1 GAATAATCTCTTGTCGTAGCAAATCCAAACCACGTGCTCAGTTAGAAGCTTGATTGTGAGAGGTT
1161737 T
66 T
1161738 TCGGTCTATA
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 66 1.00
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.30
Consensus pattern (66 bp):
GAATAATCTCTTGTCGTAGCAAATCCAAACCACGTGCTCAGTTAGAAGCTTGATTGTGAGAGGTT
T
Found at i:1167693 original size:20 final size:20
Alignment explanation
Indices: 1167670--1167738 Score: 84
Period size: 21 Copynumber: 3.4 Consensus size: 20
1167660 TACCGAAGTG
*
1167670 CCACATATTTGTCCCGAAGA
1 CCACATAATTGTCCCGAAGA
*
1167690 CCACATAATTGTCCCGGAGAA
1 CCACATAATTGTCCCGAAG-A
* *
1167711 ACACATAATTCTCCCGAATGA
1 CCACATAATTGTCCCGAA-GA
1167732 CCACATA
1 CCACATA
1167739 GACCCTCTAC
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
20 17 0.41
21 23 0.56
22 1 0.02
ACGTcount: A:0.35, C:0.30, G:0.13, T:0.22
Consensus pattern (20 bp):
CCACATAATTGTCCCGAAGA
Found at i:1168381 original size:54 final size:54
Alignment explanation
Indices: 1168315--1168453 Score: 192
Period size: 54 Copynumber: 2.6 Consensus size: 54
1168305 GAAATGGCAA
* * * *
1168315 GGGTATCGATACACTCTTCAGTGTACCGATACACAATTAACATTTGATGTTT-T
1 GGGTATCGATACACTCCTCAGTGTACCGATACACAAATAACATTCGATATTTAT
* *
1168368 GAGGTATAGATACACTCCTCAGTGTACCGATACACAAATGACATTCGATATTTAT
1 G-GGTATCGATACACTCCTCAGTGTACCGATACACAAATAACATTCGATATTTAT
*
1168423 GGGTATCGATAC-CTCCTCAGTGTCCCGATAC
1 GGGTATCGATACACTCCTCAGTGTACCGATAC
1168454 GCACTCATAC
Statistics
Matches: 76, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
53 19 0.25
54 55 0.72
55 2 0.03
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (54 bp):
GGGTATCGATACACTCCTCAGTGTACCGATACACAAATAACATTCGATATTTAT
Found at i:1174190 original size:21 final size:21
Alignment explanation
Indices: 1174162--1174225 Score: 60
Period size: 23 Copynumber: 3.0 Consensus size: 21
1174152 TCGTAATTTG
1174162 CACCGAAGTGCCACATAATTA
1 CACCGAAGTGCCACATAATTA
* *
1174183 TC-TCGAAG-GACCACATAGGGTTA
1 -CACCGAAGTG-CCACATA--ATTA
1174206 CACCGAAGTGCCACATAATT
1 CACCGAAGTGCCACATAATT
1174226 GTCCCGGAGG
Statistics
Matches: 33, Mismatches: 4, Indels: 11
0.69 0.08 0.23
Matches are distributed among these distances:
20 1 0.03
21 14 0.42
22 2 0.06
23 15 0.45
24 1 0.03
ACGTcount: A:0.34, C:0.27, G:0.19, T:0.20
Consensus pattern (21 bp):
CACCGAAGTGCCACATAATTA
Found at i:1174242 original size:21 final size:21
Alignment explanation
Indices: 1174216--1174264 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
1174206 CACCGAAGTG
* * *
1174216 CCACATAATTGTCCCGGAGGA
1 CCACATAATTCTCCAGAAGGA
1174237 CCACATAATTCTCCAGAAGGA
1 CCACATAATTCTCCAGAAGGA
1174258 CCACATA
1 CCACATA
1174265 GACCCTCTAC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.35, C:0.31, G:0.16, T:0.18
Consensus pattern (21 bp):
CCACATAATTCTCCAGAAGGA
Found at i:1174427 original size:21 final size:21
Alignment explanation
Indices: 1174398--1174447 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
1174388 AAAGAGTATA
* *
1174398 TTCACATTCAC-TGATTCCAAG
1 TTCATATTCACATG-TTCAAAG
1174419 TTCATATTCACATGTTCAAAG
1 TTCATATTCACATGTTCAAAG
1174440 TTCATATT
1 TTCATATT
1174448 TTCCTAACAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 24 0.92
22 2 0.08
ACGTcount: A:0.30, C:0.22, G:0.08, T:0.40
Consensus pattern (21 bp):
TTCATATTCACATGTTCAAAG
Found at i:1174905 original size:55 final size:56
Alignment explanation
Indices: 1174846--1174991 Score: 188
Period size: 55 Copynumber: 2.6 Consensus size: 56
1174836 CGAAATGACA
* * * * *
1174846 AGGGTATCTATAAACTCCTCAGTGTACCGATAGACAATTAAAATTTGATGTTTTG-
1 AGGGTATCGATACACTCCTCAGTGTACCGATACACAAATAAAATTCGATGTTTTGC
* * ***
1174901 AGGGTATCGATACACTCCTCAATGTATCGATACACAAATGGCATTCGATGTTTTGC
1 AGGGTATCGATACACTCCTCAGTGTACCGATACACAAATAAAATTCGATGTTTTGC
1174957 A-GGTATCGATACACTCCTCAGTGTACCGATACACA
1 AGGGTATCGATACACTCCTCAGTGTACCGATACACA
1174992 CTCATACAAT
Statistics
Matches: 78, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
55 77 0.99
56 1 0.01
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.30
Consensus pattern (56 bp):
AGGGTATCGATACACTCCTCAGTGTACCGATACACAAATAAAATTCGATGTTTTGC
Found at i:1177111 original size:138 final size:132
Alignment explanation
Indices: 1176887--1177156 Score: 406
Period size: 138 Copynumber: 2.0 Consensus size: 132
1176877 TATACTAAAG
1176887 GTGGTGATTAACTAGTATAATATAAAAATGAGTATAATATATTATATTATTTATCTAATTAATAA
1 GTGGTGATTAACTAGTATAATATAAAAATGAGTATAATATATTATATTATTTATCTAATTAATAA
1176952 AAATAGATATAATAATAATAATAAATT-ATTCA-TTCAGACTCAAATATCATATT-AAATCGGGT
66 AAATAGATATAATAATAATAAT--ATTCATTCACTT-AGACTC-AA-ATCATATTAAAATCGGGT
1177014 CAAAGTT
126 CAAAGTT
1177021 GTGGTGATTAACTAGT-T-ATATATAAAATGAGTATAAAATATATCATTATATTATTTATCTAAT
1 GTGGTGATTAACTAGTATAATATA-AAAATGAGTAT---A-ATAT-ATTATATTATTTATCTAAT
1177084 TAATAAAAATAGATATAATAATAATAATATTCATTCACTTAGACTCAAATCATATTAAAATCGGG
60 TAATAAAAATAGATATAATAATAATAATATTCATTCACTTAGACTCAAATCATATTAAAATCGGG
1177149 TCAAAGTT
125 TCAAAGTT
1177157 CGGTTCGGAT
Statistics
Matches: 127, Mismatches: 0, Indels: 16
0.89 0.00 0.11
Matches are distributed among these distances:
132 5 0.04
133 12 0.09
134 16 0.13
135 8 0.06
136 22 0.17
137 15 0.12
138 49 0.39
ACGTcount: A:0.46, C:0.07, G:0.10, T:0.37
Consensus pattern (132 bp):
GTGGTGATTAACTAGTATAATATAAAAATGAGTATAATATATTATATTATTTATCTAATTAATAA
AAATAGATATAATAATAATAATATTCATTCACTTAGACTCAAATCATATTAAAATCGGGTCAAAG
TT
Found at i:1177222 original size:15 final size:16
Alignment explanation
Indices: 1177185--1177231 Score: 69
Period size: 15 Copynumber: 3.0 Consensus size: 16
1177175 GGTAAATTAA
1177185 ATTCGGGTTGATTTCG
1 ATTCGGGTTGATTTCG
* *
1177201 GTTCGGGTTGCTTT-G
1 ATTCGGGTTGATTTCG
1177216 ATTCGGGTTGATTTCG
1 ATTCGGGTTGATTTCG
1177232 GTTCTTGGTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
15 13 0.50
16 13 0.50
ACGTcount: A:0.09, C:0.13, G:0.34, T:0.45
Consensus pattern (16 bp):
ATTCGGGTTGATTTCG
Found at i:1178461 original size:18 final size:18
Alignment explanation
Indices: 1178421--1178454 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1178411 TATAATAGCA
*
1178421 TGAATTGATGCTATGAAG
1 TGAATTCATGCTATGAAG
1178439 TGAATTCATGCT-TGAA
1 TGAATTCATGCTATGAA
1178455 ATTGAATGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.32, C:0.09, G:0.24, T:0.35
Consensus pattern (18 bp):
TGAATTCATGCTATGAAG
Found at i:1179254 original size:27 final size:27
Alignment explanation
Indices: 1179202--1179255 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 27
1179192 ATTACGATGG
*
1179202 AAGTACGATTTAGTTTTATATCAATTT
1 AAGTACGATTTAGTTTTATATAAATTT
* *
1179229 AAGTATCGTTTTATTTTTAT-TAAATTT
1 AAGTA-CGATTTAGTTTTATATAAATTT
1179256 TATATTTAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 11 0.48
28 12 0.52
ACGTcount: A:0.31, C:0.06, G:0.09, T:0.54
Consensus pattern (27 bp):
AAGTACGATTTAGTTTTATATAAATTT
Found at i:1180335 original size:16 final size:17
Alignment explanation
Indices: 1180293--1180336 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
1180283 ACATTTCACT
*
1180293 GTTATCAGATATTTACA
1 GTTATCAGATATATACA
* *
1180310 GATATTAGAT-TATACA
1 GTTATCAGATATATACA
1180326 GTTATCAGATA
1 GTTATCAGATA
1180337 CATATATCAG
Statistics
Matches: 21, Mismatches: 5, Indels: 2
0.75 0.18 0.07
Matches are distributed among these distances:
16 13 0.62
17 8 0.38
ACGTcount: A:0.39, C:0.09, G:0.14, T:0.39
Consensus pattern (17 bp):
GTTATCAGATATATACA
Found at i:1191092 original size:94 final size:94
Alignment explanation
Indices: 1190931--1191671 Score: 1259
Period size: 94 Copynumber: 7.7 Consensus size: 94
1190921 TGGAGCTGGA
1190931 AAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
1 AAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
*
1190996 ATATCCTTCGTTGTGAAGTTGAAATTGAG
66 ATATCCTTCGTTGTGAAGTTGAAATTGGG
*
1191025 AAATTGTTTATTGACAACCAGCGGTCCTTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
1 AAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
1191090 ATATCCTTCGTTGTGAAGTTGAAATTGGG
66 ATATCCTTCGTTGTGAAGTTGAAATTGGG
1191119 AAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
1 AAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
*
1191184 ATATCCTTCATTGTGAAGTTGAAATTGGG
66 ATATCCTTCGTTGTGAAGTTGAAATTGGG
1191213 AAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
1 AAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
*
1191278 ATATCCTTCGTTGTGAAGTTAAAATTGGG
66 ATATCCTTCGTTGTGAAGTTGAAATTGGG
*
1191307 AAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTATCTGGAGTCCA
1 AAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
1191372 ATATCCTTCGTTGTGAAGTTGAAATTGGG
66 ATATCCTTCGTTGTGAAGTTGAAATTGGG
1191401 AAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
1 AAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
1191466 ATATCCTTCGTTGTGAAGTTGAAATTGGTTCTGGAGCTGG
66 ATATCCTTCGTTGTGAAGTTGAAA-----T-T---G--GG
*
1191506 AAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTGGAGTCC
1 -AAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
1191571 AATATCCTTCGTTGTGAAGTTGAAATTGGCTCTTG
65 AATATCCTTCGTTGTGAAGTTGAAATTGG-----G
*
1191606 AAATTG-TTATTGACAACCAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
1 AAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
1191670 AT
66 AT
1191672 GTGAAGTTGA
Statistics
Matches: 618, Mismatches: 12, Indels: 30
0.94 0.02 0.05
Matches are distributed among these distances:
94 456 0.74
95 1 0.00
97 1 0.00
98 58 0.09
99 7 0.01
100 3 0.00
101 1 0.00
103 1 0.00
105 2 0.00
106 88 0.14
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (94 bp):
AAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
ATATCCTTCGTTGTGAAGTTGAAATTGGG
Found at i:1192532 original size:11 final size:11
Alignment explanation
Indices: 1192512--1192548 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
1192502 ACCCTAAACG
*
1192512 TTTTTCTCTTT
1 TTTTTTTCTTT
1192523 TTTTTTTC--T
1 TTTTTTTCTTT
1192532 TTTTTTTCTTT
1 TTTTTTTCTTT
1192543 TTTTTT
1 TTTTTT
1192549 CAACGTAGGA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
9 9 0.39
11 14 0.61
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (11 bp):
TTTTTTTCTTT
Found at i:1192534 original size:9 final size:9
Alignment explanation
Indices: 1192522--1192547 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
1192512 TTTTTCTCTT
1192522 TTTTTTTTC
1 TTTTTTTTC
1192531 TTTTTTTTC
1 TTTTTTTTC
1192540 TTTTTTTT
1 TTTTTTTT
1192548 TCAACGTAGG
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:0.08, G:0.00, T:0.92
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:1199705 original size:13 final size:13
Alignment explanation
Indices: 1199687--1199729 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
1199677 AAAAACATGG
1199687 AAAATAAAAAATA
1 AAAATAAAAAATA
1199700 AAAATAAAAAA-A
1 AAAATAAAAAATA
* * *
1199712 AACATGAAATATA
1 AAAATAAAAAATA
1199725 AAAAT
1 AAAAT
1199730 GCAAAATATG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
12 9 0.36
13 16 0.64
ACGTcount: A:0.79, C:0.02, G:0.02, T:0.16
Consensus pattern (13 bp):
AAAATAAAAAATA
Found at i:1199712 original size:17 final size:19
Alignment explanation
Indices: 1199687--1199728 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
1199677 AAAAACATGG
1199687 AAAATAAAAA-AT-AAAAAT
1 AAAA-AAAAACATGAAAAAT
*
1199705 AAAAAAAAACATGAAATAT
1 AAAAAAAAACATGAAAAAT
1199724 AAAAA
1 AAAAA
1199729 TGCAAAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 5 0.24
18 6 0.29
19 10 0.48
ACGTcount: A:0.81, C:0.02, G:0.02, T:0.14
Consensus pattern (19 bp):
AAAAAAAAACATGAAAAAT
Found at i:1203448 original size:4 final size:4
Alignment explanation
Indices: 1203439--1203517 Score: 65
Period size: 4 Copynumber: 19.5 Consensus size: 4
1203429 AAAATGTTAG
* *
1203439 AATA AATA AATA AATA AATAA AATA AA-A TACTA AATA AGTCA AATGA
1 AATA AATA AATA AATA AAT-A AATA AATA -AATA AATA AAT-A AAT-A
* *
1203486 AATG AATA AATA AATA AATT AA-A AA-A AATA AA
1 AATA AATA AATA AATA AATA AATA AATA AATA AA
1203518 AATTGATGAT
Statistics
Matches: 61, Mismatches: 9, Indels: 10
0.76 0.11 0.12
Matches are distributed among these distances:
3 6 0.10
4 43 0.70
5 12 0.20
ACGTcount: A:0.71, C:0.03, G:0.04, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:1203483 original size:26 final size:26
Alignment explanation
Indices: 1203444--1203514 Score: 58
Period size: 26 Copynumber: 2.8 Consensus size: 26
1203434 GTTAGAATAA
*
1203444 ATAAATAAAT-AAATAAAAT-AA-AA
1 ATAAATAAATCAAAAAAAATGAATAA
* **
1203467 TACTAAATAAGTCAAATGAAATGAATAA
1 -A-TAAATAAATCAAAAAAAATGAATAA
*
1203495 ATAAATAAATTAAAAAAAAT
1 ATAAATAAATCAAAAAAAAT
1203515 AAAAATTGAT
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
24 1 0.03
25 8 0.22
26 23 0.62
27 3 0.08
28 2 0.05
ACGTcount: A:0.69, C:0.03, G:0.04, T:0.24
Consensus pattern (26 bp):
ATAAATAAATCAAAAAAAATGAATAA
Found at i:1210509 original size:22 final size:19
Alignment explanation
Indices: 1210481--1210521 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 19
1210471 AGAAAACCAG
1210481 ACCGGTTTTGAACCGGGTCTGA
1 ACCGG-TTTG-ACC-GGTCTGA
1210503 ACCGGTTTGACCGGTCTGA
1 ACCGGTTTGACCGGTCTGA
1210522 CCCGACCCGA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.37
20 3 0.16
21 4 0.21
22 5 0.26
ACGTcount: A:0.17, C:0.24, G:0.32, T:0.27
Consensus pattern (19 bp):
ACCGGTTTGACCGGTCTGA
Found at i:1210541 original size:17 final size:17
Alignment explanation
Indices: 1210519--1210557 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
1210509 TTGACCGGTC
1210519 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
1210536 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
1210553 TGACC
1 TGACC
1210558 GTTGACCGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.18, C:0.46, G:0.23, T:0.13
Consensus pattern (17 bp):
TGACCCGACCCGACCGT
Found at i:1217807 original size:10 final size:10
Alignment explanation
Indices: 1217766--1217804 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
1217756 GGAAAACCTG
1217766 TTTGACCGAT
1 TTTGACCGAT
*
1217776 TTTGAACTGAT
1 TTTG-ACCGAT
*
1217787 TTTGACCGGT
1 TTTGACCGAT
1217797 TTTGACCG
1 TTTGACCG
1217805 GTTCGAACCG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
10 16 0.64
11 9 0.36
ACGTcount: A:0.18, C:0.18, G:0.23, T:0.41
Consensus pattern (10 bp):
TTTGACCGAT
Found at i:1217844 original size:19 final size:19
Alignment explanation
Indices: 1217822--1217860 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
1217812 CCGGTCTAAA
*
1217822 CGGTCTGAACTGGCCCGAC
1 CGGTCTGAACCGGCCCGAC
1217841 CGGTCTGAACCGGCCCGAC
1 CGGTCTGAACCGGCCCGAC
1217860 C
1 C
1217861 CAACCGACCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.15, C:0.41, G:0.31, T:0.13
Consensus pattern (19 bp):
CGGTCTGAACCGGCCCGAC
Found at i:1219467 original size:58 final size:58
Alignment explanation
Indices: 1219266--1219622 Score: 538
Period size: 58 Copynumber: 6.3 Consensus size: 58
1219256 GGGGGTTACA
* * *
1219266 CATACTAAGTGTATGAATTTTCATATTGGGCA-TTTGTGCGCAAAAAGTT-AGAAATT
1 CATACTAAGTGTATGAATTTCCGTATTGGGCACTTTGTGTGCAAAAAGTTAAGAAATT
*
1219322 CATACTAAGTGTATGAATTTCCGTATTGGGCACTTCGTGTGC-AAAAGTTAAG-AATT
1 CATACTAAGTGTATGAATTTCCGTATTGGGCACTTTGTGTGCAAAAAGTTAAGAAATT
*
1219378 C--ACTAAGTGTATGAATTTCCGTATTGGGCACTTTGCGTGCAAAAAGTTAAGAAATT
1 CATACTAAGTGTATGAATTTCCGTATTGGGCACTTTGTGTGCAAAAAGTTAAGAAATT
* *
1219434 CATACTAAGTGTATGAATTTCCATATTGTGCACTTTGTGTGC-AAAAGTTAAGAAATT
1 CATACTAAGTGTATGAATTTCCGTATTGGGCACTTTGTGTGCAAAAAGTTAAGAAATT
* *
1219491 CATACTTA-TGTATTAATTTCCGTATT--GCA-TTTGTGTGCAAAAAGTTAAGAAATT
1 CATACTAAGTGTATGAATTTCCGTATTGGGCACTTTGTGTGCAAAAAGTTAAGAAATT
* *
1219545 CATACTGAGTGTATGAATTTCCGTATTGGGCACTTTGTGTGCAAAAAGTTAAGAGATT
1 CATACTAAGTGTATGAATTTCCGTATTGGGCACTTTGTGTGCAAAAAGTTAAGAAATT
1219603 CATACTAAGTGTATGAATTT
1 CATACTAAGTGTATGAATTT
1219623 TTGTACGAAA
Statistics
Matches: 274, Mismatches: 16, Indels: 20
0.88 0.05 0.06
Matches are distributed among these distances:
53 9 0.03
54 62 0.23
55 27 0.10
56 63 0.23
57 34 0.12
58 79 0.29
ACGTcount: A:0.32, C:0.12, G:0.20, T:0.36
Consensus pattern (58 bp):
CATACTAAGTGTATGAATTTCCGTATTGGGCACTTTGTGTGCAAAAAGTTAAGAAATT
Found at i:1219467 original size:112 final size:112
Alignment explanation
Indices: 1219269--1219622 Score: 529
Period size: 111 Copynumber: 3.2 Consensus size: 112
1219259 GGTTACACAT
* * *
1219269 ACTAAGTGTATGAATTTTCATATTGGGCATTTGTGCGCAAAAAGTT-AGAAATTCATACTAAGTG
1 ACTAAGTGTATGAATTTCCGTATTGGGCATTTGTGTGCAAAAAGTTAAGAAATTCATACTAAGTG
*
1219333 TATGAATTTCCGTATTGGGCACTTCGTGTGCAAAAGTTAAGAATTC-
66 TATGAATTTCCGTATTGGGCACTTTGTGTGCAAAAGTTAAGAATTCA
*
1219379 ACTAAGTGTATGAATTTCCGTATTGGGCACTTTGCGTGCAAAAAGTTAAGAAATTCATACTAAGT
1 ACTAAGTGTATGAATTTCCGTATTGGGCA-TTTGTGTGCAAAAAGTTAAGAAATTCATACTAAGT
* *
1219444 GTATGAATTTCCATATTGTGCACTTTGTGTGCAAAAGTTAAGAAATTCA
65 GTATGAATTTCCGTATTGGGCACTTTGTGTGCAAAAGTTAAG-AATTCA
* * *
1219493 TACTTA-TGTATTAATTTCCGTATT--GCATTTGTGTGCAAAAAGTTAAGAAATTCATACTGAGT
1 -ACTAAGTGTATGAATTTCCGTATTGGGCATTTGTGTGCAAAAAGTTAAGAAATTCATACTAAGT
1219555 GTATGAATTTCCGTATTGGGCACTTTGTGTGCAAAAAGTTAAGAGATTCA
65 GTATGAATTTCCGTATTGGGCACTTTGTGTGC-AAAAGTTAAGA-ATTCA
1219605 TACTAAGTGTATGAATTT
1 -ACTAAGTGTATGAATTT
1219623 TTGTACGAAA
Statistics
Matches: 221, Mismatches: 15, Indels: 13
0.89 0.06 0.05
Matches are distributed among these distances:
110 27 0.12
111 79 0.36
112 79 0.36
113 15 0.07
114 17 0.08
115 4 0.02
ACGTcount: A:0.32, C:0.12, G:0.20, T:0.36
Consensus pattern (112 bp):
ACTAAGTGTATGAATTTCCGTATTGGGCATTTGTGTGCAAAAAGTTAAGAAATTCATACTAAGTG
TATGAATTTCCGTATTGGGCACTTTGTGTGCAAAAGTTAAGAATTCA
Found at i:1219589 original size:169 final size:167
Alignment explanation
Indices: 1219266--1219622 Score: 542
Period size: 169 Copynumber: 2.1 Consensus size: 167
1219256 GGGGGTTACA
*
1219266 CATACTAAGTGTATGAATTTTCATATTGGGCATTTGTGCGCAAAAAGTTAGAAATTCATACTAAG
1 CATACTAAGTGTATGAATTTCCATATTGGGCATTTGTGCGCAAAAAGTTAGAAATTCATACTAAG
1219331 TGTATGAATTTCCGTATTGGGCACTTCGTGTGCAAAAGTTAAGAATTCACTAAGTGTATGAATTT
66 TGTATGAATTTCCGTATT-GGCACTTCGTGTGCAAAAGTTAAGAATTCACTAAGTGTATGAATTT
1219396 CCGTATTGGGCACTTTGCGTGCAAAAAGTTAAGAAATT
130 CCGTATTGGGCACTTTGCGTGCAAAAAGTTAAGAAATT
* * *
1219434 CATACTAAGTGTATGAATTTCCATATTGTGCACTTTGTGTGC-AAAAGTTAAGAAATTCATACTT
1 CATACTAAGTGTATGAATTTCCATATTGGGCA-TTTGTGCGCAAAAAGTT-AGAAATTCATACTA
* * *
1219498 A-TGTATTAATTTCCGTATT-GCA-TTTGTGTGCAAAAAGTTAAGAAATTCATACTGAGTGTATG
64 AGTGTATGAATTTCCGTATTGGCACTTCGTGTGC-AAAAGTTAAG-AATTC--ACTAAGTGTATG
* *
1219560 AATTTCCGTATTGGGCACTTTGTGTGCAAAAAGTTAAGAGATT
125 AATTTCCGTATTGGGCACTTTGCGTGCAAAAAGTTAAGAAATT
1219603 CATACTAAGTGTATGAATTT
1 CATACTAAGTGTATGAATTT
1219623 TTGTACGAAA
Statistics
Matches: 174, Mismatches: 9, Indels: 11
0.90 0.05 0.06
Matches are distributed among these distances:
165 8 0.05
166 13 0.07
167 5 0.03
168 54 0.31
169 94 0.54
ACGTcount: A:0.32, C:0.12, G:0.20, T:0.36
Consensus pattern (167 bp):
CATACTAAGTGTATGAATTTCCATATTGGGCATTTGTGCGCAAAAAGTTAGAAATTCATACTAAG
TGTATGAATTTCCGTATTGGCACTTCGTGTGCAAAAGTTAAGAATTCACTAAGTGTATGAATTTC
CGTATTGGGCACTTTGCGTGCAAAAAGTTAAGAAATT
Found at i:1219949 original size:68 final size:68
Alignment explanation
Indices: 1219838--1220235 Score: 501
Period size: 68 Copynumber: 5.8 Consensus size: 68
1219828 ACAAGATTAA
* * *
1219838 AGGCCTAACCGTGCATTTGACAGAAATGTGTCAATCATGCCAGTTAGATGGAAGGCTAAGTGCCT
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGCTAAGTGCCT
1219903 TTG
66 TTG
* * * **
1219906 AGGCCTAACTGTGCATTTGATAGAAATGTGTCAATCATTCCAGTTAGATGAAAGGCTAAGTGTAT
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGCTAAGTGCCT
1219971 TTG
66 TTG
* * *
1219974 A-GCTCGAATTGTGCATTTGATAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGCTAAGTGCC
1 AGGC-CTAACTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGCTAA--G--
1220038 TTTGCCTTTG
61 --TGCCTTTG
** * * * * *
1220048 AGGCCTAACTGTGCATTTGGTAGAAAGATGTCAATTATGCCAATTCGATGAAAGGCTAGGTGCCT
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGCTAAGTGCCT
1220113 TTG
66 TTG
* *
1220116 AGGCCTAACTATGCATTTGACAGAAAGGTGGCAATCATGCCAGTTAGATGAAAGGCTAAGTGCCT
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGCTAAGTGCCT
1220181 TTG
66 TTG
* * * * *
1220184 AGGCCTGACTGTGCATATGACAGAAAGGTGTCAATTATGTCATTTAGATGAA
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAA
1220236 CGATTAAATA
Statistics
Matches: 286, Mismatches: 36, Indels: 16
0.85 0.11 0.05
Matches are distributed among these distances:
67 2 0.01
68 226 0.79
70 1 0.00
72 1 0.00
74 54 0.19
75 2 0.01
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.29
Consensus pattern (68 bp):
AGGCCTAACTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGCTAAGTGCCT
TTG
Found at i:1220116 original size:142 final size:142
Alignment explanation
Indices: 1219838--1220183 Score: 465
Period size: 142 Copynumber: 2.5 Consensus size: 142
1219828 ACAAGATTAA
* * * *
1219838 AGGCCTAACCGTGCATTTGACAGAAATGTGTCAATCATGCCAGTTAGATGGAAGGCTAA--G---
1 AGGCCGAACTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGCTAAGTGCCT
* *
1219898 -TGCCTTTGAGGCCTAACTGTGCATTTGATAGAAATGTGTCAATCATTCCAGTTAGATGAAAGGC
66 TTGCCTTTGAGGCCTAACTGTGCATTTGATAGAAATGTGTCAATCATGCCAATTAGATGAAAGGC
*
1219962 TAAGTGTATTTG
131 TAAGTGCATTTG
* *
1219974 A-GCTCGAATTGTGCATTTGATAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGCTAAGTGCC
1 AGGC-CGAACTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGCTAAGTGCC
* * *
1220038 TTTGCCTTTGAGGCCTAACTGTGCATTTGGTAGAAA-GATGTCAATTATGCCAATTCGATGAAAG
65 TTTGCCTTTGAGGCCTAACTGTGCATTTGATAGAAATG-TGTCAATCATGCCAATTAGATGAAAG
* *
1220102 GCTAGGTGCCTTTG
129 GCTAAGTGCATTTG
* * *
1220116 AGGCCTAACTATGCATTTGACAGAAAGGTGGCAATCATGCCAGTTAGATGAAAGGCTAAGTGCCT
1 AGGCCGAACTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGCTAAGTGCCT
1220181 TTG
66 TTG
1220184 AGGCCTGACT
Statistics
Matches: 182, Mismatches: 19, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
135 2 0.01
136 50 0.27
138 1 0.01
141 1 0.01
142 126 0.69
143 2 0.01
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.29
Consensus pattern (142 bp):
AGGCCGAACTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGCTAAGTGCCT
TTGCCTTTGAGGCCTAACTGTGCATTTGATAGAAATGTGTCAATCATGCCAATTAGATGAAAGGC
TAAGTGCATTTG
Found at i:1220211 original size:210 final size:210
Alignment explanation
Indices: 1219838--1220235 Score: 559
Period size: 210 Copynumber: 1.9 Consensus size: 210
1219828 ACAAGATTAA
* *
1219838 AGGCCTAACCGTGCATTTGACAGAAATGTGTCAATCATGCCAGTTAGATGGAAGGCTAAGTGCCT
1 AGGCCTAACCGTGCATTTGACAGAAATGTGTCAATCATGCCAATTAGATGAAAGGCTAAGTGCCT
* * * * *
1219903 TTGAGGCCTAACTGTGCATTTGATAGAAATGTGTCAATCATTCCAGTTAGATGAAAGGCTAAGTG
66 TTGAGGCCTAACTATGCATTTGACAGAAAGGTGGCAATCATGCCAGTTAGATGAAAGGCTAAGTG
* * * *
1219968 TATTTGAGCTCGAATTGTGCATTTGATAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGCTAA
131 CATTTGAGCTCGAACTGTGCATATGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGCTAA
1220033 GTGCCTTTGCCTTTG
196 GTGCCTTTGCCTTTG
* ** * * *
1220048 AGGCCTAACTGTGCATTTGGTAGAAA-GATGTCAATTATGCCAATTCGATGAAAGGCTAGGTGCC
1 AGGCCTAACCGTGCATTTGACAGAAATG-TGTCAATCATGCCAATTAGATGAAAGGCTAAGTGCC
1220112 TTTGAGGCCTAACTATGCATTTGACAGAAAGGTGGCAATCATGCCAGTTAGATGAAAGGCTAAGT
65 TTTGAGGCCTAACTATGCATTTGACAGAAAGGTGGCAATCATGCCAGTTAGATGAAAGGCTAAGT
* * * *
1220177 GCCTTTGAGGC-CTG-ACTGTGCATATGACAGAAAGGTGTCAATTATGTCATTTAGATGAA
130 GCATTTGA-GCTC-GAACTGTGCATATGACAGAAAGGTGTCAATCATGCCAGTTAGATGAA
1220236 CGATTAAATA
Statistics
Matches: 164, Mismatches: 21, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
209 1 0.01
210 160 0.98
211 3 0.02
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.29
Consensus pattern (210 bp):
AGGCCTAACCGTGCATTTGACAGAAATGTGTCAATCATGCCAATTAGATGAAAGGCTAAGTGCCT
TTGAGGCCTAACTATGCATTTGACAGAAAGGTGGCAATCATGCCAGTTAGATGAAAGGCTAAGTG
CATTTGAGCTCGAACTGTGCATATGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGCTAA
GTGCCTTTGCCTTTG
Found at i:1220634 original size:45 final size:45
Alignment explanation
Indices: 1220312--1220634 Score: 461
Period size: 45 Copynumber: 7.2 Consensus size: 45
1220302 AAGGTTGACG
*
1220312 TAATTGAAATGCATAT-GGTGCATTATTGGCATGAAAAGATGCCA
1 TAATTGAAATGCATATGGGTGCATTATCGGCATGAAAAGATGCCA
*
1220356 TAATTGAAATGCATATGGGTGCATTATCGGCAT-AAAAGGATGTCA
1 TAATTGAAATGCATATGGGTGCATTATCGGCATGAAAA-GATGCCA
** **
1220401 TAATTGAAATGCGCATGGGTGCATTATTAGCATGAAAAGATGCCA
1 TAATTGAAATGCATATGGGTGCATTATCGGCATGAAAAGATGCCA
*
1220446 TAATTGAAATGCATATGGGTGCATTATCGGCATGAAATGATGCCA
1 TAATTGAAATGCATATGGGTGCATTATCGGCATGAAAAGATGCCA
* *
1220491 TAATTGAAATGCATATGGGTGCACTATCGGCATGAAATGATGCCA
1 TAATTGAAATGCATATGGGTGCATTATCGGCATGAAAAGATGCCA
* * * * *
1220536 TAATTTAAATTCATATGGGTGCATTATAGGCATGAAAGGATTCCA
1 TAATTGAAATGCATATGGGTGCATTATCGGCATGAAAAGATGCCA
* * *
1220581 TAATTGAAATGCATATGGGTGCATTATCGGTATGAAAAGAGGCTA
1 TAATTGAAATGCATATGGGTGCATTATCGGCATGAAAAGATGCCA
*
1220626 TAAATGAAA
1 TAATTGAAA
1220635 AGGTATAATG
Statistics
Matches: 248, Mismatches: 28, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
44 20 0.08
45 224 0.90
46 4 0.02
ACGTcount: A:0.36, C:0.12, G:0.24, T:0.29
Consensus pattern (45 bp):
TAATTGAAATGCATATGGGTGCATTATCGGCATGAAAAGATGCCA
Found at i:1224005 original size:20 final size:19
Alignment explanation
Indices: 1223961--1224011 Score: 70
Period size: 17 Copynumber: 2.7 Consensus size: 19
1223951 CCGATTCAAG
1223961 TGGTATCGATACCAAAGGA
1 TGGTATCGATACCAAAGGA
*
1223980 --GTATCGATACCAGGAGGA
1 TGGTATCGATACCA-AAGGA
1223998 TGGTATCGATACCA
1 TGGTATCGATACCA
1224012 TTGAGCACAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
17 12 0.43
18 4 0.14
20 12 0.43
ACGTcount: A:0.33, C:0.18, G:0.27, T:0.22
Consensus pattern (19 bp):
TGGTATCGATACCAAAGGA
Found at i:1224480 original size:56 final size:58
Alignment explanation
Indices: 1224399--1224604 Score: 305
Period size: 56 Copynumber: 3.6 Consensus size: 58
1224389 ATGGAACCAA
* * *
1224399 GTGTGCAAAAAGTT-AGAAATTCATACTAAGTGTATGAATTTCCGTATTTGGTACTTT
1 GTGTGCAAAAAGTTAAGAAATCCATACTAAGTGTATGAATTTCCGTATTAGGCACTTT
** *
1224456 GTGTGC-AAAAGTT-AGAAATCCATACTAAGTGTATGAATTTTTGTATTGGGCACTTT
1 GTGTGCAAAAAGTTAAGAAATCCATACTAAGTGTATGAATTTCCGTATTAGGCACTTT
*
1224512 GTGTGCAAAAAGTTAAGAAATCCATATTAAGTGTATGAATTTCCGTATTAGGCAC-TT
1 GTGTGCAAAAAGTTAAGAAATCCATACTAAGTGTATGAATTTCCGTATTAGGCACTTT
*
1224569 GTGTGC-AAAAGTTAAGAAATTCATACTAAGTGTATG
1 GTGTGCAAAAAGTTAAGAAATCCATACTAAGTGTATG
1224605 TGCTTAAACA
Statistics
Matches: 136, Mismatches: 11, Indels: 5
0.89 0.07 0.03
Matches are distributed among these distances:
56 79 0.58
57 21 0.15
58 36 0.26
ACGTcount: A:0.33, C:0.11, G:0.20, T:0.35
Consensus pattern (58 bp):
GTGTGCAAAAAGTTAAGAAATCCATACTAAGTGTATGAATTTCCGTATTAGGCACTTT
Found at i:1224594 original size:114 final size:113
Alignment explanation
Indices: 1224399--1224604 Score: 342
Period size: 114 Copynumber: 1.8 Consensus size: 113
1224389 ATGGAACCAA
* * *
1224399 GTGTGCAAAAAGTTAGAAATTCATACTAAGTGTATGAATTTCCGTATTTGGTACTTTGTGTGCAA
1 GTGTGCAAAAAGTTAGAAATCCATACTAAGTGTATGAATTTCCGTATTAGGCACTTTGTGTGCAA
1224464 AAGTTAGAAATCCATACTAAGTGTATGAATTTTTGTATTGGGCACTTT
66 AAGTTAGAAATCCATACTAAGTGTATGAATTTTTGTATTGGGCACTTT
*
1224512 GTGTGCAAAAAGTTAAGAAATCCATATTAAGTGTATGAATTTCCGTATTAGGCAC-TTGTGTGCA
1 GTGTGCAAAAAGTT-AGAAATCCATACTAAGTGTATGAATTTCCGTATTAGGCACTTTGTGTGCA
*
1224576 AAAGTTAAGAAATTCATACTAAGTGTATG
65 AAAGTT-AGAAATCCATACTAAGTGTATG
1224605 TGCTTAAACA
Statistics
Matches: 86, Mismatches: 5, Indels: 3
0.91 0.05 0.03
Matches are distributed among these distances:
113 29 0.34
114 57 0.66
ACGTcount: A:0.33, C:0.11, G:0.20, T:0.35
Consensus pattern (113 bp):
GTGTGCAAAAAGTTAGAAATCCATACTAAGTGTATGAATTTCCGTATTAGGCACTTTGTGTGCAA
AAGTTAGAAATCCATACTAAGTGTATGAATTTTTGTATTGGGCACTTT
Found at i:1230568 original size:16 final size:16
Alignment explanation
Indices: 1230549--1230583 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1230539 AACATAATAT
1230549 TTTCAAAAAAAAAAAA
1 TTTCAAAAAAAAAAAA
* *
1230565 TTTCGAAATAAAAAAA
1 TTTCAAAAAAAAAAAA
1230581 TTT
1 TTT
1230584 TTGTTTTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.63, C:0.06, G:0.03, T:0.29
Consensus pattern (16 bp):
TTTCAAAAAAAAAAAA
Found at i:1233895 original size:58 final size:58
Alignment explanation
Indices: 1233803--1234046 Score: 434
Period size: 58 Copynumber: 4.2 Consensus size: 58
1233793 TAACTCAACA
*
1233803 GTATGAATTTCCGTATTGGGCATTTTGTGTGCAAAAAGTTAAGAAATTCATACTAAGT
1 GTATGAATTTCCGTATTGGGCACTTTGTGTGCAAAAAGTTAAGAAATTCATACTAAGT
* * *
1233861 GAATGAATTTCTGTATTGGGTACTTTGTGTGCAAAAAGTTAAGAAATTCATACTAAGT
1 GTATGAATTTCCGTATTGGGCACTTTGTGTGCAAAAAGTTAAGAAATTCATACTAAGT
*
1233919 GTATGAATTTCCGTATTGGGCATTTTGTGTGCAAAAAGTTAAGAAATTCATACTAAGT
1 GTATGAATTTCCGTATTGGGCACTTTGTGTGCAAAAAGTTAAGAAATTCATACTAAGT
*
1233977 GTATGAATTTCCGTATTGGGCACTTTGTGTGCAAAAAGTTAAGAGATTCATACTAAGT
1 GTATGAATTTCCGTATTGGGCACTTTGTGTGCAAAAAGTTAAGAAATTCATACTAAGT
1234035 GTATGAATTTCC
1 GTATGAATTTCC
1234047 ATATAGGAAA
Statistics
Matches: 176, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
58 176 1.00
ACGTcount: A:0.32, C:0.11, G:0.21, T:0.36
Consensus pattern (58 bp):
GTATGAATTTCCGTATTGGGCACTTTGTGTGCAAAAAGTTAAGAAATTCATACTAAGT
Found at i:1234373 original size:68 final size:68
Alignment explanation
Indices: 1234264--1234518 Score: 368
Period size: 68 Copynumber: 3.8 Consensus size: 68
1234254 ACAAGATTAA
*
1234264 AGGCCTAACTATGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGCTAAGTGACT
1 AGGCCTAACTATGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGCTAAGTGCCT
*
1234329 TTC
66 TTG
* * * *
1234332 AGGCCTAACTGTGCATTTGATAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTATGTGCCT
1 AGGCCTAACTATGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGCTAAGTGCCT
1234397 TTG
66 TTG
* *
1234400 AGGCCTAACTGTGCATTTGACATAAAGGTGTCAATCATGCCAGTTAGATG-AAGGCTAAGTGCCT
1 AGGCCTAACTATGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGCTAAGTGCCT
1234464 TTG
66 TTG
* * * * * * *
1234467 AGGCCTTACTATGCATTTCATAGAAACGTGTCAATTATGCAATTTAGATGAA
1 AGGCCTAACTATGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAA
1234519 CGGTTAAATA
Statistics
Matches: 167, Mismatches: 19, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
67 57 0.34
68 110 0.66
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.29
Consensus pattern (68 bp):
AGGCCTAACTATGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGCTAAGTGCCT
TTG
Found at i:1234515 original size:135 final size:136
Alignment explanation
Indices: 1234264--1234518 Score: 413
Period size: 135 Copynumber: 1.9 Consensus size: 136
1234254 ACAAGATTAA
1234264 AGGCCTAACTATGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGCTAAGTGACT
1 AGGCCTAACTATGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGCTAAGTGACT
* * * *
1234329 TTCAGGCCTAACTGTGCATTTGATAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTATGTG
66 TTCAGGCCTAACTATGCATTTCATAGAAACGTGTCAATTATGCAAGTTAGATGAAAGGCTATGTG
1234394 CCTTTG
131 CCTTTG
* * *
1234400 AGGCCTAACTGTGCATTTGACATAAAGGTGTCAATCATGCCAGTTAGATG-AAGGCTAAGTGCCT
1 AGGCCTAACTATGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGCTAAGTGACT
* * *
1234464 TTGAGGCCTTACTATGCATTTCATAGAAACGTGTCAATTATGCAATTTAGATGAA
66 TTCAGGCCTAACTATGCATTTCATAGAAACGTGTCAATTATGCAAGTTAGATGAA
1234519 CGGTTAAATA
Statistics
Matches: 109, Mismatches: 10, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
135 61 0.56
136 48 0.44
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.29
Consensus pattern (136 bp):
AGGCCTAACTATGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGCTAAGTGACT
TTCAGGCCTAACTATGCATTTCATAGAAACGTGTCAATTATGCAAGTTAGATGAAAGGCTATGTG
CCTTTG
Found at i:1234969 original size:45 final size:45
Alignment explanation
Indices: 1234578--1234962 Score: 549
Period size: 45 Copynumber: 8.6 Consensus size: 45
1234568 TTGTATAAAA
* *
1234578 GGCATGAAAGGATGTCATAATTAAAATGCATATGGGTGCATTATC
1 GGCATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATC
*
1234623 GGCATGAAAGGATGCCATAAATGAAATGCATATGGGTGCATTATC
1 GGCATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATC
*
1234668 GGCATGAAAGGATACCATAATTGAAATGCATATGGGTGCATTATC
1 GGCATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATC
*
1234713 GGCATGAAAGGATGCCATAATTGAAATGCTTATGGGTGCATTATC
1 GGCATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATC
* *
1234758 AGCATGAAAGGATGTCATAATTGAAATGCATATGGGTGCATTATC
1 GGCATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATC
** * * *
1234803 ATCTTGAAATGATGTCATAATTGAAATGCATATGGGTGCATTATC
1 GGCATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATC
** * *
1234848 GGCATGAAATAATGCCATAA-TGTAAATACATATGGGTGCATTATA
1 GGCATGAAAGGATGCCATAATTG-AAATGCATATGGGTGCATTATC
* *
1234893 GGCACGAAAGGATGCCATAATTGAAATGCATATGGATGCATTATC
1 GGCATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATC
* * * *
1234938 -GTATGAAAAGATGCTATAAATGAAA
1 GGCATGAAAGGATGCCATAATTGAAA
1234963 AGGCATAATG
Statistics
Matches: 307, Mismatches: 31, Indels: 5
0.90 0.09 0.01
Matches are distributed among these distances:
44 22 0.07
45 283 0.92
46 2 0.01
ACGTcount: A:0.36, C:0.12, G:0.24, T:0.28
Consensus pattern (45 bp):
GGCATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATC
Found at i:1239823 original size:21 final size:18
Alignment explanation
Indices: 1239797--1239841 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 18
1239787 TCAGTATTAT
1239797 AAAAAAGAACCAAAAGACAA
1 AAAAAAGAA-CAAAA-ACAA
*
1239817 GAAAAAAGAATAAAAACAA
1 -AAAAAAGAACAAAAACAA
1239836 AAAAAA
1 AAAAAA
1239842 TTATGAACTC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 6 0.26
19 4 0.17
20 4 0.17
21 9 0.39
ACGTcount: A:0.80, C:0.09, G:0.09, T:0.02
Consensus pattern (18 bp):
AAAAAAGAACAAAAACAA
Found at i:1240778 original size:65 final size:63
Alignment explanation
Indices: 1240698--1240857 Score: 198
Period size: 65 Copynumber: 2.5 Consensus size: 63
1240688 GAATAAATTG
* * *
1240698 AACATCGAATACATTTCATGCATCGATGCACATACTATGCATCGATGCACTCAGAG-T-TTTATG
1 AACATCGAATGCATTTGATGCATCGATGCACA-ACCATGCATCGATGCACTCAG-GCTATTT-TG
1240761 AA
63 -A
* *
1240763 AACATCGAATGCATTTGATGCATCGATGCACCAGCCATGCATCGATGCACTCTGGCTATTTTGA
1 AACATCGAATGCATTTGATGCATCGATGCA-CAACCATGCATCGATGCACTCAGGCTATTTTGA
* *
1240827 AACATCGAATGCACTTGATGCGTCGATGCAC
1 AACATCGAATGCATTTGATGCATCGATGCAC
1240858 TCTTAGTGCA
Statistics
Matches: 85, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
63 1 0.01
64 30 0.35
65 49 0.58
66 5 0.06
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.28
Consensus pattern (63 bp):
AACATCGAATGCATTTGATGCATCGATGCACAACCATGCATCGATGCACTCAGGCTATTTTGA
Found at i:1240873 original size:64 final size:64
Alignment explanation
Indices: 1240698--1240877 Score: 192
Period size: 65 Copynumber: 2.8 Consensus size: 64
1240688 GAATAAATTG
* *
1240698 AACATCGAATACATTTCATGCATCGATGCACATACTA-TGCATCGATGCACTCAGAGTTTTATGA
1 AACATCGAATGCATTTGATGCATCGATGCAC-T-CTAGTGCATCGATGCACTCAGAGTTTTATGA
1240762 A
64 A
*
1240763 AACATCGAATGCATTTGATGCATCGATGCAC-C-AGCCATGCATCGATGCACTCTG-GCTATTT-
1 AACATCGAATGCATTTGATGCATCGATGCACTCTAG---TGCATCGATGCACTCAGAG-T-TTTA
1240824 TG-A
61 TGAA
* * *
1240827 AACATCGAATGCACTTGATGCGTCGATGCACTCTTAGTGCACCGATGCACT
1 AACATCGAATGCATTTGATGCATCGATGCACTC-TAGTGCATCGATGCACT
1240878 AAGGGTCCAA
Statistics
Matches: 100, Mismatches: 6, Indels: 19
0.80 0.05 0.15
Matches are distributed among these distances:
61 1 0.01
62 1 0.01
64 44 0.44
65 49 0.49
66 3 0.03
67 2 0.02
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.28
Consensus pattern (64 bp):
AACATCGAATGCATTTGATGCATCGATGCACTCTAGTGCATCGATGCACTCAGAGTTTTATGAA
Found at i:1242901 original size:20 final size:22
Alignment explanation
Indices: 1242868--1242922 Score: 60
Period size: 20 Copynumber: 2.6 Consensus size: 22
1242858 TAACAATGAT
*
1242868 TTTGAAAGTAAAATCA-AAGA-
1 TTTGAAAATAAAATCAGAAGAG
* *
1242888 TTTGAAAATCAAATTAGAAGAG
1 TTTGAAAATAAAATCAGAAGAG
*
1242910 TTTGAAAAGAAAA
1 TTTGAAAATAAAA
1242923 ATTTGGATTT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
20 13 0.46
21 4 0.14
22 11 0.39
ACGTcount: A:0.55, C:0.04, G:0.16, T:0.25
Consensus pattern (22 bp):
TTTGAAAATAAAATCAGAAGAG
Found at i:1246737 original size:20 final size:20
Alignment explanation
Indices: 1246712--1246783 Score: 144
Period size: 20 Copynumber: 3.6 Consensus size: 20
1246702 GCCTTGAATG
1246712 TGCATCGATGCACAAGGCCA
1 TGCATCGATGCACAAGGCCA
1246732 TGCATCGATGCACAAGGCCA
1 TGCATCGATGCACAAGGCCA
1246752 TGCATCGATGCACAAGGCCA
1 TGCATCGATGCACAAGGCCA
1246772 TGCATCGATGCA
1 TGCATCGATGCA
1246784 TCCGTCGGGT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 52 1.00
ACGTcount: A:0.29, C:0.29, G:0.25, T:0.17
Consensus pattern (20 bp):
TGCATCGATGCACAAGGCCA
Found at i:1248342 original size:21 final size:21
Alignment explanation
Indices: 1248302--1248343 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1248292 TCCGGGAGCG
*
1248302 AGCTCTTCACGAGCTGCTCCT
1 AGCTCTTCACGAGCTCCTCCT
* *
1248323 AGCTCTTCTCGTGCTCCTCCT
1 AGCTCTTCACGAGCTCCTCCT
1248344 CCAGCACCGG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.10, C:0.40, G:0.17, T:0.33
Consensus pattern (21 bp):
AGCTCTTCACGAGCTCCTCCT
Found at i:1250111 original size:71 final size:72
Alignment explanation
Indices: 1250031--1250174 Score: 281
Period size: 71 Copynumber: 2.0 Consensus size: 72
1250021 GGTATATCTT
1250031 GAGGAAGTTGTAAGGTTATCTCTTTGGCCTCAAAAGAAAGAAC-AATTAGTGAATTTGTTGGAAA
1 GAGGAAGTTGTAAGGTTATCTCTTTGGCCTCAAAAGAAAGAACAAATTAGTGAATTTGTTGGAAA
1250095 ATCCTTA
66 ATCCTTA
1250102 GAGGAAGTTGTAAGGTTATCTCTTTGGCCTCAAAAGAAAGAACAAATTAGTGAATTTGTTGGAAA
1 GAGGAAGTTGTAAGGTTATCTCTTTGGCCTCAAAAGAAAGAACAAATTAGTGAATTTGTTGGAAA
1250167 ATCCTTA
66 ATCCTTA
1250174 G
1 G
1250175 TGTGGATAGC
Statistics
Matches: 72, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
71 43 0.60
72 29 0.40
ACGTcount: A:0.35, C:0.11, G:0.23, T:0.31
Consensus pattern (72 bp):
GAGGAAGTTGTAAGGTTATCTCTTTGGCCTCAAAAGAAAGAACAAATTAGTGAATTTGTTGGAAA
ATCCTTA
Found at i:1252047 original size:18 final size:19
Alignment explanation
Indices: 1252024--1252071 Score: 62
Period size: 18 Copynumber: 2.5 Consensus size: 19
1252014 ATACAATTTG
* *
1252024 GTATCGATACCCATGG-GA
1 GTATCGATACCAAGGGAGA
1252042 GTATCGATACCAAGGGTAGA
1 GTATCGATACCAAGGG-AGA
1252062 GTATCGATAC
1 GTATCGATAC
1252072 TTCCTATAGG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 14 0.54
20 12 0.46
ACGTcount: A:0.31, C:0.19, G:0.27, T:0.23
Consensus pattern (19 bp):
GTATCGATACCAAGGGAGA
Found at i:1253531 original size:32 final size:32
Alignment explanation
Indices: 1253495--1253625 Score: 122
Period size: 32 Copynumber: 3.9 Consensus size: 32
1253485 GTTTAATTAC
*
1253495 TGACATGGCACATGTCACGTCATCATTATGGA
1 TGACATGACACATGTCACGTCATCATTATGGA
* *
1253527 TGACATGATACATGGCACGTCATCACTATGAGTGGCCA
1 TGACATGACACATGTCACGTCATCA-T-T-A-TGG--A
*
1253565 CTGACATGGCACATGTCA--TCATCATTATGGA
1 -TGACATGACACATGTCACGTCATCATTATGGA
* * *
1253596 TGACATGATACATGACACGTCATCACTATG
1 TGACATGACACATGTCACGTCATCATTATG
1253626 AGTGGCCTTA
Statistics
Matches: 80, Mismatches: 10, Indels: 18
0.74 0.09 0.17
Matches are distributed among these distances:
30 14 0.17
31 1 0.01
32 32 0.40
33 4 0.05
34 2 0.03
35 2 0.03
36 4 0.05
37 6 0.08
38 1 0.01
39 14 0.17
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.27
Consensus pattern (32 bp):
TGACATGACACATGTCACGTCATCATTATGGA
Found at i:1253606 original size:69 final size:70
Alignment explanation
Indices: 1253493--1253632 Score: 255
Period size: 69 Copynumber: 2.0 Consensus size: 70
1253483 GTGTTTAATT
*
1253493 ACTGACATGGCACATGTCACGTCATCATTATGGATGACATGATACATGGCACGTCATCACTATGA
1 ACTGACATGGCACATGTCAC-TCATCATTATGGATGACATGATACATGACACGTCATCACTATGA
1253558 GTGGCC
65 GTGGCC
1253564 ACTGACATGGCACATGTCA-TCATCATTATGGATGACATGATACATGACACGTCATCACTATGAG
1 ACTGACATGGCACATGTCACTCATCATTATGGATGACATGATACATGACACGTCATCACTATGAG
1253628 TGGCC
66 TGGCC
1253633 TTACGCATGC
Statistics
Matches: 68, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
69 49 0.72
71 19 0.28
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26
Consensus pattern (70 bp):
ACTGACATGGCACATGTCACTCATCATTATGGATGACATGATACATGACACGTCATCACTATGAG
TGGCC
Found at i:1257728 original size:35 final size:35
Alignment explanation
Indices: 1257682--1257756 Score: 150
Period size: 35 Copynumber: 2.1 Consensus size: 35
1257672 TTGCTTTCAA
1257682 TCGAGGAGCGTGTTTGGCAGCACATGATTGATGAT
1 TCGAGGAGCGTGTTTGGCAGCACATGATTGATGAT
1257717 TCGAGGAGCGTGTTTGGCAGCACATGATTGATGAT
1 TCGAGGAGCGTGTTTGGCAGCACATGATTGATGAT
1257752 TCGAG
1 TCGAG
1257757 CTGCGTTATT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 40 1.00
ACGTcount: A:0.23, C:0.15, G:0.35, T:0.28
Consensus pattern (35 bp):
TCGAGGAGCGTGTTTGGCAGCACATGATTGATGAT
Found at i:1259866 original size:24 final size:24
Alignment explanation
Indices: 1259839--1259898 Score: 102
Period size: 24 Copynumber: 2.5 Consensus size: 24
1259829 GTACATGCCA
* *
1259839 ACATTTTACATTTACAAGAAACCT
1 ACATTTAAAATTTACAAGAAACCT
1259863 ACATTTAAAATTTACAAGAAACCT
1 ACATTTAAAATTTACAAGAAACCT
1259887 ACATTTAAAATT
1 ACATTTAAAATT
1259899 GTTCTGATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.47, C:0.17, G:0.03, T:0.33
Consensus pattern (24 bp):
ACATTTAAAATTTACAAGAAACCT
Found at i:1260264 original size:20 final size:22
Alignment explanation
Indices: 1260239--1260294 Score: 80
Period size: 23 Copynumber: 2.6 Consensus size: 22
1260229 CACCAAAGTG
*
1260239 CCACATA-TTTGTC-CGAATGA
1 CCACATAGTTTGTCTCGAAGGA
1260259 CCACATAGTTTTGTCTCGAAGGA
1 CCACATAG-TTTGTCTCGAAGGA
1260282 CCACATAGTTTGT
1 CCACATAGTTTGT
1260295 TTCCCGATGG
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 7 0.22
22 11 0.34
23 14 0.44
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.32
Consensus pattern (22 bp):
CCACATAGTTTGTCTCGAAGGA
Found at i:1266207 original size:16 final size:18
Alignment explanation
Indices: 1266188--1266220 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
1266178 ATAAAACACA
1266188 TTAAT-ATTTA-ATAAAC
1 TTAATAATTTATATAAAC
1266204 TTAATAATTTATATAAA
1 TTAATAATTTATATAAA
1266221 TACAAAAGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 5 0.33
18 5 0.33
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (18 bp):
TTAATAATTTATATAAAC
Found at i:1266944 original size:23 final size:23
Alignment explanation
Indices: 1266918--1266962 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
1266908 GTGCCATATA
1266918 TTTGTCCCAAATGACCACATAGT
1 TTTGTCCCAAATGACCACATAGT
*
1266941 TTTGTCTCAAATGACCACATAG
1 TTTGTCCCAAATGACCACATAG
1266963 AACCCTCGAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.31, C:0.24, G:0.13, T:0.31
Consensus pattern (23 bp):
TTTGTCCCAAATGACCACATAGT
Found at i:1267779 original size:11 final size:11
Alignment explanation
Indices: 1267763--1267797 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
1267753 TTTCATTTTG
1267763 AAATTTAACCA
1 AAATTTAACCA
1267774 AAATTTAACCA
1 AAATTTAACCA
* *
1267785 AAACTTACCCA
1 AAATTTAACCA
1267796 AA
1 AA
1267798 TCTCCTACTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.54, C:0.23, G:0.00, T:0.23
Consensus pattern (11 bp):
AAATTTAACCA
Found at i:1268253 original size:126 final size:127
Alignment explanation
Indices: 1267997--1268247 Score: 390
Period size: 126 Copynumber: 2.0 Consensus size: 127
1267987 CAAATTTAAC
1267997 ATATAAATCCTAAAAACTACCATATCAACAACATATCCCTTAAAACCCCATTTTTCAAATCCATC
1 ATATAAATCCTAAAAACTACCA-ATCAACAACATATCCCTTAAAACCCCATTTTTCAAATCCATC
1268062 AACTCAATCATCTTTTAGTTTTAATCCACCTAAAACTTCCCTTAAGCTTATATATCACCCAAAGA
65 AACTCAATCATCTTTTAGTTTTAATCCACCTAAAACTTCCCTTAAGC-T-TATATCACCCAAAGA
*
1268127 ATATAAATCCT-AAAACTAACC-ATC-TCAACATATCCCTT-AAACCCCATTTTTCAAATCCATC
1 ATATAAATCCTAAAAACT-ACCAATCAACAACATATCCCTTAAAACCCCATTTTTCAAATCCATC
1268188 ACTACTC-ATCATCTTTTAGTTTTAATCCACCT-AAACTTCCCTTAAGC-TATATCACCCAAA
65 A--ACTCAATCATCTTTTAGTTTTAATCCACCTAAAACTTCCCTTAAGCTTATATCACCCAAA
1268248 AAAGAACCAA
Statistics
Matches: 117, Mismatches: 1, Indels: 13
0.89 0.01 0.10
Matches are distributed among these distances:
123 13 0.11
126 39 0.33
127 38 0.32
128 7 0.06
129 6 0.05
130 14 0.12
ACGTcount: A:0.37, C:0.29, G:0.02, T:0.31
Consensus pattern (127 bp):
ATATAAATCCTAAAAACTACCAATCAACAACATATCCCTTAAAACCCCATTTTTCAAATCCATCA
ACTCAATCATCTTTTAGTTTTAATCCACCTAAAACTTCCCTTAAGCTTATATCACCCAAAGA
Found at i:1273002 original size:22 final size:23
Alignment explanation
Indices: 1272965--1273011 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
1272955 AACCCTAAAC
1272965 AAGCCCAAAAATCGTATCTGCTA
1 AAGCCCAAAAATCGTATCTGCTA
* *
1272988 AAGCCC-ATAATCGTATCTTCTA
1 AAGCCCAAAAATCGTATCTGCTA
1273010 AA
1 AA
1273012 CTCGCGATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 16 0.73
23 6 0.27
ACGTcount: A:0.38, C:0.26, G:0.11, T:0.26
Consensus pattern (23 bp):
AAGCCCAAAAATCGTATCTGCTA
Found at i:1275432 original size:24 final size:25
Alignment explanation
Indices: 1275405--1275463 Score: 93
Period size: 27 Copynumber: 2.3 Consensus size: 25
1275395 ATATATGGAG
1275405 GTGGTGGTATAATC-TTTTGGACAT
1 GTGGTGGTATAATCATTTTGGACAT
1275429 GTGGTGGTATAATCTAATTTTGGACAT
1 GTGGTGGTATAATC--ATTTTGGACAT
1275456 GTGGTGGT
1 GTGGTGGT
1275464 GGTGGTAGTA
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
24 14 0.44
27 18 0.56
ACGTcount: A:0.20, C:0.07, G:0.32, T:0.41
Consensus pattern (25 bp):
GTGGTGGTATAATCATTTTGGACAT
Found at i:1283240 original size:27 final size:27
Alignment explanation
Indices: 1283210--1283414 Score: 95
Period size: 27 Copynumber: 7.4 Consensus size: 27
1283200 CATTTTGGCT
1283210 GCACAGAGGTGTCAGTCCTCGATTGAA
1 GCACAGAGGTGTCAGTCCTCGATTGAA
* *
1283237 GCACAGAGGTGCTCAATCGTC--TT--A
1 GCACAGAGGTG-TCAGTCCTCGATTGAA
**
1283261 GCTATACAGAGGTGTCAGCTCC-CGGCTGAA
1 GC---ACAGAGGTGTCAG-TCCTCGATTGAA
* *** *
1283291 GCACAGAGGTGCTCAGTCATTTTTTTTAA
1 GCACAGAGGTG-TCAGTC-CTCGATTGAA
* *
1283320 CTGCATAGAGGTGTCAGTTCTCGATTGAA
1 --GCACAGAGGTGTCAGTCCTCGATTGAA
* * *
1283349 GCACAGAGGTGCTCAATCACT--TTTGGCTA
1 GCACAGAGGTG-TCAGTC-CTCGATT-G-AA
1283378 -CACAGAGGTGTCAG-CTCTCGATTGAA
1 GCACAGAGGTGTCAGTC-CTCGATTGAA
1283404 GCACAGAGGTG
1 GCACAGAGGTG
1283415 CTCAATCGTT
Statistics
Matches: 130, Mismatches: 27, Indels: 42
0.65 0.14 0.21
Matches are distributed among these distances:
24 3 0.02
26 10 0.08
27 59 0.45
28 29 0.22
29 11 0.08
30 8 0.06
31 10 0.08
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (27 bp):
GCACAGAGGTGTCAGTCCTCGATTGAA
Found at i:1283400 original size:55 final size:55
Alignment explanation
Indices: 1283122--1283421 Score: 304
Period size: 54 Copynumber: 5.5 Consensus size: 55
1283112 CTTGATTTTA
* * * * * * *
1283122 GATTGTAGCACAGAGGTGCTCAATC-CTTCTA-ATACACAGAGGTGCCAGATTTTA
1 GATTGAAGCACAGAGGTGCTCAATCACTTTTAGCTACACAGAGGTGTCAG-CTCTC
* * * *
1283176 GATTGAAGCACAAAGGTGCTCAGTCA-TTTTGGCTGCACAGAGGTGTCAG-TCCTC
1 GATTGAAGCACAGAGGTGCTCAATCACTTTTAGCTACACAGAGGTGTCAGCT-CTC
* * * *
1283230 GATTGAAGCACAGAGGTGCTCAATC-GTCTTAGCTATACAGAGGTGTCAGCTCCC
1 GATTGAAGCACAGAGGTGCTCAATCACTTTTAGCTACACAGAGGTGTCAGCTCTC
** * * * * * *
1283284 GGCTGAAGCACAGAGGTGCTCAGTCATTTTTTTTAACTGCATAGAGGTGTCAGTTCTC
1 GATTGAAGCACAGAGGTGCTCAATCA---CTTTTAGCTACACAGAGGTGTCAGCTCTC
*
1283342 GATTGAAGCACAGAGGTGCTCAATCACTTTTGGCTACACAGAGGTGTCAGCTCTC
1 GATTGAAGCACAGAGGTGCTCAATCACTTTTAGCTACACAGAGGTGTCAGCTCTC
1283397 GATTGAAGCACAGAGGTGCTCAATC
1 GATTGAAGCACAGAGGTGCTCAATC
1283422 GTTAATTCTA
Statistics
Matches: 200, Mismatches: 37, Indels: 17
0.79 0.15 0.07
Matches are distributed among these distances:
53 1 0.00
54 92 0.46
55 63 0.31
58 44 0.22
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.27
Consensus pattern (55 bp):
GATTGAAGCACAGAGGTGCTCAATCACTTTTAGCTACACAGAGGTGTCAGCTCTC
Found at i:1283670 original size:81 final size:81
Alignment explanation
Indices: 1283535--1283693 Score: 246
Period size: 81 Copynumber: 2.0 Consensus size: 81
1283525 ACGAGTTACA
** *
1283535 GAGAATGGTTCGCACACGAAATGGCAGAGCAACAAGCTCTCACAGAGGTGTAGAGCAGGAAGTTA
1 GAGAATGGTTCGCACAAAAAATGGCAGAGCAACAAGCTCTCACAGAGGTGTAGAGCAGGAAGCTA
* *
1283600 CTGAGCCGGTTGTATC
66 CCGAGCCAGTTGTATC
* * *
1283616 GAGAATGGTTCGCACAAAAAATGGCGGATCGACAAGCTCTCACAGAGGTGTAGAGCAGGAAGCTA
1 GAGAATGGTTCGCACAAAAAATGGCAGAGCAACAAGCTCTCACAGAGGTGTAGAGCAGGAAGCTA
1283681 CCGAGCCAGTTGT
66 CCGAGCCAGTTGT
1283694 GCAAGAGACT
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
81 70 1.00
ACGTcount: A:0.31, C:0.20, G:0.31, T:0.18
Consensus pattern (81 bp):
GAGAATGGTTCGCACAAAAAATGGCAGAGCAACAAGCTCTCACAGAGGTGTAGAGCAGGAAGCTA
CCGAGCCAGTTGTATC
Found at i:1289147 original size:31 final size:31
Alignment explanation
Indices: 1289079--1289147 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
1289069 ACTAAAGTTC
* * *
1289079 AATGATAAAATTAATTCAAATCTCAAATTTT
1 AATGATAAAATCAATTCAAAACTCAAAATTT
* *
1289110 AATGATAAAATCAATTTAAAACTTAAAATTT
1 AATGATAAAATCAATTCAAAACTCAAAATTT
*
1289141 AGTGATA
1 AATGATA
1289148 TTTAAAATTA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.51, C:0.07, G:0.06, T:0.36
Consensus pattern (31 bp):
AATGATAAAATCAATTCAAAACTCAAAATTT
Found at i:1294169 original size:24 final size:24
Alignment explanation
Indices: 1294107--1294157 Score: 95
Period size: 24 Copynumber: 2.2 Consensus size: 24
1294097 AGTATGAATG
1294107 TTCAAATATC-AAACAAGTTAGAA
1 TTCAAATATCAAAACAAGTTAGAA
1294130 TTCAAATATCAAAACAAGTTAGAA
1 TTCAAATATCAAAACAAGTTAGAA
1294154 TTCA
1 TTCA
1294158 TCTTTTTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 10 0.37
24 17 0.63
ACGTcount: A:0.51, C:0.14, G:0.08, T:0.27
Consensus pattern (24 bp):
TTCAAATATCAAAACAAGTTAGAA
Found at i:1297674 original size:39 final size:39
Alignment explanation
Indices: 1297615--1297704 Score: 137
Period size: 39 Copynumber: 2.3 Consensus size: 39
1297605 ATTAGATGAG
1297615 AAATACAAATAAGATAGAGTTATAGTTAATCTAAACTACT
1 AAAT-CAAATAAGATAGAGTTATAGTTAATCTAAACTACT
*
1297655 AAATCAAAT-AGAATAGAGTTATAGTTAATCTAAATTACT
1 AAATCAAATAAG-ATAGAGTTATAGTTAATCTAAACTACT
*
1297694 AATTCAAATAA
1 AAATCAAATAA
1297705 TTTACTGCTT
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
38 2 0.04
39 39 0.85
40 5 0.11
ACGTcount: A:0.51, C:0.09, G:0.09, T:0.31
Consensus pattern (39 bp):
AAATCAAATAAGATAGAGTTATAGTTAATCTAAACTACT
Found at i:1305159 original size:59 final size:59
Alignment explanation
Indices: 1305075--1305192 Score: 218
Period size: 59 Copynumber: 2.0 Consensus size: 59
1305065 TCTCAAAACG
* *
1305075 TAACATCAAATTCAGCGTAGAAGTTGATCGTTTGTTAAGCACAGCTCAAATACGTAACT
1 TAACATCAAATTCAACGTAGAAGTTGATCGTTTGTTAAGCACAGCTCAAATAAGTAACT
1305134 TAACATCAAATTCAACGTAGAAGTTGATCGTTTGTTAAGCACAGCTCAAATAAGTAACT
1 TAACATCAAATTCAACGTAGAAGTTGATCGTTTGTTAAGCACAGCTCAAATAAGTAACT
1305193 CATCTTTGCC
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
59 57 1.00
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.29
Consensus pattern (59 bp):
TAACATCAAATTCAACGTAGAAGTTGATCGTTTGTTAAGCACAGCTCAAATAAGTAACT
Found at i:1309196 original size:16 final size:16
Alignment explanation
Indices: 1309166--1309196 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1309156 TAAAACTCGA
*
1309166 CTCGAACTCGAAAAAG
1 CTCGAACTCAAAAAAG
1309182 CTCGAACTCAAAAAA
1 CTCGAACTCAAAAAA
1309197 TTTCAGGAGC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.26, G:0.13, T:0.13
Consensus pattern (16 bp):
CTCGAACTCAAAAAAG
Found at i:1309332 original size:8 final size:8
Alignment explanation
Indices: 1309321--1309349 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
1309311 ATGGACTATA
1309321 AAAAATCT
1 AAAAATCT
1309329 -AAAATCT
1 AAAAATCT
1309336 AAAAATCT
1 AAAAATCT
1309344 AAAAAT
1 AAAAAT
1309350 ACAATTACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.35
8 13 0.65
ACGTcount: A:0.66, C:0.10, G:0.00, T:0.24
Consensus pattern (8 bp):
AAAAATCT
Found at i:1319938 original size:7 final size:7
Alignment explanation
Indices: 1319926--1319982 Score: 51
Period size: 7 Copynumber: 8.1 Consensus size: 7
1319916 AATCAAATTA
1319926 AGGGTTT
1 AGGGTTT
1319933 AGGGTTT
1 AGGGTTT
**
1319940 AATGTTT
1 AGGGTTT
**
1319947 AATGTTT
1 AGGGTTT
*
1319954 AGGGCTT
1 AGGGTTT
*
1319961 ATGGTTT
1 AGGGTTT
*
1319968 AAGGTTT
1 AGGGTTT
1319975 AGGGTTT
1 AGGGTTT
1319982 A
1 A
1319983 TGGTGTAATC
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
7 41 1.00
ACGTcount: A:0.21, C:0.02, G:0.32, T:0.46
Consensus pattern (7 bp):
AGGGTTT
Found at i:1319953 original size:21 final size:22
Alignment explanation
Indices: 1319923--1319986 Score: 80
Period size: 21 Copynumber: 3.0 Consensus size: 22
1319913 TATAATCAAA
1319923 TTAAGGGTTTAGGGTTTAAT-GT
1 TTAA-GGTTTAGGGTTTAATGGT
* *
1319945 TTAATGTTTAGGGCTT-ATGGT
1 TTAAGGTTTAGGGTTTAATGGT
1319966 TTAAGGTTTAGGGTTT-ATGGT
1 TTAAGGTTTAGGGTTTAATGGT
1319987 GTAATCTAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
20 2 0.05
21 31 0.84
22 4 0.11
ACGTcount: A:0.20, C:0.02, G:0.31, T:0.47
Consensus pattern (22 bp):
TTAAGGTTTAGGGTTTAATGGT
Found at i:1324670 original size:2 final size:2
Alignment explanation
Indices: 1324663--1324692 Score: 51
Period size: 2 Copynumber: 14.5 Consensus size: 2
1324653 AATATTAGTA
1324663 AT AT AT AT AT AT AT AT AT AT AT AGT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A-T AT AT A
1324693 GTACACACAC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 25 0.93
3 2 0.07
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1325032 original size:81 final size:81
Alignment explanation
Indices: 1324860--1325028 Score: 234
Period size: 79 Copynumber: 2.1 Consensus size: 81
1324850 TACTTAGTGG
* * *
1324860 GTTTTTATAAAAATGTCGCAATAGGGTCATGTATAATGGCGTTTTTTGACAAACACCGCTAAAGA
1 GTTTTTATAAAAATGCCGCAATAGGATCATGTATAATGGCGTTTTTTGACAAACACCACTAAAGA
* * *
1324925 GTAATATTGTAGCGAC
66 ATAATACTATAGCGAC
* * *
1324941 GTTTTTATAAAAATGCCGCAATAGTATCATGTATAGT-G-TTTTTTTGACAAACACCACTAAAGA
1 GTTTTTATAAAAATGCCGCAATAGGATCATGTATAATGGCGTTTTTTGACAAACACCACTAAAGA
*
1325004 ATAATACTATAGCGGC
66 ATAATACTATAGCGAC
1325020 GTTTTTATA
1 GTTTTTATA
1325029 TAAACTCCGC
Statistics
Matches: 78, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
79 44 0.56
80 1 0.01
81 33 0.42
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.34
Consensus pattern (81 bp):
GTTTTTATAAAAATGCCGCAATAGGATCATGTATAATGGCGTTTTTTGACAAACACCACTAAAGA
ATAATACTATAGCGAC
Found at i:1328914 original size:43 final size:43
Alignment explanation
Indices: 1328817--1329015 Score: 206
Period size: 43 Copynumber: 4.7 Consensus size: 43
1328807 TTCTGCAGAG
* * *
1328817 TTTGTTCCAAAAACGCCGCTATAGATCT-AACCTTTTGCGGTA
1 TTTGTTCCAAAAACGCTGCTATAGATCTCAACCTATTGCGGCA
* * *
1328859 TTTGCTCCAAAAACGCTGCTATAGATCTCAACCTTTTGCGGCG
1 TTTGTTCCAAAAACGCTGCTATAGATCTCAACCTATTGCGGCA
* ** * *
1328902 TTT-TCTCTAAAAATACCGCTATAGATCTCGACCTATTGCGGCA
1 TTTGT-TCCAAAAACGCTGCTATAGATCTCAACCTATTGCGGCA
* * * * *
1328945 TTTGTTCCAATAGCACTACTATAGATCTCAACCTATTGCGGCG
1 TTTGTTCCAAAAACGCTGCTATAGATCTCAACCTATTGCGGCA
*
1328988 TTTGTTCCAAAAATG-TCGCTATAGATCT
1 TTTGTTCCAAAAACGCT-GCTATAGATCT
1329016 AGACATATTG
Statistics
Matches: 128, Mismatches: 25, Indels: 7
0.80 0.16 0.04
Matches are distributed among these distances:
42 27 0.21
43 100 0.78
44 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.16, T:0.33
Consensus pattern (43 bp):
TTTGTTCCAAAAACGCTGCTATAGATCTCAACCTATTGCGGCA
Found at i:1328969 original size:86 final size:85
Alignment explanation
Indices: 1328816--1329027 Score: 255
Period size: 86 Copynumber: 2.5 Consensus size: 85
1328806 TTTCTGCAGA
** * * * * *
1328816 GTTTGTTCCAAAAACGCCGCTATAGATCTAACCTTTTGCGGTATTTGCTCCAAAAACGCTGCTAT
1 GTTTGTTCCAAAAATACCGCTATAGATCTGACCTATTGCGGCATTTGCTCCAAAAACACTACTAT
*
1328881 AGATCTCAACCTTTTGCGGC
66 AGATCTCAACCTATTGCGGC
* * * *
1328901 GTTT-TCTCTAAAAATACCGCTATAGATCTCGACCTATTGCGGCATTTGTTCCAATAGCACTACT
1 GTTTGT-TCCAAAAATACCGCTATAGATCT-GACCTATTGCGGCATTTGCTCCAAAAACACTACT
1328965 ATAGATCTCAACCTATTGCGGC
64 ATAGATCTCAACCTATTGCGGC
** *
1328987 GTTTGTTCCAAAAATGTCGCTATAGATCTAGACATATTGCG
1 GTTTGTTCCAAAAATACCGCTATAGATCT-GACCTATTGCG
1329028 ACTTTTTTCC
Statistics
Matches: 107, Mismatches: 17, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
84 1 0.01
85 24 0.22
86 81 0.76
87 1 0.01
ACGTcount: A:0.26, C:0.24, G:0.17, T:0.33
Consensus pattern (85 bp):
GTTTGTTCCAAAAATACCGCTATAGATCTGACCTATTGCGGCATTTGCTCCAAAAACACTACTAT
AGATCTCAACCTATTGCGGC
Found at i:1329025 original size:43 final size:42
Alignment explanation
Indices: 1328816--1329050 Score: 204
Period size: 43 Copynumber: 5.5 Consensus size: 42
1328806 TTTCTGCAGA
* *
1328816 GTTTGTTCCAAAAACGCCGCTATAGATCTAACCTTTTGCGGT
1 GTTTGTTCCAAAAACGCCGCTATAGATCTAACCTATTGCGGC
* * * *
1328858 ATTTGCTCCAAAAACGCTGCTATAGATCTCAACCTTTTGCGGC
1 GTTTGTTCCAAAAACGCCGCTATAGATCT-AACCTATTGCGGC
* ** *
1328901 GTTT-TCTCTAAAAATACCGCTATAGATCTCGACCTATTGCGGC
1 GTTTGT-TCCAAAAACGCCGCTATAGATCT-AACCTATTGCGGC
* * * * **
1328944 ATTTGTTCCAATAGCACTACTATAGATCTCAACCTATTGCGGC
1 GTTTGTTCCAAAAACGCCGCTATAGATCT-AACCTATTGCGGC
* * * *
1328987 GTTTGTTCCAAAAATGTCGCTATAGATCTAGACATATTGCGAC
1 GTTTGTTCCAAAAACGCCGCTATAGATCTA-ACCTATTGCGGC
* **
1329030 -TTTTTTCCCCAAACGCCGCTA
1 GTTTGTTCCAAAAACGCCGCTA
1329051 AAGAACAATT
Statistics
Matches: 154, Mismatches: 35, Indels: 8
0.78 0.18 0.04
Matches are distributed among these distances:
42 43 0.28
43 110 0.71
44 1 0.01
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.32
Consensus pattern (42 bp):
GTTTGTTCCAAAAACGCCGCTATAGATCTAACCTATTGCGGC
Found at i:1331482 original size:21 final size:22
Alignment explanation
Indices: 1331458--1331506 Score: 55
Period size: 25 Copynumber: 2.1 Consensus size: 22
1331448 GTGTAGCCGG
1331458 TTGGC-GAGAGTTTGGTTGGAT
1 TTGGCGGAGAGTTTGGTTGGAT
*
1331479 TTGGCAGTGGGGAGTTTGGTTGGAT
1 TTGGC---GGAGAGTTTGGTTGGAT
1331504 TTG
1 TTG
1331507 ATTATTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
21 5 0.22
25 18 0.78
ACGTcount: A:0.12, C:0.04, G:0.45, T:0.39
Consensus pattern (22 bp):
TTGGCGGAGAGTTTGGTTGGAT
Found at i:1331811 original size:3 final size:3
Alignment explanation
Indices: 1331803--1331847 Score: 81
Period size: 3 Copynumber: 15.0 Consensus size: 3
1331793 TGGGTTGATC
*
1331803 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TCA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1331848 AAGGTCAGAC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1332266 original size:45 final size:45
Alignment explanation
Indices: 1332184--1332767 Score: 645
Period size: 45 Copynumber: 13.0 Consensus size: 45
1332174 CAGATTGAAG
* * * *
1332184 ATGACATCACTAAAA-AGTTGACTCATCTCCATGAGAAAGTTAAGA
1 ATGACATCACTAAAAGA-TTGACTCCTCTTCACGAGAAAGTCAAGA
* * *
1332229 ATGACATCATTAAAATG-TTAACTCCTCTTCACAAGAAAGTCAAGA
1 ATGACATCACTAAAA-GATTGACTCCTCTTCACGAGAAAGTCAAGA
* *
1332274 AAGACATCACTAAAAGATTGTCTCCTCTTCACGAGAAAGTCAAGA
1 ATGACATCACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGA
* ** * *
1332319 ATGACATCACTAAAAGGTTGACTCCTCTTTGCGAAAAAGTTAAGA
1 ATGACATCACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGA
* * * * * * ** *
1332364 ATGATAACACTAAGAGATTGATTCTTTTTTGCGAGAAAGTCAGGA
1 ATGACATCACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGA
* * *
1332409 ATGACAAT-ACTAAAAGATTAATTCCTCTTCAGGAGAAAGTCAAGA
1 ATGAC-ATCACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGA
* * * * * **
1332454 ATTACATCACTAGAAGGTTGATTTCTCTTCGTGAGAAAGTCAAGA
1 ATGACATCACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGA
* * * *
1332499 ATGACAACACTAAAAGAGTGACTCCTCCTCGCGAGAAAGTCAAGA
1 ATGACATCACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGA
* *
1332544 ATGACAGCACTAAAAGATTGACTGCTCTTCACGAGAAAGTCAAGA
1 ATGACATCACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGA
* *
1332589 AAGACATCACTAAAAGATTGACTCCTCTTCACGAGAAAGTTAAGA
1 ATGACATCACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGA
* *
1332634 A-GAACATCACTAAAAGATTGACTCCTCTTTACAAGAAAGTCAAGA
1 ATG-ACATCACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGA
* * *
1332679 ATTATATCACTAAAAGATTGACTCGTCTTCACGAGAAAGTCAAGA
1 ATGACATCACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGA
* * * **
1332724 ATGACATCACCAAAAAATTGACTCATCTTCGTGAGAAAGTCAAG
1 ATGACATCACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAAG
1332768 TTGAGGTTTC
Statistics
Matches: 453, Mismatches: 79, Indels: 14
0.83 0.14 0.03
Matches are distributed among these distances:
44 4 0.01
45 448 0.99
46 1 0.00
ACGTcount: A:0.40, C:0.19, G:0.17, T:0.24
Consensus pattern (45 bp):
ATGACATCACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGA
Found at i:1332867 original size:74 final size:74
Alignment explanation
Indices: 1332783--1332952 Score: 198
Period size: 74 Copynumber: 2.3 Consensus size: 74
1332773 GTTTCTAAGG
* * * * * *
1332783 AAACATTCCTAAGAAGGACTAAAACAAATTTATGGAGAAAC-AGTCCTAAGAAGGAATCTAACGA
1 AAACAATCCTAAGAATGACTAAAACAAATTTATAGAGAAACAAG-CCTAAGAAAGAATCAAACAA
*
1332847 ATTTCTAGAG
65 ATTTCTAGAA
* ** * * *
1332857 AAACGATCCTAAGAATGACTAAAATGAATTTCTAGAGAAACAAGCCTAAGAAAGACTCAAATAAA
1 AAACAATCCTAAGAATGACTAAAACAAATTTATAGAGAAACAAGCCTAAGAAAGAATCAAACAAA
1332922 TTTCTAGAA
66 TTTCTAGAA
*
1332931 AAACAATCCTAGGAATGACTAA
1 AAACAATCCTAAGAATGACTAA
1332953 CATGAATTTC
Statistics
Matches: 80, Mismatches: 15, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
74 78 0.98
75 2 0.03
ACGTcount: A:0.48, C:0.15, G:0.15, T:0.21
Consensus pattern (74 bp):
AAACAATCCTAAGAATGACTAAAACAAATTTATAGAGAAACAAGCCTAAGAAAGAATCAAACAAA
TTTCTAGAA
Found at i:1332961 original size:37 final size:36
Alignment explanation
Indices: 1332774--1332964 Score: 170
Period size: 37 Copynumber: 5.2 Consensus size: 36
1332764 CAAGTTGAGG
* * **
1332774 TTTCTA-AGGAAACATTCCTAAGAAGGACTAAAACAAA
1 TTTCTAGA-GAAACAATCCTAAGAATGACT-AAATGAA
* * * * *
1332811 TTTATGGAGAAACAGTCCTAAGAAGGAATCT-AACGAA
1 TTTCTAGAGAAACAATCCTAAGAATG-A-CTAAATGAA
*
1332848 TTTCTAGAGAAACGATCCTAAGAATGACTAAAATGAA
1 TTTCTAGAGAAACAATCCTAAGAATGACT-AAATGAA
* * *
1332885 TTTCTAGAGAAACAAGCCTAAGAAAGACTCAAATAAA
1 TTTCTAGAGAAACAATCCTAAGAATGACT-AAATGAA
* *
1332922 TTTCTAGAAAAACAATCCTAGGAATGACTAACATGAA
1 TTTCTAGAGAAACAATCCTAAGAATGACTAA-ATGAA
1332959 TTTCTA
1 TTTCTA
1332965 TACGATCCTA
Statistics
Matches: 128, Mismatches: 20, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
35 2 0.02
36 3 0.02
37 119 0.93
38 2 0.02
39 2 0.02
ACGTcount: A:0.46, C:0.15, G:0.15, T:0.24
Consensus pattern (36 bp):
TTTCTAGAGAAACAATCCTAAGAATGACTAAATGAA
Found at i:1333429 original size:24 final size:24
Alignment explanation
Indices: 1333388--1333457 Score: 65
Period size: 24 Copynumber: 3.0 Consensus size: 24
1333378 TTTCAAAAGG
* * *
1333388 TGAAAAGGTTTGACGAAAATGTTT
1 TGAAAATGTTTTAAGAAAATGTTT
*
1333412 TGAAAATGTTTTAAGAAAGA-ATTT
1 TGAAAATGTTTTAAGAAA-ATGTTT
1333436 TGAAAAATG-TTTAAG-AAATGTT
1 TG-AAAATGTTTTAAGAAAATGTT
1333458 GCCCTTACTT
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
22 1 0.03
23 4 0.11
24 26 0.68
25 7 0.18
ACGTcount: A:0.43, C:0.01, G:0.20, T:0.36
Consensus pattern (24 bp):
TGAAAATGTTTTAAGAAAATGTTT
Found at i:1334988 original size:45 final size:44
Alignment explanation
Indices: 1334906--1335218 Score: 335
Period size: 45 Copynumber: 6.9 Consensus size: 44
1334896 TTGCTTGAAT
* * *
1334906 GACATCACTAGAAA-ATTGACTTCTCTTCGCAATAAAGTCAAGAAG
1 GACATCACTA-AAAGATTGAC-TCTCTTCACGAGAAAGTCAAGAAG
* * *
1334951 GAAAACACTAAAAGATTGACTCT-TTCTCGTGAGAAAGTCAAGAATG
1 GACATCACTAAAAGATTGACTCTCTTCAC--GAGAAAGTCAAGAA-G
* * * *
1334997 G-CAACACTTAAAGATTGACTCCTCTTCACGAGAAAGTAAAGAAT
1 GACATCACTAAAAGATTGACT-CTCTTCACGAGAAAGTCAAGAAG
*
1335041 GACATCACTAAAAGATTGACTCATCTTCACGAGAAAGTAAAGAAG
1 GACATCACTAAAAGATTGACTC-TCTTCACGAGAAAGTCAAGAAG
* *
1335086 GACATCACTAAAAGATTGACTCCTCTTTACGAGAAAGTCAAGAAT
1 GACATCACTAAAAGATTGACT-CTCTTCACGAGAAAGTCAAGAAG
*
1335131 GACATCACTAAAAGATTGACTCATCTTCACGAGAAAGTCAAGAAT
1 GACATCACTAAAAGATTGACTC-TCTTCACGAGAAAGTCAAGAAG
* * * **
1335176 TACATCACCAAAAAATTGACTCATCTTCGTGAGAAAAGTCAAG
1 GACATCACTAAAAGATTGACTC-TCTTCACGAG-AAAGTCAAG
1335219 TTGAGGTTTC
Statistics
Matches: 235, Mismatches: 22, Indels: 21
0.85 0.08 0.08
Matches are distributed among these distances:
43 4 0.02
44 9 0.04
45 204 0.87
46 14 0.06
47 4 0.02
ACGTcount: A:0.42, C:0.19, G:0.16, T:0.23
Consensus pattern (44 bp):
GACATCACTAAAAGATTGACTCTCTTCACGAGAAAGTCAAGAAG
Found at i:1335048 original size:23 final size:23
Alignment explanation
Indices: 1335022--1335093 Score: 58
Period size: 23 Copynumber: 3.2 Consensus size: 23
1335012 TGACTCCTCT
1335022 TCACGAGAAAGTAAAGAATGACA
1 TCACGAGAAAGTAAAGAATGACA
* ** * * *
1335045 TCACTA-AAAG-ATTGACTCATCT
1 TCACGAGAAAGTAAAGAATGA-CA
*
1335067 TCACGAGAAAGTAAAGAAGGACA
1 TCACGAGAAAGTAAAGAATGACA
1335090 TCAC
1 TCAC
1335094 TAAAAGATTG
Statistics
Matches: 33, Mismatches: 13, Indels: 6
0.63 0.25 0.12
Matches are distributed among these distances:
21 5 0.15
22 10 0.30
23 14 0.42
24 4 0.12
ACGTcount: A:0.46, C:0.18, G:0.18, T:0.18
Consensus pattern (23 bp):
TCACGAGAAAGTAAAGAATGACA
Found at i:1335210 original size:135 final size:134
Alignment explanation
Indices: 1334902--1335211 Score: 410
Period size: 135 Copynumber: 2.3 Consensus size: 134
1334892 TGCTTTGCTT
* * * *
1334902 GAATGACATCACTAGAAAATTGACTTC-TCTTCGCAATAAAGTCAAGAAGGAAAACACTAAAAGA
1 GAATGACATCACTAAAAAATTGAC-TCATCTTCGCGAGAAAGTAAAGAAGGAAAACACTAAAAGA
* * *
1334966 TTGACTCTTTCTCGTGAGAAAGTCAAGAATGGCAACACTTAAAGATTGACTCCTCTTCACGAGAA
65 TTGACTCTTTCTCG-GAGAAAGTCAAGAATGACAACACTAAAAGATTGACTCATCTTCACGAGAA
1335031 AGTAAA
129 AGTAAA
* * * *
1335037 GAATGACATCACTAAAAGATTGACTCATCTTCACGAGAAAGTAAAGAAGGACATCACTAAAAGAT
1 GAATGACATCACTAAAAAATTGACTCATCTTCGCGAGAAAGTAAAGAAGGAAAACACTAAAAGAT
*
1335102 TGACTCCTCTT-TAC-GAGAAAGTCAAGAATGACATCACTAAAAGATTGACTCATCTTCACGAGA
66 TGACT-CT-TTCT-CGGAGAAAGTCAAGAATGACAACACTAAAAGATTGACTCATCTTCACGAGA
*
1335165 AAGTCAA
128 AAGTAAA
* * *
1335172 GAATTACATCACCAAAAAATTGACTCATCTTCGTGAGAAA
1 GAATGACATCACTAAAAAATTGACTCATCTTCGCGAGAAA
1335212 AGTCAAGTTG
Statistics
Matches: 153, Mismatches: 18, Indels: 8
0.85 0.10 0.04
Matches are distributed among these distances:
134 2 0.01
135 145 0.95
136 3 0.02
137 3 0.02
ACGTcount: A:0.42, C:0.19, G:0.16, T:0.23
Consensus pattern (134 bp):
GAATGACATCACTAAAAAATTGACTCATCTTCGCGAGAAAGTAAAGAAGGAAAACACTAAAAGAT
TGACTCTTTCTCGGAGAAAGTCAAGAATGACAACACTAAAAGATTGACTCATCTTCACGAGAAAG
TAAA
Found at i:1335275 original size:37 final size:37
Alignment explanation
Indices: 1335225--1335417 Score: 192
Period size: 37 Copynumber: 5.2 Consensus size: 37
1335215 CAAGTTGAGG
* * * * *
1335225 TTTCTAGGGAAACAATCCTGAGAATGACTAAAACAAAA
1 TTTCTAGAGAAATAATCCTAAGAAGGACTAAAA-TAAA
* * **
1335263 TTT-TAGAGAAACAATCCTAAGAAGGAATCTAATAAA
1 TTTCTAGAGAAATAATCCTAAGAAGGACTAAAATAAA
*
1335299 TTTCTAGAGAAATAATCCTAAGAAGGACTAAAATGAA
1 TTTCTAGAGAAATAATCCTAAGAAGGACTAAAATAAA
* * *
1335336 TTTCTAGAGAAATGATCCTAAGAAAGACTCAAACT-AA
1 TTTCTAGAGAAATAATCCTAAGAAGGACT-AAAATAAA
* * * * *
1335373 TTTTTAGAAAAATGATCCTAAGAATGACTAAAATGAA
1 TTTCTAGAGAAATAATCCTAAGAAGGACTAAAATAAA
1335410 TTTCTAGA
1 TTTCTAGA
1335418 TGATCCTAAG
Statistics
Matches: 132, Mismatches: 20, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
36 10 0.08
37 115 0.87
38 7 0.05
ACGTcount: A:0.47, C:0.12, G:0.15, T:0.26
Consensus pattern (37 bp):
TTTCTAGAGAAATAATCCTAAGAAGGACTAAAATAAA
Found at i:1335426 original size:33 final size:34
Alignment explanation
Indices: 1335313--1335429 Score: 121
Period size: 37 Copynumber: 3.3 Consensus size: 34
1335303 TAGAGAAATA
*
1335313 ATCCTAAGAAGGACTAAAATGAATTTCTAGAGAAATG
1 ATCCTAAGAAAGACTAAAATGAATTTCT--AG-AATG
* *
1335350 ATCCTAAGAAAGACTCAAACT-AATTTTTAGAAAAATG
1 ATCCTAAGAAAGACT-AAAATGAATTTCTAG---AATG
*
1335387 ATCCTAAGAATGACTAAAATGAATTTCTAG-ATG
1 ATCCTAAGAAAGACTAAAATGAATTTCTAGAATG
1335420 ATCCTAAGAA
1 ATCCTAAGAA
1335430 GGTCTAGAGT
Statistics
Matches: 70, Mismatches: 6, Indels: 12
0.80 0.07 0.14
Matches are distributed among these distances:
33 13 0.19
35 2 0.03
36 4 0.06
37 47 0.67
38 4 0.06
ACGTcount: A:0.46, C:0.13, G:0.15, T:0.26
Consensus pattern (34 bp):
ATCCTAAGAAAGACTAAAATGAATTTCTAGAATG
Found at i:1335911 original size:24 final size:24
Alignment explanation
Indices: 1335877--1335938 Score: 81
Period size: 24 Copynumber: 2.5 Consensus size: 24
1335867 TTTCAAAAGG
*
1335877 TGAAAAAGTTTGATG-AAGAAGTTT
1 TGAAAATGTTTGATGAAAGAA-TTT
*
1335901 TGAAAATGTTTTATGAAAGAATTT
1 TGAAAATGTTTGATGAAAGAATTT
1335925 TGAAAAATGTTTGA
1 TG-AAAATGTTTGA
1335939 AAAGTGTTGC
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
24 18 0.55
25 15 0.45
ACGTcount: A:0.42, C:0.00, G:0.21, T:0.37
Consensus pattern (24 bp):
TGAAAATGTTTGATGAAAGAATTT
Found at i:1335931 original size:25 final size:25
Alignment explanation
Indices: 1335877--1335938 Score: 85
Period size: 25 Copynumber: 2.6 Consensus size: 25
1335867 TTTCAAAAGG
1335877 TGAAAAA-GTTTGATGAAGAAGTTT
1 TGAAAAATGTTTGATGAAGAAGTTT
*
1335901 TG-AAAATGTTTTATGAAAGAA-TTT
1 TGAAAAATGTTTGATG-AAGAAGTTT
1335925 TGAAAAATGTTTGA
1 TGAAAAATGTTTGA
1335939 AAAGTGTTGC
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
23 4 0.12
24 14 0.42
25 15 0.45
ACGTcount: A:0.42, C:0.00, G:0.21, T:0.37
Consensus pattern (25 bp):
TGAAAAATGTTTGATGAAGAAGTTT
Found at i:1340701 original size:30 final size:30
Alignment explanation
Indices: 1340665--1340731 Score: 98
Period size: 30 Copynumber: 2.2 Consensus size: 30
1340655 TAAAGATTGG
*
1340665 AAAAGTTTAGGGACCAAAAGGGTAATTTTC
1 AAAAGTTTAGAGACCAAAAGGGTAATTTTC
* * *
1340695 AAAAGTTTATAGACCAAAAGTGTAATTTTG
1 AAAAGTTTAGAGACCAAAAGGGTAATTTTC
1340725 AAAAGTT
1 AAAAGTT
1340732 ATGTATCTTG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.43, C:0.07, G:0.19, T:0.30
Consensus pattern (30 bp):
AAAAGTTTAGAGACCAAAAGGGTAATTTTC
Found at i:1343835 original size:15 final size:17
Alignment explanation
Indices: 1343800--1343834 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
1343790 CAAATACAAT
1343800 GAGTGAAATAAGAGAGA
1 GAGTGAAATAAGAGAGA
1343817 GAGTGAAATAAGAGAGA
1 GAGTGAAATAAGAGAGA
1343834 G
1 G
1343835 TAAAATTCAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.51, C:0.00, G:0.37, T:0.11
Consensus pattern (17 bp):
GAGTGAAATAAGAGAGA
Found at i:1356367 original size:23 final size:23
Alignment explanation
Indices: 1356337--1356382 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
1356327 GCTCCATCCT
1356337 TGATTATAATATAAACACTTAAA
1 TGATTATAATATAAACACTTAAA
1356360 TGATTATAATATAAACACTTAAA
1 TGATTATAATATAAACACTTAAA
1356383 AGAATAAGGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.52, C:0.09, G:0.04, T:0.35
Consensus pattern (23 bp):
TGATTATAATATAAACACTTAAA
Found at i:1361290 original size:18 final size:18
Alignment explanation
Indices: 1361253--1361291 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 18
1361243 CACTATAAAA
1361253 TTAACTTCAATTACTATTT
1 TTAACTTCAATTA-TATTT
1361272 TTAACTTCAAATT-TATTT
1 TTAACTTC-AATTATATTT
1361290 TT
1 TT
1361292 TTTCAATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.37
19 8 0.42
20 4 0.21
ACGTcount: A:0.31, C:0.13, G:0.00, T:0.56
Consensus pattern (18 bp):
TTAACTTCAATTATATTT
Found at i:1363871 original size:35 final size:36
Alignment explanation
Indices: 1363796--1363904 Score: 152
Period size: 35 Copynumber: 3.0 Consensus size: 36
1363786 TCACCAATTT
1363796 AGGTTTCATAAGAAATTTGGGTATTTTT-TTATTATGAA
1 AGGTTTCATAAGAAATTT-GGTATTTTTCTTA-T-TGAA
1363834 AGGTTTCATAAGAAATTTGGTATTTTTCTTATT-AA
1 AGGTTTCATAAGAAATTTGGTATTTTTCTTATTGAA
*
1363869 AGGTTTCATATGAAATTTGAGTA-TTTTCTTATTGAA
1 AGGTTTCATAAGAAATTTG-GTATTTTTCTTATTGAA
1363905 GATTAATTGA
Statistics
Matches: 67, Mismatches: 1, Indels: 8
0.88 0.01 0.11
Matches are distributed among these distances:
35 30 0.45
36 6 0.09
37 10 0.15
38 21 0.31
ACGTcount: A:0.31, C:0.05, G:0.17, T:0.48
Consensus pattern (36 bp):
AGGTTTCATAAGAAATTTGGTATTTTTCTTATTGAA
Found at i:1367476 original size:24 final size:24
Alignment explanation
Indices: 1367449--1367501 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
1367439 AACGGATATA
*
1367449 TCAAAAATCAAAACATAAATCAGG
1 TCAAAAATCAAAACAGAAATCAGG
** * *
1367473 TCAAGTATCATATCAGAAATCAGG
1 TCAAAAATCAAAACAGAAATCAGG
1367497 TCAAA
1 TCAAA
1367502 TAAAACATAT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.51, C:0.17, G:0.11, T:0.21
Consensus pattern (24 bp):
TCAAAAATCAAAACAGAAATCAGG
Found at i:1367525 original size:26 final size:24
Alignment explanation
Indices: 1367472--1367552 Score: 65
Period size: 24 Copynumber: 3.3 Consensus size: 24
1367462 CATAAATCAG
* * *
1367472 GTCAAGTATCATATCAGAAAT-CAG
1 GTCAAATAACATATCAG-AATCCAA
1367496 GTCAAATAAAACATATCAGAATCCAA
1 GTCAAAT--AACATATCAGAATCCAA
* * * *
1367522 GTCAAGTATCAGATCAGAATCCAT
1 GTCAAATAACATATCAGAATCCAA
1367546 GTCAAAT
1 GTCAAAT
1367553 CGAAAATCAG
Statistics
Matches: 46, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
24 26 0.57
25 3 0.07
26 17 0.37
ACGTcount: A:0.44, C:0.19, G:0.14, T:0.23
Consensus pattern (24 bp):
GTCAAATAACATATCAGAATCCAA
Found at i:1371992 original size:24 final size:24
Alignment explanation
Indices: 1371960--1372006 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
1371950 TCCACTATGG
1371960 ACGCTAAATTTGTAGAATTCTTTA
1 ACGCTAAATTTGTAGAATTCTTTA
*
1371984 ACGCTAAATTTGTAGCATTCTTT
1 ACGCTAAATTTGTAGAATTCTTT
1372007 GAAACTACAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.30, C:0.15, G:0.13, T:0.43
Consensus pattern (24 bp):
ACGCTAAATTTGTAGAATTCTTTA
Found at i:1379718 original size:28 final size:30
Alignment explanation
Indices: 1379661--1379719 Score: 77
Period size: 28 Copynumber: 2.0 Consensus size: 30
1379651 TTATATGTTC
*
1379661 ATTTTATAATTATATTAAAAATTTAATATT
1 ATTTTATAATTATATTAAAAAGTTAATATT
* *
1379691 ATTTTATAATT-T-TTAAACAGTTAGTATT
1 ATTTTATAATTATATTAAAAAGTTAATATT
1379719 A
1 A
1379720 AAATTCACTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
28 14 0.54
29 1 0.04
30 11 0.42
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (30 bp):
ATTTTATAATTATATTAAAAAGTTAATATT
Found at i:1379932 original size:18 final size:19
Alignment explanation
Indices: 1379898--1379934 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1379888 GATCGAATCG
*
1379898 AGTAGTTTTATTTAATAAA
1 AGTAATTTTATTTAATAAA
1379917 AGTAATTTTA-TTAATAAA
1 AGTAATTTTATTTAATAAA
1379935 TATATTATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (19 bp):
AGTAATTTTATTTAATAAA
Found at i:1382083 original size:81 final size:81
Alignment explanation
Indices: 1382012--1382330 Score: 482
Period size: 81 Copynumber: 4.0 Consensus size: 81
1382002 CAACTAATCT
** * * * *
1382012 ATTATTCTTTTACTCAACATTGTTTAACCGTACATCTAACTGGCATAATTGACACATTTTTATCA
1 ATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACATTTCTACCA
1382077 ATTGCACAATTAGGTC
66 ATTGCACAATTAGGTC
*
1382093 ATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATT-ACACCTTTCTACCA
1 ATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACATTTCTACCA
1382157 ATTGCACAATTAGG-C
66 ATTGCACAATTAGGTC
*
1382172 ATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACATTTCTGCCA
1 ATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACATTTCTACCA
*
1382237 ATTGCACAGTTAGGTC
66 ATTGCACAATTAGGTC
* * * * * *
1382253 ATTATTCTTTTACTCAATGGTATTTAATCGTTCATCTAAATGACATAATTGACA-TTTTCTGCCA
1 ATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACATTTCTACCA
1382317 ATTGCACAATTAGG
66 ATTGCACAATTAGG
1382331 CCTCAGAGGC
Statistics
Matches: 220, Mismatches: 16, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
79 51 0.23
80 72 0.33
81 97 0.44
ACGTcount: A:0.29, C:0.21, G:0.11, T:0.39
Consensus pattern (81 bp):
ATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACATTTCTACCA
ATTGCACAATTAGGTC
Found at i:1382201 original size:160 final size:160
Alignment explanation
Indices: 1382012--1382331 Score: 498
Period size: 160 Copynumber: 2.0 Consensus size: 160
1382002 CAACTAATCT
* * * *
1382012 ATTATTCTTTTACTCAACATTGTTTAACCGTACATCTAACTGGCATAATTGACACATTTTTATCA
1 ATTATTCTTTTACTCAACAGTATTTAACCGTACATCTAACTGGCATAATTGACACATTTCTACCA
* *
1382077 ATTGCACAATTAGGTCATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAAT
66 ATTGCACAATTAGGTCATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAAATGACATAAT
1382142 T-ACACCTTTCTACCAATTGCACAATTAGGC
131 TGACA-CTTTCTACCAATTGCACAATTAGGC
* * *
1382172 ATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACATTTCTGCCA
1 ATTATTCTTTTACTCAACAGTATTTAACCGTACATCTAACTGGCATAATTGACACATTTCTACCA
* * *
1382237 ATTGCACAGTTAGGTCATTATTCTTTTACTCAATGGTATTTAATCGTTCATCTAAATGACATAAT
66 ATTGCACAATTAGGTCATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAAATGACATAAT
* *
1382302 TGACATTTTCTGCCAATTGCACAATTAGGC
131 TGACACTTTCTACCAATTGCACAATTAGGC
1382332 CTCAGAGGCA
Statistics
Matches: 145, Mismatches: 14, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
160 142 0.98
161 3 0.02
ACGTcount: A:0.29, C:0.21, G:0.11, T:0.38
Consensus pattern (160 bp):
ATTATTCTTTTACTCAACAGTATTTAACCGTACATCTAACTGGCATAATTGACACATTTCTACCA
ATTGCACAATTAGGTCATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAAATGACATAAT
TGACACTTTCTACCAATTGCACAATTAGGC
Found at i:1382399 original size:68 final size:68
Alignment explanation
Indices: 1382283--1382537 Score: 341
Period size: 68 Copynumber: 3.8 Consensus size: 68
1382273 TATTTAATCG
* * * * * *
1382283 TTCATCTAAATGACATAATTGACA-TTTTCTGCCAATTGCACAATTAGGCCTCAGAGGCACTTAG
1 TTCATCTAACTGGCATAAATGACACATTTCTGTCAATTGCACAATTAGGCCTCAAAGGCACTTAG
1382347 CCT
66 CCT
* ** * *
1382350 TTCATCTAACTGGCATAAATGACACCTTTCTGTCGTTTGCACAGTTAGGCCTCAAAGGCATTTAG
1 TTCATCTAACTGGCATAAATGACACATTTCTGTCAATTGCACAATTAGGCCTCAAAGGCACTTAG
1382415 CCT
66 CCT
* * *
1382418 TTCATCTAAGTGGCATAAATGACACATTTCTGTCAATTGCACAATTAGGCTTTAAAGGCACTTAG
1 TTCATCTAACTGGCATAAATGACACATTTCTGTCAATTGCACAATTAGGCCTCAAAGGCACTTAG
1382483 CCT
66 CCT
* * * *
1382486 TTCATCTAACTGGCATAAATGACACATTTTTGTCATTTGCATAGTTAGGCCT
1 TTCATCTAACTGGCATAAATGACACATTTCTGTCAATTGCACAATTAGGCCT
1382538 ATAATCGTTT
Statistics
Matches: 163, Mismatches: 24, Indels: 1
0.87 0.13 0.01
Matches are distributed among these distances:
67 21 0.13
68 142 0.87
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.33
Consensus pattern (68 bp):
TTCATCTAACTGGCATAAATGACACATTTCTGTCAATTGCACAATTAGGCCTCAAAGGCACTTAG
CCT
Found at i:1382508 original size:136 final size:135
Alignment explanation
Indices: 1382283--1382537 Score: 393
Period size: 136 Copynumber: 1.9 Consensus size: 135
1382273 TATTTAATCG
* * *
1382283 TTCATCTAAATGACATAATTGACATTTTCTGCCAATTGCACAATTAGGCCTCAGAGGCACTTAGC
1 TTCATCTAAATGACATAAATGACAATTTCTGCCAATTGCACAATTAGGCCTCAAAGGCACTTAGC
* *
1382348 CTTTCATCTAACTGGCATAAATGACACCTTTCTGTCGTTTGCACAGTTAGGCCTCAAAGGCATTT
66 CTTTCATCTAACTGGCATAAATGACACATTTCTGTCATTTGCACAGTTAGGCCTCAAAGGCATTT
1382413 AGCCT
131 AGCCT
* * * * *
1382418 TTCATCTAAGTGGCATAAATGACACATTTCTGTCAATTGCACAATTAGGCTTTAAAGGCACTTAG
1 TTCATCTAAATGACATAAATGACA-ATTTCTGCCAATTGCACAATTAGGCCTCAAAGGCACTTAG
* *
1382483 CCTTTCATCTAACTGGCATAAATGACACATTTTTGTCATTTGCATAGTTAGGCCT
65 CCTTTCATCTAACTGGCATAAATGACACATTTCTGTCATTTGCACAGTTAGGCCT
1382538 ATAATCGTTT
Statistics
Matches: 107, Mismatches: 12, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
135 21 0.20
136 86 0.80
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.33
Consensus pattern (135 bp):
TTCATCTAAATGACATAAATGACAATTTCTGCCAATTGCACAATTAGGCCTCAAAGGCACTTAGC
CTTTCATCTAACTGGCATAAATGACACATTTCTGTCATTTGCACAGTTAGGCCTCAAAGGCATTT
AGCCT
Found at i:1383251 original size:18 final size:19
Alignment explanation
Indices: 1383207--1383257 Score: 86
Period size: 19 Copynumber: 2.7 Consensus size: 19
1383197 ACTTCTATAC
1383207 TATGGTATCGATACCCACT
1 TATGGTATCGATACCCACT
1383226 TATGGTATCGATACCC-CT
1 TATGGTATCGATACCCACT
*
1383244 TCTGGTATCGATAC
1 TATGGTATCGATAC
1383258 TGATTTTAGG
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
18 15 0.48
19 16 0.52
ACGTcount: A:0.24, C:0.25, G:0.18, T:0.33
Consensus pattern (19 bp):
TATGGTATCGATACCCACT
Found at i:1383307 original size:20 final size:21
Alignment explanation
Indices: 1383282--1383333 Score: 70
Period size: 22 Copynumber: 2.5 Consensus size: 21
1383272 ATGTTGCCTA
*
1383282 GTATCGATACT-CTTACTATG
1 GTATCGATACTACATACTATG
1383302 GTATCGATACTACCATACTATG
1 GTATCGATACTA-CATACTATG
*
1383324 GTACCGATAC
1 GTATCGATAC
1383334 CCCCTTACGG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 11 0.39
22 17 0.61
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.33
Consensus pattern (21 bp):
GTATCGATACTACATACTATG
Found at i:1383359 original size:95 final size:93
Alignment explanation
Indices: 1383185--1383410 Score: 257
Period size: 95 Copynumber: 2.4 Consensus size: 93
1383175 TTACTACTAC
* *
1383185 CCTAGTACCGATACTTCTATACTATGGTATCGATAC--CCACTTATGGTATCGATACCCCTTCTG
1 CCTAGTATCGATAC-TCT-TACTATGGTATCGATACTACCACTTATGGTACCGATACCCCTTCTG
* *
1383248 GTATCGATACTGATTTTAGGTTTGATGTTG
64 GTATCGATACTGATTTTAGATTCGATGTTG
1383278 CCTAGTATCGATACTCTTACTATGGTATCGATACTACCA-TACTATGGTACCGATACCCCCTTAC
1 CCTAGTATCGATACTCTTACTATGGTATCGATACTACCACT--TATGGTACCGATA-CCCCTT-C
**
1383342 -GGTATCGATAACT-ATTTTTTATTCGATGTTG
62 TGGTATCGAT-ACTGATTTTAGATTCGATGTTG
* * *
1383373 CTTGGTATCGATACCCTTA-TCATGGTATCGATACTACC
1 CCTAGTATCGATACTCTTACT-ATGGTATCGATACTACC
1383411 TCTTCGGTAT
Statistics
Matches: 116, Mismatches: 9, Indels: 14
0.83 0.06 0.10
Matches are distributed among these distances:
91 17 0.15
92 4 0.03
93 16 0.14
94 13 0.11
95 62 0.53
96 4 0.03
ACGTcount: A:0.24, C:0.23, G:0.16, T:0.37
Consensus pattern (93 bp):
CCTAGTATCGATACTCTTACTATGGTATCGATACTACCACTTATGGTACCGATACCCCTTCTGGT
ATCGATACTGATTTTAGATTCGATGTTG
Found at i:1386816 original size:59 final size:59
Alignment explanation
Indices: 1386715--1386866 Score: 160
Period size: 59 Copynumber: 2.6 Consensus size: 59
1386705 AATGAATTTG
* * * ** * ** * *
1386715 GGGATGAAATTGGAAGATTTAAAAGTTTGAGGGCCAATTTAAAATGAGGGTCGTAGTTA
1 GGGATGAAATTGGAATATTAAAAAGTTTAAGAACCAAGTTAAAATGAAAGTCATAATTA
* * *
1386774 GGGATGAAATTGGAATATTCAAAAGTTTAAGAACTAAGTTAAAATGAAAGTCATAATTT
1 GGGATGAAATTGGAATATTAAAAAGTTTAAGAACCAAGTTAAAATGAAAGTCATAATTA
* *
1386833 GAGGATGAAATTGAAATATAAAAAAGTTTAAGAA
1 G-GGATGAAATTGGAATATTAAAAAGTTTAAGAA
1386867 TTGATCTAAA
Statistics
Matches: 77, Mismatches: 15, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
59 48 0.62
60 29 0.38
ACGTcount: A:0.44, C:0.04, G:0.24, T:0.28
Consensus pattern (59 bp):
GGGATGAAATTGGAATATTAAAAAGTTTAAGAACCAAGTTAAAATGAAAGTCATAATTA
Found at i:1387386 original size:31 final size:30
Alignment explanation
Indices: 1387313--1387388 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 30
1387303 AATAATTAAA
*
1387313 AAATTTATTAAACTATTATAAAAAATCATT
1 AAATTTATCAAACTATTATAAAAAATCATT
* * *
1387343 ACATTTGGTCAAACTATTA-AAAAATCATTATT
1 AAATTT-ATCAAACTATTATAAAAA--ATCATT
1387375 AAATTTATCAAACT
1 AAATTTATCAAACT
1387389 TCCCTTTTAT
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
30 10 0.27
31 17 0.46
32 10 0.27
ACGTcount: A:0.49, C:0.11, G:0.03, T:0.38
Consensus pattern (30 bp):
AAATTTATCAAACTATTATAAAAAATCATT
Found at i:1394110 original size:204 final size:204
Alignment explanation
Indices: 1393755--1394363 Score: 1076
Period size: 204 Copynumber: 3.0 Consensus size: 204
1393745 TCAGGTACTG
* * *
1393755 TAGAGGCGAGGGTGACTCTCCCAAGTTAATTTGCTCAATTCACAAACGCCAGGGGTCGAACCCTT
1 TAGATGCGAGGGTGACTCTCCCAAGTTAATTTGCTCCATTCACAAACGTCAGGGGTCGAACCCTT
*
1393820 GACCTTGCTTAAGAGACCTAGTGCCTCATCCCACTAGACCAA-CAGATTGTAAACGAATGAACGA
66 GACCTTGCTTAAGGGACCTAGTGCCTCATCCCACTAGACCAACCA-ATTGTAAACGAATGAACGA
1393884 GAACTCGAGAAGATCGAATGAGGGAAAGGAACCTGGACGTAGGGATGTAAACAAGCCAAGTCGAG
130 GAACTCGAGAAGATCGAATGAGGGAAAGGAACCTGGACGTAGGGATGTAAACAAGCCAAGTCGAG
1393949 CTCGAGTCTA
195 CTCGAGTCTA
* *
1393959 TATATGCGAGGGTGACTCTCCCAAGTTAATTTGCTCCATTCACAAACGTGAGGGGTCGAACCCTT
1 TAGATGCGAGGGTGACTCTCCCAAGTTAATTTGCTCCATTCACAAACGTCAGGGGTCGAACCCTT
1394024 GACCTTGCTTAAGGGACCTAGTGCCTCATCCCACTAGACCAACCAATTGTAAACGAATGAACGAG
66 GACCTTGCTTAAGGGACCTAGTGCCTCATCCCACTAGACCAACCAATTGTAAACGAATGAACGAG
1394089 AACTCGAGAAGATCGAATGAGGGAAAGGAACCTGGACGTAGGGATGTAAACAAGCCAAGTCGAGC
131 AACTCGAGAAGATCGAATGAGGGAAAGGAACCTGGACGTAGGGATGTAAACAAGCCAAGTCGAGC
*
1394154 TCGAGTCTG
196 TCGAGTCTA
*
1394163 TAGATGCGAGGGTGACTCTCCCAAGTTAATTTGCTCCATTCACAAACTTCAGGGGTCGAACCCTT
1 TAGATGCGAGGGTGACTCTCCCAAGTTAATTTGCTCCATTCACAAACGTCAGGGGTCGAACCCTT
* * *
1394228 GACCTTGCTTAAGGGACCTAGTGCCTCATCTCACTAGACCAACCGATTGTAAACGAATGAATGAG
66 GACCTTGCTTAAGGGACCTAGTGCCTCATCCCACTAGACCAACCAATTGTAAACGAATGAACGAG
* * *
1394293 AACTCGAGAAGAACGAATGAGGGAAAGGAACCTGGACGTAGGGATATAAACAAGCCGAGTCGAGC
131 AACTCGAGAAGATCGAATGAGGGAAAGGAACCTGGACGTAGGGATGTAAACAAGCCAAGTCGAGC
1394358 TCGAGT
196 TCGAGT
1394364 ATTGTTAAGC
Statistics
Matches: 388, Mismatches: 16, Indels: 2
0.96 0.04 0.00
Matches are distributed among these distances:
204 386 0.99
205 2 0.01
ACGTcount: A:0.32, C:0.23, G:0.25, T:0.20
Consensus pattern (204 bp):
TAGATGCGAGGGTGACTCTCCCAAGTTAATTTGCTCCATTCACAAACGTCAGGGGTCGAACCCTT
GACCTTGCTTAAGGGACCTAGTGCCTCATCCCACTAGACCAACCAATTGTAAACGAATGAACGAG
AACTCGAGAAGATCGAATGAGGGAAAGGAACCTGGACGTAGGGATGTAAACAAGCCAAGTCGAGC
TCGAGTCTA
Done.