Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009174.1 Hibiscus syriacus cultivar Beakdansim tig00112737_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: 1358226
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 7
Found at i:222773 original size:20 final size:20
Alignment explanation
Indices: 222745--222796 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 20
222735 GATTGAAGTA
* *
222745 GTATCGATACTAATGTGT-AG
1 GTATTGATACTAA-GGGTAAG
*
222765 GTATTGATACCAAGGGTAAG
1 GTATTGATACTAAGGGTAAG
*
222785 ATATTGATACTA
1 GTATTGATACTA
222797 TAATTTAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
19 3 0.12
20 23 0.88
ACGTcount: A:0.35, C:0.10, G:0.23, T:0.33
Consensus pattern (20 bp):
GTATTGATACTAAGGGTAAG
Found at i:223399 original size:15 final size:15
Alignment explanation
Indices: 223381--223415 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
223371 TATGATATAT
*
223381 GTGAATATGTGTTAA
1 GTGAATATGTGCTAA
*
223396 GTGAATGTGTGCTAA
1 GTGAATATGTGCTAA
223411 GTGAA
1 GTGAA
223416 ATGAAATACT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.31, C:0.03, G:0.31, T:0.34
Consensus pattern (15 bp):
GTGAATATGTGCTAA
Found at i:223686 original size:24 final size:24
Alignment explanation
Indices: 223625--223703 Score: 97
Period size: 24 Copynumber: 3.3 Consensus size: 24
223615 GAGTCGAGGG
* *
223625 TTCTTCGCGGTCCTTCAGGACAAA
1 TTCTACGCGGTCCTTCGGGACAAA
*
223649 TTTCTACGTGGTCCTTCGGGACAAA
1 -TTCTACGCGGTCCTTCGGGACAAA
* *
223674 TTCTACGCAGTCCTTCGAGACAAA
1 TTCTACGCGGTCCTTCGGGACAAA
223698 -TCTACG
1 TTCTACG
223704 TGGCACTTTG
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
23 6 0.12
24 21 0.44
25 21 0.44
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.29
Consensus pattern (24 bp):
TTCTACGCGGTCCTTCGGGACAAA
Found at i:232855 original size:13 final size:13
Alignment explanation
Indices: 232837--232861 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
232827 AAAAGAATAT
232837 ATAACCATTAACC
1 ATAACCATTAACC
232850 ATAACCATTAAC
1 ATAACCATTAAC
232862 TAGTATAATC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.28, G:0.00, T:0.24
Consensus pattern (13 bp):
ATAACCATTAACC
Found at i:232916 original size:3 final size:3
Alignment explanation
Indices: 232910--232975 Score: 132
Period size: 3 Copynumber: 22.0 Consensus size: 3
232900 CTTAAAAAAA
232910 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
232958 TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT
232976 CTTTACTTAT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 63 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:237487 original size:200 final size:195
Alignment explanation
Indices: 237061--237584 Score: 658
Period size: 200 Copynumber: 2.6 Consensus size: 195
237051 GCGCTTATAT
* **
237061 TGACCTATTTTCTAAGTAAACCGGTATATTTATACCGGTAACATTACAAATTTACCTATTACATT
1 TGACCTATTTTCTAA-TAAACCGGTATATTTATACAGGT-ACATTGTAAATTTACCTATTACATT
* * * *
237126 ATAATTATCAGTTTCGATGCTTTTTGGATCGATACAATTT--TAAATGTATTGACACTTTATGCA
64 ATAATTATCGGTTTCGATG-TTTTGGGATCGATAC-TTTTAATAAATGTATCGACACTTTATGCA
* * *
237189 TGCACCTCATTGGGCATTCATTCTGGAAAAAAGTATTGACACAAACTTAAAAAGTGTCGATACAT
127 TGCACCCCATTGGGCATTCATTATGGAAAAAAGTATCGACACAAACTTAAAAAGTGTCGATACAT
*
237254 TATT
192 TATC
* * * *
237258 TAGACCTATTTTCTCATCAAACCGGTATATTTCTATCGGGTACATTGTAAATTTACCTATCACAT
1 T-GACCTATTTTCTAAT-AAACCGGTATATTTATA-CAGGTACATTGTAAATTTACCTATTACAT
* * *
237323 TGTAATTATCGGTTTTGATGTTTGTGGGATCGATACTTTTAATAAATGTATCGACACTTTATGCG
63 TATAATTATCGGTTTCGATGTTT-TGGGATCGATACTTTTAATAAATGTATCGACACTTTATGCA
* * * *
237388 TGCACCCCGTTTGGCATTCATTATGGACAAAACA-TATCGACACAAATTTAAACAGTGTCGATAC
127 TGCACCCCATTGGGCATTCATTATGGA-AAAA-AGTATCGACACAAACTTAAAAAGTGTCGATAC
*
237452 TTTATGC
190 ATTAT-C
* * *
237459 TGACCTATTTTCTTATAAAATCGGTATATTTATACCAGTTACATTGTAAATTTACCTATTACATT
1 TGACCTATTTTCTAAT-AAACCGGTATATTTATA-CAGGTACATTGTAAATTTACCTATTACATT
*
237524 ATAATTATCGATTTCGATGTTATTGGGATCGATACTTTTAATAAATGTATCGACACTTTAT
64 ATAATTATCGGTTTCGATGTT-TTGGGATCGATACTTTTAATAAATGTATCGACACTTTAT
237585 ATTCTGGACA
Statistics
Matches: 284, Mismatches: 33, Indels: 17
0.85 0.10 0.05
Matches are distributed among these distances:
197 8 0.03
198 78 0.27
199 48 0.17
200 147 0.52
201 3 0.01
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.39
Consensus pattern (195 bp):
TGACCTATTTTCTAATAAACCGGTATATTTATACAGGTACATTGTAAATTTACCTATTACATTAT
AATTATCGGTTTCGATGTTTTGGGATCGATACTTTTAATAAATGTATCGACACTTTATGCATGCA
CCCCATTGGGCATTCATTATGGAAAAAAGTATCGACACAAACTTAAAAAGTGTCGATACATTATC
Found at i:237708 original size:177 final size:178
Alignment explanation
Indices: 237422--237756 Score: 489
Period size: 177 Copynumber: 1.9 Consensus size: 178
237412 GGACAAAACA
* * * * *
237422 TATCGACACAAATTTAAACAGTGTCGATACTTTATGCTGACCTATTTTCTTATAAAATCGGTATA
1 TATCGACACAAATTCAAAAAGTGTCGATACTTTATGCTGACATATTTTCTAATAAAACCGGTATA
237487 TTTATACCAGTTACATTGTAAATTTACCTATTACATTATAATTATCGA-TTTCGATGTTATTGGG
66 TTTATACCAGTTACATTGTAAATTTACCTATTACATTATAATTAT-GAGTTTCGATGTTATTGGG
237551 ATCGATACTTTTA-ATAAATGTATCGACACTTTATATTCTGGACAATAAG
130 ATCGATACTTTTAGA-AAATGTATCGACACTTTATATTCTGGACAATAAG
* * *
237600 TATCGACACAAATTCAAAAAGTGTCGATA-TATTATGTTGACATGTTTTCTAAT-TAACCGGTAT
1 TATCGACACAAATTCAAAAAGTGTCGATACT-TTATGCTGACATATTTTCTAATAAAACCGGTAT
* * * * *
237663 ATTTATATCGGTTACATTGTTAATTTACCTATTACATTATAATTATTAGTTTCGATGTTTTTGGG
65 ATTTATACCAGTTACATTGTAAATTTACCTATTACATTATAATTATGAGTTTCGATGTTATTGGG
*
237728 GTCGATACTTTTAGAAAATGTATCGACAC
130 ATCGATACTTTTAGAAAATGTATCGACAC
237757 ATATTTAGCT
Statistics
Matches: 140, Mismatches: 14, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
176 1 0.01
177 93 0.66
178 46 0.33
ACGTcount: A:0.32, C:0.14, G:0.13, T:0.41
Consensus pattern (178 bp):
TATCGACACAAATTCAAAAAGTGTCGATACTTTATGCTGACATATTTTCTAATAAAACCGGTATA
TTTATACCAGTTACATTGTAAATTTACCTATTACATTATAATTATGAGTTTCGATGTTATTGGGA
TCGATACTTTTAGAAAATGTATCGACACTTTATATTCTGGACAATAAG
Found at i:242709 original size:33 final size:33
Alignment explanation
Indices: 242670--242736 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
242660 CCATCTTAAG
242670 TTCACCCATCAACACCTCAACTTCTTTCACCAC
1 TTCACCCATCAACACCTCAACTTCTTTCACCAC
*
242703 TTCACCCCTCAACACCTCAACTTCTTTCACCAC
1 TTCACCCATCAACACCTCAACTTCTTTCACCAC
242736 T
1 T
242737 CCATCTATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.25, C:0.46, G:0.00, T:0.28
Consensus pattern (33 bp):
TTCACCCATCAACACCTCAACTTCTTTCACCAC
Found at i:242795 original size:21 final size:21
Alignment explanation
Indices: 242771--242813 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
242761 CCCTTATGCT
242771 TCTCAAGTGTCTCTTCGACTC
1 TCTCAAGTGTCTCTTCGACTC
*
242792 TCTCAAGTTTCTCTTCGACTC
1 TCTCAAGTGTCTCTTCGACTC
242813 T
1 T
242814 TGATTGTCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.14, C:0.33, G:0.12, T:0.42
Consensus pattern (21 bp):
TCTCAAGTGTCTCTTCGACTC
Found at i:245291 original size:23 final size:22
Alignment explanation
Indices: 245243--245291 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
245233 CCAGAATGTC
245243 AAGG-GGGAACCGATACCCCCA
1 AAGGAGGGAACCGATACCCCCA
* *
245264 CAGGAGGGAACCGATTCCCCCTA
1 AAGGAGGGAACCGATACCCCC-A
245287 AAGGA
1 AAGGA
245292 AAATTGTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 3 0.13
22 15 0.65
23 5 0.22
ACGTcount: A:0.33, C:0.31, G:0.29, T:0.08
Consensus pattern (22 bp):
AAGGAGGGAACCGATACCCCCA
Found at i:246211 original size:103 final size:103
Alignment explanation
Indices: 245986--246203 Score: 411
Period size: 103 Copynumber: 2.1 Consensus size: 103
245976 GTCGAGGGTC
245986 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
246051 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTAGTATATGTATATGATTCTTAAGGAATGA
246089 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
246154 TTGATTCC-TAGTATATGTATATGATTCTTAAGGAATGA
66 TTGA-TCCTTAGTATATGTATATGATTCTTAAGGAATGA
246192 TATGTGGTCCTT
1 TATGTGGTCCTT
246204 ATGGACATTA
Statistics
Matches: 113, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
103 110 0.97
104 3 0.03
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.38
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCTTAGTATATGTATATGATTCTTAAGGAATGA
Found at i:246264 original size:47 final size:47
Alignment explanation
Indices: 246210--246329 Score: 206
Period size: 47 Copynumber: 2.6 Consensus size: 47
246200 CCTTATGGAC
246210 ATTATTATATGGCACTACGGTGCAATTCTACGCGGCACTCCGGTGCA
1 ATTATTATATGGCACTACGGTGCAATTCTACGCGGCACTCCGGTGCA
*
246257 ATTATTATATGGTACTACGGTGCAATTCTACGCGGCACTCCGGTGCA
1 ATTATTATATGGCACTACGGTGCAATTCTACGCGGCACTCCGGTGCA
* *
246304 ATTA-TATGTGGCACTTCGGTGCAATT
1 ATTATTATATGGCACTACGGTGCAATT
246330 ATATGAGATG
Statistics
Matches: 69, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
46 19 0.28
47 50 0.72
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.31
Consensus pattern (47 bp):
ATTATTATATGGCACTACGGTGCAATTCTACGCGGCACTCCGGTGCA
Found at i:246330 original size:23 final size:23
Alignment explanation
Indices: 246210--246334 Score: 124
Period size: 23 Copynumber: 5.3 Consensus size: 23
246200 CCTTATGGAC
*
246210 ATTATTATATGGCACTACGGTGCA
1 ATTA-TATGTGGCACTACGGTGCA
* * * *
246234 ATTCTACGCGGCACTCCGGTGCA
1 ATTATATGTGGCACTACGGTGCA
* *
246257 ATTATTATATGGTACTACGGTGCA
1 ATTA-TATGTGGCACTACGGTGCA
* * * *
246281 ATTCTACGCGGCACTCCGGTGCA
1 ATTATATGTGGCACTACGGTGCA
*
246304 ATTATATGTGGCACTTCGGTGCA
1 ATTATATGTGGCACTACGGTGCA
246327 ATTATATG
1 ATTATATG
246335 AGATGTGGTG
Statistics
Matches: 79, Mismatches: 21, Indels: 3
0.77 0.20 0.03
Matches are distributed among these distances:
23 59 0.75
24 20 0.25
ACGTcount: A:0.24, C:0.22, G:0.23, T:0.31
Consensus pattern (23 bp):
ATTATATGTGGCACTACGGTGCA
Found at i:248029 original size:182 final size:182
Alignment explanation
Indices: 247721--248137 Score: 699
Period size: 182 Copynumber: 2.3 Consensus size: 182
247711 TACTTGTACT
* *
247721 TATTAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCGGTTTTGTCCTTTAGAGACCG
1 TATTAAAGTATCGACACTTTCAATATATCCGGTAGCGCTATACCGATTTTGTCCTTTAGAGACCG
* * * *
247786 GTTTTGTCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTTTTATAAAGTATCGACACT
66 ATTTTGTCATATTTTTACCTATTATATCGTTGTGGATCGATACATTGTTATAAAATATCGACACT
247851 TTATAGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATACTTA
131 TTATAGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATACTTA
** * * *
247903 TATTAAAGTATCGACACTTTCAATATATTTGGTCGCTCTATACTGATTTTGTCCTTTAGAGACCG
1 TATTAAAGTATCGACACTTTCAATATATCCGGTAGCGCTATACCGATTTTGTCCTTTAGAGACCG
247968 ATTTTGTCATATTTTTACCTATTATATCGTTGTGGATCGATACATTGTTATAAAATATCGACACT
66 ATTTTGTCATATTTTTACCTATTATATCGTTGTGGATCGATACATTGTTATAAAATATCGACACT
*
248033 TTATAGGCGTTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATACTTA
131 TTATAGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATACTTA
* * *
248085 TATTAAAGTATCGACAATTTCAATATATCCGGTAGCGCTTTACCGGTTTTGTC
1 TATTAAAGTATCGACACTTTCAATATATCCGGTAGCGCTATACCGATTTTGTC
248138 ATATTTTTAC
Statistics
Matches: 215, Mismatches: 20, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
182 215 1.00
ACGTcount: A:0.27, C:0.18, G:0.15, T:0.40
Consensus pattern (182 bp):
TATTAAAGTATCGACACTTTCAATATATCCGGTAGCGCTATACCGATTTTGTCCTTTAGAGACCG
ATTTTGTCATATTTTTACCTATTATATCGTTGTGGATCGATACATTGTTATAAAATATCGACACT
TTATAGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATACTTA
Found at i:248276 original size:28 final size:28
Alignment explanation
Indices: 248244--248328 Score: 170
Period size: 28 Copynumber: 3.0 Consensus size: 28
248234 TATTTCTTCA
248244 TGATTTAGACCTACTACATTATTATTAC
1 TGATTTAGACCTACTACATTATTATTAC
248272 TGATTTAGACCTACTACATTATTATTAC
1 TGATTTAGACCTACTACATTATTATTAC
248300 TGATTTAGACCTACTACATTATTATTAC
1 TGATTTAGACCTACTACATTATTATTAC
248328 T
1 T
248329 CAATATTTTC
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 57 1.00
ACGTcount: A:0.32, C:0.18, G:0.07, T:0.44
Consensus pattern (28 bp):
TGATTTAGACCTACTACATTATTATTAC
Found at i:256563 original size:20 final size:20
Alignment explanation
Indices: 256540--256646 Score: 117
Period size: 20 Copynumber: 5.3 Consensus size: 20
256530 ATTTCGCGTT
*
256540 GCGATACTGACTATCGCAAC
1 GCGATACTGACTTTCGCAAC
* **
256560 GCGATAAT-ACAAAATCGCAAC
1 GCGATACTGAC--TTTCGCAAC
*
256581 GCAATACTGACTTTCGCAAC
1 GCGATACTGACTTTCGCAAC
* *
256601 ACGATACTTACTTTCGCAAC
1 GCGATACTGACTTTCGCAAC
256621 GCGATACTGACTTTCGCAAC
1 GCGATACTGACTTTCGCAAC
*
256641 GAGATA
1 GCGATA
256647 ATACATAATC
Statistics
Matches: 72, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
19 2 0.03
20 54 0.75
21 14 0.19
22 2 0.03
ACGTcount: A:0.34, C:0.27, G:0.17, T:0.22
Consensus pattern (20 bp):
GCGATACTGACTTTCGCAAC
Found at i:256861 original size:22 final size:22
Alignment explanation
Indices: 256833--256876 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
256823 CACTCTCTCA
*
256833 CCCATCTCTGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
256855 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
256877 TATCTCCATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.43, G:0.16, T:0.20
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:257188 original size:20 final size:20
Alignment explanation
Indices: 257139--257197 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
257129 TTTATTCTCT
* **
257139 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATTGTCATTTTCG
257159 CGTTGCGATTGTCATTTTCG
1 CGTTGCGATTGTCATTTTCG
* *
257179 TGTTGCGATTTTCATTTTC
1 CGTTGCGATTGTCATTTTC
257198 AGAAACTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.15, C:0.19, G:0.22, T:0.44
Consensus pattern (20 bp):
CGTTGCGATTGTCATTTTCG
Found at i:257388 original size:25 final size:24
Alignment explanation
Indices: 257334--257388 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
257324 TGTTTATTAT
* *
257334 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
257358 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
257384 TGTTT
1 TGTTT
257389 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:259132 original size:20 final size:20
Alignment explanation
Indices: 259109--259153 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
259099 CGCAACACGA
259109 AAATGA-CTATCGCAATGCGG
1 AAATGAGCTATCGCAATGC-G
259129 AAAT-AGCTATCGCAATGCG
1 AAATGAGCTATCGCAATGCG
259148 AAATGA
1 AAATGA
259154 AAATCGCAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.40, C:0.18, G:0.22, T:0.20
Consensus pattern (20 bp):
AAATGAGCTATCGCAATGCG
Found at i:259159 original size:19 final size:19
Alignment explanation
Indices: 259137--259266 Score: 101
Period size: 19 Copynumber: 7.6 Consensus size: 19
259127 GGAAATAGCT
259137 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
259156 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
259170 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
259189 ATTGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
259203 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
259222 ATCGCAA--CG--A-CCAA
1 ATCGCAATGCGAAATGAAA
*
259236 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
259255 ATCGCAATGCGA
1 ATCGCAATGCGA
259267 TTTGTGTTTC
Statistics
Matches: 85, Mismatches: 11, Indels: 30
0.67 0.09 0.24
Matches are distributed among these distances:
14 28 0.33
15 3 0.04
16 6 0.07
17 6 0.07
18 3 0.04
19 39 0.46
ACGTcount: A:0.46, C:0.22, G:0.19, T:0.13
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:259172 original size:14 final size:14
Alignment explanation
Indices: 259153--259244 Score: 58
Period size: 14 Copynumber: 5.9 Consensus size: 14
259143 ATGCGAAATG
259153 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
259167 AAAATCGCAATGCGAAATG
1 AAAATCGCAA--CG--A-C
*
259186 AAAATTGCAACGAC
1 AAAATCGCAACGAC
*
259200 AAAATCGCAATGCGAAATG
1 AAAATCGCAA--CG--A-C
259219 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
259233 CAAATCGCAACG
1 AAAATCGCAACG
259245 CGAAATGAAA
Statistics
Matches: 61, Mismatches: 7, Indels: 20
0.69 0.08 0.23
Matches are distributed among these distances:
14 30 0.49
15 2 0.03
16 4 0.07
17 4 0.07
18 2 0.03
19 19 0.31
ACGTcount: A:0.48, C:0.23, G:0.17, T:0.12
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:259179 original size:33 final size:33
Alignment explanation
Indices: 259137--259261 Score: 223
Period size: 33 Copynumber: 3.8 Consensus size: 33
259127 GGAAATAGCT
259137 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
259170 ATCGCAATGCGAAATGAAAATTGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
259203 ATCGCAATGCGAAATGAAAATCGCAACGACCAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
259236 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
259262 TGCGATTTGT
Statistics
Matches: 88, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 88 1.00
ACGTcount: A:0.47, C:0.22, G:0.18, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:259310 original size:33 final size:33
Alignment explanation
Indices: 259273--259352 Score: 142
Period size: 33 Copynumber: 2.4 Consensus size: 33
259263 GCGATTTGTG
*
259273 TTTCGCGTTGCGATTTGGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTGGTCGTTGCGATTTTCA
*
259306 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTGGTCGTTGCGATTTTCA
259339 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
259353 AGCCATTTCC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (33 bp):
TTTCGCATTGCGATTTGGTCGTTGCGATTTTCA
Found at i:259318 original size:19 final size:19
Alignment explanation
Indices: 259294--259352 Score: 74
Period size: 19 Copynumber: 3.4 Consensus size: 19
259284 GATTTGGTCG
259294 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
259313 TTGCGA-TTT--TGTCG--
1 TTGCGATTTTCATTTCGCA
259327 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
259346 TTGCGAT
1 TTGCGAT
259353 AGCCATTTCC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 6 0.18
15 3 0.09
16 4 0.12
17 4 0.12
18 3 0.09
19 13 0.39
ACGTcount: A:0.14, C:0.19, G:0.20, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:259332 original size:14 final size:14
Alignment explanation
Indices: 259278--259336 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 14
259268 TTGTGTTTCG
*
259278 CGTTGCGATTTGGT
1 CGTTGCGATTTTGT
*
259292 CGTTGCGATTTTCATTT
1 CGTTGCGA-TTT--TGT
259309 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
259325 CGTTGCGATTTT
1 CGTTGCGATTTT
259337 CATTTCGCAT
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
14 18 0.49
15 3 0.08
16 4 0.11
17 3 0.08
18 3 0.08
19 6 0.16
ACGTcount: A:0.10, C:0.17, G:0.25, T:0.47
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:259408 original size:20 final size:20
Alignment explanation
Indices: 259339--259411 Score: 110
Period size: 20 Copynumber: 3.6 Consensus size: 20
259329 GCGATTTTCA
*
259339 TTTCGCATTGCGATAGCCAT
1 TTTCGCGTTGCGATAGCCAT
* *
259359 TTCCGCGTTACGATAGCCAT
1 TTTCGCGTTGCGATAGCCAT
*
259379 TTTCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATAGCCAT
259399 TTTCGCGTTGCGA
1 TTTCGCGTTGCGA
259412 AAGTAAGTTT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.16, C:0.25, G:0.23, T:0.36
Consensus pattern (20 bp):
TTTCGCGTTGCGATAGCCAT
Found at i:259422 original size:20 final size:20
Alignment explanation
Indices: 259379--259437 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 20
259369 CGATAGCCAT
* * *
259379 TTTCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGAAAGTAAG
259399 TTTCGCGTTGCGAAAGTAAG
1 TTTCGCGTTGCGAAAGTAAG
** *
259419 TTTCGTATTGCAAAAGTAA
1 TTTCGCGTTGCGAAAGTAA
259438 ACTATTCTTC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.25, C:0.15, G:0.24, T:0.36
Consensus pattern (20 bp):
TTTCGCGTTGCGAAAGTAAG
Found at i:259423 original size:40 final size:40
Alignment explanation
Indices: 259339--259429 Score: 101
Period size: 40 Copynumber: 2.3 Consensus size: 40
259329 GCGATTTTCA
* * *
259339 TTTCGCATTGCGATAGCCATTTCCGCGTTACGATAGCCAT
1 TTTCGCATTGCGATAGCCATTTCCGCGTTACGAAAGCAAG
* * * * *
259379 TTTCGCGTTGCGATAGTCATTTTCGCGTTGCGAAAGTAAG
1 TTTCGCATTGCGATAGCCATTTCCGCGTTACGAAAGCAAG
*
259419 TTTCGTATTGC
1 TTTCGCATTGC
259430 AAAAGTAAAC
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.19, C:0.22, G:0.23, T:0.36
Consensus pattern (40 bp):
TTTCGCATTGCGATAGCCATTTCCGCGTTACGAAAGCAAG
Found at i:259866 original size:41 final size:42
Alignment explanation
Indices: 259775--259866 Score: 109
Period size: 41 Copynumber: 2.2 Consensus size: 42
259765 GTCCGACTCA
* *
259775 CCTGTCATCCCTTAAGAGTCCCCTCTAATCGTTCAAGAGGCT
1 CCTGTCATCCCTCAAGAGTCCCCTCTAACCGTTCAAGAGGCT
* *
259817 CCTATCATCCCTCAAGAGTCTCCC-C-CACCGTTCAAGAGGC-
1 CCTGTCATCCCTCAAGAGTC-CCCTCTAACCGTTCAAGAGGCT
259857 CACTGTCATC
1 C-CTGTCATC
259867 GTTGAAGAGG
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
40 1 0.02
41 20 0.47
42 19 0.44
43 3 0.07
ACGTcount: A:0.22, C:0.38, G:0.15, T:0.25
Consensus pattern (42 bp):
CCTGTCATCCCTCAAGAGTCCCCTCTAACCGTTCAAGAGGCT
Found at i:261307 original size:14 final size:14
Alignment explanation
Indices: 261273--261311 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
261263 TTGATTGTTT
261273 AATTGATTTGTAAA
1 AATTGATTTGTAAA
*
261287 AAATGATTTGTAAA
1 AATTGATTTGTAAA
**
261301 TGTTGATTTGT
1 AATTGATTTGT
261312 TTAATTGATG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:261467 original size:19 final size:19
Alignment explanation
Indices: 261443--261485 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
261433 TCAACGAGAG
* *
261443 AATCGCAATGCGAAATGAA
1 AATCGCAATGCAAAATAAA
261462 AATCGCAATGCAAAATAAA
1 AATCGCAATGCAAAATAAA
261481 AATCG
1 AATCG
261486 TAACGAGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.51, C:0.16, G:0.16, T:0.16
Consensus pattern (19 bp):
AATCGCAATGCAAAATAAA
Found at i:261551 original size:20 final size:20
Alignment explanation
Indices: 261526--261581 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
261516 TCGCATTGCG
*
261526 ATTTTCTCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
*
261546 ATTTTCGCGTTGCGATAGTC
1 ATTTTCGCGTTGCGATAGCC
261566 ATTTTCGCGTTGCGAT
1 ATTTTCGCGTTGCGAT
261582 TTCCCCGTTG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.14, C:0.21, G:0.23, T:0.41
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:261926 original size:41 final size:41
Alignment explanation
Indices: 261828--261944 Score: 146
Period size: 41 Copynumber: 2.9 Consensus size: 41
261818 CGAAGTCAGA
* * *** * *
261828 ATCGCGTTGCGAAAGTTAGAATCGCATTGCGAAAGT-CAGT
1 ATCGCGTTGCGAAAGTCAGTATCGCATTGCGATTTTATATT
*
261868 ATCGCGTTGCGAAAGTCAGTATCGCGTTGCGATTTTATATT
1 ATCGCGTTGCGAAAGTCAGTATCGCATTGCGATTTTATATT
*
261909 ATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTT
1 ATCGCGTTGCGAAAGTCAGTATCGCATTGCGATTTT
261945 CCAAATTCGC
Statistics
Matches: 66, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
40 30 0.45
41 36 0.55
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.32
Consensus pattern (41 bp):
ATCGCGTTGCGAAAGTCAGTATCGCATTGCGATTTTATATT
Found at i:261941 original size:20 final size:20
Alignment explanation
Indices: 261813--261940 Score: 141
Period size: 20 Copynumber: 6.4 Consensus size: 20
261803 TTCAGAATCT
*
261813 CGTTGCG-AAGTCAGAATCG
1 CGTTGCGAAAGTCAGTATCG
* *
261832 CGTTGCGAAAGTTAGAATCG
1 CGTTGCGAAAGTCAGTATCG
*
261852 CATTGCGAAAGTCAGTATCG
1 CGTTGCGAAAGTCAGTATCG
261872 CGTTGCGAAAGTCAGTATCG
1 CGTTGCGAAAGTCAGTATCG
*** * *
261892 CGTTGCGATTTTATATTATCG
1 CGTTGCGAAAGT-CAGTATCG
*
261913 CGTTGCGATAGTCAGTATCG
1 CGTTGCGAAAGTCAGTATCG
*
261933 CATTGCGA
1 CGTTGCGA
261941 TTTTCCAAAT
Statistics
Matches: 92, Mismatches: 15, Indels: 3
0.84 0.14 0.03
Matches are distributed among these distances:
19 7 0.08
20 69 0.75
21 16 0.17
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.29
Consensus pattern (20 bp):
CGTTGCGAAAGTCAGTATCG
Found at i:261974 original size:20 final size:21
Alignment explanation
Indices: 261930--261981 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
261920 ATAGTCAGTA
*
261930 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
**
261951 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACAAAT
261971 TCGCATTGCGA
1 TCGCATTGCGA
261982 ATTGGGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:261980 original size:61 final size:61
Alignment explanation
Indices: 261848--261982 Score: 141
Period size: 61 Copynumber: 2.2 Consensus size: 61
261838 GAAAGTTAGA
* * *
261848 ATCGCATTGCGAAAGTCAGTATCGCGTTGCGAAAGTCAGTATCGCGTTGCGATTTTATATT
1 ATCGCATTGCGAAAGTCAGTATCGCATTGCGAAAGTCAATATCGCATTGCGATTTTATATT
* * *** *
261909 ATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTCCAA-ATTCGCATTGCGA-TTTA-CTT
1 ATCGCATTGCGAAAGTCAGTATCGCATTGCGAAAGT-CAATA-TCGCATTGCGATTTTATATT
261969 ATTCGCATTGCGAA
1 A-TCGCATTGCGAA
261983 TTGGGAAAAT
Statistics
Matches: 60, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
60 3 0.05
61 45 0.75
62 12 0.20
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.34
Consensus pattern (61 bp):
ATCGCATTGCGAAAGTCAGTATCGCATTGCGAAAGTCAATATCGCATTGCGATTTTATATT
Found at i:262081 original size:20 final size:20
Alignment explanation
Indices: 262058--262103 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
262048 GGAAACTGAT
*
262058 TTGCGATAATAGAGATCGCG
1 TTGCGATAATAGAGATCGCA
* *
262078 TTGCGA-ATTAGCGATCGCA
1 TTGCGATAATAGAGATCGCA
262097 TTGCGAT
1 TTGCGAT
262104 TTTGTTGGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.28
Consensus pattern (20 bp):
TTGCGATAATAGAGATCGCA
Found at i:270467 original size:48 final size:48
Alignment explanation
Indices: 270415--270506 Score: 112
Period size: 48 Copynumber: 1.9 Consensus size: 48
270405 ATTTTCGACT
* *
270415 TGAATTCTGTTCTGATACATTACCTGAATTATATTCTGATTTCTTATC
1 TGAATTCTGTTATGATACATGACCTGAATTATATTCTGATTTCTTATC
* * * * * *
270463 TGAATTTTGTTATGATATATGATCTGAATTTTGTTTTGATTTCT
1 TGAATTCTGTTATGATACATGACCTGAATTATATTCTGATTTCT
270507 GATATCTCCG
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
48 36 1.00
ACGTcount: A:0.24, C:0.11, G:0.13, T:0.52
Consensus pattern (48 bp):
TGAATTCTGTTATGATACATGACCTGAATTATATTCTGATTTCTTATC
Found at i:270478 original size:24 final size:24
Alignment explanation
Indices: 270451--270509 Score: 82
Period size: 24 Copynumber: 2.5 Consensus size: 24
270441 AATTATATTC
*
270451 TGATTTCTTATCTGAATTTTGTTA
1 TGATTTCTGATCTGAATTTTGTTA
* * *
270475 TGATATATGATCTGAATTTTGTTT
1 TGATTTCTGATCTGAATTTTGTTA
270499 TGATTTCTGAT
1 TGATTTCTGAT
270510 ATCTCCGTTT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.22, C:0.07, G:0.15, T:0.56
Consensus pattern (24 bp):
TGATTTCTGATCTGAATTTTGTTA
Found at i:271962 original size:189 final size:188
Alignment explanation
Indices: 271687--272064 Score: 625
Period size: 189 Copynumber: 2.0 Consensus size: 188
271677 ATTAAATTTT
* *
271687 AAATTTTAAATATATTATATATAACTTATGGGCTCAACCAAACCATTTAAAACTCAATTAATAAT
1 AAATATTAAATATATTATATATAACATATGGGCTCAACCAAACCATTTAAAACTCAATTAATAAT
*
271752 TTAAGATCTAATAAATTTTAAACCTAAATCAATATTAATTAATTAAAAAAA-TTATATACAATTT
66 TTAAGATCTAATAAATTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTTATATAAAATTT
* *
271816 TTATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTTTTGAATTTAAAAA
131 TTATTTTATAATTATATATTATTTAAATTAATTAGAAACTATTTTTTTGAA-TTAAAAA
* * * *
271875 AAATATTAAATATATTATATATAACATATGGTCTCAGTCCAAACTATTTAAAATTCAATTAATAA
1 AAATATTAAATATATTATATATAACATATGGGCTCA-ACCAAACCATTTAAAACTCAATTAATAA
*
271940 TTTAAGATAC-AATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTTATATAAAAT
65 TTTAAGAT-CTAATAAATTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTTATATAAAAT
272004 TTTTATTTTATAATTATATATTATTTAAATTAATTAGAAACTATTTTTTTGAATTAAAAA
129 TTTTATTTTATAATTATATATTATTTAAATTAATTAGAAACTATTTTTTTGAATTAAAAA
272064 A
1 A
272065 TATTTAATTT
Statistics
Matches: 177, Mismatches: 10, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
188 33 0.19
189 82 0.46
190 62 0.35
ACGTcount: A:0.47, C:0.07, G:0.03, T:0.42
Consensus pattern (188 bp):
AAATATTAAATATATTATATATAACATATGGGCTCAACCAAACCATTTAAAACTCAATTAATAAT
TTAAGATCTAATAAATTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTTATATAAAATTT
TTATTTTATAATTATATATTATTTAAATTAATTAGAAACTATTTTTTTGAATTAAAAA
Found at i:282252 original size:16 final size:17
Alignment explanation
Indices: 282223--282256 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
282213 ATAAAATATA
*
282223 TTTAAATTATTCTTAAT
1 TTTAAAATATTCTTAAT
282240 TTTAAAATA-TCTTAAT
1 TTTAAAATATTCTTAAT
282256 T
1 T
282257 AAAATTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (17 bp):
TTTAAAATATTCTTAAT
Found at i:282735 original size:31 final size:31
Alignment explanation
Indices: 282700--282796 Score: 115
Period size: 31 Copynumber: 3.1 Consensus size: 31
282690 TTAAGTTTCT
*
282700 ATTTGACTCTTAAAGTTTAGATAAAATATTA
1 ATTTGACTCTTAAACTTTAGATAAAATATTA
* * * *
282731 ATTTGACTCCTAAATTTTAGATGAAATACTA
1 ATTTGACTCTTAAACTTTAGATAAAATATTA
* *
282762 ATTTGACCCTTGAACTTTAGATAAAAT-TTCA
1 ATTTGACTCTTAAACTTTAGATAAAATATT-A
282793 ATTT
1 ATTT
282797 AACCTTCAAA
Statistics
Matches: 55, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
30 1 0.02
31 54 0.98
ACGTcount: A:0.38, C:0.11, G:0.09, T:0.41
Consensus pattern (31 bp):
ATTTGACTCTTAAACTTTAGATAAAATATTA
Found at i:284163 original size:16 final size:16
Alignment explanation
Indices: 284142--284174 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
284132 AAGAATAATT
284142 GGTAGACCCGAAAATA
1 GGTAGACCCGAAAATA
*
284158 GGTAGACCTGAAAATA
1 GGTAGACCCGAAAATA
284174 G
1 G
284175 ATGGACGCCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.42, C:0.15, G:0.27, T:0.15
Consensus pattern (16 bp):
GGTAGACCCGAAAATA
Found at i:286660 original size:21 final size:21
Alignment explanation
Indices: 286634--286690 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
286624 CATATGAAAT
286634 TTGTCCCGAAGGACCACTGTA
1 TTGTCCCGAAGGACCACTGTA
286655 TTGTCCCGAAGGACCACTGTA
1 TTGTCCCGAAGGACCACTGTA
*
286676 TTGTTCCGAAGGACC
1 TTGTCCCGAAGGACC
286691 TATGAAACCC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.23, C:0.28, G:0.25, T:0.25
Consensus pattern (21 bp):
TTGTCCCGAAGGACCACTGTA
Found at i:287129 original size:2 final size:2
Alignment explanation
Indices: 287094--287121 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
287084 AGCATATAGA
287094 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
287122 CCATATATCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:287479 original size:20 final size:22
Alignment explanation
Indices: 287444--287484 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
287434 AAATTTTTTT
287444 TTCAAACCCAGAAAA-TCACTG
1 TTCAAACCCAGAAAATTCACTG
*
287465 TTCATACCC-GAAAATTCACT
1 TTCAAACCCAGAAAATTCACT
287485 ATAACAACTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.39, C:0.29, G:0.07, T:0.24
Consensus pattern (22 bp):
TTCAAACCCAGAAAATTCACTG
Found at i:292145 original size:20 final size:20
Alignment explanation
Indices: 292116--292153 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
292106 AGTGAACAGT
*
292116 GGGGGTATCGATTCCCTATA
1 GGGGGAATCGATTCCCTATA
292136 GGGGGAATCGATTCCCTA
1 GGGGGAATCGATTCCCTA
292154 AATACATTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.21, G:0.32, T:0.26
Consensus pattern (20 bp):
GGGGGAATCGATTCCCTATA
Found at i:292868 original size:21 final size:21
Alignment explanation
Indices: 292842--292898 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
292832 CATATGAAAT
292842 TTGTCCCGAAGGACCACTGTA
1 TTGTCCCGAAGGACCACTGTA
292863 TTGTCCCGAAGGACCACTGTA
1 TTGTCCCGAAGGACCACTGTA
*
292884 TTGTTCCGAAGGACC
1 TTGTCCCGAAGGACC
292899 TATGAAACCC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.23, C:0.28, G:0.25, T:0.25
Consensus pattern (21 bp):
TTGTCCCGAAGGACCACTGTA
Found at i:293688 original size:20 final size:22
Alignment explanation
Indices: 293651--293693 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
293641 TGGAAATTTT
293651 TGTTCAAACCCAGAAAA-TCAC
1 TGTTCAAACCCAGAAAATTCAC
*
293672 TGTTCATACCC-GAAAATTCAC
1 TGTTCAAACCCAGAAAATTCAC
293693 T
1 T
293694 ATAACAACTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.37, C:0.28, G:0.09, T:0.26
Consensus pattern (22 bp):
TGTTCAAACCCAGAAAATTCAC
Found at i:294815 original size:22 final size:21
Alignment explanation
Indices: 294769--294819 Score: 66
Period size: 22 Copynumber: 2.4 Consensus size: 21
294759 CTTTCATGTC
* *
294769 TTTTTTTTTTTCGAACAGTTT
1 TTTTTTTTTTTCGAACAGCTA
*
294790 TTTTTTCTTTTTCGAACTGCTA
1 TTTTTT-TTTTTCGAACAGCTA
294812 TTTTTTTT
1 TTTTTTTT
294820 CAACATTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 8 0.31
22 18 0.69
ACGTcount: A:0.12, C:0.12, G:0.08, T:0.69
Consensus pattern (21 bp):
TTTTTTTTTTTCGAACAGCTA
Found at i:303417 original size:4 final size:4
Alignment explanation
Indices: 303403--303440 Score: 51
Period size: 4 Copynumber: 9.5 Consensus size: 4
303393 TCTAAAAAAA
*
303403 TTAT GTTAT TTAT TTAT TTAT TTAT GTA- TTAT TTAT TT
1 TTAT -TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
303441 TTAGCCATGA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
3 2 0.07
4 24 0.80
5 4 0.13
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (4 bp):
TTAT
Found at i:303988 original size:24 final size:24
Alignment explanation
Indices: 303961--304007 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
303951 CAAAATCTGA
303961 GTATTGACCAAGATCAAAGTTCGG
1 GTATTGACCAAGATCAAAGTTCGG
*
303985 GTATTGACCAAGATCAAATTTCG
1 GTATTGACCAAGATCAAAGTTCG
304008 AATACTGACT
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:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (24 bp):
GTATTGACCAAGATCAAAGTTCGG
Found at i:304016 original size:24 final size:24
Alignment explanation
Indices: 303965--304016 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
303955 ATCTGAGTAT
** *
303965 TGACCAAGATCAAAGTTCGGGTAT
1 TGACCAAGATCAAAGTTCGAATAC
*
303989 TGACCAAGATCAAATTTCGAATAC
1 TGACCAAGATCAAAGTTCGAATAC
304013 TGAC
1 TGAC
304017 TAGTACTCAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.25
Consensus pattern (24 bp):
TGACCAAGATCAAAGTTCGAATAC
Found at i:304149 original size:12 final size:12
Alignment explanation
Indices: 304128--304161 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
304118 GGTTGTGGGT
*
304128 TTTGAGATTGTG
1 TTTGATATTGTG
304140 TTTGATATTGTG
1 TTTGATATTGTG
*
304152 TTTGGTATTG
1 TTTGATATTG
304162 GAAATGTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:309656 original size:18 final size:18
Alignment explanation
Indices: 309644--309686 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
309634 ATGTCCCGAG
309644 GGACCACTATGTCCTCAA
1 GGACCACTATGTCCTCAA
309662 GGACCACTATGTCCTCAA
1 GGACCACTATGTCCTCAA
309680 GGACCAC
1 GGACCAC
309687 GTAGACCCTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.28, C:0.35, G:0.19, T:0.19
Consensus pattern (18 bp):
GGACCACTATGTCCTCAA
Found at i:311924 original size:20 final size:21
Alignment explanation
Indices: 311872--311925 Score: 58
Period size: 20 Copynumber: 2.7 Consensus size: 21
311862 TTGTGAAATT
* **
311872 AAAATTCGTGTTGCGAATTCG
1 AAAATTCGTGTTGCAAAAACG
*
311893 AAAATT-GAGTTGCAAAAAC-
1 AAAATTCGTGTTGCAAAAACG
311912 AAAATTCGTGTTGC
1 AAAATTCGTGTTGC
311926 GATTTAGAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
19 6 0.22
20 15 0.56
21 6 0.22
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30
Consensus pattern (21 bp):
AAAATTCGTGTTGCAAAAACG
Found at i:311990 original size:20 final size:20
Alignment explanation
Indices: 311961--312072 Score: 70
Period size: 20 Copynumber: 5.5 Consensus size: 20
311951 GGAAACTTGT
*
311961 GTTGCAAATTCAGAAATCGA
1 GTTGCGAATTCAGAAATCGA
* *
311981 GTTGCGAATT-TGAAATTCCGT
1 GTTGCGAATTCAGAAA-T-CGA
** *
312002 GTTGCGAATTTGGAAATCGC
1 GTTGCGAATTCAGAAATCGA
**
312022 GTTGCGAATTTGGAAATTC-A
1 GTTGCGAATTCAGAAA-TCGA
312042 CGTTGCG-ATTGCAGAAA-CTGA
1 -GTTGCGAATT-CAGAAATC-GA
312063 GTTGCGAATT
1 GTTGCGAATT
312073 TGGGAAATTC
Statistics
Matches: 75, Mismatches: 8, Indels: 17
0.75 0.08 0.17
Matches are distributed among these distances:
19 5 0.07
20 37 0.49
21 29 0.39
22 4 0.05
ACGTcount: A:0.29, C:0.14, G:0.26, T:0.31
Consensus pattern (20 bp):
GTTGCGAATTCAGAAATCGA
Found at i:312004 original size:41 final size:41
Alignment explanation
Indices: 311959--312086 Score: 129
Period size: 41 Copynumber: 3.0 Consensus size: 41
311949 AAGGAAACTT
311959 GTGTTGCAAATTCAGAAATCGAGTTGCGAATTTGAAATTC-C
1 GTGTTGC-AATTCAGAAATCGAGTTGCGAATTTGAAATTCAC
** *
312000 GTGTTGCGAATTTGGAAATCGCGTTGCGAATTTGGAAATTCAC
1 GTGTTGC-AATTCAGAAATCGAGTTGCGAATTT-GAAATTCAC
*
312043 --GTTGCGATTGCAGAAA-CTGAGTTGCGAATTTGGGAAATTCAC
1 GTGTTGCAATT-CAGAAATC-GAGTTGCGAATTT--GAAATTCAC
312085 GT
1 GT
312087 TGCAAATTTG
Statistics
Matches: 72, Mismatches: 8, Indels: 11
0.79 0.09 0.12
Matches are distributed among these distances:
40 4 0.06
41 50 0.69
42 17 0.24
43 1 0.01
ACGTcount: A:0.28, C:0.14, G:0.27, T:0.31
Consensus pattern (41 bp):
GTGTTGCAATTCAGAAATCGAGTTGCGAATTTGAAATTCAC
Found at i:312058 original size:21 final size:22
Alignment explanation
Indices: 311981--312100 Score: 98
Period size: 21 Copynumber: 5.8 Consensus size: 22
311971 CAGAAATCGA
311981 GTTGCGAATTT--GAAATTC-C
1 GTTGCGAATTTGAGAAATTCAC
*
312000 GTGTTGCGAATTTG-GAAA-TCGC
1 --GTTGCGAATTTGAGAAATTCAC
312022 GTTGCGAATTTG-GAAATTCAC
1 GTTGCGAATTTGAGAAATTCAC
* *
312043 GTTGCG-A-TTGCAGAAACTGA-
1 GTTGCGAATTTG-AGAAATTCAC
*
312063 GTTGCGAATTTGGGAAATTCAC
1 GTTGCGAATTTGAGAAATTCAC
*
312085 GTTGCAAATTTG-GAAA
1 GTTGCGAATTTGAGAAA
312101 CTGTGTTGCG
Statistics
Matches: 84, Mismatches: 7, Indels: 16
0.79 0.07 0.15
Matches are distributed among these distances:
19 3 0.04
20 23 0.27
21 39 0.46
22 19 0.23
ACGTcount: A:0.28, C:0.13, G:0.27, T:0.32
Consensus pattern (22 bp):
GTTGCGAATTTGAGAAATTCAC
Found at i:314500 original size:38 final size:38
Alignment explanation
Indices: 314444--314548 Score: 176
Period size: 38 Copynumber: 2.8 Consensus size: 38
314434 ATAGCGACTG
*
314444 CAATACTAACGAACCATGCTGTTCTTCTACGACCTGAC
1 CAATGCTAACGAACCATGCTGTTCTTCTACGACCTGAC
314482 CAATGCTAACGAACCATGCTGTTCTTCTACGACCTGAC
1 CAATGCTAACGAACCATGCTGTTCTTCTACGACCTGAC
*
314520 CAATGCTAACGAACCA-GACCGTTCTTCTA
1 CAATGCTAACGAACCATG-CTGTTCTTCTA
314549 TGAATCGGCC
Statistics
Matches: 64, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
37 1 0.02
38 63 0.98
ACGTcount: A:0.29, C:0.31, G:0.14, T:0.26
Consensus pattern (38 bp):
CAATGCTAACGAACCATGCTGTTCTTCTACGACCTGAC
Found at i:322804 original size:19 final size:20
Alignment explanation
Indices: 322782--322819 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
322772 ACAAAAATCA
*
322782 AAAAGAAAAGA-AAAAGATT
1 AAAACAAAAGAGAAAAGATT
322801 AAAACAAAAGAGAAAAGAT
1 AAAACAAAAGAGAAAAGAT
322820 GAGAGAGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.74, C:0.03, G:0.16, T:0.08
Consensus pattern (20 bp):
AAAACAAAAGAGAAAAGATT
Found at i:324029 original size:20 final size:20
Alignment explanation
Indices: 323984--324029 Score: 51
Period size: 20 Copynumber: 2.3 Consensus size: 20
323974 CGAGGGTAAA
*
323984 GATACTCCTACTTGGGTATC
1 GATACTCCTACATGGGTATC
324004 -AGTACTCCT-CATGTGGTATC
1 GA-TACTCCTACATG-GGTATC
324024 GATACT
1 GATACT
324030 ACCCTGAGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 6
0.76 0.03 0.21
Matches are distributed among these distances:
19 4 0.18
20 17 0.77
21 1 0.05
ACGTcount: A:0.22, C:0.24, G:0.20, T:0.35
Consensus pattern (20 bp):
GATACTCCTACATGGGTATC
Found at i:341290 original size:39 final size:38
Alignment explanation
Indices: 341218--341293 Score: 100
Period size: 38 Copynumber: 2.0 Consensus size: 38
341208 ATATTTTCAA
*
341218 TTTTATAAAAAAATTATATAAATATTATGAATTTAATT
1 TTTTATAAAAAAATTATATAAATATTATCAATTTAATT
* *
341256 TTTTTTAAAGAAAA-TATATAAATATTTTCCAATTTAAT
1 TTTTATAAA-AAAATTATATAAATATTAT-CAATTTAAT
341294 AAAAAAATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
38 21 0.64
39 12 0.36
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (38 bp):
TTTTATAAAAAAATTATATAAATATTATCAATTTAATT
Found at i:341460 original size:20 final size:20
Alignment explanation
Indices: 341424--341461 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
341414 ATCCTATTCC
**
341424 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
341444 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
341462 GTAAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:342927 original size:43 final size:43
Alignment explanation
Indices: 342796--343021 Score: 210
Period size: 43 Copynumber: 5.2 Consensus size: 43
342786 TATGTAATAA
* *
342796 AAACGCCGCAATAAG-TGTTGATTTTTAGCGGCGTTTTTCTTAC
1 AAACGCCGCAAT-AGTTGTTGATATTTAGCGGCGTTTTTCTCAC
* * *
342839 AAACGCCGCAAATAGATGTTGATCTTTAGCGGCGTTTTTCCCAC
1 AAACGCCGC-AATAGTTGTTGATATTTAGCGGCGTTTTTCTCAC
* * * *
342883 AAACGCTGCAGTAGTTGTTTATATTTAGCGGCGTTTTTATCAC
1 AAACGCCGCAATAGTTGTTGATATTTAGCGGCGTTTTTCTCAC
* * *
342926 AAACGCCGCAATAATTATTGAAATTTAGCGGCGTTTTT-TCCAC
1 AAACGCCGCAATAGTTGTTGATATTTAGCGGCGTTTTTCT-CAC
* ** *
342969 ACAA-GCCGCAATA-TGTGTTGAGATTTCCCGACGTTTTT-TCATAC
1 A-AACGCCGCAATAGT-TGTTGATATTTAGCGGCGTTTTTCTC--AC
343013 AAACGCCGC
1 AAACGCCGC
343022 TAAAAGATCG
Statistics
Matches: 154, Mismatches: 21, Indels: 15
0.81 0.11 0.08
Matches are distributed among these distances:
42 3 0.02
43 105 0.68
44 46 0.30
ACGTcount: A:0.26, C:0.22, G:0.19, T:0.33
Consensus pattern (43 bp):
AAACGCCGCAATAGTTGTTGATATTTAGCGGCGTTTTTCTCAC
Found at i:343015 original size:87 final size:87
Alignment explanation
Indices: 342796--343029 Score: 212
Period size: 87 Copynumber: 2.7 Consensus size: 87
342786 TATGTAATAA
** * * * *
342796 AAACGCCGCAATAAG-TGTTGATTTTTAGCGGCGTTTTTCTTACAAACGCCGCAAATAGATGTTG
1 AAACGCCGCAAT-AGTTGTTGAGATTTACCGACGTTTTTCATACAAACGCCGCAAATAGATATTG
**
342860 ATCTTTAGCGGCGTTTTTCCCAC
65 AAATTTAGCGGCGTTTTTCCCAC
* * * * * *
342883 AAACGCTGCAGTAGTTGTTTATATTTAGCGGCGTTTTT-ATCACAAACGCCGC-AATA-ATTATT
1 AAACGCCGCAATAGTTGTTGAGATTTACCGACGTTTTTCAT-ACAAACGCCGCAAATAGA-TATT
*
342945 GAAATTTAGCGGCGTTTTTTCCAC
64 GAAATTTAGCGGCGTTTTTCCCAC
*
342969 ACAA-GCCGCAATA-TGTGTTGAGATTTCCCGACGTTTTTTCATACAAACGCCGCTAAA-AGAT
1 A-AACGCCGCAATAGT-TGTTGAGATTTACCGACG-TTTTTCATACAAACGCCGC-AAATAGAT
343030 CGATACATAG
Statistics
Matches: 121, Mismatches: 16, Indels: 19
0.78 0.10 0.12
Matches are distributed among these distances:
85 2 0.02
86 52 0.43
87 60 0.50
88 4 0.03
89 3 0.02
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (87 bp):
AAACGCCGCAATAGTTGTTGAGATTTACCGACGTTTTTCATACAAACGCCGCAAATAGATATTGA
AATTTAGCGGCGTTTTTCCCAC
Found at i:343460 original size:23 final size:23
Alignment explanation
Indices: 343430--343484 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
343420 GCTGATATGT
*
343430 TGCT-TCTCTATG-TGCTGCTGC
1 TGCTCTCTCTATGTTGCCGCTGC
* *
343451 TGCCTCTCTCTGTGTTTCCGCTGC
1 TG-CTCTCTCTATGTTGCCGCTGC
343475 TGCTCTCTCT
1 TGCTCTCTCT
343485 GCTTCTCTTG
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
21 2 0.07
22 2 0.07
23 15 0.54
24 9 0.32
ACGTcount: A:0.02, C:0.35, G:0.20, T:0.44
Consensus pattern (23 bp):
TGCTCTCTCTATGTTGCCGCTGC
Found at i:343886 original size:42 final size:40
Alignment explanation
Indices: 343833--343929 Score: 113
Period size: 42 Copynumber: 2.4 Consensus size: 40
343823 GCGACGTTTA
* * *
343833 TATTAAAAACGCCGCAAAGGAACTACTCTATTACTGCGTT
1 TATTAAAAACGCCACAAAGGAACTACTATATTACGGCGTT
* * * *
343873 TTTTACGAAAACGCCACTAAGTAACTATTATATTACGGCGTT
1 TATTA--AAAACGCCACAAAGGAACTACTATATTACGGCGTT
343915 TATTAAAAACGCCAC
1 TATTAAAAACGCCAC
343930 CGAATAACAA
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
40 14 0.30
42 33 0.70
ACGTcount: A:0.36, C:0.22, G:0.13, T:0.29
Consensus pattern (40 bp):
TATTAAAAACGCCACAAAGGAACTACTATATTACGGCGTT
Found at i:347746 original size:20 final size:20
Alignment explanation
Indices: 347717--347754 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
347707 CCCCTTCAAA
*
347717 GGGGGAATCGGTTCCCTCAT
1 GGGGGAATCGATTCCCTCAT
*
347737 GGGGGGATCGATTCCCTC
1 GGGGGAATCGATTCCCTC
347755 TGCACCAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.26, G:0.37, T:0.24
Consensus pattern (20 bp):
GGGGGAATCGATTCCCTCAT
Found at i:351595 original size:22 final size:21
Alignment explanation
Indices: 351553--351592 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
351543 GAGTTTGTTT
*
351553 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTTAAAATA
351574 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
351593 ATAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.07, G:0.03, T:0.55
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAATA
Found at i:355014 original size:41 final size:41
Alignment explanation
Indices: 354949--355086 Score: 190
Period size: 41 Copynumber: 3.4 Consensus size: 41
354939 CGTTTATACA
* *
354949 AAAAAATGCCACTATTGATT-ACACTATTGTGGCGTTTGTT
1 AAAAAACGCCACTATTGATTAACACTATTGCGGCGTTTGTT
354989 AAAAAACGCCACTATTGATTAACACTATTGCGGCGTTTGTCT
1 AAAAAACGCCACTATTGATTAACACTATTGCGGCGTTTGT-T
* **
355031 -AAAAACGCCACTATTGATTATCACTATTGCGGCGTTTGAGG
1 AAAAAACGCCACTATTGATTAACACTATTGCGGCGTTTG-TT
*
355072 AATAAACGCCACTAT
1 AAAAAACGCCACTAT
355087 ATGTGTAATA
Statistics
Matches: 88, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
40 19 0.22
41 55 0.62
42 14 0.16
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Consensus pattern (41 bp):
AAAAAACGCCACTATTGATTAACACTATTGCGGCGTTTGTT
Found at i:355106 original size:83 final size:81
Alignment explanation
Indices: 354950--355109 Score: 207
Period size: 83 Copynumber: 2.0 Consensus size: 81
354940 GTTTATACAA
* * **
354950 AAAAATGCCACTATTGATTACACTATTGTGGCGTTTGTTAAAAAACGCCACTATTGATTAACACT
1 AAAAACGCCACTATTGATTACACTATTGCGGCGTTTGGGAAAAAACGCCACTATTGATTAACACT
*
355015 ATTGCGGCGTTTGTCT
66 ATTACGGCGTTTGTCT
*
355031 AAAAACGCCACTATTGATTATCACTATTGCGGCGTTTGAGGAATAAACGCCACTATATG-TGTAA
1 AAAAACGCCACTATTGATTA-CACTATTGCGGCGTTTG-GGAAAAAACGCCACTAT-TGAT-TAA
*
355095 TA-TATTACGGCGTTT
62 CACTATTACGGCGTTT
355110 TTGGTATAAA
Statistics
Matches: 68, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
81 19 0.28
82 16 0.24
83 27 0.40
84 6 0.09
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (81 bp):
AAAAACGCCACTATTGATTACACTATTGCGGCGTTTGGGAAAAAACGCCACTATTGATTAACACT
ATTACGGCGTTTGTCT
Found at i:355143 original size:42 final size:42
Alignment explanation
Indices: 355097--355225 Score: 147
Period size: 42 Copynumber: 3.1 Consensus size: 42
355087 ATGTGTAATA
355097 TATTACGGCGTTTTTGGTATAAACGCCGCTAATTTACCACTC
1 TATTACGGCGTTTTTGGTATAAACGCCGCTAATTTACCACTC
* * * * *
355139 TATTATGGCG-TTTTGCCTA-AATCGCCGCAAAATTTA-TACTC
1 TATTACGGCGTTTTTG-GTATAAACGCCGC-TAATTTACCACTC
* * *
355180 TATTGCGGCGTTTGTGGTATAAACGCCGCTAATTTACCACCC
1 TATTACGGCGTTTTTGGTATAAACGCCGCTAATTTACCACTC
355222 TATT
1 TATT
355226 GCTGCGTTAA
Statistics
Matches: 69, Mismatches: 13, Indels: 10
0.75 0.14 0.11
Matches are distributed among these distances:
41 33 0.48
42 36 0.52
ACGTcount: A:0.24, C:0.23, G:0.17, T:0.36
Consensus pattern (42 bp):
TATTACGGCGTTTTTGGTATAAACGCCGCTAATTTACCACTC
Found at i:355227 original size:42 final size:41
Alignment explanation
Indices: 355097--355225 Score: 145
Period size: 41 Copynumber: 3.1 Consensus size: 41
355087 ATGTGTAATA
355097 TATTACGGCGTTTTTGGTATAAACGCCGCTAATTTACCACTC
1 TATTACGGCG-TTTTGGTATAAACGCCGCTAATTTACCACTC
* * * * *
355139 TATTATGGCGTTTTGCCTA-AATCGCCGCAAAATTTA-TACTC
1 TATTACGGCGTTTTG-GTATAAACGCCGC-TAATTTACCACTC
* *
355180 TATTGCGGCGTTTGTGGTATAAACGCCGCTAATTTACCACCC
1 TATTACGGCGTTT-TGGTATAAACGCCGCTAATTTACCACTC
355222 TATT
1 TATT
355226 GCTGCGTTAA
Statistics
Matches: 70, Mismatches: 12, Indels: 10
0.76 0.13 0.11
Matches are distributed among these distances:
41 36 0.51
42 34 0.49
ACGTcount: A:0.24, C:0.23, G:0.17, T:0.36
Consensus pattern (41 bp):
TATTACGGCGTTTTGGTATAAACGCCGCTAATTTACCACTC
Found at i:356910 original size:16 final size:16
Alignment explanation
Indices: 356869--356930 Score: 54
Period size: 16 Copynumber: 3.9 Consensus size: 16
356859 AACTATACTC
**
356869 GAACTGAAATTAACCT
1 GAACTGAAAGCAACCT
*
356885 GAATCT-AAAGCAACTT
1 GAA-CTGAAAGCAACCT
* *
356901 GAACTGAAAGTAACCC
1 GAACTGAAAGCAACCT
*
356917 GAACCGAAAGCAAC
1 GAACTGAAAGCAAC
356931 TCAAACCGAA
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
15 2 0.06
16 32 0.89
17 2 0.06
ACGTcount: A:0.45, C:0.23, G:0.16, T:0.16
Consensus pattern (16 bp):
GAACTGAAAGCAACCT
Found at i:356915 original size:32 final size:32
Alignment explanation
Indices: 356869--356988 Score: 114
Period size: 32 Copynumber: 3.8 Consensus size: 32
356859 AACTATACTC
* * * *
356869 GAACTGAAATTAACCTGAATCTAAAGCAACTT
1 GAACTGAAAGTAACCCGAACCGAAAGCAACTT
*
356901 GAACTGAAAGTAACCCGAACCGAAAGCAACTC
1 GAACTGAAAGTAACCCGAACCGAAAGCAACTT
* * * * *
356933 AAACCGAAATTAATCCGAACCGAAAGCAACTC
1 GAACTGAAAGTAACCCGAACCGAAAGCAACTT
* * * *
356965 AAACCGAAATTAACCCGAATCGAA
1 GAACTGAAAGTAACCCGAACCGAA
356989 TTTTAACACG
Statistics
Matches: 77, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 77 1.00
ACGTcount: A:0.46, C:0.25, G:0.14, T:0.15
Consensus pattern (32 bp):
GAACTGAAAGTAACCCGAACCGAAAGCAACTT
Found at i:356937 original size:16 final size:16
Alignment explanation
Indices: 356918--356973 Score: 69
Period size: 16 Copynumber: 3.5 Consensus size: 16
356908 AAGTAACCCG
356918 AACCGAAAGCAACTCA
1 AACCGAAAGCAACTCA
** *
356934 AACCGAAATTAA-TCCG
1 AACCGAAAGCAACT-CA
356950 AACCGAAAGCAACTCA
1 AACCGAAAGCAACTCA
356966 AACCGAAA
1 AACCGAAA
356974 TTAACCCGAA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
15 1 0.03
16 30 0.94
17 1 0.03
ACGTcount: A:0.50, C:0.29, G:0.12, T:0.09
Consensus pattern (16 bp):
AACCGAAAGCAACTCA
Found at i:356944 original size:64 final size:64
Alignment explanation
Indices: 356865--356988 Score: 151
Period size: 64 Copynumber: 1.9 Consensus size: 64
356855 CTCAAACTAT
* * * * ** *
356865 ACTCGAACTGAAATTAA-CCTGAATCTAAAGCAACTTGAACTGAAAGTAACCCGAACCGAAAGCA
1 ACTCAAACCGAAATTAATCC-GAACCGAAAGCAACTCAAACCGAAAGTAACCCGAACCGAAAGCA
* *
356929 ACTCAAACCGAAATTAATCCGAACCGAAAGCAACTCAAACCGAAATTAACCCGAATCGAA
1 ACTCAAACCGAAATTAATCCGAACCGAAAGCAACTCAAACCGAAAGTAACCCGAACCGAA
356989 TTTTAACACG
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
64 48 0.96
65 2 0.04
ACGTcount: A:0.45, C:0.26, G:0.14, T:0.15
Consensus pattern (64 bp):
ACTCAAACCGAAATTAATCCGAACCGAAAGCAACTCAAACCGAAAGTAACCCGAACCGAAAGCA
Found at i:356988 original size:16 final size:16
Alignment explanation
Indices: 356901--356988 Score: 68
Period size: 16 Copynumber: 5.5 Consensus size: 16
356891 AAAGCAACTT
* *
356901 GAACTGAAAGTAACCC
1 GAACCGAAATTAACCC
** *
356917 GAACCGAAAGCAACTC
1 GAACCGAAATTAACCC
* *
356933 AAACCGAAATTAATCC
1 GAACCGAAATTAACCC
** *
356949 GAACCGAAAGCAACTC
1 GAACCGAAATTAACCC
*
356965 AAACCGAAATTAACCC
1 GAACCGAAATTAACCC
*
356981 GAATCGAA
1 GAACCGAA
356989 TTTTAACACG
Statistics
Matches: 53, Mismatches: 19, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
16 53 1.00
ACGTcount: A:0.47, C:0.27, G:0.15, T:0.11
Consensus pattern (16 bp):
GAACCGAAATTAACCC
Found at i:357934 original size:22 final size:22
Alignment explanation
Indices: 357908--357960 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
357898 ATAATCATCC
* *
357908 AACTCGATTTTTCGTACACCCG
1 AACTCGATTTATCGTACACCCA
357930 AACTCGATTTATCGTACACCCA
1 AACTCGATTTATCGTACACCCA
*
357952 AACTAGATT
1 AACTCGATT
357961 CGAACCAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.30, C:0.28, G:0.11, T:0.30
Consensus pattern (22 bp):
AACTCGATTTATCGTACACCCA
Found at i:358560 original size:22 final size:23
Alignment explanation
Indices: 358522--358564 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
358512 TTGATGGTGT
358522 TATTATTATTTAGCTTAATAAAA
1 TATTATTATTTAGCTTAATAAAA
358545 TATTA-TATTTTA-CTTAATAA
1 TATTATTA-TTTAGCTTAATAA
358565 CACAATCATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.42, C:0.05, G:0.02, T:0.51
Consensus pattern (23 bp):
TATTATTATTTAGCTTAATAAAA
Found at i:360621 original size:16 final size:19
Alignment explanation
Indices: 360589--360627 Score: 57
Period size: 16 Copynumber: 2.2 Consensus size: 19
360579 CACCCGTTCT
360589 AAAATAATTACATAAATA-
1 AAAATAATTACATAAATAG
360607 AAAATAA-TA-ATAAATAG
1 AAAATAATTACATAAATAG
360624 AAAA
1 AAAA
360628 AACCAAACAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 7 0.35
17 6 0.30
18 7 0.35
ACGTcount: A:0.72, C:0.03, G:0.03, T:0.23
Consensus pattern (19 bp):
AAAATAATTACATAAATAG
Found at i:360672 original size:33 final size:34
Alignment explanation
Indices: 360615--360734 Score: 113
Period size: 33 Copynumber: 3.5 Consensus size: 34
360605 TAAAAATAAT
* *
360615 AATAAATAG--AAAAAACCAAACATTCATT-AAA
1 AATAAATAGAAAAAAAATCAATCATTCATTAAAA
360646 AATAAATAGAAAAAAAATCAATCATTCATTAAAA
1 AATAAATAGAAAAAAAATCAATCATTCATTAAAA
*
360680 CTAATAAATAGAAAAAACCATCACACTCATTCATTCAAAA
1 --AATAAATAGAAAAAA-AATCA-A-TCATTCATT-AAAA
**
360720 TTTAAATA-AAAAAAA
1 AATAAATAGAAAAAAA
360735 TAAATTCAAA
Statistics
Matches: 74, Mismatches: 6, Indels: 13
0.80 0.06 0.14
Matches are distributed among these distances:
31 9 0.12
33 17 0.23
34 3 0.04
36 15 0.20
37 10 0.14
38 7 0.09
39 9 0.12
40 4 0.05
ACGTcount: A:0.62, C:0.13, G:0.03, T:0.23
Consensus pattern (34 bp):
AATAAATAGAAAAAAAATCAATCATTCATTAAAA
Found at i:365671 original size:2 final size:2
Alignment explanation
Indices: 365664--365700 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
365654 TTATTCTTGA
365664 AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
365701 GTCAATGTTG
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:365687 original size:17 final size:17
Alignment explanation
Indices: 365665--365698 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
365655 TATTCTTGAA
365665 TATATATATATATATAT
1 TATATATATATATATAT
365682 TATATATATATATATAT
1 TATATATATATATATAT
365699 ATGTCAATGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TATATATATATATATAT
Found at i:367539 original size:2 final size:2
Alignment explanation
Indices: 367530--367558 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
367520 TTTTTCAGAA
367530 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
367559 GAACTTATGA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:374913 original size:27 final size:27
Alignment explanation
Indices: 374883--374943 Score: 86
Period size: 27 Copynumber: 2.3 Consensus size: 27
374873 TTCATTGAAG
* *
374883 GATCTTGTGGAGTCGAGTTATTTTCTT
1 GATCTTGTGGAGTCAAGTTACTTTCTT
*
374910 GATCTTATGGAGTCAAGTTACTTTCTT
1 GATCTTGTGGAGTCAAGTTACTTTCTT
*
374937 GGTCTTG
1 GATCTTG
374944 AAGTTGAATA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.16, C:0.13, G:0.25, T:0.46
Consensus pattern (27 bp):
GATCTTGTGGAGTCAAGTTACTTTCTT
Found at i:379642 original size:12 final size:12
Alignment explanation
Indices: 379611--379715 Score: 77
Period size: 12 Copynumber: 8.8 Consensus size: 12
379601 TGAAAGCGAT
* *
379611 GAGGGAACCAGC
1 GAGGAAACCAAC
* *
379623 GAGCAAACCAAT
1 GAGGAAACCAAC
*
379635 GAGGAAACCGAC
1 GAGGAAACCAAC
*
379647 GAAGGAAA-CAAT
1 G-AGGAAACCAAC
**
379659 GAGGAAACTGAC
1 GAGGAAACCAAC
* *
379671 AAGGAAACCAAT
1 GAGGAAACCAAC
* *
379683 GCGGAAACCGAC
1 GAGGAAACCAAC
*
379695 AAGGAAACCAAC
1 GAGGAAACCAAC
379707 GAGGAAACC
1 GAGGAAACC
379716 GGTGAGAGAA
Statistics
Matches: 67, Mismatches: 24, Indels: 4
0.71 0.25 0.04
Matches are distributed among these distances:
11 6 0.09
12 55 0.82
13 6 0.09
ACGTcount: A:0.47, C:0.22, G:0.28, T:0.04
Consensus pattern (12 bp):
GAGGAAACCAAC
Found at i:379658 original size:24 final size:24
Alignment explanation
Indices: 379627--379716 Score: 137
Period size: 24 Copynumber: 3.8 Consensus size: 24
379617 ACCAGCGAGC
379627 AAACCAATGAGGAAACCGACGAAGG
1 AAACCAATGAGGAAACCGAC-AAGG
*
379652 AAA-CAATGAGGAAACTGACAAGG
1 AAACCAATGAGGAAACCGACAAGG
*
379675 AAACCAATGCGGAAACCGACAAGG
1 AAACCAATGAGGAAACCGACAAGG
*
379699 AAACCAACGAGGAAACCG
1 AAACCAATGAGGAAACCG
379717 GTGAGAGAAC
Statistics
Matches: 59, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
23 7 0.12
24 49 0.83
25 3 0.05
ACGTcount: A:0.49, C:0.21, G:0.26, T:0.04
Consensus pattern (24 bp):
AAACCAATGAGGAAACCGACAAGG
Found at i:379775 original size:12 final size:12
Alignment explanation
Indices: 379760--379822 Score: 58
Period size: 12 Copynumber: 5.2 Consensus size: 12
379750 CCGGAGAAGG
379760 AACCAGCGAGGA
1 AACCAGCGAGGA
*
379772 AACC-GACGAGGG
1 AACCAG-CGAGGA
*
379784 AACCAGCAAGGA
1 AACCAGCGAGGA
*
379796 AACC-GACGAGGG
1 AACCAG-CGAGGA
*
379808 AACCAGTGAGGA
1 AACCAGCGAGGA
379820 AAC
1 AAC
379823 TGACGAGGCA
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
11 2 0.05
12 36 0.90
13 2 0.05
ACGTcount: A:0.41, C:0.24, G:0.33, T:0.02
Consensus pattern (12 bp):
AACCAGCGAGGA
Found at i:379842 original size:24 final size:24
Alignment explanation
Indices: 379744--379830 Score: 122
Period size: 24 Copynumber: 3.6 Consensus size: 24
379734 GAGATCGACA
*
379744 AGGAAACCGGA-GAAGGAACCAGCG
1 AGGAAACC-GACGAGGGAACCAGCG
*
379768 AGGAAACCGACGAGGGAACCAGCA
1 AGGAAACCGACGAGGGAACCAGCG
*
379792 AGGAAACCGACGAGGGAACCAGTG
1 AGGAAACCGACGAGGGAACCAGCG
*
379816 AGGAAACTGACGAGG
1 AGGAAACCGACGAGG
379831 CAACTGGCGA
Statistics
Matches: 57, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
23 2 0.04
24 55 0.96
ACGTcount: A:0.40, C:0.21, G:0.37, T:0.02
Consensus pattern (24 bp):
AGGAAACCGACGAGGGAACCAGCG
Found at i:379984 original size:23 final size:24
Alignment explanation
Indices: 379939--380000 Score: 72
Period size: 23 Copynumber: 2.6 Consensus size: 24
379929 ACCGACGAGA
*
379939 GAACCAATGAGGAAACCGCTAAGG
1 GAACCAATGAGGAAAACGCTAAGG
* * *
379963 GAACCGATGA-GAAAACGGTAAGA
1 GAACCAATGAGGAAAACGCTAAGG
*
379986 AAACCAATGAGGAAA
1 GAACCAATGAGGAAA
380001 CCAACAAGGA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
23 18 0.58
24 13 0.42
ACGTcount: A:0.48, C:0.16, G:0.27, T:0.08
Consensus pattern (24 bp):
GAACCAATGAGGAAAACGCTAAGG
Found at i:381336 original size:31 final size:29
Alignment explanation
Indices: 381258--381360 Score: 106
Period size: 30 Copynumber: 3.6 Consensus size: 29
381248 AAAAAAAATG
* *
381258 AATACTTTCG-TACCTATTTTGACTAAAAA
1 AATACTTTAGATACTTATTTTGAC-AAAAA
*
381287 AATACTTTAGGTACTTATTTTGACAAAAA
1 AATACTTTAGATACTTATTTTGACAAAAA
* *
381316 AGATAAGTTTATATACTTA-TTTG--AAAAA
1 A-AT-ACTTTAGATACTTATTTTGACAAAAA
381344 AATACTTTAGATACTTA
1 AATACTTTAGATACTTA
381361 AATGAAAAAA
Statistics
Matches: 64, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
26 12 0.19
27 2 0.03
28 6 0.09
29 15 0.23
30 18 0.28
31 11 0.17
ACGTcount: A:0.42, C:0.11, G:0.09, T:0.39
Consensus pattern (29 bp):
AATACTTTAGATACTTATTTTGACAAAAA
Found at i:381352 original size:26 final size:26
Alignment explanation
Indices: 381282--381370 Score: 88
Period size: 26 Copynumber: 3.2 Consensus size: 26
381272 TATTTTGACT
*
381282 AAAAAAATACTTTAGGTACTTATTTTG
1 AAAAAAATACTTTAGATACTTA-TTTG
* *
381309 ACAAAAAAGATAAGTTTATATACTTATTTG
1 --AAAAAA-AT-ACTTTAGATACTTATTTG
**
381339 AAAAAAATACTTTAGATACTTAAATG
1 AAAAAAATACTTTAGATACTTATTTG
381365 AAAAAA
1 AAAAAA
381371 GATGATATAT
Statistics
Matches: 51, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
26 20 0.39
27 2 0.04
28 6 0.12
29 6 0.12
30 6 0.12
31 11 0.22
ACGTcount: A:0.51, C:0.07, G:0.09, T:0.34
Consensus pattern (26 bp):
AAAAAAATACTTTAGATACTTATTTG
Found at i:385159 original size:43 final size:43
Alignment explanation
Indices: 385103--385394 Score: 389
Period size: 43 Copynumber: 6.8 Consensus size: 43
385093 AGGTCTTATA
*
385103 CTTGCACATAGCAAA-AGAGCCTGGGGAAACTGTAAGGCTTACC
1 CTTGCACACAGCAAAGAGA-CCTGGGGAAACTGTAAGGCTTACC
385146 CTTGCACACAGCAAAG-GAACCT-GGGAAACTGTAAGGCTTACC
1 CTTGCACACAGCAAAGAG-ACCTGGGGAAACTGTAAGGCTTACC
* *
385188 TTTGCACACAGCAAAG-GAACCTGGGGGAACTGTAAGGCTTACC
1 CTTGCACACAGCAAAGAG-ACCTGGGGAAACTGTAAGGCTTACC
* *
385231 CTTGCACACAGCAAAGGGACCTGGGGGAACTGTAAGGCTTACC
1 CTTGCACACAGCAAAGAGACCTGGGGAAACTGTAAGGCTTACC
* * *
385274 CTTGCACACAACAAAGGGACCTGGGGGAACTGTAAGGCTTACC
1 CTTGCACACAGCAAAGAGACCTGGGGAAACTGTAAGGCTTACC
* *
385317 CTTGCACACAGCAAAGGGACCT-GAGAGAACTGTAAGGCTTACC
1 CTTGCACACAGCAAAGAGACCTGGGGA-AACTGTAAGGCTTACC
* *
385360 CTTGCACATAACAAAGAGACCTGAGGG-AACTGTAA
1 CTTGCACACAGCAAAGAGACCTG-GGGAAACTGTAA
385395 CGGTAATTAA
Statistics
Matches: 230, Mismatches: 12, Indels: 14
0.90 0.05 0.05
Matches are distributed among these distances:
42 43 0.19
43 183 0.80
44 2 0.01
45 2 0.01
ACGTcount: A:0.32, C:0.24, G:0.26, T:0.17
Consensus pattern (43 bp):
CTTGCACACAGCAAAGAGACCTGGGGAAACTGTAAGGCTTACC
Found at i:385289 original size:86 final size:86
Alignment explanation
Indices: 385103--385394 Score: 435
Period size: 86 Copynumber: 3.4 Consensus size: 86
385093 AGGTCTTATA
* * * * * *
385103 CTTGCACATAGCAAAAGAGCCTGGGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAGGAACCT
1 CTTGCACACAACAAAGGAACCTGGGGGAACTGTAAGGCTTACCCTTGCACACAGCAAAGGGACCT
*
385168 -GGGAAACTGTAAGGCTTACC
66 GGGGGAACTGTAAGGCTTACC
* *
385188 TTTGCACACAGCAAAGGAACCTGGGGGAACTGTAAGGCTTACCCTTGCACACAGCAAAGGGACCT
1 CTTGCACACAACAAAGGAACCTGGGGGAACTGTAAGGCTTACCCTTGCACACAGCAAAGGGACCT
385253 GGGGGAACTGTAAGGCTTACC
66 GGGGGAACTGTAAGGCTTACC
*
385274 CTTGCACACAACAAAGGGACCTGGGGGAACTGTAAGGCTTACCCTTGCACACAGCAAAGGGACCT
1 CTTGCACACAACAAAGGAACCTGGGGGAACTGTAAGGCTTACCCTTGCACACAGCAAAGGGACCT
* *
385339 GAGAGAACTGTAAGGCTTACC
66 GGGGGAACTGTAAGGCTTACC
* *
385360 CTTGCACATAACAAA-GAGACCTGAGGGAACTGTAA
1 CTTGCACACAACAAAGGA-ACCTGGGGGAACTGTAA
385395 CGGTAATTAA
Statistics
Matches: 190, Mismatches: 15, Indels: 3
0.91 0.07 0.01
Matches are distributed among these distances:
85 60 0.32
86 130 0.68
ACGTcount: A:0.32, C:0.24, G:0.26, T:0.17
Consensus pattern (86 bp):
CTTGCACACAACAAAGGAACCTGGGGGAACTGTAAGGCTTACCCTTGCACACAGCAAAGGGACCT
GGGGGAACTGTAAGGCTTACC
Found at i:385347 original size:129 final size:128
Alignment explanation
Indices: 385103--385394 Score: 451
Period size: 129 Copynumber: 2.3 Consensus size: 128
385093 AGGTCTTATA
* *
385103 CTTGCACATAGCAAA-AGAGCCTGGGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAGGAACC
1 CTTGCACATAGCAAAGAGA-CCTGGGGGAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACC
* * *
385167 TGGGAAACTGTAAGGCTTACCTTTGCACACAGCAAAGGAACCTGGGGGAACTGTAAGGCTTACC
65 TGGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAGGAACCTGAGAGAACTGTAAGGCTTACC
* * *
385231 CTTGCACACAGCAAAGGGACCTGGGGGAACTGTAAGGCTTACCCTTGCACACAACAAAGGGACCT
1 CTTGCACATAGCAAAGAGACCTGGGGGAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACCT
* *
385296 GGGGGAACTGTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGAGAGAACTGTAAGGCTTACC
66 -GGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAGGAACCTGAGAGAACTGTAAGGCTTACC
* *
385360 CTTGCACATAACAAAGAGACCTGAGGGAACTGTAA
1 CTTGCACATAGCAAAGAGACCTGGGGGAACTGTAA
385395 CGGTAATTAA
Statistics
Matches: 148, Mismatches: 14, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
128 57 0.39
129 91 0.61
ACGTcount: A:0.32, C:0.24, G:0.26, T:0.17
Consensus pattern (128 bp):
CTTGCACATAGCAAAGAGACCTGGGGGAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACCT
GGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAGGAACCTGAGAGAACTGTAAGGCTTACC
Found at i:397047 original size:21 final size:21
Alignment explanation
Indices: 397021--397091 Score: 76
Period size: 21 Copynumber: 3.4 Consensus size: 21
397011 AATACCCCTG
*
397021 GTATCGATACTCATATGAGGA
1 GTATCGATACTCATATGAGAA
*
397042 GTATCGATACTC-TAT-AAACA
1 GTATCGATACTCATATGAGA-A
*
397062 GTATTGATACTCA-ATGAAGAA
1 GTATCGATACTCATATG-AGAA
397083 GTATCGATA
1 GTATCGATA
397092 ATTCCACACT
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
19 1 0.02
20 17 0.41
21 21 0.51
22 2 0.05
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.30
Consensus pattern (21 bp):
GTATCGATACTCATATGAGAA
Found at i:400476 original size:21 final size:21
Alignment explanation
Indices: 400450--400495 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
400440 TCAACTTTAT
400450 CTTAGAGAACACACACATTCC
1 CTTAGAGAACACACACATTCC
400471 CTTAGAGAACACACACATTCC
1 CTTAGAGAACACACACATTCC
400492 CTTA
1 CTTA
400496 AGTTAGTCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.37, C:0.33, G:0.09, T:0.22
Consensus pattern (21 bp):
CTTAGAGAACACACACATTCC
Found at i:405280 original size:6 final size:6
Alignment explanation
Indices: 405269--405297 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
405259 AATCTATAAG
405269 AAAATA AAAATA AAAATA AAAATA AAAAT
1 AAAATA AAAATA AAAATA AAAATA AAAAT
405298 CAATGAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
AAAATA
Found at i:413694 original size:36 final size:36
Alignment explanation
Indices: 413647--413734 Score: 122
Period size: 36 Copynumber: 2.4 Consensus size: 36
413637 TCGCACTAAT
* * *
413647 CTTTGGACTAAGTTCCACTTAATTTCTTTCTGTAAC
1 CTTTGCACTAAGTTACACTTAATTTCTTTCAGTAAC
*
413683 CTTTGCACTAAGTTACACTTAATTTCTTTCAGTAAT
1 CTTTGCACTAAGTTACACTTAATTTCTTTCAGTAAC
* *
413719 CTTTACACTAAATTAC
1 CTTTGCACTAAGTTAC
413735 TATTTTCTTC
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 46 1.00
ACGTcount: A:0.27, C:0.22, G:0.08, T:0.43
Consensus pattern (36 bp):
CTTTGCACTAAGTTACACTTAATTTCTTTCAGTAAC
Found at i:415710 original size:13 final size:13
Alignment explanation
Indices: 415689--415753 Score: 85
Period size: 13 Copynumber: 5.0 Consensus size: 13
415679 AATGATGCGC
* *
415689 AATGAGCGTCCTA
1 AATGCGCGTCATA
415702 AATGCGCGTCATA
1 AATGCGCGTCATA
*
415715 AATGAGCGTCATA
1 AATGCGCGTCATA
*
415728 AATGCGTGTCATA
1 AATGCGCGTCATA
*
415741 AATACGCGTCATA
1 AATGCGCGTCATA
415754 GATTTATGAC
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 45 1.00
ACGTcount: A:0.34, C:0.20, G:0.22, T:0.25
Consensus pattern (13 bp):
AATGCGCGTCATA
Found at i:415718 original size:26 final size:26
Alignment explanation
Indices: 415689--415753 Score: 96
Period size: 26 Copynumber: 2.5 Consensus size: 26
415679 AATGATGCGC
*
415689 AATGAGCGTCCTAAATGCGCGTCATA
1 AATGAGCGTCATAAATGCGCGTCATA
*
415715 AATGAGCGTCATAAATGCGTGTCATA
1 AATGAGCGTCATAAATGCGCGTCATA
415741 AAT-ACGCGTCATA
1 AATGA-GCGTCATA
415754 GATTTATGAC
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
25 1 0.03
26 35 0.97
ACGTcount: A:0.34, C:0.20, G:0.22, T:0.25
Consensus pattern (26 bp):
AATGAGCGTCATAAATGCGCGTCATA
Found at i:416014 original size:10 final size:10
Alignment explanation
Indices: 415991--416020 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
415981 AAACAAAACA
415991 AAATAAAATC
1 AAATAAAATC
*
416001 AAATCAAATC
1 AAATAAAATC
416011 AAATAAAATC
1 AAATAAAATC
416021 CAATCCAAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.67, C:0.13, G:0.00, T:0.20
Consensus pattern (10 bp):
AAATAAAATC
Found at i:424914 original size:12 final size:12
Alignment explanation
Indices: 424897--424922 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
424887 TTATTCATAA
424897 TTGTGACGATAT
1 TTGTGACGATAT
424909 TTGTGACGATAT
1 TTGTGACGATAT
424921 TT
1 TT
424923 TTTTGTCACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.08, G:0.23, T:0.46
Consensus pattern (12 bp):
TTGTGACGATAT
Found at i:425289 original size:21 final size:21
Alignment explanation
Indices: 425248--425290 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
425238 TGATATTGAC
*
425248 TATTAATAATTTTGTCGCAAA
1 TATTAATAATTTTGGCGCAAA
*
425269 TATTAA-ACTTTTGGCGTCAAA
1 TATTAATAATTTTGGCG-CAAA
425290 T
1 T
425291 TTTTTTACGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.42
Consensus pattern (21 bp):
TATTAATAATTTTGGCGCAAA
Found at i:434749 original size:20 final size:20
Alignment explanation
Indices: 434723--434775 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
434713 TTTGTGTTAT
434723 CGGTATCGATACTACCCCATG
1 CGGTATCGATACTACCCC-TG
* *
434744 -GGTATCGAGACTAGCCCTG
1 CGGTATCGATACTACCCCTG
*
434763 CAGTATCGATACT
1 CGGTATCGATACT
434776 TCTTGAATGG
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 2 0.07
20 25 0.93
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (20 bp):
CGGTATCGATACTACCCCTG
Found at i:437069 original size:2 final size:2
Alignment explanation
Indices: 437062--437089 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
437052 AGTGTATCAA
437062 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
437090 ATATATATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:437094 original size:2 final size:2
Alignment explanation
Indices: 437089--437124 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
437079 TCTCTCTCTC
437089 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
437125 CACACACACA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:438690 original size:23 final size:23
Alignment explanation
Indices: 438664--438751 Score: 97
Period size: 23 Copynumber: 3.8 Consensus size: 23
438654 AGAGCTTTGT
* * *
438664 AGAGAGCTTTACTATGAGATTGG
1 AGAGAGTTTTACTGTGAGACTGG
* * *
438687 AGAGAGTTTTGCCGTGAGGCTGG
1 AGAGAGTTTTACTGTGAGACTGG
438710 AGAGAGTTTTGA-TGTGAGACTGG
1 AGAGAGTTTT-ACTGTGAGACTGG
*
438733 AGAGAGTTTTGCTGTGAGA
1 AGAGAGTTTTACTGTGAGA
438752 TTGAAGTTGC
Statistics
Matches: 53, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
23 53 1.00
ACGTcount: A:0.25, C:0.08, G:0.38, T:0.30
Consensus pattern (23 bp):
AGAGAGTTTTACTGTGAGACTGG
Found at i:450259 original size:13 final size:13
Alignment explanation
Indices: 450205--450253 Score: 62
Period size: 13 Copynumber: 3.8 Consensus size: 13
450195 TGCGTCATAA
*
450205 ATTTATGACGTGC
1 ATTTATGACGCGC
* *
450218 ATTTATGACACAC
1 ATTTATGACGCGC
*
450231 ATTTATGATGCGC
1 ATTTATGACGCGC
450244 ATTTATGACG
1 ATTTATGACG
450254 TTCATTGAGC
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.37
Consensus pattern (13 bp):
ATTTATGACGCGC
Found at i:455975 original size:46 final size:46
Alignment explanation
Indices: 455881--456047 Score: 201
Period size: 46 Copynumber: 3.6 Consensus size: 46
455871 TATGTTTTTT
* * *
455881 TAACCCTAAATCTAATTGAGACTTTTCTTATTCTTCTA-TTCATATTCTC
1 TAACCCTAAATCTAACTGAGA---TTCTTATTCTTC-AGTTTATCTTCTC
* *
455930 TAACCCTAAATCTAATTGAGATTCTTCTTCTTCAGTTTATCTTCTC
1 TAACCCTAAATCTAACTGAGATTCTTATTCTTCAGTTTATCTTCTC
* * *
455976 TAACCTTAAATCTAACTAAGATTCTTATTCTTCGGTTTATCTTCTC
1 TAACCCTAAATCTAACTGAGATTCTTATTCTTCAGTTTATCTTCTC
* *
456022 TAACCTTAAATCTAACTGAGACTCTT
1 TAACCCTAAATCTAACTGAGATTCTT
456048 CATCTACATT
Statistics
Matches: 107, Mismatches: 10, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
45 1 0.01
46 85 0.79
49 21 0.20
ACGTcount: A:0.27, C:0.23, G:0.06, T:0.44
Consensus pattern (46 bp):
TAACCCTAAATCTAACTGAGATTCTTATTCTTCAGTTTATCTTCTC
Found at i:459646 original size:21 final size:21
Alignment explanation
Indices: 459622--459678 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
459612 TCTGAAATGT
* *
459622 TGCTTTTCTCGCTTCTCTCTC
1 TGCTTCTCTCGCTTCTCTATC
*
459643 TGCTTCTCTCGCTGCTCTATC
1 TGCTTCTCTCGCTTCTCTATC
* *
459664 TACTTCTCTTGCTTC
1 TGCTTCTCTCGCTTC
459679 AGCTCCAGCT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.04, C:0.37, G:0.11, T:0.49
Consensus pattern (21 bp):
TGCTTCTCTCGCTTCTCTATC
Found at i:462415 original size:41 final size:41
Alignment explanation
Indices: 462342--462491 Score: 167
Period size: 41 Copynumber: 3.6 Consensus size: 41
462332 GTCTTGAGTA
* *
462342 GTGTTTGTATATATAAATACCA-TGAAAATATAAATGTATAATG
1 GTGTTTGTATA-A-AAATATCACT-AAAATATAAATGTATAACG
* * *
462385 GTGTTTGTATAAAAATATCACTAAATTATAAATTTATAGCG
1 GTGTTTGTATAAAAATATCACTAAAATATAAATGTATAACG
* * ** *
462426 GTGTTTGTATAAAAATATCATTAAAGTACGAGTGTATAACG
1 GTGTTTGTATAAAAATATCACTAAAATATAAATGTATAACG
*
462467 GTATTTGTATAAAAATATCACTAAA
1 GTGTTTGTATAAAAATATCACTAAA
462492 GTACTATTCT
Statistics
Matches: 92, Mismatches: 14, Indels: 4
0.84 0.13 0.04
Matches are distributed among these distances:
41 79 0.86
42 2 0.02
43 11 0.12
ACGTcount: A:0.43, C:0.07, G:0.14, T:0.37
Consensus pattern (41 bp):
GTGTTTGTATAAAAATATCACTAAAATATAAATGTATAACG
Found at i:462522 original size:41 final size:40
Alignment explanation
Indices: 462384--462515 Score: 158
Period size: 41 Copynumber: 3.2 Consensus size: 40
462374 AATGTATAAT
*
462384 GGTGTTTGTATAAAAATATCACTAAATTA-TAAATTTATAGC
1 GGTGTTTGTATAAAAATATCACTAAAGTACT--ATTTATAGC
* * * *
462425 GGTGTTTGTATAAAAATATCATTAAAGTACGAGTGTATAAC
1 GGTGTTTGTATAAAAATATCACTAAAGTACTA-TTTATAGC
* *
462466 GGTATTTGTATAAAAATATCACTAAAGTACTATTCTATTGC
1 GGTGTTTGTATAAAAATATCACTAAAGTACTATT-TATAGC
462507 GGTGTTTGT
1 GGTGTTTGT
462516 TGAAAAAATA
Statistics
Matches: 76, Mismatches: 12, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
40 2 0.03
41 74 0.97
ACGTcount: A:0.36, C:0.08, G:0.17, T:0.39
Consensus pattern (40 bp):
GGTGTTTGTATAAAAATATCACTAAAGTACTATTTATAGC
Found at i:463080 original size:2 final size:2
Alignment explanation
Indices: 463070--463129 Score: 92
Period size: 2 Copynumber: 32.0 Consensus size: 2
463060 ATTCATTTTT
463070 TA TA T- TA TA TA T- TA TA TA T- TA TA T- TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
463108 TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA
463130 AAATTTTAAG
Statistics
Matches: 54, Mismatches: 0, Indels: 8
0.87 0.00 0.13
Matches are distributed among these distances:
1 4 0.07
2 50 0.93
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:463630 original size:16 final size:16
Alignment explanation
Indices: 463611--463644 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
463601 TCAATTACAA
*
463611 GTTAGGTTCATAACAG
1 GTTAGGTTCAAAACAG
*
463627 GTTAGGTTGAAAACAG
1 GTTAGGTTCAAAACAG
463643 GT
1 GT
463645 CGTGTAATAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.32, C:0.09, G:0.29, T:0.29
Consensus pattern (16 bp):
GTTAGGTTCAAAACAG
Found at i:465312 original size:2 final size:2
Alignment explanation
Indices: 465305--465335 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
465295 ATTAATCGAT
465305 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
465336 CATAGTCACG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:465324 original size:109 final size:109
Alignment explanation
Indices: 465109--465311 Score: 388
Period size: 109 Copynumber: 1.9 Consensus size: 109
465099 ATAATTCGAC
465109 ATTTGATACTCATAATCGTATTAAAATTCTTGGATTAGGATTGAATTGAAGCTAACTAAGAAATT
1 ATTTGATACTCATAATCGTATTAAAATTCTTGGATTAGGATTGAATTGAAGCTAACTAAGAAATT
*
465174 AAAGCCAAATTTATTAATCGATTTTATATTAAGAAATATATAAA
66 AAAGCCAAATTTATTAATCGATTATATATTAAGAAATATATAAA
*
465218 ATTTGATACTCATAATCGTATTAAAATTCTTGGATTAGGATTGAATTGAAGCTAATTAAGAAATT
1 ATTTGATACTCATAATCGTATTAAAATTCTTGGATTAGGATTGAATTGAAGCTAACTAAGAAATT
465283 AAAGCCAAATTTATTAATCGATTATATAT
66 AAAGCCAAATTTATTAATCGATTATATAT
465312 ATATATATAT
Statistics
Matches: 92, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
109 92 1.00
ACGTcount: A:0.42, C:0.08, G:0.12, T:0.37
Consensus pattern (109 bp):
ATTTGATACTCATAATCGTATTAAAATTCTTGGATTAGGATTGAATTGAAGCTAACTAAGAAATT
AAAGCCAAATTTATTAATCGATTATATATTAAGAAATATATAAA
Done.