Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007883.1 Hibiscus syriacus cultivar Beakdansim tig00110263_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: 1590433
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 9
Found at i:942695 original size:3 final size:3
Alignment explanation
Indices: 942689--942766 Score: 74
Period size: 3 Copynumber: 27.0 Consensus size: 3
942679 CATTTTGTTT
** * *
942689 TTA TTA TTA TTA TTA AAA TTA TTA TTA TTA TTA ATA TT- GTA TATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
*
942734 TTA TTA -TA TTA -TA TTA TTA TTA -AA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
942767 CAAACAGGCC
Statistics
Matches: 60, Mismatches: 10, Indels: 10
0.75 0.12 0.12
Matches are distributed among these distances:
2 6 0.10
3 51 0.85
4 3 0.05
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:942721 original size:24 final size:25
Alignment explanation
Indices: 942689--942766 Score: 90
Period size: 24 Copynumber: 3.1 Consensus size: 25
942679 CATTTTGTTT
942689 TTATTATTATTATTA-AAATTATTA
1 TTATTATTATTATTATAAATTATTA
* *
942713 TTATTATTAATATTGTATATATTATTA
1 TTATTATTATTA-T-TATAAATTATTA
942740 -TATTA-TATTATTATTAAATTATTA
1 TTATTATTATTATTA-TAAATTATTA
942764 TTA
1 TTA
942767 CAAACAGGCC
Statistics
Matches: 45, Mismatches: 4, Indels: 9
0.78 0.07 0.16
Matches are distributed among these distances:
23 2 0.04
24 21 0.47
25 7 0.16
26 7 0.16
27 8 0.18
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (25 bp):
TTATTATTATTATTATAAATTATTA
Found at i:943897 original size:16 final size:16
Alignment explanation
Indices: 943878--943933 Score: 51
Period size: 20 Copynumber: 3.2 Consensus size: 16
943868 TTACTTTTTA
943878 TATTTAATTTTAATTT
1 TATTTAATTTTAATTT
943894 TATTT-ATTTTACTCATTGTT
1 TATTTAATTTTA---A-T-TT
943914 TATTTATATTTTAATTT
1 TATTTA-ATTTTAATTT
943931 TAT
1 TAT
943934 ATGTTTAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 13
0.72 0.00 0.28
Matches are distributed among these distances:
15 6 0.18
16 5 0.15
17 5 0.15
18 2 0.06
19 2 0.06
20 7 0.21
22 6 0.18
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.68
Consensus pattern (16 bp):
TATTTAATTTTAATTT
Found at i:943973 original size:11 final size:11
Alignment explanation
Indices: 943942--943978 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
943932 ATATGTTTAA
943942 ATTATTATTTT
1 ATTATTATTTT
*
943953 CATAATTATTTT
1 -ATTATTATTTT
943965 ATTATTATTTT
1 ATTATTATTTT
943976 ATT
1 ATT
943979 CATATAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 13 0.57
12 10 0.43
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (11 bp):
ATTATTATTTT
Found at i:944241 original size:14 final size:14
Alignment explanation
Indices: 944222--944256 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
944212 AAATAAATAA
*
944222 ATATTTTTATTAAT
1 ATATTTTAATTAAT
*
944236 ATATTTAAATTAAT
1 ATATTTTAATTAAT
944250 ATATTTT
1 ATATTTT
944257 CTTAAAAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
ATATTTTAATTAAT
Found at i:952892 original size:3 final size:3
Alignment explanation
Indices: 952884--952927 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
952874 CTAGATCATG
952884 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
952928 GTCAAGAATA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:954452 original size:74 final size:74
Alignment explanation
Indices: 954330--954470 Score: 246
Period size: 74 Copynumber: 1.9 Consensus size: 74
954320 TTTTCCAGGA
* * *
954330 AAACTTGTTTTAACCCAGACTCCAATTTAATCTACTATAAAATGGGTTTATAAACTTTTTATAGA
1 AAACTTGTTTTAACCCAAACTCCAATTTAATCTACTATAAAATGGGTTTAAAAACTTTTTACAGA
954395 AGTAGGGGG
66 AGTAGGGGG
*
954404 AAACTTGTTTTAACCCAAACTCCAATTTAATCTACTATAAAATTGGTTTAAAAACTTTTTACAGA
1 AAACTTGTTTTAACCCAAACTCCAATTTAATCTACTATAAAATGGGTTTAAAAACTTTTTACAGA
954469 AG
66 AG
954471 CAGGTTGTCA
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
74 63 1.00
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (74 bp):
AAACTTGTTTTAACCCAAACTCCAATTTAATCTACTATAAAATGGGTTTAAAAACTTTTTACAGA
AGTAGGGGG
Found at i:961310 original size:21 final size:22
Alignment explanation
Indices: 961284--961328 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
961274 CTATATAGAT
*
961284 ACGATAAAATTT-AGGGTGGGC
1 ACGATAAAATTTCAGGGTGAGC
*
961305 ACGATAAATTTTCAGGGTGAGC
1 ACGATAAAATTTCAGGGTGAGC
961327 AC
1 AC
961329 ACGCATATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.33, C:0.13, G:0.29, T:0.24
Consensus pattern (22 bp):
ACGATAAAATTTCAGGGTGAGC
Found at i:968262 original size:13 final size:15
Alignment explanation
Indices: 968244--968275 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
968234 AAATACTTCG
968244 AATAATGAT-TGA-T
1 AATAATGATATGATT
968257 AATAATGATATGATT
1 AATAATGATATGATT
968272 AATA
1 AATA
968276 GCCCAAAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 9 0.53
14 3 0.18
15 5 0.29
ACGTcount: A:0.50, C:0.00, G:0.12, T:0.38
Consensus pattern (15 bp):
AATAATGATATGATT
Found at i:968384 original size:23 final size:23
Alignment explanation
Indices: 968356--968443 Score: 94
Period size: 23 Copynumber: 3.9 Consensus size: 23
968346 TTGGGACAAA
968356 TATGTGGTACTTCGGTGCAAACC
1 TATGTGGTACTTCGGTGCAAACC
* *
968379 TATGTGGCACTTTGGTGCAAACC
1 TATGTGGTACTTCGGTGCAAACC
* *
968402 TATGTGGT-CCTCTGG-G-ACAA-T
1 TATGTGGTACTTC-GGTGCA-AACC
968423 TATGTGGTACTTCGGTGCAAA
1 TATGTGGTACTTCGGTGCAAA
968444 TTACGAGATG
Statistics
Matches: 53, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
21 11 0.21
22 11 0.21
23 31 0.58
ACGTcount: A:0.22, C:0.19, G:0.27, T:0.32
Consensus pattern (23 bp):
TATGTGGTACTTCGGTGCAAACC
Found at i:970314 original size:58 final size:58
Alignment explanation
Indices: 970244--970360 Score: 234
Period size: 58 Copynumber: 2.0 Consensus size: 58
970234 ATTTACCTCA
970244 TATTAAATAGAGACGATACTCGATCTTTAGTAAGAAAAATTTCTAAGCAAAATCATGT
1 TATTAAATAGAGACGATACTCGATCTTTAGTAAGAAAAATTTCTAAGCAAAATCATGT
970302 TATTAAATAGAGACGATACTCGATCTTTAGTAAGAAAAATTTCTAAGCAAAATCATGT
1 TATTAAATAGAGACGATACTCGATCTTTAGTAAGAAAAATTTCTAAGCAAAATCATGT
970360 T
1 T
970361 GATAATGTGT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 59 1.00
ACGTcount: A:0.43, C:0.12, G:0.14, T:0.32
Consensus pattern (58 bp):
TATTAAATAGAGACGATACTCGATCTTTAGTAAGAAAAATTTCTAAGCAAAATCATGT
Found at i:972261 original size:45 final size:45
Alignment explanation
Indices: 972197--972284 Score: 158
Period size: 45 Copynumber: 2.0 Consensus size: 45
972187 TCCTCCAATT
*
972197 AAATGATAACACGTGACACGACACATGGTACTAGAGATATATGTC
1 AAATGATAACACGTGACACGACACATGATACTAGAGATATATGTC
*
972242 AAATGATGACACGTGACACGACACATGATACTAGAGATATATG
1 AAATGATAACACGTGACACGACACATGATACTAGAGATATATG
972285 ACATCCTTCG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.41, C:0.17, G:0.20, T:0.22
Consensus pattern (45 bp):
AAATGATAACACGTGACACGACACATGATACTAGAGATATATGTC
Found at i:980259 original size:17 final size:17
Alignment explanation
Indices: 980234--980267 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
980224 TACTGCTTCC
980234 TTCGAACTGCTTGGATG
1 TTCGAACTGCTTGGATG
*
980251 TTCGGACTGCTTGGATG
1 TTCGAACTGCTTGGATG
980268 AATGAAACAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.15, C:0.18, G:0.32, T:0.35
Consensus pattern (17 bp):
TTCGAACTGCTTGGATG
Found at i:984449 original size:14 final size:14
Alignment explanation
Indices: 984430--984471 Score: 84
Period size: 14 Copynumber: 3.0 Consensus size: 14
984420 AAATATGGAA
984430 AGTGGCATCATATC
1 AGTGGCATCATATC
984444 AGTGGCATCATATC
1 AGTGGCATCATATC
984458 AGTGGCATCATATC
1 AGTGGCATCATATC
984472 GAAGGATGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (14 bp):
AGTGGCATCATATC
Found at i:984804 original size:31 final size:31
Alignment explanation
Indices: 984760--984818 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
984750 TTTTTAATAG
984760 TTTGACAAATTTAATGATCATATTGTAAAAA
1 TTTGACAAATTTAATGATCATATTGTAAAAA
*
984791 TTTGA-AAATTTTAATGATCATTTTGTAA
1 TTTGACAAA-TTTAATGATCATATTGTAA
984819 CTCTTGAAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 3 0.12
31 23 0.88
ACGTcount: A:0.41, C:0.05, G:0.10, T:0.44
Consensus pattern (31 bp):
TTTGACAAATTTAATGATCATATTGTAAAAA
Found at i:986554 original size:25 final size:25
Alignment explanation
Indices: 986526--986573 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
986516 TTTCAAGCTA
*
986526 AAAATATAATATCAAGTTCAGATCT
1 AAAATATAATATCAAATTCAGATCT
*
986551 AAAATATGATATCAAATTCAGAT
1 AAAATATAATATCAAATTCAGAT
986574 AATTAGATCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.50, C:0.10, G:0.08, T:0.31
Consensus pattern (25 bp):
AAAATATAATATCAAATTCAGATCT
Found at i:990136 original size:2 final size:2
Alignment explanation
Indices: 990060--990122 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
990050 ACATGAAAGC
990060 TA TA TA 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 TA TA TA
990102 TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
990123 CAATCTAGAT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:994628 original size:29 final size:29
Alignment explanation
Indices: 994554--994637 Score: 114
Period size: 29 Copynumber: 2.9 Consensus size: 29
994544 CCCCGTCGTT
* * **
994554 GGTCGCCAGGGCATCCATGAGAGCTAGGA
1 GGTCGCCAGGGCATCCGTGCGAGCTACAA
*
994583 GGTCACCAGGGCATCCGTGCGAGCTACAA
1 GGTCGCCAGGGCATCCGTGCGAGCTACAA
*
994612 GGTCGCCAGGGCATCCGAGCGAGCTA
1 GGTCGCCAGGGCATCCGTGCGAGCTA
994638 TGCATGAGCC
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 48 1.00
ACGTcount: A:0.23, C:0.29, G:0.36, T:0.13
Consensus pattern (29 bp):
GGTCGCCAGGGCATCCGTGCGAGCTACAA
Found at i:995155 original size:21 final size:21
Alignment explanation
Indices: 995126--995169 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
995116 AATTTAGTTA
*
995126 ATTAGTTTGTTAGTATAAATT
1 ATTAATTTGTTAGTATAAATT
* *
995147 ATTAATTTGTTAGTTTAAGTT
1 ATTAATTTGTTAGTATAAATT
995168 AT
1 AT
995170 ATTATATTAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.32, C:0.00, G:0.14, T:0.55
Consensus pattern (21 bp):
ATTAATTTGTTAGTATAAATT
Found at i:995170 original size:28 final size:28
Alignment explanation
Indices: 995139--995204 Score: 89
Period size: 28 Copynumber: 2.4 Consensus size: 28
995129 AGTTTGTTAG
995139 TATAAATTATTAATTTGTTAGTTTAAGT
1 TATAAATTATTAATTTGTTAGTTTAAGT
* *
995167 TAT-ATTATATTAGTTTGTTAGTTTAAGT
1 TATAAAT-TATTAATTTGTTAGTTTAAGT
*
995195 TATAGATTAT
1 TATAAATTAT
995205 ATTATATAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
27 2 0.06
28 29 0.91
29 1 0.03
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.55
Consensus pattern (28 bp):
TATAAATTATTAATTTGTTAGTTTAAGT
Found at i:995556 original size:17 final size:17
Alignment explanation
Indices: 995534--995583 Score: 86
Period size: 17 Copynumber: 3.1 Consensus size: 17
995524 TGATTCGAGG
995534 AAAGAAACAAGAAAGGA
1 AAAGAAACAAGAAAGGA
995551 AAAGAAACAAGAAAGGA
1 AAAGAAACAAGAAAGGA
995568 AAAG-AA-AAGAAAGGA
1 AAAGAAACAAGAAAGGA
995583 A
1 A
995584 TAAGGCATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.30
16 2 0.06
17 21 0.64
ACGTcount: A:0.72, C:0.04, G:0.24, T:0.00
Consensus pattern (17 bp):
AAAGAAACAAGAAAGGA
Found at i:999082 original size:23 final size:23
Alignment explanation
Indices: 999046--999110 Score: 116
Period size: 23 Copynumber: 2.9 Consensus size: 23
999036 ATAGTAATGA
999046 TTAT-AATA-GTCGAATTTATCT
1 TTATAAATATGTCGAATTTATCT
999067 TTATAAATATGTCGAATTTATCT
1 TTATAAATATGTCGAATTTATCT
999090 TTATAAATATGTCGAATTTAT
1 TTATAAATATGTCGAATTTAT
999111 TTTTTTACAT
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
21 4 0.10
22 4 0.10
23 34 0.81
ACGTcount: A:0.35, C:0.08, G:0.09, T:0.48
Consensus pattern (23 bp):
TTATAAATATGTCGAATTTATCT
Found at i:999276 original size:14 final size:14
Alignment explanation
Indices: 999254--999307 Score: 60
Period size: 14 Copynumber: 4.1 Consensus size: 14
999244 TATTAATATT
999254 TAATGATTTGATAA
1 TAATGATTTGATAA
* *
999268 TAAT-AATT--TAG
1 TAATGATTTGATAA
999279 TAATGATTTGATAA
1 TAATGATTTGATAA
*
999293 TAATGATTTAATAA
1 TAATGATTTGATAA
999307 T
1 T
999308 GATTACTAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
11 6 0.19
12 3 0.09
13 3 0.09
14 20 0.62
ACGTcount: A:0.44, C:0.00, G:0.11, T:0.44
Consensus pattern (14 bp):
TAATGATTTGATAA
Found at i:999283 original size:25 final size:25
Alignment explanation
Indices: 999254--999311 Score: 98
Period size: 25 Copynumber: 2.3 Consensus size: 25
999244 TATTAATATT
*
999254 TAATGATTTGATAATAATAATTTAG
1 TAATGATTTGATAATAATAATTTAA
*
999279 TAATGATTTGATAATAATGATTTAA
1 TAATGATTTGATAATAATAATTTAA
999304 TAATGATT
1 TAATGATT
999312 ACTAATAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.43, C:0.00, G:0.12, T:0.45
Consensus pattern (25 bp):
TAATGATTTGATAATAATAATTTAA
Found at i:999304 original size:11 final size:11
Alignment explanation
Indices: 999265--999435 Score: 64
Period size: 11 Copynumber: 14.6 Consensus size: 11
999255 AATGATTTGA
*
999265 TAATAATAATT
1 TAATAATGATT
*
999276 TAGTAATGATTT
1 TAATAATGA-TT
999288 GATAATAATGATT
1 --TAATAATGATT
999301 TAATAATGATT
1 TAATAATGATT
*
999312 ACTAATAATTATT
1 --TAATAATGATT
* * *
999325 TATTATTAATAT
1 TAATAATGAT-T
999337 T--TAATGATT
1 TAATAATGATT
999346 TGATAGTAATGATT
1 T-A-A-TAATGATT
*
999360 TAGTAATGATT
1 TAATAATGATT
*
999371 AGTAATAATAATT
1 --TAATAATGATT
* * *
999384 TATTATTAATAT
1 TAATAATGAT-T
999396 T--TAATGATT
1 TAATAATGATT
999405 TGATAGTAATGATT
1 T-A-A-TAATGATT
*
999419 TAGTAATGA-T
1 TAATAATGATT
999429 TAATAAT
1 TAATAAT
999436 AATGAAATGA
Statistics
Matches: 123, Mismatches: 18, Indels: 39
0.68 0.10 0.22
Matches are distributed among these distances:
9 4 0.03
10 17 0.14
11 47 0.38
12 6 0.05
13 23 0.19
14 26 0.21
ACGTcount: A:0.42, C:0.01, G:0.11, T:0.47
Consensus pattern (11 bp):
TAATAATGATT
Found at i:999350 original size:59 final size:59
Alignment explanation
Indices: 999279--999438 Score: 275
Period size: 59 Copynumber: 2.7 Consensus size: 59
999269 AATAATTTAG
* * * *
999279 TAATGATTTGATAATAATGATTTAATAATGATTACTAATAATTATTTATTATTAATATT
1 TAATGATTTGATAGTAATGATTTAGTAATGATTAATAATAATAATTTATTATTAATATT
*
999338 TAATGATTTGATAGTAATGATTTAGTAATGATTAGTAATAATAATTTATTATTAATATT
1 TAATGATTTGATAGTAATGATTTAGTAATGATTAATAATAATAATTTATTATTAATATT
999397 TAATGATTTGATAGTAATGATTTAGTAATGATTAATAATAAT
1 TAATGATTTGATAGTAATGATTTAGTAATGATTAATAATAAT
999439 GAAATGACTA
Statistics
Matches: 96, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
59 96 1.00
ACGTcount: A:0.42, C:0.01, G:0.11, T:0.47
Consensus pattern (59 bp):
TAATGATTTGATAGTAATGATTTAGTAATGATTAATAATAATAATTTATTATTAATATT
Found at i:999355 original size:21 final size:22
Alignment explanation
Indices: 999247--999420 Score: 69
Period size: 21 Copynumber: 8.4 Consensus size: 22
999237 ATTAGTTTAT
*
999247 TAATATTTAATGATTTGA-TAA
1 TAATATTTAATGATTTGATTAG
*
999268 TAATAATTTAGTAATGATTTGA-TAA
1 TAAT-A-TT--TAATGATTTGATTAG
* *
999293 TAATGATTTAAT-A-ATGATTAC
1 TAAT-ATTTAATGATTTGATTAG
* *
999314 T-A-A--TAATTATTT-ATTAT
1 TAATATTTAATGATTTGATTAG
999331 TAATATTTAATGATTTGA-TAG
1 TAATATTTAATGATTTGATTAG
* *
999352 TAATGATTTAGT-A-ATGATTAG
1 TAAT-ATTTAATGATTTGATTAG
* *
999373 T-A-A--TAATAATTT-ATTAT
1 TAATATTTAATGATTTGATTAG
999390 TAATATTTAATGATTTGA-TAG
1 TAATATTTAATGATTTGATTAG
999411 TAATGATTTA
1 TAAT-ATTTA
999421 GTAATGATTA
Statistics
Matches: 117, Mismatches: 14, Indels: 43
0.67 0.08 0.25
Matches are distributed among these distances:
16 7 0.06
17 12 0.10
18 6 0.05
19 2 0.02
20 8 0.07
21 41 0.35
22 18 0.15
23 2 0.02
24 2 0.02
25 19 0.16
ACGTcount: A:0.41, C:0.01, G:0.10, T:0.48
Consensus pattern (22 bp):
TAATATTTAATGATTTGATTAG
Found at i:999771 original size:21 final size:20
Alignment explanation
Indices: 999742--999802 Score: 54
Period size: 21 Copynumber: 3.0 Consensus size: 20
999732 TGATTACTAA
*
999742 TAATGATTTATTATTAATATT
1 TAATAATTTATTATTAATA-T
999763 TAATAATTTGA-TATTAATGAT
1 TAATAATTT-ATTATTAAT-AT
*
999784 TAAGTAA-TGATTATTAATA
1 TAA-TAATTTATTATTAATA
999803 ATGAAATTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
20 2 0.06
21 27 0.79
22 5 0.15
ACGTcount: A:0.43, C:0.00, G:0.08, T:0.49
Consensus pattern (20 bp):
TAATAATTTATTATTAATAT
Found at i:999799 original size:14 final size:13
Alignment explanation
Indices: 999782--999831 Score: 57
Period size: 14 Copynumber: 3.7 Consensus size: 13
999772 GATATTAATG
999782 ATTAAGTAATGATT
1 ATTAA-TAATGATT
999796 ATTAATAATGAAATT
1 ATTAATAATG--ATT
999811 A-TAATAATGATT
1 ATTAATAATGATT
*
999823 AATAATAAT
1 ATTAATAAT
999832 TAAATATTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
12 4 0.12
13 12 0.36
14 13 0.39
15 4 0.12
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (13 bp):
ATTAATAATGATT
Found at i:999877 original size:16 final size:16
Alignment explanation
Indices: 999858--999896 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
999848 ATTTAAATCA
*
999858 AATTTATAAATAGTTG
1 AATTTATAAATAGTCG
*
999874 AATTTATAACTAGTCG
1 AATTTATAAATAGTCG
999890 AATTTAT
1 AATTTAT
999897 CTTTATATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.41, C:0.05, G:0.10, T:0.44
Consensus pattern (16 bp):
AATTTATAAATAGTCG
Found at i:1002237 original size:8 final size:8
Alignment explanation
Indices: 1002226--1002260 Score: 61
Period size: 8 Copynumber: 4.4 Consensus size: 8
1002216 ACTTATAATA
1002226 TAATAAAC
1 TAATAAAC
1002234 TAATAAAC
1 TAATAAAC
1002242 TAATAAAC
1 TAATAAAC
*
1002250 TAACAAAC
1 TAATAAAC
1002258 TAA
1 TAA
1002261 ACTTTTTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.63, C:0.14, G:0.00, T:0.23
Consensus pattern (8 bp):
TAATAAAC
Found at i:1002239 original size:16 final size:16
Alignment explanation
Indices: 1002208--1002252 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
1002198 AAAAAAATTT
*
1002208 ATATAAT-AACTTATA
1 ATATAATAAACTAATA
1002223 ATATAATAAACTAATA
1 ATATAATAAACTAATA
1002239 A-ACTAATAAACTAA
1 ATA-TAATAAACTAA
1002253 CAAACTAAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 8 0.30
16 19 0.70
ACGTcount: A:0.60, C:0.09, G:0.00, T:0.31
Consensus pattern (16 bp):
ATATAATAAACTAATA
Found at i:1002359 original size:30 final size:30
Alignment explanation
Indices: 1002296--1002366 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 30
1002286 ACCCTTAATC
* *
1002296 AACTAATAAATTATTCTTTTATATAACTTA
1 AACTAATAAACTATTCTTTTATATAACTAA
*
1002326 AACTAATAAACTATTTTTTTATTATAA-TAA
1 AACTAATAAACTATTCTTTTA-TATAACTAA
1002356 AACT--TAAACTA
1 AACTAATAAACTA
1002367 CTAATAAACT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
28 7 0.19
30 25 0.68
31 5 0.14
ACGTcount: A:0.46, C:0.10, G:0.00, T:0.44
Consensus pattern (30 bp):
AACTAATAAACTATTCTTTTATATAACTAA
Found at i:1002613 original size:21 final size:21
Alignment explanation
Indices: 1002560--1002599 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1002550 TTTATGTATG
1002560 ATATAACTTAAACTAACAATA
1 ATATAACTTAAACTAACAATA
*
1002581 ATATAGCTTAAACTAACAA
1 ATATAACTTAAACTAACAA
1002600 ACTAATTAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.55, C:0.15, G:0.03, T:0.28
Consensus pattern (21 bp):
ATATAACTTAAACTAACAATA
Found at i:1002750 original size:15 final size:15
Alignment explanation
Indices: 1002727--1002760 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1002717 TTCTTCTTCA
*
1002727 TCTTTTCCCTTTCTC
1 TCTTCTCCCTTTCTC
*
1002742 TCTTCTCCCTTTCTT
1 TCTTCTCCCTTTCTC
1002757 TCTT
1 TCTT
1002761 TACATAACTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (15 bp):
TCTTCTCCCTTTCTC
Found at i:1003058 original size:28 final size:29
Alignment explanation
Indices: 1003027--1003095 Score: 95
Period size: 29 Copynumber: 2.4 Consensus size: 29
1003017 CGTCGGGACA
1003027 GCATGGCGACCT-ATAGGTCGCGGGGAGT
1 GCATGGCGACCTGATAGGTCGCGGGGAGT
* * *
1003055 GCATGGCGACCTGGTAGGTCGCTGGGTGT
1 GCATGGCGACCTGATAGGTCGCGGGGAGT
*
1003084 GAATGGCGACCT
1 GCATGGCGACCT
1003096 CTTCCAACGA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
28 12 0.33
29 24 0.67
ACGTcount: A:0.16, C:0.22, G:0.42, T:0.20
Consensus pattern (29 bp):
GCATGGCGACCTGATAGGTCGCGGGGAGT
Found at i:1005388 original size:21 final size:21
Alignment explanation
Indices: 1005362--1005406 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1005352 GTCTGTTCAT
*
1005362 ATTCACTAGTTCAAAGCTCAC
1 ATTCACTAGCTCAAAGCTCAC
* *
1005383 ATTCACTTGCTCAAAGTTCAC
1 ATTCACTAGCTCAAAGCTCAC
1005404 ATT
1 ATT
1005407 TCCATAATCG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.27, G:0.09, T:0.33
Consensus pattern (21 bp):
ATTCACTAGCTCAAAGCTCAC
Found at i:1005965 original size:42 final size:42
Alignment explanation
Indices: 1005887--1005966 Score: 99
Period size: 42 Copynumber: 1.9 Consensus size: 42
1005877 ATACCTTCCC
* *** *
1005887 CTGGTATCAATACTACACACACAATATTGATTCCCTCTACAT
1 CTGGTATAAATACTACACACACAATACCAATACCCTCTACAT
1005929 CTGGTATAAATACTAC-CTACACAATACCAATACCCTCT
1 CTGGTATAAATACTACAC-ACACAATACCAATACCCTCT
1005967 TCAACGAGTA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
41 1 0.03
42 31 0.97
ACGTcount: A:0.35, C:0.30, G:0.06, T:0.29
Consensus pattern (42 bp):
CTGGTATAAATACTACACACACAATACCAATACCCTCTACAT
Found at i:1007804 original size:31 final size:31
Alignment explanation
Indices: 1007735--1007807 Score: 83
Period size: 31 Copynumber: 2.4 Consensus size: 31
1007725 ACCTTCAGTG
* *
1007735 ACCACATCTTAATTAAAACGAAACAAAAGTG
1 ACCAAATCTTAATTAAAACGAAACAAAAGTA
** * **
1007766 ATTAAATCTTAATTAAAATGAAATGAAAGTA
1 ACCAAATCTTAATTAAAACGAAACAAAAGTA
1007797 ACCAAATCTTA
1 ACCAAATCTTA
1007808 TGTTTTTTAA
Statistics
Matches: 33, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.52, C:0.14, G:0.08, T:0.26
Consensus pattern (31 bp):
ACCAAATCTTAATTAAAACGAAACAAAAGTA
Found at i:1011291 original size:12 final size:13
Alignment explanation
Indices: 1011263--1011291 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1011253 TTTGGAAGGT
1011263 AAATGAAAATAAG
1 AAATGAAAATAAG
1011276 AAATGAAAAT-AG
1 AAATGAAAATAAG
1011288 AAAT
1 AAAT
1011292 ACGATACTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.38
13 10 0.62
ACGTcount: A:0.69, C:0.00, G:0.14, T:0.17
Consensus pattern (13 bp):
AAATGAAAATAAG
Found at i:1014304 original size:11 final size:11
Alignment explanation
Indices: 1014290--1014315 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1014280 TTTTGTTTAG
1014290 TTTTTCTTTTT
1 TTTTTCTTTTT
1014301 TTTTTCTTTTT
1 TTTTTCTTTTT
1014312 TTTT
1 TTTT
1014316 GTTTAGTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTTTCTTTTT
Found at i:1014315 original size:14 final size:15
Alignment explanation
Indices: 1014278--1014329 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
1014268 TATGCGGCCA
*
1014278 TTTTTTGTTTAGTTTT
1 TTTTTTGTTTA-CTTT
* *
1014294 TCTTTTTTTTTTCTTT
1 T-TTTTTGTTTACTTT
*
1014310 TTTTTTGTTTAGTTT
1 TTTTTTGTTTACTTT
1014325 TTTTT
1 TTTTT
1014330 CAAGTAATTT
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
15 16 0.55
16 5 0.17
17 8 0.28
ACGTcount: A:0.04, C:0.04, G:0.08, T:0.85
Consensus pattern (15 bp):
TTTTTTGTTTACTTT
Found at i:1017242 original size:14 final size:13
Alignment explanation
Indices: 1017223--1017265 Score: 59
Period size: 13 Copynumber: 3.2 Consensus size: 13
1017213 TTTTAATGAT
*
1017223 TATTTTTGAAAAA
1 TATTTTTTAAAAA
*
1017236 TATTTTTTAAATA
1 TATTTTTTAAAAA
1017249 TATTTTTTTAAAAA
1 TA-TTTTTTAAAAA
1017263 TAT
1 TAT
1017266 ATAAACATGA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
13 14 0.54
14 12 0.46
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (13 bp):
TATTTTTTAAAAA
Found at i:1018648 original size:59 final size:59
Alignment explanation
Indices: 1018575--1018742 Score: 336
Period size: 59 Copynumber: 2.8 Consensus size: 59
1018565 TATAGCGGTG
1018575 TATATTTTTATCTTGAAGCTTGGGATTTTAGCCTGAATTTGGTTAATTATAGTGGTGTA
1 TATATTTTTATCTTGAAGCTTGGGATTTTAGCCTGAATTTGGTTAATTATAGTGGTGTA
1018634 TATATTTTTATCTTGAAGCTTGGGATTTTAGCCTGAATTTGGTTAATTATAGTGGTGTA
1 TATATTTTTATCTTGAAGCTTGGGATTTTAGCCTGAATTTGGTTAATTATAGTGGTGTA
1018693 TATATTTTTATCTTGAAGCTTGGGATTTTAGCCTGAATTTGGTTAATTAT
1 TATATTTTTATCTTGAAGCTTGGGATTTTAGCCTGAATTTGGTTAATTAT
1018743 TGTTTGGGCT
Statistics
Matches: 109, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 109 1.00
ACGTcount: A:0.24, C:0.07, G:0.21, T:0.48
Consensus pattern (59 bp):
TATATTTTTATCTTGAAGCTTGGGATTTTAGCCTGAATTTGGTTAATTATAGTGGTGTA
Found at i:1022461 original size:16 final size:16
Alignment explanation
Indices: 1022423--1022459 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
1022413 AGAAAATGAA
1022423 ATAAAATATTTTAAAT
1 ATAAAATATTTTAAAT
*
1022439 GTAAAATA-TTTAAAT
1 ATAAAATATTTTAAAT
1022454 ATAAAA
1 ATAAAA
1022460 ATTAAATTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
15 12 0.63
16 7 0.37
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (16 bp):
ATAAAATATTTTAAAT
Found at i:1027912 original size:24 final size:23
Alignment explanation
Indices: 1027861--1027906 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
1027851 TTTATAAAAG
1027861 CTTTTCTTTTTACTTTTCAAGTT
1 CTTTTCTTTTTACTTTTCAAGTT
1027884 CTTTTCATTTTTA-TTTTCAAGTT
1 CTTTTC-TTTTTACTTTTCAAGTT
1027907 TGTTTTATGC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 16 0.73
24 6 0.27
ACGTcount: A:0.15, C:0.15, G:0.04, T:0.65
Consensus pattern (23 bp):
CTTTTCTTTTTACTTTTCAAGTT
Found at i:1032707 original size:16 final size:16
Alignment explanation
Indices: 1032665--1032717 Score: 56
Period size: 16 Copynumber: 3.3 Consensus size: 16
1032655 TCTCCATCAC
1032665 AAAAAA-TGTT-GAAA
1 AAAAAACTGTTCGAAA
* *
1032679 AAAATAGCAGTTCGAAA
1 AAAA-AACTGTTCGAAA
1032696 AAAAAACTGTTCGAAA
1 AAAAAACTGTTCGAAA
1032712 GAAAAA
1 -AAAAA
1032718 GAAAAAAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
14 4 0.13
15 1 0.03
16 13 0.42
17 13 0.42
ACGTcount: A:0.60, C:0.08, G:0.15, T:0.17
Consensus pattern (16 bp):
AAAAAACTGTTCGAAA
Found at i:1038309 original size:34 final size:33
Alignment explanation
Indices: 1038251--1038346 Score: 138
Period size: 33 Copynumber: 2.9 Consensus size: 33
1038241 ATGTGCAAAA
* *
1038251 TTGGTCACCTACCAAAGATGAATTTTCCAATAAG
1 TTGGCCACCAACC-AAGATGAATTTTCCAATAAG
*
1038285 TTGGCCACCAACCAAGATGAAATTTCCAATAAG
1 TTGGCCACCAACCAAGATGAATTTTCCAATAAG
* *
1038318 TTAGCCACCAATCAAGATGAATTTTCCAA
1 TTGGCCACCAACCAAGATGAATTTTCCAA
1038347 CTTGCCAAAT
Statistics
Matches: 56, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
33 45 0.80
34 11 0.20
ACGTcount: A:0.38, C:0.23, G:0.14, T:0.26
Consensus pattern (33 bp):
TTGGCCACCAACCAAGATGAATTTTCCAATAAG
Found at i:1042320 original size:34 final size:33
Alignment explanation
Indices: 1042262--1042357 Score: 138
Period size: 33 Copynumber: 2.9 Consensus size: 33
1042252 ATGTACAAAA
* *
1042262 TTGGTCACCTACCAAAGATGAATTTTCCAATAAG
1 TTGGCCACCAACC-AAGATGAATTTTCCAATAAG
*
1042296 TTGGCCACCAACCAAGATGAAATTTCCAATAAG
1 TTGGCCACCAACCAAGATGAATTTTCCAATAAG
* *
1042329 TTAGCCACCAATCAAGATGAATTTTCCAA
1 TTGGCCACCAACCAAGATGAATTTTCCAA
1042358 CTTGCCAAAT
Statistics
Matches: 56, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
33 45 0.80
34 11 0.20
ACGTcount: A:0.38, C:0.23, G:0.14, T:0.26
Consensus pattern (33 bp):
TTGGCCACCAACCAAGATGAATTTTCCAATAAG
Found at i:1043064 original size:33 final size:33
Alignment explanation
Indices: 1043009--1043099 Score: 146
Period size: 33 Copynumber: 2.7 Consensus size: 33
1042999 CAAAGTTGGT
*
1043009 CACCTACCAAAGATGAATTTTCCAATAAGTTGAC
1 CACCAACC-AAGATGAATTTTCCAATAAGTTGAC
* *
1043043 CACCAACCAAGATGAAATTTCCAATAAGTTGGC
1 CACCAACCAAGATGAATTTTCCAATAAGTTGAC
1043076 CACCAACCAAGATGAATTTTCCAA
1 CACCAACCAAGATGAATTTTCCAA
1043100 CTTGCCAAAT
Statistics
Matches: 53, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
33 46 0.87
34 7 0.13
ACGTcount: A:0.40, C:0.25, G:0.12, T:0.23
Consensus pattern (33 bp):
CACCAACCAAGATGAATTTTCCAATAAGTTGAC
Found at i:1053544 original size:50 final size:50
Alignment explanation
Indices: 1053469--1053570 Score: 204
Period size: 50 Copynumber: 2.0 Consensus size: 50
1053459 TTTTCTGAAA
1053469 AATGGATTGGCAATCGGCCTTTCTTGTAAAAATCTTTTCACTTTCAATTC
1 AATGGATTGGCAATCGGCCTTTCTTGTAAAAATCTTTTCACTTTCAATTC
1053519 AATGGATTGGCAATCGGCCTTTCTTGTAAAAATCTTTTCACTTTCAATTC
1 AATGGATTGGCAATCGGCCTTTCTTGTAAAAATCTTTTCACTTTCAATTC
1053569 AA
1 AA
1053571 AAAGAGCTCG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 52 1.00
ACGTcount: A:0.27, C:0.20, G:0.14, T:0.39
Consensus pattern (50 bp):
AATGGATTGGCAATCGGCCTTTCTTGTAAAAATCTTTTCACTTTCAATTC
Found at i:1054174 original size:21 final size:21
Alignment explanation
Indices: 1054149--1054188 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1054139 TACATTTCTA
*
1054149 ACTTATTTATCTGAGAAAAAG
1 ACTTATTTATCTGACAAAAAG
*
1054170 ACTTATTTATTTGACAAAA
1 ACTTATTTATCTGACAAAA
1054189 TAAGATACTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.42, C:0.10, G:0.10, T:0.38
Consensus pattern (21 bp):
ACTTATTTATCTGACAAAAAG
Found at i:1059214 original size:23 final size:23
Alignment explanation
Indices: 1059177--1059240 Score: 101
Period size: 23 Copynumber: 2.8 Consensus size: 23
1059167 CAGCTCATAT
1059177 AAATGCACCGAAGTGCCACGTAG
1 AAATGCACCGAAGTGCCACGTAG
* * *
1059200 AATTGCACCGTAGTGCCGCGTAG
1 AAATGCACCGAAGTGCCACGTAG
1059223 AAATGCACCGAAGTGCCA
1 AAATGCACCGAAGTGCCA
1059241 TATAAGGTTG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.31, C:0.27, G:0.27, T:0.16
Consensus pattern (23 bp):
AAATGCACCGAAGTGCCACGTAG
Found at i:1064333 original size:19 final size:20
Alignment explanation
Indices: 1064292--1064334 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
1064282 AAAAATTATT
* *
1064292 AATAATTTAATACTTTTTGA
1 AATAATATAATACTTTTTAA
1064312 AATAATATAATA-TTTTTAA
1 AATAATATAATACTTTTTAA
1064331 AATA
1 AATA
1064335 TTTTTGTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 10 0.48
20 11 0.52
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (20 bp):
AATAATATAATACTTTTTAA
Found at i:1064401 original size:30 final size:29
Alignment explanation
Indices: 1064364--1064496 Score: 96
Period size: 30 Copynumber: 4.6 Consensus size: 29
1064354 AATATAATTG
1064364 AATATATTATTTTAATATTAAAACTATAA
1 AATATATTATTTTAATATTAAAACTATAA
** * **
1064393 AATTATATTATTAAAAATATTTTAAA-TATTT
1 AA-TATATTATT-TTAATA-TTAAAACTATAA
* *
1064424 AATA-ATTAATTT--TATTAAAATTATATA
1 AATATATTATTTTAATATTAAAACTATA-A
* *
1064451 AATATTTTATATTAATATTAAATAC-ATAA
1 AATATATTATTTTAATATTAAA-ACTATAA
1064480 AATAATATTATTTTAAT
1 AAT-ATATTATTTTAAT
1064497 TTTTATGTTT
Statistics
Matches: 77, Mismatches: 17, Indels: 19
0.68 0.15 0.17
Matches are distributed among these distances:
25 5 0.06
26 5 0.06
27 4 0.05
28 5 0.06
29 11 0.14
30 32 0.42
31 10 0.13
32 5 0.06
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (29 bp):
AATATATTATTTTAATATTAAAACTATAA
Found at i:1064444 original size:34 final size:34
Alignment explanation
Indices: 1064400--1064466 Score: 84
Period size: 34 Copynumber: 2.0 Consensus size: 34
1064390 TAAAATTATA
*
1064400 TTATTAAAAA-TATTTTAAATATTTAATAATTAATT
1 TTATTAAAAATTA-TATAAATATTTAAT-ATTAATT
*
1064435 TTATT-AAAATTATATAAATATTTTATATTAAT
1 TTATTAAAAATTATATAAATATTTAATATTAAT
1064467 ATTAAATACA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
33 6 0.21
34 16 0.55
35 7 0.24
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (34 bp):
TTATTAAAAATTATATAAATATTTAATATTAATT
Found at i:1065683 original size:21 final size:21
Alignment explanation
Indices: 1065657--1065701 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1065647 GATTTCTGGG
* *
1065657 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
1065678 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
1065699 CAA
1 CAA
1065702 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:1065754 original size:22 final size:22
Alignment explanation
Indices: 1065726--1065789 Score: 110
Period size: 22 Copynumber: 2.9 Consensus size: 22
1065716 CCAGTATGTC
1065726 ATGGGGGAACCGATACCCCCAT
1 ATGGGGGAACCGATACCCCCAT
1065748 ATGGGGGAACCGATACCCCCAT
1 ATGGGGGAACCGATACCCCCAT
* *
1065770 AGGGGGGAACCGATTCCCCC
1 ATGGGGGAACCGATACCCCC
1065790 TAAAGGAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.25, C:0.33, G:0.30, T:0.12
Consensus pattern (22 bp):
ATGGGGGAACCGATACCCCCAT
Found at i:1066330 original size:18 final size:18
Alignment explanation
Indices: 1066307--1066341 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1066297 CTAGGAGATT
1066307 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
1066325 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
1066342 CTAGATGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAACATATAAGATAAGA
Found at i:1066427 original size:21 final size:22
Alignment explanation
Indices: 1066398--1066441 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1066388 GTTGTATGAT
1066398 AGAAAATTAT-GAAGTTATATG
1 AGAAAATTATAGAAGTTATATG
* *
1066419 AGAAGATTATAGGAGTTATATG
1 AGAAAATTATAGAAGTTATATG
1066441 A
1 A
1066442 AATTGAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.45, C:0.00, G:0.23, T:0.32
Consensus pattern (22 bp):
AGAAAATTATAGAAGTTATATG
Found at i:1067034 original size:23 final size:23
Alignment explanation
Indices: 1066990--1067034 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
1066980 ATCATTATAT
*
1066990 GGCACTATGGTGCAATTCTACGG
1 GGCACTATGGTGCAATTATACGG
*
1067013 GGCACT-TCGGTGCATTTATACG
1 GGCACTAT-GGTGCAATTATACG
1067035 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 1 0.05
23 18 0.95
ACGTcount: A:0.20, C:0.22, G:0.29, T:0.29
Consensus pattern (23 bp):
GGCACTATGGTGCAATTATACGG
Found at i:1070194 original size:21 final size:21
Alignment explanation
Indices: 1070168--1070212 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1070158 GATTTCTGGG
* *
1070168 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
1070189 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
1070210 CAA
1 CAA
1070213 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:1070819 original size:18 final size:18
Alignment explanation
Indices: 1070796--1070830 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1070786 CTAGGAGATT
1070796 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
1070814 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
1070831 CTAGATGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAACATATAAGATAAGA
Found at i:1070916 original size:21 final size:22
Alignment explanation
Indices: 1070887--1070930 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1070877 GTTGTATGAT
1070887 AGAAAATTAT-GAAGTTATATG
1 AGAAAATTATAGAAGTTATATG
* *
1070908 AGAAGATTATAGGAGTTATATG
1 AGAAAATTATAGAAGTTATATG
1070930 A
1 A
1070931 AATTGAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.45, C:0.00, G:0.23, T:0.32
Consensus pattern (22 bp):
AGAAAATTATAGAAGTTATATG
Found at i:1071525 original size:23 final size:23
Alignment explanation
Indices: 1071481--1071525 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
1071471 ATCATTATAT
* *
1071481 GGCACTACGGTGCAATTCTACGG
1 GGCACTACAGTGCAATTATACGG
* *
1071504 GGCACTTCAGTGCATTTATACG
1 GGCACTACAGTGCAATTATACG
1071526 ATCTGTGGTG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.22, C:0.24, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTACAGTGCAATTATACGG
Found at i:1072273 original size:35 final size:36
Alignment explanation
Indices: 1072232--1072302 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
1072222 TTTCATTTAC
1072232 ATTTTGTTAG-TTAAAAATAGGGTAAACTATGTGTT
1 ATTTTGTTAGTTTAAAAATAGGGTAAACTATGTGTT
1072267 ATTTTGTTAGTTTAAAAATAGGGTAAACTATGTGTT
1 ATTTTGTTAGTTTAAAAATAGGGTAAACTATGTGTT
1072303 TAGTACCTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
35 10 0.29
36 25 0.71
ACGTcount: A:0.34, C:0.03, G:0.20, T:0.44
Consensus pattern (36 bp):
ATTTTGTTAGTTTAAAAATAGGGTAAACTATGTGTT
Found at i:1073612 original size:43 final size:44
Alignment explanation
Indices: 1073559--1073641 Score: 141
Period size: 43 Copynumber: 1.9 Consensus size: 44
1073549 ATAATTTACT
1073559 AAAAAGCTTTCAATACAAAGTACAAACATTAAAATTTGAATCCC
1 AAAAAGCTTTCAATACAAAGTACAAACATTAAAATTTGAATCCC
* *
1073603 AAAAA-CTTTCAATACAAAGTACAAACGTTAAATTTTGAA
1 AAAAAGCTTTCAATACAAAGTACAAACATTAAAATTTGAA
1073642 CCATCAGGAT
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
43 32 0.86
44 5 0.14
ACGTcount: A:0.51, C:0.16, G:0.07, T:0.27
Consensus pattern (44 bp):
AAAAAGCTTTCAATACAAAGTACAAACATTAAAATTTGAATCCC
Found at i:1079647 original size:17 final size:18
Alignment explanation
Indices: 1079608--1079655 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
1079598 TGTTTCTGAG
1079608 GGAATTAGAATCTGTGAA
1 GGAATTAGAATCTGTGAA
* *
1079626 GGAATTGGAATCTGT-CA
1 GGAATTAGAATCTGTGAA
1079643 GGAATTAGAATCT
1 GGAATTAGAATCT
1079656 AATTCCATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 13 0.48
18 14 0.52
ACGTcount: A:0.35, C:0.08, G:0.27, T:0.29
Consensus pattern (18 bp):
GGAATTAGAATCTGTGAA
Found at i:1080447 original size:262 final size:245
Alignment explanation
Indices: 1080010--1080616 Score: 711
Period size: 262 Copynumber: 2.4 Consensus size: 245
1080000 CCTCCATCCG
1080010 AGACCCGACCAAAATAAAGTTTCACCTGACCCGACCCGAATATATGAATTAG-AACCCGACCCGA
1 AGACCCGACCAAAATAAAGTTTCACCT-----GACCCGAATATATGAATTAGAAACCCGACCCGA
* ** * * *
1080074 AATAATAAAAAAATTATTTTTATTCAATAAAAGCAGTGACTTAATTGGAAATATATATATATAGA
61 AATAAT-AAAAAATTATTTTTATTCAATAAAAACAACGACTTAATTGAAAAAATATATATAGAGA
* **
1080139 GGGATATTATTGTAATTATTTCTAAATATATAAGGTAATTTTATATATTTTTTGGATTGGGTCGG
125 GGGATATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATA-----T--ATT--GTCGG
1080204 GTCGGGTATTTTTCACCCTAAACCCGAA-TCCGACCCGACCCTACCCGAATATCACACTTAAAAA
181 GTCGGGTATTTTTCACCCTAAACCCGAACT-CGACCCGACCC-A----AATATCACACTTAAAAA
1080268 AA-ACC
240 AACACC
*
1080273 -GACCCGACCAAAATAAAGTTTCACCTGACCCGAATATATGAATTAGAAATCCGACCCGACCCAA
1 AGACCCGACCAAAATAAAGTTTCACCTGACCCGAATATATGAATTAG-AA----ACCCGACCCGA
1080337 AATAATAAAAAATTATTTTTATTCAATAAAAACAACGACTTAATTGAAAAAA-ATTATATAGAGA
61 AATAATAAAAAATTATTTTTATTCAATAAAAACAACGACTTAATTGAAAAAATA-TATATAGAGA
* * *
1080401 GGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATATTTTCGGGTTGGGTAT
125 GGGATATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATATTGTCGGGTCGGGTAT
* *
1080466 TTTTCACTCTAAATCCGAACTCGACCCGACCCAAATATCACACTTAAAAAAACTGACC
190 TTTTCACCCTAAACCCGAACTCGACCCGACCCAAATATCACACTTAAAAAAAC--ACC
* *
1080524 AGATCCGACCAAAATAAAGTTTCACCCAACCCGACCCGAATATATGAATTAGAAACCCGACCCGA
1 AGACCCGACCAAAATAAAGTTT----C-ACCTGACCCGAATATATGAATTAGAAACCCGACCCGA
*
1080589 AATAATAAAAAAATATTTTTATTCAATA
61 AATAATAAAAAATTATTTTTATTCAATA
1080617 TATGAATAAG
Statistics
Matches: 308, Mismatches: 19, Indels: 45
0.83 0.05 0.12
Matches are distributed among these distances:
248 19 0.06
251 3 0.01
252 58 0.19
253 40 0.13
254 1 0.00
255 3 0.01
256 3 0.01
257 44 0.14
259 1 0.00
261 1 0.00
262 119 0.39
263 16 0.05
ACGTcount: A:0.40, C:0.19, G:0.13, T:0.28
Consensus pattern (245 bp):
AGACCCGACCAAAATAAAGTTTCACCTGACCCGAATATATGAATTAGAAACCCGACCCGAAATAA
TAAAAAATTATTTTTATTCAATAAAAACAACGACTTAATTGAAAAAATATATATAGAGAGGGATA
TTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATATTGTCGGGTCGGGTATTTTTCA
CCCTAAACCCGAACTCGACCCGACCCAAATATCACACTTAAAAAAACACC
Found at i:1085275 original size:29 final size:29
Alignment explanation
Indices: 1085220--1085282 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 29
1085210 GTAAGCAATC
* **
1085220 TATTACATTACATTTTTTCATCAAAACAA
1 TATTACATTACATTTTGTCAAAAAAACAA
1085249 TATTACATTACATTTTGT-AAAAGAAACAA
1 TATTACATTACATTTTGTCAAAA-AAACAA
1085278 TATTA
1 TATTA
1085283 TGACTTTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
28 2 0.07
29 28 0.93
ACGTcount: A:0.44, C:0.13, G:0.03, T:0.40
Consensus pattern (29 bp):
TATTACATTACATTTTGTCAAAAAAACAA
Found at i:1086625 original size:60 final size:60
Alignment explanation
Indices: 1086548--1086681 Score: 171
Period size: 60 Copynumber: 2.2 Consensus size: 60
1086538 TGAGGATGAT
* * * * *
1086548 CATTTTGTAACTATTAATAGTCGAGGAACTTAACAAAGTAACATTCTATAGTCGAATGAC
1 CATTTTGTAACTTTTAATAGTCAAGGAACTTAACAAAGTAACATCCTATAATCGAAGGAC
* * * *
1086608 TATTTTGTAACTTTTAATAGTCAAGGGACTTAATAAAGTAATATCCTATAATCGAAGGAC
1 CATTTTGTAACTTTTAATAGTCAAGGAACTTAACAAAGTAACATCCTATAATCGAAGGAC
1086668 CATTTTTGT-ACTTT
1 CA-TTTTGTAACTTT
1086682 ACCCTTATAT
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
60 57 0.90
61 6 0.10
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.37
Consensus pattern (60 bp):
CATTTTGTAACTTTTAATAGTCAAGGAACTTAACAAAGTAACATCCTATAATCGAAGGAC
Found at i:1086716 original size:22 final size:22
Alignment explanation
Indices: 1086691--1086737 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
1086681 TACCCTTATA
* * *
1086691 TTTAAATAAATTTTTTAGTGTT
1 TTTAAATAAATATTTTAATATT
1086713 TTT-AATAAATATTTTAATATT
1 TTTAAATAAATATTTTAATATT
1086734 TTTA
1 TTTA
1086738 TTATAATGTA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
21 18 0.86
22 3 0.14
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (22 bp):
TTTAAATAAATATTTTAATATT
Found at i:1091542 original size:56 final size:56
Alignment explanation
Indices: 1091469--1091667 Score: 188
Period size: 56 Copynumber: 3.6 Consensus size: 56
1091459 CCCTATTTTT
* * * *
1091469 TAGATACATTCGATTTCGGGACCCCTATTTTTATGCTTCTTAATGGCAATAACTTA
1 TAGATATACTCGATTTCGGGACCCCTATTTTTATGATTCTTAATGGCAACAACTTA
* * ** **
1091525 TACATATACTCAATTTCGGGGTCTTTATTTTTATGATTCTTAATGGCAACAA-TTGA
1 TAGATATACTCGATTTCGGGACCCCTATTTTTATGATTCTTAATGGCAACAACTT-A
* * * * * * *
1091581 TTGATATACTCGATTTTGAGG-CCTCTATTTTTATGTTTATTAATGACAACAACTGA
1 TAGATATACTCGATTTCG-GGACCCCTATTTTTATGATTCTTAATGGCAACAACTTA
**
1091637 TAGATATACTCGATTTCAAGA-CCCTATTTTT
1 TAGATATACTCGATTTCGGGACCCCTATTTTT
1091668 TGGGGCCTAC
Statistics
Matches: 114, Mismatches: 25, Indels: 9
0.77 0.17 0.06
Matches are distributed among these distances:
55 12 0.11
56 99 0.87
57 3 0.03
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.42
Consensus pattern (56 bp):
TAGATATACTCGATTTCGGGACCCCTATTTTTATGATTCTTAATGGCAACAACTTA
Found at i:1092522 original size:29 final size:29
Alignment explanation
Indices: 1092489--1092546 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
1092479 AAAATAACTG
1092489 GTCAAATTAATTATAATAATTTTGAACAA
1 GTCAAATTAATTATAATAATTTTGAACAA
1092518 GTCAAATTAATTATAATAATTTTGAACAA
1 GTCAAATTAATTATAATAATTTTGAACAA
1092547 TGAGTTGTAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.48, C:0.07, G:0.07, T:0.38
Consensus pattern (29 bp):
GTCAAATTAATTATAATAATTTTGAACAA
Found at i:1099918 original size:62 final size:63
Alignment explanation
Indices: 1099842--1099960 Score: 152
Period size: 62 Copynumber: 1.9 Consensus size: 63
1099832 CACTATTTTA
* **
1099842 AAATACAAATATCGAATGCCATCGATGCATCGATGCATAAG-G-AGTGCATCGATGCACCCCAT
1 AAATACAAACATCGAATAACATCGATGCATCGATGCAT-AGTGTAGTGCATCGATGCACCCCAT
* ** *
1099904 AAATACAAACATCGAATAAGATTTATGCATCGATGCATGGTGTAGTGCATCGATGCA
1 AAATACAAACATCGAATAACATCGATGCATCGATGCATAGTGTAGTGCATCGATGCA
1099961 TACCTCCATT
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
61 1 0.02
62 33 0.69
63 14 0.29
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.24
Consensus pattern (63 bp):
AAATACAAACATCGAATAACATCGATGCATCGATGCATAGTGTAGTGCATCGATGCACCCCAT
Found at i:1100339 original size:30 final size:30
Alignment explanation
Indices: 1100305--1100373 Score: 95
Period size: 30 Copynumber: 2.3 Consensus size: 30
1100295 TTATATGAGT
* *
1100305 TATGTGATAAAGGTATGG-AAATGATATGTC
1 TATGTGATAAAGG-AAGGAAAATAATATGTC
1100335 TATGTGATAAAGGAAGGAAAATAATATGTC
1 TATGTGATAAAGGAAGGAAAATAATATGTC
*
1100365 TACGTGATA
1 TATGTGATA
1100374 CAAATTATGT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
29 3 0.09
30 32 0.91
ACGTcount: A:0.41, C:0.04, G:0.25, T:0.30
Consensus pattern (30 bp):
TATGTGATAAAGGAAGGAAAATAATATGTC
Found at i:1100614 original size:23 final size:23
Alignment explanation
Indices: 1100584--1100697 Score: 174
Period size: 23 Copynumber: 5.0 Consensus size: 23
1100574 ATTATTATAT
1100584 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
*
1100607 GGCACTACGGTGCAATTCTATGC
1 GGCACTACGGTGCAATTCTACGC
1100630 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
1100653 GGCACTTCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
* * *
1100676 GGCACTTCGGTACAATTATACG
1 GGCACTACGGTGCAATTCTACG
1100698 ACCTCACAAT
Statistics
Matches: 85, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 85 1.00
ACGTcount: A:0.22, C:0.27, G:0.25, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:1112514 original size:24 final size:24
Alignment explanation
Indices: 1112486--1112558 Score: 66
Period size: 24 Copynumber: 3.2 Consensus size: 24
1112476 GTGTGTGTTT
1112486 TTAAAATGATAAATGGGAGAAGTG
1 TTAAAATGATAAATGGGAGAAGTG
* * * *
1112510 TT-AAA-G-T-AAGGGGTG-TGTTT
1 TTAAAATGATAAATGGGAGAAG-TG
1112530 TTAAAATGATAAATGGGAGAAGTG
1 TTAAAATGATAAATGGGAGAAGTG
1112554 TTAAA
1 TTAAA
1112559 GTAAGGGGGA
Statistics
Matches: 35, Mismatches: 8, Indels: 12
0.64 0.15 0.22
Matches are distributed among these distances:
19 1 0.03
20 9 0.26
21 4 0.11
22 2 0.06
23 4 0.11
24 14 0.40
25 1 0.03
ACGTcount: A:0.41, C:0.00, G:0.29, T:0.30
Consensus pattern (24 bp):
TTAAAATGATAAATGGGAGAAGTG
Found at i:1112541 original size:44 final size:44
Alignment explanation
Indices: 1112478--1112566 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
1112468 GGGAAGAAGT
1112478 GTGTGTTTTTAAAATGATAAATGGGAGAAGTGTTAAAGTAAGGG
1 GTGTGTTTTTAAAATGATAAATGGGAGAAGTGTTAAAGTAAGGG
1112522 GTGTGTTTTTAAAATGATAAATGGGAGAAGTGTTAAAGTAAGGG
1 GTGTGTTTTTAAAATGATAAATGGGAGAAGTGTTAAAGTAAGGG
1112566 G
1 G
1112567 GAGTAATTTC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.36, C:0.00, G:0.33, T:0.31
Consensus pattern (44 bp):
GTGTGTTTTTAAAATGATAAATGGGAGAAGTGTTAAAGTAAGGG
Found at i:1113065 original size:21 final size:21
Alignment explanation
Indices: 1113035--1113089 Score: 101
Period size: 21 Copynumber: 2.6 Consensus size: 21
1113025 TTGCACTTAG
1113035 GGAACCGATTCCCTATGAGGA
1 GGAACCGATTCCCTATGAGGA
*
1113056 GGAACTGATTCCCTATGAGGA
1 GGAACCGATTCCCTATGAGGA
1113077 GGAACCGATTCCC
1 GGAACCGATTCCC
1113090 CCAAGCTCCA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.27, C:0.25, G:0.27, T:0.20
Consensus pattern (21 bp):
GGAACCGATTCCCTATGAGGA
Found at i:1116211 original size:64 final size:64
Alignment explanation
Indices: 1116141--1116282 Score: 162
Period size: 63 Copynumber: 2.2 Consensus size: 64
1116131 ATGCACATGA
* ** **
1116141 AGTGCATCGATGCACTATTTTAAAATACAAACATCGAATGCCATCGATGCATCGATGCATAAG-G
1 AGTGCATCGATGCACCACATT-AAATACAAACATCGAATAACATCGATGCATCGATGCAT-AGTG
1116205 -
64 T
* * ** *
1116205 AGTGCATCGATGCACCCCATTAAATACAAACATCGAATAAGATTTATGCATCGATGCATGGTGT
1 AGTGCATCGATGCACCACATTAAATACAAACATCGAATAACATCGATGCATCGATGCATAGTGT
1116269 AGTGCATCGATGCA
1 AGTGCATCGATGCA
1116283 TACCTCCATT
Statistics
Matches: 66, Mismatches: 10, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
62 1 0.02
63 34 0.52
64 31 0.47
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.25
Consensus pattern (64 bp):
AGTGCATCGATGCACCACATTAAATACAAACATCGAATAACATCGATGCATCGATGCATAGTGT
Found at i:1116259 original size:63 final size:64
Alignment explanation
Indices: 1116163--1116282 Score: 163
Period size: 63 Copynumber: 1.9 Consensus size: 64
1116153 CACTATTTTA
**
1116163 AAATACAAACATCGAATGCCATCGATGCATCGATGCATAAG-G-AGTGCATCGATGCACCCCATT
1 AAATACAAACATCGAATAACATCGATGCATCGATGCAT-AGTGTAGTGCATCGATGCACCCCATT
* ** *
1116226 AAATACAAACATCGAATAAGATTTATGCATCGATGCATGGTGTAGTGCATCGATGCA
1 AAATACAAACATCGAATAACATCGATGCATCGATGCATAGTGTAGTGCATCGATGCA
1116283 TACCTCCATT
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
62 1 0.02
63 34 0.69
64 14 0.29
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.23
Consensus pattern (64 bp):
AAATACAAACATCGAATAACATCGATGCATCGATGCATAGTGTAGTGCATCGATGCACCCCATT
Found at i:1116947 original size:23 final size:23
Alignment explanation
Indices: 1116917--1116998 Score: 112
Period size: 23 Copynumber: 3.6 Consensus size: 23
1116907 TGGCACTATA
*
1116917 GTGCAATTCTACGCGGCACTCCG
1 GTGCAATTCTACGCGGCACTTCG
* *
1116940 GTGTAATTCTACGTGGCACTTCG
1 GTGCAATTCTACGCGGCACTTCG
1116963 GTGCAATTCTAC-CTGGCACTTCG
1 GTGCAATTCTACGC-GGCACTTCG
*
1116986 GTGCAATTATACG
1 GTGCAATTCTACG
1116999 AGTTATGGTG
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
23 51 1.00
ACGTcount: A:0.20, C:0.27, G:0.24, T:0.29
Consensus pattern (23 bp):
GTGCAATTCTACGCGGCACTTCG
Found at i:1119748 original size:22 final size:22
Alignment explanation
Indices: 1119705--1119749 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
1119695 GATGTTTGAG
*
1119705 CAGTCATAGGGGTATTGATACC
1 CAGTCATAGGGGTATCGATACC
*
1119727 CAGTCATAGGGGTATCGGTACC
1 CAGTCATAGGGGTATCGATACC
1119749 C
1 C
1119750 TGGGTATTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.24, C:0.22, G:0.29, T:0.24
Consensus pattern (22 bp):
CAGTCATAGGGGTATCGATACC
Found at i:1119764 original size:37 final size:37
Alignment explanation
Indices: 1119714--1119785 Score: 126
Period size: 37 Copynumber: 1.9 Consensus size: 37
1119704 GCAGTCATAG
*
1119714 GGGTATTGATACCCAGTCATAGGGGTATCGGTACCCT
1 GGGTATTGATACCCAGTCATAGGGGTATCAGTACCCT
*
1119751 GGGTATTGATACCCATTCATAGGGGTATCAGTACC
1 GGGTATTGATACCCAGTCATAGGGGTATCAGTACC
1119786 TCTTAGCATT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.28
Consensus pattern (37 bp):
GGGTATTGATACCCAGTCATAGGGGTATCAGTACCCT
Found at i:1127061 original size:20 final size:20
Alignment explanation
Indices: 1127033--1127083 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
1127023 AGTGAACTTG
* *
1127033 GTATTGATACCAC-CCTGCGA
1 GTATCGATACCACACCTAC-A
1127053 GTATCGATACCACACCTACA
1 GTATCGATACCACACCTACA
1127073 GTATCGATACC
1 GTATCGATACC
1127084 CATTTATTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 24 0.86
21 4 0.14
ACGTcount: A:0.29, C:0.31, G:0.16, T:0.24
Consensus pattern (20 bp):
GTATCGATACCACACCTACA
Found at i:1135302 original size:21 final size:23
Alignment explanation
Indices: 1135276--1135325 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
1135266 GAGGGAATCA
1135276 TCCCCCCATG-A-GGGAACCGAT
1 TCCCCCCATGAAGGGGAACCGAT
** *
1135297 TCCCCCTTTGAAGGGGAACTGAT
1 TCCCCCCATGAAGGGGAACCGAT
1135320 TCCCCC
1 TCCCCC
1135326 TACAGGGGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 8 0.33
22 1 0.04
23 15 0.62
ACGTcount: A:0.20, C:0.38, G:0.22, T:0.20
Consensus pattern (23 bp):
TCCCCCCATGAAGGGGAACCGAT
Found at i:1136048 original size:21 final size:21
Alignment explanation
Indices: 1136024--1136063 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1136014 ACCGTCAACC
*
1136024 AAATCCACTTCCAAATCCTCA
1 AAATCCAATTCCAAATCCTCA
* *
1136045 AAATCTAATTCCTAATCCT
1 AAATCCAATTCCAAATCCT
1136064 AATCCTATTG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.38, C:0.33, G:0.00, T:0.30
Consensus pattern (21 bp):
AAATCCAATTCCAAATCCTCA
Found at i:1137324 original size:16 final size:18
Alignment explanation
Indices: 1137305--1137338 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
1137295 AATTTGTGGA
1137305 TTGATT-GATTT-TGAAT
1 TTGATTGGATTTATGAAT
1137321 TTGATTGGATTTATGAAT
1 TTGATTGGATTTATGAAT
1137339 GGTGAGAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 5 0.31
18 5 0.31
ACGTcount: A:0.26, C:0.00, G:0.21, T:0.53
Consensus pattern (18 bp):
TTGATTGGATTTATGAAT
Found at i:1139929 original size:13 final size:12
Alignment explanation
Indices: 1139895--1139920 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1139885 GATAACTCTA
1139895 TTTAAAAAATAG
1 TTTAAAAAATAG
1139907 TTTAAAAAATAG
1 TTTAAAAAATAG
1139919 TT
1 TT
1139921 GTACAAAATT
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:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (12 bp):
TTTAAAAAATAG
Found at i:1144138 original size:19 final size:19
Alignment explanation
Indices: 1144114--1144188 Score: 123
Period size: 19 Copynumber: 3.9 Consensus size: 19
1144104 ATGACCAATA
* *
1144114 AAATCGTAATGCGATCTTT
1 AAATCGTAACGCGATCTCT
*
1144133 AAATCGCAACGCGATCTCT
1 AAATCGTAACGCGATCTCT
1144152 AAATCGTAACGCGATCTCT
1 AAATCGTAACGCGATCTCT
1144171 AAATCGTAACGCGATCTC
1 AAATCGTAACGCGATCTC
1144189 CAGTATCGCA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 52 1.00
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.27
Consensus pattern (19 bp):
AAATCGTAACGCGATCTCT
Found at i:1144237 original size:20 final size:20
Alignment explanation
Indices: 1144214--1144387 Score: 131
Period size: 20 Copynumber: 8.6 Consensus size: 20
1144204 GTTTTCAAAT
*
1144214 TCGCAACGCGATTTTGACAA
1 TCGCAACGCGATTCTGACAA
* * *
1144234 TCGCAATGCGAATATGTA-AA
1 TCGCAACGCGATTCTG-ACAA
* *
1144254 TCGCAACGCAATTCTGACTA
1 TCGCAACGCGATTCTGACAA
**
1144274 TCGCAACGCGATAAT-ACATAA
1 TCGCAACGCGATTCTGAC--AA
*
1144295 TCGCAACGCGATTCTGACCA
1 TCGCAACGCGATTCTGACAA
1144315 TCGCAACGCGATTCTGATC-A
1 TCGCAACGCGATTCTGA-CAA
* **
1144335 TCGCAACGTGATAAT-ACATAA
1 TCGCAACGCGATTCTGAC--AA
* * *
1144356 TCGCAATGCTATTCTGACTA
1 TCGCAACGCGATTCTGACAA
1144376 TCGCAACGCGAT
1 TCGCAACGCGAT
1144388 AATACAAAAT
Statistics
Matches: 118, Mismatches: 26, Indels: 20
0.72 0.16 0.12
Matches are distributed among these distances:
18 1 0.01
19 4 0.03
20 82 0.69
21 27 0.23
22 4 0.03
ACGTcount: A:0.32, C:0.26, G:0.18, T:0.24
Consensus pattern (20 bp):
TCGCAACGCGATTCTGACAA
Found at i:1144359 original size:41 final size:41
Alignment explanation
Indices: 1144314--1144409 Score: 131
Period size: 41 Copynumber: 2.3 Consensus size: 41
1144304 GATTCTGACC
* * *
1144314 ATCGCAACGCGATTCTGA-TCATCGCAACGTGATAATACATA
1 ATCGCAATGCGATTCTGACT-ATCGCAACGCGATAATACAAA
*
1144355 ATCGCAATGCTATTCTGACTATCGCAACGCGATAATACAAA
1 ATCGCAATGCGATTCTGACTATCGCAACGCGATAATACAAA
*
1144396 ATCTCAATGCGATT
1 ATCGCAATGCGATT
1144410 TTCAAAGAGC
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
41 47 0.98
42 1 0.02
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.26
Consensus pattern (41 bp):
ATCGCAATGCGATTCTGACTATCGCAACGCGATAATACAAA
Found at i:1144385 original size:61 final size:61
Alignment explanation
Indices: 1144253--1144387 Score: 209
Period size: 61 Copynumber: 2.2 Consensus size: 61
1144243 GAATATGTAA
*
1144253 ATCGCAACGCAATTCTGACTATCGCAACGCGATAATACATAATCGCAACGCGATTCTGACC
1 ATCGCAACGCGATTCTGACTATCGCAACGCGATAATACATAATCGCAACGCGATTCTGACC
* * * *
1144314 ATCGCAACGCGATTCTGA-TCATCGCAACGTGATAATACATAATCGCAATGCTATTCTGACT
1 ATCGCAACGCGATTCTGACT-ATCGCAACGCGATAATACATAATCGCAACGCGATTCTGACC
1144375 ATCGCAACGCGAT
1 ATCGCAACGCGAT
1144388 AATACAAAAT
Statistics
Matches: 68, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
60 1 0.01
61 67 0.99
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.24
Consensus pattern (61 bp):
ATCGCAACGCGATTCTGACTATCGCAACGCGATAATACATAATCGCAACGCGATTCTGACC
Found at i:1144578 original size:22 final size:22
Alignment explanation
Indices: 1144553--1144599 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
1144543 CTACGGCGAC
1144553 ATCCGTCCCCATCTCCGACGAA
1 ATCCGTCCCCATCTCCGACGAA
1144575 ATCCGTCCCCATCTCCGACGAA
1 ATCCGTCCCCATCTCCGACGAA
1144597 ATC
1 ATC
1144600 AGTCTATCTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.23, C:0.45, G:0.13, T:0.19
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCGACGAA
Found at i:1145003 original size:20 final size:20
Alignment explanation
Indices: 1144978--1145094 Score: 68
Period size: 20 Copynumber: 6.2 Consensus size: 20
1144968 AAAATCGCAA
1144978 CGATAGTCAAATTCGCGTTG
1 CGATAGTCAAATTCGCGTTG
** **
1144998 CGATAGTCATTTTCATGTTG
1 CGATAGTCAAATTCGCGTTG
** *
1145018 CGATTTTC-ATTTCGCGTTG
1 CGATAGTCAAATTCGCGTTG
* *
1145037 CGAT--T---A-TCTCGTTA
1 CGATAGTCAAATTCGCGTTG
1145051 CGATAGTCAAATTCGCGTTG
1 CGATAGTCAAATTCGCGTTG
* ** *
1145071 CGATAATCATTTTCGTGTTG
1 CGATAGTCAAATTCGCGTTG
1145091 CGAT
1 CGAT
1145095 TTTAAGTTTC
Statistics
Matches: 73, Mismatches: 18, Indels: 12
0.71 0.17 0.12
Matches are distributed among these distances:
14 10 0.14
16 1 0.01
17 1 0.01
19 13 0.18
20 48 0.66
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.39
Consensus pattern (20 bp):
CGATAGTCAAATTCGCGTTG
Found at i:1145116 original size:73 final size:73
Alignment explanation
Indices: 1144977--1145116 Score: 192
Period size: 73 Copynumber: 1.9 Consensus size: 73
1144967 GAAAATCGCA
* * * ***
1144977 ACGATAGTCAAATTCGCGTTGCGATAGTCATTTTCATGTTGCGATTTTCATTTCGCGTTGCGATT
1 ACGATAGTCAAATTCGCGTTGCGATAATCATTTTCATGTTGCGATTTTAATTTCGAGAAACGATT
1145042 ATCTCGTT
66 ATCTCGTT
* *
1145050 ACGATAGTCAAATTCGCGTTGCGATAATCATTTTCGTGTTGCGATTTTAAGTTTC-AGAAACTAT
1 ACGATAGTCAAATTCGCGTTGCGATAATCATTTTCATGTTGCGATTTTAA-TTTCGAGAAACGAT
1145114 TAT
65 TAT
1145117 TCTTCTGCAA
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
73 54 0.93
74 4 0.07
ACGTcount: A:0.24, C:0.17, G:0.19, T:0.40
Consensus pattern (73 bp):
ACGATAGTCAAATTCGCGTTGCGATAATCATTTTCATGTTGCGATTTTAATTTCGAGAAACGATT
ATCTCGTT
Found at i:1147102 original size:20 final size:19
Alignment explanation
Indices: 1147077--1147184 Score: 75
Period size: 20 Copynumber: 5.8 Consensus size: 19
1147067 CACAACGCGA
1147077 AAATGACTATCGCAAAGCAG
1 AAATGACTATCGCAAAGC-G
*
1147097 AAATGACTATCGCAACGCG
1 AAATGACTATCGCAAAGCG
*
1147116 AATTTGACTATCGCAACAG-G
1 AA-ATGACTATCGCAA-AGCG
*
1147136 --AT-A--ATCGCAATGCG
1 AAATGACTATCGCAAAGCG
* ** *
1147150 AAATAAAAATCGCAATGCG
1 AAATGACTATCGCAAAGCG
1147169 AAAATGACTATCGCAA
1 -AAATGACTATCGCAA
1147185 CGCAAATTTA
Statistics
Matches: 71, Mismatches: 8, Indels: 18
0.73 0.08 0.19
Matches are distributed among these distances:
13 1 0.01
14 8 0.11
16 3 0.04
17 2 0.03
19 14 0.20
20 42 0.59
21 1 0.01
ACGTcount: A:0.43, C:0.20, G:0.19, T:0.19
Consensus pattern (19 bp):
AAATGACTATCGCAAAGCG
Found at i:1147217 original size:19 final size:19
Alignment explanation
Indices: 1147195--1147231 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1147185 CGCAAATTTA
1147195 GTTTCGCGTTGCGATTTTG
1 GTTTCGCGTTGCGATTTTG
*
1147214 GTTTCGCTTTGCGATTTT
1 GTTTCGCGTTGCGATTTT
1147232 CTCGTTGCGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.05, C:0.16, G:0.27, T:0.51
Consensus pattern (19 bp):
GTTTCGCGTTGCGATTTTG
Found at i:1147243 original size:33 final size:33
Alignment explanation
Indices: 1147196--1147275 Score: 106
Period size: 33 Copynumber: 2.4 Consensus size: 33
1147186 GCAAATTTAG
* * *
1147196 TTTCGCGTTGCGATTTTGGTTTCGCTTTGCGAT
1 TTTCCCGTTGCGATTTTGATTTCGCATTGCGAT
* *
1147229 TTTCTCGTTGCGATTTTTATTTCGCATTGCGAT
1 TTTCCCGTTGCGATTTTGATTTCGCATTGCGAT
*
1147262 TATCCCGTTGCGAT
1 TTTCCCGTTGCGAT
1147276 AGTCAAATTC
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.10, C:0.20, G:0.23, T:0.47
Consensus pattern (33 bp):
TTTCCCGTTGCGATTTTGATTTCGCATTGCGAT
Found at i:1147258 original size:19 final size:18
Alignment explanation
Indices: 1147191--1147262 Score: 53
Period size: 19 Copynumber: 4.0 Consensus size: 18
1147181 GCAACGCAAA
1147191 TTTAGTTTCGCGTTGCGATT
1 TTTA-TTTCGC-TTGCGATT
**
1147211 TTGGTTTCGCTTTGCGA--
1 TTTATTTCGC-TTGCGATT
*
1147228 TTT-TCTCG-TTGCGATT
1 TTTATTTCGCTTGCGATT
1147244 TTTATTTCGCATTGCGATT
1 TTTATTTCGC-TTGCGATT
1147263 ATCCCGTTGC
Statistics
Matches: 41, Mismatches: 6, Indels: 11
0.71 0.10 0.19
Matches are distributed among these distances:
14 6 0.15
16 7 0.17
17 6 0.15
19 20 0.49
20 2 0.05
ACGTcount: A:0.10, C:0.17, G:0.22, T:0.51
Consensus pattern (18 bp):
TTTATTTCGCTTGCGATT
Found at i:1147912 original size:21 final size:21
Alignment explanation
Indices: 1147822--1147921 Score: 67
Period size: 21 Copynumber: 4.8 Consensus size: 21
1147812 CCGACTCACA
* *
1147822 TGTCATTGTTCAAGAGGCCTC
1 TGTCATCGTTCAAGAGGCCCC
* * *
1147843 T-CCTATCGTTCAAGAGTCCCA
1 TGTC-ATCGTTCAAGAGGCCCC
* ** *
1147864 TATCATCCCTCAAGAGTCCCC
1 TGTCATCGTTCAAGAGGCCCC
**
1147885 TCCCATCGTTCAAGAGGCCCC
1 TGTCATCGTTCAAGAGGCCCC
* *
1147906 TGTCATCATTGAAGAG
1 TGTCATCGTTCAAGAG
1147922 TTCCCTCCCA
Statistics
Matches: 59, Mismatches: 18, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
20 1 0.02
21 57 0.97
22 1 0.02
ACGTcount: A:0.23, C:0.32, G:0.18, T:0.27
Consensus pattern (21 bp):
TGTCATCGTTCAAGAGGCCCC
Found at i:1147912 original size:42 final size:42
Alignment explanation
Indices: 1147831--1147931 Score: 112
Period size: 42 Copynumber: 2.4 Consensus size: 42
1147821 ATGTCATTGT
* * * * *
1147831 TCAAGAGGCCTCTCCTATCGTTCAAGAGTCCCATATCATCCC
1 TCAAGAGTCCCCTCCCATCGTTCAAGAGGCCCATATCATCAC
* * *
1147873 TCAAGAGTCCCCTCCCATCGTTCAAGAGGCCCCTGTCATCAT
1 TCAAGAGTCCCCTCCCATCGTTCAAGAGGCCCATATCATCAC
* *
1147915 TGAAGAGTTCCCTCCCA
1 TCAAGAGTCCCCTCCCA
1147932 CTATTCAAGT
Statistics
Matches: 49, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.23, C:0.37, G:0.16, T:0.25
Consensus pattern (42 bp):
TCAAGAGTCCCCTCCCATCGTTCAAGAGGCCCATATCATCAC
Found at i:1149501 original size:20 final size:20
Alignment explanation
Indices: 1149476--1149529 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
1149466 AGGTACAATT
*
1149476 TCGCAACGCTAAA-CTCAAAA
1 TCGCAACGCGAAAGCT-AAAA
*
1149496 TCGCAATGCGAAAGCTAAAA
1 TCGCAACGCGAAAGCTAAAA
*
1149516 TTGCAACGCGAAAG
1 TCGCAACGCGAAAG
1149530 TCAATTCGCG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 27 0.93
21 2 0.07
ACGTcount: A:0.43, C:0.24, G:0.19, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGAAAGCTAAAA
Found at i:1149598 original size:34 final size:34
Alignment explanation
Indices: 1149538--1149674 Score: 116
Period size: 34 Copynumber: 3.9 Consensus size: 34
1149528 AGTCAATTCG
* * *
1149538 CGTTGCGATAGTCTAATATGCTTTGCGATTTTCT
1 CGTTGCGATAGTCAAATACGCGTTGCGATTTTCT
* *
1149572 CGTTGCGATAGTCAAATACCCGTTGCGATAACCAAATTCGT
1 CGTTGCGATAGTCAAATACGCGTTGCGAT------TTTC-T
**
1149613 -GTTGCGATAGTCAAATTTGCGTTGCGATTTT-T
1 CGTTGCGATAGTCAAATACGCGTTGCGATTTTCT
*
1149645 GCGTTGCGATAGTCAAATTCGCGTTGCGAT
1 -CGTTGCGATAGTCAAATACGCGTTGCGAT
1149675 AATCAAATTC
Statistics
Matches: 84, Mismatches: 10, Indels: 18
0.75 0.09 0.16
Matches are distributed among these distances:
32 1 0.01
34 54 0.64
40 28 0.33
41 1 0.01
ACGTcount: A:0.22, C:0.19, G:0.23, T:0.36
Consensus pattern (34 bp):
CGTTGCGATAGTCAAATACGCGTTGCGATTTTCT
Found at i:1149629 original size:20 final size:20
Alignment explanation
Indices: 1149572--1149710 Score: 146
Period size: 20 Copynumber: 7.2 Consensus size: 20
1149562 GCGATTTTCT
* *
1149572 CGTTGCGATAGTCAAATACC
1 CGTTGCGATAGTCAAATTCG
**
1149592 CGTTGCGATAACCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* *
1149612 TGTTGCGATAGTCAAATTTG
1 CGTTGCGATAGTCAAATTCG
*
1149632 CGTTGCGAT--T----TTTG
1 CGTTGCGATAGTCAAATTCG
1149646 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* *
1149666 CGTTGCGATAATCAAATTCA
1 CGTTGCGATAGTCAAATTCG
*
1149686 CGTTACGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
1149706 CGTTG
1 CGTTG
1149711 TAATATTCAA
Statistics
Matches: 97, Mismatches: 16, Indels: 12
0.78 0.13 0.10
Matches are distributed among these distances:
14 13 0.13
16 1 0.01
18 1 0.01
20 82 0.85
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.32
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:1149647 original size:14 final size:14
Alignment explanation
Indices: 1149628--1149654 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1149618 GATAGTCAAA
1149628 TTTGCGTTGCGATT
1 TTTGCGTTGCGATT
1149642 TTTGCGTTGCGAT
1 TTTGCGTTGCGAT
1149655 AGTCAAATTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.15, G:0.30, T:0.48
Consensus pattern (14 bp):
TTTGCGTTGCGATT
Found at i:1149653 original size:74 final size:74
Alignment explanation
Indices: 1149532--1149710 Score: 252
Period size: 74 Copynumber: 2.4 Consensus size: 74
1149522 CGCGAAAGTC
* * *
1149532 AATTCGCGTTGCGATAGTCTAATATGCTTTGCGATTTTCTCGTTGCGATAGTCAAATACCCGTTG
1 AATTCGCGTTGCGATAGTCAAATTTGCGTTGCGATTTTCTCGTTGCGATAGTCAAATACCCGTTG
1149597 CGATAACCA
66 CGATAACCA
* * *
1149606 AATTCGTGTTGCGATAGTCAAATTTGCGTTGCGATTTT-TGCGTTGCGATAGTCAAATTCGCGTT
1 AATTCGCGTTGCGATAGTCAAATTTGCGTTGCGATTTTCT-CGTTGCGATAGTCAAATACCCGTT
*
1149670 GCGATAATCA
65 GCGATAACCA
* * *
1149680 AATTCACGTTACGATAGTCAAATTCGCGTTG
1 AATTCGCGTTGCGATAGTCAAATTTGCGTTG
1149711 TAATATTCAA
Statistics
Matches: 93, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
73 1 0.01
74 92 0.99
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.35
Consensus pattern (74 bp):
AATTCGCGTTGCGATAGTCAAATTTGCGTTGCGATTTTCTCGTTGCGATAGTCAAATACCCGTTG
CGATAACCA
Found at i:1149721 original size:40 final size:40
Alignment explanation
Indices: 1149646--1149722 Score: 118
Period size: 40 Copynumber: 1.9 Consensus size: 40
1149636 GCGATTTTTG
* *
1149646 CGTTGCGATAGTCAAATTCGCGTTGCGATAATCAAATTCA
1 CGTTACGATAGTCAAATTCGCGTTGCAATAATCAAATTCA
* *
1149686 CGTTACGATAGTCAAATTCGCGTTGTAATATTCAAAT
1 CGTTACGATAGTCAAATTCGCGTTGCAATAATCAAAT
1149723 GAATGTGTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Consensus pattern (40 bp):
CGTTACGATAGTCAAATTCGCGTTGCAATAATCAAATTCA
Found at i:1152091 original size:14 final size:14
Alignment explanation
Indices: 1152072--1152108 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1152062 TCTCGTGGCA
1152072 TTTTCTTCGGGGAC
1 TTTTCTTCGGGGAC
*
1152086 TTTTCTTCGGGGAT
1 TTTTCTTCGGGGAC
1152100 TTCTTCTTC
1 TT-TTCTTC
1152109 TTCTTCTTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.05, C:0.22, G:0.22, T:0.51
Consensus pattern (14 bp):
TTTTCTTCGGGGAC
Found at i:1152326 original size:24 final size:24
Alignment explanation
Indices: 1152292--1152345 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1152282 CTAAAACATC
1152292 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
1152316 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
1152340 ATCAAA
1 ATCAAA
1152346 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:1153206 original size:21 final size:21
Alignment explanation
Indices: 1153180--1153255 Score: 93
Period size: 21 Copynumber: 3.7 Consensus size: 21
1153170 GACAGTCAAA
1153180 ATCGCGTTGCGATTATGTATT
1 ATCGCGTTGCGATTATGTATT
*
1153201 ATCGCGCTGCGATTATGTATT
1 ATCGCGTTGCGATTATGTATT
* **
1153222 ATCGCGTTACGA-TA-GTCAGA
1 ATCGCGTTGCGATTATGT-ATT
1153242 ATCGCGTTGCGATT
1 ATCGCGTTGCGATT
1153256 TACATATTCG
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
19 2 0.04
20 14 0.30
21 31 0.66
ACGTcount: A:0.21, C:0.18, G:0.25, T:0.36
Consensus pattern (21 bp):
ATCGCGTTGCGATTATGTATT
Found at i:1153289 original size:22 final size:20
Alignment explanation
Indices: 1153243--1153289 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 20
1153233 ATAGTCAGAA
* *
1153243 TCGCGTTGCGATTTACATAT
1 TCGCGTTCCGATTTACAAAT
1153263 TCGCGTTCCGATTTTACAAAAT
1 TCGCGTTCCGA-TTTAC-AAAT
1153285 TCGCG
1 TCGCG
1153290 ATTTTACAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 10 0.43
21 5 0.22
22 8 0.35
ACGTcount: A:0.21, C:0.23, G:0.19, T:0.36
Consensus pattern (20 bp):
TCGCGTTCCGATTTACAAAT
Found at i:1153393 original size:20 final size:19
Alignment explanation
Indices: 1153370--1153415 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
1153360 GGAAACTGAT
* *
1153370 TTGCGATACTGGAGATCGCG
1 TTGCGAT-CTAGAGATCGCA
*
1153390 TTGCGATTTAGAGATCGCA
1 TTGCGATCTAGAGATCGCA
1153409 TTGCGAT
1 TTGCGAT
1153416 TTTGTTGGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.30
Consensus pattern (19 bp):
TTGCGATCTAGAGATCGCA
Found at i:1153405 original size:19 final size:19
Alignment explanation
Indices: 1153381--1153417 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1153371 TGCGATACTG
*
1153381 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTGCGATTTA
1153400 GAGATCGCATTGCGATTT
1 GAGATCGCATTGCGATTT
1153418 TGTTGGTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:1155676 original size:15 final size:15
Alignment explanation
Indices: 1155628--1155679 Score: 77
Period size: 15 Copynumber: 3.5 Consensus size: 15
1155618 ATATTTAGCT
*
1155628 GGGCGGGCGGATGTG
1 GGGCGGGCGGATGCG
* *
1155643 GGGAGAGCGGATGCG
1 GGGCGGGCGGATGCG
1155658 GGGCGGGCGGATGCG
1 GGGCGGGCGGATGCG
1155673 GGGCGGG
1 GGGCGGG
1155680 TAATGTCTCA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.10, C:0.15, G:0.67, T:0.08
Consensus pattern (15 bp):
GGGCGGGCGGATGCG
Found at i:1158397 original size:13 final size:13
Alignment explanation
Indices: 1158379--1158404 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1158369 TCTTTAAGAA
1158379 CATTCTATTTTAT
1 CATTCTATTTTAT
1158392 CATTCTATTTTAT
1 CATTCTATTTTAT
1158405 ATTAAATATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.15, G:0.00, T:0.62
Consensus pattern (13 bp):
CATTCTATTTTAT
Found at i:1161365 original size:7 final size:7
Alignment explanation
Indices: 1161353--1161383 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
1161343 GTCAAAGAAA
1161353 GTCAACG
1 GTCAACG
1161360 GTCAACG
1 GTCAACG
1161367 GTCAACG
1 GTCAACG
1161374 GTCAACG
1 GTCAACG
1161381 GTC
1 GTC
1161384 GGGTCGGGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.26, C:0.29, G:0.29, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:1161390 original size:5 final size:5
Alignment explanation
Indices: 1161380--1161459 Score: 70
Period size: 5 Copynumber: 14.8 Consensus size: 5
1161370 AACGGTCAAC
* * *
1161380 GGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG AGTCG GGTCAAC GGTCG
1 GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTC--G GGTCG
*
1161429 GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTC
1 GGTCG GGTCG GGTC--G GGTCG GGTCG GGTC
1161460 TGACCGGTCA
Statistics
Matches: 61, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
5 49 0.80
7 12 0.20
ACGTcount: A:0.09, C:0.23, G:0.50, T:0.19
Consensus pattern (5 bp):
GGTCG
Found at i:1161401 original size:22 final size:22
Alignment explanation
Indices: 1161373--1161459 Score: 165
Period size: 22 Copynumber: 4.0 Consensus size: 22
1161363 AACGGTCAAC
1161373 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
*
1161395 GGTCAACGGTCGGGTCGAGTCG
1 GGTCAACGGTCGGGTCGGGTCG
1161417 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
1161439 GGTCAACGGTCGGGTCGGGTC
1 GGTCAACGGTCGGGTCGGGTC
1161460 TGACCGGTCA
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 63 1.00
ACGTcount: A:0.10, C:0.23, G:0.48, T:0.18
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Done.