Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008531.1 Hibiscus syriacus cultivar Beakdansim tig00111409_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: 3817888
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 19
Found at i:1076432 original size:57 final size:56
Alignment explanation
Indices: 1076316--1076434 Score: 154
Period size: 57 Copynumber: 2.1 Consensus size: 56
1076306 AGCGCATCGA
* *
1076316 TGCATGAAATGCATTCGATGTTTCAAAATAGCCAGAGTGCATCGATGCATGGCTGG
1 TGCATCAAATGCATTCGATGTTTCAAAATAGCCAGAGTGCATCGATGCATAGCTGG
*
1076372 TGCATCAAATGCATTCGATGTTTTCATAAA-A-CTCTGAGTGCATCGATGCATAGCAT-G
1 TGCATCAAATGCATTCGATG-TTTCA-AAATAGC-CAGAGTGCATCGATGCATAGC-TGG
1076429 TGCATC
1 TGCATC
1076435 GATGGATGAA
Statistics
Matches: 56, Mismatches: 3, Indels: 7
0.85 0.05 0.11
Matches are distributed among these distances:
56 20 0.36
57 32 0.57
58 4 0.07
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (56 bp):
TGCATCAAATGCATTCGATGTTTCAAAATAGCCAGAGTGCATCGATGCATAGCTGG
Found at i:1079196 original size:23 final size:22
Alignment explanation
Indices: 1079166--1079247 Score: 85
Period size: 23 Copynumber: 3.6 Consensus size: 22
1079156 GCATGACCTT
1079166 GTGCATCGATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
* * *
1079188 AGTGCATCGGTGCACCTTC-ATG
1 -GTGCATCGATGCACATTCAAGG
*
1079210 GTGTATCGATGCACATTCAAAGG
1 GTGCATCGATGCACATTC-AAGG
*
1079233 GATGCATCGGTGCAC
1 G-TGCATCGATGCAC
1079248 TATTAAGTGT
Statistics
Matches: 47, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
21 15 0.32
22 2 0.04
23 19 0.40
24 11 0.23
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.24
Consensus pattern (22 bp):
GTGCATCGATGCACATTCAAGG
Found at i:1079222 original size:21 final size:22
Alignment explanation
Indices: 1079166--1079228 Score: 74
Period size: 21 Copynumber: 2.9 Consensus size: 22
1079156 GCATGACCTT
1079166 GTGCATCGATGCACATTCAAGGA
1 GTGCATCGATGCACATTC-AGGA
* * *
1079189 GTGCATCGGTGCACCTTCATG-
1 GTGCATCGATGCACATTCAGGA
*
1079210 GTGTATCGATGCACATTCA
1 GTGCATCGATGCACATTCA
1079229 AAGGGATGCA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
21 16 0.47
22 2 0.06
23 16 0.47
ACGTcount: A:0.24, C:0.24, G:0.25, T:0.27
Consensus pattern (22 bp):
GTGCATCGATGCACATTCAGGA
Found at i:1079258 original size:44 final size:44
Alignment explanation
Indices: 1079170--1079266 Score: 128
Period size: 44 Copynumber: 2.2 Consensus size: 44
1079160 GACCTTGTGC
*
1079170 ATCGATGCACATTCAAGGAGTGCATCGGTGCACCTTCATGGTGT
1 ATCGATGCACATTCAAGGAGTGCATCGGTGCACCTTCATAGTGT
*
1079214 ATCGATGCACATTCAAAGG-GATGCATCGGTGCA-CTATTA-AGTGT
1 ATCGATGCACATTC-AAGGAG-TGCATCGGTGCACCT-TCATAGTGT
1079258 ATCGATGCA
1 ATCGATGCA
1079267 TGAAGCACAA
Statistics
Matches: 48, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
44 30 0.62
45 18 0.38
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.27
Consensus pattern (44 bp):
ATCGATGCACATTCAAGGAGTGCATCGGTGCACCTTCATAGTGT
Found at i:1085105 original size:20 final size:20
Alignment explanation
Indices: 1085080--1085143 Score: 128
Period size: 20 Copynumber: 3.2 Consensus size: 20
1085070 GTGCATCGAC
1085080 GCATGGCTGGTGCATCAAAT
1 GCATGGCTGGTGCATCAAAT
1085100 GCATGGCTGGTGCATCAAAT
1 GCATGGCTGGTGCATCAAAT
1085120 GCATGGCTGGTGCATCAAAT
1 GCATGGCTGGTGCATCAAAT
1085140 GCAT
1 GCAT
1085144 TCGATGTTTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.25, C:0.20, G:0.30, T:0.25
Consensus pattern (20 bp):
GCATGGCTGGTGCATCAAAT
Found at i:1088533 original size:3 final size:3
Alignment explanation
Indices: 1088527--1088567 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
1088517 TTTCTTCTTG
* *
1088527 ATT ATT AAT ATT ACT ATT ATT ATT ATT A-T ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1088568 GATATGTTGA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:1089989 original size:13 final size:13
Alignment explanation
Indices: 1089973--1089997 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1089963 GTCCATATAT
1089973 TTATTTATTTAAA
1 TTATTTATTTAAA
1089986 TTATTTATTTAA
1 TTATTTATTTAA
1089998 TTTTATTCCT
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:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TTATTTATTTAAA
Found at i:1090097 original size:5 final size:5
Alignment explanation
Indices: 1090087--1090382 Score: 413
Period size: 5 Copynumber: 60.4 Consensus size: 5
1090077 TTATTTTTAT
1090087 TATTA TATTA TATTA TATT- TA-TA TTATTA TATTATA TATTA TATTA
1 TATTA TATTA TATTA TATTA TATTA -TATTA TA-T-TA TATTA TATTA
1090133 TATTA TATTA TATTA TATTA TATTA TA-T- TATTA TATTA TATTA TA-T-
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
1090179 TATTA TATTA TATTA TATTA TATTA TATTA TATT- TATTTA TATTA TATTA
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TA-TTA TATTA TATTA
1090229 TA-T- TATTA TATTA TATTA TATTA TATTA TA-TA TTATTA TATTA TATTA
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA -TATTA TATTA TATTA
*
1090277 TATTA TATTA TATTA T-TTA TTATTT TATTA TATTA TATTATA TATTA
1 TATTA TATTA TATTA TATTA -TATTA TATTA TATTA TA-T-TA TATTA
1090324 TATTA TATTA TATTA TATTA TATTA TA-TA TATTA TA-T- TATTA TATTA
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
1090371 TATTA TATTA TA
1 TATTA TATTA TA
1090383 CATTATATAT
Statistics
Matches: 267, Mismatches: 2, Indels: 44
0.85 0.01 0.14
Matches are distributed among these distances:
3 9 0.03
4 21 0.08
5 217 0.81
6 12 0.04
7 8 0.03
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
TATTA
Found at i:1093290 original size:21 final size:19
Alignment explanation
Indices: 1093246--1093284 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
1093236 TGCCAACACT
1093246 ACAAACTTCAATTTTTTTA
1 ACAAACTTCAATTTTTTTA
1093265 ACAAACTTCAATTTTTTTA
1 ACAAACTTCAATTTTTTTA
1093284 A
1 A
1093285 GACAAATCAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.38, C:0.15, G:0.00, T:0.46
Consensus pattern (19 bp):
ACAAACTTCAATTTTTTTA
Found at i:1096878 original size:20 final size:20
Alignment explanation
Indices: 1096853--1096896 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
1096843 ATGTGGTGTT
* *
1096853 TGATTAATTTTTCATGTATA
1 TGATTAACTTTTCATGCATA
*
1096873 TGATTAACTTTTCCTGCATA
1 TGATTAACTTTTCATGCATA
1096893 TGAT
1 TGAT
1096897 ATATCTAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.27, C:0.11, G:0.11, T:0.50
Consensus pattern (20 bp):
TGATTAACTTTTCATGCATA
Found at i:1101520 original size:19 final size:19
Alignment explanation
Indices: 1101480--1101544 Score: 51
Period size: 22 Copynumber: 3.2 Consensus size: 19
1101470 ATCTAATTTT
* *
1101480 GGTATCGATACCGGTAG-GG
1 GGTATCGATACC-ATAGTAG
1101499 GGTATCGATACCATAGTAGG
1 GGTATCGATACCATAGTA-G
*
1101519 GTAGTATCGATACCATGGTAAG
1 G--GTATCGATACCATAGT-AG
1101541 GGTA
1 GGTA
1101545 CCATGGTATC
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
18 3 0.08
19 12 0.32
20 5 0.13
22 17 0.45
23 1 0.03
ACGTcount: A:0.28, C:0.14, G:0.34, T:0.25
Consensus pattern (19 bp):
GGTATCGATACCATAGTAG
Found at i:1101528 original size:22 final size:23
Alignment explanation
Indices: 1101500--1101544 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
1101490 CCGGTAGGGG
1101500 GTATCGATACCATAGT-AGGGTA
1 GTATCGATACCATAGTAAGGGTA
*
1101522 GTATCGATACCATGGTAAGGGTA
1 GTATCGATACCATAGTAAGGGTA
1101545 CCATGGTATC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 15 0.71
23 6 0.29
ACGTcount: A:0.31, C:0.13, G:0.29, T:0.27
Consensus pattern (23 bp):
GTATCGATACCATAGTAAGGGTA
Found at i:1101560 original size:14 final size:14
Alignment explanation
Indices: 1101522--1101560 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
1101512 TAGTAGGGTA
1101522 GTATCGATACCATG
1 GTATCGATACCATG
** *
1101536 GTAAGGGTACCATG
1 GTATCGATACCATG
1101550 GTATCGATACC
1 GTATCGATACC
1101561 TGGCAACGTC
Statistics
Matches: 19, Mismatches: 6, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.26
Consensus pattern (14 bp):
GTATCGATACCATG
Found at i:1101996 original size:2 final size:2
Alignment explanation
Indices: 1101944--1101982 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1101934 GTTTTAATAA
1101944 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1101983 GTGCATCGAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1102074 original size:55 final size:55
Alignment explanation
Indices: 1102015--1102306 Score: 386
Period size: 55 Copynumber: 5.3 Consensus size: 55
1102005 TGTGTACTAT
* * * *
1102015 AGGCACTTTGTGTGTATATTCACGAAATTCATCATAAGTTGATGAATTACCGTAC
1 AGGCACTTTGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCGTAC
* * *
1102070 AGGCACTTTGTGTGCATATTCACGGAATTCATCATGAGTTGATAAATCATCATAC
1 AGGCACTTTGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCGTAC
* * *
1102125 AAGCACTTTGTGTGCATATTCATGGAATTCATCATGAGTTGATGAATCACCATAC
1 AGGCACTTTGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCGTAC
* * *
1102180 AGGCACTATATGTGCATATTCACGGAATTCATCATGAGTTGATGAATCATCGTAC
1 AGGCACTTTGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCGTAC
* * * ** *
1102235 ATGCACTTTGTGTGCATAATCCACGGAATTCATCATAAAATGAAGAATCACCGTAC
1 AGGCACTTTGTGTGCAT-ATTCACGGAATTCATCATGAGTTGATGAATCACCGTAC
* *
1102291 AAGCACTATGTGTGCA
1 AGGCACTTTGTGTGCA
1102307 GCCCACAAAA
Statistics
Matches: 208, Mismatches: 28, Indels: 1
0.88 0.12 0.00
Matches are distributed among these distances:
55 162 0.78
56 46 0.22
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Consensus pattern (55 bp):
AGGCACTTTGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCGTAC
Found at i:1102343 original size:110 final size:110
Alignment explanation
Indices: 1102017--1102306 Score: 427
Period size: 110 Copynumber: 2.6 Consensus size: 110
1102007 TGTACTATAG
* * * *
1102017 GCACTTTGTGTGTATATTCACGAAATTCATCATAAGTTGATGAATTACCGTACAGGCACTTTGTG
1 GCACTTTGTGTGCATATTCACGGAATTCATCATAAGTTGATGAATCACCGTACAGGCACTATGTG
* *
1102082 TGCATATTCACGGAATTCATCATGAGTTGATAAATCATCATACAA
66 TGCATATTCACGGAATTCATCATGAGTTGATGAATCATCGTACAA
* * * *
1102127 GCACTTTGTGTGCATATTCATGGAATTCATCATGAGTTGATGAATCACCATACAGGCACTATATG
1 GCACTTTGTGTGCATATTCACGGAATTCATCATAAGTTGATGAATCACCGTACAGGCACTATGTG
*
1102192 TGCATATTCACGGAATTCATCATGAGTTGATGAATCATCGTACAT
66 TGCATATTCACGGAATTCATCATGAGTTGATGAATCATCGTACAA
* ** * *
1102237 GCACTTTGTGTGCATAATCCACGGAATTCATCATAAAATGAAGAATCACCGTACAAGCACTATGT
1 GCACTTTGTGTGCAT-ATTCACGGAATTCATCATAAGTTGATGAATCACCGTACAGGCACTATGT
1102302 GTGCA
65 GTGCA
1102307 GCCCACAAAA
Statistics
Matches: 159, Mismatches: 20, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
110 114 0.72
111 45 0.28
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Consensus pattern (110 bp):
GCACTTTGTGTGCATATTCACGGAATTCATCATAAGTTGATGAATCACCGTACAGGCACTATGTG
TGCATATTCACGGAATTCATCATGAGTTGATGAATCATCGTACAA
Found at i:1102351 original size:110 final size:110
Alignment explanation
Indices: 1102015--1102351 Score: 426
Period size: 110 Copynumber: 3.1 Consensus size: 110
1102005 TGTGTACTAT
* * * *
1102015 AGGCACTTTGTGTGTATATTCACGAAATTCATCATAAGTTGATGAATTACCGTACAGGCACTTTG
1 AGGCACTTTGTGTGCATATTCACGGAATTCATCATAAGTTGATGAATCACCGTACAGGCACTATG
* *
1102080 TGTGCATATTCACGGAATTCATCATGAGTTGATAAATCATCATAC
66 TGTGCATATTCACGGAATTCATCATGAGTTGATGAATCATCGTAC
* * * * *
1102125 AAGCACTTTGTGTGCATATTCATGGAATTCATCATGAGTTGATGAATCACCATACAGGCACTATA
1 AGGCACTTTGTGTGCATATTCACGGAATTCATCATAAGTTGATGAATCACCGTACAGGCACTATG
1102190 TGTGCATATTCACGGAATTCATCATGAGTTGATGAATCATCGTAC
66 TGTGCATATTCACGGAATTCATCATGAGTTGATGAATCATCGTAC
* * ** * *
1102235 ATGCACTTTGTGTGCATAATCCACGGAATTCATCATAAAATGAAGAATCACCGTACAAGCACTAT
1 AGGCACTTTGTGTGCAT-ATTCACGGAATTCATCATAAGTTGATGAATCACCGTACAGGCACTAT
*** ** * *
1102300 GTGTGCA-GCCCACAAAATTCATCATGGGTTGATGAATTC-TCGTAT
65 GTGTGCATATTCACGGAATTCATCATGAGTTGATGAA-TCATCGTAC
1102345 AGGCACT
1 AGGCACT
1102352 AATAGTGCAC
Statistics
Matches: 196, Mismatches: 29, Indels: 4
0.86 0.13 0.02
Matches are distributed among these distances:
110 149 0.76
111 47 0.24
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (110 bp):
AGGCACTTTGTGTGCATATTCACGGAATTCATCATAAGTTGATGAATCACCGTACAGGCACTATG
TGTGCATATTCACGGAATTCATCATGAGTTGATGAATCATCGTAC
Found at i:1108514 original size:20 final size:19
Alignment explanation
Indices: 1108489--1108543 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 19
1108479 TGATTGAATC
*
1108489 AGTATCGATACCTATGAGG
1 AGTATCGATACCTATAAGG
*
1108508 TAGTATCAATACCATAATAAGG
1 -AGTATCGATACC-T-ATAAGG
*
1108530 GGTATCGATACCTA
1 AGTATCGATACCTA
1108544 GAAACATCGA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
19 1 0.03
20 12 0.41
21 11 0.38
22 5 0.17
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.27
Consensus pattern (19 bp):
AGTATCGATACCTATAAGG
Found at i:1108617 original size:22 final size:22
Alignment explanation
Indices: 1108584--1108627 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1108574 CTGATAGGGG
1108584 GTATCGTACCATAGT-AGGGTA
1 GTATCGTACCATAGTAAGGGTA
*
1108605 GTATCGATACCATGGTAAGGGTA
1 GTATCG-TACCATAGTAAGGGTA
1108628 TCGATATCTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 6 0.30
22 8 0.40
23 6 0.30
ACGTcount: A:0.30, C:0.14, G:0.30, T:0.27
Consensus pattern (22 bp):
GTATCGTACCATAGTAAGGGTA
Found at i:1108630 original size:20 final size:20
Alignment explanation
Indices: 1108582--1108633 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 20
1108572 TACTGATAGG
*
1108582 GGGTATCG-TACCATAGTAG
1 GGGTATCGATACCATAGTAA
*
1108601 GGTAGTATCGATACCATGGTAA
1 GG--GTATCGATACCATAGTAA
1108623 GGGTATCGATA
1 GGGTATCGATA
1108634 TCTGGCAACA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
19 2 0.07
20 9 0.32
21 6 0.21
22 11 0.39
ACGTcount: A:0.29, C:0.13, G:0.31, T:0.27
Consensus pattern (20 bp):
GGGTATCGATACCATAGTAA
Found at i:1109107 original size:55 final size:55
Alignment explanation
Indices: 1109041--1109307 Score: 367
Period size: 55 Copynumber: 4.9 Consensus size: 55
1109031 CTATGTGTAC
* * * *
1109041 TACAGGCACTTTGTGTGCATATTCACGAAATTCATTATAAGTTGATGAATTATCG
1 TACAGGCACTTTGTGTGCATATTCACGGAATTCATCATAAGTTGATGAATCACCG
* *
1109096 TACAGGCACTTTGTGTGCATATTTACGGAATTCATCATGAGTTGATGAATCACCG
1 TACAGGCACTTTGTGTGCATATTCACGGAATTCATCATAAGTTGATGAATCACCG
* *
1109151 TACAGACACTTTGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCG
1 TACAGGCACTTTGTGTGCATATTCACGGAATTCATCATAAGTTGATGAATCACCG
*
1109206 TACAGGCACTTTGTGTGCATATTCCATGGAATTCATCATAAGTTGATGAATCACCG
1 TACAGGCACTTTGTGTGCATATT-CACGGAATTCATCATAAGTTGATGAATCACCG
* * * * **
1109262 TATAGACACTATGTGTGCAGCA--CACGGAATTCATCATGGGTTGATG
1 TACAGGCACTTTGTGTGCA-TATTCACGGAATTCATCATAAGTTGATG
1109308 GATTCTCGTA
Statistics
Matches: 192, Mismatches: 18, Indels: 5
0.89 0.08 0.02
Matches are distributed among these distances:
54 21 0.11
55 124 0.65
56 46 0.24
57 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32
Consensus pattern (55 bp):
TACAGGCACTTTGTGTGCATATTCACGGAATTCATCATAAGTTGATGAATCACCG
Found at i:1114307 original size:16 final size:17
Alignment explanation
Indices: 1114257--1114307 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 17
1114247 AAAAAAATTA
1114257 AATTTGAAAGTTAGAGT
1 AATTTGAAAGTTAGAGT
*
1114274 GA-TT-AAA-TTAAGAGT
1 AATTTGAAAGTT-AGAGT
1114289 AATTTGAAAGTTA-AGT
1 AATTTGAAAGTTAGAGT
1114305 AAT
1 AAT
1114308 CAAATTAATG
Statistics
Matches: 28, Mismatches: 2, Indels: 9
0.72 0.05 0.23
Matches are distributed among these distances:
14 2 0.07
15 9 0.32
16 10 0.36
17 5 0.18
18 2 0.07
ACGTcount: A:0.45, C:0.00, G:0.20, T:0.35
Consensus pattern (17 bp):
AATTTGAAAGTTAGAGT
Found at i:1116893 original size:2 final size:2
Alignment explanation
Indices: 1116886--1116915 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1116876 GATAATAACA
1116886 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1116916 TAGATTTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1117243 original size:2 final size:2
Alignment explanation
Indices: 1117238--1117263 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1117228 TTGTCCGATT
1117238 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
1117264 GTTTGTAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1117315 original size:36 final size:34
Alignment explanation
Indices: 1117249--1117625 Score: 198
Period size: 36 Copynumber: 10.5 Consensus size: 34
1117239 ATATATATAT
* **
1117249 ATATATATATATATAG-TTTGTAAATGTTTTTGAA
1 ATATATA-ATATATAGTTTTGAAAACATTTTTGAA
* *
1117283 ATCACATAATATATAGTTTTGAAAACGATTTTTTTAA
1 AT-ATATAATATATAGTTTTGAAAAC-A-TTTTTGAA
**
1117320 ATATATAATATATA-TTTAAAAAAACA-TTTTGAAA
1 ATATATAATATATAGTTT-TGAAAACATTTTTG-AA
* * **
1117354 ATATATAATATATGGTTTTTAAAACATTTTAAAA
1 ATATATAATATATAGTTTTGAAAACATTTTTGAA
* * *
1117388 ACTTAGATAATATATAGTTTAGAAATCA-TTTTGAAAA
1 A--TATATAATATATAGTTTTGAAAACATTTTTG--AA
* *
1117425 TATATATAATATATAGTTTTTTTAAAACA-TTCTGAAAA
1 -ATATATAATATATAG--TTTTGAAAACATTTTTG--AA
* * *
1117463 ACTTATATAATATATAATTTTAAAAATATTTTTGAAAA
1 A--TATATAATATATAGTTTTGAAAACATTTTTG--AA
* * *
1117501 ATTATGTAATATATAGTTTTAAAAAATATTTTTTGAAA
1 A-TATATAATATATAGTTTT-GAAAACA-TTTTTG-AA
*
1117539 ACTTATATAATAT-T--TTTT-AAATCATTTTTGAAA
1 A--TATATAATATATAGTTTTGAAAACATTTTTG-AA
*
1117572 ACTATATGATATATAGTTTTGAAAACTTATTTTT-AA
1 A-TATATAATATATAGTTTTGAAAAC--ATTTTTGAA
*
1117608 AAATATAATATATAGTTT
1 ATATATAATATATAGTTT
1117626 AAAGATGTTT
Statistics
Matches: 276, Mismatches: 40, Indels: 53
0.75 0.11 0.14
Matches are distributed among these distances:
32 9 0.03
33 15 0.05
34 38 0.14
35 43 0.16
36 60 0.22
37 38 0.14
38 44 0.16
39 29 0.11
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.45
Consensus pattern (34 bp):
ATATATAATATATAGTTTTGAAAACATTTTTGAA
Found at i:1117351 original size:70 final size:69
Alignment explanation
Indices: 1117288--1117628 Score: 232
Period size: 70 Copynumber: 4.8 Consensus size: 69
1117278 TTGAAATCAC
** *
1117288 ATAATATATAGTTTTGAAAACGATTTTTTTAAA-TATATAATATATA-TTTAAAAAAACATTTTG
1 ATAATATATAGTTTTGAAAAC-A-TTTTAAAAACTAGATAATATATAGTTT-AAAAAACATTTTG
1117351 AAAATAT
63 AAAATAT
* * * *
1117358 ATAATATATGGTTTTTAAAACATTTTAAAAACTTAGATAATATATAGTTTAGAAATCATTTTGAA
1 ATAATATATAGTTTTGAAAACATTTTAAAAAC-TAGATAATATATAGTTTAAAAAACATTTTG-A
1117423 AATATAT
64 AA-ATAT
* * * * * *
1117430 ATAATATATAGTTTTTTTAAAACATTCTGAAAAACTTATATAATATATAATTTTAAAAATATTTT
1 ATAATATATAG--TTTTGAAAACATT-TTAAAAAC-TAGATAATATATAGTTTAAAAAACA-TTT
1117495 TGAAAAATTAT
61 TG-AAAA-TAT
* * * * * * *
1117506 GTAATATATAGTTTTAAAAAATATTTTTTGAAAACTTATATAATAT-T--TTT-TAAATCATTTT
1 ATAATATATAGTTTT-GAAAACA--TTTTAAAAAC-TAGATAATATATAGTTTAAAAAACA-TTT
1117567 TGAAAACTAT
61 TGAAAA-TAT
*
1117577 ATGATATATAGTTTTGAAAACTTATTTTTAAAAA-T--ATAATATATAGTTTAAA
1 ATAATATATAGTTTTGAAAAC--A-TTTTAAAAACTAGATAATATATAGTTTAAA
1117629 GATGTTTTTT
Statistics
Matches: 222, Mismatches: 30, Indels: 37
0.77 0.10 0.13
Matches are distributed among these distances:
67 7 0.03
68 8 0.04
69 2 0.01
70 49 0.22
71 36 0.16
72 25 0.11
73 3 0.01
74 17 0.08
75 34 0.15
76 39 0.18
77 2 0.01
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (69 bp):
ATAATATATAGTTTTGAAAACATTTTAAAAACTAGATAATATATAGTTTAAAAAACATTTTGAAA
ATAT
Found at i:1117511 original size:37 final size:38
Alignment explanation
Indices: 1117288--1117625 Score: 215
Period size: 36 Copynumber: 9.4 Consensus size: 38
1117278 TTGAAATCAC
* ** **
1117288 ATAATATATAGTTTTGAAAACGATTTTT-TTAAA-TAT
1 ATAATATATAGTTTTAAAAAATATTTTTGAAAAATTAT
* *
1117324 ATAATATATA-TTTAAAAAAACA-TTTTG-AAAA-TAT
1 ATAATATATAGTTTTAAAAAATATTTTTGAAAAATTAT
* * * *
1117358 ATAATATATGGTTTT-TAAAACA-TTTT-AAAAACTTAG
1 ATAATATATAGTTTTAAAAAATATTTTTGAAAAA-TTAT
*
1117394 ATAATATATAG-TTT-AGAAATCA-TTTTG-AAAATATAT
1 ATAATATATAGTTTTAAAAAAT-ATTTTTGAAAAAT-TAT
** * *
1117430 ATAATATATAGTTTTTTTAAAACA-TTCTGAAAAACTTAT
1 ATAATATATAG-TTTTAAAAAATATTTTTGAAAAA-TTAT
*
1117469 ATAATATATAATTTT-AAAAATATTTTTGAAAAATTAT
1 ATAATATATAGTTTTAAAAAATATTTTTGAAAAATTAT
* *
1117506 GTAATATATAGTTTTAAAAAATATTTTTTGAAAACTTAT
1 ATAATATATAGTTTTAAAAAATA-TTTTTGAAAAATTAT
*
1117545 ATAATAT-T--TTTT---AAATCATTTTTG-AAAACTAT
1 ATAATATATAGTTTTAAAAAAT-ATTTTTGAAAAATTAT
* **
1117577 ATGATATATAGTTTTGAAAACTTATTTTT--AAAA--AT
1 ATAATATATAGTTTT-AAAAAATATTTTTGAAAAATTAT
1117612 ATAATATATAGTTT
1 ATAATATATAGTTT
1117626 AAAGATGTTT
Statistics
Matches: 246, Mismatches: 32, Indels: 49
0.75 0.10 0.15
Matches are distributed among these distances:
32 12 0.05
33 11 0.04
34 34 0.14
35 37 0.15
36 48 0.20
37 26 0.11
38 35 0.14
39 42 0.17
40 1 0.00
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.45
Consensus pattern (38 bp):
ATAATATATAGTTTTAAAAAATATTTTTGAAAAATTAT
Found at i:1118862 original size:22 final size:23
Alignment explanation
Indices: 1118810--1118862 Score: 61
Period size: 25 Copynumber: 2.2 Consensus size: 23
1118800 TATTTAACCC
* * *
1118810 TTTTCTTTTTCACTCTTTTTATT
1 TTTTTTTTTTCACTATTATTATT
1118833 TTGGTTTTTTTTCACTATTATTATT
1 TT--TTTTTTTTCACTATTATTATT
1118858 TTTTT
1 TTTTT
1118863 AATTTTTATT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
23 5 0.20
25 20 0.80
ACGTcount: A:0.11, C:0.11, G:0.04, T:0.74
Consensus pattern (23 bp):
TTTTTTTTTTCACTATTATTATT
Found at i:1118886 original size:4 final size:4
Alignment explanation
Indices: 1118853--1118936 Score: 54
Period size: 4 Copynumber: 21.5 Consensus size: 4
1118843 TTCACTATTA
* *
1118853 TTAT TTTT TTAA TT-T TTAT TTAT CTCTAT TTAT TTAT TTAT TTAT TT-T
1 TTAT TTAT TTAT TTAT TTAT TTAT -T-TAT TTAT TTAT TTAT TTAT TTAT
* *
1118901 ATTA- TTA- TTAT TAAA TTAT TGT-T TT-T TTAT TTAT TT
1 -TTAT TTAT TTAT TTAT TTAT T-TAT TTAT TTAT TTAT TT
1118937 TTCTTTTGAC
Statistics
Matches: 64, Mismatches: 8, Indels: 16
0.73 0.09 0.18
Matches are distributed among these distances:
3 13 0.20
4 45 0.70
5 3 0.05
6 3 0.05
ACGTcount: A:0.24, C:0.02, G:0.01, T:0.73
Consensus pattern (4 bp):
TTAT
Found at i:1119783 original size:21 final size:20
Alignment explanation
Indices: 1119751--1119940 Score: 174
Period size: 21 Copynumber: 9.2 Consensus size: 20
1119741 CATTGCGATT
1119751 TTGGACTATCGCAA-CGAAC
1 TTGGACTATCGCAACCGAAC
*
1119770 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAAC-CGAAC
*
1119793 TTCGACTATCGCAA-CGAAC
1 TTGGACTATCGCAACCGAAC
*
1119812 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAAC-CGAAC
* *
1119835 GTCGACTATCGCAA-CGAAC
1 TTGGACTATCGCAACCGAAC
*
1119854 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAAC-CGAAC
*
1119877 TTCGACTATCGCAA-CGAAC
1 TTGGACTATCGCAACCGAAC
1119896 TTGGACTATCGCAACGCGAAC
1 TTGGACTATCGCAAC-CGAAC
* *
1119917 TTGGACTATCG-AAACGAAT
1 TTGGACTATCGCAACCGAAC
1119936 TTGGA
1 TTGGA
1119941 AAATCGCATT
Statistics
Matches: 141, Mismatches: 16, Indels: 28
0.76 0.09 0.15
Matches are distributed among these distances:
19 52 0.37
20 2 0.01
21 58 0.41
23 29 0.21
ACGTcount: A:0.34, C:0.25, G:0.21, T:0.20
Consensus pattern (20 bp):
TTGGACTATCGCAACCGAAC
Found at i:1119813 original size:42 final size:42
Alignment explanation
Indices: 1119754--1119948 Score: 317
Period size: 42 Copynumber: 4.7 Consensus size: 42
1119744 TGCGATTTTG
1119754 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
*
1119796 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACGTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
1119838 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
* *
1119880 GACTATCGCAACGAACTTGGACT--ATCGCAACGCGAACTTG
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
* *
1119920 GACTATCGAAACGAATTTGG-A-AAATCGCA
1 GACTATCGCAACGAACTTGGAATAAATCGCA
1119949 TTGCGATAGT
Statistics
Matches: 144, Mismatches: 7, Indels: 6
0.92 0.04 0.04
Matches are distributed among these distances:
40 40 0.28
42 104 0.72
ACGTcount: A:0.35, C:0.25, G:0.21, T:0.19
Consensus pattern (42 bp):
GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
Found at i:1119939 original size:19 final size:19
Alignment explanation
Indices: 1119751--1119940 Score: 110
Period size: 19 Copynumber: 9.3 Consensus size: 19
1119741 CATTGCGATT
*
1119751 TTGGACTATCGCAACGAAC
1 TTGGACTATCGAAACGAAC
* *
1119770 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCG-AA-ACGAAC
* *
1119793 TTCGACTATCGCAACGAAC
1 TTGGACTATCGAAACGAAC
* *
1119812 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCG-AA-ACGAAC
* * *
1119835 GTCGACTATCGCAACGAAC
1 TTGGACTATCGAAACGAAC
* *
1119854 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCG-AA-ACGAAC
* *
1119877 TTCGACTATCGCAACGAAC
1 TTGGACTATCGAAACGAAC
*
1119896 TTGGACTATCGCAACGCGAAC
1 TTGGACTATCG-AA-ACGAAC
*
1119917 TTGGACTATCGAAACGAAT
1 TTGGACTATCGAAACGAAC
1119936 TTGGA
1 TTGGA
1119941 AAATCGCATT
Statistics
Matches: 127, Mismatches: 30, Indels: 28
0.69 0.16 0.15
Matches are distributed among these distances:
19 49 0.39
20 6 0.05
21 40 0.31
22 3 0.02
23 29 0.23
ACGTcount: A:0.34, C:0.25, G:0.21, T:0.20
Consensus pattern (19 bp):
TTGGACTATCGAAACGAAC
Found at i:1128314 original size:28 final size:25
Alignment explanation
Indices: 1128256--1128319 Score: 74
Period size: 28 Copynumber: 2.4 Consensus size: 25
1128246 TTGTTATTAT
* *
1128256 TAAAATATTAATTTCTACTTATTAT
1 TAAAATATTAATTTCTACTTATAAA
*
1128281 TAAAATATTAATTTTTACACTTTATAAA
1 TAAAATATTAATTTCT--AC-TTATAAA
1128309 TAAAATATTAA
1 TAAAATATTAA
1128320 GAATAATATA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
25 15 0.45
27 2 0.06
28 16 0.48
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (25 bp):
TAAAATATTAATTTCTACTTATAAA
Found at i:1128377 original size:21 final size:21
Alignment explanation
Indices: 1128347--1128400 Score: 60
Period size: 20 Copynumber: 2.7 Consensus size: 21
1128337 GAAATAAAAA
*
1128347 TATTA-TAAAATATATTA-AT
1 TATTATTAAAATATAGTATAT
1128366 TATTTATTAAAATA-AGTATAT
1 TA-TTATTAAAATATAGTATAT
*
1128387 TATTATTATAATAT
1 TATTATTAAAATAT
1128401 TAAAATAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
19 2 0.07
20 16 0.55
21 11 0.38
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (21 bp):
TATTATTAAAATATAGTATAT
Found at i:1128415 original size:28 final size:27
Alignment explanation
Indices: 1128354--1128422 Score: 81
Period size: 28 Copynumber: 2.6 Consensus size: 27
1128344 AAATATTATA
*
1128354 AAATATATTA-ATTAT-TTATTAAAAT
1 AAATATATTATATTATAATATTAAAAT
*
1128379 AAGTATATTATTATTATAATATTAAAAT
1 AAATATATTA-TATTATAATATTAAAAT
1128407 AAA-ATTATTATATTAT
1 AAATA-TATTATATTAT
1128423 GCTTTAAAGT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
25 9 0.24
27 12 0.32
28 16 0.43
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (27 bp):
AAATATATTATATTATAATATTAAAAT
Found at i:1131769 original size:18 final size:18
Alignment explanation
Indices: 1131742--1131776 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1131732 TCCGAATACA
*
1131742 AAATGGGTATCGATACTC
1 AAATGAGTATCGATACTC
1131760 AAATGAGTATCGATACT
1 AAATGAGTATCGATACT
1131777 ACTTTACATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (18 bp):
AAATGAGTATCGATACTC
Found at i:1134695 original size:20 final size:20
Alignment explanation
Indices: 1134672--1134710 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1134662 TATAGCATCG
1134672 ATACTATATGAACAGTACCA
1 ATACTATATGAACAGTACCA
*
1134692 ATACTATATGAATAGTACC
1 ATACTATATGAACAGTACC
1134711 GATATTGTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.44, C:0.18, G:0.10, T:0.28
Consensus pattern (20 bp):
ATACTATATGAACAGTACCA
Found at i:1134875 original size:21 final size:21
Alignment explanation
Indices: 1134851--1134927 Score: 52
Period size: 24 Copynumber: 3.6 Consensus size: 21
1134841 TACTCAAAGG
*
1134851 AGTATCGATACTACTTTACATAGT
1 AGTATCGATACTACTATAC--A-T
* *
1134875 AGTATCGATACTACACATA-GT
1 AGTATCGATACTAC-TATACAT
*
1134896 AGTATCGATACCA-TGA-ACAT
1 AGTATCGATACTACT-ATACAT
1134916 AGTATCGATACT
1 AGTATCGATACT
1134928 GGTCAGACCC
Statistics
Matches: 43, Mismatches: 7, Indels: 10
0.72 0.12 0.17
Matches are distributed among these distances:
19 1 0.02
20 13 0.30
21 13 0.30
24 14 0.33
25 2 0.05
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.31
Consensus pattern (21 bp):
AGTATCGATACTACTATACAT
Found at i:1134882 original size:24 final size:21
Alignment explanation
Indices: 1134851--1134906 Score: 85
Period size: 21 Copynumber: 2.5 Consensus size: 21
1134841 TACTCAAAGG
1134851 AGTATCGATACTACTTTACATAGT
1 AGTATCGATACTAC---ACATAGT
1134875 AGTATCGATACTACACATAGT
1 AGTATCGATACTACACATAGT
1134896 AGTATCGATAC
1 AGTATCGATAC
1134907 CATGAACATA
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
21 18 0.56
24 14 0.44
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32
Consensus pattern (21 bp):
AGTATCGATACTACACATAGT
Found at i:1137725 original size:53 final size:53
Alignment explanation
Indices: 1137643--1137838 Score: 250
Period size: 53 Copynumber: 3.7 Consensus size: 53
1137633 GTCCGCTCTA
* * *
1137643 TCTTG-TTCAGGGATTAATGAACTCGAACAATCTTCTAAAAATGGGTTCACTCCC
1 TCTTGCTTCAGGGAGT-A-GAACTCGAACAATCTTCTGAAAACGGGTTCACTCCC
* * ***
1137697 TCTTGCTTGAGGGGGTAGAACTCGAACAATCTTCTGTCCACGGGTTCACTCCC
1 TCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGAAAACGGGTTCACTCCC
* *** *
1137750 TCTTGCTTCAGGGAGTAGAACTTGAACAATCTTCTGCTTACGGGTTCGCTCCC
1 TCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGAAAACGGGTTCACTCCC
1137803 TCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTG
1 TCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTG
1137839 GTGTGATTCT
Statistics
Matches: 125, Mismatches: 16, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
53 112 0.90
54 6 0.05
55 7 0.06
ACGTcount: A:0.23, C:0.25, G:0.21, T:0.31
Consensus pattern (53 bp):
TCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGAAAACGGGTTCACTCCC
Found at i:1138385 original size:42 final size:42
Alignment explanation
Indices: 1138338--1138607 Score: 222
Period size: 42 Copynumber: 6.2 Consensus size: 42
1138328 TTACAAATTA
*
1138338 CCCGAAGGATTTAATCATCATGCTCGAAAGACTTAGTGATGG
1 CCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGG
* *
1138380 CCCGAAGGACTTCATCATCATGCTCGAAAGACTTACTGATGG
1 CCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGG
* *
1138422 CCCGAAGGACTTCATCATCATGCTCGAAAGACTTACTGATGG
1 CCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGG
* * ** * * * **
1138464 CACTTACTGATGGGTTTGCTTCA-CTACT-CTTCCGTGAAGGCTTA-TAAATTA
1 C-C---C-GAAGGATTT-AATCATC-A-TGC-T-CG-AAAGACTTACT-GATGG
* * *
1138515 CCCTAAGGATTTAATCATCATGCTCGAAAGACATACTGATTG
1 CCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGG
* * * *
1138557 CTCTAAGGATTTAAGCATCATGCTCGAAAGACTTATTGATGG
1 CCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGG
1138599 CCCGAAGGA
1 CCCGAAGGA
1138608 CTTACTAAGT
Statistics
Matches: 184, Mismatches: 29, Indels: 30
0.76 0.12 0.12
Matches are distributed among these distances:
42 135 0.73
43 4 0.02
44 2 0.01
45 5 0.03
46 8 0.04
47 8 0.04
48 6 0.03
49 2 0.01
50 4 0.02
51 10 0.05
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.28
Consensus pattern (42 bp):
CCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGG
Found at i:1138412 original size:22 final size:21
Alignment explanation
Indices: 1138351--1138456 Score: 85
Period size: 20 Copynumber: 5.0 Consensus size: 21
1138341 GAAGGATTTA
1138351 ATCATCATGCTCGAAAGACTT
1 ATCATCATGCTCGAAAGACTT
* * * *
1138372 AGTGAT--GGCCCGAAGGACTT
1 A-TCATCATGCTCGAAAGACTT
1138392 CATCATCATGCTCGAAAGACTT
1 -ATCATCATGCTCGAAAGACTT
* * *
1138414 A-C-TGATGGCCCGAAGGACTT
1 ATCATCAT-GCTCGAAAGACTT
1138434 CATCATCATGCTCGAAAGACTT
1 -ATCATCATGCTCGAAAGACTT
1138456 A
1 A
1138457 CTGATGGCAC
Statistics
Matches: 63, Mismatches: 14, Indels: 16
0.68 0.15 0.17
Matches are distributed among these distances:
19 3 0.05
20 26 0.41
21 5 0.08
22 26 0.41
23 3 0.05
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.25
Consensus pattern (21 bp):
ATCATCATGCTCGAAAGACTT
Found at i:1138470 original size:13 final size:13
Alignment explanation
Indices: 1138452--1138476 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1138442 TGCTCGAAAG
1138452 ACTTACTGATGGC
1 ACTTACTGATGGC
1138465 ACTTACTGATGG
1 ACTTACTGATGG
1138477 GTTTGCTTCA
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:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (13 bp):
ACTTACTGATGGC
Found at i:1143075 original size:13 final size:13
Alignment explanation
Indices: 1143053--1143085 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
1143043 AAATACATGT
1143053 AATG-CAAATGCA
1 AATGACAAATGCA
1143065 AATGACAAATGCA
1 AATGACAAATGCA
1143078 AAT-ACAAA
1 AATGACAAA
1143086 AGGTGTCATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.58, C:0.15, G:0.12, T:0.15
Consensus pattern (13 bp):
AATGACAAATGCA
Found at i:1147571 original size:23 final size:23
Alignment explanation
Indices: 1147545--1147594 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
1147535 TATATACATT
*
1147545 CATATCATAAAGGACAAAAATAA
1 CATATCACAAAGGACAAAAATAA
*
1147568 CATATCACAAAGGACAAAAGTAA
1 CATATCACAAAGGACAAAAATAA
1147591 CATA
1 CATA
1147595 AAATAAAAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.58, C:0.16, G:0.10, T:0.16
Consensus pattern (23 bp):
CATATCACAAAGGACAAAAATAA
Found at i:1151075 original size:23 final size:23
Alignment explanation
Indices: 1151049--1151093 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1151039 CAGTCATTCA
**
1151049 GGATAATTCTACGTGGTCCTTCG
1 GGATAATTCTACACGGTCCTTCG
*
1151072 GGATATTTCTACACGGTCCTTC
1 GGATAATTCTACACGGTCCTTC
1151094 TGGACATCTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.18, C:0.24, G:0.22, T:0.36
Consensus pattern (23 bp):
GGATAATTCTACACGGTCCTTCG
Found at i:1151923 original size:20 final size:20
Alignment explanation
Indices: 1151894--1151932 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1151884 AGGTTTTTGT
* *
1151894 AAAACCAATTGTTTTTATTG
1 AAAACAAATTATTTTTATTG
1151914 AAAACAAATTATTTTTATT
1 AAAACAAATTATTTTTATT
1151933 TTATTTTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.41, C:0.08, G:0.05, T:0.46
Consensus pattern (20 bp):
AAAACAAATTATTTTTATTG
Found at i:1154430 original size:11 final size:11
Alignment explanation
Indices: 1154414--1154443 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
1154404 AAGAAACATG
1154414 AGAATGTGAAT
1 AGAATGTGAAT
1154425 AGAATGTGAAT
1 AGAATGTGAAT
1154436 AGAATGTG
1 AGAATGTG
1154444 TGTAGTTAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (11 bp):
AGAATGTGAAT
Found at i:1155383 original size:15 final size:15
Alignment explanation
Indices: 1155363--1155393 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1155353 ATACTGAGGT
1155363 AGTAGTATCGATACC
1 AGTAGTATCGATACC
*
1155378 AGTAGTATCGGTACC
1 AGTAGTATCGATACC
1155393 A
1 A
1155394 ATGATTAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (15 bp):
AGTAGTATCGATACC
Found at i:1159468 original size:21 final size:22
Alignment explanation
Indices: 1159444--1159496 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
1159434 ATTTCTACAC
*
1159444 GGTCCTTCTGGACA-TCTATGT
1 GGTCCTTCGGGACATTCTATGT
1159465 GGTCCTTCGGGACATTCTATGT
1 GGTCCTTCGGGACATTCTATGT
1159487 GG-CACTTCGG
1 GGTC-CTTCGG
1159497 TGCAAATTTC
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 14 0.48
22 15 0.52
ACGTcount: A:0.13, C:0.25, G:0.28, T:0.34
Consensus pattern (22 bp):
GGTCCTTCGGGACATTCTATGT
Found at i:1160764 original size:55 final size:54
Alignment explanation
Indices: 1160650--1160777 Score: 159
Period size: 55 Copynumber: 2.3 Consensus size: 54
1160640 TCATTTGGTG
* *
1160650 AAGAGACATGACTTTTGGTGAAAAGTCACAACTTTTAATAAATACACCTCTTAGG
1 AAGAGACATGACTTTTGGTGAAAAGTCACAACTTTT-AGAAATACACCTCTTAGA
* ** * *
1160705 AAGAGACATGACTTTTGGTGAAAAGTCACAACTTTT-GAAATGCCATTTTTTCATA
1 AAGAGACATGACTTTTGGTGAAAAGTCACAACTTTTAGAAAT-ACACCTCTT-AGA
1160760 AAGAGACATGACTTTTGG
1 AAGAGACATGACTTTTGG
1160778 ATGGACCTCT
Statistics
Matches: 64, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
53 4 0.06
54 5 0.08
55 55 0.86
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (54 bp):
AAGAGACATGACTTTTGGTGAAAAGTCACAACTTTTAGAAATACACCTCTTAGA
Found at i:1161291 original size:46 final size:47
Alignment explanation
Indices: 1161238--1161327 Score: 137
Period size: 48 Copynumber: 1.9 Consensus size: 47
1161228 GTTAAACTCA
* *
1161238 TGTTTTTAGAATTTTAGTTT-AAATATTTTAGGAATTATCTTTTACT
1 TGTTTTTAGAATTTTAGTTTAAAATATCTTAAGAATTATCTTTTACT
*
1161284 TGTTTTTAGGATTTTAGTTTAAAAATATCTTAAGAATTATCTTT
1 TGTTTTTAGAATTTTAGTTT-AAAATATCTTAAGAATTATCTTT
1161328 AGGAATTATA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
46 19 0.49
48 20 0.51
ACGTcount: A:0.30, C:0.04, G:0.11, T:0.54
Consensus pattern (47 bp):
TGTTTTTAGAATTTTAGTTTAAAATATCTTAAGAATTATCTTTTACT
Found at i:1161304 original size:23 final size:23
Alignment explanation
Indices: 1161237--1161306 Score: 61
Period size: 23 Copynumber: 3.0 Consensus size: 23
1161227 AGTTAAACTC
*
1161237 ATGTTTTTAGAATTTTAGTTTAA
1 ATGTTTTTAGGATTTTAGTTTAA
* * ** *
1161260 AT-ATTTTAGGAATTATCTTTTAC
1 ATGTTTTTAGG-ATTTTAGTTTAA
*
1161283 TTGTTTTTAGGATTTTAGTTTAA
1 ATGTTTTTAGGATTTTAGTTTAA
1161306 A
1 A
1161307 AATATCTTAA
Statistics
Matches: 32, Mismatches: 13, Indels: 4
0.65 0.27 0.08
Matches are distributed among these distances:
22 6 0.19
23 19 0.59
24 7 0.22
ACGTcount: A:0.29, C:0.03, G:0.13, T:0.56
Consensus pattern (23 bp):
ATGTTTTTAGGATTTTAGTTTAA
Found at i:1161355 original size:24 final size:24
Alignment explanation
Indices: 1161325--1161379 Score: 101
Period size: 24 Copynumber: 2.3 Consensus size: 24
1161315 AAGAATTATC
1161325 TTTAGGAATTATATCTTCCTTGTT
1 TTTAGGAATTATATCTTCCTTGTT
*
1161349 TTTAGGAATTATATTTTCCTTGTT
1 TTTAGGAATTATATCTTCCTTGTT
1161373 TTTAGGA
1 TTTAGGA
1161380 TTTTTGAAGG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.22, C:0.09, G:0.15, T:0.55
Consensus pattern (24 bp):
TTTAGGAATTATATCTTCCTTGTT
Found at i:1162722 original size:24 final size:24
Alignment explanation
Indices: 1162695--1162789 Score: 95
Period size: 24 Copynumber: 4.0 Consensus size: 24
1162685 AAACGGAGAT
*
1162695 ATCAGAATTCAAAACAGAATTCAG
1 ATCAGAATTCAGAACAGAATTCAG
* *
1162719 ATCAG-ATATCAGAACCGAATCCAG
1 ATCAGAAT-TCAGAACAGAATTCAG
*
1162743 ATCAGAAATCAGAACAGAATTCAG
1 ATCAGAATTCAGAACAGAATTCAG
* * *
1162767 GTCATGTATAC-GAACAGAATTCA
1 ATCA-GAATTCAGAACAGAATTCA
1162790 AGTCGGGAAA
Statistics
Matches: 58, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
23 2 0.03
24 52 0.90
25 4 0.07
ACGTcount: A:0.45, C:0.19, G:0.16, T:0.20
Consensus pattern (24 bp):
ATCAGAATTCAGAACAGAATTCAG
Found at i:1162724 original size:12 final size:12
Alignment explanation
Indices: 1162697--1162766 Score: 70
Period size: 12 Copynumber: 5.8 Consensus size: 12
1162687 ACGGAGATAT
*
1162697 CAGAATTCAAAA
1 CAGAATTCAGAA
*
1162709 CAGAATTCAGAT
1 CAGAATTCAGAA
1162721 CAG-ATATCAGAA
1 CAGAAT-TCAGAA
* * *
1162733 CCGAATCCAGAT
1 CAGAATTCAGAA
*
1162745 CAGAAATCAGAA
1 CAGAATTCAGAA
1162757 CAGAATTCAG
1 CAGAATTCAG
1162767 GTCATGTATA
Statistics
Matches: 45, Mismatches: 11, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
11 2 0.04
12 41 0.91
13 2 0.04
ACGTcount: A:0.47, C:0.20, G:0.16, T:0.17
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:1165122 original size:30 final size:30
Alignment explanation
Indices: 1165049--1165122 Score: 103
Period size: 30 Copynumber: 2.5 Consensus size: 30
1165039 TTTTACTATT
* *
1165049 GGTCAAATTCAAAGGTCAACGGGTTGACCC
1 GGTCAAAGTCAACGGTCAACGGGTTGACCC
* * *
1165079 GGTCAAAGCCAACGGTTAACGGGTTGACTC
1 GGTCAAAGTCAACGGTCAACGGGTTGACCC
1165109 GGTCAAAGTCAACG
1 GGTCAAAGTCAACG
1165123 AGTTGACCCA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.30, C:0.23, G:0.28, T:0.19
Consensus pattern (30 bp):
GGTCAAAGTCAACGGTCAACGGGTTGACCC
Found at i:1171918 original size:22 final size:22
Alignment explanation
Indices: 1171893--1171947 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
1171883 TCAGGAGTTA
* *
1171893 CAGGAGTTATTTGATTTAATTC
1 CAGGAGTTATATGATATAATTC
* * *
1171915 CAGGGGTTACATGATATAATTT
1 CAGGAGTTATATGATATAATTC
1171937 CAGGAGTTATA
1 CAGGAGTTATA
1171948 ACAGCTGAAT
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.31, C:0.09, G:0.22, T:0.38
Consensus pattern (22 bp):
CAGGAGTTATATGATATAATTC
Found at i:1175345 original size:29 final size:29
Alignment explanation
Indices: 1175310--1175391 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
1175300 AAACTAAATT
*
1175310 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
1175339 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
1175368 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
1175392 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:1178391 original size:29 final size:29
Alignment explanation
Indices: 1178356--1178437 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
1178346 AAACTAAATT
*
1178356 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
1178385 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
1178414 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
1178438 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:1179615 original size:16 final size:16
Alignment explanation
Indices: 1179596--1179637 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
1179586 TAAACTTCAA
1179596 ATTTAAAATATAAAAT
1 ATTTAAAATATAAAAT
*
1179612 ATTTAAAGA-ATTAAAT
1 ATTTAAA-ATATAAAAT
*
1179628 ATTAAAAATA
1 ATTTAAAATA
1179638 GAAATTAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 1 0.05
16 20 0.91
17 1 0.05
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (16 bp):
ATTTAAAATATAAAAT
Found at i:1180303 original size:2 final size:2
Alignment explanation
Indices: 1180296--1180327 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1180286 ATTTTTAATA
1180296 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1180328 TTCTAAATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1185335 original size:19 final size:19
Alignment explanation
Indices: 1185311--1185348 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
1185301 TATTGCAGAA
1185311 TTAGGCTTGTAAATGAGAT
1 TTAGGCTTGTAAATGAGAT
1185330 TTAGGCTTGTAAATGAGAT
1 TTAGGCTTGTAAATGAGAT
1185349 AAAAGAGATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.05, G:0.26, T:0.37
Consensus pattern (19 bp):
TTAGGCTTGTAAATGAGAT
Found at i:1186094 original size:21 final size:22
Alignment explanation
Indices: 1186060--1186104 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
1186050 GGTTTTTCGG
1186060 ATGATGAAATAAA-TAAATAAA
1 ATGATGAAATAAATTAAATAAA
1186081 ATGAGTGAAA-AAATTAAATAAA
1 ATGA-TGAAATAAATTAAATAAA
1186103 AT
1 AT
1186105 AAAGGTAGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 7 0.32
22 15 0.68
ACGTcount: A:0.64, C:0.00, G:0.11, T:0.24
Consensus pattern (22 bp):
ATGATGAAATAAATTAAATAAA
Found at i:1188432 original size:21 final size:21
Alignment explanation
Indices: 1188402--1188449 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
1188392 TAATTTTCAA
*
1188402 ACATTATTGCACCTAATTTTG
1 ACATTGTTGCACCTAATTTTG
1188423 ACATTGTTGCACCTAATTTTG
1 ACATTGTTGCACCTAATTTTG
1188444 ACATTG
1 ACATTG
1188450 CAATATTAGG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.27, C:0.19, G:0.12, T:0.42
Consensus pattern (21 bp):
ACATTGTTGCACCTAATTTTG
Found at i:1193083 original size:21 final size:21
Alignment explanation
Indices: 1193053--1193100 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
1193043 TAATTTTCAA
*
1193053 ACATTATTGCACCTAATTTTG
1 ACATTGTTGCACCTAATTTTG
1193074 ACATTGTTGCACCTAATTTTG
1 ACATTGTTGCACCTAATTTTG
1193095 ACATTG
1 ACATTG
1193101 CAATATTAGG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.27, C:0.19, G:0.12, T:0.42
Consensus pattern (21 bp):
ACATTGTTGCACCTAATTTTG
Found at i:1195930 original size:15 final size:15
Alignment explanation
Indices: 1195910--1195946 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
1195900 ATATTTAGAT
*
1195910 GGGCGGGCGGATGTG
1 GGGCGGGCGGATGCG
1195925 GGGCGGGCGGATGCG
1 GGGCGGGCGGATGCG
1195940 GGGCGGG
1 GGGCGGG
1195947 TAATGTCTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.05, C:0.16, G:0.70, T:0.08
Consensus pattern (15 bp):
GGGCGGGCGGATGCG
Found at i:1199987 original size:21 final size:20
Alignment explanation
Indices: 1199963--1200001 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
1199953 TAAATGATTG
1199963 GCCTCGAGGTCGTAAAAAACA
1 GCCTCGAGGTCG-AAAAAACA
* *
1199984 GCCTTGAGGTTGAAAAAA
1 GCCTCGAGGTCGAAAAAA
1200002 TTGCGATCGT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 6 0.38
21 10 0.62
ACGTcount: A:0.38, C:0.18, G:0.26, T:0.18
Consensus pattern (20 bp):
GCCTCGAGGTCGAAAAAACA
Found at i:1201447 original size:2 final size:2
Alignment explanation
Indices: 1201440--1201481 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1201430 TTTTATAGAA
1201440 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1201482 TATGAGGTAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1202509 original size:60 final size:60
Alignment explanation
Indices: 1202393--1202535 Score: 173
Period size: 60 Copynumber: 2.4 Consensus size: 60
1202383 GATGAATTCG
* ** * *
1202393 GGGATGAAATTGGAATATTT-AAAGTTTGGGGACTAGTTTAGAAAGAAGGATATAGTTTA
1 GGGATGAAATTAGAATATTTAAAAGTTTCAGGACTAATTTAGAAAGAAGAATATAGTTTA
* * * *
1202452 GGGATGAAATTAAAATATTTAAAAGTTTCAGGATTAATTTAGAATG-AGAATCGTAGTTTA
1 GGGATGAAATTAGAATATTTAAAAGTTTCAGGACTAATTTAGAAAGAAGAAT-ATAGTTTA
*
1202512 GGGATGAAATTAGAATATTCAAAA
1 GGGATGAAATTAGAATATTTAAAA
1202536 ATTGAAAGAC
Statistics
Matches: 71, Mismatches: 11, Indels: 3
0.84 0.13 0.04
Matches are distributed among these distances:
59 22 0.31
60 49 0.69
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.32
Consensus pattern (60 bp):
GGGATGAAATTAGAATATTTAAAAGTTTCAGGACTAATTTAGAAAGAAGAATATAGTTTA
Found at i:1202551 original size:60 final size:60
Alignment explanation
Indices: 1202445--1202560 Score: 151
Period size: 60 Copynumber: 1.9 Consensus size: 60
1202435 AAGAAGGATA
* * ** * ** *
1202445 TAGTTTAGGGATGAAATTAAAATATTTAAAAGTTTCAGGATTAATTTAGAATGAGAATCG
1 TAGTTTAGGGATGAAATTAAAATATTCAAAAATTGAAAGACCAATTTAAAATGAGAATCG
*
1202505 TAGTTTAGGGATGAAATTAGAATATTCAAAAATTGAAAGACCAATTTAAAATGAGA
1 TAGTTTAGGGATGAAATTAAAATATTCAAAAATTGAAAGACCAATTTAAAATGAGA
1202561 GTTATAATTT
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
60 47 1.00
ACGTcount: A:0.45, C:0.04, G:0.19, T:0.32
Consensus pattern (60 bp):
TAGTTTAGGGATGAAATTAAAATATTCAAAAATTGAAAGACCAATTTAAAATGAGAATCG
Found at i:1211497 original size:22 final size:22
Alignment explanation
Indices: 1211479--1211525 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
1211469 TTTGTCCCTT
1211479 ATGATGCGTAGAAATGTCCCAA
1 ATGATGCGTAGAAATGTCCCAA
*
1211501 ATGATGCGTAGAAATGTCCCGA
1 ATGATGCGTAGAAATGTCCCAA
1211523 ATG
1 ATG
1211526 CCCATATATA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.34, C:0.17, G:0.26, T:0.23
Consensus pattern (22 bp):
ATGATGCGTAGAAATGTCCCAA
Found at i:1211540 original size:21 final size:21
Alignment explanation
Indices: 1211514--1211572 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
1211504 ATGCGTAGAA
* * *
1211514 ATGTCCCGAATGCCCATATAT
1 ATGTCCCGAATGACCACATAG
1211535 ATGTCCCGAATGACCACATAG
1 ATGTCCCGAATGACCACATAG
* *
1211556 ATGTCCCAAAGGACCAC
1 ATGTCCCGAATGACCAC
1211573 TCCTTAAGGA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.32, C:0.31, G:0.17, T:0.20
Consensus pattern (21 bp):
ATGTCCCGAATGACCACATAG
Found at i:1211974 original size:19 final size:19
Alignment explanation
Indices: 1211947--1212002 Score: 53
Period size: 19 Copynumber: 3.0 Consensus size: 19
1211937 TCATGTAACC
*
1211947 ACATATATCTTATCTCATA
1 ACATTTATCTTATCTCATA
* *
1211966 ACATTTATCATATATGCAT-
1 ACATTTATCTTATCT-CATA
*
1211985 ACATTCA-CTTATCTCATA
1 ACATTTATCTTATCTCATA
1212003 TCATATAATT
Statistics
Matches: 29, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
17 3 0.10
18 5 0.17
19 18 0.62
20 3 0.10
ACGTcount: A:0.36, C:0.21, G:0.02, T:0.41
Consensus pattern (19 bp):
ACATTTATCTTATCTCATA
Found at i:1215470 original size:21 final size:22
Alignment explanation
Indices: 1215446--1215488 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1215436 AGGCTCCATT
* *
1215446 GTCGGCCA-CGCATCGGTCGCC
1 GTCGACCACCGCATCGATCGCC
1215467 GTCGACCACCGCATCGATCGCC
1 GTCGACCACCGCATCGATCGCC
1215489 ATCACTTGTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.14, C:0.44, G:0.28, T:0.14
Consensus pattern (22 bp):
GTCGACCACCGCATCGATCGCC
Found at i:1216811 original size:118 final size:119
Alignment explanation
Indices: 1216600--1217139 Score: 622
Period size: 119 Copynumber: 4.6 Consensus size: 119
1216590 AACTTGAGCG
* * ** * * *
1216600 AAAGGTTGAACAAGTTCTTCTCATTATGAAATTCTTCTTCCTTTTTGGATGCGTTCTTCTTAATA
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATTGGATGAGTTCTTCTCATTA
* *
1216665 TGAACCCAT-TCATTGGAAATGTTGATCCACCTCCTTCTATGATGGATTTGAG-A
66 TGAACCCCTCT-ATTGCAAATGTTGATCCACCTCCTTCTATGATGGATTTGAGAA
* * * *
1216718 AAAGGTTGAACAAGTTCTTCTCATTATAAATTTCTTCTCCCTCATTGGATGAGTTATTCTCATTG
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATTGGATGAGTTCTTCTCATTA
* * * *
1216783 TGAACCCCTCTATTGCAAATGTTTATCCACCTCCTTCTGTGACGGATTTAAG-A
66 TGAACCCCTCTATTGCAAATGTTGATCCACCTCCTTCTATGATGGATTTGAGAA
* * * *
1216836 AAAGG-TGCACAAGTTCTTCTCATTATGAACTTATTCTCCATCATTGGATGAGTTCTTATCATTA
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATTGGATGAGTTCTTCTCATTA
* * * * *
1216900 TGGACCCCTCTATTTCAAATGTTAATCCACCTCATTCTGTGATGGATTTGAGAA
66 TGAACCCCTCTATTGCAAATGTTGATCCACCTCCTTCTATGATGGATTTGAGAA
* * * * * *
1216954 AAAGGTTGAACAAGTTCCTCTCATTATGAACTTCTTGTTCCT-TTTCAGACGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATT-GGATGAGTTCTTCTCATT
* ** * * * *
1217018 ATGAATCATTCCATTGGAAATGTTGGTCTACCTCCTTCTATGATGGATTTGAGAA
65 ATGAACCCCTCTATTGCAAATGTTGATCCACCTCCTTCTATGATGGATTTGAGAA
* * ** *
1217073 AAATGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCTCTCACCGGGTGAGTTCTTCTCCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATTGGATGAGTTCTTCT-CATT
1217138 AT
65 AT
1217140 TTGAAAACCT
Statistics
Matches: 353, Mismatches: 63, Indels: 10
0.83 0.15 0.02
Matches are distributed among these distances:
117 97 0.27
118 113 0.32
119 137 0.39
120 6 0.02
ACGTcount: A:0.25, C:0.21, G:0.15, T:0.39
Consensus pattern (119 bp):
AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATTGGATGAGTTCTTCTCATTA
TGAACCCCTCTATTGCAAATGTTGATCCACCTCCTTCTATGATGGATTTGAGAA
Found at i:1219384 original size:136 final size:136
Alignment explanation
Indices: 1219137--1219385 Score: 372
Period size: 136 Copynumber: 1.8 Consensus size: 136
1219127 ATTCATTCAG
* * *
1219137 TGATAGGTGTTGATATGAATAGTGCCCCTCCGGGGGACATCATACATAATAGGGCAATTATAACC
1 TGATAGGTGTTGATATGAATAGTGCCCCACCAGGGGACATCACACATAATAGGGCAATTATAACC
* *
1219202 AATTTTCTGACAAAAAGGAAAGACACATCCCACAAGAAGTGATTTCACCACATTGTTGCGTCCCT
66 AATTTTCTGACAAAAAAGAAAGACACATCCCACAAGAAGCGATTTCACCACATTGTTGCGTCCCT
1219267 CAAACA
131 CAAACA
* * *
1219273 TGATAGGTGTTGATATGAATATTGCCCCACCAGGGGACATTACACATAATAGGGTAATTATAACC
1 TGATAGGTGTTGATATGAATAGTGCCCCACCAGGGGACATCACACATAATAGGGCAATTATAACC
* * *** *
1219338 TATTTTCTGACAAAAAAGAAAGGCGTGTCCCACAAGAAGCGCTTTCAC
66 AATTTTCTGACAAAAAAGAAAGACACATCCCACAAGAAGCGATTTCAC
1219386 GTGAATAGTA
Statistics
Matches: 99, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
136 99 1.00
ACGTcount: A:0.35, C:0.21, G:0.20, T:0.25
Consensus pattern (136 bp):
TGATAGGTGTTGATATGAATAGTGCCCCACCAGGGGACATCACACATAATAGGGCAATTATAACC
AATTTTCTGACAAAAAAGAAAGACACATCCCACAAGAAGCGATTTCACCACATTGTTGCGTCCCT
CAAACA
Found at i:1225841 original size:17 final size:17
Alignment explanation
Indices: 1225821--1225857 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
1225811 TTATTAATTA
1225821 TTTTTATTCTAATATTT
1 TTTTTATTCTAATATTT
* *
1225838 TTTTTATTTTAATGTTT
1 TTTTTATTCTAATATTT
1225855 TTT
1 TTT
1225858 AAAGTTATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.19, C:0.03, G:0.03, T:0.76
Consensus pattern (17 bp):
TTTTTATTCTAATATTT
Found at i:1236741 original size:20 final size:20
Alignment explanation
Indices: 1236718--1236756 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1236708 CCTAAAATGA
1236718 AAAAAAGA-AAAGGAAAAGAG
1 AAAAAAGAGAAA-GAAAAGAG
*
1236738 AAAAAGGAGAAAGAAAAGA
1 AAAAAAGAGAAAGAAAAGA
1236757 AAATAAGGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (20 bp):
AAAAAAGAGAAAGAAAAGAG
Found at i:1238086 original size:107 final size:106
Alignment explanation
Indices: 1237908--1238149 Score: 369
Period size: 107 Copynumber: 2.3 Consensus size: 106
1237898 CTTTCAGAGT
* * *
1237908 CAATTTCAACTTCACAACGAAGGATATTGGACTCAATACAGCACAAGCTCAACTTCACGGCGAAG
1 CAATTTCAACTTCACAGCGAAGGATATTGAACCCAATACAGCACAAGCTCAACTTCACGGCGAAG
* * *
1237973 GGGCGGCTGACTGTCAACAAACAATTCCCCAATTTCATATC
66 GGGCGGCTGACTGTCAACAAACAATTCCCCAATTCCAGAAC
*
1238014 CAATTTCAACTTCACAGCGAAGGATATTGAACCCAAATATAGCACAAGCTCAACTTCACGGCGAA
1 CAATTTCAACTTCACAGCGAAGGATATTGAACCC-AATACAGCACAAGCTCAACTTCACGGCGAA
** *
1238079 GGGGCGGCTGACTGTCAACAAACAATTTTCCAGTTCCAGAAC
65 GGGGCGGCTGACTGTCAACAAACAATTCCCCAATTCCAGAAC
1238121 CAATTTCAACTTCAC-GACGAAGGATATTG
1 CAATTTCAACTTCACAG-CGAAGGATATTG
1238150 GACTTGGAGC
Statistics
Matches: 124, Mismatches: 10, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
106 32 0.26
107 92 0.74
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (106 bp):
CAATTTCAACTTCACAGCGAAGGATATTGAACCCAATACAGCACAAGCTCAACTTCACGGCGAAG
GGGCGGCTGACTGTCAACAAACAATTCCCCAATTCCAGAAC
Found at i:1238925 original size:2 final size:2
Alignment explanation
Indices: 1238913--1238952 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
1238903 TGAAATGAAC
*
1238913 AT AT AT TT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1238953 TGTATAAATA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:1240563 original size:19 final size:19
Alignment explanation
Indices: 1240541--1240600 Score: 68
Period size: 19 Copynumber: 3.2 Consensus size: 19
1240531 TCATATTTTA
* *
1240541 TTTTTCTTTTGTTTTGTTT
1 TTTTTCTTTTGTTTTATGT
1240560 TTTTTCGTTTT-TTTTATGT
1 TTTTTC-TTTTGTTTTATGT
* *
1240579 ATTTGCTTTTGTTTTATGT
1 TTTTTCTTTTGTTTTATGT
1240598 TTT
1 TTT
1240601 CATATTTTTC
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
18 4 0.12
19 26 0.76
20 4 0.12
ACGTcount: A:0.05, C:0.05, G:0.12, T:0.78
Consensus pattern (19 bp):
TTTTTCTTTTGTTTTATGT
Found at i:1242341 original size:38 final size:37
Alignment explanation
Indices: 1242290--1242377 Score: 126
Period size: 38 Copynumber: 2.4 Consensus size: 37
1242280 TTTTTACCCT
1242290 AAACCCGACCCGAC-CTGAC-CTGAATATCACACTTAAAA
1 AAACCCGACCCGACTC-GACTC-GAATATCACACTT-AAA
1242328 AAACCCGACCCGACTCGACTCGAATATCACACTTAAA
1 AAACCCGACCCGACTCGACTCGAATATCACACTTAAA
*
1242365 AAACCCGATCCGA
1 AAACCCGACCCGA
1242378 ACCGAACAAA
Statistics
Matches: 47, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
37 15 0.32
38 30 0.64
39 2 0.04
ACGTcount: A:0.39, C:0.35, G:0.11, T:0.15
Consensus pattern (37 bp):
AAACCCGACCCGACTCGACTCGAATATCACACTTAAA
Found at i:1242660 original size:222 final size:212
Alignment explanation
Indices: 1242398--1242861 Score: 702
Period size: 222 Copynumber: 2.2 Consensus size: 212
1242388 ATAAAGTTTT
* * *
1242398 ATCCGACCCGACCCAACCCGAAATAATAAAAAATTATTTTTATTTAATAAAAACATTGACTTAAT
1 ATCCAACCCGACCCGACCCGAAATAATAAAAAATTATTTTTATTTAATAAAAACAGTGACTTAAT
* *
1242463 TCGACCCGACCCGAATTATATATATTTTCGGGGCGGTCCGGTTTTTTTCACCCTAAACCCGAACC
66 TCGACCCGACCCGAA-T-TATATATTTTCGGGGCAGTCCGGGTTTTTTCACCCTAAACCCG-A--
*
1242528 CGACCCGACCCGAATATCACACTTAAAAAAACCCGA-CCTGACCCGAACAAAATAAAGTTTCATC
126 --ACCCGACCCGAATATCACACTTAAAAAAACCCGATCC-GACCCGAACAAAATAAAGTTTCACC
1242592 CGACCCGACCCGAATATATGAATTAG
188 CGACCCGACCCGAATA-ATGAATTAG
1242618 AAATCCAACCCGACCCGACCCGAAATAATAAAAAATTATTTTTATTTAATAAAAACAGTGACTTA
1 --ATCCAACCCGACCCGACCCGAAATAATAAAAAATTATTTTTATTTAATAAAAACAGTGACTTA
* * *
1242683 ATTCGACCCGACCTGAATTATATATTTTCGGGTCAGTCCGGGTTTTTTCACCCTAAACCTGAACC
64 ATTCGACCCGACCCGAATTATATATTTTCGGGGCAGTCCGGGTTTTTTCACCCTAAACCCGAACC
*
1242748 CGACCCGAATATCACACTTAAAAAAACCCGATCCGACCCGACCAAAATAAAGTTTCACCCGACCC
129 CGACCCGAATATCACACTTAAAAAAACCCGATCCGACCCGAACAAAATAAAGTTTCACCCGACCC
*
1242813 GACTCGAATAATGAATTAG
194 GACCCGAATAATGAATTAG
1242832 A---AACCCGACCCGACCCGAAATAATAAAAAA
1 ATCCAACCCGACCCGACCCGAAATAATAAAAAA
1242862 AATACTTTTA
Statistics
Matches: 230, Mismatches: 11, Indels: 15
0.90 0.04 0.06
Matches are distributed among these distances:
209 29 0.13
212 1 0.00
214 9 0.04
215 72 0.31
216 2 0.01
219 1 0.00
220 39 0.17
221 1 0.00
222 76 0.33
ACGTcount: A:0.37, C:0.27, G:0.12, T:0.23
Consensus pattern (212 bp):
ATCCAACCCGACCCGACCCGAAATAATAAAAAATTATTTTTATTTAATAAAAACAGTGACTTAAT
TCGACCCGACCCGAATTATATATTTTCGGGGCAGTCCGGGTTTTTTCACCCTAAACCCGAACCCG
ACCCGAATATCACACTTAAAAAAACCCGATCCGACCCGAACAAAATAAAGTTTCACCCGACCCGA
CCCGAATAATGAATTAG
Found at i:1247457 original size:18 final size:18
Alignment explanation
Indices: 1247415--1247490 Score: 79
Period size: 18 Copynumber: 4.4 Consensus size: 18
1247405 TATAATTCAT
1247415 TAGTATATATAAATTATA
1 TAGTATATATAAATTATA
*
1247433 TGGTATATATAAATTATA
1 TAGTATATATAAATTATA
*
1247451 TA-T-TATAT-AGTTCAT-
1 TAGTATATATAAATT-ATA
* *
1247466 TAGTATATATAGACTATA
1 TAGTATATATAAATTATA
1247484 TAGTATA
1 TAGTATA
1247491 AATTAATAAT
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
15 5 0.11
16 8 0.17
17 8 0.17
18 26 0.55
ACGTcount: A:0.43, C:0.03, G:0.09, T:0.45
Consensus pattern (18 bp):
TAGTATATATAAATTATA
Found at i:1247711 original size:160 final size:160
Alignment explanation
Indices: 1247541--1247864 Score: 630
Period size: 160 Copynumber: 2.0 Consensus size: 160
1247531 ATTAAATTAA
1247541 TTATATTAAATGATTTATTTATTGATTATTAATTTTATTAGATTAAAAATTAAATTATATAAAAT
1 TTATATTAAATGATTTATTTATTGATTATTAATTTTATTAGATTAAAAATTAAATTATATAAAAT
1247606 ATCAATAAGTTTATATCGTTATTATAATGTATAAATGATTAATAATTTAAATATAATTTAACATA
66 ATCAATAAGTTTATATCGTTATTATAATGTATAAATGATTAATAATTTAAATATAATTTAACATA
1247671 AAATTTTAATTTATATATATATACATGGTT
131 AAATTTTAATTTATATATATATACATGGTT
*
1247701 TTATATTAAATGATTTATTTATTGATTATTAATTTTATTAGATTAAAAATTAGATTATATAAAAT
1 TTATATTAAATGATTTATTTATTGATTATTAATTTTATTAGATTAAAAATTAAATTATATAAAAT
*
1247766 ATGAATAAGTTTATATCGTTATTATAATGTATAAATGATTAATAATTTAAATATAATTTAACATA
66 ATCAATAAGTTTATATCGTTATTATAATGTATAAATGATTAATAATTTAAATATAATTTAACATA
1247831 AAATTTTAATTTATATATATATACATGGTT
131 AAATTTTAATTTATATATATATACATGGTT
1247861 TTAT
1 TTAT
1247865 TTACTATGAT
Statistics
Matches: 162, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
160 162 1.00
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (160 bp):
TTATATTAAATGATTTATTTATTGATTATTAATTTTATTAGATTAAAAATTAAATTATATAAAAT
ATCAATAAGTTTATATCGTTATTATAATGTATAAATGATTAATAATTTAAATATAATTTAACATA
AAATTTTAATTTATATATATATACATGGTT
Found at i:1253540 original size:20 final size:20
Alignment explanation
Indices: 1253515--1253575 Score: 59
Period size: 20 Copynumber: 2.9 Consensus size: 20
1253505 TTTTGGTGCA
*
1253515 GAGGGAATCGATACCCCCAT
1 GAGGGAACCGATACCCCCAT
* *
1253535 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATACCCCC-AT
*
1253556 GAAGGGGAACCGATTCCCCC
1 G-A-GGGAACCGATACCCCC
1253576 CCACAGGGGA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
20 16 0.46
21 2 0.06
22 1 0.03
23 16 0.46
ACGTcount: A:0.25, C:0.33, G:0.26, T:0.16
Consensus pattern (20 bp):
GAGGGAACCGATACCCCCAT
Found at i:1255903 original size:15 final size:15
Alignment explanation
Indices: 1255883--1255914 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
1255873 AAGCGTTTTA
1255883 AAGAGGAGTAGTGTT
1 AAGAGGAGTAGTGTT
1255898 AAGAGGAGTAGTGTT
1 AAGAGGAGTAGTGTT
1255913 AA
1 AA
1255915 AGTAAGGGGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.38, T:0.25
Consensus pattern (15 bp):
AAGAGGAGTAGTGTT
Found at i:1260813 original size:175 final size:175
Alignment explanation
Indices: 1260522--1260862 Score: 673
Period size: 175 Copynumber: 1.9 Consensus size: 175
1260512 CAAGTTCTTT
1260522 AAGAACTATATCGATTGAGCAAGTGCATTTCTATACTTGTGGCTTCATTCTATTCACTTTGATTC
1 AAGAACTATATCGATTGAGCAAGTGCATTTCTATACTTGTGGCTTCATTCTATTCACTTTGATTC
1260587 TTATAATTCATAGATTCAATATCTATTGGGTTTAAGACACTTCTACCATCCCTCAAGCAAGTTTA
66 TTATAATTCATAGATTCAATATCTATTGGGTTTAAGACACTTCTACCATCCCTCAAGCAAGTTTA
1260652 TAAAGAGCGGGGCTTTGCTACTTAGCATTGTTTCTTAGATTGAGC
131 TAAAGAGCGGGGCTTTGCTACTTAGCATTGTTTCTTAGATTGAGC
*
1260697 AAGAACTATATCGATTGAGCAAGTGTATTTCTATACTTGTGGCTTCATTCTATTCACTTTGATTC
1 AAGAACTATATCGATTGAGCAAGTGCATTTCTATACTTGTGGCTTCATTCTATTCACTTTGATTC
1260762 TTATAATTCATAGATTCAATATCTATTGGGTTTAAGACACTTCTACCATCCCTCAAGCAAGTTTA
66 TTATAATTCATAGATTCAATATCTATTGGGTTTAAGACACTTCTACCATCCCTCAAGCAAGTTTA
1260827 TAAAGAGCGGGGCTTTGCTACTTAGCATTGTTTCTT
131 TAAAGAGCGGGGCTTTGCTACTTAGCATTGTTTCTT
1260863 CATCGACAAG
Statistics
Matches: 165, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
175 165 1.00
ACGTcount: A:0.27, C:0.18, G:0.16, T:0.38
Consensus pattern (175 bp):
AAGAACTATATCGATTGAGCAAGTGCATTTCTATACTTGTGGCTTCATTCTATTCACTTTGATTC
TTATAATTCATAGATTCAATATCTATTGGGTTTAAGACACTTCTACCATCCCTCAAGCAAGTTTA
TAAAGAGCGGGGCTTTGCTACTTAGCATTGTTTCTTAGATTGAGC
Found at i:1261043 original size:20 final size:20
Alignment explanation
Indices: 1260998--1261043 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
1260988 TCATTAATTC
*
1260998 ATTTCTATTTCATTTACTTA
1 ATTTTTATTTCATTTACTTA
1261018 AGTTTTTATTTCATTT-CTTA
1 A-TTTTTATTTCATTTACTTA
1261038 TATTTT
1 -ATTTT
1261044 CTTTAACTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 9 0.39
21 14 0.61
ACGTcount: A:0.22, C:0.11, G:0.02, T:0.65
Consensus pattern (20 bp):
ATTTTTATTTCATTTACTTA
Found at i:1264287 original size:14 final size:14
Alignment explanation
Indices: 1264264--1264293 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1264254 ATAACAACTT
*
1264264 AGGAGTTGAATTTG
1 AGGAGCTGAATTTG
1264278 AGGAGCTGAATTTG
1 AGGAGCTGAATTTG
1264292 AG
1 AG
1264294 CTTAACAAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.30, C:0.03, G:0.37, T:0.30
Consensus pattern (14 bp):
AGGAGCTGAATTTG
Found at i:1266026 original size:103 final size:104
Alignment explanation
Indices: 1265689--1266023 Score: 419
Period size: 103 Copynumber: 3.2 Consensus size: 104
1265679 CTTGAAATTG
* *******
1265689 TTTTTCTTAAAATCAATTTTGTCTCACTTGAGGCAGTTTTCCTTTGATTTTTTTTTTTTTGAAAT
1 TTTTTCTTAAAATCAATTTTGTCTCACTTGAGGCAGTTTTCCCTTGAAAACAAATTTTTTGAAAT
1265754 TGTTTCACTCGAAACAAAAATTTATTCCATTTGAGATGA
66 TGTTTCACTCGAAACAAAAATTTATTCCATTTGAGATGA
* * * **
1265793 TTTTTCTTAAAATTAATTTTGTCTCACTTGAGACAGGTTTCCCTTGAAACACAAA-AATTTGAAA
1 TTTTTCTTAAAATCAATTTTGTCTCACTTGAGGCAGTTTTCCCTTGAAA-ACAAATTTTTTGAAA
* *
1265857 TT-TTTCACTCGAAACAAAAATTTA-TCTCACTTGAAATTG-
65 TTGTTTCACTCGAAACAAAAATTTATTC-CATTTGAGA-TGA
* * *
1265896 TTTTTCTTAAAATCAATTTCGTCTCGCTTGAGGCAATTTTCCCTT-AAAACAAATTTTTTGAAAT
1 TTTTTCTTAAAATCAATTTTGTCTCACTTGAGGCAGTTTTCCCTTGAAAACAAATTTTTTGAAAT
* *
1265960 TGTTTCGCTTGAAACAAAAATTTATTCCATTTGAGATGA
66 TGTTTCACTCGAAACAAAAATTTATTCCATTTGAGATGA
*
1265999 TTTTTCTTAAAATGAATTTTGTCTC
1 TTTTTCTTAAAATCAATTTTGTCTC
1266024 GCTCGAAAAA
Statistics
Matches: 195, Mismatches: 29, Indels: 15
0.82 0.12 0.06
Matches are distributed among these distances:
101 5 0.03
102 16 0.08
103 118 0.61
104 56 0.29
ACGTcount: A:0.30, C:0.15, G:0.11, T:0.44
Consensus pattern (104 bp):
TTTTTCTTAAAATCAATTTTGTCTCACTTGAGGCAGTTTTCCCTTGAAAACAAATTTTTTGAAAT
TGTTTCACTCGAAACAAAAATTTATTCCATTTGAGATGA
Found at i:1266137 original size:104 final size:106
Alignment explanation
Indices: 1266029--1266240 Score: 299
Period size: 104 Copynumber: 2.0 Consensus size: 106
1266019 GTCTCGCTCG
*
1266029 AAAAAAAATTCAACTCACTTGAAATTGT-TTT-TTAAAATCAATTTCGTCTCGCTTGAGAC-AGT
1 AAAAAAAATTCAACTCACTTGAAATTCTCTTTCTTAAAATCAATTTCGTCTCGCTTGAGACAAGT
* * * *
1266091 TTCCCTTGGAACAC-AAATTTTGAAATTGTTTCGCTCAAAAC
66 TTCCCTTGAAACACAAAAATTTAAAATTGTTT-ACTCAAAAC
* * *
1266132 -AAAAAAATTCATCTCACTTGAAATTCTCTTTCTTAAAATCAATTTCGTCTCGCTTGAGCCAATT
1 AAAAAAAATTCAACTCACTTGAAATTCTCTTTCTTAAAATCAATTTCGTCTCGCTTGAGACAAGT
*
1266196 TTCCCTTGAAACACAAAAATTTAAAATTGTTTACTCGAAAC
66 TTCCCTTGAAACACAAAAATTTAAAATTGTTTACTCAAAAC
1266237 AAAA
1 AAAA
1266241 TTTTATCTCA
Statistics
Matches: 95, Mismatches: 9, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
102 25 0.26
103 3 0.03
104 27 0.28
105 22 0.23
106 18 0.19
ACGTcount: A:0.37, C:0.19, G:0.09, T:0.34
Consensus pattern (106 bp):
AAAAAAAATTCAACTCACTTGAAATTCTCTTTCTTAAAATCAATTTCGTCTCGCTTGAGACAAGT
TTCCCTTGAAACACAAAAATTTAAAATTGTTTACTCAAAAC
Found at i:1266182 original size:159 final size:160
Alignment explanation
Indices: 1265864--1266185 Score: 413
Period size: 159 Copynumber: 2.0 Consensus size: 160
1265854 AAATTTTTCA
* * *
1265864 CTCGAAACAAAAATTTATCTCACTTGAAATTGTTTTTCTTAAAATCAATTTCGTCTCGCTTGAGG
1 CTCGAAACAAAAATTCAACTCACTTGAAATTGTTTTTCTTAAAATCAATTTCGTCTCGCTTGAGA
* ** * *
1265929 CAATTTTCCCTTAAAACAAATTTTTTGAAATTGTTTCGCTTGAAACAAAAATTTATTCCATTTGA
66 CAAGTTTCCCTTAAAACAAA-TTTTTGAAATTGTTTCGCTCAAAACAAAAATTCATTCCACTTGA
* * * *
1265994 GATGATTTTTCTTAAAATGAATTTTGTCTCG
130 AATGATCTTTCTTAAAATCAATTTCGTCTCG
1266025 CTCGAAA-AAAAATTCAACTCACTTGAAATTG-TTTT-TTAAAATCAATTTCGTCTCGCTTGAGA
1 CTCGAAACAAAAATTCAACTCACTTGAAATTGTTTTTCTTAAAATCAATTTCGTCTCGCTTGAGA
*
1266087 C-AGTTTCCCTTGGAACACAAA-TTTTGAAATTGTTTCGCTCAAAACAAAAAAATTCA-TCTCAC
66 CAAGTTTCCCTT--AAAACAAATTTTTGAAATTGTTTCGCTCAAAAC--AAAAATTCATTC-CAC
**
1266149 TTGAAATTCTCTTTCTTAAAATCAATTTCGTCTCG
126 TTGAAATGATCTTTCTTAAAATCAATTTCGTCTCG
1266184 CT
1 CT
1266186 TGAGCCAATT
Statistics
Matches: 141, Mismatches: 15, Indels: 12
0.84 0.09 0.07
Matches are distributed among these distances:
157 31 0.22
158 29 0.21
159 52 0.37
160 22 0.16
161 7 0.05
ACGTcount: A:0.33, C:0.18, G:0.11, T:0.39
Consensus pattern (160 bp):
CTCGAAACAAAAATTCAACTCACTTGAAATTGTTTTTCTTAAAATCAATTTCGTCTCGCTTGAGA
CAAGTTTCCCTTAAAACAAATTTTTGAAATTGTTTCGCTCAAAACAAAAATTCATTCCACTTGAA
ATGATCTTTCTTAAAATCAATTTCGTCTCG
Found at i:1266646 original size:44 final size:44
Alignment explanation
Indices: 1266598--1266716 Score: 177
Period size: 44 Copynumber: 2.7 Consensus size: 44
1266588 TCTTTTGCTC
*
1266598 GATTCTATCACAGAATGAGATAGATCAGCATCAACATTTTGTTT
1 GATTCTATCACAGAATGAGATAGATCAACATCAACATTTTGTTT
*
1266642 GATTCTATCACAGAA-GAAGATAGATCAATATCAACATTTTGTTT
1 GATTCTATCACAGAATG-AGATAGATCAACATCAACATTTTGTTT
* * *
1266686 GATTCTATCACAAAATGAGGTGGATCAACAT
1 GATTCTATCACAGAATGAGATAGATCAACAT
1266717 TATCATTCCT
Statistics
Matches: 67, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
43 1 0.01
44 65 0.97
45 1 0.01
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.32
Consensus pattern (44 bp):
GATTCTATCACAGAATGAGATAGATCAACATCAACATTTTGTTT
Found at i:1269720 original size:139 final size:139
Alignment explanation
Indices: 1269451--1269723 Score: 347
Period size: 139 Copynumber: 2.0 Consensus size: 139
1269441 GTTTGTTTAA
* * * * *
1269451 TTTCACATTTAGTTTTTAAATTAGGTGAATTTTTAATTTGGTCCTCACTTTTGCTCGAGGTTCCG
1 TTTCACATTTAGTCTTTAAATTAGGAGAATTCTTAATTTGATCCTCACTTTTCCTCGAGGTTCCG
* * ** * * *
1269516 AATTAATTATTCGATATGGCATACTTGGATAAAATTAATTGGGATTAATATTAGAGCCTCCATTT
66 AATTAATTATTCGATATCGCATAATTGGATAAAATTAATTAAGATTAATAGTAGAACCTCAATTT
1269581 TAGGCCTAT
131 TAGGCCTAT
* *
1269590 TTTCATATTTAGTCTTTAAATTAGGAGAATTCTTAATTTGATCCTCACTTTTCCTTGAGGTTCC-
1 TTTCACATTTAGTCTTTAAATTAGGAGAATTCTTAATTTGATCCTCACTTTTCCTCGAGGTTCCG
*
1269654 AATTTAATTATTCGA-ATCGCATAATT-GATTAAAATTAATTTAAG-TTAATAGTATAACCTACA
66 AA-TTAATTATTCGATATCGCATAATTGGA-TAAAATTAA-TTAAGATTAATAGTAGAACCT-CA
1269716 ATTTTAGG
127 ATTTTAGG
1269724 TTTAATCCTT
Statistics
Matches: 115, Mismatches: 15, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
137 2 0.02
138 32 0.28
139 81 0.70
ACGTcount: A:0.30, C:0.13, G:0.14, T:0.43
Consensus pattern (139 bp):
TTTCACATTTAGTCTTTAAATTAGGAGAATTCTTAATTTGATCCTCACTTTTCCTCGAGGTTCCG
AATTAATTATTCGATATCGCATAATTGGATAAAATTAATTAAGATTAATAGTAGAACCTCAATTT
TAGGCCTAT
Found at i:1270631 original size:22 final size:21
Alignment explanation
Indices: 1270586--1270631 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1270576 ATTTCATTTT
* * *
1270586 AATTAATTTTTTATTTTCAGA
1 AATTAATTTTTTATATTAAAA
1270607 AATTAATTTTTTAATATTAAAA
1 AATTAATTTTTT-ATATTAAAA
1270629 AAT
1 AAT
1270632 ATGTCAGGTG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 12 0.57
22 9 0.43
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (21 bp):
AATTAATTTTTTATATTAAAA
Found at i:1272103 original size:12 final size:14
Alignment explanation
Indices: 1272086--1272126 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 14
1272076 ACTAATTTTT
1272086 TATAAATAT-TA-A
1 TATAAATATATATA
1272098 TATAAATATATATA
1 TATAAATATATATA
*
1272112 TATATATATATATA
1 TATAAATATATATA
1272126 T
1 T
1272127 TAGTTTAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
12 9 0.35
13 2 0.08
14 15 0.58
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (14 bp):
TATAAATATATATA
Found at i:1272110 original size:2 final size:2
Alignment explanation
Indices: 1272097--1272126 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1272087 ATAAATATTA
*
1272097 AT AT AA 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
1272127 TAGTTTAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1274034 original size:66 final size:62
Alignment explanation
Indices: 1273902--1274042 Score: 178
Period size: 66 Copynumber: 2.2 Consensus size: 62
1273892 ACATTTTGTA
*
1273902 TACCGATGCACAACCATGCATCGATGCACTCCTGATTTTAATGAAACATCGAATGAATTTTATG
1 TACCGATGCACAACCATGCATCGATGCACTCATGATTTT-ATGAAACATCGAATGAA-TTTATG
*
1273966 TACCGATGCACTAACCATGCATCGATGCATCTTCATGCTCTTT-TGAAACATCGAATGTAA-TTA
1 TACCGATGCAC-AACCATGCATCGATGCA-C-TCATGAT-TTTATGAAACATCGAATG-AATTTA
1274029 GTG
61 -TG
1274032 TACCGATGCAC
1 TACCGATGCAC
1274043 CCCTAGTGTA
Statistics
Matches: 69, Mismatches: 2, Indels: 10
0.85 0.02 0.12
Matches are distributed among these distances:
64 11 0.16
65 20 0.29
66 28 0.41
67 7 0.10
68 3 0.04
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.30
Consensus pattern (62 bp):
TACCGATGCACAACCATGCATCGATGCACTCATGATTTTATGAAACATCGAATGAATTTATG
Found at i:1284059 original size:20 final size:20
Alignment explanation
Indices: 1284034--1284082 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
1284024 TTTCGAGTCA
1284034 AGTCGAGTTTAAGAAATTCG
1 AGTCGAGTTTAAGAAATTCG
1284054 AGTCGAGTTTAAGAAATTCG
1 AGTCGAGTTTAAGAAATTCG
1284074 AGTCGAGTT
1 AGTCGAGTT
1284083 GTTCGAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.33, C:0.10, G:0.27, T:0.31
Consensus pattern (20 bp):
AGTCGAGTTTAAGAAATTCG
Found at i:1284079 original size:25 final size:25
Alignment explanation
Indices: 1284025--1284081 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 25
1284015 TTGAAATTTT
*
1284025 TTCGAGTCAAGTCGAGTTTAAGAAA
1 TTCGAGTCGAGTCGAGTTTAAGAAA
1284050 -T----TCGAGTCGAGTTTAAGAAA
1 TTCGAGTCGAGTCGAGTTTAAGAAA
1284070 TTCGAGTCGAGT
1 TTCGAGTCGAGT
1284082 TGTTCGAGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 10
0.70 0.03 0.27
Matches are distributed among these distances:
20 18 0.69
21 1 0.04
24 1 0.04
25 6 0.23
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.30
Consensus pattern (25 bp):
TTCGAGTCGAGTCGAGTTTAAGAAA
Found at i:1286832 original size:7 final size:7
Alignment explanation
Indices: 1286820--1286844 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1286810 AATTAGATTA
1286820 GGATGTC
1 GGATGTC
1286827 GGATGTC
1 GGATGTC
1286834 GGATGTC
1 GGATGTC
1286841 GGAT
1 GGAT
1286845 ATGTAAATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.16, C:0.12, G:0.44, T:0.28
Consensus pattern (7 bp):
GGATGTC
Found at i:1288944 original size:23 final size:24
Alignment explanation
Indices: 1288914--1288971 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 24
1288904 TTATTATTGA
1288914 TAAAAATATAAA-AAAAT-ATATTT
1 TAAAAATATAAATAAAATAAT-TTT
*
1288937 TAAAAATAATAAATCAAATAATTTT
1 TAAAAAT-ATAAATAAAATAATTTT
*
1288962 TAAATATATA
1 TAAAAATATA
1288972 TTTTACAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
23 7 0.23
24 8 0.27
25 13 0.43
26 2 0.07
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (24 bp):
TAAAAATATAAATAAAATAATTTT
Found at i:1290040 original size:29 final size:29
Alignment explanation
Indices: 1290005--1290086 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
1289995 AAACTAAATT
*
1290005 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
1290034 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
1290063 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
1290087 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:1292106 original size:25 final size:25
Alignment explanation
Indices: 1292057--1292122 Score: 78
Period size: 25 Copynumber: 2.6 Consensus size: 25
1292047 AACAATATAC
* **
1292057 ATAATCGTGTAATAAAAATTGACGA
1 ATAATCGTGTCATAAAAATAAACGA
*
1292082 ATAATCGTGTCATAAAAGTAAACGA
1 ATAATCGTGTCATAAAAATAAACGA
* *
1292107 ACAATTGTGTCATAAA
1 ATAATCGTGTCATAAA
1292123 TGTAGACAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.47, C:0.11, G:0.15, T:0.27
Consensus pattern (25 bp):
ATAATCGTGTCATAAAAATAAACGA
Found at i:1293853 original size:28 final size:28
Alignment explanation
Indices: 1293809--1293864 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
1293799 CCACCGTTGC
* *
1293809 TTTCAAGCATTAGCTCGACAATATAATG
1 TTTCAAGCATGAGCTCGACAACATAATG
*
1293837 TTTCAAGCACTGA-CTCGACGACATAATG
1 TTTCAAGCA-TGAGCTCGACAACATAATG
1293865 AAAACAAAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 22 0.92
29 2 0.08
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.29
Consensus pattern (28 bp):
TTTCAAGCATGAGCTCGACAACATAATG
Found at i:1294805 original size:20 final size:20
Alignment explanation
Indices: 1294780--1294817 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1294770 GCACACCAAA
**
1294780 TTCTCAAATTATCTCAAATC
1 TTCTCAAACCATCTCAAATC
1294800 TTCTCAAACCATCTCAAA
1 TTCTCAAACCATCTCAAA
1294818 GCCCAAACCC
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:0.37, C:0.29, G:0.00, T:0.34
Consensus pattern (20 bp):
TTCTCAAACCATCTCAAATC
Found at i:1294841 original size:17 final size:17
Alignment explanation
Indices: 1294802--1294844 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
1294792 CTCAAATCTT
* *
1294802 CTCAAACCATCTCAAAG
1 CTCAAACCCTCTCAAAA
* *
1294819 CCCAAACCCTCTTAAAA
1 CTCAAACCCTCTCAAAA
1294836 CTCAAACCC
1 CTCAAACCC
1294845 AGTCAAATAT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.40, C:0.42, G:0.02, T:0.16
Consensus pattern (17 bp):
CTCAAACCCTCTCAAAA
Found at i:1297087 original size:60 final size:60
Alignment explanation
Indices: 1296991--1297110 Score: 170
Period size: 60 Copynumber: 2.0 Consensus size: 60
1296981 TTCCACGCTG
* * * * *
1296991 TCGACATTTAGGTCGAACAAGCTGGTAGTTGCATGCCTTCCCCTTGAA-CTTGAAGGCATC
1 TCGACATTGAGGTCGAACAAGCTCGCAGTTGAATGCC-TCCCCCTGAAGCTTGAAGGCATC
*
1297051 TCGACATTGAGGTCGAAGAAGCTCGCAGTTGAATGCCTCCCCCTGAAGCTTGAAGGCATC
1 TCGACATTGAGGTCGAACAAGCTCGCAGTTGAATGCCTCCCCCTGAAGCTTGAAGGCATC
1297111 ATATCAAATG
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
59 9 0.17
60 44 0.83
ACGTcount: A:0.24, C:0.26, G:0.25, T:0.25
Consensus pattern (60 bp):
TCGACATTGAGGTCGAACAAGCTCGCAGTTGAATGCCTCCCCCTGAAGCTTGAAGGCATC
Found at i:1298692 original size:29 final size:30
Alignment explanation
Indices: 1298659--1298719 Score: 97
Period size: 29 Copynumber: 2.1 Consensus size: 30
1298649 ATGCCCGTTT
*
1298659 TTCCAGTTTAGTGCCTAACGTTT-ATTTCA
1 TTCCAGTTTAGTGCCTAACGTTTCATTCCA
*
1298688 TTCCAGTTTGGTGCCTAACGTTTCATTCCA
1 TTCCAGTTTAGTGCCTAACGTTTCATTCCA
1298718 TT
1 TT
1298720 ACTTAAAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 22 0.76
30 7 0.24
ACGTcount: A:0.18, C:0.23, G:0.15, T:0.44
Consensus pattern (30 bp):
TTCCAGTTTAGTGCCTAACGTTTCATTCCA
Found at i:1299201 original size:17 final size:16
Alignment explanation
Indices: 1299175--1299209 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 16
1299165 CGGGTTAGTG
1299175 TTAGGATTTTGAGGTT
1 TTAGGATTTTGAGGTT
1299191 TTAGAGATTTTGAGGTT
1 TTAG-GATTTTGAGGTT
1299208 TT
1 TT
1299210 GAGTAATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.20, C:0.00, G:0.29, T:0.51
Consensus pattern (16 bp):
TTAGGATTTTGAGGTT
Found at i:1299288 original size:27 final size:28
Alignment explanation
Indices: 1299233--1299288 Score: 71
Period size: 27 Copynumber: 2.0 Consensus size: 28
1299223 GAAATAAGGG
**
1299233 TTTTTATAAATATAATAATATTTTTAAT
1 TTTTTATAAATATAATAATATTTAAAAT
1299261 TTTTTAT-AATATAATAA-ATTTCAAAAT
1 TTTTTATAAATATAATAATATTT-AAAAT
1299288 T
1 T
1299289 ATGAGATTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 4 0.16
27 14 0.56
28 7 0.28
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.54
Consensus pattern (28 bp):
TTTTTATAAATATAATAATATTTAAAAT
Found at i:1308342 original size:2 final size:2
Alignment explanation
Indices: 1308335--1308367 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1308325 TAGTGATGTG
1308335 TA 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 TA T
1308368 CATGTATTCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1322750 original size:21 final size:20
Alignment explanation
Indices: 1322664--1322821 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
1322654 AAATGACCAA
**
1322664 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
1322683 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
1322703 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
1322723 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
1322744 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
1322765 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
1322785 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
1322806 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
1322822 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:1322850 original size:20 final size:20
Alignment explanation
Indices: 1322788--1323017 Score: 232
Period size: 20 Copynumber: 11.5 Consensus size: 20
1322778 CGATTTTCCA
* ** *
1322788 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
1322808 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
1322828 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1322848 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
1322868 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
1322888 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1322908 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1322928 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
1322948 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
1322968 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
1322988 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
1323008 AAATCACAAC
1 AAATCGCAAC
1323018 ACTGAAATTT
Statistics
Matches: 176, Mismatches: 28, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 172 0.98
21 2 0.01
ACGTcount: A:0.37, C:0.25, G:0.19, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:1323739 original size:24 final size:24
Alignment explanation
Indices: 1323700--1323746 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1323690 AAATTTGGTC
1323700 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
1323724 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
1323747 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:1326296 original size:34 final size:33
Alignment explanation
Indices: 1326228--1326368 Score: 239
Period size: 33 Copynumber: 4.2 Consensus size: 33
1326218 CGGAAATTAC
1326228 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
* *
1326261 AATCCCAAC-ATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAACGA-GAGAATCGCAATGC-GAAATGAA
1326295 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
1326328 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
1326361 AATCGCAA
1 AATCGCAA
1326369 TGCGAAATGA
Statistics
Matches: 101, Mismatches: 4, Indels: 6
0.91 0.04 0.05
Matches are distributed among these distances:
32 1 0.01
33 70 0.69
34 29 0.29
35 1 0.01
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.13
Consensus pattern (33 bp):
AATCGCAACGAGAGAATCGCAATGCGAAATGAA
Found at i:1326314 original size:14 final size:14
Alignment explanation
Indices: 1326295--1326349 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
1326285 CGGAAATGAA
1326295 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
1326309 AATCGCAATGCGAAATGAA
1 AATCGCAA--CG--A-GAG
1326328 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1326342 AATCGCAA
1 AATCGCAA
1326350 TGCGAAATGA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.45, C:0.20, G:0.24, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1326317 original size:67 final size:67
Alignment explanation
Indices: 1326209--1326368 Score: 243
Period size: 67 Copynumber: 2.4 Consensus size: 67
1326199 GCATTTGACT
** * *
1326209 ATCGCAACACGGAAATTACAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAAC-ATG
1 ATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAACGA-G
1326273 AAA
65 AAA
*
1326276 ATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGAGA
1 ATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAACGAGA
*
1326341 GA
66 AA
1326343 ATCGCAATGC-GAAATGAAAATCGCAA
1 ATCGCAATGCGGAAATGAAAATCGCAA
1326369 TGCGAAATGA
Statistics
Matches: 86, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
66 16 0.19
67 69 0.80
68 1 0.01
ACGTcount: A:0.46, C:0.20, G:0.21, T:0.13
Consensus pattern (67 bp):
ATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAACGAGA
AA
Done.