Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold160
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: 5021213
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 92036 characters in sequence are not A, C, G, or T
File 7 of 30
Found at i:1061742 original size:149 final size:151
Alignment explanation
Indices: 1061469--1061739 Score: 318
Period size: 149 Copynumber: 1.8 Consensus size: 151
1061459 CTTCATTTCC
*
1061469 TTTTTTTCCTTTGTCCTCAAAGAGTAGGGCGCACTTCTTTTCCCTTTATCCTCAAAGAGCAGGAT
1 TTTTTTTCCTTTGTCCTCAAAGAGTAGGACGCACTTCTTTTCCCTTTATCCTCAAAGAGCAGGAT
* * * ** *
1061534 GCACTTCATTTCCTTTTCTCCCTTTGTCTTTAAAGAGTAGGACGTACTTCTTTTCCCTTTGTTCT
66 GCACTTCATTTCCTTTTCTCCCTTTGTCCTCAAAGAGCAGGACCCACTTCTTCTCCCTTTGTTCT
1061599 CAGAGAGCAGGACATACTTCA
131 CAGAGAGCAGGACATACTTCA
* * * * *
1061620 TTTTTTTCC-TTGTCCTCAAA-AGGTAGGATGCACTT-TTTTTCCTTTGTCTTCAAGGAGCAGGA
1 TTTTTTTCCTTTGTCCTCAAAGA-GTAGGACGCACTTCTTTTCCCTTTATCCTCAAAGAGCAGGA
** * * *
1061682 TGCATTCTTTTTTTCCTTTT-T-CCTTTGTCCTCAAGGAGCATGACCCATTTCATTCTCC
65 TGCA--CTTCATTTCCTTTTCTCCCTTTGTCCTCAAAGAGCAGGACCCACTTC-TTCTCC
1061740 TTTTTCCTCT
Statistics
Matches: 99, Mismatches: 17, Indels: 9
0.79 0.14 0.07
Matches are distributed among these distances:
149 50 0.51
150 28 0.28
151 21 0.21
ACGTcount: A:0.18, C:0.25, G:0.15, T:0.41
Consensus pattern (151 bp):
TTTTTTTCCTTTGTCCTCAAAGAGTAGGACGCACTTCTTTTCCCTTTATCCTCAAAGAGCAGGAT
GCACTTCATTTCCTTTTCTCCCTTTGTCCTCAAAGAGCAGGACCCACTTCTTCTCCCTTTGTTCT
CAGAGAGCAGGACATACTTCA
Found at i:1062102 original size:31 final size:31
Alignment explanation
Indices: 1061869--1062189 Score: 169
Period size: 31 Copynumber: 9.8 Consensus size: 31
1061859 TCTTTTTTTT
* *
1061869 AGCCCACACGAGTTGGTGGCACCCT-AGTCAA
1 AGCCCACACAAGCTGGTGGCA-CCTGAGTCAA
* ** * * *
1061900 AGCTCGTACAAGCTAGTGGCACTTAAGTCAA
1 AGCCCACACAAGCTGGTGGCACCTGAGTCAA
** * * * *
1061931 AGCCTGCACAAGTTGGCGACAACTGAGTCAA
1 AGCCCACACAAGCTGGTGGCACCTGAGTCAA
** *
1061962 AGCCCACACAAGCTAATGGCACCTAAGTCTAAGTCTA
1 AGCCCACACAAGCTGGTGGCACCT--G----AGTCAA
* * ** *
1061999 AGCCTACACGAA-TTGGTGGCACCCAAGTCTA
1 AGCCCACAC-AAGCTGGTGGCACCTGAGTCAA
* * *
1062030 AGCCCGCAAAAGCTGGCGGCACCTGAGTCAA
1 AGCCCACACAAGCTGGTGGCACCTGAGTCAA
**
1062061 AGCTTACACAAGCTGGTGGCACCTGAGTCAA
1 AGCCCACACAAGCTGGTGGCACCTGAGTCAA
* *
1062092 AGCCCCCACAAGATGGTGGCACCTAAGCCAGAGTCAA
1 AGCCCACACAAGCTGGTGGCACCT------GAGTCAA
* *
1062129 AGCCCATACAAGCTGGTGGCACCTAAGTTTAAATCAA
1 AGCCCACACAAGCTGGTGGCACCT--G----AGTCAA
1062166 AGCCCACACAAGCTGGTGGCACCT
1 AGCCCACACAAGCTGGTGGCACCT
1062190 AAGTTCGAGT
Statistics
Matches: 216, Mismatches: 55, Indels: 32
0.71 0.18 0.11
Matches are distributed among these distances:
30 4 0.02
31 130 0.60
33 3 0.01
37 77 0.36
38 2 0.01
ACGTcount: A:0.31, C:0.29, G:0.23, T:0.17
Consensus pattern (31 bp):
AGCCCACACAAGCTGGTGGCACCTGAGTCAA
Found at i:1062112 original size:130 final size:130
Alignment explanation
Indices: 1061869--1062118 Score: 311
Period size: 130 Copynumber: 1.9 Consensus size: 130
1061859 TCTTTTTTTT
* * * * * * *
1061869 AGCCCACACGAGTTGGTGGCACCCTAGTCAAAGCTCGTACAAGCTAGTGGCACTTAAGTCAAAGC
1 AGCCCACACGAATTGGTGGCACCCAAGTCAAAGCCCGCAAAAGCTAGCGGCACCTAAGTCAAAGC
* * *
1061934 CTGCACAAGTTGGCGACAACTGAGTCAAAGCCCACACAAGCTAATGGCACCTAAGTCTAAGTCTA
66 CTACACAAGCTGGCGACAACTGAGTCAAAGCCCACACAAGATAATGGCACCTAAGTCTAAGTCTA
* * * *
1061999 AGCCTACACGAATTGGTGGCACCCAAGTCTAAGCCCGCAAAAGCTGGCGGCACCTGAGTCAAAGC
1 AGCCCACACGAATTGGTGGCACCCAAGTCAAAGCCCGCAAAAGCTAGCGGCACCTAAGTCAAAGC
* * * * * **
1062064 TTACACAAGCTGGTGGCACCTGAGTCAAAGCCCCCACAAGATGGTGGCACCTAAG
66 CTACACAAGCTGGCGACAACTGAGTCAAAGCCCACACAAGATAATGGCACCTAAG
1062119 CCAGAGTCAA
Statistics
Matches: 99, Mismatches: 21, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
130 99 1.00
ACGTcount: A:0.30, C:0.29, G:0.24, T:0.17
Consensus pattern (130 bp):
AGCCCACACGAATTGGTGGCACCCAAGTCAAAGCCCGCAAAAGCTAGCGGCACCTAAGTCAAAGC
CTACACAAGCTGGCGACAACTGAGTCAAAGCCCACACAAGATAATGGCACCTAAGTCTAAGTCTA
Found at i:1062132 original size:130 final size:130
Alignment explanation
Indices: 1061869--1062156 Score: 310
Period size: 130 Copynumber: 2.2 Consensus size: 130
1061859 TCTTTTTTTT
* * * * * * *
1061869 AGCCCACACGAGTTGGTGGCACCCTAGTCAAAGCTCGTACAAGCTAGTGGCACTTAAGTCAAAGC
1 AGCCCACACGAATTGGTGGCACCCAAGTCAAAGCCCGCAAAAGCTAGCGGCACCTAAGTCAAAGC
* * * * *
1061934 CTGCACAAGTTGGCGACAACTGAGTCAAAGCCCACACAAGCTAATGGCACCTAAGTCTAAGTCTA
66 CTACACAAGCTGGCGACAACTGAGTCAAAGCCCACACAAGATAATGGCACCTAAGTCCAAGTCAA
* * * *
1061999 AGCCTACACGAATTGGTGGCACCCAAGTCTAAGCCCGCAAAAGCTGGCGGCACCTGAGTCAAAGC
1 AGCCCACACGAATTGGTGGCACCCAAGTCAAAGCCCGCAAAAGCTAGCGGCACCTAAGTCAAAGC
* * * * * **
1062064 TTACACAAGCTGGTGGCACCTGAGTCAAAGCCCCCACAAGATGGTGGCACCTAAG-CCAGAGTCA
66 CTACACAAGCTGGCGACAACTGAGTCAAAGCCCACACAAGATAATGGCACCTAAGTCCA-AGTCA
1062128 A
130 A
* * *
1062129 AGCCCATAC-AAGCTGGTGGCACCTAAGT
1 AGCCCACACGAA-TTGGTGGCACCCAAGT
1062157 TTAAATCAAA
Statistics
Matches: 129, Mismatches: 27, Indels: 4
0.81 0.17 0.03
Matches are distributed among these distances:
129 4 0.03
130 125 0.97
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.17
Consensus pattern (130 bp):
AGCCCACACGAATTGGTGGCACCCAAGTCAAAGCCCGCAAAAGCTAGCGGCACCTAAGTCAAAGC
CTACACAAGCTGGCGACAACTGAGTCAAAGCCCACACAAGATAATGGCACCTAAGTCCAAGTCAA
Found at i:1062140 original size:37 final size:38
Alignment explanation
Indices: 1062085--1062202 Score: 152
Period size: 37 Copynumber: 3.2 Consensus size: 38
1062075 GGTGGCACCT
* *
1062085 GAGTCAAAGCCCCCACAAGATGGTGGCACCTAAG-CCA
1 GAGTCAAAGCCCACACAAGCTGGTGGCACCTAAGTCCA
* **
1062122 GAGTCAAAGCCCATACAAGCTGGTGGCACCTAAGTTTA
1 GAGTCAAAGCCCACACAAGCTGGTGGCACCTAAGTCCA
* *
1062160 -AATCAAAGCCCACACAAGCTGGTGGCACCTAAGTTC-
1 GAGTCAAAGCCCACACAAGCTGGTGGCACCTAAGTCCA
1062196 GAGTCAA
1 GAGTCAA
1062203 GTCCACATTA
Statistics
Matches: 70, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
37 69 0.99
38 1 0.01
ACGTcount: A:0.33, C:0.28, G:0.23, T:0.16
Consensus pattern (38 bp):
GAGTCAAAGCCCACACAAGCTGGTGGCACCTAAGTCCA
Found at i:1062805 original size:20 final size:20
Alignment explanation
Indices: 1062780--1062818 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
1062770 GTATTCAATT
1062780 AGTGAATGTATCGATACATA
1 AGTGAATGTATCGATACATA
1062800 AGTGAATGTATCGATACAT
1 AGTGAATGTATCGATACAT
1062819 GTCTCAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.10, G:0.21, T:0.31
Consensus pattern (20 bp):
AGTGAATGTATCGATACATA
Found at i:1064295 original size:20 final size:19
Alignment explanation
Indices: 1064256--1064292 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
1064246 TTTCATCAAC
1064256 AAGTTCTTGATCTTGGGGA
1 AAGTTCTTGATCTTGGGGA
1064275 AAGTTCTTGATCTTGGGG
1 AAGTTCTTGATCTTGGGG
1064293 GAACATTAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.19, C:0.11, G:0.32, T:0.38
Consensus pattern (19 bp):
AAGTTCTTGATCTTGGGGA
Found at i:1064406 original size:26 final size:26
Alignment explanation
Indices: 1064377--1064427 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
1064367 TTTTAGGTTT
1064377 TGCCAAAGCCTTGATTCTCCCTTAAC
1 TGCCAAAGCCTTGATTCTCCCTTAAC
1064403 TGCCAAAGCCTTGATTCTCCCTTAA
1 TGCCAAAGCCTTGATTCTCCCTTAA
1064428 GTGTATGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.24, C:0.33, G:0.12, T:0.31
Consensus pattern (26 bp):
TGCCAAAGCCTTGATTCTCCCTTAAC
Found at i:1068361 original size:113 final size:113
Alignment explanation
Indices: 1068157--1068361 Score: 331
Period size: 113 Copynumber: 1.8 Consensus size: 113
1068147 CTCCTACAAG
* * * *
1068157 GCTGTGGACTCTAATATATGGTTTTGGACTGTCTTTTTGTGACATTGTCTAATTGGGATTATATT
1 GCTGTGAACTCTAATATATAGTTTTGGACTGTCCTTTTGTAACATTGTCTAATTGGGATTATATT
* *
1068222 TTTATCATGATGAAGTCAGGGTTGCTACTGCTAAGTTCGGGAATCAAT
66 TTGATCATAATGAAGTCAGGGTTGCTACTGCTAAGTTCGGGAATCAAT
*
1068270 GCTGTGAACTCTAATATATAGTTTTGGACTGTCCTTTTGTAACATTTTCTAATTGGGATTATATT
1 GCTGTGAACTCTAATATATAGTTTTGGACTGTCCTTTTGTAACATTGTCTAATTGGGATTATATT
1068335 TTGATCATAATGAAGTCATGGG-TGCTA
66 TTGATCATAATGAAGTCA-GGGTTGCTA
1068362 AGTTTGGGAC
Statistics
Matches: 84, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
113 81 0.96
114 3 0.04
ACGTcount: A:0.24, C:0.12, G:0.22, T:0.41
Consensus pattern (113 bp):
GCTGTGAACTCTAATATATAGTTTTGGACTGTCCTTTTGTAACATTGTCTAATTGGGATTATATT
TTGATCATAATGAAGTCAGGGTTGCTACTGCTAAGTTCGGGAATCAAT
Found at i:1070448 original size:28 final size:28
Alignment explanation
Indices: 1070408--1070462 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
1070398 AGTCATATGA
1070408 TAACCATAAGATCAAATCCGTGAATGTC
1 TAACCATAAGATCAAATCCGTGAATGTC
*
1070436 TAACCATAAGATCAAATCGGTGAATGT
1 TAACCATAAGATCAAATCCGTGAATGT
1070463 TTTGATGAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.40, C:0.18, G:0.16, T:0.25
Consensus pattern (28 bp):
TAACCATAAGATCAAATCCGTGAATGTC
Found at i:1074490 original size:13 final size:13
Alignment explanation
Indices: 1074472--1074498 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1074462 ACATTATGCT
1074472 TTGTATCGATACA
1 TTGTATCGATACA
1074485 TTGTATCGATACA
1 TTGTATCGATACA
1074498 T
1 T
1074499 GCTCACTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1074585 original size:13 final size:13
Alignment explanation
Indices: 1074567--1074593 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1074557 TTATCACTAT
1074567 TTGTATCGATACA
1 TTGTATCGATACA
1074580 TTGTATCGATACA
1 TTGTATCGATACA
1074593 T
1 T
1074594 GAGAAAATTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1081302 original size:290 final size:290
Alignment explanation
Indices: 1080782--1081361 Score: 991
Period size: 290 Copynumber: 2.0 Consensus size: 290
1080772 AACACCTAGG
* * * *
1080782 CAACCCTATCCAAGTCGCGATCGGTACTCCCAGGTCGCAATCGGGCAGCCCCCACACCTATCGCC
1 CAACCCTATCCAAGTCACGATCGGTACTCCCAGGTCGAAACCGGGCAGCCCCCACACCTATCACC
*
1080847 TAGAACACCCGAAACCTTCCGATTTTTCACCGAAATCATTTTTAACTCGTCCAATGGCTCCTCAA
66 TAGAACACCCAAAACCTTCCGATTTTTCACCGAAATCATTTTTAACTCGTCCAATGGCTCCTCAA
* *
1080912 ATGAAATTATCCTCACAACGACGCACTCGAGGTGCTTTCTCCCCTAATCCGCAAAATCAAACCTT
131 ATGAAATTACCCTCACAACGACGCACTCGAGGTGCTTCCTCCCCTAATCCGCAAAATCAAACCTT
*
1080977 TTTCGAAGGTTGTTTTCGAACTCAAGCCAACCTCGAACATTTTAACCGTACTTTTTCC-CGGTTG
196 CTTCGAAGGTTGTTTTCGAACTCAAGCCAACCTCGAACATTTTAACCGTAC-TTTTCCTCGGTTG
*
1081041 GCTGTCCGACCATGTCGCGCGGTCGACATGA
260 GCTGTCCGACCATGTCGCGCGGTCAACATGA
*
1081072 CAACCCTATCCAGGTCACGATCGGTACTCCCAGGTCGAAACCGGGCAGCCCCCACACCTATCACC
1 CAACCCTATCCAAGTCACGATCGGTACTCCCAGGTCGAAACCGGGCAGCCCCCACACCTATCACC
* * *
1081137 TAGAACACCTAAAACCTTTCGATTTTTCACCGAAATCATTTTTAACTCGTCCAATGGCTCCTCGA
66 TAGAACACCCAAAACCTTCCGATTTTTCACCGAAATCATTTTTAACTCGTCCAATGGCTCCTCAA
* *
1081202 ATGAAATTACCCTCACAACGACGCACTCGAGGTGCTTCCTCCTCTAATCTGCAAAATCAAACCTT
131 ATGAAATTACCCTCACAACGACGCACTCGAGGTGCTTCCTCCCCTAATCCGCAAAATCAAACCTT
1081267 CTTCGAAGGTTGTTTTCGAACTCAAGCCAACCTCGAACATTTTAACCGTACTTTTCCTCGGTTGG
196 CTTCGAAGGTTGTTTTCGAACTCAAGCCAACCTCGAACATTTTAACCGTACTTTTCCTCGGTTGG
**
1081332 CTGTTTGACCATGTCGCGCGGTCAACATGA
261 CTGTCCGACCATGTCGCGCGGTCAACATGA
1081362 AATATCTCAG
Statistics
Matches: 272, Mismatches: 17, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
289 6 0.02
290 266 0.98
ACGTcount: A:0.25, C:0.32, G:0.17, T:0.26
Consensus pattern (290 bp):
CAACCCTATCCAAGTCACGATCGGTACTCCCAGGTCGAAACCGGGCAGCCCCCACACCTATCACC
TAGAACACCCAAAACCTTCCGATTTTTCACCGAAATCATTTTTAACTCGTCCAATGGCTCCTCAA
ATGAAATTACCCTCACAACGACGCACTCGAGGTGCTTCCTCCCCTAATCCGCAAAATCAAACCTT
CTTCGAAGGTTGTTTTCGAACTCAAGCCAACCTCGAACATTTTAACCGTACTTTTCCTCGGTTGG
CTGTCCGACCATGTCGCGCGGTCAACATGA
Found at i:1083131 original size:13 final size:13
Alignment explanation
Indices: 1083113--1083139 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1083103 ACATTATGCT
1083113 TTGTATCGATACA
1 TTGTATCGATACA
1083126 TTGTATCGATACA
1 TTGTATCGATACA
1083139 T
1 T
1083140 GCTCACTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1083171 original size:20 final size:19
Alignment explanation
Indices: 1083123--1083179 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
1083113 TTGTATCGAT
1083123 ACATTGTATCGATACATGC
1 ACATTGTATCGATACATGC
* * *
1083142 TCACTGTATCGATACATGG
1 ACATTGTATCGATACATGC
1083161 ACAATTGTATCGATACATG
1 AC-ATTGTATCGATACATG
1083180 AGATTGGCAG
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 17 0.53
20 15 0.47
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32
Consensus pattern (19 bp):
ACATTGTATCGATACATGC
Found at i:1083245 original size:13 final size:13
Alignment explanation
Indices: 1083224--1083254 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1083214 CGATACATGG
*
1083224 TACAATGTATCGA
1 TACATTGTATCGA
1083237 TACATTGTATCGA
1 TACATTGTATCGA
1083250 TACAT
1 TACAT
1083255 GAGGAAATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.35
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:1083251 original size:33 final size:34
Alignment explanation
Indices: 1083209--1083277 Score: 97
Period size: 33 Copynumber: 2.1 Consensus size: 34
1083199 TATCACTATC
*
1083209 TGTATCGATACATG-GTACAA-TGTATCGATACAT
1 TGTATCGATACATGAGGA-AATTGTATCGATACAT
*
1083242 TGTATCGATACATGAGGAAATTGTATCGTTACAT
1 TGTATCGATACATGAGGAAATTGTATCGATACAT
1083276 TG
1 TG
1083278 CTTGTAACGG
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
33 16 0.50
34 16 0.50
ACGTcount: A:0.32, C:0.13, G:0.20, T:0.35
Consensus pattern (34 bp):
TGTATCGATACATGAGGAAATTGTATCGATACAT
Found at i:1084280 original size:17 final size:17
Alignment explanation
Indices: 1084258--1084292 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1084248 ACTATTTTAA
* *
1084258 ATTTTAACTATTTGTTT
1 ATTTTAAATATTTCTTT
1084275 ATTTTAAATATTTCTTT
1 ATTTTAAATATTTCTTT
1084292 A
1 A
1084293 CTCATAAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.29, C:0.06, G:0.03, T:0.63
Consensus pattern (17 bp):
ATTTTAAATATTTCTTT
Found at i:1088097 original size:2 final size:2
Alignment explanation
Indices: 1088090--1088121 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1088080 ATCTTACTAA
1088090 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
1088122 TACCATGTTA
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:1089975 original size:22 final size:20
Alignment explanation
Indices: 1089943--1089984 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 20
1089933 TTTTAATATT
*
1089943 TTAATTTTTAAATATATTTA
1 TTAATTTTTAAAAATATTTA
1089963 TTAAGTTTATTAAAAATATTTA
1 TTAA-TTT-TTAAAAATATTTA
1089985 CTAAAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 4 0.21
21 3 0.16
22 12 0.63
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (20 bp):
TTAATTTTTAAAAATATTTA
Found at i:1090562 original size:13 final size:14
Alignment explanation
Indices: 1090531--1090565 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
1090521 TGATACTTTT
1090531 TTTTTAAATTAATA
1 TTTTTAAATTAATA
*
1090545 TTTTTAAATTATTA
1 TTTTTAAATTAATA
1090559 TTTTTAA
1 TTTTTAA
1090566 TCTTAACTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
TTTTTAAATTAATA
Found at i:1092808 original size:33 final size:34
Alignment explanation
Indices: 1092739--1092815 Score: 88
Period size: 33 Copynumber: 2.3 Consensus size: 34
1092729 CAGAGGAAAA
* *
1092739 GATAAATT-TTTGTTAAATCAATATAATCAAAGT
1 GATAAATTATTTGTTAAATAAAAATAATCAAAGT
*
1092772 GATAAATTATTT-TTAAATAAAAATAAGT-AAATT
1 GATAAATTATTTGTTAAATAAAAATAA-TCAAAGT
*
1092805 GATAATTTATT
1 GATAAATTATT
1092816 ATATAAAGAT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
33 34 0.89
34 4 0.11
ACGTcount: A:0.48, C:0.03, G:0.08, T:0.42
Consensus pattern (34 bp):
GATAAATTATTTGTTAAATAAAAATAATCAAAGT
Found at i:1093849 original size:14 final size:14
Alignment explanation
Indices: 1093830--1093858 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1093820 TTTTTAACGA
1093830 AAAAAATTTTGAAC
1 AAAAAATTTTGAAC
1093844 AAAAAATTTTGAAC
1 AAAAAATTTTGAAC
1093858 A
1 A
1093859 GTTGCTCCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.59, C:0.07, G:0.07, T:0.28
Consensus pattern (14 bp):
AAAAAATTTTGAAC
Found at i:1094566 original size:20 final size:21
Alignment explanation
Indices: 1094527--1094570 Score: 72
Period size: 22 Copynumber: 2.1 Consensus size: 21
1094517 TTAAGTATAG
1094527 ATGTTTTTCAAGCATAAAAATA
1 ATGTTTTTCAAG-ATAAAAATA
1094549 ATGTTTTTCAAG-TAAAAATA
1 ATGTTTTTCAAGATAAAAATA
1094569 AT
1 AT
1094571 TCAAAATATC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 10 0.45
22 12 0.55
ACGTcount: A:0.45, C:0.07, G:0.09, T:0.39
Consensus pattern (21 bp):
ATGTTTTTCAAGATAAAAATA
Found at i:1095299 original size:36 final size:34
Alignment explanation
Indices: 1095250--1095341 Score: 118
Period size: 36 Copynumber: 2.7 Consensus size: 34
1095240 TGAGTGATTA
*
1095250 AGAGGTTCTATCTTAGCCTTTGAAAAAGATGAGG
1 AGAGGTTCTATCTTAGCCTTTGAAAAAGATAAGG
*
1095284 AGAAAGGTTCTATCTTAGCCTGTG-AAAAGATAAGG
1 AG--AGGTTCTATCTTAGCCTTTGAAAAAGATAAGG
*
1095319 AG-GTTTCTATCTTAG-CTTTGAAA
1 AGAGGTTCTATCTTAGCCTTTGAAA
1095342 GATAGTGTTG
Statistics
Matches: 51, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
31 4 0.08
32 14 0.27
34 2 0.04
35 12 0.24
36 19 0.37
ACGTcount: A:0.33, C:0.12, G:0.24, T:0.32
Consensus pattern (34 bp):
AGAGGTTCTATCTTAGCCTTTGAAAAAGATAAGG
Found at i:1096446 original size:21 final size:21
Alignment explanation
Indices: 1096420--1096462 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1096410 AATCAACCAT
* *
1096420 TCAAGATGATGATGAAGATGA
1 TCAAGAGGATGATGAAAATGA
*
1096441 TCAAGAGGTTGATGAAAATGA
1 TCAAGAGGATGATGAAAATGA
1096462 T
1 T
1096463 GAAATGGCTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.42, C:0.05, G:0.28, T:0.26
Consensus pattern (21 bp):
TCAAGAGGATGATGAAAATGA
Found at i:1096939 original size:32 final size:30
Alignment explanation
Indices: 1096892--1097012 Score: 118
Period size: 32 Copynumber: 3.8 Consensus size: 30
1096882 ACAATACTAT
*
1096892 TTTTCAAGGCTAAGATAGAAACCTCCCCATC
1 TTTTCACGGCTAAGATAG-AACCTCCCCATC
*
1096923 TTTTCACGAGCTAAGATAAAACCTCTTCCCTATC
1 TTTTCACG-GCTAAGATAGAACCTC--CCC-ATC
* *
1096957 TTTTGCA-GGTTAAGATAGAACCTCCCTATC
1 TTTT-CACGGCTAAGATAGAACCTCCCCATC
*
1096987 TTTTACAAAGGCTAAGATAGAACCTC
1 TTTT-C-ACGGCTAAGATAGAACCTC
1097013 TACATTATTT
Statistics
Matches: 76, Mismatches: 7, Indels: 13
0.79 0.07 0.14
Matches are distributed among these distances:
30 8 0.11
31 16 0.21
32 25 0.33
33 17 0.22
34 8 0.11
35 2 0.03
ACGTcount: A:0.31, C:0.26, G:0.13, T:0.30
Consensus pattern (30 bp):
TTTTCACGGCTAAGATAGAACCTCCCCATC
Found at i:1097036 original size:64 final size:63
Alignment explanation
Indices: 1096887--1097043 Score: 183
Period size: 64 Copynumber: 2.4 Consensus size: 63
1096877 ACCTTACAAT
* *
1096887 ACTATTTTTCAAGGCTAAGATAGAAACCTCCCCATCTTTTCACGAGCTAAGATAAAACCTCTTC
1 ACTATTTTTCAAGGCTAAGATAG-AACCTCCCCATCTTTTCAAGAGCTAAGATAAAACCTCTAC
* * * *
1096951 CCTATCTTTTGC-AGGTTAAGATAGAACCTCCCTATCTTTTACAA-AGGCTAAGATAGAACCTCT
1 ACTAT-TTTT-CAAGGCTAAGATAGAACCTCCCCATCTTTT-CAAGA-GCTAAGATAAAACCTCT
1097014 AC
62 AC
* *
1097016 ATTATTTTTTAAGGCTAAGATAGAACCT
1 ACTATTTTTCAAGGCTAAGATAGAACCT
1097044 TTGAATCACT
Statistics
Matches: 78, Mismatches: 10, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
64 40 0.51
65 37 0.47
66 1 0.01
ACGTcount: A:0.32, C:0.23, G:0.13, T:0.32
Consensus pattern (63 bp):
ACTATTTTTCAAGGCTAAGATAGAACCTCCCCATCTTTTCAAGAGCTAAGATAAAACCTCTAC
Found at i:1098191 original size:13 final size:13
Alignment explanation
Indices: 1098173--1098198 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1098163 CAATTTTTTG
1098173 TGTATCGATACAT
1 TGTATCGATACAT
1098186 TGTATCGATACAT
1 TGTATCGATACAT
1098199 ACTTGCTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1098284 original size:20 final size:20
Alignment explanation
Indices: 1098259--1098331 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
1098249 ATCTTTTTTT
1098259 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
1098279 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
1098300 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
1098320 ATGTATCGATAC
1 ATGTATCGATAC
1098332 TTTGAGTTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:1098310 original size:41 final size:42
Alignment explanation
Indices: 1098237--1098331 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 42
1098227 CTGCCAAGAA
*
1098237 ATGTATCGATACATCTTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTTCATGTATCGATACATTGCAAC
1098279 ATGTATCGATACATC-TTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTTCATGTATCGATACATTGCAAC
1098320 ATGTATCGATAC
1 ATGTATCGATAC
1098332 TTTGAGTTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
41 37 0.71
42 15 0.29
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.40
Consensus pattern (42 bp):
ATGTATCGATACATCTTTTTTCATGTATCGATACATTGCAAC
Found at i:1098969 original size:17 final size:17
Alignment explanation
Indices: 1098937--1098983 Score: 76
Period size: 17 Copynumber: 2.7 Consensus size: 17
1098927 CTCTCCTTTG
*
1098937 TCTCCCCCGTTTAAAAAA
1 TCTCCCCC-TTAAAAAAA
1098955 TCTCCCCCTTAAAAAAA
1 TCTCCCCCTTAAAAAAA
1098972 TCTCCCCCTTAA
1 TCTCCCCCTTAA
1098984 TCAAGTAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
17 20 0.71
18 8 0.29
ACGTcount: A:0.32, C:0.38, G:0.02, T:0.28
Consensus pattern (17 bp):
TCTCCCCCTTAAAAAAA
Found at i:1100809 original size:13 final size:13
Alignment explanation
Indices: 1100791--1100829 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
1100781 ATAATCACCC
*
1100791 TGTATCGATACAG
1 TGTATCGATACAA
1100804 TGTATCGATACAA
1 TGTATCGATACAA
1100817 TGTATCGATACAA
1 TGTATCGATACAA
1100830 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1100840 original size:20 final size:20
Alignment explanation
Indices: 1100815--1100893 Score: 70
Period size: 20 Copynumber: 3.7 Consensus size: 20
1100805 GTATCGATAC
1100815 AATGTATCGATACAAAGAAA
1 AATGTATCGATACAAAGAAA
*
1100835 AATGTATCGATACATAGAATTTCCA
1 AATGTATCGATACAAAGAA-----A
*
1100860 GATGTATCGATACACAA-AAA
1 AATGTATCGATACA-AAGAAA
*
1100880 CATGTATCGATACA
1 AATGTATCGATACA
1100894 TTTTGGACAT
Statistics
Matches: 49, Mismatches: 4, Indels: 12
0.75 0.06 0.18
Matches are distributed among these distances:
20 32 0.65
25 16 0.33
26 1 0.02
ACGTcount: A:0.46, C:0.15, G:0.14, T:0.25
Consensus pattern (20 bp):
AATGTATCGATACAAAGAAA
Found at i:1102928 original size:15 final size:15
Alignment explanation
Indices: 1102908--1102938 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1102898 ATTTCGTTTG
*
1102908 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
1102923 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
1102938 G
1 G
1102939 GACATTTTTA
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:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:1107018 original size:13 final size:13
Alignment explanation
Indices: 1107000--1107025 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1106990 CAATTTTTTG
1107000 TGTATCGATACAT
1 TGTATCGATACAT
1107013 TGTATCGATACAT
1 TGTATCGATACAT
1107026 ACTTGCTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1107090 original size:21 final size:21
Alignment explanation
Indices: 1107064--1107139 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
1107054 CTGCCAAGAA
*
1107064 ATGTATCGATACATCTTTTTT
1 ATGTATCGATACATCTTTTTC
****
1107085 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
1107105 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
1107126 ATGTATCGATACAT
1 ATGTATCGATACAT
1107140 TGCAACATGT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:1107110 original size:20 final size:20
Alignment explanation
Indices: 1107085--1107157 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
1107075 CATCTTTTTT
1107085 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
1107105 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
1107126 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
1107146 ATGTATCGATAC
1 ATGTATCGATAC
1107158 TTTGAGTTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:1107121 original size:41 final size:41
Alignment explanation
Indices: 1107064--1107157 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
1107054 CTGCCAAGAA
*
1107064 ATGTATCGATACATCTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1107105 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1107146 ATGTATCGATAC
1 ATGTATCGATAC
1107158 TTTGAGTTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:1107538 original size:22 final size:22
Alignment explanation
Indices: 1107513--1107554 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
1107503 GATGAGGAGT
1107513 GATGTATCGATACATGAACAGC
1 GATGTATCGATACATGAACAGC
*
1107535 GATGTATTGATACATGAACA
1 GATGTATCGATACATGAACA
1107555 ATGATCAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.38, C:0.14, G:0.21, T:0.26
Consensus pattern (22 bp):
GATGTATCGATACATGAACAGC
Found at i:1107626 original size:13 final size:13
Alignment explanation
Indices: 1107608--1107632 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1107598 TACCAGTTTT
1107608 ATGTATCGATATA
1 ATGTATCGATATA
1107621 ATGTATCGATAT
1 ATGTATCGATAT
1107633 GAAGTAAAAT
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:0.08, G:0.16, T:0.40
Consensus pattern (13 bp):
ATGTATCGATATA
Found at i:1113386 original size:23 final size:20
Alignment explanation
Indices: 1113336--1113449 Score: 122
Period size: 20 Copynumber: 5.5 Consensus size: 20
1113326 TAACTAGATA
* *
1113336 TATCGATACATTGAACAATA
1 TATCGATACATTGAAGAATG
*
1113356 TATCGATACATTTGGGTAGAATG
1 TATCGATACA-TT--GAAGAATG
1113379 TATCGATACATTGAAGAATG
1 TATCGATACATTGAAGAATG
* * *
1113399 TATCGATAAATTCATA-CATG
1 TATCGATACATTGA-AGAATG
*
1113419 TATCGATACATTGAAAAATG
1 TATCGATACATTGAAGAATG
1113439 TATCGATACAT
1 TATCGATACAT
1113450 CTGGGTAAAA
Statistics
Matches: 79, Mismatches: 10, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.01
20 58 0.73
21 3 0.04
22 2 0.03
23 15 0.19
ACGTcount: A:0.39, C:0.12, G:0.16, T:0.32
Consensus pattern (20 bp):
TATCGATACATTGAAGAATG
Found at i:1114282 original size:45 final size:46
Alignment explanation
Indices: 1114162--1114285 Score: 160
Period size: 49 Copynumber: 2.7 Consensus size: 46
1114152 AGATGAGAGG
** *
1114162 AGTGCCAATGTGCCAATTCAAGGCCAGTGACATTGGGCTAAGGGAAA
1 AGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGGCTAA-GGAAA
*
1114209 AGTGAACCAATGTGCTGATTCAAGGCCAGCGACATTGGGCTAA-TAAA
1 AGTG--CCAATGTGCTGATTCAAGGCCAGCGACATTGGGCTAAGGAAA
* *
1114256 AGTGCCAATATGCTGATTCAATGCCAGCGA
1 AGTGCCAATGTGCTGATTCAAGGCCAGCGA
1114286 TATCGGACTT
Statistics
Matches: 69, Mismatches: 6, Indels: 6
0.85 0.07 0.07
Matches are distributed among these distances:
45 24 0.35
47 11 0.16
49 34 0.49
ACGTcount: A:0.32, C:0.20, G:0.27, T:0.21
Consensus pattern (46 bp):
AGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGGCTAAGGAAA
Found at i:1114413 original size:28 final size:28
Alignment explanation
Indices: 1114366--1114880 Score: 575
Period size: 28 Copynumber: 17.9 Consensus size: 28
1114356 TTTCAAAAAA
* *
1114366 GGTGCCACTAACTTGTGTGGGCTTTGAAGG
1 GGTGCCACTGAC-T-TGTGGGCTTTGAAAG
*
1114396 GGTACCACTGACTTGTGGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* *
1114424 GGTGCCACTGATTTGTGTGGGCTTCGAAAG
1 GGTGCCACTGA-CT-TGTGGGCTTTGAAAG
*
1114454 GGTATGCCACTAACTTGTGGGCTTTGAAAG
1 GG--TGCCACTGACTTGTGGGCTTTGAAAG
* *
1114484 GGTGCCATTGGCTTGTGGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* *
1114512 AGTATGCCACTGACTTGTGGGCTTTAAAAG
1 -G-GTGCCACTGACTTGTGGGCTTTGAAAG
*
1114542 GGTGCCACTGACTTGTGGGCTTTGAAGG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
*
1114570 GGTACCACTGACTTGTGGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* *
1114598 GGTGCCACTGATTTGTGTGGGCTTCGAAAG
1 GGTGCCACTGA-CT-TGTGGGCTTTGAAAG
*
1114628 GGTATGCCACTAACTTGTGGGCTTTGAAAG
1 GG--TGCCACTGACTTGTGGGCTTTGAAAG
* * *
1114658 GGTGCCATTGGCTTGTGGGCTTTGTAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* * *
1114686 GATGCCATTGACTTGTGGTCTTTTG-AAG
1 GGTGCCACTGACTTGTGGGC-TTTGAAAG
*
1114714 AGATGCCACTGACTTGTGGGCTTTGAAAG
1 -GGTGCCACTGACTTGTGGGCTTTGAAAG
* *
1114743 GATGCCACTGACTTGTGGGCGTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* * *
1114771 GATGCCACTAACTTATGGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
*
1114799 GGTGCCACTGACTTGTGGGCTTTGAAAA
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* * * *
1114827 GATGCTACAGATTTGTGGGC-TTGAAAAG
1 GGTGCCACTGACTTGTGGGCTTTG-AAAG
* *
1114855 GATGCCACTGACTTATGGGCTTTGAA
1 GGTGCCACTGACTTGTGGGCTTTGAA
1114881 GAGATGAACG
Statistics
Matches: 417, Mismatches: 53, Indels: 32
0.83 0.11 0.06
Matches are distributed among these distances:
27 3 0.01
28 266 0.64
29 33 0.08
30 97 0.23
31 2 0.00
32 16 0.04
ACGTcount: A:0.21, C:0.17, G:0.33, T:0.30
Consensus pattern (28 bp):
GGTGCCACTGACTTGTGGGCTTTGAAAG
Found at i:1114658 original size:174 final size:173
Alignment explanation
Indices: 1114361--1114877 Score: 706
Period size: 174 Copynumber: 3.0 Consensus size: 173
1114351 TTTTTTTTCA
* *
1114361 AAAAAGGTGCCACTAACTTGTGTGGGCTTTGAAGGGGTACCACTGACTTGTGGGCTTTGAAAGGG
1 AAAAGGGTGCCACTGAC-T-TGTGGGCTTTGAAGGGGTACCACTGACTTGTGGGCTTTGAAAGGG
1114426 TGCCACTGATTTGTGTGGGCTTCGAAAGGGTATGCCACTAACTTGTGGGCTTTGAAAGGGTGCCA
64 TGCCACTGATTTGTGTGGGCTTCGAAAGGGTATGCCACTAACTTGTGGGCTTTGAAAGGGTGCCA
1114491 TTGGCTTGTGGGCTTTGAAAGAGTATGCCACTGACTTGTGGGCTTT
129 TTGGCTTGTGGGCTTTGAAAGAG-ATGCCACTGACTTGTGGGCTTT
1114537 AAAAGGGTGCCACTGACTTGTGGGCTTTGAAGGGGTACCACTGACTTGTGGGCTTTGAAAGGGTG
1 AAAAGGGTGCCACTGACTTGTGGGCTTTGAAGGGGTACCACTGACTTGTGGGCTTTGAAAGGGTG
1114602 CCACTGATTTGTGTGGGCTTCGAAAGGGTATGCCACTAACTTGTGGGCTTTGAAAGGGTGCCATT
66 CCACTGATTTGTGTGGGCTTCGAAAGGGTATGCCACTAACTTGTGGGCTTTGAAAGGGTGCCATT
* * *
1114667 GGCTTGTGGGCTTTGTAAG-GATGCCATTGACTTGTGGTCTTT
131 GGCTTGTGGGCTTTGAAAGAGATGCCACTGACTTGTGGGCTTT
** * * * * * *
1114709 TGAAGAGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCGTTGAAAGGAT
1 AAAAG-GGTGCCACTGACTTGTGGGCTTTGAAGGGGTACCACTGACTTGTGGGCTTTGAAAGGGT
** * * * * * * *
1114774 GCCACT-AACT-TATGGGCTTTGAAAGGG--TGCCACTGACTTGTGGGCTTTGAAAAGATGCTAC
65 GCCACTGATTTGTGTGGGCTTCGAAAGGGTATGCCACTAACTTGTGGGCTTTGAAAGGGTGCCAT
* ** *
1114835 AGATTTGTGGGC-TTGAAA-AGGATGCCACTGACTTATGGGCTTT
130 TGGCTTGTGGGCTTTGAAAGA-GATGCCACTGACTTGTGGGCTTT
1114878 GAAGAGATGA
Statistics
Matches: 309, Mismatches: 29, Indels: 13
0.88 0.08 0.04
Matches are distributed among these distances:
168 5 0.02
169 58 0.19
171 15 0.05
172 25 0.08
173 60 0.19
174 130 0.42
175 1 0.00
176 15 0.05
ACGTcount: A:0.21, C:0.16, G:0.32, T:0.30
Consensus pattern (173 bp):
AAAAGGGTGCCACTGACTTGTGGGCTTTGAAGGGGTACCACTGACTTGTGGGCTTTGAAAGGGTG
CCACTGATTTGTGTGGGCTTCGAAAGGGTATGCCACTAACTTGTGGGCTTTGAAAGGGTGCCATT
GGCTTGTGGGCTTTGAAAGAGATGCCACTGACTTGTGGGCTTT
Found at i:1120772 original size:33 final size:33
Alignment explanation
Indices: 1120735--1120801 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1120725 TTCAACGATT
1120735 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
1120768 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
1120801 T
1 T
1120802 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:1120773 original size:13 final size:13
Alignment explanation
Indices: 1120755--1120779 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1120745 CATAAAATGT
1120755 TGTATCGATACAA
1 TGTATCGATACAA
1120768 TGTATCGATACA
1 TGTATCGATACA
1120780 TATTTTTTTG
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:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1120863 original size:13 final size:13
Alignment explanation
Indices: 1120845--1120869 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1120835 ATTACTCACA
1120845 TGTATCGATACAT
1 TGTATCGATACAT
1120858 TGTATCGATACA
1 TGTATCGATACA
1120870 CTGATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1121006 original size:52 final size:52
Alignment explanation
Indices: 1120878--1120998 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
1120868 CACTGATCTT
*
1120878 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
1120930 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1120982 TGTATCGATACATGCAG
1 TGTATCGATACATGCAG
1120999 ATAAATTTTC
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:1128223 original size:15 final size:15
Alignment explanation
Indices: 1128203--1128236 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1128193 TCCAAACACA
*
1128203 AAAAAAAGAAAAAAG
1 AAAAAAACAAAAAAG
*
1128218 AAAAAAACAAAACAG
1 AAAAAAACAAAAAAG
1128233 AAAA
1 AAAA
1128237 TCTCGGTGAG
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:0.85, C:0.06, G:0.09, T:0.00
Consensus pattern (15 bp):
AAAAAAACAAAAAAG
Found at i:1129368 original size:65 final size:61
Alignment explanation
Indices: 1129252--1129430 Score: 268
Period size: 65 Copynumber: 2.8 Consensus size: 61
1129242 ATACCTTTTT
1129252 AAAGTCCACGACTCAGTGGCAATCTCTTCTCAAAGTCCACGACTCAGTGGCAATCTCTGCTC
1 AAAGTCCACGACTCAGTGGC-ATCTCTTCTCAAAGTCCACGACTCAGTGGCAATCTCTGCTC
* * *
1129314 AAAGTCCACGACTCAGTGGCATCTTTTCCTTTTTAAAGTCCACGACTCAGTGGCAATCTCTTCTC
1 AAAGTCCACGACTCAGTGGCATC---T-CTTCTCAAAGTCCACGACTCAGTGGCAATCTCTGCTC
*
1129379 AAAGTCCACGACTCAGTGGCAATCTCTGCTCAAAGTCCACGACTCAGTGGCA
1 AAAGTCCACGACTCAGTGGC-ATCTCTTCTCAAAGTCCACGACTCAGTGGCA
1129431 TTTTTTCTTC
Statistics
Matches: 106, Mismatches: 6, Indels: 10
0.87 0.05 0.08
Matches are distributed among these distances:
61 3 0.03
62 44 0.42
63 1 0.01
64 1 0.01
65 54 0.51
66 3 0.03
ACGTcount: A:0.26, C:0.31, G:0.18, T:0.26
Consensus pattern (61 bp):
AAAGTCCACGACTCAGTGGCATCTCTTCTCAAAGTCCACGACTCAGTGGCAATCTCTGCTC
Found at i:1129409 original size:96 final size:96
Alignment explanation
Indices: 1129245--1129437 Score: 377
Period size: 96 Copynumber: 2.0 Consensus size: 96
1129235 TCTTCAAATA
1129245 CCTTTTTAAAGTCCACGACTCAGTGGCAATCTCTTCTCAAAGTCCACGACTCAGTGGCAATCTCT
1 CCTTTTTAAAGTCCACGACTCAGTGGCAATCTCTTCTCAAAGTCCACGACTCAGTGGCAATCTCT
1129310 GCTCAAAGTCCACGACTCAGTGGCATCTTTT
66 GCTCAAAGTCCACGACTCAGTGGCATCTTTT
1129341 CCTTTTTAAAGTCCACGACTCAGTGGCAATCTCTTCTCAAAGTCCACGACTCAGTGGCAATCTCT
1 CCTTTTTAAAGTCCACGACTCAGTGGCAATCTCTTCTCAAAGTCCACGACTCAGTGGCAATCTCT
*
1129406 GCTCAAAGTCCACGACTCAGTGGCATTTTTT
66 GCTCAAAGTCCACGACTCAGTGGCATCTTTT
1129437 C
1 C
1129438 TTCAAAGCCC
Statistics
Matches: 96, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
96 96 1.00
ACGTcount: A:0.24, C:0.30, G:0.17, T:0.30
Consensus pattern (96 bp):
CCTTTTTAAAGTCCACGACTCAGTGGCAATCTCTTCTCAAAGTCCACGACTCAGTGGCAATCTCT
GCTCAAAGTCCACGACTCAGTGGCATCTTTT
Found at i:1129444 original size:31 final size:31
Alignment explanation
Indices: 1129252--1129430 Score: 279
Period size: 31 Copynumber: 5.7 Consensus size: 31
1129242 ATACCTTTTT
1129252 AAAGTCCACGACTCAGTGGCAATCTCTTCTC
1 AAAGTCCACGACTCAGTGGCAATCTCTTCTC
*
1129283 AAAGTCCACGACTCAGTGGCAATCTCTGCTC
1 AAAGTCCACGACTCAGTGGCAATCTCTTCTC
* *
1129314 AAAGTCCACGACTCAGTGGC-ATCTTTTCCTTTTT
1 AAAGTCCACGACTCAGTGGCAATC---T-CTTCTC
1129348 AAAGTCCACGACTCAGTGGCAATCTCTTCTC
1 AAAGTCCACGACTCAGTGGCAATCTCTTCTC
*
1129379 AAAGTCCACGACTCAGTGGCAATCTCTGCTC
1 AAAGTCCACGACTCAGTGGCAATCTCTTCTC
1129410 AAAGTCCACGACTCAGTGGCA
1 AAAGTCCACGACTCAGTGGCA
1129431 TTTTTTCTTC
Statistics
Matches: 136, Mismatches: 7, Indels: 10
0.89 0.05 0.07
Matches are distributed among these distances:
30 3 0.02
31 105 0.77
32 1 0.01
33 1 0.01
34 23 0.17
35 3 0.02
ACGTcount: A:0.26, C:0.31, G:0.18, T:0.26
Consensus pattern (31 bp):
AAAGTCCACGACTCAGTGGCAATCTCTTCTC
Found at i:1129554 original size:34 final size:34
Alignment explanation
Indices: 1129408--1129917 Score: 561
Period size: 34 Copynumber: 14.8 Consensus size: 34
1129398 CAATCTCTGC
* * * *
1129408 TCAAAGTCCACGACTCAGTGGCA--TTTTT-TCT
1 TCAAAGCCCACAACTCCGTGGCACCTTTTTCTTT
* *
1129439 TCAAAGCCCACAACTTCGTGGCACCTTTTCCCTTT
1 TCAAAGCCCACAACTCCGTGGCACCTTTT-TCTTT
* *
1129474 TCAAAGCCCACAACTCCGTGGCACTTCCTTTTCCTT
1 TCAAAGCCCACAACTCCGTGGCAC--CTTTTTCTTT
* *
1129510 T-AAAGCCCACAACTCCGTGGCACATTCTTCTTT
1 TCAAAGCCCACAACTCCGTGGCACCTTTTTCTTT
*
1129543 TCAAAGCCCACAACTCCGTGGCACTTTTTTCATCTT
1 TCAAAGCCCACAACTCCGTGGCACCTTTTTC-T-TT
*
1129579 T--AAGTCCACAACTCCGTGGCACCTTTTTCTTT
1 TCAAAGCCCACAACTCCGTGGCACCTTTTTCTTT
*
1129611 TTAAAGCCCACAACTCCGTGGCACCTTTTTCTTT
1 TCAAAGCCCACAACTCCGTGGCACCTTTTTCTTT
* *
1129645 TTAAAGCCCACAACTCTGTGGCACACTTTTTCTTT
1 TCAAAGCCCACAACTCCGTGGCAC-CTTTTTCTTT
* *
1129680 TTAAAGCCCACAACTCTGTGGCACTCTTTTTCCCTTT
1 TCAAAGCCCACAACTCCGTGGCAC-CTTTTT--CTTT
1129717 TCAAAGCCCACAACTCCGTGGCACCTTTTTCTTT
1 TCAAAGCCCACAACTCCGTGGCACCTTTTTCTTT
* *
1129751 TTAAAGCCCACAACTCCGTGGCACTCTTTTTC-CT
1 TCAAAGCCCACAACTCCGTGGCAC-CTTTTTCTTT
* *
1129785 TCTAAGCCCACAACTCCGTGGCACTCTTTTTC-CT
1 TCAAAGCCCACAACTCCGTGGCAC-CTTTTTCTTT
*
1129819 TCTAAGCCCACAACTCCGTGGCACTCTTTTTTTCCTTT
1 TCAAAGCCCACAACTCCGTGGCAC-C--TTTTT-CTTT
* * *
1129857 TTAAAGCCCACAACTCTGTGGCACCTTGTTCTTT
1 TCAAAGCCCACAACTCCGTGGCACCTTTTTCTTT
* * * *
1129891 T-TAAGTCCACAACTTCGTGGCATCTTT
1 TCAAAGCCCACAACTCCGTGGCACCTTT
1129918 CACCCTTCCT
Statistics
Matches: 422, Mismatches: 38, Indels: 36
0.85 0.08 0.07
Matches are distributed among these distances:
31 19 0.05
32 3 0.01
33 32 0.08
34 197 0.47
35 99 0.23
36 18 0.04
37 32 0.08
38 22 0.05
ACGTcount: A:0.20, C:0.33, G:0.12, T:0.35
Consensus pattern (34 bp):
TCAAAGCCCACAACTCCGTGGCACCTTTTTCTTT
Found at i:1129764 original size:140 final size:139
Alignment explanation
Indices: 1129438--1129917 Score: 645
Period size: 140 Copynumber: 3.5 Consensus size: 139
1129428 GCATTTTTTC
* * * *
1129438 TTCAAAGCCCACAACTTCGTGGCACCTTTTCCCTTTTCAAAGCCCACAACTCCGTGGCACTTCCT
1 TTCAAAGCCCACAACTCCGTGGCACCTTTT-TCTTTTTAAAGCCCACAACTCCGTGGCAC-TCTT
* * *
1129503 TTTCCTTTAAAGCCCACAACTCCGTGGCACA-TTCTTCTTTTCAAAGCCCACAACTCCGTGGCAC
64 TTTCTTTTAAAGCCCACAACTCCGTGGCACACTTTTTCTTTTTAAAGCCCACAACTCCGTGGCAC
*
1129567 T-TTTTTCATCT
129 TCTTTTTCCT-T
*
1129578 TT--AAGTCCACAACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACAACTCCGTGGCAC-CTTTT
1 TTCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACAACTCCGTGGCACTCTTTT
* *
1129640 TCTTTTTAAAGCCCACAACTCTGTGGCACACTTTTTCTTTTTAAAGCCCACAACTCTGTGGCACT
66 TC-TTTTAAAGCCCACAACTCCGTGGCACACTTTTTCTTTTTAAAGCCCACAACTCCGTGGCACT
1129705 CTTTTTCCCTT
130 CTTTTT-CCTT
1129716 TTCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACAACTCCGTGGCACTCTTTT
1 TTCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACAACTCCGTGGCACTCTTTT
* * * *
1129781 TCCTTCT-AAGCCCACAACTCCGTGGCACTCTTTTTCCTTCT-AAGCCCACAACTCCGTGGCACT
66 T-CTTTTAAAGCCCACAACTCCGTGGCACACTTTTTCTTTTTAAAGCCCACAACTCCGTGGCACT
1129844 CTTTTTTTCCTT
130 C--TTTTTCCTT
* * * * *
1129856 TTTAAAGCCCACAACTCTGTGGCACCTTGTTCTTTTT-AAGTCCACAACTTCGTGGCA-TCTTT
1 TTCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACAACTCCGTGGCACTCTTT
1129918 CACCCTTCCT
Statistics
Matches: 307, Mismatches: 23, Indels: 22
0.87 0.07 0.06
Matches are distributed among these distances:
135 6 0.02
136 25 0.08
137 58 0.19
138 37 0.12
139 42 0.14
140 124 0.40
141 14 0.05
142 1 0.00
ACGTcount: A:0.20, C:0.33, G:0.12, T:0.35
Consensus pattern (139 bp):
TTCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACAACTCCGTGGCACTCTTTT
TCTTTTAAAGCCCACAACTCCGTGGCACACTTTTTCTTTTTAAAGCCCACAACTCCGTGGCACTC
TTTTTCCTT
Found at i:1130055 original size:49 final size:48
Alignment explanation
Indices: 1129991--1130827 Score: 1041
Period size: 49 Copynumber: 17.8 Consensus size: 48
1129981 GCAACCCTTC
* * *
1129991 TAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-CTTCATCTT
1130040 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA---C--CTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACTTCATCTT
* * *
1130083 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGACACCTTTATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-CTTCATCTT
1130132 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA---C--CTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACTTCATCTT
* * * *
1130175 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTTATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-CTTCATCTT
* *
1130224 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGG----T-ACCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACTTCATCTT
* * *
1130267 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-CTTCATCTT
1130316 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA---C--CTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACTTCATCTT
* *
1130359 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACATTTTCCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC---TT-CATCTT
*
1130411 TAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGGCA---C--CTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACTTCATCTT
* * * *
1130454 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCATCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-CTTCATCTT
*
1130503 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-CTTCATCTT
*
1130552 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACTTCATCTT
*
1130600 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-CTTCATCTT
* * *
1130649 TAAATCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTCACCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACTTCATCTT
1130697 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA---C--CTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACTTCATCTT
* * *
1130740 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATCGGCACCTTTTCCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-C--TT-CATCTT
*
1130792 TAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTG
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTG
1130828 ACATCCTTTT
Statistics
Matches: 688, Mismatches: 57, Indels: 83
0.83 0.07 0.10
Matches are distributed among these distances:
43 233 0.34
44 1 0.00
45 4 0.01
47 1 0.00
48 92 0.13
49 281 0.41
50 2 0.00
52 74 0.11
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.31
Consensus pattern (48 bp):
TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACTTCATCTT
Found at i:1130104 original size:22 final size:22
Alignment explanation
Indices: 1130037--1130104 Score: 54
Period size: 22 Copynumber: 3.1 Consensus size: 22
1130027 GCATCTTCAT
1130037 CTTTAAGTCCAATGTAGCTGGC
1 CTTTAAGTCCAATGTAGCTGGC
* * *
1130059 CTTGAA-TCAGCACAT-TGGC--AC
1 CTTTAAGTC--CA-ATGTAGCTGGC
1130080 CTTTAAGTCCAATGTAGCTGGC
1 CTTTAAGTCCAATGTAGCTGGC
1130102 CTT
1 CTT
1130105 GACTCAGCAC
Statistics
Matches: 33, Mismatches: 6, Indels: 14
0.62 0.11 0.26
Matches are distributed among these distances:
19 2 0.06
20 5 0.15
21 8 0.24
22 11 0.33
23 5 0.15
24 2 0.06
ACGTcount: A:0.24, C:0.25, G:0.21, T:0.31
Consensus pattern (22 bp):
CTTTAAGTCCAATGTAGCTGGC
Found at i:1130153 original size:92 final size:92
Alignment explanation
Indices: 1129986--1130836 Score: 1238
Period size: 92 Copynumber: 9.1 Consensus size: 92
1129976 CGGTGGCAAC
* *
1129986 CCTTCTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATG
1 CCTT-TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATG
1130051 TAGCTGGCCTTGAATCAGCACATTGGCA
65 TAGCTGGCCTTGAATCAGCACATTGGCA
* * * * *
1130079 CCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGACACCTTTATCTTTAAGTCCAATGT
1 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGT
1130144 AGCTGGCCTTGAATCAGCACATTGGCA
66 AGCTGGCCTTGAATCAGCACATTGGCA
* * *
1130171 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTTATCTTTAAGTCCAATGT
1 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGT
* *
1130236 AGCTGGCCTTGACTCAGCACATTGGTA
66 AGCTGGCCTTGAATCAGCACATTGGCA
* *
1130263 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGT
1 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGT
1130328 AGCTGGCCTTGAATCAGCACATTGGCA
66 AGCTGGCCTTGAATCAGCACATTGGCA
* *
1130355 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACATTTTCCATCTTTAAGTTCAA
1 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC--CTT-CATCTTTAAGTCCAA
1130420 TGTAGCTGGCCTTGAATCAGCACATTGGCA
63 TGTAGCTGGCCTTGAATCAGCACATTGGCA
* * *
1130450 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCATCATCTTTAAGTCCAATGT
1 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGT
*
1130515 AGCTGGCCTTGACTCAGCACATTGGCA
66 AGCTGGCCTTGAATCAGCACATTGGCA
* *
1130542 CCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC-TCATCTTTAAGTC
1 ----C--CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTC
*
1130606 CAATGTAGCTGGCCTTGACTCAGCACATTGGCA
60 CAATGTAGCTGGCCTTGAATCAGCACATTGGCA
* * * *
1130639 CCTTCATCTTTAAATCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC-TCACCTTTAAGTC
1 ----C--CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTC
1130703 CAATGTAGCTGGCCTTGAATCAGCACATTGGCA
60 CAATGTAGCTGGCCTTGAATCAGCACATTGGCA
* *
1130736 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATCGGCACCTTTTCCATCTTTAAGTTCAA
1 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACC--TT-CATCTTTAAGTCCAA
*
1130801 TGTAGCTGGCCTTGAATCAGCACATTGACA
63 TGTAGCTGGCCTTGAATCAGCACATTGGCA
1130831 TCCTTT
1 -CCTTT
1130837 TTCATCATCT
Statistics
Matches: 702, Mismatches: 42, Indels: 25
0.91 0.05 0.03
Matches are distributed among these distances:
91 40 0.06
92 339 0.48
93 6 0.01
94 3 0.00
95 128 0.18
96 6 0.01
97 140 0.20
98 40 0.06
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.31
Consensus pattern (92 bp):
CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGT
AGCTGGCCTTGAATCAGCACATTGGCA
Found at i:1133186 original size:33 final size:33
Alignment explanation
Indices: 1133149--1133215 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1133139 TTCAACGATT
1133149 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
1133182 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
1133215 T
1 T
1133216 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:1133187 original size:13 final size:13
Alignment explanation
Indices: 1133169--1133193 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1133159 CATAAAATGT
1133169 TGTATCGATACAA
1 TGTATCGATACAA
1133182 TGTATCGATACA
1 TGTATCGATACA
1133194 TATTTTTTTG
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:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1133277 original size:13 final size:13
Alignment explanation
Indices: 1133259--1133283 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1133249 ATTACTCACA
1133259 TGTATCGATACAT
1 TGTATCGATACAT
1133272 TGTATCGATACA
1 TGTATCGATACA
1133284 CTGATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1133420 original size:52 final size:52
Alignment explanation
Indices: 1133292--1133412 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
1133282 CACTGATCTT
*
1133292 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
1133344 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1133396 TGTATCGATACATGCAG
1 TGTATCGATACATGCAG
1133413 ATAAATTTTC
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:1144108 original size:20 final size:20
Alignment explanation
Indices: 1144077--1144193 Score: 101
Period size: 20 Copynumber: 5.7 Consensus size: 20
1144067 TTTTAACTAG
*
1144077 ATGTACCGATACATTGAACA
1 ATGTATCGATACATTGAACA
* * *
1144097 ATATATCGATACATCTGGGTAGA
1 ATGTATCGATACAT-T--GAACA
* *
1144120 ATGTATCAATACATTGAAGA
1 ATGTATCGATACATTGAACA
* * *
1144140 ATGTATTGATAAATTCATAC-
1 ATGTATCGATACATTGA-ACA
*
1144160 ATGTATCGATACATTGAAAA
1 ATGTATCGATACATTGAACA
1144180 ATGTATCGATACAT
1 ATGTATCGATACAT
1144194 CTGGGTAAAA
Statistics
Matches: 76, Mismatches: 16, Indels: 10
0.75 0.16 0.10
Matches are distributed among these distances:
19 1 0.01
20 57 0.75
21 2 0.03
22 1 0.01
23 15 0.20
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.32
Consensus pattern (20 bp):
ATGTATCGATACATTGAACA
Found at i:1145574 original size:21 final size:21
Alignment explanation
Indices: 1145545--1145597 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
1145535 CTTGCAACTT
*
1145545 ATTTCTTTTCTCCTCTAATTC
1 ATTTATTTTCTCCTCTAATTC
**
1145566 ATTTATTTTCTTTTCTAATTC
1 ATTTATTTTCTCCTCTAATTC
* *
1145587 ACTTAATTTCT
1 ATTTATTTTCT
1145598 TTTCAAGAAG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.19, C:0.21, G:0.00, T:0.60
Consensus pattern (21 bp):
ATTTATTTTCTCCTCTAATTC
Found at i:1145598 original size:21 final size:21
Alignment explanation
Indices: 1145558--1145601 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
1145548 TCTTTTCTCC
* *
1145558 TCTAATTCATTTATTTTCTTT
1 TCTAATTCACTTAATTTCTTT
1145579 TCTAATTCACTTAATTTCTTT
1 TCTAATTCACTTAATTTCTTT
1145600 TC
1 TC
1145602 AAGAAGATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.20, C:0.18, G:0.00, T:0.61
Consensus pattern (21 bp):
TCTAATTCACTTAATTTCTTT
Found at i:1146602 original size:20 final size:20
Alignment explanation
Indices: 1146577--1146651 Score: 114
Period size: 20 Copynumber: 3.8 Consensus size: 20
1146567 TTTTACCCAG
1146577 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * *
1146597 ATGTATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
*
1146617 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTTTTCA
1146637 ATGTATCGATACATT
1 ATGTATCGATACATT
1146652 CCGTCTTTTT
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:1156459 original size:10 final size:10
Alignment explanation
Indices: 1156442--1156547 Score: 77
Period size: 10 Copynumber: 11.2 Consensus size: 10
1156432 CATCCTTCAT
1156442 AACCAAAAAA
1 AACCAAAAAA
*
1156452 AGCCAAAAAA
1 AACCAAAAAA
1156462 CAA--AAAAAA
1 -AACCAAAAAA
*
1156471 AA-CAGAAAA
1 AACCAAAAAA
1156480 AACCAAAAAAA
1 AACC-AAAAAA
*
1156491 AAACAAAAAA
1 AACCAAAAAA
1156501 AACC--AAAA
1 AACCAAAAAA
1156509 AA--AAAAAA
1 AACCAAAAAA
1156517 AA-C-AAAAA
1 AACCAAAAAA
*
1156525 AACAAAAAAA
1 AACCAAAAAA
*
1156535 AAACAAGAAAA
1 AACCAA-AAAA
1156546 AA
1 AA
1156548 AATAAACAGA
Statistics
Matches: 77, Mismatches: 9, Indels: 19
0.73 0.09 0.18
Matches are distributed among these distances:
8 21 0.27
9 13 0.17
10 28 0.36
11 15 0.19
ACGTcount: A:0.84, C:0.13, G:0.03, T:0.00
Consensus pattern (10 bp):
AACCAAAAAA
Found at i:1156460 original size:1 final size:1
Alignment explanation
Indices: 1156456--1156549 Score: 80
Period size: 1 Copynumber: 94.0 Consensus size: 1
1156446 AAAAAAAGCC
* * * ** * ** *
1156456 AAAAAACAAAAAAAAAACAGAAAAAACCAAAAAAAAAACAAAAAAAACCAAAAAAAAAAAAAACA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * *
1156521 AAAAAACAAAAAAAAAACAAGAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1156550 TAAACAGAAA
Statistics
Matches: 73, Mismatches: 20, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
1 73 1.00
ACGTcount: A:0.87, C:0.11, G:0.02, T:0.00
Consensus pattern (1 bp):
A
Found at i:1156470 original size:11 final size:11
Alignment explanation
Indices: 1156456--1156549 Score: 120
Period size: 11 Copynumber: 8.5 Consensus size: 11
1156446 AAAAAAAGCC
1156456 AAAAAACAAAA
1 AAAAAACAAAA
*
1156467 AAAAAAC-AGA
1 AAAAAACAAAA
*
1156477 AAAAACCAAAA
1 AAAAAACAAAA
1156488 AAAAAAC-AAA
1 AAAAAACAAAA
*
1156498 AAAAACCAAAA
1 AAAAAACAAAA
*
1156509 AAAAAAAAAACA
1 AAAAAACAAA-A
1156521 AAAAAACAAAA
1 AAAAAACAAAA
1156532 AAAAAACAAGAA
1 AAAAAACAA-AA
1156544 AAAAAA
1 AAAAAA
1156550 TAAACAGAAA
Statistics
Matches: 71, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
10 17 0.24
11 36 0.51
12 18 0.25
ACGTcount: A:0.87, C:0.11, G:0.02, T:0.00
Consensus pattern (11 bp):
AAAAAACAAAA
Found at i:1156470 original size:21 final size:21
Alignment explanation
Indices: 1156446--1156537 Score: 75
Period size: 21 Copynumber: 4.3 Consensus size: 21
1156436 CTTCATAACC
1156446 AAAAAAAGCCAAAAAACAAAA
1 AAAAAAAGCCAAAAAACAAAA
*
1156467 AAAAAACAG--AAAAAACCAAA
1 AAAAAA-AGCCAAAAAACAAAA
*
1156487 AAAAAAA-CAAAAAAAACCAAAAA
1 AAAAAAAGC-CAAAAAA-C-AAAA
**
1156510 AAAAAAAAACAAAAAA-ACAAA
1 AAAAAAAGCCAAAAAACA-AAA
1156531 AAAAAAA
1 AAAAAAA
1156538 CAAGAAAAAA
Statistics
Matches: 59, Mismatches: 4, Indels: 16
0.75 0.05 0.20
Matches are distributed among these distances:
19 1 0.02
20 17 0.29
21 22 0.37
22 3 0.05
23 16 0.27
ACGTcount: A:0.86, C:0.12, G:0.02, T:0.00
Consensus pattern (21 bp):
AAAAAAAGCCAAAAAACAAAA
Found at i:1157869 original size:28 final size:28
Alignment explanation
Indices: 1157772--1158157 Score: 470
Period size: 28 Copynumber: 13.5 Consensus size: 28
1157762 CATTCATCTC
* *
1157772 TTCAAAGCCCACAAGTTAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCA-TCCT
* * *
1157801 TTCAAAGCCTACACGAGTCGGTGGCAACTCTT
1 TTCAAAGCC--CACAAGTCAGTGGC-A-TCCT
* *
1157833 TTTAAAGCCCACAAGTTAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
*
1157861 TTCAAAGCCCACAAGTCAGTGGCATGCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
*
1157889 TTCAAAGCCCACAAGTCAGTGGCATGCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
*
1157917 TTCAAAGCCCACAAGTCAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCA-TCCT
*
1157946 TTCAAAGCCCACAAGTCAGTGGCATCAT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
1157974 TTCAAAGCCCACAAGTCAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* *
1158002 TTCAAAGCCCACAAGTCAATGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
*
1158030 TTCAAAGCCCACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* *
1158058 TTCAAAACCCACAAGTTAGTGGCA-CCTT
1 TTCAAAGCCCACAAGTCAGTGGCATCC-T
* *
1158086 TTCAAAGCCCACAAGCCAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCA-TCCT
* * *
1158115 TTTAAAGTCCACAAG-CTAGTGGCAACTCTT
1 TTCAAAGCCCACAAGTC-AGTGGC-A-TCCT
1158145 TTCAAAGCCCACA
1 TTCAAAGCCCACA
1158158 TAAGTGAGTG
Statistics
Matches: 320, Mismatches: 28, Indels: 17
0.88 0.08 0.05
Matches are distributed among these distances:
27 2 0.01
28 208 0.65
29 56 0.17
30 29 0.09
31 11 0.03
32 14 0.04
ACGTcount: A:0.29, C:0.30, G:0.18, T:0.23
Consensus pattern (28 bp):
TTCAAAGCCCACAAGTCAGTGGCATCCT
Found at i:1157977 original size:113 final size:113
Alignment explanation
Indices: 1157766--1158177 Score: 519
Period size: 113 Copynumber: 3.6 Consensus size: 113
1157756 CTAGAACATT
* * *
1157766 CATCTCTTCAAAGCCCACAAGTTAGTGGCACTCTTTTCAAAGCCTACACGAGTCGGTGGCAACTC
1 CATCT-TTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCC--CACAAGTCAGTGGC-ACTC
* *
1157831 TTTTTAAAGCCCACAAGTTAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGG
62 TTTTCAAAGCCCACAAGTTAGTGGCATCATTTCAAAGCCCACAAGTCAGTGG
1157883 CATGCTTTCAAAGCCCACAAGTCAGTGGCA-TGC-TTTCAAAGCCCACAAGTCAGTGGCACTCTT
1 CAT-CTTTCAAAGCCCACAAGTCAGTGGCACT-CTTTTCAAAGCCCACAAGTCAGTGGCACTCTT
*
1157946 TTCAAAGCCCACAAGTCAGTGGCATCATTTCAAAGCCCACAAGTCAGTGG
64 TTCAAAGCCCACAAGTTAGTGGCATCATTTCAAAGCCCACAAGTCAGTGG
* * *
1157996 CATCCTTTCAAAGCCCACAAGTCAATGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCAC-CCTT
1 CAT-CTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCTTT
* * * *
1158059 TCAAAACCCACAAGTTAGTGGCACCTTTTCAAAGCCCACAAGCCAGTGG
65 TCAAAGCCCACAAGTTAGTGGCATCATTTCAAAGCCCACAAGTCAGTGG
* * *
1158108 CACTCTTTTTAAAGTCCACAAG-CTAGTGGCAACTCTTTTCAAAGCCCACATAAGTGAGTGGCAC
1 CA-TC-TTTCAAAGCCCACAAGTC-AGTGGC-ACTCTTTTCAAAGCCCAC--AAGTCAGTGGCAC
*
1158172 TTTTTT
60 TCTTTT
1158178 TTTAAAAAAA
Statistics
Matches: 262, Mismatches: 21, Indels: 23
0.86 0.07 0.08
Matches are distributed among these distances:
112 52 0.20
113 127 0.48
114 14 0.05
115 14 0.05
116 11 0.04
117 39 0.15
118 5 0.02
ACGTcount: A:0.29, C:0.29, G:0.18, T:0.24
Consensus pattern (113 bp):
CATCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCTTTT
CAAAGCCCACAAGTTAGTGGCATCATTTCAAAGCCCACAAGTCAGTGG
Found at i:1159086 original size:20 final size:20
Alignment explanation
Indices: 1159061--1159135 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
1159051 TTTTACCCAG
*
1159061 ATGTATCGATACGTTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
1159081 ATGTATCGCTACATGTATGA
1 ATGTATCGATACATTTTTCA
* *
1159101 ATATATCGATACATTCTTCA
1 ATGTATCGATACATTTTTCA
1159121 ATGTATCGATACATT
1 ATGTATCGATACATT
1159136 CTATCTTTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.31, C:0.16, G:0.13, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:1163503 original size:32 final size:31
Alignment explanation
Indices: 1163453--1163608 Score: 167
Period size: 32 Copynumber: 4.9 Consensus size: 31
1163443 CCTTACAACA
*
1163453 CTATCTTTCAAGGCTAAGATAGAACC-CTCC
1 CTATCTTTCAAGGCTAAGATAAAACCTCTCC
*
1163483 CTATCGTTTCACAGGCTAAGATAAAACCTTTTCC
1 CTATC-TTTCA-AGGCTAAGATAAAACC-TCTCC
*
1163517 CTATCTTTTGC-AGGCTAAGATAGAA-C-CTCC
1 CTATC-TTT-CAAGGCTAAGATAAAACCTCTCC
*
1163547 CTATCTTTTACAAAGGCTAAGATAAAACCTCTACA
1 CTATC-TTT-C-AAGGCTAAGATAAAACCTCT-CC
1163582 CTATCTTTCAAGGCTAAGATAAAACCT
1 CTATCTTTCAAGGCTAAGATAAAACCT
1163609 TTCAATCACT
Statistics
Matches: 108, Mismatches: 8, Indels: 18
0.81 0.06 0.13
Matches are distributed among these distances:
30 18 0.17
31 5 0.05
32 47 0.44
33 15 0.14
34 16 0.15
35 7 0.06
ACGTcount: A:0.33, C:0.26, G:0.12, T:0.29
Consensus pattern (31 bp):
CTATCTTTCAAGGCTAAGATAAAACCTCTCC
Found at i:1163541 original size:65 final size:65
Alignment explanation
Indices: 1163450--1163607 Score: 223
Period size: 65 Copynumber: 2.4 Consensus size: 65
1163440 TAACCTTACA
* *
1163450 ACACTATCTTTCAAGGCTAAGATAGAACCCTCCCTATCGTTT-CACAGGCTAAGATAAAACCTTT
1 ACACTATCTTTCAAGGCTAAGATAGAACCCTCCCTATCGTTTACAAAGGCTAAGATAAAACCTCT
* * *
1163514 TCCCTATCTTTTGC-AGGCTAAGATAGAA-CCTCCCTATCTTTTACAAAGGCTAAGATAAAACCT
1 ACACTATC-TTT-CAAGGCTAAGATAGAACCCTCCCTATCGTTTACAAAGGCTAAGATAAAACCT
1163577 CT
64 CT
*
1163579 ACACTATCTTTCAAGGCTAAGATAAAACC
1 ACACTATCTTTCAAGGCTAAGATAGAACC
1163608 TTTCAATCAC
Statistics
Matches: 81, Mismatches: 8, Indels: 9
0.83 0.08 0.09
Matches are distributed among these distances:
63 1 0.01
64 35 0.43
65 44 0.54
66 1 0.01
ACGTcount: A:0.34, C:0.26, G:0.12, T:0.28
Consensus pattern (65 bp):
ACACTATCTTTCAAGGCTAAGATAGAACCCTCCCTATCGTTTACAAAGGCTAAGATAAAACCTCT
Found at i:1164082 original size:22 final size:22
Alignment explanation
Indices: 1164057--1164098 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
1164047 GTGATGAGCA
*
1164057 GTGATGTATCGATACATGAATG
1 GTGATGTATCAATACATGAATG
1164079 GTGATGTATCAATACATGAA
1 GTGATGTATCAATACATGAA
1164099 CAATGATCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.36, C:0.10, G:0.24, T:0.31
Consensus pattern (22 bp):
GTGATGTATCAATACATGAATG
Found at i:1164105 original size:22 final size:22
Alignment explanation
Indices: 1164058--1164105 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
1164048 TGATGAGCAG
* ***
1164058 TGATGTATCGATACATGAATGG
1 TGATGTATCAATACATGAACAA
1164080 TGATGTATCAATACATGAACAA
1 TGATGTATCAATACATGAACAA
1164102 TGAT
1 TGAT
1164106 CAACAGTAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.38, C:0.10, G:0.21, T:0.31
Consensus pattern (22 bp):
TGATGTATCAATACATGAACAA
Found at i:1164776 original size:21 final size:21
Alignment explanation
Indices: 1164752--1164792 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1164742 AAAGAGTTGG
1164752 AAAA-GAAAATAAGTGAGTTAC
1 AAAACGAAAATAA-TGAGTTAC
*
1164773 AAAACGAAAATGATGAGTTA
1 AAAACGAAAATAATGAGTTA
1164793 ACTAATAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.56, C:0.05, G:0.20, T:0.20
Consensus pattern (21 bp):
AAAACGAAAATAATGAGTTAC
Found at i:1167675 original size:20 final size:21
Alignment explanation
Indices: 1167636--1167679 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
1167626 TTAAGTATAG
1167636 ATGTTTTCCAAGCATAAAAATA
1 ATGTTTTCCAAG-ATAAAAATA
*
1167658 ATGTTTTTCAAG-TAAAAATA
1 ATGTTTTCCAAGATAAAAATA
1167678 AT
1 AT
1167680 TCAAAGTATC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 10 0.48
22 11 0.52
ACGTcount: A:0.45, C:0.09, G:0.09, T:0.36
Consensus pattern (21 bp):
ATGTTTTCCAAGATAAAAATA
Found at i:1167898 original size:13 final size:13
Alignment explanation
Indices: 1167880--1167906 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1167870 AAAACTCACT
1167880 TTGTATCGATACA
1 TTGTATCGATACA
1167893 TTGTATCGATACA
1 TTGTATCGATACA
1167906 T
1 T
1167907 GATGAATTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1167917 original size:20 final size:20
Alignment explanation
Indices: 1167892--1167943 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
1167882 GTATCGATAC
1167892 ATTGTATCGATACATGATGA
1 ATTGTATCGATACATGATGA
*
1167912 ATTGTATCGATACATGGTGA
1 ATTGTATCGATACATGATGA
1167932 ATTGTATCGATA
1 ATTGTATCGATA
1167944 TATTGAGCGC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.33, C:0.10, G:0.21, T:0.37
Consensus pattern (20 bp):
ATTGTATCGATACATGATGA
Found at i:1168425 original size:36 final size:34
Alignment explanation
Indices: 1168376--1168467 Score: 102
Period size: 36 Copynumber: 2.7 Consensus size: 34
1168366 TAAGTGATTA
1168376 AGAGGTTCTATCTTAGCCTTTGAAAAAGATAGGG
1 AGAGGTTCTATCTTAGCCTTTGAAAAAGATAGGG
* *
1168410 AGAAAGGTTCTATCTTAG-ATCGTG-AAAAGATAGGG
1 AG--AGGTTCTATCTTAGCCT-TTGAAAAAGATAGGG
*
1168445 AG-GTTTCTATCTTAGCC-TTGAAA
1 AGAGGTTCTATCTTAGCCTTTGAAA
1168468 GATAGTGTTG
Statistics
Matches: 48, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
31 2 0.04
32 14 0.29
34 2 0.04
35 14 0.29
36 16 0.33
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (34 bp):
AGAGGTTCTATCTTAGCCTTTGAAAAAGATAGGG
Found at i:1168950 original size:24 final size:24
Alignment explanation
Indices: 1168923--1168988 Score: 71
Period size: 24 Copynumber: 2.7 Consensus size: 24
1168913 ATTTTAGACG
* *
1168923 TAATATAAAAATATGATATAAATA
1 TAATATAAAAATATAATATAAAAA
**
1168947 TAATATATTTAATA-AATATAAAAA
1 TAATATA-AAAATATAATATAAAAA
1168971 TAATATAATAAATATAAT
1 TAATATAA-AAATATAAT
1168989 GTAATAAACA
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
24 26 0.79
25 7 0.21
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (24 bp):
TAATATAAAAATATAATATAAAAA
Found at i:1175038 original size:78 final size:77
Alignment explanation
Indices: 1174950--1175120 Score: 243
Period size: 78 Copynumber: 2.2 Consensus size: 77
1174940 AAAGGTATAG
* * * * *
1174950 AAAATGACCTTACGGGATATGTTTTGACATGAAAGTGCTACATAACCCTAAAAGGCTCGATTTTG
1 AAAATGACCTTAAGGGATATGTTTTGACATGAAAGTGCCACATAACCCTAAAAGACTCCATTTTC
* *
1175015 ATGGAAATATTCT
66 ATGGAAA-AGTAT
* * *
1175028 ACAATGACCTTAAGGGATATGTTTTGACATGAATGTGCCACATAACCCTAAAAGATTCCATTTTC
1 AAAATGACCTTAAGGGATATGTTTTGACATGAAAGTGCCACATAACCCTAAAAGACTCCATTTTC
1175093 ATGGAAAAGTAT
66 ATGGAAAAGTAT
1175105 AAAATGACCTTAAGGG
1 AAAATGACCTTAAGGG
1175121 TTTTATTTTT
Statistics
Matches: 82, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
77 18 0.22
78 64 0.78
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.29
Consensus pattern (77 bp):
AAAATGACCTTAAGGGATATGTTTTGACATGAAAGTGCCACATAACCCTAAAAGACTCCATTTTC
ATGGAAAAGTAT
Found at i:1175372 original size:72 final size:72
Alignment explanation
Indices: 1175238--1175378 Score: 176
Period size: 72 Copynumber: 2.0 Consensus size: 72
1175228 TACATGTTTG
* * * * *
1175238 GACTTGGAAAAATTGCTAAAAGATCCTTATAGGTTTGGCCAACATATGAAATACACTTAAAATGA
1 GACTTGAAAAAATTGCTAAAAGATCCATATAGGTTCGACCAACATATGAAATACACTCAAAATGA
1175303 ATGTCTA
66 ATGTCTA
* * * *
1175310 GACTTGAAAAAATTGCTAAAAGTTCCATATATGTTCGACCAAC-TCATGAAATGCCCTCAAAATG
1 GACTTGAAAAAATTGCTAAAAGATCCATATAGGTTCGACCAACAT-ATGAAATACACTCAAAATG
*
1175374 CATGT
65 AATGT
1175379 TTGGATTTTA
Statistics
Matches: 58, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
71 1 0.02
72 57 0.98
ACGTcount: A:0.39, C:0.17, G:0.16, T:0.28
Consensus pattern (72 bp):
GACTTGAAAAAATTGCTAAAAGATCCATATAGGTTCGACCAACATATGAAATACACTCAAAATGA
ATGTCTA
Found at i:1176587 original size:148 final size:148
Alignment explanation
Indices: 1176392--1176907 Score: 571
Period size: 148 Copynumber: 3.5 Consensus size: 148
1176382 AGTTTTGGGA
* ** * *
1176392 AAAAATGTTAAAAGGTCCTTAAGGTCCACCATTGACTTAGAAGTGCCCAATGATCCTAGAGGACT
1 AAAAATGCTAAAATATCCTTAAGGTCTACCATTGACTTAGAAGTGCCCAGTGATCCTA-AGGACT
* * * * ** *
1176457 TGAAAGAGAAAAAACAAACCTATTCCTAATTCATACCTTTGATGTAGAAG-TGGGCTC-AGTAGT
65 TGAAAAAGTAAAAACAAACCCATTCCTAATTCATACCTTCGACATAGAAGCT-GACTCGA-TAGT
1176520 CTTATAGGATTAGGTTTCAGG
128 CTTATAGGATTAGGTTTCAGG
*
1176541 -AAAATGCTAAAATATTCC-TAAGGTCTACCATTGACTTAGAACTGCCCAGTGATCCTAAGGGAC
1 AAAAATGCTAAAATA-TCCTTAAGGTCTACCATTGACTTAGAAGTGCCCAGTGATCCTAA-GGAC
*
1176604 TTGAAAAAGTAAAAACAAACCCATTCCGAATTCATACCTTCGACATAGAAGCTGACTCGATAGTC
64 TTGAAAAAGTAAAAACAAACCCATTCCTAATTCATACCTTCGACATAGAAGCTGACTCGATAGTC
**
1176669 TTATAGGATTAGGTTTTGGG
129 TTATAGGATTAGGTTTCAGG
**
1176689 AAAAATGCTAAAATATCCTTAAGGTCTACCATTGACTTAG-AGTGCCTGGTGATCCTAAAGGACT
1 AAAAATGCTAAAATATCCTTAAGGTCTACCATTGACTTAGAAGTGCCCAGTGATCCT-AAGGACT
* * * * * * *
1176753 TGAAAAAGTAAAAACAAACCCACTCCTAATTTATACCTTCGGCATATAAACGGAC-CAGGTAGTC
65 TGAAAAAGTAAAAACAAACCCATTCCTAATTCATACCTTCGACATAGAAGCTGACTC-GATAGTC
* * * *
1176817 TCATAAGACTAGGTTTTGAGG
129 TTATAGGATTAGG-TTTCAGG
* * * ** * *
1176838 -AAAATGCTAACATATCCCTAAGGTTTATTATCGACTTAGAAGTGCCTAGTGATCCTAAGTGACT
1 AAAAATGCTAAAATATCCTTAAGGTCTACCATTGACTTAGAAGTGCCCAGTGATCCTAAG-GACT
1176902 T-AAAAA
65 TGAAAAA
1176908 TGGTTGTAAA
Statistics
Matches: 317, Mismatches: 39, Indels: 23
0.84 0.10 0.06
Matches are distributed among these distances:
147 2 0.01
148 248 0.78
149 67 0.21
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.27
Consensus pattern (148 bp):
AAAAATGCTAAAATATCCTTAAGGTCTACCATTGACTTAGAAGTGCCCAGTGATCCTAAGGACTT
GAAAAAGTAAAAACAAACCCATTCCTAATTCATACCTTCGACATAGAAGCTGACTCGATAGTCTT
ATAGGATTAGGTTTCAGG
Found at i:1177435 original size:16 final size:16
Alignment explanation
Indices: 1177406--1177457 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
1177396 AAGGTTATCT
1177406 TTATTAATTTTATTTTGA
1 TTATT-ATTTTATTTT-A
*
1177424 TTATTA-TTTATTTAA
1 TTATTATTTTATTTTA
*
1177439 TTTTTATTTTATTTTA
1 TTATTATTTTATTTTA
1177455 TTA
1 TTA
1177458 AAAAAATCAT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 6 0.21
16 17 0.59
17 1 0.03
18 5 0.17
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (16 bp):
TTATTATTTTATTTTA
Found at i:1177456 original size:21 final size:21
Alignment explanation
Indices: 1177406--1177452 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
1177396 AAGGTTATCT
* *
1177406 TTATTAATTTTATTTTGATTA
1 TTATTTATTTAATTTTGATTA
*
1177427 TTATTTATTTAATTTTTATT-
1 TTATTTATTTAATTTTGATTA
1177447 TTATTT
1 TTATTT
1177453 TATTAAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 6 0.26
21 17 0.74
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (21 bp):
TTATTTATTTAATTTTGATTA
Found at i:1178230 original size:20 final size:20
Alignment explanation
Indices: 1178205--1178259 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
1178195 GTTGGGCTCA
* *
1178205 ATGTATCGATACATTTTACC
1 ATGTATCGATACAATTCACC
* *
1178225 ATGTATCGATATAATTCATC
1 ATGTATCGATACAATTCACC
1178245 ATGTATCGATACAAT
1 ATGTATCGATACAAT
1178260 GTATCAATAC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.38
Consensus pattern (20 bp):
ATGTATCGATACAATTCACC
Found at i:1178355 original size:13 final size:13
Alignment explanation
Indices: 1178337--1178361 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1178327 TACTATGAAC
1178337 ATGTATCGATACA
1 ATGTATCGATACA
1178350 ATGTATCGATAC
1 ATGTATCGATAC
1178362 TAAGCAATAT
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:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1179091 original size:15 final size:15
Alignment explanation
Indices: 1179071--1179100 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1179061 CTTTTTAAAG
1179071 TTCTAAAACAAATAT
1 TTCTAAAACAAATAT
1179086 TTCTAAAACAAATAT
1 TTCTAAAACAAATAT
1179101 ATTGCAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.33
Consensus pattern (15 bp):
TTCTAAAACAAATAT
Found at i:1180237 original size:21 final size:21
Alignment explanation
Indices: 1180191--1180245 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
1180181 TTTTTACTTA
*
1180191 AAAACATTTGATTTAAAGCTCG
1 AAAACATTT-ATTCAAAGCTCG
* *
1180213 AAAACATTTATTCATAGCTCT
1 AAAACATTTATTCAAAGCTCG
1180234 AAAACATTTATT
1 AAAACATTTATT
1180246 GATATTGAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 21 0.70
22 9 0.30
ACGTcount: A:0.42, C:0.15, G:0.07, T:0.36
Consensus pattern (21 bp):
AAAACATTTATTCAAAGCTCG
Found at i:1181887 original size:22 final size:20
Alignment explanation
Indices: 1181862--1181911 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 20
1181852 ACACTAGGTG
*
1181862 TGGGAGCTGCCCAATTGCGACC
1 TGGGAG-TG-CCAATCGCGACC
*
1181884 TGGGAGTGCCGATCGCGACC
1 TGGGAGTGCCAATCGCGACC
*
1181904 TGGAAGTG
1 TGGGAGTG
1181912 GCTGCCTAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 17 0.68
21 2 0.08
22 6 0.24
ACGTcount: A:0.18, C:0.26, G:0.38, T:0.18
Consensus pattern (20 bp):
TGGGAGTGCCAATCGCGACC
Found at i:1183742 original size:16 final size:17
Alignment explanation
Indices: 1183705--1183742 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
1183695 TTTTATCAAC
*
1183705 ATTTTCTCTATTAAAAC
1 ATTTTCTCTATTAAAAA
*
1183722 CTTTT-TCTATTAAAAA
1 ATTTTCTCTATTAAAAA
1183738 ATTTT
1 ATTTT
1183743 GAAAGCCTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.34, C:0.13, G:0.00, T:0.53
Consensus pattern (17 bp):
ATTTTCTCTATTAAAAA
Found at i:1187765 original size:13 final size:13
Alignment explanation
Indices: 1187747--1187804 Score: 56
Period size: 13 Copynumber: 4.9 Consensus size: 13
1187737 CAATTCTTCA
1187747 TGTATCGATACAT
1 TGTATCGATACAT
*
1187760 TGTATCGATACAA
1 TGTATCGATACAT
*
1187773 TG--T-G--CCA-
1 TGTATCGATACAT
1187780 TGTATCGATACAT
1 TGTATCGATACAT
1187793 TGTATCGATACA
1 TGTATCGATACA
1187805 ATGTGCCATG
Statistics
Matches: 36, Mismatches: 3, Indels: 12
0.71 0.06 0.24
Matches are distributed among these distances:
7 2 0.06
8 2 0.06
9 1 0.03
10 2 0.06
11 1 0.03
12 2 0.06
13 26 0.72
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1187771 original size:33 final size:33
Alignment explanation
Indices: 1187729--1187824 Score: 160
Period size: 33 Copynumber: 2.9 Consensus size: 33
1187719 TGGGACAATT
1187729 TATCGATACAAT-T-CTTCATGTATCGATACATTG
1 TATCGATACAATGTGC--CATGTATCGATACATTG
1187762 TATCGATACAATGTGCCATGTATCGATACATTG
1 TATCGATACAATGTGCCATGTATCGATACATTG
1187795 TATCGATACAATGTGCCATGTATCGATACA
1 TATCGATACAATGTGCCATGTATCGATACA
1187825 AATAGTGGTA
Statistics
Matches: 61, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
33 59 0.97
34 1 0.02
35 1 0.02
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (33 bp):
TATCGATACAATGTGCCATGTATCGATACATTG
Found at i:1187785 original size:20 final size:20
Alignment explanation
Indices: 1187760--1187825 Score: 83
Period size: 20 Copynumber: 3.6 Consensus size: 20
1187750 ATCGATACAT
1187760 TGTATCGATACAATGTGCCA
1 TGTATCGATACAATGTGCCA
1187780 TGTATCGATAC-A--T----
1 TGTATCGATACAATGTGCCA
1187793 TGTATCGATACAATGTGCCA
1 TGTATCGATACAATGTGCCA
1187813 TGTATCGATACAA
1 TGTATCGATACAA
1187826 ATAGTGGTAG
Statistics
Matches: 39, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
13 11 0.28
14 1 0.03
16 1 0.03
17 1 0.03
19 1 0.03
20 24 0.62
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (20 bp):
TGTATCGATACAATGTGCCA
Found at i:1187898 original size:19 final size:19
Alignment explanation
Indices: 1187853--1187910 Score: 84
Period size: 19 Copynumber: 3.1 Consensus size: 19
1187843 ACTGCCAGTT
1187853 TCATGTATCGATACAATTG
1 TCATGTATCGATACAATTG
1187872 TCCATGTATCGATACAA-TG
1 T-CATGTATCGATACAATTG
1187891 ATCATGTATCGATAC-ATTG
1 -TCATGTATCGATACAATTG
1187910 T
1 T
1187911 ATCGATACAA
Statistics
Matches: 36, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
18 2 0.06
19 18 0.50
20 16 0.44
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (19 bp):
TCATGTATCGATACAATTG
Found at i:1187913 original size:13 final size:12
Alignment explanation
Indices: 1187874--1187952 Score: 59
Period size: 13 Copynumber: 7.2 Consensus size: 12
1187864 TACAATTGTC
1187874 CATGTATCGATA
1 CATGTATCGATA
1187886 CA---AT-GAT-
1 CATGTATCGATA
1187893 CATGTATCGATA
1 CATGTATCGATA
1187905 CATTGTATCGATA
1 CA-TGTATCGATA
* *
1187918 CA---AACCATA
1 CATGTATCGATA
1187927 -ATGTATCGATA
1 CATGTATCGATA
1187938 CATTGTATCGATA
1 CA-TGTATCGATA
1187951 CA
1 CA
1187953 AAGCATAATG
Statistics
Matches: 52, Mismatches: 4, Indels: 21
0.68 0.05 0.27
Matches are distributed among these distances:
7 2 0.04
8 4 0.08
9 7 0.13
10 2 0.04
11 8 0.15
12 5 0.10
13 24 0.46
ACGTcount: A:0.37, C:0.18, G:0.14, T:0.32
Consensus pattern (12 bp):
CATGTATCGATA
Found at i:1187933 original size:20 final size:19
Alignment explanation
Indices: 1187908--1187972 Score: 70
Period size: 20 Copynumber: 3.6 Consensus size: 19
1187898 ATCGATACAT
1187908 TGTATCGATACAAACCATAA
1 TGTATCGATACAAA-CATAA
1187928 TGTATCGAT----ACAT--
1 TGTATCGATACAAACATAA
1187941 TGTATCGATACAAAGCATAA
1 TGTATCGATACAAA-CATAA
1187961 TGTATCGATACA
1 TGTATCGATACA
1187973 TCTGGATGGG
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 9 0.24
15 3 0.08
16 1 0.03
17 1 0.03
18 3 0.08
20 21 0.55
ACGTcount: A:0.40, C:0.17, G:0.14, T:0.29
Consensus pattern (19 bp):
TGTATCGATACAAACATAA
Found at i:1187936 original size:33 final size:33
Alignment explanation
Indices: 1187876--1187973 Score: 153
Period size: 33 Copynumber: 3.0 Consensus size: 33
1187866 CAATTGTCCA
** *
1187876 TGTATCGATAC-AATGATCATGTATCGATACAT
1 TGTATCGATACAAACCATAATGTATCGATACAT
1187908 TGTATCGATACAAACCATAATGTATCGATACAT
1 TGTATCGATACAAACCATAATGTATCGATACAT
*
1187941 TGTATCGATACAAAGCATAATGTATCGATACAT
1 TGTATCGATACAAACCATAATGTATCGATACAT
1187974 CTGGATGGGT
Statistics
Matches: 61, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
32 11 0.18
33 50 0.82
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.32
Consensus pattern (33 bp):
TGTATCGATACAAACCATAATGTATCGATACAT
Found at i:1190157 original size:13 final size:14
Alignment explanation
Indices: 1190126--1190166 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 14
1190116 AATAGTGCCC
*
1190126 ATGTATCGATACTG
1 ATGTATCGATACTA
1190140 A-GTATCGATAC-A
1 ATGTATCGATACTA
*
1190152 ATGTATCAATACTA
1 ATGTATCGATACTA
1190166 A
1 A
1190167 GAACACTGTA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
12 1 0.04
13 19 0.83
14 3 0.13
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.32
Consensus pattern (14 bp):
ATGTATCGATACTA
Found at i:1194245 original size:20 final size:20
Alignment explanation
Indices: 1194220--1194257 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
1194210 TGCTGCTAGT
1194220 TTCATGTATCGATACAATTC
1 TTCATGTATCGATACAATTC
1194240 TTCATGTATCGATACAAT
1 TTCATGTATCGATACAAT
1194258 AAACATGTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.18, G:0.11, T:0.39
Consensus pattern (20 bp):
TTCATGTATCGATACAATTC
Found at i:1194266 original size:19 final size:20
Alignment explanation
Indices: 1194222--1194277 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 20
1194212 CTGCTAGTTT
***
1194222 CATGTATCGATACAATTCTT
1 CATGTATCGATACAATTAAA
1194242 CATGTATCGATACAA-TAAA
1 CATGTATCGATACAATTAAA
* *
1194261 CATGTATTGATATAATT
1 CATGTATCGATACAATT
1194278 TATCGATACA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.38, C:0.14, G:0.11, T:0.38
Consensus pattern (20 bp):
CATGTATCGATACAATTAAA
Found at i:1194976 original size:22 final size:22
Alignment explanation
Indices: 1194923--1194977 Score: 85
Period size: 22 Copynumber: 2.5 Consensus size: 22
1194913 TTCTTTAAAT
1194923 TAAAAATT-TTCTCCCCCTTAA
1 TAAAAATTCTTCTCCCCCTTAA
*
1194944 TAAAAAATCTTCTCCCCCTTAA
1 TAAAAATTCTTCTCCCCCTTAA
*
1194966 TAAAATTTCTTC
1 TAAAAATTCTTC
1194978 CTTTAAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 7 0.23
22 23 0.77
ACGTcount: A:0.35, C:0.27, G:0.00, T:0.38
Consensus pattern (22 bp):
TAAAAATTCTTCTCCCCCTTAA
Found at i:1203101 original size:19 final size:20
Alignment explanation
Indices: 1203077--1203128 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
1203067 TACAATTCTT
**
1203077 CATGTATCGATACATTG-AA
1 CATGTATCGATACAAAGCAA
1203096 CATGTATCGATACAAAGCAA
1 CATGTATCGATACAAAGCAA
*
1203116 TATGTATCGATAC
1 CATGTATCGATAC
1203129 TTCTGTGCTT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.52
20 14 0.48
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.29
Consensus pattern (20 bp):
CATGTATCGATACAAAGCAA
Found at i:1204763 original size:13 final size:13
Alignment explanation
Indices: 1204745--1204784 Score: 71
Period size: 13 Copynumber: 3.1 Consensus size: 13
1204735 ACATTATGCT
*
1204745 TTGTATTGATACA
1 TTGTATCGATACA
1204758 TTGTATCGATACA
1 TTGTATCGATACA
1204771 TTGTATCGATACA
1 TTGTATCGATACA
1204784 T
1 T
1204785 ACACAATTGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.30, C:0.12, G:0.15, T:0.42
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1204872 original size:33 final size:33
Alignment explanation
Indices: 1204835--1204899 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
1204825 TACCACTGTT
* ** *
1204835 TGTATCGATACATGGCACATTGTATCGATACAA
1 TGTATCAATACATGAAAAATTGTATCGATACAA
1204868 TGTATCAATACATGAAAAATTGTATCGATACA
1 TGTATCAATACATGAAAAATTGTATCGATACA
1204900 TTATCCCAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (33 bp):
TGTATCAATACATGAAAAATTGTATCGATACAA
Found at i:1205164 original size:8 final size:8
Alignment explanation
Indices: 1205151--1205181 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
1205141 AGTTTTACTT
1205151 ATTTTCTC
1 ATTTTCTC
1205159 ATTTTCTC
1 ATTTTCTC
1205167 ATTTTTCTC
1 A-TTTTCTC
1205176 ATTTTC
1 ATTTTC
1205182 AAGAGCTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 14 0.64
9 8 0.36
ACGTcount: A:0.13, C:0.23, G:0.00, T:0.65
Consensus pattern (8 bp):
ATTTTCTC
Found at i:1205172 original size:9 final size:9
Alignment explanation
Indices: 1205152--1205180 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
1205142 GTTTTACTTA
1205152 TTTTCTCA-
1 TTTTCTCAT
1205160 TTTTCTCAT
1 TTTTCTCAT
1205169 TTTTCTCAT
1 TTTTCTCAT
1205178 TTT
1 TTT
1205181 CAAGAGCTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 8 0.40
9 12 0.60
ACGTcount: A:0.10, C:0.21, G:0.00, T:0.69
Consensus pattern (9 bp):
TTTTCTCAT
Found at i:1208085 original size:17 final size:17
Alignment explanation
Indices: 1208044--1208112 Score: 102
Period size: 17 Copynumber: 3.8 Consensus size: 17
1208034 AGGGCATATT
1208044 AAGTATGTGATGCGCGTATTA
1 AAGTATGTGAT--GCG-A-TA
1208065 AAGTATGTGATGCGATA
1 AAGTATGTGATGCGATA
1208082 AAGTATGTGATGCGATA
1 AAGTATGTGATGCGATA
1208099 AAGTATGTGATGCG
1 AAGTATGTGATGCG
1208113 CGTATTAAGG
Statistics
Matches: 48, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
17 33 0.69
18 1 0.02
19 3 0.06
21 11 0.23
ACGTcount: A:0.32, C:0.07, G:0.30, T:0.30
Consensus pattern (17 bp):
AAGTATGTGATGCGATA
Found at i:1211045 original size:13 final size:13
Alignment explanation
Indices: 1211027--1211052 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1211017 CATTGAATGA
1211027 TGTATCGATACAT
1 TGTATCGATACAT
1211040 TGTATCGATACAT
1 TGTATCGATACAT
1211053 GGGTTACTAT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1213541 original size:19 final size:21
Alignment explanation
Indices: 1213517--1213570 Score: 69
Period size: 19 Copynumber: 2.7 Consensus size: 21
1213507 AACCCTTGAA
*
1213517 TGTATCGATACATGA-TC-AT
1 TGTATCGATACATGACACAAT
1213536 TGTATCGATACAT-ACACAAT
1 TGTATCGATACATGACACAAT
*
1213556 TGTATCGATGCATGA
1 TGTATCGATACATGA
1213571 AACTGGCAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
18 1 0.03
19 14 0.47
20 14 0.47
21 1 0.03
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (21 bp):
TGTATCGATACATGACACAAT
Found at i:1213559 original size:20 final size:19
Alignment explanation
Indices: 1213517--1213571 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 19
1213507 AACCCTTGAA
*
1213517 TGTATCGATACATGATCAT
1 TGTATCGATACATGAACAT
1213536 TGTATCGATACAT-ACACAAT
1 TGTATCGATACATGA-AC-AT
*
1213556 TGTATCGATGCATGAA
1 TGTATCGATACATGAA
1213572 ACTGGCAGTA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
18 1 0.03
19 14 0.45
20 15 0.48
21 1 0.03
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (19 bp):
TGTATCGATACATGAACAT
Found at i:1215732 original size:22 final size:24
Alignment explanation
Indices: 1215702--1215745 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
1215692 TCTCTCAATC
1215702 TCTTCAAG-AATTATACCCCAAAT
1 TCTTCAAGAAATTATACCCCAAAT
1215725 TCTT-AAGAAATTATACCCCAA
1 TCTTCAAGAAATTATACCCCAA
1215746 GGTTGAATAC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 3 0.15
23 17 0.85
ACGTcount: A:0.41, C:0.25, G:0.05, T:0.30
Consensus pattern (24 bp):
TCTTCAAGAAATTATACCCCAAAT
Found at i:1216739 original size:145 final size:145
Alignment explanation
Indices: 1216422--1216840 Score: 472
Period size: 145 Copynumber: 2.9 Consensus size: 145
1216412 TGGATTACCG
** * * *
1216422 GGATAC-TTCTACGTCGAACCTACCCCCTAGAGGCATTTTCGTAATTTTTCAAGATCGAGTCTTA
1 GGATACTTTCTACGTCGAAAGTACACCCTA-AGGCATTTTCGTAATTTTTTAAGATCGAGTCCTA
*
1216486 GGTTGTCACTCTTATGCCAAAGGTGTACATATAGGATAGATTCAATATTTTCAACCCTTTTCAAG
65 GGTTGTCACTCTTATGCCAAAGGTGTACATATAGGATAGATTCAATCTTTTCAACCCTTTTCAAG
* * *
1216551 TCTTTTATGGTTACTA
130 TCCTTTAGGGGTACTA
* * * *
1216567 GGATACTTT-TACGTCGAAAGCA-ACCCTAAGGACATTTTCGTAATTTTTTTAGGTTTGAGTCCT
1 GGATACTTTCTACGTCGAAAGTACACCCTAAGG-CATTTTCGTAA-TTTTTTAAGATCGAGTCCT
* *
1216630 AGGTTGTCACTCTTATGCCAAAGGTGTACACATAGGATAGATCCAATCTTTTCAACCCTTTTCAA
64 AGGTTGTCACTCTTATGCCAAAGGTGTACATATAGGATAGATTCAATCTTTTCAACCCTTTTCAA
* *
1216695 GTCCTTTGGGGGTA-TC
129 GTCCTTTAGGGGTACTA
* * * * * * *
1216711 GGGTA-TTTCTACGTCGAAGGTACTCCCTAGGGCATTTTCATAA-TTTCTAAAATCGAGTCCTAG
1 GGATACTTTCTACGTCGAAAGTACACCCTAAGGCATTTTCGTAATTTTTTAAGATCGAGTCCTAG
* ** * * * * * *
1216774 GTTATCACTCTTACACCGAAGGTGCACATATAGGATAGGTTCACTCTTTACAACCCTTTTCACGT
66 GTTGTCACTCTTATGCCAAAGGTGTACATATAGGATAGATTCAATCTTTTCAACCCTTTTCAAGT
1216839 CC
131 CC
1216841 CTTAAGATCA
Statistics
Matches: 230, Mismatches: 39, Indels: 13
0.82 0.14 0.05
Matches are distributed among these distances:
142 71 0.31
143 6 0.03
144 42 0.18
145 109 0.47
146 2 0.01
ACGTcount: A:0.26, C:0.22, G:0.18, T:0.35
Consensus pattern (145 bp):
GGATACTTTCTACGTCGAAAGTACACCCTAAGGCATTTTCGTAATTTTTTAAGATCGAGTCCTAG
GTTGTCACTCTTATGCCAAAGGTGTACATATAGGATAGATTCAATCTTTTCAACCCTTTTCAAGT
CCTTTAGGGGTACTA
Found at i:1217089 original size:143 final size:143
Alignment explanation
Indices: 1216830--1217093 Score: 361
Period size: 143 Copynumber: 1.8 Consensus size: 143
1216820 TTTACAACCC
* **
1216830 TTTTCACGTCCCTTAAGATCACCGAGCACTTCTAAGTTGATGGTAAACCTTAAGGATATGTTAGC
1 TTTTCAAGTCCCTTAAGATCACCGAGCACTTCTAAGTCAATGGTAAACCTTAAGGATATGTTAGC
* * ** * *
1216895 ATATTCCCCAAAACCTACTCCTATAAGACTACTGAGTTTGCTTTTATGCCAAAGGTTAGGAGTGA
66 ATATTCCCCAAAACCTAATCCTATAAGACTACTGAATCCGCTTCTACGCCAAAGGTTAGGAGTGA
1216960 GTTTGTTTTTACT
131 GTTTGTTTTTACT
* * * *
1216973 TTTTCAAGTCCTTTAGGATCACC-AGGCACTTCTAAGTCAATGGTAGACC-TAAGGGATATTTTA
1 TTTTCAAGTCCCTTAAGATCACCGA-GCACTTCTAAGTCAATGGTAAACCTTAA-GGATATGTTA
* *
1217036 GCATTTTCCCCAAAACTTAATCCTATAAGACTACTGAATCCGCTTCTACGCCAAAGGT
64 GCATATTCCCCAAAACCTAATCCTATAAGACTACTGAATCCGCTTCTACGCCAAAGGT
1217094 ATGAATTAAA
Statistics
Matches: 104, Mismatches: 15, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
142 4 0.04
143 100 0.96
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.33
Consensus pattern (143 bp):
TTTTCAAGTCCCTTAAGATCACCGAGCACTTCTAAGTCAATGGTAAACCTTAAGGATATGTTAGC
ATATTCCCCAAAACCTAATCCTATAAGACTACTGAATCCGCTTCTACGCCAAAGGTTAGGAGTGA
GTTTGTTTTTACT
Found at i:1221157 original size:166 final size:164
Alignment explanation
Indices: 1220710--1221210 Score: 505
Period size: 166 Copynumber: 3.0 Consensus size: 164
1220700 ATTCCTTTTA
1220710 TTTCATGAGTTATTG-ATTTTCTT-TTGGAATTCTCCTTA-TTTTAAAATACGACA-TTTTCTAC
1 TTTCATGAGTT-TTGAATTTT-TTCTTGGAATTC-CCTTATTTTTAAAA-ACGACAGTTTTCTAC
* * * * * *
1220771 TCCGTAAATATTTTCGAAGGAATTTTTCTCGGTTTTTAATTTTTATAATTCATAAAATATTATTA
62 TCCGTAAATGTTTTTGGAGGAATTTTTCTAGGTTTTTAATTTTTAAAATTCAT-CAATATTATTA
* * * * *
1220836 TTTAATTCATGTTAAATCAGTTTTCAAAAATTCACTCAT
126 TTTAATTCATATTAAATCAGTTTTGAAAAATTAAATTAT
* * * * * * *
1220875 CTTT-ATGAGTTTTTCATTTTTTTCCTTGAAACTCACTTATTTTTGAAATAC-AGAGTTTTCTAC
1 -TTTCATGAG-TTTTGAATTTTTT-CTTGGAATTCCCTTATTTTT-AAAAACGACAGTTTTCTAC
* * *
1220938 TCCGTAAATGTTTTTGGAAGG-ATTGTTCTTGGTTTTTAATTTTCAAAATTCATCAGATATTATT
62 TCCGTAAATGTTTTTGG-AGGAATTTTTCTAGGTTTTTAATTTTTAAAATTCATCA-ATATTATT
*
1221002 ATTTAATTCATATTAAATCAGTTTTGGAAAATTAAATTAT
125 ATTTAATTCATATTAAATCAGTTTTGAAAAATTAAATTAT
1221042 TTTCATGAGTTTTGAATTTTTTCTTCGGAATTCCCTTATTTCTTAAAAACGA-AGTTTTCTACTC
1 TTTCATGAGTTTTGAATTTTTTCTT-GGAATTCCCTTATTT-TTAAAAACGACAGTTTTCTACTC
* * * ** *
1221106 TGTAAATGTTTTTGGGGGAATTTTTCTAGATTTAAAATTTTTAAAATTCATCCAATATTGTTATT
64 CGTAAATGTTTTTGGAGGAATTTTTCTAGGTTTTTAATTTTTAAAATTCAT-CAATATTATTATT
* * * * * *
1221171 AAACTCTTATTAAATTAGTTTTGCAAAATTCAATTTAT
128 TAATTCATATTAAATCAGTTTTGAAAAATT-AAATTAT
1221209 TT
1 TT
1221211 CTTTTTTTTT
Statistics
Matches: 277, Mismatches: 42, Indels: 31
0.79 0.12 0.09
Matches are distributed among these distances:
165 14 0.05
166 134 0.48
167 123 0.44
168 6 0.02
ACGTcount: A:0.30, C:0.12, G:0.10, T:0.49
Consensus pattern (164 bp):
TTTCATGAGTTTTGAATTTTTTCTTGGAATTCCCTTATTTTTAAAAACGACAGTTTTCTACTCCG
TAAATGTTTTTGGAGGAATTTTTCTAGGTTTTTAATTTTTAAAATTCATCAATATTATTATTTAA
TTCATATTAAATCAGTTTTGAAAAATTAAATTAT
Found at i:1223491 original size:141 final size:139
Alignment explanation
Indices: 1223114--1223477 Score: 432
Period size: 140 Copynumber: 2.6 Consensus size: 139
1223104 TTAGTCATTT
* * * *
1223114 TTTTTTAAGATTTCTAATATTCTTATGGTTTTTCGTAGGGGTATAGAAGTTTTTAAAACTTTTC-
1 TTTTTAAAGATTTCTAATATTC-TATGG-CTTTCGTAGGGGTATAGAAATTTTCAAAACTTTTCT
* *
1223178 ATATCTTTTCAGGTCTTTATTAAGGTACGAAATGAATTTTTAAAAAATTAAAAATTAAATAAAAA
64 AT-TCTTTTCAGTTCTCTATTAAGGTACGAAATGAATTTTTAAAAAATTAAAAATTAAATAAAAA
*
1223243 TTATTATTTTAA
128 TTATTATTTAAA
* * * *
1223255 TTTTTAAAGATTTCTAATATCCTATGGCTATCTGTAGGGGTATAGAAATCTTCAAAACTTTTCTT
1 TTTTTAAAGATTTCTAATATTCTATGGCTTTC-GTAGGGGTATAGAAATTTTCAAAACTTTTCTA
* * *
1223320 TTCTTTTC-GATTCTCCATTAAGGTACGAAATGAATTTTT-GAAAATTAAAAATTAAATTAAAAT
65 TTCTTTTCAG-TTCTCTATTAAGGTACGAAATGAATTTTTAAAAAATTAAAAATTAAATAAAAAT
1223383 TATTATTTAAA
129 TATTATTTAAA
* * * *
1223394 TCTTTCT-TAGATTTCTATTATTTCTATGGCCTTTCGTAGAGGTGTAGAAATTTTCAAAACTTTT
1 T-TTT-TAAAGATTTCTAATA-TTCTATGG-CTTTCGTAGGGGTATAGAAATTTTCAAAACTTTT
*
1223458 CGTATTC-TCTCAGTTCTCTA
62 C-TATTCTTTTCAGTTCTCTA
1223478 AAAGGGTATG
Statistics
Matches: 190, Mismatches: 24, Indels: 18
0.82 0.10 0.08
Matches are distributed among these distances:
139 37 0.19
140 79 0.42
141 65 0.34
142 9 0.05
ACGTcount: A:0.33, C:0.11, G:0.12, T:0.45
Consensus pattern (139 bp):
TTTTTAAAGATTTCTAATATTCTATGGCTTTCGTAGGGGTATAGAAATTTTCAAAACTTTTCTAT
TCTTTTCAGTTCTCTATTAAGGTACGAAATGAATTTTTAAAAAATTAAAAATTAAATAAAAATTA
TTATTTAAA
Found at i:1223938 original size:156 final size:153
Alignment explanation
Indices: 1223632--1224396 Score: 852
Period size: 156 Copynumber: 4.9 Consensus size: 153
1223622 ACTTTATGTT
* ** * *
1223632 GAAAGTATACCCATAAGGGCATTTTAGTAACTTTTTAGAACTAACTCCTAGGTTATCACTAGGTC
1 GAAAGTAT-CCC-T-AGGGCATTTTTGTAA-TTTTTAGAACCGACTCCTAGGTTGTCACCAGGTC
* * * * * * *
1223697 CACTTTTATGCTAAATGTAGGTATTTAGGATAGGTTCATCCCATCTAAAATCTTTTTCAAGCTCT
62 TACTTTTATGCCAAATGTGGGTATTTAGGATAGGTTCACCCCATCTATAATCCTTTTCAAGCCCT
* * *
1223762 TTCAGGGGTATCGGGCACTTCTACGTT
127 TTTAGGGGTATCGGGTACTTCTACGTC
* * *
1223789 GAAGGTATCACCTAGGTGCATTTTTGTAATTTTCTAGAACCGACTCCTAGGTTGTCATCGGGTCT
1 GAAAGTATC-CCTAGG-GCATTTTTGTAATTTT-TAGAACCGACTCCTAGGTTGTCACCAGGTCT
*
1223854 ACTTTTATGCCAAAGGTGGGTATTTAGGATAGGTTCACCCCATCTATAATCCTTTTCAAGCCCTT
63 ACTTTTATGCCAAATGTGGGTATTTAGGATAGGTTCACCCCATCTATAATCCTTTTCAAGCCCTT
*
1223919 TTAGGGGTATCGGGTACTTCTACATC
128 TTAGGGGTATCGGGTACTTCTACGTC
* ** * * *
1223945 GAAAGTATCCCCTAGAGGTATTTTCATAATTTTTAAGAATCGACTCTTAGGTTGTCACCTAGTTC
1 GAAAGTAT-CCCTAG-GGCATTTTTGTAATTTTT-AGAACCGACTCCTAGGTTGTCACC-AGGTC
* * * * *
1224010 GA-TTTTACGCCAAATGAGGGTATTTAGGATAGGTTCACTCCATCTATAATCCTTTTCAAGCACT
62 TACTTTTATGCCAAATGTGGGTATTTAGGATAGGTTCACCCCATCTATAATCCTTTTCAAGCCCT
*
1224074 TTTAGGGGTATC-GGTCACTTCTATGTC
127 TTTAGGGGTATCGGGT-ACTTCTACGTC
* ** * *
1224101 GAAGGTATCCCTTAGGAGCA-TTTTCAAATTTTTTTAGAACTGACTCTTAGGTTGTCACCAGGTC
1 GAAAGTATCCC-TAGG-GCATTTTTGTAA--TTTTTAGAACCGACTCCTAGGTTGTCACCAGGTC
** * *
1224165 TGTTTTTATGCCAAAGGTGGGTATTTAGGATAGGTTCATCCCATCTATAATCCTTTTCAAGCCCT
62 TACTTTTATGCCAAATGTGGGTATTTAGGATAGGTTCACCCCATCTATAATCCTTTTCAAGCCCT
* * *
1224230 TTTAGAGGTATCAGGTACTTCTACGTG
127 TTTAGGGGTATCGGGTACTTCTACGTC
* * ** *
1224257 GAAAGTATTCCTTAGGGGCATTTTTGTAATTTTTTAGAATCGACTCCTAGGTTGTCTTCGGGTCT
1 GAAAGTA-TCCCTA-GGGCATTTTTGTAA-TTTTTAGAACCGACTCCTAGGTTGTCACCAGGTCT
* * * *
1224322 ATTTTTATGCCAAATGTGGGTATTTTGGATAGGTTCACCCCATCTATAATCTTTTTTTAAGCCCT
63 ACTTTTATGCCAAATGTGGGTATTTAGGATAGGTTCACCCCATCTATAATC-CTTTTCAAGCCCT
1224387 TTTAGGGGTA
127 TTTAGGGGTA
1224397 CTGGGCACTT
Statistics
Matches: 517, Mismatches: 73, Indels: 36
0.83 0.12 0.06
Matches are distributed among these distances:
155 24 0.05
156 439 0.85
157 54 0.10
ACGTcount: A:0.24, C:0.19, G:0.20, T:0.37
Consensus pattern (153 bp):
GAAAGTATCCCTAGGGCATTTTTGTAATTTTTAGAACCGACTCCTAGGTTGTCACCAGGTCTACT
TTTATGCCAAATGTGGGTATTTAGGATAGGTTCACCCCATCTATAATCCTTTTCAAGCCCTTTTA
GGGGTATCGGGTACTTCTACGTC
Done.