Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009610.1 Hibiscus syriacus cultivar Beakdansim tig00116996_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3811333
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 15 of 18
Found at i:3073503 original size:20 final size:20
Alignment explanation
Indices: 3073478--3073534 Score: 87
Period size: 20 Copynumber: 2.9 Consensus size: 20
3073468 GTGATTTTCC
3073478 TAAATCGCAATGCGAATACG
1 TAAATCGCAATGCGAATACG
* *
3073498 TAAATCGTAATACGAATACG
1 TAAATCGCAATGCGAATACG
*
3073518 TAAATCGCAACGCGAAT
1 TAAATCGCAATGCGAAT
3073535 CTGGCTATCG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.42, C:0.19, G:0.18, T:0.21
Consensus pattern (20 bp):
TAAATCGCAATGCGAATACG
Found at i:3073759 original size:22 final size:22
Alignment explanation
Indices: 3073731--3073796 Score: 114
Period size: 22 Copynumber: 3.0 Consensus size: 22
3073721 GGCGACATCC
3073731 GTCCCCATCTCCGACGAAATCA
1 GTCCCCATCTCCGACGAAATCA
*
3073753 GTCCCCATCTCCGACGATATCA
1 GTCCCCATCTCCGACGAAATCA
*
3073775 GTCTCCATCTCCGACGAAATCA
1 GTCCCCATCTCCGACGAAATCA
3073797 TTCACGGTCA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.26, C:0.39, G:0.14, T:0.21
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCA
Found at i:3074175 original size:20 final size:20
Alignment explanation
Indices: 3074150--3074219 Score: 104
Period size: 20 Copynumber: 3.5 Consensus size: 20
3074140 TTTTCATTTT
*
3074150 GCGTTGCGATAGTTAAATTC
1 GCGTTGCGATAGTCAAATTC
3074170 GCGTTGCGATAGTCAAATTC
1 GCGTTGCGATAGTCAAATTC
**
3074190 GCGTTGCGATAGTCATTTTC
1 GCGTTGCGATAGTCAAATTC
*
3074210 GTGTTGCGAT
1 GCGTTGCGAT
3074220 TTTAAGTTTC
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.20, C:0.17, G:0.27, T:0.36
Consensus pattern (20 bp):
GCGTTGCGATAGTCAAATTC
Found at i:3076142 original size:20 final size:20
Alignment explanation
Indices: 3076117--3076168 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
3076107 AGAATAGTTT
*
3076117 ACTATCACAATGCGAAAATG
1 ACTATCACAACGCGAAAATG
*
3076137 ACTATCGCAACGCGAAAATG
1 ACTATCACAACGCGAAAATG
3076157 ACTATCACAACG
1 ACTATCACAACG
3076169 AGAGAATCGC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.42, C:0.25, G:0.15, T:0.17
Consensus pattern (20 bp):
ACTATCACAACGCGAAAATG
Found at i:3076186 original size:34 final size:34
Alignment explanation
Indices: 3076140--3076294 Score: 127
Period size: 34 Copynumber: 4.4 Consensus size: 34
3076130 GAAAATGACT
* * *
3076140 ATCGCAACGCGAAAATGACTATCACAACGAGAGA
1 ATCGCAATGCGAAAATGACTATCGCAACGAAAGA
**
3076174 ATCGCAATGCG-AAATGAAAATCGCAAC-AACA-A
1 ATCGCAATGCGAAAATGACTATCGCAACGAA-AGA
* *
3076206 AGTCGCAACGCAAAAATGACTATCGCAATGCGAAAATGA
1 A-TCGCAATGCGAAAATGACTATCGCAA--CG-AAA-GA
**
3076245 CTATCGCAATGCGAATTTGACTATCGCAACGAAAGA
1 --ATCGCAATGCGAAAATGACTATCGCAACGAAAGA
*
3076281 ATCGCAATGTGAAA
1 ATCGCAATGCGAAA
3076295 TAAAAATCGC
Statistics
Matches: 95, Mismatches: 15, Indels: 22
0.72 0.11 0.17
Matches are distributed among these distances:
32 3 0.03
33 22 0.23
34 35 0.37
36 3 0.03
37 4 0.04
38 4 0.04
39 1 0.01
40 22 0.23
41 1 0.01
ACGTcount: A:0.43, C:0.21, G:0.19, T:0.16
Consensus pattern (34 bp):
ATCGCAATGCGAAAATGACTATCGCAACGAAAGA
Found at i:3076233 original size:20 final size:20
Alignment explanation
Indices: 3076208--3076275 Score: 91
Period size: 20 Copynumber: 3.4 Consensus size: 20
3076198 AACAACAAAG
*
3076208 TCGCAACGCAAAAATGACTA
1 TCGCAACGCGAAAATGACTA
*
3076228 TCGCAATGCGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
* **
3076248 TCGCAATGCGAATTTGACTA
1 TCGCAACGCGAAAATGACTA
3076268 TCGCAACG
1 TCGCAACG
3076276 AAAGAATCGC
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.37, C:0.24, G:0.19, T:0.21
Consensus pattern (20 bp):
TCGCAACGCGAAAATGACTA
Found at i:3076398 original size:20 final size:20
Alignment explanation
Indices: 3076320--3076391 Score: 108
Period size: 20 Copynumber: 3.6 Consensus size: 20
3076310 GATTCTCTCG
*
3076320 TTGCGATAGTCAAATTCGCT
1 TTGCGATAGTCAAATTCGCA
*
3076340 TTGCGATAGTTAAATTCGCA
1 TTGCGATAGTCAAATTCGCA
**
3076360 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCAAATTCGCA
3076380 TTGCGATAGTCA
1 TTGCGATAGTCA
3076392 TTTTCGCGTT
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.25, C:0.18, G:0.21, T:0.36
Consensus pattern (20 bp):
TTGCGATAGTCAAATTCGCA
Found at i:3076981 original size:21 final size:21
Alignment explanation
Indices: 3076890--3076994 Score: 95
Period size: 21 Copynumber: 5.0 Consensus size: 21
3076880 GACTCACCTG
*
3076890 TCATCGTTCAAGAGGCCTCCCC
1 TCATCGTTCAAGAGGCC-CCTC
*
3076912 T-ATCGTTCAAGAGGCCCCTA
1 TCATCGTTCAAGAGGCCCCTC
** *
3076932 TCATCCCTCAAGAGTCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
* * * *
3076953 CCACCGTTCAAGAGGCCACTG
1 TCATCGTTCAAGAGGCCCCTC
* *
3076974 TCATCGTTGAAGAGGTCCCTC
1 TCATCGTTCAAGAGGCCCCTC
3076995 CCAACATTCT
Statistics
Matches: 63, Mismatches: 19, Indels: 3
0.74 0.22 0.04
Matches are distributed among these distances:
20 3 0.05
21 59 0.94
22 1 0.02
ACGTcount: A:0.21, C:0.37, G:0.19, T:0.23
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:3076987 original size:42 final size:42
Alignment explanation
Indices: 3076887--3076997 Score: 118
Period size: 42 Copynumber: 2.6 Consensus size: 42
3076877 CCCGACTCAC
* * * *
3076887 CTGTCATCGTTCAAGAGGCCTCC-CCTATCGTTCAAGAGGCCC
1 CTGTCATCGTTCAAGAGTCC-CCTCCCACCGTTCAAGAGGCCA
* **
3076929 CTATCATCCCTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCA
1 CTGTCATCGTTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCA
*
3076971 CTGTCATCGTTGAAGAGGT-CCCTCCCA
1 CTGTCATCGTTCAAGA-GTCCCCTCCCA
3076998 ACATTCTAGA
Statistics
Matches: 56, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
41 2 0.04
42 52 0.93
43 2 0.04
ACGTcount: A:0.21, C:0.38, G:0.19, T:0.23
Consensus pattern (42 bp):
CTGTCATCGTTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCA
Found at i:3078657 original size:20 final size:20
Alignment explanation
Indices: 3078622--3078718 Score: 135
Period size: 20 Copynumber: 4.9 Consensus size: 20
3078612 GTTGTGATTT
*
3078622 TCATTT-CGCATTGCGATAG
1 TCATTTCCGCGTTGCGATAG
3078641 TCATTTCCGCGTTGCGATAG
1 TCATTTCCGCGTTGCGATAG
*
3078661 TCAATTCCGCGTTGCGATAG
1 TCATTTCCGCGTTGCGATAG
**
3078681 TCATTTCCATGTTGCGATAG
1 TCATTTCCGCGTTGCGATAG
3078701 TCATATT-CGCGTTGCGAT
1 TCAT-TTCCGCGTTGCGAT
3078719 TTTCGCGTTG
Statistics
Matches: 69, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
19 6 0.09
20 61 0.88
21 2 0.03
ACGTcount: A:0.19, C:0.23, G:0.23, T:0.36
Consensus pattern (20 bp):
TCATTTCCGCGTTGCGATAG
Found at i:3078725 original size:14 final size:14
Alignment explanation
Indices: 3078706--3078732 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3078696 GATAGTCATA
3078706 TTCGCGTTGCGATT
1 TTCGCGTTGCGATT
3078720 TTCGCGTTGCGAT
1 TTCGCGTTGCGAT
3078733 AGTCAAATGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.22, G:0.30, T:0.41
Consensus pattern (14 bp):
TTCGCGTTGCGATT
Found at i:3081181 original size:24 final size:25
Alignment explanation
Indices: 3081147--3081201 Score: 85
Period size: 24 Copynumber: 2.2 Consensus size: 25
3081137 CTGAAAAATC
3081147 ATCAAAATCCGAGTATTGACC-AAG
1 ATCAAAATCCGAGTATTGACCAAAG
* *
3081171 ATCAAAGTCCGGGTATTGACCAAAG
1 ATCAAAATCCGAGTATTGACCAAAG
3081196 ATCAAA
1 ATCAAA
3081202 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
24 19 0.68
25 9 0.32
ACGTcount: A:0.42, C:0.20, G:0.18, T:0.20
Consensus pattern (25 bp):
ATCAAAATCCGAGTATTGACCAAAG
Found at i:3082070 original size:20 final size:20
Alignment explanation
Indices: 3082045--3082091 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
3082035 AAATTCAGTA
*
3082045 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCGCG
*
3082065 TTGCGATAGTCAGATTCGCG
1 TTGCGATAGTCAGAATCGCG
3082085 TTGCGAT
1 TTGCGAT
3082092 TTACATATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.21, C:0.19, G:0.28, T:0.32
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCGCG
Found at i:3082101 original size:20 final size:20
Alignment explanation
Indices: 3082078--3082190 Score: 181
Period size: 20 Copynumber: 5.7 Consensus size: 20
3082068 CGATAGTCAG
* *
3082078 ATTCGCGTTGCGATTTACAT
1 ATTCGCATTGCGATTTACGT
*
3082098 ATTCGCATTGCAATTTACGT
1 ATTCGCATTGCGATTTACGT
3082118 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* *
3082138 ATTTGCATTGTGATTTACGT
1 ATTCGCATTGCGATTTACGT
3082158 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
3082178 ATTCGCATTGCGA
1 ATTCGCATTGCGA
3082191 ATTAGGAAAA
Statistics
Matches: 85, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 85 1.00
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.41
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:3082211 original size:21 final size:21
Alignment explanation
Indices: 3082187--3082232 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
3082177 TATTCGCATT
3082187 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* *
3082208 GCGAATTTGGAAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
3082229 GCGA
1 GCGA
3082233 TAGTCAGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.39, C:0.17, G:0.26, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:3097364 original size:44 final size:44
Alignment explanation
Indices: 3097278--3097364 Score: 147
Period size: 44 Copynumber: 2.0 Consensus size: 44
3097268 TCAAAAAAAA
* *
3097278 TTAAAATCAGTTAATCATTTTTACACTTTAAAGTCAATTTTTTT
1 TTAAAATCAGTTAATCATTTTTACACTTTAAAATCAAATTTTTT
*
3097322 TTAAAATCAGTTAATCATTTTTACACTTTAAAATTAAATTTTT
1 TTAAAATCAGTTAATCATTTTTACACTTTAAAATCAAATTTTT
3097365 AAAGATTTGT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.37, C:0.10, G:0.03, T:0.49
Consensus pattern (44 bp):
TTAAAATCAGTTAATCATTTTTACACTTTAAAATCAAATTTTTT
Found at i:3108605 original size:60 final size:58
Alignment explanation
Indices: 3108509--3108686 Score: 164
Period size: 60 Copynumber: 3.0 Consensus size: 58
3108499 TATAAGTCCT
** * *
3108509 CAAACTATG-ACACTCATTCT-AAATTAATCCTCAAACTTTTGAACATTCCAAATTCATCC
1 CAAACTATGAAC-CTCATT-TGAAATTGGTCCCCAAACTTTTGAA-ATTCCAATTTCATCC
* *
3108568 ACAAACTAT-AACCATCATTTGAAATTGGTCCCTAAACTTTTAGGAATTCCAATTTCATTCC
1 -CAAACTATGAACC-TCATTTGAAATTGGTCCCCAAACTTTT-GAAATTCCAATTTCA-TCC
* * * * *
3108629 CAATCTATGATCCTCATTTTATATTGGTCCCCAAACTTTTGAATATTTCAATTTCATC
1 CAAACTATGAACCTCATTTGAAATTGGTCCCCAAACTTTTGAA-ATTCCAATTTCATC
3108687 TTCTATCTTT
Statistics
Matches: 98, Mismatches: 13, Indels: 15
0.78 0.10 0.12
Matches are distributed among these distances:
59 6 0.06
60 84 0.86
61 8 0.08
ACGTcount: A:0.33, C:0.24, G:0.06, T:0.37
Consensus pattern (58 bp):
CAAACTATGAACCTCATTTGAAATTGGTCCCCAAACTTTTGAAATTCCAATTTCATCC
Found at i:3108850 original size:60 final size:59
Alignment explanation
Indices: 3108727--3108887 Score: 162
Period size: 60 Copynumber: 2.7 Consensus size: 59
3108717 TATTGGAACG
* * * * *
3108727 TTCAAAAGTTTGGGATCAATTTAGAATGAGGGTTATAGTTTGTGGATGAATTTGGAATT
1 TTCAAAAGTTTGGGATCAATTTAGAATGAGAGTCATAGTTTGTGGATGAAATTAGAATA
* * * *
3108786 TTCAAAATTTTGGGGATTAATTTAGAATGAGAGTCATGGTTTAG-GGATGAAATTATAATA
1 TTCAAAAGTTT-GGGATCAATTTAGAATGAGAGTCATAGTTT-GTGGATGAAATTAGAATA
* * * * *
3108846 TTCAAATGTTTAGGGACCAATCTATAATGAGGGTCATAGTTT
1 TTCAAAAGTTT-GGGATCAATTTAGAATGAGAGTCATAGTTT
3108888 CAAGATGTAT
Statistics
Matches: 82, Mismatches: 18, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
59 10 0.12
60 71 0.87
61 1 0.01
ACGTcount: A:0.33, C:0.06, G:0.24, T:0.37
Consensus pattern (59 bp):
TTCAAAAGTTTGGGATCAATTTAGAATGAGAGTCATAGTTTGTGGATGAAATTAGAATA
Found at i:3112117 original size:20 final size:20
Alignment explanation
Indices: 3112094--3112132 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
3112084 AAATATAAAC
*
3112094 AAATAAAATTAAAACAATAA
1 AAATAAAACTAAAACAATAA
**
3112114 AAATACCACTAAAACAATA
1 AAATAAAACTAAAACAATA
3112133 TATTTTAAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.69, C:0.13, G:0.00, T:0.18
Consensus pattern (20 bp):
AAATAAAACTAAAACAATAA
Found at i:3113532 original size:3 final size:3
Alignment explanation
Indices: 3113524--3113616 Score: 159
Period size: 3 Copynumber: 30.7 Consensus size: 3
3113514 AATATATATT
*
3113524 TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
3113572 TAG TAA TAA TAA TAA TAA TAA TAA TAA TAA TTAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TA
3113617 TGGATAAAAA
Statistics
Matches: 85, Mismatches: 4, Indels: 2
0.93 0.04 0.02
Matches are distributed among these distances:
3 82 0.96
4 3 0.04
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:3114187 original size:113 final size:113
Alignment explanation
Indices: 3113935--3114606 Score: 1175
Period size: 113 Copynumber: 6.0 Consensus size: 113
3113925 AGAATTATGC
* * * *
3113935 AAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * * * *
3114000 TATGAAC-TTCTCCGGAAAAGATAATCCATCAATTGATGAATTCAGGT
66 TATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTCAGGT
*
3114047 AAAAGGTTGAACAAATTCTTCTAATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* *
3114112 TATGAACTTTCTCTGGAAAAGATGATCCCTCAAATGATGGATTCAGGT
66 TATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTCAGGT
3114160 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
*
3114225 TATGAACTTTCTCTGGAAAAGCTGATCCCTCAAATGATGGATTCAGGT
66 TATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTCAGGT
3114273 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
*
3114338 TATGAACTTTCTCTGGAAAAGCCGATCCATCAAATGATGGATTCAGGT
66 TATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTCAGGT
3114386 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
3114451 TATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTCAGGT
66 TATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTCAGGT
3114499 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* ** *
3114564 TATGAACTTTCTCTGGAAAAGCTAATCTTTCAAATGATAGATT
66 TATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATT
3114607 TGAATCTTTG
Statistics
Matches: 541, Mismatches: 18, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
112 68 0.13
113 473 0.87
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (113 bp):
AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
TATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTCAGGT
Found at i:3115554 original size:82 final size:83
Alignment explanation
Indices: 3115450--3115991 Score: 898
Period size: 82 Copynumber: 6.6 Consensus size: 83
3115440 CATACCAAAC
*
3115450 CAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTTTAAACTCAATGATT
1 CAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAATGATT
3115515 G-TTCTGTCCAACCAGAT
66 GATTCTGTCCAACCAGAT
* * *
3115532 CAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCCAAATTCAATGCTT
1 CAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAATGATT
*
3115597 GATTCTGTCCAATCAGAT
66 GATTCTGTCCAACCAGAT
*
3115615 CAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAATGCTT
1 CAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAATGATT
*
3115680 GATTCTGTCCAATCAGAT
66 GATTCTGTCCAACCAGAT
3115698 CAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAATGATT
1 CAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAATGATT
3115763 G-TTCTGTCCAACCAGAT
66 GATTCTGTCCAACCAGAT
3115780 CAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAATGATT
1 CAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAATGATT
3115845 G-TTCTGTCCAACCAGAT
66 GATTCTGTCCAACCAGAT
* *
3115862 CAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAGCACATTCATCTTCCT-AATTCAATGA
1 CAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-GCAAATTCATCTT-CTAAACTCAATGA
* *
3115925 TTGATTCTG-CTAAACCAGGT
64 TTGATTCTGTC-CAACCAGAT
**
3115945 CAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCAT
1 CAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCAT
3115992 TTGTTCTATT
Statistics
Matches: 438, Mismatches: 16, Indels: 11
0.94 0.03 0.02
Matches are distributed among these distances:
81 2 0.00
82 218 0.50
83 217 0.50
84 1 0.00
ACGTcount: A:0.36, C:0.23, G:0.13, T:0.28
Consensus pattern (83 bp):
CAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAATGATT
GATTCTGTCCAACCAGAT
Found at i:3117055 original size:5 final size:5
Alignment explanation
Indices: 3117047--3117106 Score: 61
Period size: 5 Copynumber: 11.8 Consensus size: 5
3117037 TTTTTTCCTT
* *
3117047 TTTTC TTTTTT TTTTC TTTTC TTTT- TTTCCTC TTTTC TTTTC TTTTT
1 TTTTC -TTTTC TTTTC TTTTC TTTTC TTT--TC TTTTC TTTTC TTTTC
3117094 TTTTC -TTTC TTTT
1 TTTTC TTTTC TTTT
3117107 TCTTCAAGCA
Statistics
Matches: 46, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
4 7 0.15
5 31 0.67
6 5 0.11
7 3 0.07
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTC
Found at i:3117061 original size:11 final size:11
Alignment explanation
Indices: 3117045--3117107 Score: 65
Period size: 13 Copynumber: 5.4 Consensus size: 11
3117035 TCTTTTTTCC
3117045 TTTTTTCTTTT
1 TTTTTTCTTTT
3117056 TTTTTTCTTTTCT
1 TTTTTTC-TTT-T
3117069 TTTTTTCCTCTTT
1 TTTTTT-CT-TTT
*
3117082 TCTTTTC-TTT
1 TTTTTTCTTTT
3117092 TTTTTTCTTTCT
1 TTTTTTCTTT-T
3117104 TTTT
1 TTTT
3117108 CTTCAAGCAT
Statistics
Matches: 44, Mismatches: 2, Indels: 11
0.77 0.04 0.19
Matches are distributed among these distances:
10 9 0.20
11 9 0.20
12 9 0.20
13 14 0.32
14 3 0.07
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTTTCTTTT
Found at i:3117067 original size:31 final size:30
Alignment explanation
Indices: 3117031--3117101 Score: 106
Period size: 32 Copynumber: 2.3 Consensus size: 30
3117021 CTTGACCCCC
* *
3117031 TTTTTCTTTTTTCCTTTTTTCTTTTTTTTT
1 TTTTTCTTTTTTCCTCTTTTCTTTTCTTTT
3117061 TCTTTTCTTTTTTTCCTCTTTTCTTTTCTTTT
1 T-TTTTC-TTTTTTCCTCTTTTCTTTTCTTTT
3117093 TTTTTCTTT
1 TTTTTCTTT
3117102 CTTTTTCTTC
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
30 4 0.11
31 10 0.27
32 23 0.62
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (30 bp):
TTTTTCTTTTTTCCTCTTTTCTTTTCTTTT
Found at i:3117096 original size:40 final size:39
Alignment explanation
Indices: 3117031--3117108 Score: 61
Period size: 41 Copynumber: 1.9 Consensus size: 39
3117021 CTTGACCCCC
* * *
3117031 TTTTTCTTTTTTCCTT-TTTTCTTTTTTTTTTCTTTTCTT
1 TTTTTCTTTTTTCTTTCTTTTC-TTTTTTTCTCTTTTCCT
* *
3117070 TTTTTCCTCTTTTCTTTTCTTTTTTTTTCTTTCT-TTTTC
1 TTTTT-CTTTTTTC-TTTCTTTTCTTTT-TTTCTCTTTTC
3117109 TTCAAGCATA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
39 5 0.16
40 7 0.23
41 11 0.35
42 8 0.26
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (39 bp):
TTTTTCTTTTTTCTTTCTTTTCTTTTTTTCTCTTTTCCT
Found at i:3127769 original size:24 final size:23
Alignment explanation
Indices: 3127737--3127782 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
3127727 ATAAAAAATG
3127737 AAATAATATATATAAATACTATAA
1 AAATAATATATATAAATA-TATAA
* *
3127761 AAATAATATGTATATATATATA
1 AAATAATATATATAAATATATA
3127783 TAAACAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (23 bp):
AAATAATATATATAAATATATAA
Found at i:3128524 original size:20 final size:20
Alignment explanation
Indices: 3128501--3128539 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
3128491 AAATATAAAC
*
3128501 AAATAAAATTAAAACAATAA
1 AAATAAAACTAAAACAATAA
**
3128521 AAATACCACTAAAACAATA
1 AAATAAAACTAAAACAATA
3128540 TATTTTAAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.69, C:0.13, G:0.00, T:0.18
Consensus pattern (20 bp):
AAATAAAACTAAAACAATAA
Found at i:3129944 original size:3 final size:3
Alignment explanation
Indices: 3129936--3130090 Score: 220
Period size: 3 Copynumber: 51.7 Consensus size: 3
3129926 AATATATATT
* *
3129936 TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAG
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * *
3129984 TAA TAA TAA TAA TAA TAA TAA TAT TAT TAT TAT TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * *
3130032 TAA TAA TAA TAA TAA TAG TAA TAA TAA TAA TAA TAA TAT TAT TAT TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
3130080 TAA TAA TAA TA
1 TAA TAA TAA TA
3130091 TGGATAAAAA
Statistics
Matches: 142, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 142 1.00
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:3133934 original size:31 final size:31
Alignment explanation
Indices: 3133899--3133958 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
3133889 TAGTTGTATG
* *
3133899 AATTATTTAAATTTCAGTATTGTAAAACTAA
1 AATTATTTAAATCTCAGTATTGCAAAACTAA
*
3133930 AATTATTTAAATCTCGGTATTGCAAAACT
1 AATTATTTAAATCTCAGTATTGCAAAACT
3133959 CGTTTAAGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.42, C:0.10, G:0.08, T:0.40
Consensus pattern (31 bp):
AATTATTTAAATCTCAGTATTGCAAAACTAA
Found at i:3136201 original size:23 final size:24
Alignment explanation
Indices: 3136173--3136217 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
3136163 ATTTAATTAA
3136173 ATAAATTA-TAATTTAAATTAATT
1 ATAAATTAGTAATTTAAATTAATT
* *
3136196 ATAAATTAGTTATTTAATTTAA
1 ATAAATTAGTAATTTAAATTAA
3136218 AATATTTAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (24 bp):
ATAAATTAGTAATTTAAATTAATT
Found at i:3136237 original size:22 final size:22
Alignment explanation
Indices: 3136201--3136247 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
3136191 TAATTATAAA
3136201 TTAGTTATTTAATTTAAAATAT
1 TTAGTTATTTAATTTAAAATAT
3136223 TTAGTTATTTAATTTAAAATAT
1 TTAGTTATTTAATTTAAAATAT
3136245 TTA
1 TTA
3136248 ATTTATATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.55
Consensus pattern (22 bp):
TTAGTTATTTAATTTAAAATAT
Found at i:3136294 original size:26 final size:25
Alignment explanation
Indices: 3136230--3136297 Score: 64
Period size: 26 Copynumber: 2.6 Consensus size: 25
3136220 TATTTAGTTA
3136230 TTTAATTTAAAATATTTAATTTATAT
1 TTTAATTTAAAA-ATTTAATTTATAT
* * * * *
3136256 ATAAATTAAAAAAATTTAATTTTTTT
1 TTTAATT-TAAAAATTTAATTTATAT
3136282 GTTTAATTTAAAAATT
1 -TTTAATTTAAAAATT
3136298 GATTAATAAT
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
26 23 0.72
27 9 0.28
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (25 bp):
TTTAATTTAAAAATTTAATTTATAT
Found at i:3136443 original size:29 final size:29
Alignment explanation
Indices: 3136396--3136479 Score: 82
Period size: 29 Copynumber: 2.9 Consensus size: 29
3136386 AAAAAAATCG
* *
3136396 ATTAATTCGGTTCGGTTAATAAATTTT-A
1 ATTAATTTGGTTCGATTAATAAATTTTCA
* *
3136424 TATTAATTTGGTTTGATTAAT-ATTTTTCA
1 -ATTAATTTGGTTCGATTAATAAATTTTCA
*
3136453 ATAAATTTTGGTTCGATTAACTAAATT
1 ATTAA-TTTGGTTCGATTAA-TAAATT
3136480 GAATTAATCG
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
28 9 0.20
29 31 0.70
30 1 0.02
31 3 0.07
ACGTcount: A:0.32, C:0.06, G:0.12, T:0.50
Consensus pattern (29 bp):
ATTAATTTGGTTCGATTAATAAATTTTCA
Found at i:3136468 original size:138 final size:139
Alignment explanation
Indices: 3136296--3136580 Score: 378
Period size: 138 Copynumber: 2.1 Consensus size: 139
3136286 AATTTAAAAA
* **
3136296 TTGATTAATAATTTTTTAAATAAATTTTGATTCGATTAATTAAATCGTTTTAACCGAATTTTTAT
1 TTGATTAATAATTTTTTAAATAAATTTTGATTCGATTAACTAAATCGAATTAACCGAATTTTTAT
* * * *
3136361 TTCAATTAATTCGGTTAATAATTATAAAAAAATCGATTAATTCGGTTCGGTTAATAAATTTTATA
66 TTCAATTAATTCGGTTAATAATT-TAAAAAAATAGATTAATTC-ATTCGATTAATAAATTTTAAA
* *
3136426 TTAA-TTTGGT
129 TAAATTTTAGT
* * * * *
3136436 TTGATTAAT-A-TTTTTCAATAAATTTTGGTTCGATTAACTAAATTGAATTAATCGAATTTTTGT
1 TTGATTAATAATTTTTTAAATAAATTTTGATTCGATTAACTAAATCGAATTAACCGAATTTTTAT
* * *
3136499 TTTAATTAATTCGTTTAATAATTTAAAAAAATAGATTAATTCATTCGATTAATAATTTTTAAATA
66 TTCAATTAATTCGGTTAATAATTTAAAAAAATAGATTAATTCATTCGATTAATAAATTTTAAATA
3136564 AATTTTAGT
131 AATTTTAGT
3136573 TTGATTAA
1 TTGATTAA
3136581 CTAAATCAAA
Statistics
Matches: 127, Mismatches: 17, Indels: 5
0.85 0.11 0.03
Matches are distributed among these distances:
136 20 0.16
137 31 0.24
138 66 0.52
139 1 0.01
140 9 0.07
ACGTcount: A:0.38, C:0.06, G:0.09, T:0.48
Consensus pattern (139 bp):
TTGATTAATAATTTTTTAAATAAATTTTGATTCGATTAACTAAATCGAATTAACCGAATTTTTAT
TTCAATTAATTCGGTTAATAATTTAAAAAAATAGATTAATTCATTCGATTAATAAATTTTAAATA
AATTTTAGT
Found at i:3136657 original size:64 final size:66
Alignment explanation
Indices: 3136589--3136713 Score: 166
Period size: 69 Copynumber: 1.9 Consensus size: 66
3136579 AACTAAATCA
* *
3136589 AATTAACCGATTT-TTTTA-ACAT-TTAATCGAATTAAAATTTATTTAAAAATTATTAACCAAAC
1 AATTAACCGATTTATTTTATA-ATAGTAATCGAATCAAAATTTATTTAAAAATTATTAACCAAAC
3136651 TT
65 TT
*
3136653 AATTAACCGATTTATTTTATTTAATCAGTAATCGAATCGAAATTTATTTAAAAATTATTAA
1 AATTAACCGATTTATTTTA--TAAT-AGTAATCGAATCAAAATTTATTTAAAAATTATTAA
3136714 TCGAACTGGA
Statistics
Matches: 52, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
64 13 0.25
65 5 0.10
67 2 0.04
68 1 0.02
69 31 0.60
ACGTcount: A:0.43, C:0.10, G:0.05, T:0.42
Consensus pattern (66 bp):
AATTAACCGATTTATTTTATAATAGTAATCGAATCAAAATTTATTTAAAAATTATTAACCAAACT
T
Found at i:3136858 original size:17 final size:16
Alignment explanation
Indices: 3136823--3136866 Score: 61
Period size: 17 Copynumber: 2.7 Consensus size: 16
3136813 AAAAAATTAC
* *
3136823 AATTAATTTAAATAAT
1 AATTTATTTAAAAAAT
3136839 AATTTATTTAAACAAAT
1 AATTTATTTAAA-AAAT
3136856 AATTTATTTAA
1 AATTTATTTAA
3136867 TTTTTTATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
16 11 0.44
17 14 0.56
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
AATTTATTTAAAAAAT
Found at i:3137896 original size:18 final size:18
Alignment explanation
Indices: 3137873--3137909 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
3137863 TTGGAATGTT
* *
3137873 TATGAAGGAATTAGAATC
1 TATGAAAGAATTAAAATC
3137891 TATGAAAGAATTAAAATC
1 TATGAAAGAATTAAAATC
3137909 T
1 T
3137910 GTCAGGAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.49, C:0.05, G:0.16, T:0.30
Consensus pattern (18 bp):
TATGAAAGAATTAAAATC
Found at i:3145802 original size:23 final size:24
Alignment explanation
Indices: 3145743--3145802 Score: 61
Period size: 23 Copynumber: 2.6 Consensus size: 24
3145733 ATACTTATTG
*
3145743 ATTATTATGATTATTTGAAAAAAT
1 ATTATTATGATTATGTGAAAAAAT
* * *
3145767 ATTA-TACGTTTATGTGTAAAAAT
1 ATTATTATGATTATGTGAAAAAAT
*
3145790 TTTATTATG-TTAT
1 ATTATTATGATTAT
3145803 ATTTTCGTTC
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
23 22 0.76
24 7 0.24
ACGTcount: A:0.38, C:0.02, G:0.10, T:0.50
Consensus pattern (24 bp):
ATTATTATGATTATGTGAAAAAAT
Found at i:3152688 original size:18 final size:18
Alignment explanation
Indices: 3152665--3152700 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
3152655 GAGGGATTAT
*
3152665 TAGTGGTCCTTCGGGACA
1 TAGTGGTCATTCGGGACA
3152683 TAGTGGTCATTCGGGACA
1 TAGTGGTCATTCGGGACA
3152701 AATATTCAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.19, C:0.19, G:0.33, T:0.28
Consensus pattern (18 bp):
TAGTGGTCATTCGGGACA
Found at i:3157169 original size:23 final size:23
Alignment explanation
Indices: 3157136--3157187 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
3157126 ATTATTATAT
3157136 GGCACTACGGTACAATTCTACGC
1 GGCACTACGGTACAATTCTACGC
* * *
3157159 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTACAATTCTACGC
3157182 GGCACT
1 GGCACT
3157188 TCAGTGCAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.21, C:0.31, G:0.25, T:0.23
Consensus pattern (23 bp):
GGCACTACGGTACAATTCTACGC
Found at i:3157194 original size:23 final size:23
Alignment explanation
Indices: 3157148--3157203 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
3157138 CACTACGGTA
*
3157148 CAATTCTACGCGGCACTCCGGTG
1 CAATTCTACGCGGCACTCCAGTG
* *
3157171 CAATTCTACGTGGCACTTCAGTG
1 CAATTCTACGCGGCACTCCAGTG
*
3157194 CAATTATACG
1 CAATTCTACG
3157204 AGCTGTGGTG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.23, C:0.29, G:0.21, T:0.27
Consensus pattern (23 bp):
CAATTCTACGCGGCACTCCAGTG
Found at i:3158554 original size:71 final size:71
Alignment explanation
Indices: 3158471--3158606 Score: 272
Period size: 71 Copynumber: 1.9 Consensus size: 71
3158461 TCAAGCCATC
3158471 ATGTCTAGATCGAATTAAAGAATTACAAGCTAGAGATGAAAAGTGTTCAAAGAAGATACAACAAA
1 ATGTCTAGATCGAATTAAAGAATTACAAGCTAGAGATGAAAAGTGTTCAAAGAAGATACAACAAA
3158536 TAAGGA
66 TAAGGA
3158542 ATGTCTAGATCGAATTAAAGAATTACAAGCTAGAGATGAAAAGTGTTCAAAGAAGATACAACAAA
1 ATGTCTAGATCGAATTAAAGAATTACAAGCTAGAGATGAAAAGTGTTCAAAGAAGATACAACAAA
3158607 CTTATATGAA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 65 1.00
ACGTcount: A:0.49, C:0.10, G:0.19, T:0.21
Consensus pattern (71 bp):
ATGTCTAGATCGAATTAAAGAATTACAAGCTAGAGATGAAAAGTGTTCAAAGAAGATACAACAAA
TAAGGA
Found at i:3159954 original size:18 final size:18
Alignment explanation
Indices: 3159931--3159965 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
3159921 AGGGATTATC
*
3159931 AGTGGTCCTTCGGGACAT
1 AGTGGTCATTCGGGACAT
3159949 AGTGGTCATTCGGGACA
1 AGTGGTCATTCGGGACA
3159966 AATATTCAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.20, C:0.20, G:0.34, T:0.26
Consensus pattern (18 bp):
AGTGGTCATTCGGGACAT
Found at i:3164074 original size:2 final size:2
Alignment explanation
Indices: 3164062--3164111 Score: 54
Period size: 2 Copynumber: 26.5 Consensus size: 2
3164052 TTTGAAAAAC
*
3164062 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT -T GA- AA AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT
3164102 AT AT -T AT AT A
1 AT AT AT AT AT A
3164112 GTTTTAAAAC
Statistics
Matches: 42, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
1 4 0.10
2 38 0.90
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (2 bp):
AT
Found at i:3164146 original size:41 final size:40
Alignment explanation
Indices: 3164096--3164257 Score: 138
Period size: 40 Copynumber: 4.1 Consensus size: 40
3164086 TATATTGAAA
*
3164096 ATATATATATTATATAGTTTTAAAACATTTTGAAGATATAT
1 ATATATATATTATATAGTTTTAAAACATTTTGAA-AAATAT
* * *
3164137 ATATATATATAATATAATTTTTGAAACATTTTTG--AAA-A-
1 ATATATATATTATAT-AGTTTTAAAACA-TTTTGAAAAATAT
* * * *
3164175 CTACATA-A-TATATAGTTTTGCAAACATTTTTAAAAATAT
1 ATATATATATTATATAGTTTT-AAAACATTTTGAAAAATAT
* * * *
3164214 ATATATATAATATATATTTTTAAAATATTTTTAAAAATAT
1 ATATATATATTATATAGTTTTAAAACATTTTGAAAAATAT
3164254 ATAT
1 ATAT
3164258 TTTATAGTTT
Statistics
Matches: 97, Mismatches: 15, Indels: 19
0.74 0.11 0.15
Matches are distributed among these distances:
35 9 0.09
36 9 0.09
37 4 0.04
38 6 0.06
39 6 0.06
40 24 0.25
41 24 0.25
42 10 0.10
43 5 0.05
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (40 bp):
ATATATATATTATATAGTTTTAAAACATTTTGAAAAATAT
Found at i:3164185 original size:34 final size:34
Alignment explanation
Indices: 3164145--3164224 Score: 99
Period size: 35 Copynumber: 2.3 Consensus size: 34
3164135 ATATATATAT
*
3164145 ATAATATAATTTTTG-AAACATTTTTGAAAACTAC
1 ATAATATAATTTTTGCAAACATTTTT-AAAAATAC
* *
3164179 ATAATATATAGTTTTGCAAACATTTTTAAAAATAT
1 ATAATATA-ATTTTTGCAAACATTTTTAAAAATAC
3164214 ATATATATAAT
1 ATA-ATATAAT
3164225 ATATATTTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
34 8 0.21
35 16 0.41
36 15 0.38
ACGTcount: A:0.46, C:0.06, G:0.05, T:0.42
Consensus pattern (34 bp):
ATAATATAATTTTTGCAAACATTTTTAAAAATAC
Found at i:3164193 original size:77 final size:75
Alignment explanation
Indices: 3164039--3164268 Score: 209
Period size: 75 Copynumber: 3.1 Consensus size: 75
3164029 TCCGATGCTC
* * * * * * * * *
3164039 GTTTAGAAAACAGTTTGAAAAACATATA-ATAT-ATATATATATAT-ATATATATTGAAAATATA
1 GTTTTGAAAACATTTTGAAAAATATATATATATAATATATATTTTTAAAACATTTTTAAAA-ATA
* *
3164101 TATATTATATA
65 CATAATATATA
*
3164112 GTTTT-AAAACATTTTGAAGATATATATATATATATAATATA-ATTTTTGAAACATTTTTGAAAA
1 GTTTTGAAAACATTTTGAA-A-A-ATATATATATATAATATATATTTTTAAAACATTTTT-AAAA
*
3164175 CTACATAATATATA
62 ATACATAATATATA
* * * *
3164189 GTTTTGCAAACATTTTTAAAAATATATATATATAATATATATTTTTAAAATATTTTTAAAAATAT
1 GTTTTGAAAACATTTTGAAAAATATATATATATAATATATATTTTTAAAACATTTTTAAAAATAC
* *
3164254 ATATTTTATA
66 ATAATATATA
3164264 GTTTT
1 GTTTT
3164269 TGGAAATAGT
Statistics
Matches: 128, Mismatches: 20, Indels: 16
0.78 0.12 0.10
Matches are distributed among these distances:
72 12 0.09
73 5 0.04
74 1 0.01
75 43 0.34
76 24 0.19
77 28 0.22
78 15 0.12
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.45
Consensus pattern (75 bp):
GTTTTGAAAACATTTTGAAAAATATATATATATAATATATATTTTTAAAACATTTTTAAAAATAC
ATAATATATA
Found at i:3164200 original size:36 final size:34
Alignment explanation
Indices: 3164145--3164222 Score: 97
Period size: 34 Copynumber: 2.3 Consensus size: 34
3164135 ATATATATAT
* *
3164145 ATAATATA-ATTTTTGAAACATTTTTGAAAACTAC
1 ATAATATATAGTTTTGAAACATTTTT-AAAAATAC
*
3164179 ATAATATATAGTTTTGCAAACATTTTTAAAAATAT
1 ATAATATATAGTTTTG-AAACATTTTTAAAAATAC
3164214 AT-ATATATA
1 ATAATATATA
3164223 ATATATATTT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
34 15 0.38
35 14 0.36
36 10 0.26
ACGTcount: A:0.46, C:0.06, G:0.05, T:0.42
Consensus pattern (34 bp):
ATAATATATAGTTTTGAAACATTTTTAAAAATAC
Found at i:3164254 original size:36 final size:36
Alignment explanation
Indices: 3164139--3164257 Score: 116
Period size: 36 Copynumber: 3.2 Consensus size: 36
3164129 AGATATATAT
* *
3164139 ATATATATAATATA-ATTTTTGAAACATTTTTGAAA
1 ATATATATAATATATATTTTTAAAACATTTTTAAAA
* * **
3164174 A-CTACATAATATATAGTTTTGCAAACATTTTTAAAAATA
1 ATATATATAATATATA-TTTTTAAAACATTTTT--AAA-A
*
3164213 TATATATATAATATATATTTTTAAAATATTTTTAAAA
1 -ATATATATAATATATATTTTTAAAACATTTTTAAAA
3164250 ATATATAT
1 ATATATAT
3164258 TTTATAGTTT
Statistics
Matches: 67, Mismatches: 10, Indels: 13
0.74 0.11 0.14
Matches are distributed among these distances:
34 10 0.15
35 2 0.03
36 22 0.33
37 1 0.01
38 5 0.07
39 1 0.01
40 14 0.21
41 12 0.18
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.45
Consensus pattern (36 bp):
ATATATATAATATATATTTTTAAAACATTTTTAAAA
Found at i:3164276 original size:36 final size:36
Alignment explanation
Indices: 3164139--3164301 Score: 98
Period size: 36 Copynumber: 4.4 Consensus size: 36
3164129 AGATATATAT
** *
3164139 ATATATATAATATAATTTTT-GAAACATTTTTGAAAA
1 ATATATATTTTATAGTTTTTGGAAACATTTTT-AAAA
* * * * *
3164175 CTACATAATATATAG-TTTTGCAAACATTTTTAAAA
1 ATATATATTTTATAGTTTTTGGAAACATTTTTAAAA
** *
3164210 ATATATATATATAATATA-TATTTTTAAAATATTTTTAAAA
1 ATATATAT-T-T--TATAGT-TTTTGGAAACATTTTTAAAA
* * *
3164250 ATATATATTTTATAGTTTTTGGAAATAGTTTTTATAT
1 ATATATATTTTATAGTTTTTGGAAACA-TTTTTAAAA
3164287 ATAATATATTATTAT
1 AT-ATATATT-TTAT
3164302 TATTATTTAT
Statistics
Matches: 99, Mismatches: 17, Indels: 19
0.73 0.13 0.14
Matches are distributed among these distances:
35 13 0.13
36 34 0.34
37 10 0.10
38 8 0.08
39 9 0.09
40 25 0.25
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (36 bp):
ATATATATTTTATAGTTTTTGGAAACATTTTTAAAA
Found at i:3164289 original size:75 final size:73
Alignment explanation
Indices: 3164132--3164295 Score: 188
Period size: 75 Copynumber: 2.2 Consensus size: 73
3164122 ATTTTGAAGA
* *
3164132 TATATATATATATATAATATAATTTTTGAAACATTTTTGAAAACTACATAATATATAGTTTTGCA
1 TATATATATATATATAATATAATTTTTAAAACATTTTTGAAAAATACATAATATATAGTTTTGCA
3164197 AACATTTT
66 AACATTTT
* * * * *
3164205 TAAAAATATATATATATAATATATATTTTTAAAATATTTTT-AAAAATATATATTTTATAGTTTT
1 T--ATATATATATATATAATATA-ATTTTTAAAACATTTTTGAAAAATACATAATATATAG-TTT
* *
3164269 TGGAAATAGTTTT
62 TGCAAACA-TTTT
3164282 TATATATA-ATATAT
1 TATATATATATATAT
3164296 TATTATTATT
Statistics
Matches: 76, Mismatches: 10, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
73 1 0.01
74 6 0.08
75 40 0.53
76 24 0.32
77 5 0.07
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (73 bp):
TATATATATATATATAATATAATTTTTAAAACATTTTTGAAAAATACATAATATATAGTTTTGCA
AACATTTT
Found at i:3165371 original size:29 final size:30
Alignment explanation
Indices: 3165337--3165397 Score: 90
Period size: 29 Copynumber: 2.1 Consensus size: 30
3165327 GATTTTTAGC
3165337 TTCAATTTGATCC-ATAAA-TTTTGATTTAT
1 TTCAATTTGATCCTATAAACTTTT-ATTTAT
*
3165366 TTCAATTTGATCCTTTAAACTTTTATTTAT
1 TTCAATTTGATCCTATAAACTTTTATTTAT
3165396 TT
1 TT
3165398 TTTATTTACT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
29 13 0.45
30 12 0.41
31 4 0.14
ACGTcount: A:0.28, C:0.11, G:0.05, T:0.56
Consensus pattern (30 bp):
TTCAATTTGATCCTATAAACTTTTATTTAT
Found at i:3169459 original size:31 final size:31
Alignment explanation
Indices: 3169389--3169504 Score: 144
Period size: 31 Copynumber: 3.7 Consensus size: 31
3169379 CCGAAGGACC
** *
3169389 TGTCCATATGT-TCTTAAGAACATAGGTAATCC
1 TGTCCATATGTCTCGAAAG-ACATAGGTAAT-A
* *
3169421 TGTCCATATATCTCGAAAGACATAGGTAATT
1 TGTCCATATGTCTCGAAAGACATAGGTAATA
*
3169452 TGTCCATATGTCTCTAAAGACATAGGTAATA
1 TGTCCATATGTCTCGAAAGACATAGGTAATA
*
3169483 TATCCATATGTCTCGAAAGACA
1 TGTCCATATGTCTCGAAAGACA
3169505 GATAACCCTC
Statistics
Matches: 74, Mismatches: 9, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
31 48 0.65
32 21 0.28
33 5 0.07
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (31 bp):
TGTCCATATGTCTCGAAAGACATAGGTAATA
Found at i:3169675 original size:14 final size:15
Alignment explanation
Indices: 3169656--3169685 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
3169646 CATCAATCTC
3169656 ATATCATATAA-CAT
1 ATATCATATAATCAT
3169670 ATATCATATAATCAT
1 ATATCATATAATCAT
3169685 A
1 A
3169686 CTATTCATAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.50, C:0.13, G:0.00, T:0.37
Consensus pattern (15 bp):
ATATCATATAATCAT
Found at i:3171172 original size:17 final size:16
Alignment explanation
Indices: 3171150--3171186 Score: 58
Period size: 17 Copynumber: 2.3 Consensus size: 16
3171140 TATAAGCATC
3171150 CAAATTCAAACAATCCA
1 CAAATTCAAAC-ATCCA
3171167 CAAATTCAAACATCCA
1 CAAATTCAAACATCCA
3171183 -AAAT
1 CAAAT
3171187 GTTAAAACAG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 4 0.20
16 5 0.25
17 11 0.55
ACGTcount: A:0.54, C:0.27, G:0.00, T:0.19
Consensus pattern (16 bp):
CAAATTCAAACATCCA
Found at i:3177066 original size:117 final size:117
Alignment explanation
Indices: 3176846--3177066 Score: 270
Period size: 117 Copynumber: 1.9 Consensus size: 117
3176836 CTTTCAAATC
*
3176846 GAAATTTTCTTTTTCAATAATTTCAAATTTCATTTTTGAAAGCTCTATATCCTGCGTCAAGATTT
1 GAAAATTTCTTTTTCAATAATTTCAAATTTCATTTTTGAAAGCTCTATATCCTGCGTCAAGATTT
* *
3176911 CATTTTGATTTTCAAAATCCATTTTCGTTTCTAGAAGAAGTTTGTTTAATTT
66 CATTTTGATTTTCAAAATCCATTTTAGTTTCTAAAAGAAGTTTGTTTAATTT
* * * * *
3176963 GAAAATTTCTTTTTCAA-AGTTTTCAGATTTCGTTTTTGAAAGCTCTA-ACTCCTTTC-TCAATA
1 GAAAATTTCTTTTTCAATA-ATTTCAAATTTCATTTTTGAAAGCTCTATA-TCC-TGCGTCAAGA
* * **
3177025 TTTTATTTTGATTTTCTAAATCTGTTTTAGCTTTC-AAAAGAA
63 TTTCATTTTGATTTTCAAAATCCATTTTAG-TTTCTAAAAGAA
3177067 TATCATTTTT
Statistics
Matches: 88, Mismatches: 12, Indels: 8
0.81 0.11 0.07
Matches are distributed among these distances:
116 2 0.02
117 80 0.91
118 6 0.07
ACGTcount: A:0.28, C:0.14, G:0.10, T:0.48
Consensus pattern (117 bp):
GAAAATTTCTTTTTCAATAATTTCAAATTTCATTTTTGAAAGCTCTATATCCTGCGTCAAGATTT
CATTTTGATTTTCAAAATCCATTTTAGTTTCTAAAAGAAGTTTGTTTAATTT
Found at i:3178382 original size:19 final size:21
Alignment explanation
Indices: 3178346--3178387 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
3178336 CCGTTGAACA
3178346 GGGGGAATCGGTACCCCT-TG
1 GGGGGAATCGGTACCCCTCTG
*
3178366 GGGGGAATCGGT-TCCCTCTG
1 GGGGGAATCGGTACCCCTCTG
3178386 GG
1 GG
3178388 CAATCTACCC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.12, C:0.24, G:0.43, T:0.21
Consensus pattern (21 bp):
GGGGGAATCGGTACCCCTCTG
Found at i:3182801 original size:85 final size:84
Alignment explanation
Indices: 3182658--3182982 Score: 359
Period size: 85 Copynumber: 3.8 Consensus size: 84
3182648 TCTCAACCTA
*
3182658 TTACAGCATAGCTCAAGGTGAGAAGGTCTATCTGTCAACAAAGACAC-TCGAGTTCGATTACATT
1 TTACAGCATAGCTCAAGGAGAGAAGGT-TATCTGTCAACAAAGAC-CTTCGAGTTCGATTACATT
*
3182722 CAGCTCAATGACATATCAAAT
64 CAGCTCAAGGACATATCAAAT
* * *
3182743 TTACAGCATAGCTCAAGGAAAGAAGAGTTATCTGTTAACAAAGACCTTCGAATTCGATTACATTC
1 TTACAGCATAGCTCAAGGAGAGAAG-GTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTC
*
3182808 AGCTTAAGGACATATCAAAT
65 AGCTCAAGGACATATCAAAT
* ** * * * * * *
3182828 TTAAAATATAACTCAAGGCGAGAAGGGTTATCTGTCAACAAATACCTTCTAGTTTGATTCCATTC
1 TTACAGCATAGCTCAAGGAGAGAA-GGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTC
* *
3182893 AGCTCAAGGGCATGTCAAAT
65 AGCTCAAGGACATATCAAAT
* * * * * *
3182913 TTACAGCATAGCTTAAGCCGAGA-AAAGATATATGTCAACAAACA-CTGTCGAGTTCGATTCCAT
1 TTACAGCATAGCTCAAG--GAGAGAAGGTTATCTGTCAACAAAGACCT-TCGAGTTCGATTACAT
3182976 TCAGCTC
63 TCAGCTC
3182983 GACAACACAT
Statistics
Matches: 201, Mismatches: 33, Indels: 12
0.82 0.13 0.05
Matches are distributed among these distances:
84 3 0.01
85 190 0.95
86 5 0.02
87 3 0.01
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.27
Consensus pattern (84 bp):
TTACAGCATAGCTCAAGGAGAGAAGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCA
GCTCAAGGACATATCAAAT
Found at i:3182971 original size:170 final size:170
Alignment explanation
Indices: 3182669--3182981 Score: 407
Period size: 170 Copynumber: 1.8 Consensus size: 170
3182659 TACAGCATAG
* *
3182669 CTCAAGGTGAGAAGGTCTATCTGTCAACAAAGACACTCGAGTTCGATTACATTCAGCTCAATGAC
1 CTCAAGGCGAGAAGGTCTATCTGTCAACAAAGACACTCGAGTTCGATTACATTCAGCTCAAGGAC
* * * * * *
3182734 ATATCAAATTTACAGCATAGCTCAAGGAAAGAAGAGTTATCTGTTAACAAAGACCTTCGAATTCG
66 ATATCAAATTTACAGCATAGCTCAAGCAAAGAAAAGATATATGTCAACAAACACCTTCGAATTCG
3182799 ATTACATTCAGCTTAAGGACATATCAAATTTAAAATATAA
131 ATTACATTCAGCTTAAGGACATATCAAATTTAAAATATAA
* * * *
3182839 CTCAAGGCGAGAAGGGT-TATCTGTCAACAAATAC-CTTCTAGTTTGATTCCATTCAGCTCAAGG
1 CTCAAGGCGAGAA-GGTCTATCTGTCAACAAAGACAC-TCGAGTTCGATTACATTCAGCTCAAGG
* * * ** *
3182902 GCATGTCAAATTTACAGCATAGCTTAAGCCGAGAAAAGATATATGTCAACAAACA-CTGTCGAGT
64 ACATATCAAATTTACAGCATAGCTCAAGCAAAGAAAAGATATATGTCAACAAACACCT-TCGAAT
*
3182966 TCGATTCCATTCAGCT
128 TCGATTACATTCAGCT
3182982 CGACAACACA
Statistics
Matches: 121, Mismatches: 19, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
169 3 0.02
170 115 0.95
171 3 0.02
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.27
Consensus pattern (170 bp):
CTCAAGGCGAGAAGGTCTATCTGTCAACAAAGACACTCGAGTTCGATTACATTCAGCTCAAGGAC
ATATCAAATTTACAGCATAGCTCAAGCAAAGAAAAGATATATGTCAACAAACACCTTCGAATTCG
ATTACATTCAGCTTAAGGACATATCAAATTTAAAATATAA
Found at i:3183781 original size:35 final size:35
Alignment explanation
Indices: 3183742--3183923 Score: 109
Period size: 36 Copynumber: 4.8 Consensus size: 35
3183732 AATATATATA
3183742 TTTGAAAATATATATATTATATAGTTTTAAAACAT
1 TTTGAAAATATATATATTATATAGTTTTAAAACAT
* * **
3183777 TTTGAATATATATATATATATATA-TATATAATATAGTT
1 TTTGAAAATATATATAT-TATATAGT-TTTAA-A-ACAT
*
3183815 TTTGAAAACATTTTTGAAAACTATATAATATATAGTTTTGAAAACAT
1 TTTG-AAA-A----T----A-TATATATTATATAGTTTT-AAAACAT
* * * *
3183862 TTTAAAAAAATATATAATATATAGTTTTAAAATATT
1 TTTGAAAATATATATATTATATAGTTTTAAAACA-T
3183898 TTTGAAAATATATAT-TT-TATAGTTTT
1 TTTGAAAATATATATATTATATAGTTTT
3183924 TAGAAAGATT
Statistics
Matches: 114, Mismatches: 15, Indels: 37
0.69 0.09 0.22
Matches are distributed among these distances:
34 9 0.08
35 23 0.20
36 42 0.37
37 2 0.02
38 6 0.05
39 2 0.02
40 1 0.01
44 1 0.01
45 1 0.01
46 3 0.03
47 5 0.04
48 10 0.09
49 9 0.08
ACGTcount: A:0.45, C:0.02, G:0.06, T:0.47
Consensus pattern (35 bp):
TTTGAAAATATATATATTATATAGTTTTAAAACAT
Found at i:3183789 original size:2 final size:2
Alignment explanation
Indices: 3183782--3183811 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
3183772 AACATTTTGA
3183782 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3183812 GTTTTTGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3183804 original size:49 final size:50
Alignment explanation
Indices: 3183749--3183848 Score: 145
Period size: 47 Copynumber: 2.1 Consensus size: 50
3183739 ATATTTGAAA
*
3183749 ATATATATATTATATAG-TTTT-AAAACA-TTTTGAATATATATATATAT
1 ATATATATATAATATAGTTTTTGAAAACATTTTTGAATATATATATATAT
*
3183796 ATATATATATAATATAGTTTTTGAAAACATTTTTGAAAACTATATA-ATAT
1 ATATATATATAATATAGTTTTTGAAAACATTTTTGAATA-TATATATATAT
3183846 ATA
1 ATA
3183849 GTTTTGAAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
47 16 0.34
48 4 0.09
49 6 0.13
50 15 0.32
51 6 0.13
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (50 bp):
ATATATATATAATATAGTTTTTGAAAACATTTTTGAATATATATATATAT
Found at i:3183861 original size:36 final size:35
Alignment explanation
Indices: 3183796--3183923 Score: 159
Period size: 36 Copynumber: 3.5 Consensus size: 35
3183786 ATATATATAT
3183796 ATATATATATAATATAGTTTTTGAAAACATTTTTGAAA
1 ATATATA-AT-ATATAG-TTTTGAAAACATTTTTGAAA
**
3183834 ACTATATAATATATAGTTTTGAAAACATTTTAAAAAA
1 A-TATATAATATATAGTTTTGAAAACATTTT-TGAAA
*
3183871 ATATATAATATATAGTTTT-AAAATATTTTTGAAA
1 ATATATAATATATAGTTTTGAAAACATTTTTGAAA
* *
3183905 ATATATATTTTATAGTTTT
1 ATATATAATATATAGTTTT
3183924 TAGAAAGATT
Statistics
Matches: 81, Mismatches: 7, Indels: 8
0.84 0.07 0.08
Matches are distributed among these distances:
34 20 0.25
35 9 0.11
36 33 0.41
37 10 0.12
38 3 0.04
39 6 0.07
ACGTcount: A:0.45, C:0.02, G:0.06, T:0.46
Consensus pattern (35 bp):
ATATATAATATATAGTTTTGAAAACATTTTTGAAA
Found at i:3185663 original size:17 final size:17
Alignment explanation
Indices: 3185641--3185676 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
3185631 TGATGTGATT
*
3185641 AATGAAATCGAAACATC
1 AATGAAATCAAAACATC
3185658 AATGAAATCAAAACATC
1 AATGAAATCAAAACATC
3185675 AA
1 AA
3185677 GGATCGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.58, C:0.17, G:0.08, T:0.17
Consensus pattern (17 bp):
AATGAAATCAAAACATC
Found at i:3193031 original size:15 final size:14
Alignment explanation
Indices: 3193011--3193052 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
3193001 AGATCCTCTG
3193011 AATCATTCAGCGCTT
1 AATCATTCA-CGCTT
*
3193026 AATCATTCA-ACTT
1 AATCATTCACGCTT
3193039 AATCATTCAACGCT
1 AATCATTC-ACGCT
3193053 CATTCTGAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
13 11 0.48
14 1 0.04
15 11 0.48
ACGTcount: A:0.33, C:0.26, G:0.07, T:0.33
Consensus pattern (14 bp):
AATCATTCACGCTT
Found at i:3193041 original size:13 final size:13
Alignment explanation
Indices: 3193023--3193049 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3193013 TCATTCAGCG
3193023 CTTAATCATTCAA
1 CTTAATCATTCAA
3193036 CTTAATCATTCAA
1 CTTAATCATTCAA
3193049 C
1 C
3193050 GCTCATTCTG
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:0.37, C:0.26, G:0.00, T:0.37
Consensus pattern (13 bp):
CTTAATCATTCAA
Found at i:3193717 original size:20 final size:21
Alignment explanation
Indices: 3193692--3193733 Score: 77
Period size: 20 Copynumber: 2.0 Consensus size: 21
3193682 CCCTTCTAAG
3193692 TATTAGTTTAACAC-AATGTA
1 TATTAGTTTAACACAAATGTA
3193712 TATTAGTTTAACACAAATGTA
1 TATTAGTTTAACACAAATGTA
3193733 T
1 T
3193734 TAAACCATGA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.67
21 7 0.33
ACGTcount: A:0.40, C:0.10, G:0.10, T:0.40
Consensus pattern (21 bp):
TATTAGTTTAACACAAATGTA
Found at i:3201085 original size:21 final size:21
Alignment explanation
Indices: 3201059--3201100 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
3201049 GTTCAGTCTC
3201059 AGGTTTCATAGTCCGTTTCGT
1 AGGTTTCATAGTCCGTTTCGT
3201080 AGGTTTCATAGTCCGTTTCGT
1 AGGTTTCATAGTCCGTTTCGT
3201101 CTTGATCCCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.14, C:0.19, G:0.24, T:0.43
Consensus pattern (21 bp):
AGGTTTCATAGTCCGTTTCGT
Found at i:3201853 original size:11 final size:11
Alignment explanation
Indices: 3201837--3201866 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
3201827 AAATATATCA
3201837 ATTATTTTTTT
1 ATTATTTTTTT
3201848 ATTATTTTTTT
1 ATTATTTTTTT
3201859 ATT-TTTTT
1 ATTATTTTT
3201867 ATTTTTTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 5 0.26
11 14 0.74
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (11 bp):
ATTATTTTTTT
Found at i:3201862 original size:19 final size:17
Alignment explanation
Indices: 3201838--3201882 Score: 72
Period size: 17 Copynumber: 2.5 Consensus size: 17
3201828 AATATATCAA
3201838 TTATTTTTTTATTATTTTT
1 TTATTTTTTTA-T-TTTTT
3201857 TTATTTTTTTATTTTTT
1 TTATTTTTTTATTTTTT
3201874 TTATTTTTT
1 TTATTTTTT
3201883 CGTTTTTTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
17 14 0.54
18 1 0.04
19 11 0.42
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (17 bp):
TTATTTTTTTATTTTTT
Found at i:3201864 original size:9 final size:9
Alignment explanation
Indices: 3201841--3201882 Score: 59
Period size: 9 Copynumber: 4.6 Consensus size: 9
3201831 ATATCAATTA
3201841 TTTTTTTAT
1 TTTTTTTAT
3201850 TATTTTTT-T
1 T-TTTTTTAT
3201859 ATTTTTTTAT
1 -TTTTTTTAT
3201869 TTTTTTTAT
1 TTTTTTTAT
3201878 TTTTT
1 TTTTT
3201883 CGTTTTTTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
9 22 0.73
10 8 0.27
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (9 bp):
TTTTTTTAT
Found at i:3201868 original size:16 final size:16
Alignment explanation
Indices: 3201843--3201896 Score: 63
Period size: 17 Copynumber: 3.2 Consensus size: 16
3201833 ATCAATTATT
3201843 TTTTTATTATTTTTTTA
1 TTTTT-TTATTTTTTTA
3201860 TTTTTTTATTTTTTTTA
1 TTTTTTTA-TTTTTTTA
** *
3201877 TTTTTTCGTTTTTTCA
1 TTTTTTTATTTTTTTA
3201893 TTTT
1 TTTT
3201897 ATATTTCTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
16 14 0.42
17 19 0.58
ACGTcount: A:0.11, C:0.04, G:0.02, T:0.83
Consensus pattern (16 bp):
TTTTTTTATTTTTTTA
Found at i:3201872 original size:8 final size:8
Alignment explanation
Indices: 3201843--3201896 Score: 63
Period size: 8 Copynumber: 6.5 Consensus size: 8
3201833 ATCAATTATT
3201843 TTTTTATTA
1 TTTTT-TTA
3201852 TTTTTTTA
1 TTTTTTTA
3201860 TTTTTTTA
1 TTTTTTTA
3201868 TTTTTTTTA
1 -TTTTTTTA
**
3201877 TTTTTTCG
1 TTTTTTTA
*
3201885 TTTTTTCA
1 TTTTTTTA
3201893 TTTT
1 TTTT
3201897 ATATTTCTTA
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
8 28 0.68
9 13 0.32
ACGTcount: A:0.11, C:0.04, G:0.02, T:0.83
Consensus pattern (8 bp):
TTTTTTTA
Found at i:3201877 original size:25 final size:26
Alignment explanation
Indices: 3201842--3201901 Score: 77
Period size: 25 Copynumber: 2.3 Consensus size: 26
3201832 TATCAATTAT
* *
3201842 TTTTTTATTATTTTTTTATTTTTTTA
1 TTTTTTATTATTTTTTCATTTTTTCA
*
3201868 TTTTTT-TTATTTTTTCGTTTTTTCA
1 TTTTTTATTATTTTTTCATTTTTTCA
*
3201893 TTTTATATT
1 TTTTTTATT
3201902 TCTTAATATG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
25 21 0.72
26 8 0.28
ACGTcount: A:0.13, C:0.03, G:0.02, T:0.82
Consensus pattern (26 bp):
TTTTTTATTATTTTTTCATTTTTTCA
Found at i:3208265 original size:20 final size:20
Alignment explanation
Indices: 3208236--3208282 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
3208226 AGTGAAGGGA
3208236 TGTACCGATACCCTATAGTG
1 TGTACCGATACCCTATAGTG
*
3208256 TGTACTGATACCCTATAGTG
1 TGTACCGATACCCTATAGTG
3208276 TGTACCG
1 TGTACCG
3208283 GTACACTTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.23, C:0.23, G:0.21, T:0.32
Consensus pattern (20 bp):
TGTACCGATACCCTATAGTG
Found at i:3209585 original size:12 final size:12
Alignment explanation
Indices: 3209570--3209602 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
3209560 TTAATCATAT
*
3209570 GAATAATGATAA
1 GAATAATAATAA
3209582 GAATAATAATAA
1 GAATAATAATAA
3209594 GAATAATAA
1 GAATAATAA
3209603 AATGATATGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.64, C:0.00, G:0.12, T:0.24
Consensus pattern (12 bp):
GAATAATAATAA
Found at i:3209640 original size:24 final size:24
Alignment explanation
Indices: 3209620--3209871 Score: 242
Period size: 24 Copynumber: 10.7 Consensus size: 24
3209610 TGTGTATGTA
* *
3209620 TATGCATATGCATATGCGTATGCG
1 TATGCGTATGCGTATGCGTATGCG
* *
3209644 TATGCATATGCGTATGGGTATGCG
1 TATGCGTATGCGTATGCGTATGCG
* *
3209668 TATGGGTATGCGTATGGGTATGCG
1 TATGCGTATGCGTATGCGTATGCG
* *
3209692 TATGGGTATGCATATG-GTATG-G
1 TATGCGTATGCGTATGCGTATGCG
*
3209714 TATG-GTATGGGTATG-GTATGCG
1 TATGCGTATGCGTATGCGTATGCG
*
3209736 TATGCGTATGCGTATGCGTATGCA
1 TATGCGTATGCGTATGCGTATGCG
3209760 TATGCGTATGCGTATGCGTATGCG
1 TATGCGTATGCGTATGCGTATGCG
* ** * *
3209784 TATGCATATATGTATGTGTATGTG
1 TATGCGTATGCGTATGCGTATGCG
** * * *
3209808 TATATGTATGTGTATGTGTATGTG
1 TATGCGTATGCGTATGCGTATGCG
* * * *
3209832 TATGTGTATGTGTATGTGTATGTG
1 TATGCGTATGCGTATGCGTATGCG
* *
3209856 TATGTGTATGTGTATG
1 TATGCGTATGCGTATG
3209872 TATATGTGTA
Statistics
Matches: 205, Mismatches: 20, Indels: 6
0.89 0.09 0.03
Matches are distributed among these distances:
21 14 0.07
22 10 0.05
23 15 0.07
24 166 0.81
ACGTcount: A:0.20, C:0.08, G:0.33, T:0.39
Consensus pattern (24 bp):
TATGCGTATGCGTATGCGTATGCG
Found at i:3209798 original size:18 final size:18
Alignment explanation
Indices: 3209620--3209871 Score: 242
Period size: 18 Copynumber: 14.2 Consensus size: 18
3209610 TGTGTATGTA
* *
3209620 TATGCATATGCATATGCG
1 TATGCGTATGCGTATGCG
*
3209638 TATGCGTATGCATATGCG
1 TATGCGTATGCGTATGCG
* *
3209656 TATGGGTATGCGTATGGG
1 TATGCGTATGCGTATGCG
*
3209674 TATGCGTATGGGTATGCG
1 TATGCGTATGCGTATGCG
* *
3209692 TATGGGTATGCATATG-G
1 TATGCGTATGCGTATGCG
*
3209709 TATG-GTATG-GTATGGG
1 TATGCGTATGCGTATGCG
3209725 TATG-GTATGCGTATGCG
1 TATGCGTATGCGTATGCG
*
3209742 TATGCGTATGCGTATGCA
1 TATGCGTATGCGTATGCG
3209760 TATGCGTATGCGTATGCG
1 TATGCGTATGCGTATGCG
* **
3209778 TATGCGTATGCATATATG
1 TATGCGTATGCGTATGCG
* * **
3209796 TATGTGTATGTGTATATG
1 TATGCGTATGCGTATGCG
* * *
3209814 TATGTGTATGTGTATGTG
1 TATGCGTATGCGTATGCG
* * *
3209832 TATGTGTATGTGTATGTG
1 TATGCGTATGCGTATGCG
* * *
3209850 TATGTGTATGTGTATGTG
1 TATGCGTATGCGTATGCG
3209868 TATG
1 TATG
3209872 TATATGTGTA
Statistics
Matches: 210, Mismatches: 21, Indels: 6
0.89 0.09 0.03
Matches are distributed among these distances:
15 4 0.02
16 15 0.07
17 15 0.07
18 176 0.84
ACGTcount: A:0.20, C:0.08, G:0.33, T:0.39
Consensus pattern (18 bp):
TATGCGTATGCGTATGCG
Found at i:3209918 original size:6 final size:6
Alignment explanation
Indices: 3209608--3209906 Score: 219
Period size: 6 Copynumber: 50.5 Consensus size: 6
3209598 AATAAAATGA
* ** ** * * ** *
3209608 TATGTG TATGTA TATGCA TATGCA TATGCG TATGCG TATGCA TATGCG
1 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
* * * * * * * **
3209656 TATGGG TATGCG TATGGG TATGCG TATGGG TATGCG TATGGG TATGCA
1 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
* * * *
3209704 TATG-G TATG-G TATG-G TATGGG TATG-G TATGCG TATGCG TATGCG
1 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
* ** * * * * ** *
3209748 TATGCG TATGCA TATGCG TATGCG TATGCG TATGCG TATGCA TATATG
1 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
*
3209796 TATGTG TATGTG TATATG TATGTG TATGTG TATGTG TATGTG TATGTG
1 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
* * *
3209844 TATGTG TATGTG TATGTG TATGTG TATGTA TATGTG TATATG TATATG
1 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
* *
3209892 TATATG TATATG TAT
1 TATGTG TATGTG TAT
3209907 ATGTTTATGT
Statistics
Matches: 264, Mismatches: 27, Indels: 4
0.89 0.09 0.01
Matches are distributed among these distances:
5 19 0.07
6 245 0.93
ACGTcount: A:0.22, C:0.07, G:0.30, T:0.41
Consensus pattern (6 bp):
TATGTG
Found at i:3215352 original size:6 final size:6
Alignment explanation
Indices: 3215252--3215351 Score: 155
Period size: 6 Copynumber: 16.7 Consensus size: 6
3215242 ATAACTAAGA
* * *
3215252 TATGTG TATGTG TATGTG TATGCG TATGCG TATGCG TATGCG TATGCG
1 TATGCG TATGCG TATGCG TATGCG TATGCG TATGCG TATGCG TATGCG
* *
3215300 TATGCA TATGCG TATGCG TATGCG TATGCG TATGCG TATGCG TATGTG
1 TATGCG TATGCG TATGCG TATGCG TATGCG TATGCG TATGCG TATGCG
3215348 TATG
1 TATG
3215352 TTTTGATGCA
Statistics
Matches: 90, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 90 1.00
ACGTcount: A:0.18, C:0.12, G:0.32, T:0.38
Consensus pattern (6 bp):
TATGCG
Found at i:3215865 original size:31 final size:30
Alignment explanation
Indices: 3215830--3215893 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 30
3215820 ATTTACTGCG
*
3215830 TAGGCACCTAAAAGTGTAACGTAGAAAACGT
1 TAGGCACCTAAAAGTGTAA-GTAGAAAACAT
*
3215861 TAGGCACCTAAAAGTGTAAGTCGAAAACAT
1 TAGGCACCTAAAAGTGTAAGTAGAAAACAT
3215891 TAG
1 TAG
3215894 ATATCTATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 12 0.39
31 19 0.61
ACGTcount: A:0.42, C:0.16, G:0.22, T:0.20
Consensus pattern (30 bp):
TAGGCACCTAAAAGTGTAAGTAGAAAACAT
Found at i:3219115 original size:34 final size:34
Alignment explanation
Indices: 3219077--3219150 Score: 87
Period size: 34 Copynumber: 2.2 Consensus size: 34
3219067 GAAGGTAAAA
*
3219077 TATTTTACTATATTATAATAAATTAA-TATTTTAT
1 TATTTTACTAAATTATAATAAATTAACT-TTTTAT
* * * *
3219111 TATTTTATTAAATTGTATTATATTAACTTTTTAT
1 TATTTTACTAAATTATAATAAATTAACTTTTTAT
3219145 TATTTT
1 TATTTT
3219151 TTGCAGTTAT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
34 33 0.97
35 1 0.03
ACGTcount: A:0.35, C:0.03, G:0.01, T:0.61
Consensus pattern (34 bp):
TATTTTACTAAATTATAATAAATTAACTTTTTAT
Found at i:3220099 original size:21 final size:21
Alignment explanation
Indices: 3220056--3220101 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
3220046 TACAATACTA
**
3220056 ATTTAGTATATTAATAATTTT
1 ATTTAGTATATTAATAAAATT
3220077 ATTTAGTATA-TAATCAAAATT
1 ATTTAGTATATTAAT-AAAATT
3220098 ATTT
1 ATTT
3220102 CATTGAACAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 4 0.18
21 18 0.82
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.52
Consensus pattern (21 bp):
ATTTAGTATATTAATAAAATT
Found at i:3221360 original size:13 final size:13
Alignment explanation
Indices: 3221342--3221367 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3221332 ACATTTCATT
3221342 ATTTTTTTATTTA
1 ATTTTTTTATTTA
3221355 ATTTTTTTATTTA
1 ATTTTTTTATTTA
3221368 CCAACAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (13 bp):
ATTTTTTTATTTA
Found at i:3222215 original size:19 final size:20
Alignment explanation
Indices: 3222193--3222245 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
3222183 AAATCGCAAC
3222193 GCGATTTT-AGTTTCGCGTT
1 GCGATTTTAAGTTTCGCGTT
* *
3222212 GCGATTTTCATTTTCGCGTT
1 GCGATTTTAAGTTTCGCGTT
3222232 GCGATTTTAAGTTT
1 GCGATTTTAAGTTT
3222246 AAGAAACTAC
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 8 0.27
20 22 0.73
ACGTcount: A:0.13, C:0.15, G:0.23, T:0.49
Consensus pattern (20 bp):
GCGATTTTAAGTTTCGCGTT
Found at i:3223759 original size:42 final size:42
Alignment explanation
Indices: 3223700--3223796 Score: 140
Period size: 42 Copynumber: 2.3 Consensus size: 42
3223690 CCCCACTTCG
* * * * *
3223700 AGAGCCATCGCCTGATCGAGCCGATTCTACAGCTCGACACCC
1 AGAGCCATCACCTGATCGAGCCGATTATACACCTCCACAACC
*
3223742 AGAGCCATCACCTGATCGAGCCGATTATACACCTCCACAACG
1 AGAGCCATCACCTGATCGAGCCGATTATACACCTCCACAACC
3223784 AGAGCCATCACCT
1 AGAGCCATCACCT
3223797 ATTCCATCAC
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.28, C:0.37, G:0.19, T:0.16
Consensus pattern (42 bp):
AGAGCCATCACCTGATCGAGCCGATTATACACCTCCACAACC
Found at i:3223939 original size:21 final size:21
Alignment explanation
Indices: 3223915--3223963 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
3223905 GGGGAGTTAC
* * *
3223915 GTGATGAGGTTAGTGCTTTGT
1 GTGATGAGGTCAGTACTTTAT
* *
3223936 GTGAGGAGGTCGGTACTTTAT
1 GTGATGAGGTCAGTACTTTAT
3223957 GTGATGA
1 GTGATGA
3223964 TAATGGTGCA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.18, C:0.06, G:0.39, T:0.37
Consensus pattern (21 bp):
GTGATGAGGTCAGTACTTTAT
Found at i:3224001 original size:21 final size:21
Alignment explanation
Indices: 3223977--3224026 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
3223967 TGGTGCATGG
*
3223977 CGTGATGAGGTA-CGGTCTTTA
1 CGTGATGAGGTAGAGGT-TTTA
*
3223998 CGTGGTGAGGTAGAGGTTTTA
1 CGTGATGAGGTAGAGGTTTTA
*
3224019 CGCGATGA
1 CGTGATGA
3224027 CAATGGTGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 21 0.88
22 3 0.12
ACGTcount: A:0.20, C:0.12, G:0.38, T:0.30
Consensus pattern (21 bp):
CGTGATGAGGTAGAGGTTTTA
Found at i:3225902 original size:20 final size:20
Alignment explanation
Indices: 3225877--3225949 Score: 74
Period size: 20 Copynumber: 3.6 Consensus size: 20
3225867 CTTTCGCAAC
**
3225877 GCGAAAGTCAAATTCACGTT
1 GCGAAAGTCAAATTCACAAT
* **
3225897 GCGAAAGTAAAATTTGCAAT
1 GCGAAAGTCAAATTCACAAT
* *
3225917 GCGAAAGTCAAATTCGCAAC
1 GCGAAAGTCAAATTCACAAT
*
3225937 ACGAAAGTCAAAT
1 GCGAAAGTCAAAT
3225950 GCGCGTTGCA
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.42, C:0.18, G:0.19, T:0.21
Consensus pattern (20 bp):
GCGAAAGTCAAATTCACAAT
Found at i:3226001 original size:20 final size:20
Alignment explanation
Indices: 3225978--3226016 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
3225968 TTTCGTGTTT
3225978 CGAATTTGA-TTTTCGCAACG
1 CGAATTTGACTTTT-GCAACG
3225998 CGAATTTGACTTTTGCAAC
1 CGAATTTGACTTTTGCAAC
3226017 AATTGCAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.36
Consensus pattern (20 bp):
CGAATTTGACTTTTGCAACG
Found at i:3226291 original size:18 final size:18
Alignment explanation
Indices: 3226268--3226303 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
3226258 AAGTCGGTTG
3226268 TGATTGAAATTTTGATTT
1 TGATTGAAATTTTGATTT
**
3226286 TGATTGCGATTTTGATTT
1 TGATTGAAATTTTGATTT
3226304 CCTTTTGCTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.22, C:0.03, G:0.19, T:0.56
Consensus pattern (18 bp):
TGATTGAAATTTTGATTT
Found at i:3228743 original size:12 final size:12
Alignment explanation
Indices: 3228722--3228755 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
3228712 GGTTGTGGGT
*
3228722 TTTGAGATTGTG
1 TTTGATATTGTG
3228734 TTTGATATTGTG
1 TTTGATATTGTG
*
3228746 TTTGGTATTG
1 TTTGATATTG
3228756 GAAATGTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:3229555 original size:20 final size:19
Alignment explanation
Indices: 3229508--3229596 Score: 65
Period size: 20 Copynumber: 4.5 Consensus size: 19
3229498 CAAAACATTT
*
3229508 GTGTTGCGAAAATAAAA-C
1 GTGTTGCGAAATTAAAATC
* *
3229526 CTGCTGCGAAATTAAAATTC
1 GTGTTGCGAAATTAAAA-TC
3229546 GTGTTGCG-AATTCGAAAATC
1 GTGTTGCGAAATT--AAAATC
* * *
3229566 GAGTTGCGAATTTGAAATTC
1 GTGTTGCGAAATT-AAAATC
3229586 AGTGTTGCGAA
1 -GTGTTGCGAA
3229597 TTTGGAAATC
Statistics
Matches: 56, Mismatches: 9, Indels: 9
0.76 0.12 0.12
Matches are distributed among these distances:
18 14 0.25
19 4 0.07
20 22 0.39
21 16 0.29
ACGTcount: A:0.34, C:0.13, G:0.24, T:0.29
Consensus pattern (19 bp):
GTGTTGCGAAATTAAAATC
Found at i:3229598 original size:41 final size:40
Alignment explanation
Indices: 3229530--3229689 Score: 132
Period size: 40 Copynumber: 4.0 Consensus size: 40
3229520 TAAAACCTGC
* *
3229530 TGCGAAATTAAAATTCGTGTTGCGAATTCGAAAATCG-AGT
1 TGCGAATTTGAAATTCGTGTTGCGAATTCGAAAATCGCA-T
* *
3229570 TGCGAATTTGAAATTCAGTGTTGCGAATTTGGAAATCGCAT
1 TGCGAATTTGAAATTC-GTGTTGCGAATTCGAAAATCGCAT
* * * *
3229611 TGCGAATTTG-ACTTCTGTGTTGCGATTTAC-AGATTCGCAT
1 TGCGAATTTGAAATTC-GTGTTGCGAATT-CGAAAATCGCAT
* * *
3229651 TGCG-ATTT-ACATATTCGCGTTGTGAATTTGAAAATCGCA
1 TGCGAATTTGA-A-ATTCGTGTTGCGAATTCGAAAATCGCA
3229690 ATGTGATTTA
Statistics
Matches: 95, Mismatches: 18, Indels: 14
0.75 0.14 0.11
Matches are distributed among these distances:
39 4 0.04
40 57 0.60
41 33 0.35
42 1 0.01
ACGTcount: A:0.28, C:0.14, G:0.23, T:0.35
Consensus pattern (40 bp):
TGCGAATTTGAAATTCGTGTTGCGAATTCGAAAATCGCAT
Found at i:3229633 original size:20 final size:19
Alignment explanation
Indices: 3229541--3229635 Score: 82
Period size: 20 Copynumber: 4.7 Consensus size: 19
3229531 GCGAAATTAA
*
3229541 AATTCGTGTTGCGAATTCG
1 AATTCGTGTTGCGAATTTG
* *
3229560 AAAATCGAGTTGCGAATTTG
1 -AATTCGTGTTGCGAATTTG
3229580 AAATTCAGTGTTGCGAATTTGG
1 -AATTC-GTGTTGCGAATTT-G
* **
3229602 AAATCGCATTGCGAATTTG
1 AATTCGTGTTGCGAATTTG
*
3229621 ACTTCTGTGTTGCGA
1 AATTC-GTGTTGCGA
3229636 TTTACAGATT
Statistics
Matches: 60, Mismatches: 12, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
19 4 0.07
20 39 0.65
21 16 0.27
22 1 0.02
ACGTcount: A:0.26, C:0.14, G:0.25, T:0.35
Consensus pattern (19 bp):
AATTCGTGTTGCGAATTTG
Found at i:3229653 original size:20 final size:20
Alignment explanation
Indices: 3229630--3229668 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
3229620 GACTTCTGTG
3229630 TTGCGATTTACAGATTCGCA
1 TTGCGATTTACAGATTCGCA
*
3229650 TTGCGATTTACATATTCGC
1 TTGCGATTTACAGATTCGC
3229669 GTTGTGAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.23, C:0.21, G:0.18, T:0.38
Consensus pattern (20 bp):
TTGCGATTTACAGATTCGCA
Found at i:3229718 original size:40 final size:40
Alignment explanation
Indices: 3229645--3229720 Score: 98
Period size: 40 Copynumber: 1.9 Consensus size: 40
3229635 ATTTACAGAT
* * **
3229645 TCGCATTGCGATTTACATATTCGCGTTGTGAATTTGAAAA
1 TCGCAATGCGATTTACATATTCGCATTACGAATTTGAAAA
* *
3229685 TCGCAATGTGATTTATATATTCGCATTACGAATTTG
1 TCGCAATGCGATTTACATATTCGCATTACGAATTTG
3229721 GAAACTGTGT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 30 1.00
ACGTcount: A:0.28, C:0.14, G:0.18, T:0.39
Consensus pattern (40 bp):
TCGCAATGCGATTTACATATTCGCATTACGAATTTGAAAA
Found at i:3239471 original size:36 final size:37
Alignment explanation
Indices: 3239400--3239484 Score: 111
Period size: 37 Copynumber: 2.3 Consensus size: 37
3239390 ATCCCATTAT
*
3239400 CATTTTTC-AACAAACATCTACCAAACTTTGAAAAAC
1 CATTTTTCAAAGAAACATCTACCAAACTTTGAAAAAC
* * *
3239436 TATTTTTCAAAGAAACATTTATCAAACTTTG-AAAAC
1 CATTTTTCAAAGAAACATCTACCAAACTTTGAAAAAC
3239472 CATTTTTTCAAAG
1 CA-TTTTTCAAAG
3239485 TTGGTTGTCA
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
36 13 0.31
37 29 0.69
ACGTcount: A:0.42, C:0.19, G:0.05, T:0.34
Consensus pattern (37 bp):
CATTTTTCAAAGAAACATCTACCAAACTTTGAAAAAC
Found at i:3243377 original size:498 final size:499
Alignment explanation
Indices: 3242415--3243411 Score: 1721
Period size: 498 Copynumber: 2.0 Consensus size: 499
3242405 TCAAATTTCT
3242415 TTTGAGGCCATGAATATGTCTCACTCCTTTCAACGTCCAGGTGGTCTAGTTTGACAACTTTAATC
1 TTTGAGGCCATGAATATGTCT-ACTCCTTTCAACGTCCAGGTGGTCTAGTTTGACAACTTTAATC
*
3242480 GGATGTTTCCTTTTCCGACGATCTTCAAGGTTTCATCATCAGCTAGATGAACATTCCCAAAATCA
65 GGATGTCTCCTTTTCCGACGATCTTCAAGGTTTCATCATCAGCTAGATGAACATTCCCAAAATCA
* * *
3242545 CCATTGACATAGTTCTTCATGATTTCTCGGCATGGGGTGGAGTGGATAGATGCCCCTGAATCCAA
130 CCATTGACATAGTTCTTCATGATTTCTCGGCATGGGGTGGAGTGGAAAAATGCCCATGAATCCAA
* * *
3242610 GATCCATGATTCAATCGGAGTGTTGACGTTTAGAATCATGGCATCACCTGTCTCCTCTGTCATGT
195 GATCCATGATTCAATCAGAGTGTTGACGCTTAGAATCATGACATCACCTGTCTCCTCTGTCATGT
* * *
3242675 TGGCAGATTCCTGTGCACCAGTATCTTTCTTCAGTGTTCAACAATCTCTTTTAAAGTGACCCTTC
260 TGGCAGATTCCTATGCACCAGTATCTTTCTTCAGTGCTCAACAATCTCTTTTAAAATGACCCTTC
*
3242740 TTGTCACAATTATAACAGGTAAAATCTTTAATTCCTGTTCTTGATTTGCCCCTTATGGATTTCGA
325 TTGCCACAATTATAACAGGTAAAATCTTTAATTCCTGTTCTTGATTTGCCCCTTATGGATTTCGA
*
3242805 TCTGCCACGATTTGAATTTCTTTCTGAAGTTCTCCCTCTGGACTCCGTTTGCAAGGCTGAGGAGG
390 TCTGCCACGATTTGAATTTCTTTCTGAAGTTCTCCCTCTGGACTCCGTGTGCAAGGCTGAGGAGG
*
3242870 TTGATGCTTCACCCGATTCTCTCCATCGAATTTCTTCGCTCAGTG
455 TTAATGCTTCACCCGATTCTCTCCATCGAATTTCTTCGCTCAGTG
*
3242915 TTTGAGGCCA-GTAATATGTCT-CTCCTTTCAACGTCCAGGTGGTCTGGTTTGACAACTTTAATC
1 TTTGAGGCCATG-AATATGTCTACTCCTTTCAACGTCCAGGTGGTCTAGTTTGACAACTTTAATC
* *
3242978 GGATGTCTCCTTTTCTGACGATCTTCAAGGTTTCATCATCAGCTAGATGAACATTTCCAAAATCA
65 GGATGTCTCCTTTTCCGACGATCTTCAAGGTTTCATCATCAGCTAGATGAACATTCCCAAAATCA
3243043 CCATTGACATAGTTC-TCAATGATTTCTCGGCATGGGGTGGAGTGGAAAAATGCCCATGAATCCA
130 CCATTGACATAGTTCTTC-ATGATTTCTCGGCATGGGGTGGAGTGGAAAAATGCCCATGAATCCA
*
3243107 AGATTCATGATTCAATCAGAGTGTTGACGCTTAGAATCATGACATCACCTGTCTCCTCTGTCATG
194 AGATCCATGATTCAATCAGAGTGTTGACGCTTAGAATCATGACATCACCTGTCTCCTCTGTCATG
* *
3243172 TTGGCAGATTCCTATGCACCGGTATCTTTCTTCAGTGCTCGACAATCTCTTTTAAAATGACCCTT
259 TTGGCAGATTCCTATGCACCAGTATCTTTCTTCAGTGCTCAACAATCTCTTTTAAAATGACCCTT
** * *
3243237 CTTGCCACAATTATAACAGGTAAAATCTTTCTTTTCTGTTCTTGATTTGCCCCTTCTGGATTTCG
324 CTTGCCACAATTATAACAGGTAAAATCTTTAATTCCTGTTCTTGATTTGCCCCTTATGGATTTCG
*
3243302 ATCTGCCACGATTTGAATTTCTTTCTGAAGTTCTCCCTCTGGACTTCGTGTGCAAGGCTGAGGAG
389 ATCTGCCACGATTTGAATTTCTTTCTGAAGTTCTCCCTCTGGACTCCGTGTGCAAGGCTGAGGAG
*
3243367 GTTAATGCTTCACCCGATTCTCTCCGTCGAATTTCTTCGCTCAGT
454 GTTAATGCTTCACCCGATTCTCTCCATCGAATTTCTTCGCTCAGT
3243412 ACCAGATCAC
Statistics
Matches: 470, Mismatches: 25, Indels: 6
0.94 0.05 0.01
Matches are distributed among these distances:
497 2 0.00
498 448 0.95
499 1 0.00
500 19 0.04
ACGTcount: A:0.22, C:0.24, G:0.19, T:0.35
Consensus pattern (499 bp):
TTTGAGGCCATGAATATGTCTACTCCTTTCAACGTCCAGGTGGTCTAGTTTGACAACTTTAATCG
GATGTCTCCTTTTCCGACGATCTTCAAGGTTTCATCATCAGCTAGATGAACATTCCCAAAATCAC
CATTGACATAGTTCTTCATGATTTCTCGGCATGGGGTGGAGTGGAAAAATGCCCATGAATCCAAG
ATCCATGATTCAATCAGAGTGTTGACGCTTAGAATCATGACATCACCTGTCTCCTCTGTCATGTT
GGCAGATTCCTATGCACCAGTATCTTTCTTCAGTGCTCAACAATCTCTTTTAAAATGACCCTTCT
TGCCACAATTATAACAGGTAAAATCTTTAATTCCTGTTCTTGATTTGCCCCTTATGGATTTCGAT
CTGCCACGATTTGAATTTCTTTCTGAAGTTCTCCCTCTGGACTCCGTGTGCAAGGCTGAGGAGGT
TAATGCTTCACCCGATTCTCTCCATCGAATTTCTTCGCTCAGTG
Found at i:3244548 original size:37 final size:36
Alignment explanation
Indices: 3244489--3244608 Score: 172
Period size: 35 Copynumber: 3.3 Consensus size: 36
3244479 ATCCCATTAT
* *
3244489 CATTTTTC-AACAAACATCTACCAAACTTTGAAAAA
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAA
*
3244524 CTATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 C-ATTTTTCAAAGAAACATTTACCAAACTTTGAAAAA
*
3244561 CA-TTTTCAAAGAAACATTTACCAAACTTTGAAAAT
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAA
3244596 CATTTTTTCAAAG
1 CA-TTTTTCAAAG
3244609 TTGGTTATCA
Statistics
Matches: 77, Mismatches: 4, Indels: 6
0.89 0.05 0.07
Matches are distributed among these distances:
35 35 0.45
36 8 0.10
37 34 0.44
ACGTcount: A:0.43, C:0.19, G:0.05, T:0.33
Consensus pattern (36 bp):
CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAA
Found at i:3244564 original size:21 final size:20
Alignment explanation
Indices: 3244537--3244600 Score: 59
Period size: 20 Copynumber: 3.4 Consensus size: 20
3244527 TTTTTCAAAG
3244537 AAACATTTACCAAACTTTGA
1 AAACATTTACCAAACTTTGA
*
3244557 AAACCATTT-TCAAA----G-
1 AAA-CATTTACCAAACTTTGA
3244572 AAACATTTACCAAACTTTGA
1 AAACATTTACCAAACTTTGA
3244592 AAATCATTT
1 AAA-CATTT
3244601 TTTCAAAGTT
Statistics
Matches: 34, Mismatches: 2, Indels: 15
0.67 0.04 0.29
Matches are distributed among these distances:
14 5 0.15
15 7 0.21
16 1 0.03
19 1 0.03
20 10 0.29
21 10 0.29
ACGTcount: A:0.45, C:0.19, G:0.05, T:0.31
Consensus pattern (20 bp):
AAACATTTACCAAACTTTGA
Found at i:3250514 original size:35 final size:37
Alignment explanation
Indices: 3250475--3250547 Score: 98
Period size: 36 Copynumber: 2.0 Consensus size: 37
3250465 TTCATTAAAC
*
3250475 ATTTTTAT-ATTTTCAA-TTTTGTAAA-AAAATATATA
1 ATTTTTATGAATTT-AATTTTTGTAAAGAAAATATATA
*
3250510 ATTTTTATGAATTTAATTTTTTTAAAGAAAATATATA
1 ATTTTTATGAATTTAATTTTTGTAAAGAAAATATATA
3250547 A
1 A
3250548 ATATTTTTCA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
35 10 0.30
36 12 0.36
37 11 0.33
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.51
Consensus pattern (37 bp):
ATTTTTATGAATTTAATTTTTGTAAAGAAAATATATA
Found at i:3250775 original size:20 final size:20
Alignment explanation
Indices: 3250750--3250820 Score: 126
Period size: 20 Copynumber: 3.5 Consensus size: 20
3250740 TTCTGACTAT
3250750 GTAAATCGCAATGCGAATAC
1 GTAAATCGCAATGCGAATAC
3250770 GTAAATCGCAATGCGAATAC
1 GTAAATCGCAATGCGAATAC
3250790 GTAAATCGCAATGCGAAT-C
1 GTAAATCGCAATGCGAATAC
3250809 TGTAAATCGCAA
1 -GTAAATCGCAA
3250821 CGAGATTCTG
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
19 1 0.02
20 49 0.98
ACGTcount: A:0.39, C:0.20, G:0.20, T:0.21
Consensus pattern (20 bp):
GTAAATCGCAATGCGAATAC
Found at i:3250830 original size:20 final size:20
Alignment explanation
Indices: 3250749--3250830 Score: 69
Period size: 20 Copynumber: 4.1 Consensus size: 20
3250739 ATTCTGACTA
* *
3250749 TGTAAATCGCAATGCGAATAC
1 TGTAAATCGCAACGAGAAT-C
* *
3250770 -GTAAATCGCAATGCGAATAC
1 TGTAAATCGCAACGAGAAT-C
* *
3250790 -GTAAATCGCAATGCGAATC
1 TGTAAATCGCAACGAGAATC
*
3250809 TGTAAATCGCAACGAGATTC
1 TGTAAATCGCAACGAGAATC
3250829 TG
1 TG
3250831 ACTATCGCAA
Statistics
Matches: 57, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
19 1 0.02
20 56 0.98
ACGTcount: A:0.37, C:0.20, G:0.21, T:0.23
Consensus pattern (20 bp):
TGTAAATCGCAACGAGAATC
Found at i:3251709 original size:24 final size:24
Alignment explanation
Indices: 3251682--3251735 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
3251672 GTATTCGAAA
3251682 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
3251706 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
3251730 TTTGAT
1 TTTGAT
3251736 GATTTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:3254195 original size:20 final size:19
Alignment explanation
Indices: 3254170--3254214 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
3254160 CAACGCGGAA
3254170 ATCGCAAC-GCGAATATGACT
1 ATCGCAACAG-GAA-ATGACT
3254190 ATCGCAACATGGAAATGACT
1 ATCGCAACA-GGAAATGACT
3254210 ATCGC
1 ATCGC
3254215 TGTAACCCCC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 19 0.83
21 3 0.13
22 1 0.04
ACGTcount: A:0.36, C:0.24, G:0.20, T:0.20
Consensus pattern (19 bp):
ATCGCAACAGGAAATGACT
Found at i:3254678 original size:41 final size:41
Alignment explanation
Indices: 3254633--3254860 Score: 322
Period size: 41 Copynumber: 5.6 Consensus size: 41
3254623 ATTCGCGTTG
*
3254633 CATTTCGCGTTGCGATAGT-TGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTCT-AAAGTCGCGTTGCGATTTTC
*
3254674 CATTTCGCGTTGCGATAGTCTACAGTCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTCTAAAGTCGCGTTGCGATTTTC
*
3254715 CATTTCGCGTTGCGATAGTCTACAGTCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTCTAAAGTCGCGTTGCGATTTTC
*
3254756 CATTTCGCGTTGCGATAGT-TGAAATTCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTCT-AAAGTCGCGTTGCGATTTTC
* *
3254797 CATTTCGCGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTCTAAAGTCG-CGTTGCGATTTTC
*
3254839 CAAATT--CGTTGCGATAGT-TAAA
1 C-ATTTCGCGTTGCGATAGTCTAAA
3254861 AAAAAAGATT
Statistics
Matches: 173, Mismatches: 9, Indels: 11
0.90 0.05 0.06
Matches are distributed among these distances:
40 4 0.02
41 150 0.87
42 16 0.09
43 3 0.02
ACGTcount: A:0.18, C:0.21, G:0.24, T:0.37
Consensus pattern (41 bp):
CATTTCGCGTTGCGATAGTCTAAAGTCGCGTTGCGATTTTC
Found at i:3254683 original size:20 final size:20
Alignment explanation
Indices: 3254658--3254812 Score: 161
Period size: 20 Copynumber: 7.6 Consensus size: 20
3254648 TAGTTGAAAA
3254658 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
* * *
3254678 TCGCGTTGCGATAGTCTACA-G
1 TCGCGTTGCGAT--TTTCCATT
3254699 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
* * *
3254719 TCGCGTTGCGATAGTCTACA-G
1 TCGCGTTGCGAT--TTTCCATT
3254740 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
* ** *
3254760 TCGCGTTGCGATAGTTGAAAT
1 TCGCGTTGCGAT-TTTCCATT
3254781 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
3254801 TCGCGTTGCGAT
1 TCGCGTTGCGAT
3254813 AGTCTACAGT
Statistics
Matches: 108, Mismatches: 20, Indels: 14
0.76 0.14 0.10
Matches are distributed among these distances:
19 8 0.07
20 52 0.48
21 40 0.37
22 8 0.07
ACGTcount: A:0.14, C:0.23, G:0.25, T:0.38
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCATT
Found at i:3254852 original size:123 final size:122
Alignment explanation
Indices: 3254633--3254856 Score: 387
Period size: 123 Copynumber: 1.8 Consensus size: 122
3254623 ATTCGCGTTG
3254633 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACA
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACA
*
3254698 GTCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTCGCGTTGCGATTTTC
66 GTCGCGTTGCGATTTTCCAATTC-CGTTGCGATAGTCTACAGTCGCGTTGCGATTTTC
*
3254756 CATTTCGCGTTGCGATAGTTGAAATTCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACA
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACA
*
3254821 GTTGTCGTTGCGATTTTCCAAATT-CGTTGCGATAGT
66 GTCG-CGTTGCGATTTTCC-AATTCCGTTGCGATAGT
3254857 TAAAAAAAAA
Statistics
Matches: 96, Mismatches: 3, Indels: 4
0.93 0.03 0.04
Matches are distributed among these distances:
123 79 0.82
124 14 0.15
125 3 0.03
ACGTcount: A:0.17, C:0.21, G:0.24, T:0.38
Consensus pattern (122 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACA
GTCGCGTTGCGATTTTCCAATTCCGTTGCGATAGTCTACAGTCGCGTTGCGATTTTC
Found at i:3254971 original size:5 final size:6
Alignment explanation
Indices: 3254934--3254970 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
3254924 GACACGTATT
*
3254934 ACCATG ACCACG ACCACG ACCACG ACC-CG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
3254971 CAAGACGAGA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
5 10 0.33
6 20 0.67
ACGTcount: A:0.30, C:0.51, G:0.16, T:0.03
Consensus pattern (6 bp):
ACCACG
Found at i:3255479 original size:6 final size:6
Alignment explanation
Indices: 3255463--3255518 Score: 105
Period size: 6 Copynumber: 9.5 Consensus size: 6
3255453 GTCCGTCTCG
3255463 GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
3255510 GGTCGT GGT
1 GGTCGT GGT
3255519 AATACGTGTC
Statistics
Matches: 50, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 5 0.10
6 45 0.90
ACGTcount: A:0.00, C:0.16, G:0.52, T:0.32
Consensus pattern (6 bp):
GGTCGT
Found at i:3255637 original size:20 final size:20
Alignment explanation
Indices: 3255612--3255649 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
3255602 ACAACGAATT
3255612 TGGAAAATCGCAACGCGAAA
1 TGGAAAATCGCAACGCGAAA
3255632 TGGAAAATCGCAACGCGA
1 TGGAAAATCGCAACGCGA
3255650 TTTTCAACTA
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:0.42, C:0.21, G:0.26, T:0.11
Consensus pattern (20 bp):
TGGAAAATCGCAACGCGAAA
Found at i:3255678 original size:21 final size:21
Alignment explanation
Indices: 3255617--3255678 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 21
3255607 GAATTTGGAA
*
3255617 AATCGCAACGCGAAATGGAA-
1 AATCGCAACGCGAAATGCAAC
** *
3255637 AATCGCAACGCGATTTTCAAC
1 AATCGCAACGCGAAATGCAAC
*
3255658 TATCGCAACGCGAAATGCAAC
1 AATCGCAACGCGAAATGCAAC
3255679 GCGAATTTGC
Statistics
Matches: 33, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
20 16 0.48
21 17 0.52
ACGTcount: A:0.39, C:0.26, G:0.19, T:0.16
Consensus pattern (21 bp):
AATCGCAACGCGAAATGCAAC
Found at i:3255746 original size:20 final size:20
Alignment explanation
Indices: 3255723--3255791 Score: 75
Period size: 20 Copynumber: 3.4 Consensus size: 20
3255713 TCAACTATCA
3255723 CAACGCGAAATGGAAAATCG
1 CAACGCGAAATGGAAAATCG
** ** *
3255743 CAACGCGATCTCCAACTATCG
1 CAACGCGAAATGGAA-AATCG
*
3255764 CAACGCGAAATGGAAAAACG
1 CAACGCGAAATGGAAAATCG
3255784 CAACGCGA
1 CAACGCGA
3255792 TTTTCAACTA
Statistics
Matches: 37, Mismatches: 11, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
20 22 0.59
21 15 0.41
ACGTcount: A:0.41, C:0.28, G:0.22, T:0.10
Consensus pattern (20 bp):
CAACGCGAAATGGAAAATCG
Found at i:3255751 original size:60 final size:62
Alignment explanation
Indices: 3255590--3255751 Score: 142
Period size: 60 Copynumber: 2.7 Consensus size: 62
3255580 AAAATCTTTT
* *
3255590 TTTTTAACTATCACAA--CGAATTTGGAAAATCGCAACGCGA-AATGGAAAATCGCAACGCGA
1 TTTTCAACTATCACAACGCGAA-ATGGAAAATCGCAACGCGATAATGGAAAATCGCAACGCGA
* * * * * ***
3255650 TTTTCAACTATCGCAACGCGAAAT-G-CAA-CGCGAATTTGCGATGATGG-AGATCGCGTTGCGA
1 TTTTCAACTATCACAACGCGAAATGGAAAATCGC-AA--CGCGATAATGGAAAATCGCAACGCGA
3255711 -TTTCAACTATCACAACGCGAAATGGAAAATCGCAACGCGAT
1 TTTTCAACTATCACAACGCGAAATGGAAAATCGCAACGCGAT
3255752 CTCCAACTAT
Statistics
Matches: 80, Mismatches: 13, Indels: 18
0.72 0.12 0.16
Matches are distributed among these distances:
58 3 0.04
59 4 0.05
60 42 0.52
61 16 0.20
62 12 0.15
63 3 0.04
ACGTcount: A:0.35, C:0.22, G:0.21, T:0.22
Consensus pattern (62 bp):
TTTTCAACTATCACAACGCGAAATGGAAAATCGCAACGCGATAATGGAAAATCGCAACGCGA
Found at i:3255768 original size:41 final size:41
Alignment explanation
Indices: 3255714--3255816 Score: 161
Period size: 41 Copynumber: 2.5 Consensus size: 41
3255704 GTTGCGATTT
* *
3255714 CAACTATCACAACGCGAAATGGAAAATCGCAACGCGATCTC
1 CAACTATCGCAACGCGAAATGGAAAAACGCAACGCGATCTC
* *
3255755 CAACTATCGCAACGCGAAATGGAAAAACGCAACGCGATTTT
1 CAACTATCGCAACGCGAAATGGAAAAACGCAACGCGATCTC
*
3255796 CAACTATCGCAATGCGAAATG
1 CAACTATCGCAACGCGAAATG
3255817 CAACGTGAAT
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 57 1.00
ACGTcount: A:0.39, C:0.26, G:0.18, T:0.17
Consensus pattern (41 bp):
CAACTATCGCAACGCGAAATGGAAAAACGCAACGCGATCTC
Found at i:3255820 original size:21 final size:21
Alignment explanation
Indices: 3255714--3255820 Score: 83
Period size: 21 Copynumber: 5.2 Consensus size: 21
3255704 GTTGCGATTT
*
3255714 CAACTATCACAACGCGAAATG
1 CAACTATCGCAACGCGAAATG
* * ** *
3255735 GAA-AATCGCAACGCGATCTC
1 CAACTATCGCAACGCGAAATG
3255755 CAACTATCGCAACGCGAAATG
1 CAACTATCGCAACGCGAAATG
* * * ** *
3255776 GAA-AAACGCAACGCGATTTT
1 CAACTATCGCAACGCGAAATG
*
3255796 CAACTATCGCAATGCGAAATG
1 CAACTATCGCAACGCGAAATG
3255817 CAAC
1 CAAC
3255821 GTGAATTTGT
Statistics
Matches: 60, Mismatches: 24, Indels: 4
0.68 0.27 0.05
Matches are distributed among these distances:
20 28 0.47
21 32 0.53
ACGTcount: A:0.39, C:0.27, G:0.18, T:0.16
Consensus pattern (21 bp):
CAACTATCGCAACGCGAAATG
Found at i:3257208 original size:17 final size:17
Alignment explanation
Indices: 3257186--3257226 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
3257176 AACGGTCAAC
*
3257186 GGTCAACGGTCGGGTCG
1 GGTCAACAGTCGGGTCG
3257203 GGTCAACAGTCGGGTCG
1 GGTCAACAGTCGGGTCG
3257220 GGTCAAC
1 GGTCAAC
3257227 CCGGTTCAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.17, C:0.24, G:0.41, T:0.17
Consensus pattern (17 bp):
GGTCAACAGTCGGGTCG
Found at i:3257244 original size:19 final size:19
Alignment explanation
Indices: 3257220--3257283 Score: 94
Period size: 19 Copynumber: 3.4 Consensus size: 19
3257210 AGTCGGGTCG
*
3257220 GGTCAACCCGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
3257239 GGTCAAACCGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
*
3257258 GGTCAAACCGG-TCAAACC
1 GGTCAAACCGGTTCAGACC
3257276 GGTTCAAA
1 GG-TCAAA
3257284 ACTGGTCAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
18 8 0.19
19 34 0.81
ACGTcount: A:0.28, C:0.31, G:0.25, T:0.16
Consensus pattern (19 bp):
GGTCAAACCGGTTCAGACC
Done.