Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D13
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: 60343961
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 596159 characters in sequence are not A, C, G, or T
File 102 of 204
Found at i:31748765 original size:150 final size:152
Alignment explanation
Indices: 31748536--31748814 Score: 379
Period size: 150 Copynumber: 1.8 Consensus size: 152
31748526 GAGATTCCAT
* *
31748536 GTAAGACCATGTCTGGGACATGGCATTGGCATCCTTGAGATCATGAGACGTCCCATGTAAGACCA
1 GTAAGACCATGTCTAGGACATGGCATGGGCATCC-T--GATCATGAGACGTCCCATGTAAGACCA
* * * **
31748601 TGTCTGGGACATGGCATTGGCACCG-AGATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGG
63 TATCTGGGACATGGCATTGGCA--GTACATGAAACATCCCATGTAAGACCATGTCTGGGACATGG
31748665 CGTTCGCACCGAGATGAGAGATCCCCC
126 CGTTCGCACCGAGATGAGAGATCCCCC
31748692 GTAAGACCATGTCTAGGACATGGCATGGGCA-CC-GAT-ATGAGAAC-TCCCATGTAAGACCATA
1 GTAAGACCATGTCTAGGACATGGCATGGGCATCCTGATCATGAG-ACGTCCCATGTAAGACCATA
* * *
31748753 TCTGGGATATGGCATTTGCAGTACATGAAACATCCCATGTATGACCATGTCTGGGACATGGC
65 TCTGGGACATGGCATTGGCAGTACATGAAACATCCCATGTAAGACCATGTCTGGGACATGGC
31748815 TTTGGCATGT
Statistics
Matches: 111, Mismatches: 10, Indels: 11
0.84 0.08 0.08
Matches are distributed among these distances:
148 1 0.01
149 35 0.32
150 39 0.35
151 5 0.05
155 2 0.02
156 29 0.26
ACGTcount: A:0.27, C:0.23, G:0.28, T:0.22
Consensus pattern (152 bp):
GTAAGACCATGTCTAGGACATGGCATGGGCATCCTGATCATGAGACGTCCCATGTAAGACCATAT
CTGGGACATGGCATTGGCAGTACATGAAACATCCCATGTAAGACCATGTCTGGGACATGGCGTTC
GCACCGAGATGAGAGATCCCCC
Found at i:31760728 original size:6 final size:6
Alignment explanation
Indices: 31760717--31760743 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
31760707 TGTAAAAATT
31760717 AAATAA AAATAA AAATAA AAATAA AAA
1 AAATAA AAATAA AAATAA AAATAA AAA
31760744 ATAGTTAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAATAA
Found at i:31764987 original size:46 final size:46
Alignment explanation
Indices: 31764934--31765021 Score: 167
Period size: 46 Copynumber: 1.9 Consensus size: 46
31764924 TATAAATGTG
31764934 TCACATGAGTCACATGAGTCAAATGAGAATACTTGGAGATAACACA
1 TCACATGAGTCACATGAGTCAAATGAGAATACTTGGAGATAACACA
*
31764980 TCACATGAGTCACATGAGTCAAATGAGAATAGTTGGAGATAA
1 TCACATGAGTCACATGAGTCAAATGAGAATACTTGGAGATAA
31765022 ATGAAAGTAT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.41, C:0.15, G:0.22, T:0.23
Consensus pattern (46 bp):
TCACATGAGTCACATGAGTCAAATGAGAATACTTGGAGATAACACA
Found at i:31770284 original size:20 final size:21
Alignment explanation
Indices: 31770242--31770286 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
31770232 TGCTAAAGTT
**
31770242 AAAA-AAATCATAAATATCCA
1 AAAATAAATCATAAATATAAA
31770262 AAAATAAAT-ATAAATATAAA
1 AAAATAAATCATAAATATAAA
31770282 AAAAT
1 AAAAT
31770287 TAAAGAAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 18 0.82
21 4 0.18
ACGTcount: A:0.71, C:0.07, G:0.00, T:0.22
Consensus pattern (21 bp):
AAAATAAATCATAAATATAAA
Found at i:31792301 original size:62 final size:62
Alignment explanation
Indices: 31792212--31792393 Score: 294
Period size: 62 Copynumber: 2.9 Consensus size: 62
31792202 AAGTGATTAC
* ** * *
31792212 TTAATATTAAATTAAATTTAATGTTTATCTTG-TAGATAAATATTCTATTATTTTAATAAAAT
1 TTAATATTAAATTTAATCCAATATTTATCTTGATA-ATAAATATTATATTATTTTAATAAAAT
31792274 TTAATATTAAATTTAATCCAATATTTATCTTGATAATAAATATTATATTATTTTAATAAAAT
1 TTAATATTAAATTTAATCCAATATTTATCTTGATAATAAATATTATATTATTTTAATAAAAT
*
31792336 TTAATATTAAATTTAATCCAATATTTATCTTGATAATAAATATTATATTAATTTAATA
1 TTAATATTAAATTTAATCCAATATTTATCTTGATAATAAATATTATATTATTTTAATA
31792394 TTAAAGTGAT
Statistics
Matches: 113, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
62 111 0.98
63 2 0.02
ACGTcount: A:0.44, C:0.04, G:0.03, T:0.49
Consensus pattern (62 bp):
TTAATATTAAATTTAATCCAATATTTATCTTGATAATAAATATTATATTATTTTAATAAAAT
Found at i:31793326 original size:9 final size:9
Alignment explanation
Indices: 31793304--31793342 Score: 51
Period size: 9 Copynumber: 4.1 Consensus size: 9
31793294 ATATATCTGT
*
31793304 TTTATAATTT
1 TTTAT-ATTA
31793314 TTTATATTA
1 TTTATATTA
31793323 TTTATATTA
1 TTTATATTA
31793332 TTTAATATTA
1 TTT-ATATTA
31793342 T
1 T
31793343 AATTGTGATA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
9 15 0.56
10 12 0.44
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (9 bp):
TTTATATTA
Found at i:31793328 original size:19 final size:19
Alignment explanation
Indices: 31793304--31793342 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
31793294 ATATATCTGT
*
31793304 TTTATAATT-TTTTATATTA
1 TTTAT-ATTATTTAATATTA
31793323 TTTATATTATTTAATATTA
1 TTTATATTATTTAATATTA
31793342 T
1 T
31793343 AATTGTGATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 3 0.17
19 15 0.83
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
TTTATATTATTTAATATTA
Found at i:31803147 original size:21 final size:23
Alignment explanation
Indices: 31803108--31803150 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 23
31803098 TTTTGAGATT
31803108 TTGATATTTTATAATTTTTTATA
1 TTGATATTTTATAATTTTTTATA
31803131 TTGA-ATTTTAT-ATTTTTTAT
1 TTGATATTTTATAATTTTTTAT
31803151 TAAATAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 9 0.45
22 7 0.35
23 4 0.20
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (23 bp):
TTGATATTTTATAATTTTTTATA
Found at i:31803159 original size:22 final size:22
Alignment explanation
Indices: 31803113--31803171 Score: 61
Period size: 21 Copynumber: 2.7 Consensus size: 22
31803103 AGATTTTGAT
*
31803113 ATTTTATAATTTTTTA-TATTGA
1 ATTTTAT-ATTTTTTATTAATGA
31803135 ATTTTATATTTTTTATTAAAT-A
1 ATTTTATATTTTTTATT-AATGA
*
31803157 ATTTT-GATTTTTTAT
1 ATTTTATATTTTTTAT
31803172 AATTTTATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
21 17 0.52
22 14 0.42
23 2 0.06
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (22 bp):
ATTTTATATTTTTTATTAATGA
Found at i:31804365 original size:50 final size:50
Alignment explanation
Indices: 31804308--31804440 Score: 133
Period size: 50 Copynumber: 2.7 Consensus size: 50
31804298 TTAAACATAA
* *
31804308 TTAACATATAAGATGCATAAATGCATGGCTTAA-TTAAAATGCAAACTTAT
1 TTAACATATAAGATGCAT-AATGCATGACATAATTTAAAATGCAAACTTAT
* * * * * *
31804358 TTAACATATGAGTTTCATAATGCATGACATAATTTAATATGCAAACTGAA
1 TTAACATATAAGATGCATAATGCATGACATAATTTAAAATGCAAACTTAT
* * * * *
31804408 TTAATATATGAGTTACATAATGCATGAAATAAT
1 TTAACATATAAGATGCATAATGCATGACATAAT
31804441 CAAATGCAAA
Statistics
Matches: 71, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
49 12 0.17
50 59 0.83
ACGTcount: A:0.44, C:0.11, G:0.12, T:0.34
Consensus pattern (50 bp):
TTAACATATAAGATGCATAATGCATGACATAATTTAAAATGCAAACTTAT
Found at i:31804491 original size:32 final size:33
Alignment explanation
Indices: 31804450--31804513 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
31804440 TCAAATGCAA
**
31804450 AACATATAATGTAAAACATAA-TTAAAGATGCT
1 AACATATAATACAAAACATAATTTAAAGATGCT
31804482 AACATATAATACAAAACATAATTTAAAGATGC
1 AACATATAATACAAAACATAATTTAAAGATGC
31804514 AAACTTATGA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 19 0.66
33 10 0.34
ACGTcount: A:0.55, C:0.11, G:0.08, T:0.27
Consensus pattern (33 bp):
AACATATAATACAAAACATAATTTAAAGATGCT
Found at i:31805380 original size:13 final size:12
Alignment explanation
Indices: 31805350--31805392 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 12
31805340 ATTTTTATAT
31805350 AATAAATTATTC
1 AATAAATTATTC
*
31805362 ATATAATTTACTTC
1 A-ATAAATTA-TTC
31805376 AATAAAATTATTC
1 AAT-AAATTATTC
31805389 AATA
1 AATA
31805393 TTAAAATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
12 2 0.08
13 15 0.58
14 9 0.35
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.42
Consensus pattern (12 bp):
AATAAATTATTC
Found at i:31813972 original size:19 final size:20
Alignment explanation
Indices: 31813948--31814001 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 20
31813938 AATACCAACT
*
31813948 TAAAAATATCGATACT-TTA
1 TAAAAATATCGATACTCGTA
*
31813967 TAAAAATATCGATACTCGTG
1 TAAAAATATCGATACTCGTA
*
31813987 GAAAAATATCGATAC
1 TAAAAATATCGATAC
31814002 CACTGGGGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
19 16 0.52
20 15 0.48
ACGTcount: A:0.46, C:0.13, G:0.11, T:0.30
Consensus pattern (20 bp):
TAAAAATATCGATACTCGTA
Found at i:31816139 original size:20 final size:20
Alignment explanation
Indices: 31816094--31816152 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 20
31816084 AACAATTTTA
*
31816094 AATCAAGTGC-AAATGATTTT
1 AATCAAGT-CAAAATGATTTC
*
31816114 AGTCAAGTCAAAATGATTTC
1 AATCAAGTCAAAATGATTTC
* *
31816134 AATCAAGTTAAAATAATTT
1 AATCAAGTCAAAATGATTT
31816153 TAAAATGATT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
19 1 0.03
20 32 0.97
ACGTcount: A:0.44, C:0.10, G:0.12, T:0.34
Consensus pattern (20 bp):
AATCAAGTCAAAATGATTTC
Found at i:31820588 original size:16 final size:16
Alignment explanation
Indices: 31820555--31820589 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
31820545 AAGATATTAG
* *
31820555 AAATAAAAAATTATAT
1 AAATAAAAAATAAAAT
31820571 AAATAAAAAATAAAAT
1 AAATAAAAAATAAAAT
31820587 AAA
1 AAA
31820590 ATTAGAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (16 bp):
AAATAAAAAATAAAAT
Found at i:31823667 original size:21 final size:21
Alignment explanation
Indices: 31823642--31823682 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
31823632 TGTTAATACA
*
31823642 AATTTCAATTTCTTTTCTAAT
1 AATTTCAATCTCTTTTCTAAT
*
31823663 AATTTCAATCTGTTTTCTAA
1 AATTTCAATCTCTTTTCTAA
31823683 ATTCCTAGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.15, G:0.02, T:0.54
Consensus pattern (21 bp):
AATTTCAATCTCTTTTCTAAT
Found at i:31825144 original size:27 final size:27
Alignment explanation
Indices: 31825109--31825175 Score: 84
Period size: 27 Copynumber: 2.5 Consensus size: 27
31825099 CCCAATTTTA
* *
31825109 CTTCAGTAAATTTTTGACGATTTTACC
1 CTTCAGTAAAATTTTGAAGATTTTACC
*
31825136 CTTCGGTAAAATTTTGAAGATTTTACTC
1 CTTCAGTAAAATTTTGAAGATTTTAC-C
31825164 C-T-AGTAAAATTT
1 CTTCAGTAAAATTT
31825176 CGAGAAAATA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
26 9 0.26
27 24 0.69
28 2 0.06
ACGTcount: A:0.30, C:0.15, G:0.12, T:0.43
Consensus pattern (27 bp):
CTTCAGTAAAATTTTGAAGATTTTACC
Found at i:31825330 original size:6 final size:6
Alignment explanation
Indices: 31825319--31825345 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
31825309 GGATTGTAAT
31825319 TTTCCA TTTCCA TTTCCA TTTCCA TTT
1 TTTCCA TTTCCA TTTCCA TTTCCA TTT
31825346 TTGGAAACTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.30, G:0.00, T:0.56
Consensus pattern (6 bp):
TTTCCA
Found at i:31827526 original size:28 final size:28
Alignment explanation
Indices: 31827475--31827530 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
31827465 ATTTAAACTC
31827475 ATGTCACACATCTATAAAATATTTCTTT
1 ATGTCACACATCTATAAAATATTTCTTT
31827503 ATGTCACACATCTATAAAATATTTCTTT
1 ATGTCACACATCTATAAAATATTTCTTT
31827531 TTATCATTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.36, C:0.18, G:0.04, T:0.43
Consensus pattern (28 bp):
ATGTCACACATCTATAAAATATTTCTTT
Found at i:31830255 original size:15 final size:14
Alignment explanation
Indices: 31830219--31830258 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
31830209 AACTTTCAAT
**
31830219 ACTTATTTTTTTAC
1 ACTTATTTTTCGAC
31830233 ACTTATTTTTCGAC
1 ACTTATTTTTCGAC
31830247 ACTTAATTTTTC
1 ACTT-ATTTTTC
31830259 AGTTTATCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 16 0.70
15 7 0.30
ACGTcount: A:0.23, C:0.17, G:0.03, T:0.57
Consensus pattern (14 bp):
ACTTATTTTTCGAC
Found at i:31830692 original size:43 final size:43
Alignment explanation
Indices: 31830634--31830736 Score: 152
Period size: 43 Copynumber: 2.4 Consensus size: 43
31830624 GTTTATAGAA
* *
31830634 ACAAAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGGTTTCTCC
1 ACAAAA-GCCGCTAAAGGTCATGTTCCTTAGCGGCGCTTTCTCC
* * *
31830678 ACAAATGCTGCTAAAGGTCATGTTCCTTAGCGGCGCTTTTTCC
1 ACAAAAGCCGCTAAAGGTCATGTTCCTTAGCGGCGCTTTCTCC
31830721 ACAAAAGCCGCTAAAG
1 ACAAAAGCCGCTAAAG
31830737 AACATGGCTT
Statistics
Matches: 52, Mismatches: 7, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
43 47 0.90
44 5 0.10
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.26
Consensus pattern (43 bp):
ACAAAAGCCGCTAAAGGTCATGTTCCTTAGCGGCGCTTTCTCC
Found at i:31830751 original size:43 final size:42
Alignment explanation
Indices: 31830634--31830819 Score: 135
Period size: 43 Copynumber: 4.3 Consensus size: 42
31830624 GTTTATAGAA
** * * *
31830634 ACAAAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGGTTTCTCC
1 ACAAAA-GCCGCTAAAGAACATGCT-TTTAGCGGCGCTTTTTCC
* * **
31830678 ACAAATGCTGCTAAAGGTCATG-TTCCTTAGCGGCGCTTTTTCC
1 ACAAAAGCCGCTAAAGAACATGCTT--TTAGCGGCGCTTTTTCC
*
31830721 ACAAAAGCCGCTAAAGAACATGGCTTTTAGC-G-ACTTTTTCCC
1 ACAAAAGCCGCTAAAGAACAT-GCTTTTAGCGGCGCTTTTT-CC
* * * * *
31830763 ACAAACGCCGCTATAGAACTTGACTTTTAGTGGCGCTTTTTCA
1 ACAAAAGCCGCTAAAGAACATG-CTTTTAGCGGCGCTTTTTCC
*
31830806 ATCAAACGCCGCTA
1 A-CAAAAGCCGCTA
31830820 TTGTTTGGTG
Statistics
Matches: 118, Mismatches: 15, Indels: 18
0.78 0.10 0.12
Matches are distributed among these distances:
41 8 0.07
42 29 0.25
43 55 0.47
44 24 0.20
45 2 0.02
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.28
Consensus pattern (42 bp):
ACAAAAGCCGCTAAAGAACATGCTTTTAGCGGCGCTTTTTCC
Found at i:31830817 original size:44 final size:42
Alignment explanation
Indices: 31830704--31830820 Score: 130
Period size: 42 Copynumber: 2.7 Consensus size: 42
31830694 GTCATGTTCC
* * *
31830704 TTAGCGGCGCTTTTTCCACAAAAGCCGCTAAAGAACATGGCTT
1 TTAG-GGCGCTTTTTCCACAAACGCCGCTATAGAACATGACTT
*
31830747 TTA--GCGACTTTTTCCCACAAACGCCGCTATAGAACTTGACTT
1 TTAGGGCG-CTTTTT-CCACAAACGCCGCTATAGAACATGACTT
*
31830789 TTAGTGGCGCTTTTTCAATCAAACGCCGCTAT
1 TTAG-GGCGCTTTTTCCA-CAAACGCCGCTAT
31830821 TGTTTGGTGG
Statistics
Matches: 63, Mismatches: 5, Indels: 11
0.80 0.06 0.14
Matches are distributed among these distances:
40 3 0.05
41 6 0.10
42 27 0.43
43 5 0.08
44 19 0.30
45 3 0.05
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.30
Consensus pattern (42 bp):
TTAGGGCGCTTTTTCCACAAACGCCGCTATAGAACATGACTT
Found at i:31831261 original size:87 final size:87
Alignment explanation
Indices: 31831167--31831343 Score: 291
Period size: 87 Copynumber: 2.0 Consensus size: 87
31831157 TTCTGCTCTG
* *
31831167 CTCTGCTTCCCTTGCTGCAGCCTCTGCTTCTCTCGATGCCGCATCTACTTTAAGTTGTAGCTGGA
1 CTCTGCTTCCCTCGCTGCAGCCTCTGCTTCCCTCGATGCCGCATCTACTTTAAGTTGTAGCTGGA
*
31831232 GTTCTTCATATTTCTTTTGAAC
66 GTTCTTCATATTTCCTTTGAAC
* * * *
31831254 CTCTGCTTCTCTCGCTGCAGCCTCTGCTTCCCTCGCTGCCGCCTCTGCTTTAAGTTGTAGCTGGA
1 CTCTGCTTCCCTCGCTGCAGCCTCTGCTTCCCTCGATGCCGCATCTACTTTAAGTTGTAGCTGGA
31831319 GTTCTTCATATTTCCTTTGAAC
66 GTTCTTCATATTTCCTTTGAAC
31831341 CTC
1 CTC
31831344 AACTGTGGTC
Statistics
Matches: 83, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
87 83 1.00
ACGTcount: A:0.12, C:0.32, G:0.18, T:0.39
Consensus pattern (87 bp):
CTCTGCTTCCCTCGCTGCAGCCTCTGCTTCCCTCGATGCCGCATCTACTTTAAGTTGTAGCTGGA
GTTCTTCATATTTCCTTTGAAC
Found at i:31831277 original size:21 final size:21
Alignment explanation
Indices: 31831253--31831303 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
31831243 TTCTTTTGAA
*
31831253 CCTCTGCTTCTCTCGCTGCAG
1 CCTCTGCTTCCCTCGCTGCAG
*
31831274 CCTCTGCTTCCCTCGCTGCCG
1 CCTCTGCTTCCCTCGCTGCAG
31831295 CCTCTGCTT
1 CCTCTGCTT
31831304 TAAGTTGTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.02, C:0.47, G:0.18, T:0.33
Consensus pattern (21 bp):
CCTCTGCTTCCCTCGCTGCAG
Found at i:31834982 original size:31 final size:31
Alignment explanation
Indices: 31834889--31834984 Score: 174
Period size: 31 Copynumber: 3.1 Consensus size: 31
31834879 GGCAAATTAC
*
31834889 AAGAGTAATTGAATCCTAATAAAACTCTTTC
1 AAGAGTAATTGAATCCTAATAAAACTCTTTA
31834920 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
1 AAGAGTAATTGAATCCTAAT-AAAACTCTTTA
31834952 AAGAGTAATTGAATCCTAATAAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAACTCTTTA
31834983 AA
1 AA
31834985 ATTATCTAAG
Statistics
Matches: 63, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
31 33 0.52
32 30 0.48
ACGTcount: A:0.46, C:0.14, G:0.09, T:0.31
Consensus pattern (31 bp):
AAGAGTAATTGAATCCTAATAAAACTCTTTA
Found at i:31841123 original size:31 final size:31
Alignment explanation
Indices: 31841030--31841125 Score: 165
Period size: 31 Copynumber: 3.1 Consensus size: 31
31841020 GGCAAATTAC
*
31841030 AAGAGTAATTGAATCCTAATAAAACTCTTTC
1 AAGAGTAATTGAATCCTAATAAAACTCTTTA
*
31841061 AAGAGTAAATGAATCCTAATAAAAACTCTTTA
1 AAGAGTAATTGAATCCTAAT-AAAACTCTTTA
31841093 AAGAGTAATTGAATCCTAATAAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAACTCTTTA
31841124 AA
1 AA
31841126 ATTATCTAAG
Statistics
Matches: 61, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
31 32 0.52
32 29 0.48
ACGTcount: A:0.47, C:0.14, G:0.09, T:0.30
Consensus pattern (31 bp):
AAGAGTAATTGAATCCTAATAAAACTCTTTA
Found at i:31843762 original size:16 final size:16
Alignment explanation
Indices: 31843743--31844040 Score: 125
Period size: 16 Copynumber: 17.9 Consensus size: 16
31843733 TATTTGGTAA
*
31843743 ATTATGTAGGTTATGT
1 ATTATGTAAGTTATGT
*
31843759 ATTATATAAGTTATGT
1 ATTATGTAAGTTATGT
*
31843775 AAGTTGTGT-A-TTATGTT
1 -A-TTATGTAAGTTATG-T
* *
31843792 AGTTGTGT-A-CTATGT
1 A-TTATGTAAGTTATGT
*
31843807 AAGTTATGTAAGTTAGGT
1 -A-TTATGTAAGTTATGT
*
31843825 ATTATGTATGTTATGT
1 ATTATGTAAGTTATGT
*
31843841 ATTATGTATGTTATGT
1 ATTATGTAAGTTATGT
*
31843857 ATAATATTAATTAAGTTATGT
1 AT--TA-T--GTAAGTTATGT
* *
31843878 ATAATATTAATTAAGTTGTGT
1 AT--TA-T--GTAAGTTATGT
* *
31843899 ATAATGTAAGTTGTGT
1 ATTATGTAAGTTATGT
31843915 ATTATGTAAGTTATGT
1 ATTATGTAAGTTATGT
*
31843931 ATTATGT-A-TTATGC
1 ATTATGTAAGTTATGT
*
31843945 ATTATGTATGTTATGT
1 ATTATGTAAGTTATGT
*
31843961 ATAATAT-TAA-TTAAG-
1 AT--TATGTAAGTTATGT
*
31843976 -TTGTG-AA-TTATGT
1 ATTATGTAAGTTATGT
*
31843989 ATTATGTATGTTATGTAT
1 ATTATGTAAGTTATG--T
* *
31844007 ATTATTAATTAAGTTGTGT
1 ATTA-T--GTAAGTTATGT
31844026 ATTATGTAAGTTATG
1 ATTATGTAAGTTATG
31844041 CAAGTTTATA
Statistics
Matches: 226, Mismatches: 31, Indels: 50
0.74 0.10 0.16
Matches are distributed among these distances:
12 8 0.04
14 17 0.08
15 3 0.01
16 125 0.55
17 7 0.03
18 20 0.09
19 8 0.04
21 38 0.17
ACGTcount: A:0.31, C:0.01, G:0.18, T:0.50
Consensus pattern (16 bp):
ATTATGTAAGTTATGT
Found at i:31843813 original size:25 final size:25
Alignment explanation
Indices: 31843785--31843841 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
31843775 AAGTTGTGTA
*
31843785 TTATGTTAGTT-GTGTACTATGTAAG
1 TTATGTAAGTTAG-GTACTATGTAAG
* *
31843810 TTATGTAAGTTAGGTATTATGTATG
1 TTATGTAAGTTAGGTACTATGTAAG
31843835 TTATGTA
1 TTATGTA
31843842 TTATGTATGT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
25 27 0.96
26 1 0.04
ACGTcount: A:0.26, C:0.02, G:0.23, T:0.49
Consensus pattern (25 bp):
TTATGTAAGTTAGGTACTATGTAAG
Found at i:31843858 original size:9 final size:9
Alignment explanation
Indices: 31843802--31843858 Score: 59
Period size: 9 Copynumber: 6.8 Consensus size: 9
31843792 AGTTGTGTAC
*
31843802 TATGTAAGT
1 TATGTATGT
*
31843811 TATGTAAGT
1 TATGTATGT
*
31843820 TAGGTA--T
1 TATGTATGT
31843827 TATGTATGT
1 TATGTATGT
31843836 TATGTA--T
1 TATGTATGT
31843843 TATGTATGT
1 TATGTATGT
31843852 TATGTAT
1 TATGTAT
31843859 AATATTAATT
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
7 13 0.31
9 29 0.69
ACGTcount: A:0.28, C:0.00, G:0.21, T:0.51
Consensus pattern (9 bp):
TATGTATGT
Found at i:31843864 original size:21 final size:21
Alignment explanation
Indices: 31843840--31844013 Score: 87
Period size: 21 Copynumber: 8.2 Consensus size: 21
31843830 GTATGTTATG
31843840 TATTATGTATGTTATGTATAA
1 TATTATGTATGTTATGTATAA
*
31843861 TATTAAT-TAAGTTATGTATAA
1 TATT-ATGTATGTTATGTATAA
* *
31843882 TATTAAT-TAAGTTGTGTATAA
1 TATT-ATGTATGTTATGTATAA
* *
31843903 T-GTAAGT-TGTGTAT-TATGTAA
1 TATTATGTATGT-TATGTA--TAA
* *
31843924 -GTTATGTA--TTATGTATTA
1 TATTATGTATGTTATGTATAA
31843942 TGCATTATGTATGTTATGTATAA
1 T--ATTATGTATGTTATGTATAA
* * * *
31843965 TATTAAT-TAAGTTGTGAATTATG
1 TATT-ATGTATGTTATGTA-TA-A
*
31843988 TATTATGTATGTTATGTATAT
1 TATTATGTATGTTATGTATAA
31844009 TATTA
1 TATTA
31844014 ATTAAGTTGT
Statistics
Matches: 117, Mismatches: 19, Indels: 34
0.69 0.11 0.20
Matches are distributed among these distances:
18 2 0.02
19 8 0.07
20 7 0.06
21 68 0.58
22 10 0.09
23 22 0.19
ACGTcount: A:0.33, C:0.01, G:0.16, T:0.51
Consensus pattern (21 bp):
TATTATGTATGTTATGTATAA
Found at i:31843916 original size:74 final size:73
Alignment explanation
Indices: 31843815--31844027 Score: 201
Period size: 74 Copynumber: 2.9 Consensus size: 73
31843805 GTAAGTTATG
* *
31843815 TAAGTTAG-GTATTATGTATGTTATGTATTATGTATGTTATGTATAATATTAATTAAGTTATGTA
1 TAAGTT-GTGTATAATGTAAGTT-TGTATTATGTATGTTATGTATAATATTAATTAAGTTATGTA
31843879 TAATATTAAT
64 TAATATTAAT
* *
31843889 TAAGTTGTGTATAATGTAAGTTGTGTATTATGTAAGTTATGTATTATGTATTATGCATTATGTAT
1 TAAGTTGTGTATAATGTAAGTT-TGTATTATGTATGTTATGTA-TA-ATATTA---ATTA---A-
31843954 GTTATGTATAATATTAAT
56 GTTATGTATAATATTAAT
* *
31843972 TAAGTTGTG---AAT-T-A---TGTATTATGTATGTTATGTATATTATTAATTAAGTTGTGTAT
1 TAAGTTGTGTATAATGTAAGTTTGTATTATGTATGTTATGTATAATATTAATTAAGTTATGTAT
31844028 TATGTAAGTT
Statistics
Matches: 121, Mismatches: 8, Indels: 29
0.77 0.05 0.18
Matches are distributed among these distances:
65 8 0.07
66 1 0.01
69 4 0.03
72 5 0.04
73 3 0.02
74 56 0.46
75 2 0.02
76 5 0.04
78 1 0.01
79 5 0.04
80 3 0.02
82 1 0.01
83 27 0.22
ACGTcount: A:0.32, C:0.00, G:0.17, T:0.50
Consensus pattern (73 bp):
TAAGTTGTGTATAATGTAAGTTTGTATTATGTATGTTATGTATAATATTAATTAAGTTATGTATA
ATATTAAT
Found at i:31843922 original size:7 final size:7
Alignment explanation
Indices: 31843912--31843953 Score: 57
Period size: 7 Copynumber: 5.7 Consensus size: 7
31843902 ATGTAAGTTG
31843912 TGTATTA
1 TGTATTA
31843919 TGTAAGTTA
1 TGT-A-TTA
31843928 TGTATTA
1 TGTATTA
31843935 TGTATTA
1 TGTATTA
*
31843942 TGCATTA
1 TGTATTA
31843949 TGTAT
1 TGTAT
31843954 GTTATGTATA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
7 23 0.74
8 2 0.06
9 6 0.19
ACGTcount: A:0.29, C:0.02, G:0.17, T:0.52
Consensus pattern (7 bp):
TGTATTA
Found at i:31843993 original size:44 final size:44
Alignment explanation
Indices: 31843938--31844033 Score: 165
Period size: 44 Copynumber: 2.2 Consensus size: 44
31843928 TGTATTATGT
*
31843938 ATTATGCATTATGTATGTTATGTATAATATTAATTAAGTTGTGA
1 ATTATGTATTATGTATGTTATGTATAATATTAATTAAGTTGTGA
* *
31843982 ATTATGTATTATGTATGTTATGTATATTATTAATTAAGTTGTGT
1 ATTATGTATTATGTATGTTATGTATAATATTAATTAAGTTGTGA
31844026 ATTATGTA
1 ATTATGTA
31844034 AGTTATGCAA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
44 49 1.00
ACGTcount: A:0.32, C:0.01, G:0.16, T:0.51
Consensus pattern (44 bp):
ATTATGTATTATGTATGTTATGTATAATATTAATTAAGTTGTGA
Found at i:31844003 original size:83 final size:81
Alignment explanation
Indices: 31843823--31844011 Score: 226
Period size: 83 Copynumber: 2.3 Consensus size: 81
31843813 TGTAAGTTAG
31843823 GTATTATGTATGTTATGT-ATTATGTATGTTATGTATAATATTAATTAAGTTATGTATAATATTA
1 GTATTATGTATGTTATGTAATTATGTA-GTTATGTATAATATTAATTAAGTTATGTATAATATTA
*
31843887 ATTAAGTTGTGTATAAT
65 ATTAAGTTGTGAATAAT
* * *
31843904 GTAAGTTGTGTA--TTATGTAAGTTATGTA-TTATGTATTATGCATT-ATGTATGTTATGTATAA
1 GT-A-TTATGTATGTTATGTAA-TTATGTAGTTATGTATAAT--ATTAAT-TAAGTTATGTATAA
*
31843965 TATTAATTAAGTTGTGAATTAT
60 TATTAATTAAGTTGTGAATAAT
31843987 GTATTATGTATGTTATGTATATTAT
1 GTATTATGTATGTTATGTA-ATTAT
31844012 TAATTAAGTT
Statistics
Matches: 92, Mismatches: 6, Indels: 18
0.79 0.05 0.16
Matches are distributed among these distances:
81 24 0.26
82 5 0.05
83 62 0.67
84 1 0.01
ACGTcount: A:0.32, C:0.01, G:0.16, T:0.51
Consensus pattern (81 bp):
GTATTATGTATGTTATGTAATTATGTAGTTATGTATAATATTAATTAAGTTATGTATAATATTAA
TTAAGTTGTGAATAAT
Found at i:31844057 original size:37 final size:37
Alignment explanation
Indices: 31843983--31844063 Score: 94
Period size: 37 Copynumber: 2.2 Consensus size: 37
31843973 AAGTTGTGAA
* * *
31843983 TTATGTATTATGTATGTTATGTATATTATTAATTAAG
1 TTATGTATTATGTAAGTTATGCATAGTATTAATTAAG
*
31844020 TTGTGTATTATGTAAGTTATGCA-AGT-TTATATATAAG
1 TTATGTATTATGTAAGTTATGCATAGTATTA-AT-TAAG
31844057 TTATGTA
1 TTATGTA
31844064 AGTATATCAC
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
35 3 0.08
36 4 0.11
37 30 0.81
ACGTcount: A:0.32, C:0.01, G:0.16, T:0.51
Consensus pattern (37 bp):
TTATGTATTATGTAAGTTATGCATAGTATTAATTAAG
Found at i:31844318 original size:126 final size:123
Alignment explanation
Indices: 31844087--31844319 Score: 308
Period size: 126 Copynumber: 1.8 Consensus size: 123
31844077 TATGTATCTT
* * *
31844087 ATTTATAATTATTTTTAAAATTATAAAATTTATTACTAATAAATTTGAAATGTAGGTTATATATC
1 ATTTACAATTATTTTTAAAATTATAAAATTTATTACTAATAAAATTGAAATATAGGTTATATATC
* * **
31844152 CATACCATATATAGGGTGATATATTAAAAAAATAGGTTTTAATATTTAAAAAAAAAATAAA
66 CATACCATATATA--G-AAAATATTAAAAAAATAAATTTTAATATTTAAAAAAAAAATAAA
31844213 ATTTACAATTATTTTTAAAATTATAAAATTTATTGAC-AATAAAATTGAAATATAGGTTATATAT
1 ATTTACAATTATTTTTAAAATTATAAAATTTATT-ACTAATAAAATTGAAATATAGGTTATATAT
*
31844277 CCATACCATATATA-AAAATTTTAAATATATATATAAATTTTAA
65 CCATACCATATATAGAAAATATTAAA-A-A-A-ATAAATTTTAA
31844320 GTAATGTAAT
Statistics
Matches: 94, Mismatches: 8, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
122 8 0.09
123 1 0.01
124 1 0.01
125 1 0.01
126 81 0.86
127 2 0.02
ACGTcount: A:0.48, C:0.05, G:0.06, T:0.41
Consensus pattern (123 bp):
ATTTACAATTATTTTTAAAATTATAAAATTTATTACTAATAAAATTGAAATATAGGTTATATATC
CATACCATATATAGAAAATATTAAAAAAATAAATTTTAATATTTAAAAAAAAAATAAA
Found at i:31844338 original size:18 final size:18
Alignment explanation
Indices: 31844315--31844403 Score: 101
Period size: 18 Copynumber: 4.8 Consensus size: 18
31844305 ATATATAAAT
31844315 TTTAAGTAATGTAATATA
1 TTTAAGTAATGTAATATA
31844333 TTTAAGTAATGTAAGTTATAAA
1 TTTAAGTAATGTAA--TAT--A
*
31844355 TTTTAGTAA-GTAATATA
1 TTTAAGTAATGTAATATA
*
31844372 TTTAAGTAATCTAATATA
1 TTTAAGTAATGTAATATA
*
31844390 TTTTAGTAA-GTAAT
1 TTTAAGTAATGTAAT
31844404 GTAAGTAATG
Statistics
Matches: 61, Mismatches: 5, Indels: 11
0.79 0.06 0.14
Matches are distributed among these distances:
17 13 0.21
18 29 0.48
19 3 0.05
20 3 0.05
21 4 0.07
22 9 0.15
ACGTcount: A:0.43, C:0.01, G:0.11, T:0.45
Consensus pattern (18 bp):
TTTAAGTAATGTAATATA
Found at i:31844365 original size:17 final size:17
Alignment explanation
Indices: 31844343--31844400 Score: 64
Period size: 17 Copynumber: 3.4 Consensus size: 17
31844333 TTTAAGTAAT
*
31844343 GTAAGTTATAAATTTTA
1 GTAAGTTATATATTTTA
* *
31844360 GTAAGTAATATATTTAA
1 GTAAGTTATATATTTTA
31844377 GTAA-TCTAATATATTTTA
1 GTAAGT-T-ATATATTTTA
31844395 GTAAGT
1 GTAAGT
31844401 AATGTAAGTA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
16 1 0.03
17 18 0.55
18 13 0.39
19 1 0.03
ACGTcount: A:0.41, C:0.02, G:0.12, T:0.45
Consensus pattern (17 bp):
GTAAGTTATATATTTTA
Found at i:31844374 original size:39 final size:37
Alignment explanation
Indices: 31844307--31844450 Score: 141
Period size: 39 Copynumber: 3.8 Consensus size: 37
31844297 TTAAATATAT
*
31844307 ATATAAATTTTAAGTAATGTAATATATTTAAGTAATGTA
1 ATATAAATTTT-AGTAA-GTAATATATTTAAGTAATCTA
31844346 AGTTATAAATTTTAGTAAGTAATATATTTAAGTAATCTA
1 A--TATAAATTTTAGTAAGTAATATATTTAAGTAATCTA
* ** *
31844385 ATAT--ATTTTAGTAAGTAATGTAAGTAATGTAATAT-
1 ATATAAATTTTAGTAAGTAATATATTTAA-GTAATCTA
* *
31844420 ATACTTAAATTTTAGTAAGTCATGTATTTAA
1 ATA--TAAATTTTAGTAAGTAATATATTTAA
31844451 CATTCTGTTA
Statistics
Matches: 90, Mismatches: 8, Indels: 14
0.80 0.07 0.12
Matches are distributed among these distances:
35 23 0.26
36 6 0.07
37 4 0.04
39 42 0.47
40 5 0.06
41 10 0.11
ACGTcount: A:0.43, C:0.02, G:0.11, T:0.44
Consensus pattern (37 bp):
ATATAAATTTTAGTAAGTAATATATTTAAGTAATCTA
Found at i:31845158 original size:12 final size:14
Alignment explanation
Indices: 31845135--31845167 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
31845125 CTTCAAAAAT
31845135 TAGAAGAACAAAC-
1 TAGAAGAACAAACA
31845148 TAGAA-AACAAACA
1 TAGAAGAACAAACA
31845161 TAGAAGA
1 TAGAAGA
31845168 TTGGTACTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 7 0.39
13 10 0.56
14 1 0.06
ACGTcount: A:0.64, C:0.12, G:0.15, T:0.09
Consensus pattern (14 bp):
TAGAAGAACAAACA
Found at i:31846325 original size:337 final size:337
Alignment explanation
Indices: 31845710--31847043 Score: 2059
Period size: 337 Copynumber: 4.0 Consensus size: 337
31845700 TAATAGAAAT
* * *
31845710 AGAAAATGCTAAGTTAAAATTGGTGTACATAAACGGCGTCGTTTAGCCAAAATTTTAAGACACTT
1 AGAAAATACTAAGTTAAAATTAGTGTACAGAAACGGCGTCGTTTAGCCAAAATTTTAAGACACTT
* * * *
31845775 TTGCGGCGTTTCTAAAAAAACGCCGCTATTTCTTGTACATTTG-CAGCGCTTCTAGAAAAGCGCC
66 TTGCGGCGTTTCTAGAAAAACGCCGCTATTGCTTGTACATTTGCCGGCGTTTCTA-AAAAGCGCC
** ** *
31845839 ACTAAAAAGCAAAGTTCTAATTTGAAACGGCGTCGTTTAATAAAGCTTTAATGCACATTTCTGGC
130 ACTAAAAATTAAAGTTCTAATCCGAAACGGCGCCGTTTAATAAAGCTTTAATGCACATTTCTGGC
31845904 ATTTTCTGTAAAAACGCCACTAAAATTTAATTTGCTTAAGCTAAACGGCGTCGTTTAGCCAATAT
195 ATTTTCTGTAAAAACGCCACTAAAATTTAATTTGCTTAAGCTAAACGGCGTCGTTTAGCCAATAT
* * *
31845969 TTTAAGTCACTTTTGCGGCGTTTCCTGAACAAAATGCCACTATAAATTAACAGAAATGGCGCCAT
260 TTTAAGTCACTTTTGCGGCGTTTCCTGAACAAAACGCCACTATAAATTAACAGAAACGGCGCCGT
31846034 TGGATTAATATAG
325 TGGATTAATATAG
* * *
31846047 AGAAAATACTAAGTTAAAATTCGTGTACAAAAACGGTGTCGTTTAGCCAAAATTTTAAGACACTT
1 AGAAAATACTAAGTTAAAATTAGTGTACAGAAACGGCGTCGTTTAGCCAAAATTTTAAGACACTT
*
31846112 TTGCGGCGTTTCTAGAAAAACGCCGCTATTGCTTGTACATTTGCCGG-GTTTCTTAAAAATCGCC
66 TTGCGGCGTTTCTAGAAAAACGCCGCTATTGCTTGTACATTTGCCGGCGTTTC-TAAAAAGCGCC
* *
31846176 ACTAAAAATTAAAGTTCTAATCCGAAACGGTGCCGTTTAATAAAGCTTTAATGCACATTTTTGGC
130 ACTAAAAATTAAAGTTCTAATCCGAAACGGCGCCGTTTAATAAAGCTTTAATGCACATTTCTGGC
** ** *
31846241 GCTTTCTGTAAAAACGCCACTAAAATTTAATTTGCTTAAGCTAAACAACGTCGTTTACCCAATAT
195 ATTTTCTGTAAAAACGCCACTAAAATTTAATTTGCTTAAGCTAAACGGCGTCGTTTAGCCAATAT
* * * *
31846306 TTTAAGTCATTTTTGCGGCGTTTCCTGAACAAAACCCCACTATAAATTAACAGAAACGGTGTCGT
260 TTTAAGTCACTTTTGCGGCGTTTCCTGAACAAAACGCCACTATAAATTAACAGAAACGGCGCCGT
31846371 TGGATTAATATAG
325 TGGATTAATATAG
* **
31846384 AGAAAATACTAAGTTAAAATTTGTGTACAGAAACGATGTCGTTTAGCCAAAATTTTAAGACACTT
1 AGAAAATACTAAGTTAAAATTAGTGTACAGAAACGGCGTCGTTTAGCCAAAATTTTAAGACACTT
* *
31846449 TTGCGGCGTTTCTAGAAAAATGCCGCTATTGCTTGTACATTTG-CGGCGTTTCTAAGAAGCGCCA
66 TTGCGGCGTTTCTAGAAAAACGCCGCTATTGCTTGTACATTTGCCGGCGTTTCTAAAAAGCGCCA
* *
31846513 CTAAAAATTAAAGTTCTAATCCAAAACGGCGCCGTTTAATAAAGCTTTAATGCACATTTCTGGCT
131 CTAAAAATTAAAGTTCTAATCCGAAACGGCGCCGTTTAATAAAGCTTTAATGCACATTTCTGGCA
*
31846578 TTTTCTGTAAAAACGCCACTAAAATTTAATTTGCTTAAGCTAAACGTCGTCGTTTAGCCAATATT
196 TTTTCTGTAAAAACGCCACTAAAATTTAATTTGCTTAAGCTAAACGGCGTCGTTTAGCCAATATT
* * * * *
31846643 TTAAGTCGCTTTTGCGGTGTTTCCTAAACAAAACGCCACTATAAATTAACAGAAACAGCGTCGTT
261 TTAAGTCACTTTTGCGGCGTTTCCTGAACAAAACGCCACTATAAATTAACAGAAACGGCGCCGTT
31846708 GGATTAATATAG
326 GGATTAATATAG
* * * **
31846720 AGAAAATGCTAAGTTAAAATTAGTGTATAGAAACAGCGTCGTTTAGCCAAAATACTAAGACACTT
1 AGAAAATACTAAGTTAAAATTAGTGTACAGAAACGGCGTCGTTTAGCCAAAATTTTAAGACACTT
* * * *
31846785 TTGCGGCGTTTCTCGAATAAACGCCGCAATTGCTTGTACATTT-CCGGTGTTTCTAAGAAGCGCC
66 TTGCGGCGTTTCTAGAA-AAACGCCGCTATTGCTTGTACATTTGCCGGCGTTTCTAAAAAGCGCC
*
31846849 AATAAAAATTAAAGTTCTAATCCGAAACGGCGCCGTTTAATAAAGCTTTAATGCACATTTCTGGC
130 ACTAAAAATTAAAGTTCTAATCCGAAACGGCGCCGTTTAATAAAGCTTTAATGCACATTTCTGGC
* * *
31846914 ATTTTCTTTAAAAACGCCACTAACAA-TTAATTTTCTTAAGCTAAACGGCATCGTTTAGCCAATA
195 ATTTTCTGTAAAAACGCCACTAA-AATTTAATTTGCTTAAGCTAAACGGCGTCGTTTAGCCAATA
* * *
31846978 TTTTAAGTCACTATTGCGGCGTTTCATGAAC-AAACGCCACTAAAAATTAACAGAAACGGCGCCG
259 TTTTAAGTCACTTTTGCGGCGTTTCCTGAACAAAACGCCACTATAAATTAACAGAAACGGCGCCG
31847042 TT
324 TT
31847044 TTATTAAGCT
Statistics
Matches: 915, Mismatches: 76, Indels: 13
0.91 0.08 0.01
Matches are distributed among these distances:
336 310 0.34
337 599 0.65
338 6 0.01
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (337 bp):
AGAAAATACTAAGTTAAAATTAGTGTACAGAAACGGCGTCGTTTAGCCAAAATTTTAAGACACTT
TTGCGGCGTTTCTAGAAAAACGCCGCTATTGCTTGTACATTTGCCGGCGTTTCTAAAAAGCGCCA
CTAAAAATTAAAGTTCTAATCCGAAACGGCGCCGTTTAATAAAGCTTTAATGCACATTTCTGGCA
TTTTCTGTAAAAACGCCACTAAAATTTAATTTGCTTAAGCTAAACGGCGTCGTTTAGCCAATATT
TTAAGTCACTTTTGCGGCGTTTCCTGAACAAAACGCCACTATAAATTAACAGAAACGGCGCCGTT
GGATTAATATAG
Found at i:31846997 original size:673 final size:673
Alignment explanation
Indices: 31845710--31847036 Score: 2095
Period size: 673 Copynumber: 2.0 Consensus size: 673
31845700 TAATAGAAAT
* * *
31845710 AGAAAATGCTAAGTTAAAATTGGTGTACATAAACGGCGTCGTTTAGCCAAAATTTTAAGACACTT
1 AGAAAATACTAAGTTAAAATTGGTGTACAGAAACGACGTCGTTTAGCCAAAATTTTAAGACACTT
*
31845775 TTGCGGCGTTTCTAAAAAAACGCCGCTATTTCTTGTACATTTGCAGCGCTTCTAGAAAAGCGCCA
66 TTGCGGCGTTTCTAAAAAAACGCCGCTATTGCTTGTACATTTGCAGCGCTTCTAGAAAAGCGCCA
*** *
31845840 CTAAAAAGCAAAGTTCTAATTTGAAACGGCGTCGTTTAATAAAGCTTTAATGCACATTTCTGGCA
131 CTAAAAAGCAAAGTTCTAATCCAAAACGGCGCCGTTTAATAAAGCTTTAATGCACATTTCTGGCA
31845905 TTTTCTGTAAAAACGCCACTAAAATTTAATTTGCTTAAGCTAAACGGCGTCGTTTAGCCAATATT
196 TTTTCTGTAAAAACGCCACTAAAATTTAATTTGCTTAAGCTAAACGGCGTCGTTTAGCCAATATT
* * **
31845970 TTAAGTCACTTTTGCGGCGTTTCCTGAACAAAATGCCACTATAAATTAACAGAAATGGCGCCATT
261 TTAAGTCACTTTTGCGGCGTTTCCTAAACAAAACGCCACTATAAATTAACAGAAACAGCGCCATT
* * *
31846035 GGATTAATATAGAGAAAATACTAAGTTAAAATTCGTGTACAAAAACGGTGTCGTTTAGCCAAAAT
326 GGATTAATATAGAGAAAATACTAAGTTAAAATTAGTGTACAAAAACAGCGTCGTTTAGCCAAAAT
** *
31846100 TTTAAGACACTTTTGCGGCGTTTCTAGAAAAACGCCGCTATTGCTTGTACATTTGCCGGGTTTCT
391 ACTAAGACACTTTTGCGGCGTTTCTAGAAAAACGCCGCAATTGCTTGTACATTTGCCGGGTTTCT
* * *
31846165 TAAAAATCGCCACTAAAAATTAAAGTTCTAATCCGAAACGGTGCCGTTTAATAAAGCTTTAATGC
456 TAAAAAGCGCCAATAAAAATTAAAGTTCTAATCCGAAACGGCGCCGTTTAATAAAGCTTTAATGC
* * *
31846230 ACATTTTTGGCGCTTTCTGTAAAAACGCCACTAAAATTTAATTTGCTTAAGCTAAACAACGTCGT
521 ACATTTCTGGCACTTTCTGTAAAAACGCCACTAAAATTTAATTTGCTTAAGCTAAACAACATCGT
* * * *
31846295 TTACCCAATATTTTAAGTCATTTTTGCGGCGTTTCCTGAACAAAACCCCACTATAAATTAACAGA
586 TTACCCAATATTTTAAGTCACTATTGCGGCGTTTCATGAAC-AAACCCCACTAAAAATTAACAGA
31846360 AACGGTGTCGTTGGATTAATATAG
650 AACGGTGTCGTTGGATTAATATAG
* *
31846384 AGAAAATACTAAGTTAAAATTTGTGTACAGAAACGATGTCGTTTAGCCAAAATTTTAAGACACTT
1 AGAAAATACTAAGTTAAAATTGGTGTACAGAAACGACGTCGTTTAGCCAAAATTTTAAGACACTT
* * * * *
31846449 TTGCGGCGTTTCTAGAAAAATGCCGCTATTGCTTGTACATTTGCGGCGTTTCTA-AGAAGCGCCA
66 TTGCGGCGTTTCTAAAAAAACGCCGCTATTGCTTGTACATTTGCAGCGCTTCTAGAAAAGCGCCA
** *
31846513 CTAAAAATTAAAGTTCTAATCCAAAACGGCGCCGTTTAATAAAGCTTTAATGCACATTTCTGGCT
131 CTAAAAAGCAAAGTTCTAATCCAAAACGGCGCCGTTTAATAAAGCTTTAATGCACATTTCTGGCA
*
31846578 TTTTCTGTAAAAACGCCACTAAAATTTAATTTGCTTAAGCTAAACGTCGTCGTTTAGCCAATATT
196 TTTTCTGTAAAAACGCCACTAAAATTTAATTTGCTTAAGCTAAACGGCGTCGTTTAGCCAATATT
* * * *
31846643 TTAAGTCGCTTTTGCGGTGTTTCCTAAACAAAACGCCACTATAAATTAACAGAAACAGCGTCGTT
261 TTAAGTCACTTTTGCGGCGTTTCCTAAACAAAACGCCACTATAAATTAACAGAAACAGCGCCATT
* * *
31846708 GGATTAATATAGAGAAAATGCTAAGTTAAAATTAGTGTATAGAAACAGCGTCGTTTAGCCAAAAT
326 GGATTAATATAGAGAAAATACTAAGTTAAAATTAGTGTACAAAAACAGCGTCGTTTAGCCAAAAT
*
31846773 ACTAAGACACTTTTGCGGCGTTTCTCGAATAAACGCCGCAATTGCTTGTACATTT-CCGGTGTTT
391 ACTAAGACACTTTTGCGGCGTTTCTAGAA-AAACGCCGCAATTGCTTGTACATTTGCCGG-GTTT
*
31846837 C-TAAGAAGCGCCAATAAAAATTAAAGTTCTAATCCGAAACGGCGCCGTTTAATAAAGCTTTAAT
454 CTTAAAAAGCGCCAATAAAAATTAAAGTTCTAATCCGAAACGGCGCCGTTTAATAAAGCTTTAAT
* * * **
31846901 GCACATTTCTGGCATTTTCTTTAAAAACGCCACTAACAA-TTAATTTTCTTAAGCTAAACGGCAT
519 GCACATTTCTGGCACTTTCTGTAAAAACGCCACTAA-AATTTAATTTGCTTAAGCTAAACAACAT
* *
31846965 CGTTTAGCCAATATTTTAAGTCACTATTGCGGCGTTTCATGAACAAACGCCACTAAAAATTAACA
583 CGTTTACCCAATATTTTAAGTCACTATTGCGGCGTTTCATGAACAAACCCCACTAAAAATTAACA
31847030 GAAACGG
648 GAAACGG
31847037 CGCCGTTTTA
Statistics
Matches: 595, Mismatches: 55, Indels: 8
0.90 0.08 0.01
Matches are distributed among these distances:
672 26 0.04
673 429 0.72
674 140 0.24
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.31
Consensus pattern (673 bp):
AGAAAATACTAAGTTAAAATTGGTGTACAGAAACGACGTCGTTTAGCCAAAATTTTAAGACACTT
TTGCGGCGTTTCTAAAAAAACGCCGCTATTGCTTGTACATTTGCAGCGCTTCTAGAAAAGCGCCA
CTAAAAAGCAAAGTTCTAATCCAAAACGGCGCCGTTTAATAAAGCTTTAATGCACATTTCTGGCA
TTTTCTGTAAAAACGCCACTAAAATTTAATTTGCTTAAGCTAAACGGCGTCGTTTAGCCAATATT
TTAAGTCACTTTTGCGGCGTTTCCTAAACAAAACGCCACTATAAATTAACAGAAACAGCGCCATT
GGATTAATATAGAGAAAATACTAAGTTAAAATTAGTGTACAAAAACAGCGTCGTTTAGCCAAAAT
ACTAAGACACTTTTGCGGCGTTTCTAGAAAAACGCCGCAATTGCTTGTACATTTGCCGGGTTTCT
TAAAAAGCGCCAATAAAAATTAAAGTTCTAATCCGAAACGGCGCCGTTTAATAAAGCTTTAATGC
ACATTTCTGGCACTTTCTGTAAAAACGCCACTAAAATTTAATTTGCTTAAGCTAAACAACATCGT
TTACCCAATATTTTAAGTCACTATTGCGGCGTTTCATGAACAAACCCCACTAAAAATTAACAGAA
ACGGTGTCGTTGGATTAATATAG
Found at i:31848489 original size:40 final size:41
Alignment explanation
Indices: 31848419--31848530 Score: 109
Period size: 40 Copynumber: 2.8 Consensus size: 41
31848409 GCGCTTTATC
** **
31848419 AAAAACGCCGCTACTACAGCGAGCATTAGCGACGCAACACA
1 AAAAACGCCGCTAAAACCCCGAGCATTAGCGACGCAACACA
* * ** **
31848460 AAAAACGCCGCTAAAGCCCCGAGCA-TAGCGGCGCATTATT
1 AAAAACGCCGCTAAAACCCCGAGCATTAGCGACGCAACACA
* *
31848500 ATAAACGCCGCTAAAACCTCGAGCATTAGCG
1 AAAAACGCCGCTAAAACCCCGAGCATTAGCG
31848531 GCGATATTCT
Statistics
Matches: 57, Mismatches: 13, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
40 32 0.56
41 25 0.44
ACGTcount: A:0.36, C:0.30, G:0.21, T:0.13
Consensus pattern (41 bp):
AAAAACGCCGCTAAAACCCCGAGCATTAGCGACGCAACACA
Found at i:31857803 original size:21 final size:21
Alignment explanation
Indices: 31857779--31857819 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
31857769 GCCTAAGATG
* *
31857779 TGAATTGAATTGAATTGAATA
1 TGAACTGAATTAAATTGAATA
*
31857800 TGAACTGTATTAAATTGAAT
1 TGAACTGAATTAAATTGAAT
31857820 TAAATTTACT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.41, C:0.02, G:0.17, T:0.39
Consensus pattern (21 bp):
TGAACTGAATTAAATTGAATA
Found at i:31860434 original size:21 final size:21
Alignment explanation
Indices: 31860410--31860450 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
31860400 TAAGATAAAT
31860410 AAATATTTATC-TTAATATTTA
1 AAATATTTATCATT-ATATTTA
*
31860431 AAATTTTTATCATTATATTT
1 AAATATTTATCATTATATTT
31860451 TTTTTAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.56
Consensus pattern (21 bp):
AAATATTTATCATTATATTTA
Found at i:31865678 original size:19 final size:20
Alignment explanation
Indices: 31865647--31865687 Score: 75
Period size: 19 Copynumber: 2.1 Consensus size: 20
31865637 GTGCTGAATA
31865647 TAAGTATGTAATTACATGCT
1 TAAGTATGTAATTACATGCT
31865667 TAAGTA-GTAATTACATGCT
1 TAAGTATGTAATTACATGCT
31865686 TA
1 TA
31865688 TGTTATTCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.37, C:0.10, G:0.15, T:0.39
Consensus pattern (20 bp):
TAAGTATGTAATTACATGCT
Found at i:31867597 original size:19 final size:19
Alignment explanation
Indices: 31867573--31867612 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
31867563 CTTGGAGCGA
31867573 ACGGATCGCCTAAAGCCGT
1 ACGGATCGCCTAAAGCCGT
31867592 ACGGATCGCCTAAAGCCGT
1 ACGGATCGCCTAAAGCCGT
31867611 AC
1 AC
31867613 AGATTGCGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.28, C:0.33, G:0.25, T:0.15
Consensus pattern (19 bp):
ACGGATCGCCTAAAGCCGT
Found at i:31868990 original size:22 final size:23
Alignment explanation
Indices: 31868962--31869004 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
31868952 AAATGCCCTC
31868962 TTTTATTATTCA-ATTTATTGGA
1 TTTTATTATTCATATTTATTGGA
*
31868984 TTTTATTATTCATTTTTATTG
1 TTTTATTATTCATATTTATTG
31869005 AAAATAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.23, C:0.05, G:0.07, T:0.65
Consensus pattern (23 bp):
TTTTATTATTCATATTTATTGGA
Found at i:31870944 original size:21 final size:21
Alignment explanation
Indices: 31870918--31870964 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
31870908 AATAAACACC
*
31870918 AAAAATTTATTTTAAAAATAA
1 AAAAATATATTTTAAAAATAA
*
31870939 AAAAATATATTTTAAAATTAA
1 AAAAATATATTTTAAAAATAA
31870960 AAAAA
1 AAAAA
31870965 ATTAAAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (21 bp):
AAAAATATATTTTAAAAATAA
Found at i:31870972 original size:30 final size:29
Alignment explanation
Indices: 31870931--31871010 Score: 92
Period size: 30 Copynumber: 2.7 Consensus size: 29
31870921 AATTTATTTT
31870931 AAAAATAAAAAAATA-TATTTTAAAATTAAA
1 AAAAATAAAAAAA-AGTATTTTAAAA-TAAA
*
31870961 AAAAATTAAAAAAAGTATTTTAAAATAAA
1 AAAAATAAAAAAAAGTATTTTAAAATAAA
*
31870990 AAATAA-AAAATAAAAATATTT
1 AAA-AATAAAA-AAAAGTATTT
31871011 ATTATATTCG
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
29 11 0.25
30 33 0.75
ACGTcount: A:0.70, C:0.00, G:0.01, T:0.29
Consensus pattern (29 bp):
AAAAATAAAAAAAAGTATTTTAAAATAAA
Found at i:31871553 original size:8 final size:8
Alignment explanation
Indices: 31871542--31871566 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
31871532 TACTATTTAA
31871542 AAAATATT
1 AAAATATT
31871550 AAAATATT
1 AAAATATT
31871558 AAAATATT
1 AAAATATT
31871566 A
1 A
31871567 TCTTTTAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (8 bp):
AAAATATT
Found at i:31873668 original size:24 final size:28
Alignment explanation
Indices: 31873618--31873668 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 28
31873608 CTACGATGAC
*
31873618 TAATTAATTTAATTTTCACTTCGAATTT
1 TAATTAATTTAATTTGCACTTCGAATTT
31873646 TAATT-ATTT-ATTTGCA-TTC-AATT
1 TAATTAATTTAATTTGCACTTCGAATT
31873669 CAATAATAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
24 4 0.18
25 3 0.14
26 6 0.27
27 4 0.18
28 5 0.23
ACGTcount: A:0.31, C:0.10, G:0.04, T:0.55
Consensus pattern (28 bp):
TAATTAATTTAATTTGCACTTCGAATTT
Found at i:31877512 original size:16 final size:15
Alignment explanation
Indices: 31877491--31877529 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
31877481 TTAAATTATG
*
31877491 GATATGTGTGTATTGT
1 GATATGTGTGTA-TAT
*
31877507 GATATGTGTTTATAT
1 GATATGTGTGTATAT
31877522 GATATGTG
1 GATATGTG
31877530 ACCATTATGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 10 0.48
16 11 0.52
ACGTcount: A:0.23, C:0.00, G:0.28, T:0.49
Consensus pattern (15 bp):
GATATGTGTGTATAT
Found at i:31877605 original size:39 final size:35
Alignment explanation
Indices: 31877562--31877659 Score: 124
Period size: 35 Copynumber: 2.7 Consensus size: 35
31877552 AACATGTTTT
*
31877562 TGAGTATTGTGATATATGCTTGAATGTTATGTGATTATA
1 TGAGTATTGTGATATATGCTTAAATG---T-TGATTATA
*
31877601 TGAGTATTGTGATATATGCTTAAATGTTGCTTATA
1 TGAGTATTGTGATATATGCTTAAATGTTGATTATA
* *
31877636 TGTGTAATGTGATATATGCTTAAA
1 TGAGTATTGTGATATATGCTTAAA
31877660 AGTGAATATG
Statistics
Matches: 55, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
35 29 0.53
36 1 0.02
39 25 0.45
ACGTcount: A:0.30, C:0.04, G:0.21, T:0.45
Consensus pattern (35 bp):
TGAGTATTGTGATATATGCTTAAATGTTGATTATA
Found at i:31885465 original size:24 final size:24
Alignment explanation
Indices: 31885432--31885481 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
31885422 GATTTATTTC
31885432 TTTTGAAAGACCTACTTTGTATCT
1 TTTTGAAAGACCTACTTTGTATCT
*
31885456 TTTTGGAAGACCTACTTTGTATCT
1 TTTTGAAAGACCTACTTTGTATCT
31885480 TT
1 TT
31885482 CACTATTTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.22, C:0.16, G:0.14, T:0.48
Consensus pattern (24 bp):
TTTTGAAAGACCTACTTTGTATCT
Found at i:31888499 original size:15 final size:15
Alignment explanation
Indices: 31888476--31888506 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
31888466 TTACACTAAC
*
31888476 TATAGTATTTAAAAA
1 TATAATATTTAAAAA
31888491 TATAATATTTAAAAA
1 TATAATATTTAAAAA
31888506 T
1 T
31888507 GAAAGGTGTG
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:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (15 bp):
TATAATATTTAAAAA
Found at i:31892456 original size:109 final size:107
Alignment explanation
Indices: 31892292--31892613 Score: 448
Period size: 109 Copynumber: 3.0 Consensus size: 107
31892282 GATTAAGATA
* * * *
31892292 TAAAAGGATATTTGGCTATTTGGTCCAACGAGAAAATCGAAACCCAGCTCATTAGGGCACGTTTC
1 TAAAAGGATATTTGGCTATTAGGTCGAACGAGAAAATCGAAACCCAACACATTAGGGCACGTTT-
31892357 CTCGAATTTCCAAGA-GCAAAACATTGCCTTATTTTGAAATTTTT
65 CTCGAATTTCCAA-ACGCAAAACATTGCCTTATTTTGAAA-TTTT
* * * *
31892401 TAAAAGGATATTCGACTATCAGGTCGAACGAGAAAATCGAAACCCAACACATTAGGGTACGTTTT
1 TAAAAGGATATTTGGCTATTAGGTCGAACGAGAAAATCGAAACCCAACACATTAGGGCACG-TTT
*
31892466 CTCGTATTTCCAAACGCAAAACATTGCCTTATTTTGAAATTTT
65 CTCGAATTTCCAAACGCAAAACATTGCCTTATTTTGAAATTTT
*
31892509 TAAAAGGATATTTGGCAATTAGGTCGAACGAGAAAAATCGAAACCCAACACATTAGGGCACGCTT
1 TAAAAGGATATTTGGCTATTAGGTCGAACGAG-AAAATCGAAACCCAACACATTAGGGCACG-TT
* * * * *
31892574 TCTCGAACTTCAAAATGCAAAATATTGCCTTATTTAGAAA
64 TCTCGAATTTCCAAACGCAAAACATTGCCTTATTTTGAAA
31892614 AATTTTCTTT
Statistics
Matches: 189, Mismatches: 21, Indels: 6
0.88 0.10 0.03
Matches are distributed among these distances:
108 33 0.17
109 153 0.81
110 3 0.02
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.29
Consensus pattern (107 bp):
TAAAAGGATATTTGGCTATTAGGTCGAACGAGAAAATCGAAACCCAACACATTAGGGCACGTTTC
TCGAATTTCCAAACGCAAAACATTGCCTTATTTTGAAATTTT
Found at i:31892664 original size:21 final size:21
Alignment explanation
Indices: 31892640--31892685 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
31892630 GTATGGTGTT
* *
31892640 AATATGCATGATG-GAATAATA
1 AATATG-ATAATGTGAATAAAA
31892661 AATATGATAATGTGAATAAAA
1 AATATGATAATGTGAATAAAA
31892682 AATA
1 AATA
31892686 ATATGAGCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 5 0.23
21 17 0.77
ACGTcount: A:0.54, C:0.02, G:0.15, T:0.28
Consensus pattern (21 bp):
AATATGATAATGTGAATAAAA
Found at i:31893266 original size:3 final size:3
Alignment explanation
Indices: 31893250--31893283 Score: 50
Period size: 3 Copynumber: 11.0 Consensus size: 3
31893240 AAAATAAAAC
*
31893250 TAA TAA TAGT TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA
31893284 ACTAAATAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 26 0.93
4 2 0.07
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:31893585 original size:53 final size:53
Alignment explanation
Indices: 31893505--31893611 Score: 205
Period size: 53 Copynumber: 2.0 Consensus size: 53
31893495 AAGAAAAGAA
31893505 AGAAAAGAGGGGCAAATTGCAATACGCCGCAAAATCGGAGGAACTGCGCGCAC
1 AGAAAAGAGGGGCAAATTGCAATACGCCGCAAAATCGGAGGAACTGCGCGCAC
*
31893558 AGAAAAGAGGGGCAAATTGCAATACGCCGCAAAATCGGAGGGACTGCGCGCAC
1 AGAAAAGAGGGGCAAATTGCAATACGCCGCAAAATCGGAGGAACTGCGCGCAC
31893611 A
1 A
31893612 AATAGCCCAA
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.37, C:0.22, G:0.31, T:0.09
Consensus pattern (53 bp):
AGAAAAGAGGGGCAAATTGCAATACGCCGCAAAATCGGAGGAACTGCGCGCAC
Found at i:31895387 original size:21 final size:22
Alignment explanation
Indices: 31895346--31895387 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
31895336 TTTTATTTTT
*
31895346 AAAATCATGAAAAGAATTATAG
1 AAAATCATGAAAAGAAATATAG
*
31895368 AAAATCAT-AAAATAAATATA
1 AAAATCATGAAAAGAAATATA
31895388 TCATACAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.64, C:0.05, G:0.07, T:0.24
Consensus pattern (22 bp):
AAAATCATGAAAAGAAATATAG
Found at i:31895443 original size:36 final size:33
Alignment explanation
Indices: 31895390--31895493 Score: 95
Period size: 37 Copynumber: 3.0 Consensus size: 33
31895380 TAAATATATC
*
31895390 ATACAAAAATATTTAAAAATTTAAAAAATATAGAAA
1 ATACAAAAA-ATGTAAAAA-TTAAAAAATATA-AAA
*
31895426 ATACAAAAAAGTGTAAAAAATTATAAAATTATTAAAA
1 ATACAAAAAA-TGT-AAAAATTA-AAAAATA-TAAAA
*
31895463 ATGA-AAAAAATGTTAAAA-TAAAAAATATAAA
1 AT-ACAAAAAATGTAAAAATTAAAAAATATAAA
31895494 TTATATAAAC
Statistics
Matches: 59, Mismatches: 4, Indels: 14
0.77 0.05 0.18
Matches are distributed among these distances:
32 4 0.07
33 6 0.10
34 2 0.03
35 5 0.08
36 17 0.29
37 22 0.37
38 3 0.05
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (33 bp):
ATACAAAAAATGTAAAAATTAAAAAATATAAAA
Found at i:31895453 original size:27 final size:26
Alignment explanation
Indices: 31895404--31895487 Score: 73
Period size: 27 Copynumber: 3.2 Consensus size: 26
31895394 AAAAATATTT
* *
31895404 AAAAATTTAAAAAATATAGAAAATACA
1 AAAAATGTAAAAAATATATAAAATA-A
*
31895431 AAAAAGTGTAAAAAAT-TATAAAATTATT
1 AAAAA-TGTAAAAAATATATAAAA-TA-A
* *
31895459 AAAAATGAAAAAAATGT-TAAAATAA
1 AAAAATGTAAAAAATATATAAAATAA
31895484 AAAA
1 AAAA
31895488 TATAAATTAT
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
25 4 0.08
26 2 0.04
27 25 0.52
28 17 0.35
ACGTcount: A:0.69, C:0.01, G:0.06, T:0.24
Consensus pattern (26 bp):
AAAAATGTAAAAAATATATAAAATAA
Found at i:31895525 original size:16 final size:16
Alignment explanation
Indices: 31895450--31895526 Score: 50
Period size: 16 Copynumber: 4.8 Consensus size: 16
31895440 AAAAAATTAT
*
31895450 AAAATTATTAAAAATGA
1 AAAATTATGAAAAAT-A
* *
31895467 AAAA-AATGTTAAAATA
1 AAAATTATG-AAAAATA
* *
31895483 AAAAATAT-AAATTATA
1 AAAATTATGAAA-AATA
* *
31895499 TAAACTATGAAAAATA
1 AAAATTATGAAAAATA
31895515 AAAATTATGAAA
1 AAAATTATGAAA
31895527 TAATGTTTTA
Statistics
Matches: 45, Mismatches: 11, Indels: 9
0.69 0.17 0.14
Matches are distributed among these distances:
15 2 0.04
16 29 0.64
17 14 0.31
ACGTcount: A:0.66, C:0.01, G:0.05, T:0.27
Consensus pattern (16 bp):
AAAATTATGAAAAATA
Found at i:31895898 original size:25 final size:26
Alignment explanation
Indices: 31895863--31895924 Score: 69
Period size: 24 Copynumber: 2.5 Consensus size: 26
31895853 TTTTTCTATA
31895863 TTTTC-ATAATTTTTA-AAACTTTAT
1 TTTTCTATAATTTTTATAAACTTTAT
* **
31895887 TTTTCTATAATTTCTATAATTTTTAT
1 TTTTCTATAATTTTTATAAACTTTAT
31895913 TTTT-T-TAATTTT
1 TTTTCTATAATTTT
31895925 AATATTTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
24 11 0.34
25 10 0.31
26 11 0.34
ACGTcount: A:0.27, C:0.06, G:0.00, T:0.66
Consensus pattern (26 bp):
TTTTCTATAATTTTTATAAACTTTAT
Found at i:31895921 original size:15 final size:16
Alignment explanation
Indices: 31895903--31895937 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
31895893 ATAATTTCTA
*
31895903 TAATTTTTAT-TTTTT
1 TAATTTTAATATTTTT
31895918 TAATTTTAATATTTTT
1 TAATTTTAATATTTTT
31895934 TAAT
1 TAAT
31895938 ATGTTATGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TAATTTTAATATTTTT
Found at i:31896065 original size:26 final size:27
Alignment explanation
Indices: 31896036--31896104 Score: 72
Period size: 26 Copynumber: 2.6 Consensus size: 27
31896026 CACTTTTCTA
*
31896036 TATTTTTCATAAATTTT-TTATTTTT-T
1 TATTTTTCAT-AATTTTAATATTTTTAT
* *
31896062 TATTTTTTATGATTTTAATATTTTTAT
1 TATTTTTCATAATTTTAATATTTTTAT
31896089 TATTTTAT-ATAATTTT
1 TATTTT-TCATAATTTT
31896105 TATTGAATTT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
25 5 0.14
26 16 0.44
27 14 0.39
28 1 0.03
ACGTcount: A:0.26, C:0.01, G:0.01, T:0.71
Consensus pattern (27 bp):
TATTTTTCATAATTTTAATATTTTTAT
Found at i:31896069 original size:17 final size:17
Alignment explanation
Indices: 31896049--31896105 Score: 51
Period size: 18 Copynumber: 3.2 Consensus size: 17
31896039 TTTTCATAAA
**
31896049 TTTTTTATTTTTTTATT
1 TTTTTTATTTTAATATT
*
31896066 TTTTATGATTTTAATATT
1 TTTT-TTATTTTAATATT
*
31896084 TTTATTATTTTATATAATT
1 TTTTTTATTTTA-AT-ATT
31896103 TTT
1 TTT
31896106 ATTGAATTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
17 11 0.34
18 15 0.47
19 6 0.19
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.75
Consensus pattern (17 bp):
TTTTTTATTTTAATATT
Found at i:31896083 original size:18 final size:18
Alignment explanation
Indices: 31896065--31896107 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
31896055 ATTTTTTTAT
31896065 TTTTTATGATTTTA-ATA
1 TTTTTATGATTTTATATA
*
31896082 TTTTTATTATTTTATATAA
1 TTTTTATGATTTTATAT-A
31896101 TTTTTAT
1 TTTTTAT
31896108 TGAATTTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 13 0.57
18 2 0.09
19 8 0.35
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (18 bp):
TTTTTATGATTTTATATA
Found at i:31896103 original size:27 final size:26
Alignment explanation
Indices: 31896054--31896104 Score: 75
Period size: 27 Copynumber: 1.9 Consensus size: 26
31896044 ATAAATTTTT
* *
31896054 TATTTTTTTATTTTTTATGATTTTAA
1 TATTTTTTTATTTTATATAATTTTAA
31896080 TATTTTTATTATTTTATATAATTTT
1 TATTTTT-TTATTTTATATAATTTT
31896105 TATTGAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (26 bp):
TATTTTTTTATTTTATATAATTTTAA
Found at i:31904882 original size:24 final size:24
Alignment explanation
Indices: 31904850--31904897 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
31904840 TTTATTGCAA
31904850 TATTGAGTGGCTTGACCACAACGT
1 TATTGAGTGGCTTGACCACAACGT
*
31904874 TATTGAGTGGCTTGACCATAACGT
1 TATTGAGTGGCTTGACCACAACGT
31904898 GCAACTTGTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (24 bp):
TATTGAGTGGCTTGACCACAACGT
Found at i:31904985 original size:63 final size:63
Alignment explanation
Indices: 31904845--31904999 Score: 195
Period size: 63 Copynumber: 2.5 Consensus size: 63
31904835 GTAGTTTTAT
*
31904845 TGCAATATTGAGTGGCTTGACCACAACGTTATTGAGTGGCTTGACCATAACGTGCAACTTGTC
1 TGCAATATTGAGTGGCTTGACCACAACGTTATTGAGTGGCTTGACCATAACGAGCAACTTGTC
* * * * ** * * *
31904908 TGCGATAGTGAGTGG-TTTAGCCATAACGTTATTTTGTGGTTTGACCATAATGAGTAACTTGTC
1 TGCAATATTGAGTGGCTTGA-CCACAACGTTATTGAGTGGCTTGACCATAACGAGCAACTTGTC
*
31904971 TGCAATATTCAGTGGCTTGACCACAACGT
1 TGCAATATTGAGTGGCTTGACCACAACGT
31905000 GCAACTTGAA
Statistics
Matches: 75, Mismatches: 15, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
62 3 0.04
63 69 0.92
64 3 0.04
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.33
Consensus pattern (63 bp):
TGCAATATTGAGTGGCTTGACCACAACGTTATTGAGTGGCTTGACCATAACGAGCAACTTGTC
Found at i:31922628 original size:28 final size:26
Alignment explanation
Indices: 31922596--31922649 Score: 81
Period size: 28 Copynumber: 2.0 Consensus size: 26
31922586 GAAGCTAACT
31922596 AAACTATCAACTAAAACCAACTAAAAAA
1 AAACTATCAACTAAAACC--CTAAAAAA
*
31922624 AAACTATGAACTAAAACCCTAAAAAA
1 AAACTATCAACTAAAACCCTAAAAAA
31922650 TAAGGAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 8 0.32
28 17 0.68
ACGTcount: A:0.63, C:0.20, G:0.02, T:0.15
Consensus pattern (26 bp):
AAACTATCAACTAAAACCCTAAAAAA
Found at i:31924411 original size:25 final size:26
Alignment explanation
Indices: 31924378--31924437 Score: 86
Period size: 26 Copynumber: 2.3 Consensus size: 26
31924368 GAATTTTCCC
31924378 AAAATTTTATCGG-GGTAAAATCGTA
1 AAAATTTTATCGGCGGTAAAATCGTA
* * *
31924403 AAAAATTTATCGGCGGTGAAATCGTC
1 AAAATTTTATCGGCGGTAAAATCGTA
31924429 AAAATTTTA
1 AAAATTTTA
31924438 CTGGAGTAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
25 12 0.40
26 18 0.60
ACGTcount: A:0.40, C:0.10, G:0.18, T:0.32
Consensus pattern (26 bp):
AAAATTTTATCGGCGGTAAAATCGTA
Found at i:31924648 original size:28 final size:28
Alignment explanation
Indices: 31924616--31924708 Score: 73
Period size: 28 Copynumber: 3.2 Consensus size: 28
31924606 ATATAACATG
31924616 AAGGGGGCGGCAACCCTAGTAGAAATAC
1 AAGGGGGCGGCAACCCTAGTAGAAATAC
* * * * *
31924644 AAGGGTGAGTCATTCACCTCTCA-TATAACAT-G
1 AAGGGGGCGGCA---ACC-CT-AGTAGAA-ATAC
31924676 AAGGGGGCGGCAACCCTAGTAGAAATAC
1 AAGGGGGCGGCAACCCTAGTAGAAATAC
31924704 AAGGG
1 AAGGG
31924709 TGAGTCATTC
Statistics
Matches: 47, Mismatches: 10, Indels: 16
0.64 0.14 0.22
Matches are distributed among these distances:
27 3 0.06
28 20 0.43
29 3 0.06
31 3 0.06
32 15 0.32
33 3 0.06
ACGTcount: A:0.34, C:0.20, G:0.29, T:0.16
Consensus pattern (28 bp):
AAGGGGGCGGCAACCCTAGTAGAAATAC
Found at i:31924692 original size:60 final size:60
Alignment explanation
Indices: 31924599--31924721 Score: 246
Period size: 60 Copynumber: 2.0 Consensus size: 60
31924589 GAGGCCTAAA
31924599 ACCTCTCATATAACATGAAGGGGGCGGCAACCCTAGTAGAAATACAAGGGTGAGTCATTC
1 ACCTCTCATATAACATGAAGGGGGCGGCAACCCTAGTAGAAATACAAGGGTGAGTCATTC
31924659 ACCTCTCATATAACATGAAGGGGGCGGCAACCCTAGTAGAAATACAAGGGTGAGTCATTC
1 ACCTCTCATATAACATGAAGGGGGCGGCAACCCTAGTAGAAATACAAGGGTGAGTCATTC
31924719 ACC
1 ACC
31924722 CCTCTCCTAC
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 63 1.00
ACGTcount: A:0.33, C:0.23, G:0.24, T:0.20
Consensus pattern (60 bp):
ACCTCTCATATAACATGAAGGGGGCGGCAACCCTAGTAGAAATACAAGGGTGAGTCATTC
Found at i:31926215 original size:7 final size:7
Alignment explanation
Indices: 31926203--31926235 Score: 57
Period size: 7 Copynumber: 4.6 Consensus size: 7
31926193 CAAAACTCGG
31926203 AATAATA
1 AATAATA
31926210 AATAATAA
1 AATAAT-A
31926218 AATAATA
1 AATAATA
31926225 AATAATA
1 AATAATA
31926232 AATA
1 AATA
31926236 CAATATTGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
7 18 0.72
8 7 0.28
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (7 bp):
AATAATA
Found at i:31926223 original size:15 final size:15
Alignment explanation
Indices: 31926203--31926233 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
31926193 CAAAACTCGG
31926203 AATAATAAATAATAA
1 AATAATAAATAATAA
31926218 AATAATAAATAATAA
1 AATAATAAATAATAA
31926233 A
1 A
31926234 TACAATATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (15 bp):
AATAATAAATAATAA
Found at i:31927137 original size:21 final size:24
Alignment explanation
Indices: 31927085--31927146 Score: 79
Period size: 24 Copynumber: 2.6 Consensus size: 24
31927075 TCACAAATTT
* *
31927085 CACTATCACTATCATCATAGTTTG
1 CACTATTACAATCATCATAGTTTG
**
31927109 CACTATTACAATCATCATAGTTCA
1 CACTATTACAATCATCATAGTTTG
*
31927133 CATTATTACAATCA
1 CACTATTACAATCA
31927147 ACTTCTTCAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.35, C:0.24, G:0.05, T:0.35
Consensus pattern (24 bp):
CACTATTACAATCATCATAGTTTG
Found at i:31927940 original size:12 final size:12
Alignment explanation
Indices: 31927923--31927947 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
31927913 ATTTTATAAC
31927923 ATAAATATTGTT
1 ATAAATATTGTT
31927935 ATAAATATTGTT
1 ATAAATATTGTT
31927947 A
1 A
31927948 ATATCCTCTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (12 bp):
ATAAATATTGTT
Found at i:31935696 original size:2 final size:2
Alignment explanation
Indices: 31935689--31935733 Score: 63
Period size: 2 Copynumber: 22.5 Consensus size: 2
31935679 ACATTCCTTT
* * *
31935689 GA GA GA GA GT GT GA GA GA GA GA GA GA GG GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
31935731 GA G
1 GA G
31935734 TACGTGTGTG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.42, C:0.00, G:0.53, T:0.04
Consensus pattern (2 bp):
GA
Found at i:31936697 original size:20 final size:20
Alignment explanation
Indices: 31936672--31936724 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
31936662 AAACTATAAT
31936672 TGCAAAAAAG-TTCAAGCATG
1 TGCAAAAAAGATT-AAGCATG
**
31936692 TGCAAAAAAGATTGGGCATG
1 TGCAAAAAAGATTAAGCATG
31936712 TGC-AAAAAGATTA
1 TGCAAAAAAGATTA
31936725 TCGTCTCAGT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
19 9 0.31
20 18 0.62
21 2 0.07
ACGTcount: A:0.45, C:0.11, G:0.23, T:0.21
Consensus pattern (20 bp):
TGCAAAAAAGATTAAGCATG
Found at i:31938870 original size:14 final size:15
Alignment explanation
Indices: 31938843--31938871 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
31938833 TGATTTACAG
31938843 GGGAAGAGAGAAAGA
1 GGGAAGAGAGAAAGA
31938858 GGGAAGA-AGAAAGA
1 GGGAAGAGAGAAAGA
31938872 AAATGGAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (15 bp):
GGGAAGAGAGAAAGA
Found at i:31940809 original size:16 final size:16
Alignment explanation
Indices: 31940790--31940851 Score: 54
Period size: 16 Copynumber: 3.9 Consensus size: 16
31940780 ATTTTAATAA
31940790 AATTTAATATTAAATT
1 AATTTAATATTAAATT
* **
31940806 AATTTGATATTTATCTT
1 AATTTAATA-TTAAATT
* * *
31940823 GA-TAAATATTATATT
1 AATTTAATATTAAATT
31940838 AATTTAATATTAAA
1 AATTTAATATTAAA
31940852 ATGATTAAGT
Statistics
Matches: 34, Mismatches: 10, Indels: 4
0.71 0.21 0.08
Matches are distributed among these distances:
15 7 0.21
16 21 0.62
17 6 0.18
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.50
Consensus pattern (16 bp):
AATTTAATATTAAATT
Found at i:31940994 original size:25 final size:25
Alignment explanation
Indices: 31940958--31941005 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
31940948 TTGTAGAGAT
31940958 AAAATTTTCTAAAGAGATTATTTCAG
1 AAAATTTTCTAAAGAGATT-TTTCAG
*
31940984 AAAA-TTTCTAAAGATATTTTTC
1 AAAATTTTCTAAAGAGATTTTTC
31941006 TGATTTATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 4 0.19
25 13 0.62
26 4 0.19
ACGTcount: A:0.42, C:0.08, G:0.08, T:0.42
Consensus pattern (25 bp):
AAAATTTTCTAAAGAGATTTTTCAG
Found at i:31944455 original size:20 final size:19
Alignment explanation
Indices: 31944430--31944493 Score: 74
Period size: 20 Copynumber: 3.2 Consensus size: 19
31944420 GCTTGTATAG
31944430 GTTTGCACTTTGGTGCCTCT
1 GTTTGCACTTT-GTGCCTCT
*
31944450 GTTTGCACTTCAGTGCCTCT
1 GTTTGCACTT-TGTGCCTCT
* *
31944470 GATCGCACATTTGTGCCTCT
1 GTTTGCAC-TTTGTGCCTCT
31944490 GTTT
1 GTTT
31944494 TGCATATATG
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
20 34 0.94
21 2 0.06
ACGTcount: A:0.09, C:0.27, G:0.22, T:0.42
Consensus pattern (19 bp):
GTTTGCACTTTGTGCCTCT
Found at i:31946860 original size:12 final size:14
Alignment explanation
Indices: 31946838--31946869 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
31946828 TACAAACGTG
31946838 AGAATCAGATA-AC
1 AGAATCAGATACAC
31946851 AGAA-CAGATACAC
1 AGAATCAGATACAC
31946864 AGAATC
1 AGAATC
31946870 CTACCCCCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
12 6 0.35
13 10 0.59
14 1 0.06
ACGTcount: A:0.53, C:0.19, G:0.16, T:0.12
Consensus pattern (14 bp):
AGAATCAGATACAC
Found at i:31949691 original size:327 final size:327
Alignment explanation
Indices: 31949092--31949740 Score: 1037
Period size: 327 Copynumber: 2.0 Consensus size: 327
31949082 AGAGCTTCGC
* * *
31949092 TAACTTTTGCAGAGAGTAGTCCATCCAAATCGGAGTAAAATAGGTAAACTTGGTCAGTCGACCCA
1 TAACTTTTCCAGAGAGTAGTCCATCCAAACCGGAATAAAATAGGTAAACTTGGTCAGTCGACCCA
* * * * *
31949157 TGATGACCCAAACAGAACCCTTTTTAGTGGGTGTCAAGGGTAACCCACTAACAAAGTCCATTGTC
66 CGATAACCCAAACAGAACCCTTTTTAGTGGGTGTCAAGGGCAACCCACTAACAAAGTCCATCGCC
* *
31949222 ACTCGTTCTCATTTCCATAAAAGAATCTTAACAGGTTGTAGTAAACCAAAAGGCAAATGGTGCTC
131 ACTCGTTCTCATTTCCATAAAAGAATCTTAACAGGTTGTAGCAAACCAAAAGGAAAATGGTGCTC
* * * * *
31949287 AGCCTTAACTTGCTGGCACGTTAGACAATGAGCAACAAAATCTGTTCCCTCTCGTTTCAAACTCG
196 AGCCTTAACTTACTGACACGTTAGACAATGAGCAACAAAATCTATTACCTCTCGTTTAAAACTCG
*
31949352 GCCACCAATACAATTCACTGAGATCCCGATACATCTTATTACCACCGGGATGTATAACATAATGC
261 GCCACCAATACAATTCACTGAGATCCCGATACATCTTATTACCACCGGAATGTATAACATAATGC
31949417 CT
326 CT
**
31949419 TAACTTTTCCAGAGAGTAGTCCATCCAAACCGGAATAAAATAGGTGGACTTGGTCAGTCGACCCA
1 TAACTTTTCCAGAGAGTAGTCCATCCAAACCGGAATAAAATAGGTAAACTTGGTCAGTCGACCCA
31949484 CGATAACCCAAACAGAACCCTTTTTAGTGGGTGTCAAGGGCAACCCACTAACAAAGTCCATCGCC
66 CGATAACCCAAACAGAACCCTTTTTAGTGGGTGTCAAGGGCAACCCACTAACAAAGTCCATCGCC
* *** *
31949549 ACTCGTTCTTATTTCCATAAAAGAATCTTAACAGGTTGTAGCAAACTGGAAGGAAAATGGTGTTC
131 ACTCGTTCTCATTTCCATAAAAGAATCTTAACAGGTTGTAGCAAACCAAAAGGAAAATGGTGCTC
* * *
31949614 AGCCTTAACTTACTGATAGGTTAGACAATGAGCAACAAAATCTATTACCTCTGGTTTAAAACTCG
196 AGCCTTAACTTACTGACACGTTAGACAATGAGCAACAAAATCTATTACCTCTCGTTTAAAACTCG
* * *
31949679 GCCACTAATACAATTCACTGAGATCCCGATACATCTTATTACCGCCGGAATGTATAGCATAA
261 GCCACCAATACAATTCACTGAGATCCCGATACATCTTATTACCACCGGAATGTATAACATAA
31949741 GGGCTACCAT
Statistics
Matches: 293, Mismatches: 29, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
327 293 1.00
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.26
Consensus pattern (327 bp):
TAACTTTTCCAGAGAGTAGTCCATCCAAACCGGAATAAAATAGGTAAACTTGGTCAGTCGACCCA
CGATAACCCAAACAGAACCCTTTTTAGTGGGTGTCAAGGGCAACCCACTAACAAAGTCCATCGCC
ACTCGTTCTCATTTCCATAAAAGAATCTTAACAGGTTGTAGCAAACCAAAAGGAAAATGGTGCTC
AGCCTTAACTTACTGACACGTTAGACAATGAGCAACAAAATCTATTACCTCTCGTTTAAAACTCG
GCCACCAATACAATTCACTGAGATCCCGATACATCTTATTACCACCGGAATGTATAACATAATGC
CT
Found at i:31950093 original size:62 final size:62
Alignment explanation
Indices: 31950016--31950135 Score: 231
Period size: 62 Copynumber: 1.9 Consensus size: 62
31950006 AATCAATAAC
31950016 CGCTCTACGACTGAGAGCATCGGCCACCAAATTGGACTTACCAGGATGATACTCTATCGTGT
1 CGCTCTACGACTGAGAGCATCGGCCACCAAATTGGACTTACCAGGATGATACTCTATCGTGT
*
31950078 CGCTCTATGACTGAGAGCATCGGCCACCAAATTGGACTTACCAGGATGATACTCTATC
1 CGCTCTACGACTGAGAGCATCGGCCACCAAATTGGACTTACCAGGATGATACTCTATC
31950136 ATGTAGTCAT
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 57 1.00
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.24
Consensus pattern (62 bp):
CGCTCTACGACTGAGAGCATCGGCCACCAAATTGGACTTACCAGGATGATACTCTATCGTGT
Found at i:31952593 original size:25 final size:25
Alignment explanation
Indices: 31952553--31952663 Score: 177
Period size: 25 Copynumber: 4.4 Consensus size: 25
31952543 GAGATTCATG
* *
31952553 AACTCACGCCTACAAGCATTAACAT
1 AACTCACACCTACAAGCATCAACAT
* * *
31952578 AGCTCGCGCCTACAAGCATCAACAT
1 AACTCACACCTACAAGCATCAACAT
31952603 AACTCACACCTACAAGCATCAACAT
1 AACTCACACCTACAAGCATCAACAT
31952628 AACTCACACCTACAAGCATCAACAT
1 AACTCACACCTACAAGCATCAACAT
31952653 AACTCACACCT
1 AACTCACACCT
31952664 TAGAAGGCAG
Statistics
Matches: 80, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 80 1.00
ACGTcount: A:0.40, C:0.36, G:0.07, T:0.17
Consensus pattern (25 bp):
AACTCACACCTACAAGCATCAACAT
Found at i:31968966 original size:70 final size:69
Alignment explanation
Indices: 31968846--31969029 Score: 244
Period size: 70 Copynumber: 2.7 Consensus size: 69
31968836 AACCCAAAAG
* * *
31968846 GTTAATGAGAGTTAAAAGCTCCCAACTGTCATTCTAAGGCTAACAGGTTCAATA-CAACAGCCCT
1 GTTAGTGAGAGTTAAAAGCTCCCAACTGTCATTCTAAGGCTCACAAGTTCAATATCAA-AGCCC-
31968910 TAAACA
64 TAAACA
* * * *
31968916 GTTAGTGAGAGTTAAAAGCTCCCAACTATCATTCTAATGCTCGCAAGTTCAATATCAAAGCTCTA
1 GTTAGTGAGAGTTAAAAGCTCCCAACTGTCATTCTAAGGCTCACAAGTTCAATATCAAAGCCCTA
31968981 AACA
66 AACA
* * * *
31968985 GTTAGCGATAGTTAAAAGCTCCCAGCTGTCATTTTAAGGCTCACA
1 GTTAGTGAGAGTTAAAAGCTCCCAACTGTCATTCTAAGGCTCACA
31969030 GGTTTAACAT
Statistics
Matches: 99, Mismatches: 14, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
69 44 0.44
70 52 0.53
71 3 0.03
ACGTcount: A:0.35, C:0.22, G:0.16, T:0.27
Consensus pattern (69 bp):
GTTAGTGAGAGTTAAAAGCTCCCAACTGTCATTCTAAGGCTCACAAGTTCAATATCAAAGCCCTA
AACA
Found at i:31969172 original size:58 final size:56
Alignment explanation
Indices: 31969063--31969238 Score: 194
Period size: 58 Copynumber: 3.1 Consensus size: 56
31969053 CAGCTCACGA
* * *
31969063 ATTTACATTCCCGACTAATTATTTCAAAAA-AAGGCCTAAGTTCAAAACAACTTGCGG
1 ATTTACATTCCCTACTAAGTATTTCAAAAATAA-GCCTAAGTT-AAAACAACTTGAGG
* * *
31969120 ATTTACATT-CCTAGCTGAGTATTTCAGAAAATATGCCTAAGTTGAAAACAACTCGAGG
1 ATTTACATTCCCTA-CTAAGTATTTCA-AAAATAAGCCTAAGTT-AAAACAACTTGAGG
* * *
31969178 GTTTACATTCCCTACTAATTATATCAAAAAATAAGCCTAAGCTTAAAACAACTTGAGG
1 ATTTACATTCCCTACTAAGTATTTC-AAAAATAAGCCTAAG-TTAAAACAACTTGAGG
31969236 ATT
1 ATT
31969239 CACAATCGAT
Statistics
Matches: 99, Mismatches: 14, Indels: 11
0.80 0.11 0.09
Matches are distributed among these distances:
56 3 0.03
57 19 0.19
58 69 0.70
59 8 0.08
ACGTcount: A:0.39, C:0.19, G:0.13, T:0.30
Consensus pattern (56 bp):
ATTTACATTCCCTACTAAGTATTTCAAAAATAAGCCTAAGTTAAAACAACTTGAGG
Found at i:31970880 original size:15 final size:16
Alignment explanation
Indices: 31970850--31970881 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
31970840 ACTTTAGGGG
31970850 CAAAAATGTAATTTTT
1 CAAAAATGTAATTTTT
*
31970866 CAAAAATGTGATTTTT
1 CAAAAATGTAATTTTT
31970882 GGACTTGATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.06, G:0.09, T:0.44
Consensus pattern (16 bp):
CAAAAATGTAATTTTT
Found at i:31971224 original size:51 final size:50
Alignment explanation
Indices: 31971102--31971400 Score: 320
Period size: 51 Copynumber: 5.9 Consensus size: 50
31971092 AGTGAAAGTG
* ** * *
31971102 ATGGTCACGTGTGTAGTACTATGTTCAGGCTACTACGTGTACTAGAAT-G-
1 ATGGTCACATGTGTAGTACTATGAGCAGGCTACTACGTGTA-TCGGATAGT
** * * * *
31971151 ATAGGTCGTATATGTAGTACTATGAGCAGGCTACTATGAGTACCGGATAGCT
1 AT-GGTCACATGTGTAGTACTATGAGCAGGCTACTACGTGTATCGGATAG-T
* * *
31971203 -TCGATCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATAGT
1 AT-GGTCACATGTGTAGTACTATGAGCAGGCTACTACGTGTATCGGATAGT
31971253 GATGGTCACATGTGTAGTACTATGTA-CAGGCTACTACGTGTATCGGATAGT
1 -ATGGTCACATGTGTAGTACTATG-AGCAGGCTACTACGTGTATCGGATAGT
*
31971304 GATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATAGT
1 -ATGGTCACATGTGTAGTACTATGAGCAGGCTACTACGTGTATCGGATAGT
* * *
31971355 GATGGTCACATGTCTAGTACTATGTA-CAGGCTACTATGTGAATCGG
1 -ATGGTCACATGTGTAGTACTATG-AGCAGGCTACTACGTGTATCGG
31971401 TATCATTAAT
Statistics
Matches: 212, Mismatches: 29, Indels: 16
0.82 0.11 0.06
Matches are distributed among these distances:
49 5 0.02
50 33 0.16
51 173 0.82
52 1 0.00
ACGTcount: A:0.25, C:0.16, G:0.27, T:0.31
Consensus pattern (50 bp):
ATGGTCACATGTGTAGTACTATGAGCAGGCTACTACGTGTATCGGATAGT
Found at i:31971319 original size:25 final size:25
Alignment explanation
Indices: 31971239--31971367 Score: 67
Period size: 25 Copynumber: 5.1 Consensus size: 25
31971229 AGGCTACTAC
31971239 GTGTATCGGATAGTGATGGTCACAT
1 GTGTATCGGATAGTGATGGTCACAT
* * *
31971264 GTGTA--GTACTA-TGTACAGG-CTACTAC
1 GTGTATCGGA-TAGTG-A-TGGTC-AC-AT
31971290 GTGTATCGGATAGTGATGGTCACAT
1 GTGTATCGGATAGTGATGGTCACAT
* *
31971315 GTGTA--GTACTATGTGCA-GG-CTACTAC
1 GTGTATCGGA-TA-GTG-ATGGTC-AC-AT
31971341 GTGTATCGGATAGTGATGGTCACAT
1 GTGTATCGGATAGTGATGGTCACAT
31971366 GT
1 GT
31971368 CTAGTACTAT
Statistics
Matches: 76, Mismatches: 10, Indels: 36
0.62 0.08 0.30
Matches are distributed among these distances:
23 6 0.08
24 7 0.09
25 26 0.34
26 24 0.32
27 7 0.09
28 6 0.08
ACGTcount: A:0.24, C:0.15, G:0.29, T:0.32
Consensus pattern (25 bp):
GTGTATCGGATAGTGATGGTCACAT
Found at i:31971320 original size:102 final size:102
Alignment explanation
Indices: 31971098--31971400 Score: 411
Period size: 102 Copynumber: 3.0 Consensus size: 102
31971088 TGAAAGTGAA
* * **
31971098 AGTGATGGTCACGTGTGTAGTACTATGTTCAGGCTACTACGTGTA-CTAGA-A-TGATAGGTCGT
1 AGTGATGGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATC-GGATAGTGAT-GGTCAC
* * *
31971160 ATATGTAGTACTATG-AGCAGGCTACTATGAGTACCGGAT
64 ATGTGTAGTACTATGTA-CAGGCTACTATGTGTATCGGAT
*
31971199 AGCT--TCGATCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATAGTGATGGTCAC
1 AG-TGAT-GGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATAGTGATGGTCAC
*
31971262 ATGTGTAGTACTATGTACAGGCTACTACGTGTATCGGAT
64 ATGTGTAGTACTATGTACAGGCTACTATGTGTATCGGAT
*
31971301 AGTGATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATAGTGATGGTCACAT
1 AGTGATGGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATAGTGATGGTCACAT
* *
31971366 GTCTAGTACTATGTACAGGCTACTATGTGAATCGG
66 GTGTAGTACTATGTACAGGCTACTATGTGTATCGG
31971401 TATCATTAAT
Statistics
Matches: 180, Mismatches: 14, Indels: 15
0.86 0.07 0.07
Matches are distributed among these distances:
100 1 0.01
101 42 0.23
102 131 0.73
103 6 0.03
ACGTcount: A:0.25, C:0.16, G:0.28, T:0.31
Consensus pattern (102 bp):
AGTGATGGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATAGTGATGGTCACAT
GTGTAGTACTATGTACAGGCTACTATGTGTATCGGAT
Found at i:31971385 original size:153 final size:152
Alignment explanation
Indices: 31971098--31971400 Score: 389
Period size: 153 Copynumber: 2.0 Consensus size: 152
31971088 TGAAAGTGAA
* * **
31971098 AGTGATGGTCACGTGTGTAGTACTATGTTCAGGCTACTACGTGTACTAGAATGATAGGTCGTATA
1 AGTGATGGTCACATGTGTAGTACTATGTACAGGCTACTACGTGTACTAGAATGATAGGTCACATA
* * * *
31971163 TGTAGTACTATGAGCAGGCTACTATGAGTACCGGATAGCTTCGATCACGTGTGTAGTACTATGTG
66 TGTAGTACTATGAGCAGGCTACTACGAGTACCGGATAGCTTCGATCACATGTCTAGTACTATGTA
*
31971228 CAGGCTACTACGTGTATCGGAT
131 CAGGCTACTACGTGAATCGGAT
*
31971250 AGTGATGGTCACATGTGTAGTACTATGTACAGGCTACTACGTGTA-TCGGATAGTGAT-GGTCAC
1 AGTGATGGTCACATGTGTAGTACTATGTACAGGCTACTACGTGTACT-AGA-A-TGATAGGTCAC
* * * * *
31971313 ATGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATAG-TGAT-GGTCACATGTCTAGTACT
63 ATATGTAGTACTATGAGCAGGCTACTACGAGTACCGGATAGCT--TCGATCACATGTCTAGTACT
*
31971376 ATGTACAGGCTACTATGTGAATCGG
126 ATGTACAGGCTACTACGTGAATCGG
31971401 TATCATTAAT
Statistics
Matches: 130, Mismatches: 16, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
151 1 0.01
152 46 0.35
153 78 0.60
154 5 0.04
ACGTcount: A:0.25, C:0.16, G:0.28, T:0.31
Consensus pattern (152 bp):
AGTGATGGTCACATGTGTAGTACTATGTACAGGCTACTACGTGTACTAGAATGATAGGTCACATA
TGTAGTACTATGAGCAGGCTACTACGAGTACCGGATAGCTTCGATCACATGTCTAGTACTATGTA
CAGGCTACTACGTGAATCGGAT
Found at i:31971639 original size:16 final size:16
Alignment explanation
Indices: 31971618--31971649 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
31971608 TGATTGAAAG
31971618 TGAAAAAGTAAAATTA
1 TGAAAAAGTAAAATTA
31971634 TGAAAAAGTAAAATTA
1 TGAAAAAGTAAAATTA
31971650 GCAACAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.62, C:0.00, G:0.12, T:0.25
Consensus pattern (16 bp):
TGAAAAAGTAAAATTA
Found at i:31978024 original size:5 final size:5
Alignment explanation
Indices: 31978014--31978038 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
31978004 GCATTCGTTG
31978014 TTCTT TTCTT TTCTT TTCTT TTCTT
1 TTCTT TTCTT TTCTT TTCTT TTCTT
31978039 GTTTTGTTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
TTCTT
Found at i:31978600 original size:19 final size:19
Alignment explanation
Indices: 31978578--31978614 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
31978568 TTATTAAAAT
* *
31978578 TTAAAAATATATAAAATTA
1 TTAAAAAAACATAAAATTA
31978597 TTAAAAAAACATAAAATT
1 TTAAAAAAACATAAAATT
31978615 CAATCCAACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (19 bp):
TTAAAAAAACATAAAATTA
Found at i:31986272 original size:15 final size:16
Alignment explanation
Indices: 31986254--31986291 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
31986244 TGTTAACAGC
*
31986254 TTAATAATTAACT-AT
1 TTAATAATTAAATAAT
31986269 TTAA-AATTAAATAAT
1 TTAATAATTAAATAAT
31986284 TTAATAAT
1 TTAATAAT
31986292 ATTTTCTCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 7 0.35
15 10 0.50
16 3 0.15
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAATAATTAAATAAT
Found at i:31986452 original size:7 final size:7
Alignment explanation
Indices: 31986442--31986511 Score: 113
Period size: 7 Copynumber: 9.9 Consensus size: 7
31986432 AAGGATTGGG
31986442 AATTGAA
1 AATTGAA
31986449 AATTGAA
1 AATTGAA
31986456 AATTGAA
1 AATTGAA
*
31986463 AATTGAT
1 AATTGAA
*
31986470 GATTGAAA
1 AATTG-AA
31986478 AATTGAA
1 AATTGAA
31986485 AATTGAA
1 AATTGAA
31986492 AATTGAA
1 AATTGAA
31986499 AATTGAA
1 AATTGAA
31986506 AATTGA
1 AATTGA
31986512 GGATTGAGGA
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
7 53 0.91
8 5 0.09
ACGTcount: A:0.54, C:0.00, G:0.16, T:0.30
Consensus pattern (7 bp):
AATTGAA
Found at i:31986511 original size:36 final size:36
Alignment explanation
Indices: 31986442--31986511 Score: 122
Period size: 36 Copynumber: 1.9 Consensus size: 36
31986432 AAGGATTGGG
**
31986442 AATTGAAAATTGAAAATTGAAAATTGATGATTGAAA
1 AATTGAAAATTGAAAATTGAAAATTGAAAATTGAAA
31986478 AATTGAAAATTGAAAATTGAAAATTGAAAATTGA
1 AATTGAAAATTGAAAATTGAAAATTGAAAATTGA
31986512 GGATTGAGGA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.54, C:0.00, G:0.16, T:0.30
Consensus pattern (36 bp):
AATTGAAAATTGAAAATTGAAAATTGAAAATTGAAA
Found at i:31986517 original size:14 final size:14
Alignment explanation
Indices: 31986443--31986532 Score: 99
Period size: 14 Copynumber: 6.4 Consensus size: 14
31986433 AGGATTGGGA
*
31986443 ATTGAAAATTGAAA
1 ATTGAAAATTGAAG
*
31986457 ATTGAAAATTGATG
1 ATTGAAAATTGAAG
*
31986471 ATTGAAAAATTGAAA
1 ATTG-AAAATTGAAG
*
31986486 ATTGAAAATTGAAA
1 ATTGAAAATTGAAG
*
31986500 ATTGAAAATTGAGG
1 ATTGAAAATTGAAG
** *
31986514 ATTGAGGATTGAGG
1 ATTGAAAATTGAAG
31986528 ATTGA
1 ATTGA
31986533 GAACTTAGGA
Statistics
Matches: 67, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
14 55 0.82
15 12 0.18
ACGTcount: A:0.48, C:0.00, G:0.22, T:0.30
Consensus pattern (14 bp):
ATTGAAAATTGAAG
Found at i:31986533 original size:14 final size:14
Alignment explanation
Indices: 31986443--31986554 Score: 73
Period size: 14 Copynumber: 7.9 Consensus size: 14
31986433 AGGATTGGGA
* **
31986443 ATTGAAAATTGAAA
1 ATTGAGAATTGAGG
* *
31986457 ATTGAAAATTGATG
1 ATTGAGAATTGAGG
* **
31986471 ATTGAAAAATTGAAA
1 ATTG-AGAATTGAGG
* **
31986486 ATTGAAAATTGAAA
1 ATTGAGAATTGAGG
*
31986500 ATTGAAAATTGAGG
1 ATTGAGAATTGAGG
*
31986514 ATTGAGGATTGAGG
1 ATTGAGAATTGAGG
31986528 ATTGAGAACTT-AGG
1 ATTGAGAA-TTGAGG
*
31986542 ATTGAGTATTGAG
1 ATTGAGAATTGAG
31986555 TTGAAAAGAA
Statistics
Matches: 85, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
13 2 0.02
14 69 0.81
15 14 0.16
ACGTcount: A:0.45, C:0.01, G:0.24, T:0.30
Consensus pattern (14 bp):
ATTGAGAATTGAGG
Found at i:31986555 original size:7 final size:7
Alignment explanation
Indices: 31986507--31986554 Score: 62
Period size: 7 Copynumber: 6.9 Consensus size: 7
31986497 AAAATTGAAA
31986507 ATTGAGG
1 ATTGAGG
31986514 ATTGAGG
1 ATTGAGG
31986521 ATTGAGG
1 ATTGAGG
*
31986528 ATTGAGA
1 ATTGAGG
31986535 ACTT-AGG
1 A-TTGAGG
*
31986542 ATTGAGT
1 ATTGAGG
31986549 ATTGAG
1 ATTGAG
31986555 TTGAAAAGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
6 2 0.06
7 32 0.89
8 2 0.06
ACGTcount: A:0.31, C:0.02, G:0.35, T:0.31
Consensus pattern (7 bp):
ATTGAGG
Found at i:31986889 original size:10 final size:9
Alignment explanation
Indices: 31986866--31986987 Score: 59
Period size: 10 Copynumber: 12.7 Consensus size: 9
31986856 TTGGATTGTT
*
31986866 TTTTTATTA
1 TTTTTATAA
31986875 TTTTTATAA
1 TTTTTATAA
*
31986884 TATTTTATTTA
1 T-TTTTA-TAA
31986895 TATTTTA-ACA
1 T-TTTTATA-A
31986905 -TTTTATAA
1 TTTTTATAA
*
31986913 TATTTTATGA
1 T-TTTTATAA
* *
31986923 TTTTTTTATT
1 TTTTTATA-A
*
31986933 TTTTTAGAA
1 TTTTTATAA
31986942 TTTTTATCAA
1 TTTTTAT-AA
**
31986952 TTAATAGTAA
1 TTTTTA-TAA
*
31986962 TTTTTATATT
1 TTTTTATA-A
31986972 TTTTTATAA
1 TTTTTATAA
31986981 TATTTTA
1 T-TTTTA
31986988 AACTACATCT
Statistics
Matches: 85, Mismatches: 17, Indels: 21
0.69 0.14 0.17
Matches are distributed among these distances:
8 6 0.07
9 24 0.28
10 45 0.53
11 10 0.12
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (9 bp):
TTTTTATAA
Found at i:31986891 original size:19 final size:19
Alignment explanation
Indices: 31986867--31986987 Score: 70
Period size: 19 Copynumber: 6.3 Consensus size: 19
31986857 TGGATTGTTT
31986867 TTTTATTATTTTTATAATA
1 TTTTATTATTTTTATAATA
* *
31986886 TTTTATTTATATTT-TAACA
1 TTTTA-TTATTTTTATAATA
* * *
31986905 TTTTATAATATTTTATGATTT
1 TTTTATTAT-TTTTAT-AATA
*
31986926 TTTTATT-TTTTTAGAAT-
1 TTTTATTATTTTTATAATA
* **
31986943 TTTTATCAATTAATAGTAAT-
1 TTTTAT-TATTTTTA-TAATA
*
31986963 TTTTATATTTTTTTATAATA
1 TTTTAT-TATTTTTATAATA
31986983 TTTTA
1 TTTTA
31986988 AACTACATCT
Statistics
Matches: 75, Mismatches: 19, Indels: 15
0.69 0.17 0.14
Matches are distributed among these distances:
17 6 0.08
18 5 0.07
19 30 0.40
20 27 0.36
21 7 0.09
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (19 bp):
TTTTATTATTTTTATAATA
Found at i:31986937 original size:29 final size:27
Alignment explanation
Indices: 31986864--31986948 Score: 82
Period size: 29 Copynumber: 3.0 Consensus size: 27
31986854 ATTTGGATTG
31986864 TTTTTTTATTATTTTTATAATATTTTAT
1 TTTTTTTATT-TTTTTATAATATTTTAT
***
31986892 TTATATTTTAACATTTTATAATATTTTAT
1 TT-T-TTTTATTTTTTTATAATATTTTAT
*
31986921 GATTTTTTTATTTTTTTAGAAT-TTTTAT
1 --TTTTTTTATTTTTTTATAATATTTTAT
31986949 CAATTAATAG
Statistics
Matches: 46, Mismatches: 7, Indels: 8
0.75 0.11 0.13
Matches are distributed among these distances:
28 8 0.17
29 30 0.65
30 6 0.13
31 2 0.04
ACGTcount: A:0.27, C:0.01, G:0.02, T:0.69
Consensus pattern (27 bp):
TTTTTTTATTTTTTTATAATATTTTAT
Found at i:31987208 original size:18 final size:18
Alignment explanation
Indices: 31987185--31987220 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
31987175 CAAACGATTT
*
31987185 TGTCTTAACCTGTAATAA
1 TGTCTTAACCTGGAATAA
*
31987203 TGTCTTAATCTGGAATAA
1 TGTCTTAACCTGGAATAA
31987221 GATACTTTCT
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:0.33, C:0.14, G:0.14, T:0.39
Consensus pattern (18 bp):
TGTCTTAACCTGGAATAA
Found at i:31988140 original size:16 final size:16
Alignment explanation
Indices: 31988088--31988140 Score: 63
Period size: 16 Copynumber: 3.3 Consensus size: 16
31988078 GAAAGACCCT
31988088 AAAAATTTAAG-CTCAA
1 AAAAATTTAAGTC-CAA
* *
31988104 AAAAATTTAAATCCGA
1 AAAAATTTAAGTCCAA
*
31988120 AAAAATTCAAGTCCAA
1 AAAAATTTAAGTCCAA
31988136 AAAAA
1 AAAAA
31988141 CTAAAACTGA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
16 30 0.97
17 1 0.03
ACGTcount: A:0.60, C:0.13, G:0.06, T:0.21
Consensus pattern (16 bp):
AAAAATTTAAGTCCAA
Found at i:31998029 original size:166 final size:165
Alignment explanation
Indices: 31997733--31998289 Score: 731
Period size: 166 Copynumber: 3.4 Consensus size: 165
31997723 GGAAAGTGTC
* * * *
31997733 GCAAATAATTAAGCAGAACACTGTCGTTTAACTTTGACATGTAGTGGCACTAGCAGCGTTTATCT
1 GCAAATAATTAAGCAGAACACCGTCGTTTAACTTTGACCTGTAGTGGCACTAGCGGCGTTTTTCT
* * * *
31997798 GGAAACGCCGATAAAGATCCAGCATTTGCGGCGCTTATAAAATAACGCCGCTAATGA-CTGGTAC
66 GGAAACGCCGGTAAAGATCAAGCATTTGCGGTGCTTATAAAA-AACGCCGCTAAAGATC-GGTAC
* *
31997862 ATTAGCGGCGCTACCACAAAAACGCCACTAATGCTCA
129 ATTAGCGGCGCTACTACAAAAACACCACTAATGCTCA
* * *
31997899 GCAAATAATTAAACAGAACGCCGTCGTTTAACTTTGACCTGTAGTGGCACTAGCGGCGTTTTTCC
1 GCAAATAATTAAGCAGAACACCGTCGTTTAACTTTGACCTGTAGTGGCACTAGCGGCGTTTTTCT
* * * *
31997964 GTAAACGCCGGTAAAGATCTAGTATTTGCGGTGCTTATAACAAAACGCCACTAAAGATCGGTACA
66 GGAAACGCCGGTAAAGATCAAGCATTTGCGGTGCTTATAA-AAAACGCCGCTAAAGATCGGTACA
* * * *
31998029 TTATCGGTGCTACTACAAAAACTCCACTAATGCTCT
130 TTAGCGGCGCTACTACAAAAACACCACTAATGCTCA
* *
31998065 GCAAATAATTAAGCAGAAAACCATCGTTTAACTTTGACCTGTAGTGGCACTAGCGGCGTTTATT-
1 GCAAATAATTAAGCAGAACACCGTCGTTTAACTTTGACCTGTAGTGGCACTAGCGGCGTTT-TTC
* * * *
31998129 TGGAAACACCGGTAAAGATCAAGCAGTTACGGTGCTTATATTAAAACGCCGCTAAAGATCGGTAC
65 TGGAAACGCCGGTAAAGATCAAGCATTTGCGGTGCTTATA-AAAAACGCCGCTAAAGATCGGTAC
* * * *
31998194 ATTAGCGACGCTGCTATAAAAACACCACTAATGCTCC
129 ATTAGCGGCGCTACTACAAAAACACCACTAATGCTCA
* * ** *
31998231 GTAAATAATTAAGCATAATGCCGTCGTTTAACTTTGACTTGTAGTGGCACTAGCGGCGT
1 GCAAATAATTAAGCAGAACACCGTCGTTTAACTTTGACCTGTAGTGGCACTAGCGGCGT
31998290 CTTTATACAA
Statistics
Matches: 342, Mismatches: 45, Indels: 8
0.87 0.11 0.02
Matches are distributed among these distances:
166 337 0.99
167 5 0.01
ACGTcount: A:0.32, C:0.22, G:0.20, T:0.26
Consensus pattern (165 bp):
GCAAATAATTAAGCAGAACACCGTCGTTTAACTTTGACCTGTAGTGGCACTAGCGGCGTTTTTCT
GGAAACGCCGGTAAAGATCAAGCATTTGCGGTGCTTATAAAAAACGCCGCTAAAGATCGGTACAT
TAGCGGCGCTACTACAAAAACACCACTAATGCTCA
Found at i:31998700 original size:23 final size:24
Alignment explanation
Indices: 31998649--31998694 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
31998639 GTCTTAGTTA
31998649 CTATTCATGGTTTAACAGGTTAGG
1 CTATTCATGGTTTAACAGGTTAGG
*
31998673 CTATT-ATGGTTTAA-GGGTTAGG
1 CTATTCATGGTTTAACAGGTTAGG
31998695 GTTATTGATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 7 0.33
23 9 0.43
24 5 0.24
ACGTcount: A:0.24, C:0.09, G:0.28, T:0.39
Consensus pattern (24 bp):
CTATTCATGGTTTAACAGGTTAGG
Found at i:31998812 original size:14 final size:14
Alignment explanation
Indices: 31998773--31998815 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
31998763 TTACTTTAGT
*
31998773 GTTTACTGTTTATG
1 GTTTAGTGTTTATG
* *
31998787 CTATAG-GTTTATG
1 GTTTAGTGTTTATG
31998800 GTTTAGTGTTTATG
1 GTTTAGTGTTTATG
31998814 GT
1 GT
31998816 GTACGTTTTC
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.16, C:0.05, G:0.26, T:0.53
Consensus pattern (14 bp):
GTTTAGTGTTTATG
Found at i:31998903 original size:22 final size:22
Alignment explanation
Indices: 31998845--31998904 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 22
31998835 GTTGAATGTT
* *
31998845 TAGGGGTGAG-GGCTTAGGGTT
1 TAGGGGTTAGTGGCTTAGGGTC
*
31998866 TAGGGGTTA-TAAGCTTAGGGTC
1 TAGGGGTTAGT-GGCTTAGGGTC
31998888 TAGGGGTTAGTGGCTTA
1 TAGGGGTTAGTGGCTTA
31998905 AAGTTGCTGG
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
21 8 0.25
22 23 0.72
23 1 0.03
ACGTcount: A:0.18, C:0.07, G:0.43, T:0.32
Consensus pattern (22 bp):
TAGGGGTTAGTGGCTTAGGGTC
Found at i:31999047 original size:28 final size:28
Alignment explanation
Indices: 31999016--31999078 Score: 83
Period size: 28 Copynumber: 2.2 Consensus size: 28
31999006 TAGGGTGTGT
*
31999016 ATTTACGGTTTAA-AGATTAAGGTTTAGG
1 ATTTA-GGTTTAAGAGATTAAGGTTTACG
* *
31999044 ATTTAGTTTTAAGAGTTTAAGGTTTACG
1 ATTTAGGTTTAAGAGATTAAGGTTTACG
31999072 ATTTAGG
1 ATTTAGG
31999079 GTGTATGTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
27 6 0.20
28 24 0.80
ACGTcount: A:0.30, C:0.03, G:0.24, T:0.43
Consensus pattern (28 bp):
ATTTAGGTTTAAGAGATTAAGGTTTACG
Found at i:31999076 original size:14 final size:14
Alignment explanation
Indices: 31999016--31999076 Score: 54
Period size: 14 Copynumber: 4.4 Consensus size: 14
31999006 TAGGGTGTGT
*
31999016 ATTTACGGTTTAAAG
1 ATTTAAGGTTT-AAG
*
31999031 A-TTAAGGTTTAGG
1 ATTTAAGGTTTAAG
*
31999044 ATTT-AGTTTTAAG
1 ATTTAAGGTTTAAG
*
31999057 AGTTTAAGGTTTACG
1 A-TTTAAGGTTTAAG
31999072 ATTTA
1 ATTTA
31999077 GGGTGTATGT
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
13 11 0.30
14 17 0.46
15 9 0.24
ACGTcount: A:0.31, C:0.03, G:0.21, T:0.44
Consensus pattern (14 bp):
ATTTAAGGTTTAAG
Found at i:31999169 original size:21 final size:21
Alignment explanation
Indices: 31999145--31999197 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
31999135 GGCTAAAGGC
31999145 TTATGGTTTAGGGTTTAAAT-T
1 TTATGGTTTAGGGTTT-AATGT
** *
31999166 TTATATTTTAAGGTTTAATGT
1 TTATGGTTTAGGGTTTAATGT
*
31999187 TTAAGGTTTAG
1 TTATGGTTTAG
31999198 CTAAAAACAT
Statistics
Matches: 24, Mismatches: 7, Indels: 2
0.73 0.21 0.06
Matches are distributed among these distances:
20 3 0.12
21 21 0.88
ACGTcount: A:0.26, C:0.00, G:0.21, T:0.53
Consensus pattern (21 bp):
TTATGGTTTAGGGTTTAATGT
Found at i:31999708 original size:83 final size:83
Alignment explanation
Indices: 31999609--31999837 Score: 263
Period size: 83 Copynumber: 2.8 Consensus size: 83
31999599 TAACAATTTG
* * *
31999609 CCAATGCGGCACCGTTTTTGTACTGGAATAAAAATAATAGTGGCGTTTTTTAGGAAAACGCCGCA
1 CCAATGCGGCGCCGTTTCTGTACTGGAATAAAAATAATAGTGGCGTTTTTTAGGAAAACGCTGCA
31999674 AGGATTTATTAAACTTTC
66 AGGATTTATTAAACTTTC
* * ** *
31999692 CCAATGTGGCGTCGTTTCTGTACTGGGAA-AAATTTGATAGTGGCGTTTTTTAGGAAAA---TGC
1 CCAATGCGGCGCCGTTTCTGTACT-GGAATAAAAATAATAGTGGCGTTTTTTAGGAAAACGCTGC
* * *
31999753 -ATGATTTATTAAATTTTT
65 AAGGATTTATTAAACTTTC
** *
31999771 CCAATGCGGCGCCGTTTCTGTACT-TCATAAAAATCTAATATTGGCGTTTTTTAGGAAAACGCTG
1 CCAATGCGGCGCCGTTTCTGTACTGGAATAAAAA--TAATAGTGGCGTTTTTTAGGAAAACGCTG
31999835 CAA
64 CAA
31999838 AAATGAATTA
Statistics
Matches: 119, Mismatches: 19, Indels: 15
0.78 0.12 0.10
Matches are distributed among these distances:
77 1 0.01
78 3 0.03
79 37 0.31
80 24 0.20
83 49 0.41
84 5 0.04
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.34
Consensus pattern (83 bp):
CCAATGCGGCGCCGTTTCTGTACTGGAATAAAAATAATAGTGGCGTTTTTTAGGAAAACGCTGCA
AGGATTTATTAAACTTTC
Done.