Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007744.1 Hibiscus syriacus cultivar Beakdansim tig00110007_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: 4276731
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 14 of 16
Found at i:3321606 original size:15 final size:14
Alignment explanation
Indices: 3321573--3321616 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
3321563 TTAATTTGGG
**
3321573 GATTTAGGGTTAGA
1 GATTTAGGGTTTTA
3321587 GATTTAGGGATTTTA
1 GATTTAGGG-TTTTA
*
3321602 GATTTAAGGTTTTA
1 GATTTAGGGTTTTA
3321616 G
1 G
3321617 GGATTAGGGT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
14 15 0.58
15 11 0.42
ACGTcount: A:0.27, C:0.00, G:0.30, T:0.43
Consensus pattern (14 bp):
GATTTAGGGTTTTA
Found at i:3325830 original size:13 final size:13
Alignment explanation
Indices: 3325805--3325843 Score: 60
Period size: 13 Copynumber: 2.9 Consensus size: 13
3325795 GTGCTTTTAA
3325805 CTTTTCTTTCTTTT
1 CTTTTC-TTCTTTT
3325819 CTTTTCTTCTTTT
1 CTTTTCTTCTTTT
*
3325832 GTTTTCTTCTTT
1 CTTTTCTTCTTT
3325844 GAGTGCTTGC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 18 0.75
14 6 0.25
ACGTcount: A:0.00, C:0.21, G:0.03, T:0.77
Consensus pattern (13 bp):
CTTTTCTTCTTTT
Found at i:3328498 original size:2 final size:2
Alignment explanation
Indices: 3328139--3328490 Score: 106
Period size: 2 Copynumber: 173.0 Consensus size: 2
3328129 ATTAATACTT
* *
3328139 TA TA TT TA TA TA TA T- TA AA GTA TGA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA -TA T-A TA TA TA TA TA TA TA TA TA
* * * * *
3328182 TA CA T- TT TA TA CTT TA TA TA TG TA TA TA TA AA CTA TA TA TA TA
1 TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA
* * *
3328225 TA TA GCA TA AA GTA T- TA AA GTA TGA TA TA TA TA TA TA TA TA TA
1 TA TA -TA TA TA -TA TA TA TA -TA T-A TA TA TA TA TA TA TA TA TA
* * * * * *
3328268 TA CTA TA TA AA CTT TT TA TT TA -A TA CTT TA TA TC TA TA CT- TA
1 TA -TA TA TA TA -TA TA TA TA TA TA TA -TA TA TA TA TA TA -TA TA
* * *
3328310 TA TA TA TA TA TA CTT TA -A TA GTT TA TA TA TT TA TA TA TA CT-
1 TA TA TA TA TA TA -TA TA TA TA -TA TA TA TA TA TA TA TA TA -TA
* * * * *
3328351 TT TA TA CTA TA TA GTG TA TA TA CA TA TA TA CTT TT TA T- TA TA
1 TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA -TA TA TA TA TA TA
* * * ** *
3328393 TA CT- TA TA TCC T- TT TG CC TT TA TA TA TA TA TA TA TA TA TA TA
1 TA -TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
3328435 TA TA TA TA CT- TT TA TA T- TA -A TA TA TA TA CT- TA TA TT TA TA
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA
3328475 TA TA -A T- TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA
3328491 ACTATATACT
Statistics
Matches: 260, Mismatches: 52, Indels: 76
0.67 0.13 0.20
Matches are distributed among these distances:
1 16 0.06
2 219 0.84
3 25 0.10
ACGTcount: A:0.41, C:0.06, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3330563 original size:31 final size:31
Alignment explanation
Indices: 3330518--3330584 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 31
3330508 ATTTATCTTA
* ** *
3330518 TTCCCAATGTTAATTACTAATTGTTCTTTTG
1 TTCCCAATGCTAATTACTAATTACTCTTTTC
* *
3330549 TTCCCCATGCTAATTATTAATTACTCTTTTC
1 TTCCCAATGCTAATTACTAATTACTCTTTTC
3330580 TTCCC
1 TTCCC
3330585 TGTGTATATT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.21, C:0.24, G:0.06, T:0.49
Consensus pattern (31 bp):
TTCCCAATGCTAATTACTAATTACTCTTTTC
Found at i:3330606 original size:40 final size:40
Alignment explanation
Indices: 3330556--3330634 Score: 113
Period size: 40 Copynumber: 2.0 Consensus size: 40
3330546 TTGTTCCCCA
**
3330556 TGCTAATTATTAATTACTCTTTTCTTCCCTGTGTATATTC
1 TGCTAATTATTAATTACTCTTTTCTTCCCCATGTATATTC
* **
3330596 TGCTAGTTATTAATTGTTCTTTTCTTCCCCATGTATATT
1 TGCTAATTATTAATTACTCTTTTCTTCCCCATGTATATT
3330635 ATGCAACGGT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.19, C:0.19, G:0.09, T:0.53
Consensus pattern (40 bp):
TGCTAATTATTAATTACTCTTTTCTTCCCCATGTATATTC
Found at i:3335985 original size:136 final size:138
Alignment explanation
Indices: 3335825--3336169 Score: 424
Period size: 138 Copynumber: 2.5 Consensus size: 138
3335815 TATTGAGTCG
* * * * *
3335825 AATAATCAAAATGGAACCTCGAACATAAGCAAGGACCAAAATAAAAATTCCCCTAAATTCAAGGA
1 AATAATTAAAATGGAACCTCGAACAAAAGCGAGGACCAAATTAAAAATTCCCCTAAATTAAAGGA
* * * * * *
3335890 TTAAA-GTGAAATTAAAACTATA-TAGAGGCTCTAGTTATTAATCTAGTCAATATTAGCCAATTA
66 CTAAATATGAAATTAAAACTAAAGTAGAGGCTCTAATTATTAACCTAGTCAATATTAACCAATTA
3335953 TTAGATCA
131 TTAGATCA
* * **
3335961 AATAATTAAAATGGAACCTCGAACAAAAGCGAGAACCAAATTAAGAATTCAACTAAATTAAAGGA
1 AATAATTAAAATGGAACCTCGAACAAAAGCGAGGACCAAATTAAAAATTCCCCTAAATTAAAGGA
* ** * * * *
3336026 CTAAATATGAGATTAAGCCTAAAGTGGAGGTTCTAATTATTAACCTAGTTAATTTTAACCAATTA
66 CTAAATATGAAATTAAAACTAAAGTAGAGGCTCTAATTATTAACCTAGTCAATATTAACCAATTA
* *
3336091 TTGGATCG
131 TTAGATCA
** * *
3336099 AATAATTAAAATGGAACCTCGGGCAAAAGCGATGACCAAATTAAAATTTCCCCTAAATTAAAGGA
1 AATAATTAAAATGGAACCTCGAACAAAAGCGAGGACCAAATTAAAAATTCCCCTAAATTAAAGGA
3336164 CTAAAT
66 CTAAAT
3336170 TAAAAGGAGT
Statistics
Matches: 175, Mismatches: 32, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
136 60 0.34
137 12 0.07
138 103 0.59
ACGTcount: A:0.45, C:0.15, G:0.14, T:0.26
Consensus pattern (138 bp):
AATAATTAAAATGGAACCTCGAACAAAAGCGAGGACCAAATTAAAAATTCCCCTAAATTAAAGGA
CTAAATATGAAATTAAAACTAAAGTAGAGGCTCTAATTATTAACCTAGTCAATATTAACCAATTA
TTAGATCA
Found at i:3337269 original size:20 final size:21
Alignment explanation
Indices: 3337244--3337283 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
3337234 GTATGTTATG
*
3337244 GTAATGGGTTAATTG-ATTGT
1 GTAATGGGTAAATTGTATTGT
3337264 GTAATGGGTAAATTGTATTG
1 GTAATGGGTAAATTGTATTG
3337284 GAGGAATGGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.28, C:0.00, G:0.30, T:0.42
Consensus pattern (21 bp):
GTAATGGGTAAATTGTATTGT
Found at i:3337939 original size:23 final size:23
Alignment explanation
Indices: 3337901--3337960 Score: 68
Period size: 23 Copynumber: 2.5 Consensus size: 23
3337891 TCTCTTTCTC
3337901 TCTATTTTTTCAATTTTTCTCATTTT
1 TCTATTTTTT--ATTTTTC-CATTTT
*
3337927 T-TATTTTTTATTTTTCCTTTTT
1 TCTATTTTTTATTTTTCCATTTT
*
3337949 TCTCTTTTTTAT
1 TCTATTTTTTAT
3337961 CAATTAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
22 6 0.19
23 16 0.52
25 8 0.26
26 1 0.03
ACGTcount: A:0.12, C:0.13, G:0.00, T:0.75
Consensus pattern (23 bp):
TCTATTTTTTATTTTTCCATTTT
Found at i:3338342 original size:44 final size:44
Alignment explanation
Indices: 3338276--3338393 Score: 121
Period size: 44 Copynumber: 2.7 Consensus size: 44
3338266 GTGGCGATGG
* * *
3338276 TGCTGATA-CAACTCCTTATGTGATGGAATCGAACAAAATGTTGA
1 TGCTGA-ACCAACTCATTATGTGATGGAATCGAACAAAAGGGTGA
* * * * * * *
3338320 TGCTGATCTACCTCATTCTGTGATAGAATCGAGCAAAAGGGTGT
1 TGCTGAACCAACTCATTATGTGATGGAATCGAACAAAAGGGTGA
*
3338364 TGCTGAACCAACTCCTTATGTGATGGAATC
1 TGCTGAACCAACTCATTATGTGATGGAATC
3338394 CGAAGGTATT
Statistics
Matches: 57, Mismatches: 16, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
44 57 1.00
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.30
Consensus pattern (44 bp):
TGCTGAACCAACTCATTATGTGATGGAATCGAACAAAAGGGTGA
Found at i:3338725 original size:66 final size:66
Alignment explanation
Indices: 3338585--3338727 Score: 160
Period size: 66 Copynumber: 2.2 Consensus size: 66
3338575 TTAAAAGAAA
* * * * * * **
3338585 TTTGTTTCAAGAGAAGCAATCTCATGTGAGATAAAATTTTATTTTAAGTGAAACAATTTCGAAGT
1 TTTGTTTCAAGAAAAACAATCTCAAGTGAGATAAAATCTTATTTCAAGTGAAACAAATTAAAAGT
3338650 T
66 T
* * ** * *
3338651 TGTATTTCAAGAAAAATTATCTCAAGTGAGATAAAATCTTGTTTCAAGTGAAACAAATTAAAATT
1 TTTGTTTCAAGAAAAACAATCTCAAGTGAGATAAAATCTTATTTCAAGTGAAACAAATTAAAAGT
3338716 T
66 T
3338717 TTTGTTTCAAG
1 TTTGTTTCAAG
3338728 GGAAAAGCTG
Statistics
Matches: 61, Mismatches: 16, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
66 61 1.00
ACGTcount: A:0.38, C:0.09, G:0.15, T:0.38
Consensus pattern (66 bp):
TTTGTTTCAAGAAAAACAATCTCAAGTGAGATAAAATCTTATTTCAAGTGAAACAAATTAAAAGT
T
Found at i:3340978 original size:91 final size:91
Alignment explanation
Indices: 3340814--3341405 Score: 709
Period size: 91 Copynumber: 6.5 Consensus size: 91
3340804 TGGAAAATTA
* ** * * *
3340814 ATTATGAACTTATTCTCCCTCATTGGATGAGTTCTTCTCATTATAAACTCTACACTAGAAATGTT
1 ATTATGAACTTCTTCTCCCTTGTTGGATGAGTTCTTCTCATTATGAACTCTCCACTAGGAATGTT
* * *
3340879 G-GTTCAAGGTCGAATAAGTTCTTCTC
66 GAG-CCAAGGTTGAACAAGTTCTTCTC
* * * * *
3340905 ATTATGAACTTTTTCTCCCTTGTAGGA-CATGTTGTTCTCATTATGAACTCTCCACTAGGAATAT
1 ATTATGAACTTCTTCTCCCTTGTTGGATGA-GTTCTTCTCATTATGAACTCTCCACTAGGAATGT
3340969 TGAGCCAAGGTTGAACAAGCTT-TTCTC
65 TGAGCCAAGGTTGAACAAG-TTCTTCTC
* * * * *
3340996 ATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTATCATTATGAACTCTTCA-TTGGAAACGT
1 ATTATGAACTTCTTCTCCCTTGTTGGATGAGTTCTTCTCATTATGAACTCTCCACTAGG-AATGT
* * * *
3341060 TGATCAAAAGTTGAATAAGTTCTTCTC
65 TGAGCCAAGGTTGAACAAGTTCTTCTC
* * **
3341087 ATTATGAACTTTTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAACTCTCCACTAAAAATGTT
1 ATTATGAACTTCTTCTCCCTTGTTGGATGAGTTCTTCTCATTATGAACTCTCCACTAGGAATGTT
* *
3341152 GAGTCAAGGTTGAATAAGTTCTTCTC
66 GAGCCAAGGTTGAACAAGTTCTTCTC
3341178 ATTATGAACTTCTTCTCCCTTGTTGGATGAGTTCTTCTCATTATGAACTCTCCACT-GGAAATGT
1 ATTATGAACTTCTTCTCCCTTGTTGGATGAGTTCTTCTCATTATGAACTCTCCACTAGG-AATGT
3341242 TGAGCCAAGGTTGAACAAGTTCTTCTC
65 TGAGCCAAGGTTGAACAAGTTCTTCTC
** *
3341269 ATTATGAACTTCTTCT--C-TAAT-GATGTGTTCTTCTCATTATGAACTCTCCACT-GGAAATGT
1 ATTATGAACTTCTTCTCCCTTGTTGGATGAGTTCTTCTCATTATGAACTCTCCACTAGG-AATGT
* * *
3341329 TGATCCAAGGTGGAACAAGTTATTCTC
65 TGAGCCAAGGTTGAACAAGTTCTTCTC
* * * *
3341356 ATTATGAACTTCTTCTCCCTCGTCGAATGAGTTCTTCTTATTATGAACTC
1 ATTATGAACTTCTTCTCCCTTGTTGGATGAGTTCTTCTCATTATGAACTC
3341406 CTCGCTGGAA
Statistics
Matches: 432, Mismatches: 57, Indels: 24
0.84 0.11 0.05
Matches are distributed among these distances:
87 78 0.18
88 2 0.00
89 2 0.00
90 6 0.01
91 339 0.78
92 5 0.01
ACGTcount: A:0.25, C:0.20, G:0.16, T:0.39
Consensus pattern (91 bp):
ATTATGAACTTCTTCTCCCTTGTTGGATGAGTTCTTCTCATTATGAACTCTCCACTAGGAATGTT
GAGCCAAGGTTGAACAAGTTCTTCTC
Found at i:3341127 original size:182 final size:181
Alignment explanation
Indices: 3340814--3341425 Score: 797
Period size: 182 Copynumber: 3.4 Consensus size: 181
3340804 TGGAAAATTA
* * * * *
3340814 ATTATGAACTTATTCTCCCTCATTGGATGAGTTCTTCTCATTATAAACTCTACACTAGAAATGTT
1 ATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAACTCTTCACTGGAAATGTT
* * * * *
3340879 GGTTC-AAGGTCGAATAAGTTCTTCTCATTATGAACTTTTTCTCCCTTGTAGGA-CATGTTGTTC
66 -GATCAAAGGTTGAATAAGTTCTTCTCATTATGAACTTTTTCTCCC-TGTTGGATGA-GTTCTTC
*
3340942 TCATTATGAACTCTCCACTAGGAATATTGAGCCAAGGTTGAACAAGCTT-TTCTC
128 TCATTATGAACTCTCCACTAGGAATGTTGAGCCAAGGTTGAACAAG-TTATTCTC
* * *
3340996 ATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTATCATTATGAACTCTTCATTGGAAACGTT
1 ATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAACTCTTCACTGGAAATGTT
*
3341061 GATCAAAAGTTGAATAAGTTCTTCTCATTATGAACTTTTTCTCCCTCGTTGGATGAGTTCTTCTC
66 GATCAAAGGTTGAATAAGTTCTTCTCATTATGAACTTTTTCTCCCT-GTTGGATGAGTTCTTCTC
** * * *
3341126 ATTATGAACTCTCCACTAAAAATGTTGAGTCAAGGTTGAATAAGTTCTTCTC
130 ATTATGAACTCTCCACTAGGAATGTTGAGCCAAGGTTGAACAAGTTATTCTC
* *
3341178 ATTATGAACTTCTTCTCCCTTGTTGGATGAGTTCTTCTCATTATGAACTCTCCACTGGAAATGTT
1 ATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAACTCTTCACTGGAAATGTT
* * * * ** *
3341243 GAGCCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCT--CTAAT-GATGTGTTCTTCTCA
66 GATCAAAGGTTGAATAAGTTCTTCTCATTATGAACTTTTTCTCCCTGTTGGATGAGTTCTTCTCA
* *
3341305 TTATGAACTCTCCACT-GGAAATGTTGATCCAAGGTGGAACAAGTTATTCTC
131 TTATGAACTCTCCACTAGG-AATGTTGAGCCAAGGTTGAACAAGTTATTCTC
* * * * *
3341356 ATTATGAACTTCTTCTCCCTCGTCGAATGAGTTCTTCTTATTATGAACTCCTCGCTGGAAATGTT
1 ATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAACTCTTCACTGGAAATGTT
3341421 GATCA
66 GATCA
3341426 GTTTATCTTC
Statistics
Matches: 377, Mismatches: 48, Indels: 14
0.86 0.11 0.03
Matches are distributed among these distances:
178 118 0.31
179 1 0.00
180 2 0.01
181 6 0.02
182 249 0.66
183 1 0.00
ACGTcount: A:0.25, C:0.20, G:0.16, T:0.38
Consensus pattern (181 bp):
ATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAACTCTTCACTGGAAATGTT
GATCAAAGGTTGAATAAGTTCTTCTCATTATGAACTTTTTCTCCCTGTTGGATGAGTTCTTCTCA
TTATGAACTCTCCACTAGGAATGTTGAGCCAAGGTTGAACAAGTTATTCTC
Found at i:3341772 original size:36 final size:38
Alignment explanation
Indices: 3341725--3341990 Score: 234
Period size: 39 Copynumber: 7.0 Consensus size: 38
3341715 TGATTTTGCA
* * *
3341725 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTC-G
1 TTTCAAGGGAAACTATCTCAAGCGAGACAAAACTTCTG
* * * * * *
3341761 TTTCAAGAGAAAATGTTTCAAGTGAGAGAAAA-TT-TG
1 TTTCAAGGGAAACTATCTCAAGCGAGACAAAACTTCTG
* * * *
3341797 TTTCAAGGGAAACTGTCTCAAGAGAGATAAAATCTTCTA
1 TTTCAAGGGAAACTATCTCAAGCGAGACAAAA-CTTCTG
* *
3341836 TTTCGAGGGAAACTATCTCAAGCGAGACAAAATCTTCTA
1 TTTCAAGGGAAACTATCTCAAGCGAGACAAAA-CTTCTG
* *
3341875 TTTCGAGGGAAACTATCTCAAGCGAGATAAAATCTTCTG
1 TTTCAAGGGAAACTATCTCAAGCGAGACAAAA-CTTCTG
* * *
3341914 TTTCGAGGGAAACAATCTCAAGCGAGACAAAATATTCTG
1 TTTCAAGGGAAACTATCTCAAGCGAGACAAAA-CTTCTG
** ** *
3341953 TTTTGAGACAAACTATCTCAAGCGAGATAAAATCTTCT
1 TTTCAAGGGAAACTATCTCAAGCGAGACAAAA-CTTCT
3341991 TTAAAACAAT
Statistics
Matches: 201, Mismatches: 25, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
36 58 0.29
38 2 0.01
39 141 0.70
ACGTcount: A:0.38, C:0.16, G:0.19, T:0.27
Consensus pattern (38 bp):
TTTCAAGGGAAACTATCTCAAGCGAGACAAAACTTCTG
Found at i:3341855 original size:39 final size:39
Alignment explanation
Indices: 3341797--3341990 Score: 280
Period size: 39 Copynumber: 5.0 Consensus size: 39
3341787 AGAAAATTTG
* * *
3341797 TTTCAAGGGAAACTGTCTCAAGAGAGATAAAATCTTCTA
1 TTTCGAGGGAAACTATCTCAAGCGAGATAAAATCTTCTA
*
3341836 TTTCGAGGGAAACTATCTCAAGCGAGACAAAATCTTCTA
1 TTTCGAGGGAAACTATCTCAAGCGAGATAAAATCTTCTA
*
3341875 TTTCGAGGGAAACTATCTCAAGCGAGATAAAATCTTCTG
1 TTTCGAGGGAAACTATCTCAAGCGAGATAAAATCTTCTA
* * * *
3341914 TTTCGAGGGAAACAATCTCAAGCGAGACAAAATATTCTG
1 TTTCGAGGGAAACTATCTCAAGCGAGATAAAATCTTCTA
* **
3341953 TTTTGAGACAAACTATCTCAAGCGAGATAAAATCTTCT
1 TTTCGAGGGAAACTATCTCAAGCGAGATAAAATCTTCT
3341991 TTAAAACAAT
Statistics
Matches: 140, Mismatches: 15, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 140 1.00
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.27
Consensus pattern (39 bp):
TTTCGAGGGAAACTATCTCAAGCGAGATAAAATCTTCTA
Found at i:3342368 original size:13 final size:13
Alignment explanation
Indices: 3342345--3342406 Score: 72
Period size: 13 Copynumber: 4.6 Consensus size: 13
3342335 ATTTTTTTAA
3342345 TAACTAGTGAACAG
1 TAAC-AGTGAACAG
*
3342359 TAACAGTGAACAT
1 TAACAGTGAACAG
*
3342372 TATTC-GTGAACAG
1 TA-ACAGTGAACAG
3342385 TAACAGTGAACAG
1 TAACAGTGAACAG
3342398 TGAACAGTG
1 T-AACAGTG
3342407 TATCGATGCA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
12 1 0.02
13 28 0.68
14 12 0.29
ACGTcount: A:0.40, C:0.15, G:0.23, T:0.23
Consensus pattern (13 bp):
TAACAGTGAACAG
Found at i:3342398 original size:7 final size:7
Alignment explanation
Indices: 3342350--3342406 Score: 59
Period size: 7 Copynumber: 8.6 Consensus size: 7
3342340 TTTAATAACT
3342350 AGTGAAC
1 AGTGAAC
3342357 AGT-AAC
1 AGTGAAC
3342363 AGTGAAC
1 AGTGAAC
* *
3342370 A-TTATTC
1 AGTGA-AC
3342377 -GTGAAC
1 AGTGAAC
3342383 AGT-AAC
1 AGTGAAC
3342389 AGTGAAC
1 AGTGAAC
3342396 AGTGAAC
1 AGTGAAC
3342403 AGTG
1 AGTG
3342407 TATCGATGCA
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
6 15 0.37
7 26 0.63
ACGTcount: A:0.40, C:0.14, G:0.25, T:0.21
Consensus pattern (7 bp):
AGTGAAC
Found at i:3342981 original size:47 final size:45
Alignment explanation
Indices: 3342905--3343030 Score: 166
Period size: 47 Copynumber: 2.8 Consensus size: 45
3342895 TATAAAATCT
* *
3342905 CTTACCATTTATCCCATAAGCTTTGTAAGCTTATTTTACCAAAATA
1 CTTACCATTTATTCCATAAGC-TCGTAAGCTTATTTTACCAAAATA
* *
3342951 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTATCAATATA
1 CTTACCATTT--ATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
*
3342998 CTTGCCA-TTATT-CATAAGCTCGTAAGCTTATTT
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTT
3343031 GCATACTTAC
Statistics
Matches: 73, Mismatches: 5, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
43 21 0.29
44 3 0.04
46 12 0.16
47 27 0.37
48 10 0.14
ACGTcount: A:0.31, C:0.21, G:0.08, T:0.40
Consensus pattern (45 bp):
CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
Found at i:3347982 original size:13 final size:13
Alignment explanation
Indices: 3347964--3347990 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3347954 TATATTATCC
3347964 TAATCGTAACCAT
1 TAATCGTAACCAT
3347977 TAATCGTAACCAT
1 TAATCGTAACCAT
3347990 T
1 T
3347991 GTTGATATCA
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:0.22, G:0.07, T:0.33
Consensus pattern (13 bp):
TAATCGTAACCAT
Found at i:3350051 original size:45 final size:46
Alignment explanation
Indices: 3350002--3350102 Score: 150
Period size: 47 Copynumber: 2.2 Consensus size: 46
3349992 TATAAAATCT
3350002 CTTACCATTT-ATCCCATAAGCTCGTAAGCTTATTTTACCAAAATA
1 CTTACCATTTAATCCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* * *
3350047 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTATCAATATA
1 CTTACCATTT-AATCCCATAAGCTCGTAAGCTTATTTTACCAAAATA
*
3350094 CTTTCCATT
1 CTTACCATT
3350103 ATTCATAATA
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
45 10 0.20
47 40 0.80
ACGTcount: A:0.32, C:0.23, G:0.06, T:0.40
Consensus pattern (46 bp):
CTTACCATTTAATCCCATAAGCTCGTAAGCTTATTTTACCAAAATA
Found at i:3354714 original size:14 final size:15
Alignment explanation
Indices: 3354694--3354730 Score: 51
Period size: 13 Copynumber: 2.6 Consensus size: 15
3354684 GCAAATGAAA
3354694 AGATGCAAAAATGAG
1 AGATGCAAAAATGAG
*
3354709 AG-TGC-AAAATGTG
1 AGATGCAAAAATGAG
3354722 AGATGCAAA
1 AGATGCAAA
3354731 TGCAACAAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 4
0.79 0.04 0.17
Matches are distributed among these distances:
13 9 0.47
14 6 0.32
15 4 0.21
ACGTcount: A:0.49, C:0.08, G:0.27, T:0.16
Consensus pattern (15 bp):
AGATGCAAAAATGAG
Found at i:3356808 original size:23 final size:23
Alignment explanation
Indices: 3356782--3356829 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
3356772 AAAATATATT
3356782 TATTAATATTTCTAATA-ATATAA
1 TATT-ATATTTCTAATATATATAA
* *
3356805 TATTATATTTTTAATATGTATAA
1 TATTATATTTCTAATATATATAA
3356828 TA
1 TA
3356830 AAATAATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 11 0.50
23 11 0.50
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (23 bp):
TATTATATTTCTAATATATATAA
Found at i:3356810 original size:26 final size:24
Alignment explanation
Indices: 3356757--3356810 Score: 58
Period size: 23 Copynumber: 2.2 Consensus size: 24
3356747 ATCAAAAAAA
3356757 ATTATTAAAATATTTAAAATATAT
1 ATTATTAAAATATTTAAAATATAT
*
3356781 -TTATTAATAT-TTCTAATAATATAAT
1 ATTATTAAAATATT-TAA-AATAT-AT
3356806 ATTAT
1 ATTAT
3356811 ATTTTTAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
22 2 0.08
23 12 0.48
24 5 0.20
25 2 0.08
26 4 0.16
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (24 bp):
ATTATTAAAATATTTAAAATATAT
Found at i:3356821 original size:31 final size:32
Alignment explanation
Indices: 3356776--3356836 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 32
3356766 ATATTTAAAA
* * *
3356776 TATATTTATTAATATTTCTAATAATATAATAT
1 TATATTTATTAATATGTATAATAAAATAATAT
3356808 TATATTT-TTAATATGTATAATAAAATAAT
1 TATATTTATTAATATGTATAATAAAATAAT
3356837 CAATTACATT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 19 0.73
32 7 0.27
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (32 bp):
TATATTTATTAATATGTATAATAAAATAATAT
Found at i:3357006 original size:19 final size:19
Alignment explanation
Indices: 3356966--3357019 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 19
3356956 TAATAACGGA
*
3356966 TAATATT-ATTT-ATATATT
1 TAATATTAATTTAATA-ATC
3356984 TAATATTAATTTAATAATC
1 TAATATTAATTTAATAATC
* *
3357003 TAATAATATTTTAATAA
1 TAATATTAATTTAATAA
3357020 ATATTTAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
18 7 0.23
19 21 0.68
20 3 0.10
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (19 bp):
TAATATTAATTTAATAATC
Found at i:3357132 original size:32 final size:33
Alignment explanation
Indices: 3357117--3357177 Score: 74
Period size: 32 Copynumber: 1.9 Consensus size: 33
3357107 TTCAATAAAA
* *
3357117 TATACCAATATTAATATTTT-TATTAATAAAAT
1 TATAACAATAATAATATTTTATATTAATAAAAT
*
3357149 TATAATAATAATAATATTTTA-A-TAATAAA
1 TATAACAATAATAATATTTTATATTAATAAA
3357178 TAAATTATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
31 7 0.28
32 18 0.72
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.44
Consensus pattern (33 bp):
TATAACAATAATAATATTTTATATTAATAAAAT
Found at i:3357162 original size:17 final size:17
Alignment explanation
Indices: 3357140--3357208 Score: 63
Period size: 17 Copynumber: 4.1 Consensus size: 17
3357130 ATATTTTTAT
3357140 TAATAAAATTATAATAA
1 TAATAAAATTATAATAA
* *
3357157 TAATAATATTTTAATAA
1 TAATAAAATTATAATAA
**
3357174 TAA-ATAAATTATTTTAA
1 TAATA-AAATTATAATAA
3357191 TAATTAAAA--ATAATAA
1 TAA-TAAAATTATAATAA
3357207 TA
1 TA
3357209 TTGAGTTTTA
Statistics
Matches: 41, Mismatches: 8, Indels: 7
0.73 0.14 0.12
Matches are distributed among these distances:
16 8 0.20
17 29 0.71
18 3 0.07
19 1 0.02
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TAATAAAATTATAATAA
Found at i:3357173 original size:20 final size:20
Alignment explanation
Indices: 3357150--3357205 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
3357140 TAATAAAATT
3357150 ATAATAATAATAATATTTTA
1 ATAATAATAATAATATTTTA
*
3357170 ATAATAAATAA-ATTATTTTA
1 ATAAT-AATAATAATATTTTA
*
3357190 ATAATTAAAAATAATA
1 ATAA-TAATAATAATA
3357206 ATATTGAGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
20 21 0.70
21 9 0.30
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
ATAATAATAATAATATTTTA
Found at i:3357345 original size:14 final size:14
Alignment explanation
Indices: 3357322--3357357 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
3357312 CCAAATATAG
*
3357322 TAAAACGTTTTTCA
1 TAAAATGTTTTTCA
3357336 TAAAATGTTTTTCA
1 TAAAATGTTTTTCA
*
3357350 GAAAATGT
1 TAAAATGT
3357358 AATTCCTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.39, C:0.08, G:0.11, T:0.42
Consensus pattern (14 bp):
TAAAATGTTTTTCA
Found at i:3358207 original size:54 final size:53
Alignment explanation
Indices: 3358149--3358752 Score: 308
Period size: 54 Copynumber: 11.2 Consensus size: 53
3358139 TGTAGTTCCG
* * * *
3358149 ATACGGTAATTCACAAAATTATTATGAATTACGTGGGGTGCACACATAATGCCA
1 ATACGGAAATTC-TAAACTTATTATGAATTACGTAGGGTGCACACATAATGCCA
* * * * * *
3358203 ATACGAAAATTCTAAACTAATTATGAATTTCTTAGGTTGCACACATATTGCCA
1 ATACGGAAATTCTAAACTTATTATGAATTACGTAGGGTGCACACATAATGCCA
* * * * *** * * *
3358256 ATATGGAAACTCGTAAACTTATTATGAATTTCTTAATTTACACACACAACGCCA
1 ATACGGAAATTC-TAAACTTATTATGAATTACGTAGGGTGCACACATAATGCCA
* * * * * * * * * *
3358310 ATACGAAAATTCATAAACTCATTATGAATTTCTTAAGTTGCATACACAGTGTCA
1 ATACGGAAATTC-TAAACTTATTATGAATTACGTAGGGTGCACACATAATGCCA
* * * * * * * *
3358364 ATACGGAAATTCATTAACTCATTATGAATTTCTTAAGTTGCAGACATAGTGCCA
1 ATACGGAAATTC-TAAACTTATTATGAATTACGTAGGGTGCACACATAATGCCA
* * * * * * *
3358418 ATACGGAAATTTATAAACTTATTATGAATTTCTTAAGTTACACACACAATGCCA
1 ATACGGAAA-TTCTAAACTTATTATGAATTACGTAGGGTGCACACATAATGCCA
* * * * * * * *
3358472 ATACGAAAATTCATAAACTCATTATGAATTTCTTAAGTTGTACACACAATGCCA
1 ATACGGAAATTC-TAAACTTATTATGAATTACGTAGGGTGCACACATAATGCCA
* * * * * * * * * * *
3358526 ATACGAAAATTCATAAAGTCATTATAAATTTCTTAAGTTGGACACACAGTGCCA
1 ATACGGAAATTC-TAAACTTATTATGAATTACGTAGGGTGCACACATAATGCCA
* * * * * * * * ** * *
3358580 ACACGAAAATTCATAAACTCATTATGAATTTCTTAAGTTGAACACATTGTACTA
1 ATACGGAAATTC-TAAACTTATTATGAATTACGTAGGGTGCACACATAATGCCA
* * * * * **
3358634 ATACGGAAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACATCGTGCCA
1 ATACGGAAATTC-TAAACTTATTATGAATTACGTAGGGTGCACACATAATGCCA
* * * * * *
3358688 ATACGGAAATTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAGTGCCA
1 ATACGGAAATTC-TAAACTTATTATGAATTACGTAGGGTGCACACATAATGCCA
3358742 ATACGGTAAAT
1 ATACGG-AAAT
3358753 ACAATACATA
Statistics
Matches: 477, Mismatches: 69, Indels: 7
0.86 0.12 0.01
Matches are distributed among these distances:
53 44 0.09
54 427 0.90
55 6 0.01
ACGTcount: A:0.39, C:0.18, G:0.12, T:0.32
Consensus pattern (53 bp):
ATACGGAAATTCTAAACTTATTATGAATTACGTAGGGTGCACACATAATGCCA
Found at i:3358437 original size:162 final size:162
Alignment explanation
Indices: 3358187--3358752 Score: 780
Period size: 162 Copynumber: 3.5 Consensus size: 162
3358177 TTACGTGGGG
* * * * * *
3358187 TGCACACATAATGCCAATACGAAAATTC-TAAACTAATTATGAATTTCTTAGGTTGCACACATAT
1 TGCACACACAGTGCCAATACGAAAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACACAG
* * * * *
3358251 TGCCAATATGGAAACTCGTAAACTTATTATGAATTTCTTAATTTACACACACAACGCCAATACGA
66 TGCCAATACGGAAATTCATAAACTTATTATGAATTTCTTAAGTTACACACACAATGCCAATACGA
3358316 AAATTCATAAACTCATTATGAATTTCTTAAGT
131 AAATTCATAAACTCATTATGAATTTCTTAAGT
* * * * * *
3358348 TGCATACACAGTGTCAATACGGAAATTCATTAACTCATTATGAATTTCTTAAGTTGCAGACATAG
1 TGCACACACAGTGCCAATACGAAAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACACAG
*
3358413 TGCCAATACGGAAATTTATAAACTTATTATGAATTTCTTAAGTTACACACACAATGCCAATACGA
66 TGCCAATACGGAAATTCATAAACTTATTATGAATTTCTTAAGTTACACACACAATGCCAATACGA
3358478 AAATTCATAAACTCATTATGAATTTCTTAAGT
131 AAATTCATAAACTCATTATGAATTTCTTAAGT
* * * * *
3358510 TGTACACACAATGCCAATACGAAAATTCATAAAGTCATTATAAATTTCTTAAGTTGGACACACAG
1 TGCACACACAGTGCCAATACGAAAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACACAG
* * * * * *
3358575 TGCCAACACGAAAATTCATAAACTCATTATGAATTTCTTAAGTT-GA-ACACATTGTACTAATAC
66 TGCCAATACGGAAATTCATAAACTTATTATGAATTTCTTAAGTTACACACACAATG--CCAATAC
*
3358638 GGAAATTCATAAACTCATTATGAATTTCTTAAGT
129 GAAAATTCATAAACTCATTATGAATTTCTTAAGT
* *
3358672 TGCACACATC-GTGCCAATACGGAAATTCATAAACTTATTATGAATTTCTTAAGTTGCACACACA
1 TGCACACA-CAGTGCCAATACGAAAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACACA
3358736 GTGCCAATACGGTAAAT
65 GTGCCAATACGG-AAAT
3358753 ACAATACATA
Statistics
Matches: 356, Mismatches: 44, Indels: 8
0.87 0.11 0.02
Matches are distributed among these distances:
160 7 0.02
161 24 0.07
162 320 0.90
163 5 0.01
ACGTcount: A:0.39, C:0.18, G:0.11, T:0.32
Consensus pattern (162 bp):
TGCACACACAGTGCCAATACGAAAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACACAG
TGCCAATACGGAAATTCATAAACTTATTATGAATTTCTTAAGTTACACACACAATGCCAATACGA
AAATTCATAAACTCATTATGAATTTCTTAAGT
Found at i:3358747 original size:108 final size:108
Alignment explanation
Indices: 3358187--3358746 Score: 750
Period size: 108 Copynumber: 5.2 Consensus size: 108
3358177 TTACGTGGGG
* * * * *
3358187 TGCACACATAATGCCAATACGAAAATTC-TAAACTAATTATGAATTTCTTAGGTTGCACACATAT
1 TGCACACACAATGCCAATACGAAAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACACAG
* * * * *
3358251 TGCCAATATGGAAACTCGTAAACTTATTATGAATTTCTTAATT
66 TGCCAATACGGAAATTCATAAACTCATTATGAATTTCTTAAGT
* * *
3358294 TACACACACAACGCCAATACGAAAATTCATAAACTCATTATGAATTTCTTAAGTTGCATACACAG
1 TGCACACACAATGCCAATACGAAAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACACAG
* *
3358359 TGTCAATACGGAAATTCATTAACTCATTATGAATTTCTTAAGT
66 TGCCAATACGGAAATTCATAAACTCATTATGAATTTCTTAAGT
* * * * * * * *
3358402 TGCAGACATAGTGCCAATACGGAAATTTATAAACTTATTATGAATTTCTTAAGTTACACACACAA
1 TGCACACACAATGCCAATACGAAAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACACAG
*
3358467 TGCCAATACGAAAATTCATAAACTCATTATGAATTTCTTAAGT
66 TGCCAATACGGAAATTCATAAACTCATTATGAATTTCTTAAGT
* * * *
3358510 TGTACACACAATGCCAATACGAAAATTCATAAAGTCATTATAAATTTCTTAAGTTGGACACACAG
1 TGCACACACAATGCCAATACGAAAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACACAG
* *
3358575 TGCCAACACGAAAATTCATAAACTCATTATGAATTTCTTAAGT
66 TGCCAATACGGAAATTCATAAACTCATTATGAATTTCTTAAGT
* * *
3358618 TG-A-ACACATTGTACTAATACGGAAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACAT
1 TGCACACACAATG--CCAATACGAAAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACA-
*
3358681 C-GTGCCAATACGGAAATTCATAAACTTATTATGAATTTCTTAAGT
63 CAGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCTTAAGT
*
3358726 TGCACACACAGTGCCAATACG
1 TGCACACACAATGCCAATACG
3358747 GTAAATACAA
Statistics
Matches: 394, Mismatches: 53, Indels: 11
0.86 0.12 0.02
Matches are distributed among these distances:
106 7 0.02
107 26 0.07
108 352 0.89
109 2 0.01
110 7 0.02
ACGTcount: A:0.39, C:0.18, G:0.11, T:0.32
Consensus pattern (108 bp):
TGCACACACAATGCCAATACGAAAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACACAG
TGCCAATACGGAAATTCATAAACTCATTATGAATTTCTTAAGT
Found at i:3359216 original size:21 final size:21
Alignment explanation
Indices: 3359186--3359262 Score: 136
Period size: 21 Copynumber: 3.7 Consensus size: 21
3359176 TCGATACCCA
*
3359186 CATCAATATCGATACTAAATG
1 CATCAGTATCGATACTAAATG
3359207 CATCAGTATCGATACTAAATG
1 CATCAGTATCGATACTAAATG
*
3359228 CATCAGCATCGATACTAAATG
1 CATCAGTATCGATACTAAATG
3359249 CATCAGTATCGATA
1 CATCAGTATCGATA
3359263 TTGTTCATCG
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 53 1.00
ACGTcount: A:0.39, C:0.21, G:0.13, T:0.27
Consensus pattern (21 bp):
CATCAGTATCGATACTAAATG
Found at i:3361656 original size:246 final size:244
Alignment explanation
Indices: 3361185--3361668 Score: 799
Period size: 246 Copynumber: 2.0 Consensus size: 244
3361175 GTTGCAGGAG
* * * *
3361185 CATTAATCAATCCAAATGGCATTACCAAAATTTGTAGTGTCCATATCGAGTCCGAAAAGTTATCT
1 CATTAATCAACCCAAATCGCATTACCAAAATTCGTAGTGTCCATATCAAGTCCGAAAAGTTATCT
* *
3361250 TTGAAATATCATCCTTTTTATCTTTAATTGGTGGTACCCCGACCTCAGGTCTATCTTAGAGAACA
66 TTGAAATATCATCCTTTTTATCTTTAATTGGTGGTACCCCAACCTCAGGTCTACCTTAGAGAACA
* * * *
3361315 CTGTTGCACCTTTCAATTAATCGAATGGATCATCAATCCTCAGAAGAGGATATTTATTCTTTATC
131 CTGCTACACCTTTCAATTAATCGAATAGATCATCAATCATCAGAAGAGGATATTTATTCTTTATC
3361380 GTTACTTTGTTTAACTGACGGTAGTCGATACATAATCACATAGTCGATA
196 GTTACTTTGTTTAACTGACGGTAGTCGATACATAATCACATAGTCGATA
*
3361429 CATTAATCAACCCAAATCGCTTTACCATAAATTCGTAGTGTCCATATCAAGTCCGAAAAGTTATC
1 CATTAATCAACCCAAATCGCATTACCA-AAATTCGTAGTGTCCATATCAAGTCCGAAAAGTTATC
3361494 TTTGAAATATCATCCTCTTTTATCTTTAATTGGTGGTACCCCAACCTCAGGTCTACCTTAGAGAA
65 TTTGAAATATCATCCT-TTTTATCTTTAATTGGTGGTACCCCAACCTCAGGTCTACCTTAGAGAA
* * *
3361559 CACTGCTACGCCTTTCAATTGATCGAATAGATCATCAATCATCGGAAGAGGATATTTATTCTTTA
129 CACTGCTACACCTTTCAATTAATCGAATAGATCATCAATCATCAGAAGAGGATATTTATTCTTTA
*
3361624 TCGTTA-TTATGTTTAACTGACGGTATTCGATACATAATCACATAG
194 TCGTTACTT-TGTTTAACTGACGGTAGTCGATACATAATCACATAG
3361669 ACCTGACCTT
Statistics
Matches: 222, Mismatches: 15, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
244 24 0.11
245 53 0.24
246 145 0.65
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.35
Consensus pattern (244 bp):
CATTAATCAACCCAAATCGCATTACCAAAATTCGTAGTGTCCATATCAAGTCCGAAAAGTTATCT
TTGAAATATCATCCTTTTTATCTTTAATTGGTGGTACCCCAACCTCAGGTCTACCTTAGAGAACA
CTGCTACACCTTTCAATTAATCGAATAGATCATCAATCATCAGAAGAGGATATTTATTCTTTATC
GTTACTTTGTTTAACTGACGGTAGTCGATACATAATCACATAGTCGATA
Found at i:3364343 original size:54 final size:54
Alignment explanation
Indices: 3364292--3364870 Score: 723
Period size: 54 Copynumber: 10.9 Consensus size: 54
3364282 CCGATACGGT
* * * ** *
3364292 AATTCACAAACTCATTATGAATTACATGGGGTGCACACATAGTGCCAATACGAA
1 AATTCATAAACTCATTATGAATTTCTTAAGTTGCACACATAGTGCCAATACGAA
* *
3364346 AATTCATAAACTAATTATGAATTTCTTAGGTTGCACACATAGTGCCAATAC-AGA
1 AATTCATAAACTCATTATGAATTTCTTAAGTTGCACACATAGTGCCAATACGA-A
* * *
3364400 AATTCATAAACTTATTATGAATTTCTTAAGTT--ATACACAGTGCCAATACGAA
1 AATTCATAAACTCATTATGAATTTCTTAAGTTGCACACATAGTGCCAATACGAA
* * *
3364452 AATTCATAAACTCGTTATGAATTTCTTAAGTTGCATACACAGTGCCAATAC-AA
1 AATTCATAAACTCATTATGAATTTCTTAAGTTGCACACATAGTGCCAATACGAA
* * * *
3364505 ATTTCATAAACTCATTATGAATTTCTTATGTTGCACACACAATGCC---A--AA
1 AATTCATAAACTCATTATGAATTTCTTAAGTTGCACACATAGTGCCAATACGAA
* * * * *
3364554 AATTGATAAACTCATTATGAATTTCTTAAGTTGTACACATAGTGCCAAAATGGA
1 AATTCATAAACTCATTATGAATTTCTTAAGTTGCACACATAGTGCCAATACGAA
* * * *
3364608 AATTCATAAACACATTATGAATTTCTTATGTCGCACACATAGTGCTAATACGAA
1 AATTCATAAACTCATTATGAATTTCTTAAGTTGCACACATAGTGCCAATACGAA
* * *
3364662 AATTCATAAACTCATTATCAATTTCTTAAGTTGCACACACAATGCCAATACGAA
1 AATTCATAAACTCATTATGAATTTCTTAAGTTGCACACATAGTGCCAATACGAA
* * *
3364716 AATTTATAAACTCATTATGAGTTTCTTAAGTTGCACACATAGTGCCAATACGGA
1 AATTCATAAACTCATTATGAATTTCTTAAGTTGCACACATAGTGCCAATACGAA
* *
3364770 AATTCATAAACTCATTATGAATTTCTTAAGTTGCACATATAGTACCAATACGAA
1 AATTCATAAACTCATTATGAATTTCTTAAGTTGCACACATAGTGCCAATACGAA
* * *
3364824 AATTCATAAACTC---ATGAATTTCTTAACTTGCATACACAGTGCCAATA
1 AATTCATAAACTCATTATGAATTTCTTAAGTTGCACACATAGTGCCAATA
3364871 AGGTAAATGC
Statistics
Matches: 460, Mismatches: 56, Indels: 21
0.86 0.10 0.04
Matches are distributed among these distances:
49 42 0.09
50 1 0.00
51 29 0.06
52 47 0.10
53 45 0.10
54 296 0.64
ACGTcount: A:0.39, C:0.18, G:0.11, T:0.32
Consensus pattern (54 bp):
AATTCATAAACTCATTATGAATTTCTTAAGTTGCACACATAGTGCCAATACGAA
Found at i:3365215 original size:20 final size:20
Alignment explanation
Indices: 3365192--3365234 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
3365182 CTGGTATCGG
3365192 TACCCCTTCTTTGGTAGCGA
1 TACCCCTTCTTTGGTAGCGA
*
3365212 TACCCCTTCTTTGGTATCGA
1 TACCCCTTCTTTGGTAGCGA
3365232 TAC
1 TAC
3365235 TTCTATACTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.16, C:0.30, G:0.16, T:0.37
Consensus pattern (20 bp):
TACCCCTTCTTTGGTAGCGA
Found at i:3366116 original size:15 final size:16
Alignment explanation
Indices: 3366093--3366126 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
3366083 CGAATATTTC
3366093 TTAGAAATTTAGC-AG
1 TTAGAAATTTAGCAAG
*
3366108 TTAGTAATTTAGCAAG
1 TTAGAAATTTAGCAAG
3366124 TTA
1 TTA
3366127 ATGTTTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.38, C:0.06, G:0.18, T:0.38
Consensus pattern (16 bp):
TTAGAAATTTAGCAAG
Found at i:3368401 original size:140 final size:138
Alignment explanation
Indices: 3368180--3368448 Score: 296
Period size: 140 Copynumber: 1.9 Consensus size: 138
3368170 ATATTTTAGG
* * * *
3368180 TTTAGTCCTTTAATTTAGGAGAATTCTTAATGCGGTCCTCACTTTTGCTCAATGTTTCATTTTAA
1 TTTAGTCATTTAATTTAGGAAAATTCTTAATGCGGTCCTCACTTTTGCTCAAGGTTCCATTTTAA
* * * *
3368245 TTATTATATTCAATAA-TTAGTTTAAAATTTG-TTAGG-TTAATATTTAGAGCCTCCA-TTTTAG
66 TTATTAGACTCAATAATTTA--TTAAAA-ATGATTAGGATTAATA-TTAGAGCCTACATTTTTAG
3368306 GTTGAATTTCAC
127 GTTGAATTTCAC
* ** *
3368318 TTTAGTCATTTAATTTATGAAAATT-TTCAATTTGGTCCTCACTTTTATGCTCGAGGTTCCATTT
1 TTTAGTCATTTAATTTAGGAAAATTCTT-AATGCGGTCCTCAC-TTT-TGCTCAAGGTTCCATTT
** * *
3368382 TGGTTATTCGACTCAATAATTTATTAAAAATGATTTGGATTAATATTAGAGCCTACATTTTTAGG
63 TAATTATTAGACTCAATAATTTATTAAAAATGATTAGGATTAATATTAGAGCCTACATTTTTAGG
3368447 TT
128 TT
3368449 TAATCTTCTA
Statistics
Matches: 108, Mismatches: 16, Indels: 12
0.79 0.12 0.09
Matches are distributed among these distances:
137 2 0.02
138 36 0.33
139 24 0.22
140 43 0.40
141 3 0.03
ACGTcount: A:0.28, C:0.13, G:0.13, T:0.46
Consensus pattern (138 bp):
TTTAGTCATTTAATTTAGGAAAATTCTTAATGCGGTCCTCACTTTTGCTCAAGGTTCCATTTTAA
TTATTAGACTCAATAATTTATTAAAAATGATTAGGATTAATATTAGAGCCTACATTTTTAGGTTG
AATTTCAC
Found at i:3374281 original size:19 final size:19
Alignment explanation
Indices: 3374257--3374294 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
3374247 TTTGGCTGCA
3374257 CTCTAATAGGGGAAACCCT
1 CTCTAATAGGGGAAACCCT
3374276 CTCTAATAGGGGAAACCCT
1 CTCTAATAGGGGAAACCCT
3374295 AGGGTTTTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (19 bp):
CTCTAATAGGGGAAACCCT
Found at i:3375120 original size:131 final size:130
Alignment explanation
Indices: 3374905--3375349 Score: 460
Period size: 131 Copynumber: 3.4 Consensus size: 130
3374895 GTATGGAAAA
* * *
3374905 TTTGATTCACTTCGCTGCTCTTCAGGGAAGA-TAAATCCAACTTGATTTGCTTCAATGCTCTTCA
1 TTTGATCCACTTCGCTGCTCTTCAGGGAAGATTAAATCGAAC-CGATTTGCTTCAATGCTCTTCA
* * * * * * **
3374969 GGAAAATCAAATTTGAAAGAAGAAGAATCTGCTCTATTACTCTTTATAGGAGATCAAACATGTAA
65 GGAAAACCAAATCTAAAAGAAGAAGAATCTGCTCCACTACTCTTTAGAGGAGATCAAACACATAA
3375034 T
130 T
* ** * *
3375035 TTTGATCCATTTCGCTGCTCTTCAATGAAGATTAAAACAGAACCGATTTGCTTCATTGCTCTTCA
1 TTTGATCCACTTCGCTGCTCTTCAGGGAAGATTAAATC-GAACCGATTTGCTTCAATGCTCTTCA
* * * * * *
3375100 GGAACACCAAATCTAAAAGAAGAAGAATCTGATCCACTACTCTTTAGGGGATATTAGACACATAA
65 GGAAAACCAAATCTAAAAGAAGAAGAATCTGCTCCACTACTCTTTAGAGGAGATCAAACACATAA
3375165 T
130 T
* * * * *
3375166 TTTGATCCACTTCACTGCTCTTCAGGGAAGATTGAATCTGAATCGATTTGCTTGACTGCTCTTCA
1 TTTGATCCACTTCGCTGCTCTTCAGGGAAGATTAAATC-GAACCGATTTGCTTCAATGCTCTTCA
* * * * ** *
3375231 GGAAGACCAAATCTAAAAGAACAAGAATCTGCTCCGCTACTCTTTAGGGGAGATCGGACTCGAGA
65 GGAAAACCAAATCTAAAAGAAGAAGAATCTGCTCCACTACTCTTTAGAGGAGATC--AAAC-ACA
* *
3375296 AAAC
127 TAAT
* * * *
3375300 TTTGATCCACTTCTCTGCTCTTTAGGGAAGATTGAATCAGAATCGATTTG
1 TTTGATCCACTTCGCTGCTCTTCAGGGAAGATTAAATC-GAACCGATTTG
3375350 TGTCACAGCT
Statistics
Matches: 264, Mismatches: 46, Indels: 6
0.84 0.15 0.02
Matches are distributed among these distances:
130 27 0.10
131 181 0.69
132 3 0.01
133 2 0.01
134 51 0.19
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Consensus pattern (130 bp):
TTTGATCCACTTCGCTGCTCTTCAGGGAAGATTAAATCGAACCGATTTGCTTCAATGCTCTTCAG
GAAAACCAAATCTAAAAGAAGAAGAATCTGCTCCACTACTCTTTAGAGGAGATCAAACACATAAT
Found at i:3375569 original size:240 final size:241
Alignment explanation
Indices: 3375137--3375583 Score: 664
Period size: 240 Copynumber: 1.9 Consensus size: 241
3375127 TCTGATCCAC
* * * *
3375137 TACTCTTTAGGGGATATTAGACACATAATTTTGATCCACTTCACTGCTCTTCAGGGAAGATTGAA
1 TACTCTTTAGGGGAGATCAGACACATAATTTTGATCCACTTCACTGCTCTTCAGGGAAAATTAAA
*
3375202 TCTGAATCGATTTGCTTGACTGCTCTTCAGGAAGACCAAATCTAAAAGAACAAGAATCTGCTCCG
66 TCTGAATCGATTTGCTTGACTGCTATTCAGGAAGACCAAATCTAAAAGAACAAGAATCTGCTCCG
** * *
3375267 CTACTCTTTAGGGGAGATCGGACTCGAGAAAACTTTGATCCACTTCTCTGCTCTTTAGGGAAGAT
131 CTACTCTTTAGGGGAGATCAAACTCGAGAAAACTTTGATCCACTTCACTGCTCTTCAGGGAAGAT
3375332 TGAATCAGAATCGATTTGTGTCACAGCTATTCAGGATCTGCTCAAA
196 TGAATCAGAATCGATTTGTGTCACAGCTATTCAGGATCTGCTCAAA
* * ** *
3375378 TACTTTTTAGGGGAGATCAGCCACATAATTTTGATCCACTTTGCTGCT-TTTAGGGAAAATTAAA
1 TACTCTTTAGGGGAGATCAGACACATAATTTTGATCCACTTCACTGCTCTTCAGGGAAAATTAAA
* * * * * **
3375442 TCTGGATTGATTTGCCTT-ACTGTTATTCAGGAAGACCAAATCTGAAAGAAGAAGAATCTGCTTT
66 TCTGAATCGATTTG-CTTGACTGCTATTCAGGAAGACCAAATCTAAAAGAACAAGAATCTGCTCC
* *
3375506 GCTACTCTTTAGGGGAGATCAAACTTGAGAAAACTTTGATCCACTTCACTGCTCTTCAGGGAAGG
130 GCTACTCTTTAGGGGAGATCAAACTCGAGAAAACTTTGATCCACTTCACTGCTCTTCAGGGAAGA
3375571 TTGAATCAGAATC
195 TTGAATCAGAATC
3375584 AGAATCAATT
Statistics
Matches: 182, Mismatches: 23, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
240 137 0.75
241 45 0.25
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Consensus pattern (241 bp):
TACTCTTTAGGGGAGATCAGACACATAATTTTGATCCACTTCACTGCTCTTCAGGGAAAATTAAA
TCTGAATCGATTTGCTTGACTGCTATTCAGGAAGACCAAATCTAAAAGAACAAGAATCTGCTCCG
CTACTCTTTAGGGGAGATCAAACTCGAGAAAACTTTGATCCACTTCACTGCTCTTCAGGGAAGAT
TGAATCAGAATCGATTTGTGTCACAGCTATTCAGGATCTGCTCAAA
Found at i:3375766 original size:91 final size:89
Alignment explanation
Indices: 3375637--3375810 Score: 267
Period size: 91 Copynumber: 1.9 Consensus size: 89
3375627 AAGAGGGCAG
* * ** *
3375637 ATCTACTCCACTACTCTTTAGGGGAGATTAGACACGTAATTTTGATCCACTTTGCTGCTCTTCAC
1 ATCTACTCCACTACTCTTCAGGGGAGATCAGACACGTAATTTTGAT-CACTTCACTGCTCTTCAA
3375702 GGAAGATTGAATCTGAAAGTAGAAGA
65 GGAAGATTGAATC-GAAAGTAGAAGA
* *
3375728 ATCTGCTCCACTACTCTTCAGGGGAGATCATACACGTAATTTTGATCACTTCACTGCTCTTCAAG
1 ATCTACTCCACTACTCTTCAGGGGAGATCAGACACGTAATTTTGATCACTTCACTGCTCTTCAAG
3375793 GAAGATTGAATCGAAAGT
66 GAAGATTGAATCGAAAGT
3375811 GATTTGCTTA
Statistics
Matches: 76, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
89 6 0.08
90 28 0.37
91 42 0.55
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.30
Consensus pattern (89 bp):
ATCTACTCCACTACTCTTCAGGGGAGATCAGACACGTAATTTTGATCACTTCACTGCTCTTCAAG
GAAGATTGAATCGAAAGTAGAAGA
Found at i:3375953 original size:135 final size:132
Alignment explanation
Indices: 3375711--3376118 Score: 430
Period size: 135 Copynumber: 3.1 Consensus size: 132
3375701 CGGAAGATTG
* * * *
3375711 AATCTGAAAGTAGAAGAATCTGCTCCACTACTCTTCAGGGGAGATC--ATACACG-TAATTTTGA
1 AATCTGAAAGAAGAAGAATCTGCTCCACTACTCTTTAGGGGAGATCAAATAGA-GAAAATTTTGA
* * *
3375773 T-CACTTCACTGCTCTTCAAGGAAGATTGAATCGAAAGTGATTTGCTTAGCTTCTCTTCAGGAAG
65 TCCACTTCGCTGCTCTTCAAGGAAGATTGAATTGAAATTGATTTGCTTA-CTTCTCTTCAGGAAG
3375837 ACCA
129 ACCA
* * * *
3375841 AATCTGAAAGGAGAAAGAATCTTCTCCACTACTCTTTAGGGGATATCAAATTGGAGAAAATTTTG
1 AATCTGAAAGAAG-AAGAATCTGCTCCACTACTCTTTAGGGGAGATCAAA-TAGAGAAAATTTTG
* * * * *
3375906 ATCCACTTTGCTGCTCTTTAAGGAAGATTGAATTGAAATTTATTTGCTTCACTACTCTTTAGGAA
64 ATCCACTTCGCTGCTCTTCAAGGAAGATTGAATTGAAATTGATTTGCTT-ACTTCTCTTCAGGAA
3375971 GACCA
128 GACCA
* * * * * **
3375976 AATCTAAAAGAAGAATAATCTGCTCCGCTACTCTTTAGGGTAGATCAAACTCGAGAAAAAAATTG
1 AATCTGAAAGAAGAAGAATCTGCTCCACTACTCTTTAGGGGAGATCAAA-TAGAG-AAAATTTTG
* * * * * *
3376041 ATCCACTTCGCTGCTCTTCAGGGAAGATT-AAATCAAACTTGATATACTTTACTTCTCTTCAAGA
64 ATCCACTTCGCTGCTCTTCAAGGAAGATTGAATTGAAA-TTGATTTGC-TTACTTCTCTTCAGGA
3376105 AGACCA
127 AGACCA
*
3376111 AATTTGAA
1 AATCTGAA
3376119 GGTTTAGAAT
Statistics
Matches: 229, Mismatches: 39, Indels: 15
0.81 0.14 0.05
Matches are distributed among these distances:
130 12 0.05
131 30 0.13
133 2 0.01
134 52 0.23
135 130 0.57
136 3 0.01
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Consensus pattern (132 bp):
AATCTGAAAGAAGAAGAATCTGCTCCACTACTCTTTAGGGGAGATCAAATAGAGAAAATTTTGAT
CCACTTCGCTGCTCTTCAAGGAAGATTGAATTGAAATTGATTTGCTTACTTCTCTTCAGGAAGAC
CA
Found at i:3390843 original size:22 final size:21
Alignment explanation
Indices: 3390792--3390844 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
3390782 GAGAGAAAAG
3390792 AAAA-TGAAACTGTAGTTAAA
1 AAAATTGAAACTGTAGTTAAA
* *
3390812 AAAATTGAAAGTGTAGTTGAA
1 AAAATTGAAACTGTAGTTAAA
*
3390833 AAACTTGGAAAC
1 AAAATT-GAAAC
3390845 GAAAAGAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 4 0.15
21 19 0.70
22 4 0.15
ACGTcount: A:0.51, C:0.06, G:0.19, T:0.25
Consensus pattern (21 bp):
AAAATTGAAACTGTAGTTAAA
Found at i:3399961 original size:15 final size:16
Alignment explanation
Indices: 3399941--3399972 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
3399931 CCTTGGAGTG
3399941 TATTGGTGAGGT-TTT
1 TATTGGTGAGGTATTT
3399956 TATTGGTGAGGTATTT
1 TATTGGTGAGGTATTT
3399972 T
1 T
3399973 TCATTTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.16, C:0.00, G:0.31, T:0.53
Consensus pattern (16 bp):
TATTGGTGAGGTATTT
Found at i:3403157 original size:22 final size:21
Alignment explanation
Indices: 3403106--3403158 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
3403096 GAGAGAAAAG
3403106 AAAA-TGAAACTGTAGTTAAA
1 AAAATTGAAACTGTAGTTAAA
* *
3403126 AAAATTGAAAGTGTAGTTGAA
1 AAAATTGAAACTGTAGTTAAA
*
3403147 AAACTTGGAAAC
1 AAAATT-GAAAC
3403159 GAAAAGAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 4 0.15
21 19 0.70
22 4 0.15
ACGTcount: A:0.51, C:0.06, G:0.19, T:0.25
Consensus pattern (21 bp):
AAAATTGAAACTGTAGTTAAA
Found at i:3408754 original size:227 final size:227
Alignment explanation
Indices: 3408359--3408817 Score: 918
Period size: 227 Copynumber: 2.0 Consensus size: 227
3408349 AGGGTCAATC
3408359 CAAAAAGAAGCACAAGGCTCATGTAGCTACATGGAGCGATGAAGAAGGTTCCGATGAAGAGGAAT
1 CAAAAAGAAGCACAAGGCTCATGTAGCTACATGGAGCGATGAAGAAGGTTCCGATGAAGAGGAAT
3408424 AAGAAGTTACAAACTTGTGCTTGATGTCTATCGGGGAATATTCTAAGCTAACCTCTAACTCATTC
66 AAGAAGTTACAAACTTGTGCTTGATGTCTATCGGGGAATATTCTAAGCTAACCTCTAACTCATTC
3408489 GATTTGGATGAATTATCTTATGATGAGTTATTAGAGGATTATAATGGGTTGGGTTCGGATTATAA
131 GATTTGGATGAATTATCTTATGATGAGTTATTAGAGGATTATAATGGGTTGGGTTCGGATTATAA
3408554 GAATCTATTTTCAAAATACAAAAATGATATTT
196 GAATCTATTTTCAAAATACAAAAATGATATTT
3408586 CAAAAAGAAGCACAAGGCTCATGTAGCTACATGGAGCGATGAAGAAGGTTCCGATGAAGAGGAAT
1 CAAAAAGAAGCACAAGGCTCATGTAGCTACATGGAGCGATGAAGAAGGTTCCGATGAAGAGGAAT
3408651 AAGAAGTTACAAACTTGTGCTTGATGTCTATCGGGGAATATTCTAAGCTAACCTCTAACTCATTC
66 AAGAAGTTACAAACTTGTGCTTGATGTCTATCGGGGAATATTCTAAGCTAACCTCTAACTCATTC
3408716 GATTTGGATGAATTATCTTATGATGAGTTATTAGAGGATTATAATGGGTTGGGTTCGGATTATAA
131 GATTTGGATGAATTATCTTATGATGAGTTATTAGAGGATTATAATGGGTTGGGTTCGGATTATAA
3408781 GAATCTATTTTCAAAATACAAAAATGATATTT
196 GAATCTATTTTCAAAATACAAAAATGATATTT
3408813 CAAAA
1 CAAAA
3408818 TTGAAAAACG
Statistics
Matches: 232, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
227 232 1.00
ACGTcount: A:0.36, C:0.12, G:0.22, T:0.30
Consensus pattern (227 bp):
CAAAAAGAAGCACAAGGCTCATGTAGCTACATGGAGCGATGAAGAAGGTTCCGATGAAGAGGAAT
AAGAAGTTACAAACTTGTGCTTGATGTCTATCGGGGAATATTCTAAGCTAACCTCTAACTCATTC
GATTTGGATGAATTATCTTATGATGAGTTATTAGAGGATTATAATGGGTTGGGTTCGGATTATAA
GAATCTATTTTCAAAATACAAAAATGATATTT
Found at i:3412724 original size:22 final size:23
Alignment explanation
Indices: 3412694--3412747 Score: 83
Period size: 23 Copynumber: 2.4 Consensus size: 23
3412684 CAGAGGGAAT
*
3412694 CGATACCCCC-TTGAAGGAGAAC
1 CGATTCCCCCTTTGAAGGAGAAC
*
3412716 CGATTCCCCCTTTGAAGGGGAAC
1 CGATTCCCCCTTTGAAGGAGAAC
3412739 CGATTCCCC
1 CGATTCCCC
3412748 TAGGGGAATC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
22 9 0.31
23 20 0.69
ACGTcount: A:0.24, C:0.35, G:0.22, T:0.19
Consensus pattern (23 bp):
CGATTCCCCCTTTGAAGGAGAAC
Found at i:3412748 original size:22 final size:22
Alignment explanation
Indices: 3412688--3412748 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 22
3412678 ATAGGGCAGA
* * *
3412688 GGGAATCGATACCCCCTTGAAG
1 GGGAACCGATTCCCCTTTGAAG
*
3412710 GAGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATT-CCCCTTTGAAG
3412733 GGGAACCGATTCCCCT
1 GGGAACCGATTCCCCT
3412749 AGGGGAATCG
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
22 13 0.39
23 20 0.61
ACGTcount: A:0.25, C:0.31, G:0.25, T:0.20
Consensus pattern (22 bp):
GGGAACCGATTCCCCTTTGAAG
Found at i:3412754 original size:18 final size:18
Alignment explanation
Indices: 3412731--3412765 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3412721 CCCCCTTTGA
*
3412731 AGGGGAACCGATTCCCCT
1 AGGGGAACCGATACCCCT
*
3412749 AGGGGAATCGATACCCC
1 AGGGGAACCGATACCCC
3412766 CCTGGGGTTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.31, G:0.29, T:0.14
Consensus pattern (18 bp):
AGGGGAACCGATACCCCT
Found at i:3416598 original size:19 final size:19
Alignment explanation
Indices: 3416574--3416618 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
3416564 TATGAATGAA
*
3416574 TAAAATGC-AGTGCAGAAAG
1 TAAAATGCGA-TGCAAAAAG
*
3416593 TAAAATACGATGCAAAAAG
1 TAAAATGCGATGCAAAAAG
3416612 TAAAATG
1 TAAAATG
3416619 TGGATGCTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 21 0.95
20 1 0.05
ACGTcount: A:0.53, C:0.09, G:0.20, T:0.18
Consensus pattern (19 bp):
TAAAATGCGATGCAAAAAG
Found at i:3420740 original size:18 final size:19
Alignment explanation
Indices: 3420709--3420755 Score: 71
Period size: 18 Copynumber: 2.6 Consensus size: 19
3420699 TTAATGAGAT
*
3420709 ATTTAAAT-AATAAAAGCG
1 ATTTAAATAAATAAAAGCA
3420727 A-TTAAATAAATAAAAGCA
1 ATTTAAATAAATAAAAGCA
3420745 ATTTAAATAAA
1 ATTTAAATAAA
3420756 AAATAAGAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 6 0.23
18 11 0.42
19 9 0.35
ACGTcount: A:0.62, C:0.04, G:0.06, T:0.28
Consensus pattern (19 bp):
ATTTAAATAAATAAAAGCA
Found at i:3425501 original size:13 final size:12
Alignment explanation
Indices: 3425480--3425513 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
3425470 ATGCTTGAAT
3425480 AAATAAAAACAA
1 AAATAAAAACAA
*
3425492 AAAGTAAAAATAA
1 AAA-TAAAAACAA
3425505 AAATAAAAA
1 AAATAAAAA
3425514 ATAAAGTAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.82, C:0.03, G:0.03, T:0.12
Consensus pattern (12 bp):
AAATAAAAACAA
Found at i:3425502 original size:19 final size:19
Alignment explanation
Indices: 3425480--3425518 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
3425470 ATGCTTGAAT
*
3425480 AAATAAAAACAAAAAGTAA
1 AAATAAAAACAAAAAATAA
*
3425499 AAATAAAAATAAAAAATAA
1 AAATAAAAACAAAAAATAA
3425518 A
1 A
3425519 GTAGAATTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.82, C:0.03, G:0.03, T:0.13
Consensus pattern (19 bp):
AAATAAAAACAAAAAATAA
Found at i:3425506 original size:5 final size:6
Alignment explanation
Indices: 3425480--3425518 Score: 51
Period size: 6 Copynumber: 6.2 Consensus size: 6
3425470 ATGCTTGAAT
*
3425480 AAATAA AAACAA AAAGTAA AAATAA AAATAAA AAATAA A
1 AAATAA AAATAA AAA-TAA AAATAA AAAT-AA AAATAA A
3425519 GTAGAATTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
6 18 0.62
7 11 0.38
ACGTcount: A:0.82, C:0.03, G:0.03, T:0.13
Consensus pattern (6 bp):
AAATAA
Found at i:3427099 original size:55 final size:55
Alignment explanation
Indices: 3427014--3427552 Score: 762
Period size: 55 Copynumber: 9.8 Consensus size: 55
3427004 TGACACAATT
*
3427014 TGTGCAAAACTAAGAAATTCATAATGAGTTTATGAATTTTCGTATGGGCACTTTG
1 TGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTTCGTATGGGCACTTTG
* * * *
3427069 TGTGCAAAACTACGAATTTCATAATAAGTTTATGAATTTTCATATGGTCACTTTG
1 TGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTTCGTATGGGCACTTTG
* * * *
3427124 TGTGCAAAACTAAAAAATTCATAATAAGTTTATGAATTTCCATATGAGCACTTTG
1 TGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTTCGTATGGGCACTTTG
* *
3427179 TGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTAT-GTATAGGCACTTTC
1 TGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTT-TCGTATGGGCACTTTG
* ** * *
3427234 TGTGCAAAACAAAGAAAAGCATAATAAGTTTATGAATTTTCGTATGGACAATTTG
1 TGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTTCGTATGGGCACTTTG
* * * * *
3427289 TTTGCAAAACTAAGAAATTTATAATAGGTTTATGAATTTTCGTATGGGCAATGTG
1 TGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTTCGTATGGGCACTTTG
* *
3427344 TATGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTTTGTATGGGCACTTTG
1 TGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTTCGTATGGGCACTTTG
* * * *
3427399 TATGCAAAACTAAGAAATTCATAATAAGTTAATGAA-TTTCTGTATAGGCACTGTG
1 TGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTTC-GTATGGGCACTTTG
*
3427454 TGTGCAAAACTAAGAAATTCATTATAAGTTTATGAA-TTTCTGTATGGGCA-TTGTG
1 TGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTTC-GTATGGGCACTT-TG
3427509 TGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTTCGTA
1 TGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTTCGTA
3427553 CTGGTAGTGG
Statistics
Matches: 431, Mismatches: 48, Indels: 10
0.88 0.10 0.02
Matches are distributed among these distances:
54 5 0.01
55 422 0.98
56 4 0.01
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.36
Consensus pattern (55 bp):
TGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTTCGTATGGGCACTTTG
Found at i:3437062 original size:20 final size:21
Alignment explanation
Indices: 3437025--3437063 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
3437015 AATCACATTG
**
3437025 AAAATTCAGAAAGTTTATACA
1 AAAATTCAGAAACATTATACA
3437046 AAAATTCA-AAACATTATA
1 AAAATTCAGAAACATTATA
3437064 TAAATTTCTC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.56, C:0.10, G:0.05, T:0.28
Consensus pattern (21 bp):
AAAATTCAGAAACATTATACA
Found at i:3439705 original size:11 final size:11
Alignment explanation
Indices: 3439691--3439739 Score: 73
Period size: 11 Copynumber: 4.5 Consensus size: 11
3439681 GGTGTTAGAG
3439691 TGTTATTAGTT
1 TGTTATTAGTT
*
3439702 TGTTA-TGGTT
1 TGTTATTAGTT
*
3439712 TGTTATTAGCT
1 TGTTATTAGTT
3439723 TGTTATTAGTT
1 TGTTATTAGTT
3439734 TGTTAT
1 TGTTAT
3439740 GTTGGTTACT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
10 9 0.27
11 24 0.73
ACGTcount: A:0.16, C:0.02, G:0.20, T:0.61
Consensus pattern (11 bp):
TGTTATTAGTT
Found at i:3439716 original size:21 final size:22
Alignment explanation
Indices: 3439691--3439739 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 22
3439681 GGTGTTAGAG
* *
3439691 TGTTATTAGTTTGTTA-TGGTT
1 TGTTATTAGCTTGTTATTAGTT
3439712 TGTTATTAGCTTGTTATTAGTT
1 TGTTATTAGCTTGTTATTAGTT
3439734 TGTTAT
1 TGTTAT
3439740 GTTGGTTACT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 15 0.60
22 10 0.40
ACGTcount: A:0.16, C:0.02, G:0.20, T:0.61
Consensus pattern (22 bp):
TGTTATTAGCTTGTTATTAGTT
Found at i:3440968 original size:11 final size:11
Alignment explanation
Indices: 3440954--3441002 Score: 55
Period size: 11 Copynumber: 4.5 Consensus size: 11
3440944 AATGTTAGAG
3440954 TGTTATTAGTT
1 TGTTATTAGTT
*
3440965 TGTTA-TGGTT
1 TGTTATTAGTT
**
3440975 TGTTATTAGCC
1 TGTTATTAGTT
*
3440986 TATTATTAGTT
1 TGTTATTAGTT
3440997 TGTTAT
1 TGTTAT
3441003 GTTGGTTACT
Statistics
Matches: 29, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
10 9 0.31
11 20 0.69
ACGTcount: A:0.18, C:0.04, G:0.18, T:0.59
Consensus pattern (11 bp):
TGTTATTAGTT
Found at i:3443252 original size:11 final size:12
Alignment explanation
Indices: 3443234--3443262 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
3443224 TCTGTGTGAT
3443234 ATATATGAAAAA
1 ATATATGAAAAA
3443246 A-ATATGAAAAA
1 ATATATGAAAAA
3443257 ATATAT
1 ATATAT
3443263 ATTTATTGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.66, C:0.00, G:0.07, T:0.28
Consensus pattern (12 bp):
ATATATGAAAAA
Found at i:3443990 original size:16 final size:17
Alignment explanation
Indices: 3443965--3444007 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
3443955 CCCTTATATA
3443965 TATACACACG-CGCACG
1 TATACACACGCCGCACG
*
3443981 TATACGCACGCTCGCACG
1 TATACACACGC-CGCACG
3443999 TATACACAC
1 TATACACAC
3444008 TTCCATTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 9 0.39
18 14 0.61
ACGTcount: A:0.30, C:0.37, G:0.16, T:0.16
Consensus pattern (17 bp):
TATACACACGCCGCACG
Found at i:3445964 original size:2 final size:2
Alignment explanation
Indices: 3445957--3445988 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3445947 TATGGTAGAG
3445957 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3445989 TAGAGAAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3446075 original size:14 final size:14
Alignment explanation
Indices: 3446056--3446082 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3446046 TTCACGTTAT
3446056 TGGAATATACATTC
1 TGGAATATACATTC
3446070 TGGAATATACATT
1 TGGAATATACATT
3446083 TGCATTCTAG
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:0.37, C:0.11, G:0.15, T:0.37
Consensus pattern (14 bp):
TGGAATATACATTC
Found at i:3446090 original size:20 final size:20
Alignment explanation
Indices: 3446065--3446102 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3446055 TTGGAATATA
*
3446065 CATTCTGGAATATACATTTG
1 CATTCTAGAATATACATTTG
*
3446085 CATTCTAGAATATGCATT
1 CATTCTAGAATATACATT
3446103 GTTAACATGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.39
Consensus pattern (20 bp):
CATTCTAGAATATACATTTG
Found at i:3447792 original size:35 final size:34
Alignment explanation
Indices: 3447740--3447842 Score: 143
Period size: 35 Copynumber: 2.9 Consensus size: 34
3447730 CGTCTATAGT
*
3447740 AGAACGAAGGGAGGCATCGCACTTTCGATTCAAGA
1 AGAACGAA-GGAAGCATCGCACTTTCGATTCAAGA
**
3447775 AGAACAGAAGGAAGCATCGCACTTTCGATTCAATT
1 AGAAC-GAAGGAAGCATCGCACTTTCGATTCAAGA
*
3447810 AGAATGGAAGGAAGCATCGCACTTTCGATTCAA
1 AGAA-CGAAGGAAGCATCGCACTTTCGATTCAA
3447843 CTAGAATGGA
Statistics
Matches: 62, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
35 59 0.95
36 3 0.05
ACGTcount: A:0.36, C:0.19, G:0.24, T:0.20
Consensus pattern (34 bp):
AGAACGAAGGAAGCATCGCACTTTCGATTCAAGA
Found at i:3447848 original size:35 final size:35
Alignment explanation
Indices: 3447753--3447852 Score: 155
Period size: 35 Copynumber: 2.9 Consensus size: 35
3447743 ACGAAGGGAG
** **
3447753 GCATCGCACTTTCGATTCAAGAAGAACAGAAGGAA
1 GCATCGCACTTTCGATTCAACTAGAATGGAAGGAA
*
3447788 GCATCGCACTTTCGATTCAATTAGAATGGAAGGAA
1 GCATCGCACTTTCGATTCAACTAGAATGGAAGGAA
3447823 GCATCGCACTTTCGATTCAACTAGAATGGA
1 GCATCGCACTTTCGATTCAACTAGAATGGA
3447853 TGATTTACTA
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 60 1.00
ACGTcount: A:0.35, C:0.20, G:0.22, T:0.23
Consensus pattern (35 bp):
GCATCGCACTTTCGATTCAACTAGAATGGAAGGAA
Found at i:3447980 original size:20 final size:20
Alignment explanation
Indices: 3447957--3447997 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
3447947 GAGAATATTG
*
3447957 GAATATGCATTCTGGAATAT
1 GAATATGCATTCTAGAATAT
*
3447977 GAATTTGCATTCTAGAATAT
1 GAATATGCATTCTAGAATAT
3447997 G
1 G
3447998 CATTGTTAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.34, C:0.10, G:0.20, T:0.37
Consensus pattern (20 bp):
GAATATGCATTCTAGAATAT
Found at i:3449464 original size:27 final size:26
Alignment explanation
Indices: 3449432--3449568 Score: 91
Period size: 27 Copynumber: 5.6 Consensus size: 26
3449422 ATACATAAAG
*
3449432 GCATGAACGAATGCTATAATTTAAAAT
1 GCATGAACGGATGC-ATAATTTAAAAT
* *
3449459 GCATGAAAGGATGC---A-TT--AAG
1 GCATGAACGGATGCATAATTTAAAAT
* *
3449479 GCATGAACGAATGCCATAATTGAAAAT
1 GCATGAACGGATG-CATAATTTAAAAT
* *
3449506 GCATGAAAGGATG---AA--T-AAAG
1 GCATGAACGGATGCATAATTTAAAAT
3449526 GCATGAACGGATGCCATAATTTAAAAT
1 GCATGAACGGATG-CATAATTTAAAAT
*
3449553 GCATGAAAGGATGCAT
1 GCATGAACGGATGCAT
3449569 TAAGGCATGA
Statistics
Matches: 82, Mismatches: 14, Indels: 29
0.66 0.11 0.23
Matches are distributed among these distances:
20 28 0.34
21 1 0.01
22 2 0.02
23 3 0.04
24 3 0.04
25 1 0.01
26 4 0.05
27 40 0.49
ACGTcount: A:0.43, C:0.12, G:0.23, T:0.23
Consensus pattern (26 bp):
GCATGAACGGATGCATAATTTAAAAT
Found at i:3449469 original size:47 final size:47
Alignment explanation
Indices: 3449399--3449607 Score: 285
Period size: 47 Copynumber: 4.4 Consensus size: 47
3449389 AAACCAATTT
*
3449399 CATAATTGAAAATACATGAAAGGATACATAAAGGCATGAACGAATGC
1 CATAATTGAAAATGCATGAAAGGATACATAAAGGCATGAACGAATGC
* * * *
3449446 TATAATTTAAAATGCATGAAAGGATGCATTAAGGCATGAACGAATGC
1 CATAATTGAAAATGCATGAAAGGATACATAAAGGCATGAACGAATGC
*
3449493 CATAATTGAAAATGCATGAAAGGATGA-ATAAAGGCATGAACGGATGC
1 CATAATTGAAAATGCATGAAAGGAT-ACATAAAGGCATGAACGAATGC
* * * * *
3449540 CATAATTTAAAATGCATGAAAGGATGCATTAAGGCATGAATGGATGC
1 CATAATTGAAAATGCATGAAAGGATACATAAAGGCATGAACGAATGC
* *
3449587 CATAATTGGAAATGCTTGAAA
1 CATAATTGAAAATGCATGAAA
3449608 AGGGTGTATT
Statistics
Matches: 143, Mismatches: 17, Indels: 4
0.87 0.10 0.02
Matches are distributed among these distances:
47 143 1.00
ACGTcount: A:0.44, C:0.11, G:0.22, T:0.23
Consensus pattern (47 bp):
CATAATTGAAAATGCATGAAAGGATACATAAAGGCATGAACGAATGC
Found at i:3449560 original size:94 final size:94
Alignment explanation
Indices: 3449399--3449607 Score: 339
Period size: 94 Copynumber: 2.2 Consensus size: 94
3449389 AAACCAATTT
* *
3449399 CATAATTGAAAATACATGAAAGGATACATAAAGGCATGAACGAATGCTATAATTTAAAATGCATG
1 CATAATTGAAAATGCATGAAAGGATACATAAAGGCATGAACGAATGCCATAATTTAAAATGCATG
3449464 AAAGGATGCATTAAGGCATGAACGAATGC
66 AAAGGATGCATTAAGGCATGAACGAATGC
*
3449493 CATAATTGAAAATGCATGAAAGGATGA-ATAAAGGCATGAACGGATGCCATAATTTAAAATGCAT
1 CATAATTGAAAATGCATGAAAGGAT-ACATAAAGGCATGAACGAATGCCATAATTTAAAATGCAT
* *
3449557 GAAAGGATGCATTAAGGCATGAATGGATGC
65 GAAAGGATGCATTAAGGCATGAACGAATGC
* *
3449587 CATAATTGGAAATGCTTGAAA
1 CATAATTGAAAATGCATGAAA
3449608 AGGGTGTATT
Statistics
Matches: 107, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
94 106 0.99
95 1 0.01
ACGTcount: A:0.44, C:0.11, G:0.22, T:0.23
Consensus pattern (94 bp):
CATAATTGAAAATGCATGAAAGGATACATAAAGGCATGAACGAATGCCATAATTTAAAATGCATG
AAAGGATGCATTAAGGCATGAACGAATGC
Found at i:3450412 original size:33 final size:33
Alignment explanation
Indices: 3450370--3450455 Score: 154
Period size: 33 Copynumber: 2.6 Consensus size: 33
3450360 GTTAAAGAAA
3450370 AGTGCAACAAAAAATGTTAAAAAAGCTTAACAT
1 AGTGCAACAAAAAATGTTAAAAAAGCTTAACAT
3450403 AGTGCAACAAAAAATGTTAAAAAAGCTTAACAT
1 AGTGCAACAAAAAATGTTAAAAAAGCTTAACAT
**
3450436 AGTGCAACCTAAAATGTTAA
1 AGTGCAACAAAAAATGTTAA
3450456 TTATTTCTTA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 51 1.00
ACGTcount: A:0.52, C:0.13, G:0.13, T:0.22
Consensus pattern (33 bp):
AGTGCAACAAAAAATGTTAAAAAAGCTTAACAT
Found at i:3450582 original size:21 final size:23
Alignment explanation
Indices: 3450538--3450587 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 23
3450528 AATTACAAAA
*
3450538 AATTAACATTTTAGGTTGCTCTC
1 AATTAACATTTTAGGTTGCGCTC
*
3450561 -ATTAATATTTTA-GTTGCGCTC
1 AATTAACATTTTAGGTTGCGCTC
3450582 AATTAA
1 AATTAA
3450588 AAATGTTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 8 0.33
22 16 0.67
ACGTcount: A:0.30, C:0.14, G:0.12, T:0.44
Consensus pattern (23 bp):
AATTAACATTTTAGGTTGCGCTC
Found at i:3453957 original size:29 final size:31
Alignment explanation
Indices: 3453925--3454010 Score: 95
Period size: 32 Copynumber: 2.8 Consensus size: 31
3453915 GGGCCTGAGA
*
3453925 GCCTACCCAAGAAA-AT-TCGGGGCCACGGG
1 GCCTACCCAAGAAACATCTCAGGGCCACGGG
* *
3453954 GCCTACCTAAGAAAACATCTTAGGGCCACGGG
1 GCCTACCCAAG-AAACATCTCAGGGCCACGGG
* **
3453986 GCCTACCCGAGAATGATCTCAGGGC
1 GCCTACCCAAGAAACATCTCAGGGC
3454011 TGCAGAGCCT
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
29 10 0.22
30 3 0.07
31 13 0.28
32 20 0.43
ACGTcount: A:0.28, C:0.30, G:0.28, T:0.14
Consensus pattern (31 bp):
GCCTACCCAAGAAACATCTCAGGGCCACGGG
Found at i:3457418 original size:20 final size:20
Alignment explanation
Indices: 3457393--3457446 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
3457383 CATGAACAGT
3457393 AAGTTTCGAAACTTCTGATA
1 AAGTTTCGAAACTTCTGATA
*
3457413 AAGTTTTC-AAAATTCTGATA
1 AAG-TTTCGAAACTTCTGATA
*
3457433 AAGTTTTGAAACTT
1 AAGTTTCGAAACTT
3457447 GGGCTTTTGG
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 3 0.10
20 22 0.76
21 4 0.14
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.39
Consensus pattern (20 bp):
AAGTTTCGAAACTTCTGATA
Found at i:3458767 original size:20 final size:21
Alignment explanation
Indices: 3458742--3458783 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
3458732 AGTTATGGTC
3458742 ATTTCTAGCCG-TTGGGGATG
1 ATTTCTAGCCGTTTGGGGATG
*
3458762 ATTTCTAGTCGTTTGGGGATG
1 ATTTCTAGCCGTTTGGGGATG
3458783 A
1 A
3458784 AATCTCTGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.17, C:0.12, G:0.33, T:0.38
Consensus pattern (21 bp):
ATTTCTAGCCGTTTGGGGATG
Found at i:3459173 original size:20 final size:20
Alignment explanation
Indices: 3459148--3459194 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
3459138 TTAAATGGAC
*
3459148 TTTGAATTATTTTTGAA-AAA
1 TTTGAATTA-CTTTGAATAAA
*
3459168 TTTGAAATACTTTGAATAAA
1 TTTGAATTACTTTGAATAAA
3459188 TTT-AATT
1 TTTGAATT
3459195 CATGTCCAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 9 0.39
20 14 0.61
ACGTcount: A:0.40, C:0.02, G:0.09, T:0.49
Consensus pattern (20 bp):
TTTGAATTACTTTGAATAAA
Found at i:3459809 original size:13 final size:13
Alignment explanation
Indices: 3459758--3459816 Score: 64
Period size: 13 Copynumber: 4.5 Consensus size: 13
3459748 GTCATAAATA
*
3459758 TATGACGCGCATT
1 TATGACGCACATT
* *
3459771 TTTGACACACATT
1 TATGACGCACATT
*
3459784 TATGACACACATT
1 TATGACGCACATT
*
3459797 TATGACGCGCATT
1 TATGACGCACATT
*
3459810 AATGACG
1 TATGACG
3459817 TTCATTGAGT
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 39 1.00
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.31
Consensus pattern (13 bp):
TATGACGCACATT
Found at i:3459885 original size:85 final size:85
Alignment explanation
Indices: 3459794--3460007 Score: 283
Period size: 85 Copynumber: 2.5 Consensus size: 85
3459784 TATGACACAC
* * **
3459794 ATTTATGACGCGCAT-TAATGACGTT-CATTGAGTGTCATTTTAGCCCCCGCCATAAAT-TAAG-
1 ATTTATGACACGCATGT-ATGAC-TTACATTGCGTGTCATTGAAGCCCCCGCCATAAATCT--GC
3459855 ATGACACACATTTGTGCGTCATAA
62 ATGACACACATTTGTGCGTCATAA
* * *
3459879 ATTTATGACACGCATGTATGACTTACATTGCGCGTCATTGAAGCCCCCGTCATAAATCTGCTTGA
1 ATTTATGACACGCATGTATGACTTACATTGCGTGTCATTGAAGCCCCCGCCATAAATCTGCATGA
* *
3459944 CATACATTTGTGTGTCATAA
66 CACACATTTGTGCGTCATAA
3459964 ATTTATGACACGCATGTATGACTTACATTGCGTGTCATTGAAGC
1 ATTTATGACACGCATGTATGACTTACATTGCGTGTCATTGAAGC
3460008 ACACGTCATT
Statistics
Matches: 115, Mismatches: 10, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
84 3 0.03
85 110 0.96
86 2 0.02
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (85 bp):
ATTTATGACACGCATGTATGACTTACATTGCGTGTCATTGAAGCCCCCGCCATAAATCTGCATGA
CACACATTTGTGCGTCATAA
Found at i:3460045 original size:85 final size:84
Alignment explanation
Indices: 3459856--3460046 Score: 231
Period size: 85 Copynumber: 2.2 Consensus size: 84
3459846 TAAATTAAGA
* * *
3459856 TGACACACATTTGTGCGTCATAAATTTATGACACGCATGTATGACTTACATTGCGCGTCATTGAA
1 TGACAAACATTGGTGTGTCATAAATTTATGACACGCATGTATGACTTACATTGCGCGTCATTGAA
* * ***
3459921 GCCCCCGTCATAAATCTGC
66 GCACACGTCATAAAAAAGC
* * *
3459940 TTGACATACATTTGTGTGTCATAAATTTATGACACGCATGTATGACTTACATTGCGTGTCATTGA
1 -TGACAAACATTGGTGTGTCATAAATTTATGACACGCATGTATGACTTACATTGCGCGTCATTGA
3460005 AGCACACGTCATTAAAAAAGAC
65 AGCACACGTCA-TAAAAAAG-C
* *
3460027 -GACAAACGTTGGTTTGTCAT
1 TGACAAACATTGGTGTGTCAT
3460047 GATTGTATTT
Statistics
Matches: 92, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
85 86 0.93
86 5 0.05
87 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.31
Consensus pattern (84 bp):
TGACAAACATTGGTGTGTCATAAATTTATGACACGCATGTATGACTTACATTGCGCGTCATTGAA
GCACACGTCATAAAAAAGC
Found at i:3460071 original size:2 final size:2
Alignment explanation
Indices: 3460064--3460099 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3460054 TTTTGTAAAT
3460064 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3460100 GATTGACAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3462505 original size:39 final size:40
Alignment explanation
Indices: 3462456--3462538 Score: 116
Period size: 39 Copynumber: 2.1 Consensus size: 40
3462446 TTTCTTTCTT
* *
3462456 TTTTTCCCTTTTCGGTGTCCCTTCTCCTTT-CTCCTCTTCC
1 TTTTTCCCTTTGCAGTGTCCCTTCTCCTTTAC-CCTCTTCC
*
3462496 TTTTT-CCTTTGCAGTGTTCCTTCTCCTTTACCCTCTTCC
1 TTTTTCCCTTTGCAGTGTCCCTTCTCCTTTACCCTCTTCC
3462535 TTTT
1 TTTT
3462539 CTTTCTCTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
39 33 0.85
40 6 0.15
ACGTcount: A:0.02, C:0.36, G:0.07, T:0.54
Consensus pattern (40 bp):
TTTTTCCCTTTGCAGTGTCCCTTCTCCTTTACCCTCTTCC
Found at i:3466441 original size:15 final size:15
Alignment explanation
Indices: 3466416--3466471 Score: 67
Period size: 15 Copynumber: 3.7 Consensus size: 15
3466406 GATGCTTTTT
*
3466416 TTTTCCTTCTTTGATG
1 TTTT-CTTCTTTGACG
*
3466432 TTTTCTTCTTTGACA
1 TTTTCTTCTTTGACG
*
3466447 TTTTCTTCTTAGACG
1 TTTTCTTCTTTGACG
*
3466462 TTGTCTTCTT
1 TTTTCTTCTT
3466472 ACCCCATGAA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
15 31 0.89
16 4 0.11
ACGTcount: A:0.09, C:0.20, G:0.11, T:0.61
Consensus pattern (15 bp):
TTTTCTTCTTTGACG
Found at i:3467820 original size:29 final size:28
Alignment explanation
Indices: 3467778--3467838 Score: 113
Period size: 29 Copynumber: 2.1 Consensus size: 28
3467768 TGGTGCCACA
3467778 AAATTGATACAATGTATACAAGGACATC
1 AAATTGATACAATGTATACAAGGACATC
3467806 GAAATTGATACAATGTATACAAGGACATC
1 -AAATTGATACAATGTATACAAGGACATC
3467835 AAAT
1 AAAT
3467839 AAGATCTGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 4 0.12
29 28 0.88
ACGTcount: A:0.48, C:0.13, G:0.15, T:0.25
Consensus pattern (28 bp):
AAATTGATACAATGTATACAAGGACATC
Found at i:3470948 original size:19 final size:20
Alignment explanation
Indices: 3470909--3470949 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
3470899 TCAAAACTTC
* *
3470909 ATTTTGTTTTGCAAAATCAA
1 ATTTTGCTTTGCAAAACCAA
3470929 ATTTTGCTTT-CAAAACCAA
1 ATTTTGCTTTGCAAAACCAA
3470948 AT
1 AT
3470950 CTTTTTCAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.37, C:0.15, G:0.07, T:0.41
Consensus pattern (20 bp):
ATTTTGCTTTGCAAAACCAA
Found at i:3471449 original size:15 final size:15
Alignment explanation
Indices: 3471429--3471461 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
3471419 CGCATACTTT
3471429 CTTCTTATTTTATTC
1 CTTCTTATTTTATTC
3471444 CTTCTTATTTTATTC
1 CTTCTTATTTTATTC
3471459 CTT
1 CTT
3471462 TTTCTTGTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.12, C:0.21, G:0.00, T:0.67
Consensus pattern (15 bp):
CTTCTTATTTTATTC
Found at i:3471466 original size:18 final size:18
Alignment explanation
Indices: 3471425--3471467 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 18
3471415 GCAACGCATA
3471425 CTTTCTTCTTATTTTATTC
1 CTTT-TTCTTATTTTATTC
3471444 C---TTCTTATTTTATTC
1 CTTTTTCTTATTTTATTC
3471459 CTTTTTCTT
1 CTTTTTCTT
3471468 GTCATTCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 7
0.75 0.00 0.25
Matches are distributed among these distances:
15 15 0.71
18 5 0.24
19 1 0.05
ACGTcount: A:0.09, C:0.21, G:0.00, T:0.70
Consensus pattern (18 bp):
CTTTTTCTTATTTTATTC
Found at i:3473141 original size:20 final size:20
Alignment explanation
Indices: 3473116--3473162 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
3473106 TTAAATGGAC
*
3473116 TTTGAATTATTTTTGAA-AAA
1 TTTGAATTA-CTTTGAATAAA
*
3473136 TTTGAAATACTTTGAATAAA
1 TTTGAATTACTTTGAATAAA
3473156 TTT-AATT
1 TTTGAATT
3473163 CATGTCCAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 9 0.39
20 14 0.61
ACGTcount: A:0.40, C:0.02, G:0.09, T:0.49
Consensus pattern (20 bp):
TTTGAATTACTTTGAATAAA
Found at i:3473972 original size:10 final size:10
Alignment explanation
Indices: 3473944--3473973 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
3473934 AAAGTATTAC
*
3473944 TATATATATA
1 TATATATACA
3473954 TATATATACA
1 TATATATACA
3473964 TATATATACA
1 TATATATACA
3473974 CACACACACA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (10 bp):
TATATATACA
Found at i:3473976 original size:2 final size:2
Alignment explanation
Indices: 3473971--3473995 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3473961 ACATATATAT
3473971 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
3473996 TATATATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:3474000 original size:2 final size:2
Alignment explanation
Indices: 3473995--3474023 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
3473985 ACACACACAC
3473995 AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3474024 TTGCTAAAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3480037 original size:24 final size:24
Alignment explanation
Indices: 3480005--3480075 Score: 67
Period size: 24 Copynumber: 2.9 Consensus size: 24
3479995 CTCTCCTTGG
*
3480005 CTTTACTTCTTTTTTTTTGAAATT
1 CTTTTCTTCTTTTTTTTTGAAATT
3480029 CTTTTCTTCTTCTTTTTTCTG--ATT
1 CTTTTCTTCTT-TTTTTT-TGAAATT
3480053 -TTCTTCTTCTTTTTATCTTTGAA
1 CTT-TTCTTCTTTTT-T-TTTGAA
3480076 CTCCTTTGAT
Statistics
Matches: 39, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
23 5 0.13
24 24 0.62
25 8 0.21
26 2 0.05
ACGTcount: A:0.11, C:0.17, G:0.04, T:0.68
Consensus pattern (24 bp):
CTTTTCTTCTTTTTTTTTGAAATT
Found at i:3480071 original size:11 final size:11
Alignment explanation
Indices: 3480027--3480065 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
3480017 TTTTTTGAAA
3480027 TTCTTTTCTTC
1 TTCTTTTCTTC
3480038 TTCTTTT-TTC
1 TTCTTTTCTTC
**
3480048 TGATTTTCTTC
1 TTCTTTTCTTC
3480059 TTCTTTT
1 TTCTTTT
3480066 TATCTTTGAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
10 8 0.35
11 15 0.65
ACGTcount: A:0.03, C:0.21, G:0.03, T:0.74
Consensus pattern (11 bp):
TTCTTTTCTTC
Found at i:3480372 original size:16 final size:19
Alignment explanation
Indices: 3480333--3480372 Score: 50
Period size: 16 Copynumber: 2.3 Consensus size: 19
3480323 TGGACTTAAT
3480333 AAATGGATAATAATAAAAG
1 AAATGGATAATAATAAAAG
*
3480352 TAATGGA-AAT-A-AAAAG
1 AAATGGATAATAATAAAAG
3480368 AAATG
1 AAATG
3480373 AGAGAGATAG
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
16 9 0.47
17 1 0.05
18 3 0.16
19 6 0.32
ACGTcount: A:0.62, C:0.00, G:0.17, T:0.20
Consensus pattern (19 bp):
AAATGGATAATAATAAAAG
Found at i:3481214 original size:116 final size:116
Alignment explanation
Indices: 3481010--3481246 Score: 474
Period size: 116 Copynumber: 2.0 Consensus size: 116
3481000 TGTATCATGT
3481010 CCTTTGATGATTTAGGCCTCCAATGGGTGTGATATCTTCACCAACATGCTCCTTGGTGAAAGAGC
1 CCTTTGATGATTTAGGCCTCCAATGGGTGTGATATCTTCACCAACATGCTCCTTGGTGAAAGAGC
3481075 ATATTTATGGGCAACATCATTCATGAAAGGTCACAATGTTTGGAAAGGTAA
66 ATATTTATGGGCAACATCATTCATGAAAGGTCACAATGTTTGGAAAGGTAA
3481126 CCTTTGATGATTTAGGCCTCCAATGGGTGTGATATCTTCACCAACATGCTCCTTGGTGAAAGAGC
1 CCTTTGATGATTTAGGCCTCCAATGGGTGTGATATCTTCACCAACATGCTCCTTGGTGAAAGAGC
3481191 ATATTTATGGGCAACATCATTCATGAAAGGTCACAATGTTTGGAAAGGTAA
66 ATATTTATGGGCAACATCATTCATGAAAGGTCACAATGTTTGGAAAGGTAA
3481242 CCTTT
1 CCTTT
3481247 CATGTTTGAG
Statistics
Matches: 121, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
116 121 1.00
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.31
Consensus pattern (116 bp):
CCTTTGATGATTTAGGCCTCCAATGGGTGTGATATCTTCACCAACATGCTCCTTGGTGAAAGAGC
ATATTTATGGGCAACATCATTCATGAAAGGTCACAATGTTTGGAAAGGTAA
Found at i:3483127 original size:2 final size:2
Alignment explanation
Indices: 3483120--3483171 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
3483110 TTAAAACCCT
3483120 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3483162 TA TA TA TA TA
1 TA TA TA TA TA
3483172 ATAACATATT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3485454 original size:121 final size:114
Alignment explanation
Indices: 3485247--3485481 Score: 389
Period size: 121 Copynumber: 2.0 Consensus size: 114
3485237 CAAATCCTCC
*
3485247 ACTAATCTGAAGCTATTAATTTGGCGGCGCAGGTGATATCCCTTGGGATTTCTGCATTTTGTTTA
1 ACTAATCTGAAGCTATTAATTTGGCGGCGCAGGTGATATCCCTTAGGATTTCTGCATTTTGTTTA
3485312 ATATTTTGGGCCACTTGGGCTACATAAATTTAGGACCTAGTTTGGGTTT
66 ATATTTTGGGCCACTTGGGCTACATAAATTTAGGACCTAGTTTGGGTTT
*
3485361 ACTAATCTGAAGCTATTAATTTGGCGGCGCAGGTGGCAGGTGATATCTCTTAGGATTTCTGCATT
1 ACTAATCTGAAGCTATTAATTTGGC-G-GC-----GCAGGTGATATCCCTTAGGATTTCTGCATT
3485426 TTGTTTAATATTTTGGGCCACTTGGGCTACATAAATTTAGGACCTAGTTTGGGTTT
59 TTGTTTAATATTTTGGGCCACTTGGGCTACATAAATTTAGGACCTAGTTTGGGTTT
3485482 TAATTGATTA
Statistics
Matches: 112, Mismatches: 2, Indels: 7
0.93 0.02 0.06
Matches are distributed among these distances:
114 25 0.22
115 1 0.01
116 2 0.02
121 84 0.75
ACGTcount: A:0.22, C:0.15, G:0.24, T:0.38
Consensus pattern (114 bp):
ACTAATCTGAAGCTATTAATTTGGCGGCGCAGGTGATATCCCTTAGGATTTCTGCATTTTGTTTA
ATATTTTGGGCCACTTGGGCTACATAAATTTAGGACCTAGTTTGGGTTT
Found at i:3491445 original size:3 final size:3
Alignment explanation
Indices: 3491434--3491467 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
3491424 TCTAAAAAAA
3491434 TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
3491468 CATATTACAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:3492517 original size:16 final size:16
Alignment explanation
Indices: 3492493--3492523 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3492483 TTCCTCTTTG
3492493 ACTTATTTTTTTATTA
1 ACTTATTTTTTTATTA
*
3492509 ACTTTTTTTTTTATT
1 ACTTATTTTTTTATT
3492524 TTTTATGTTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.19, C:0.06, G:0.00, T:0.74
Consensus pattern (16 bp):
ACTTATTTTTTTATTA
Found at i:3493280 original size:18 final size:19
Alignment explanation
Indices: 3493247--3493285 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
3493237 AAAATATTAA
*
3493247 ATTTAAGTTTTAATTATTT
1 ATTTAAGTTCTAATTATTT
3493266 ATTTAA-TTCTAATTATTT
1 ATTTAAGTTCTAATTATTT
3493284 AT
1 AT
3493286 CATTGATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.62
Consensus pattern (19 bp):
ATTTAAGTTCTAATTATTT
Found at i:3498978 original size:20 final size:20
Alignment explanation
Indices: 3498949--3498987 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3498939 TTTCCACCAC
*
3498949 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGATCCTAA
*
3498969 ATGCATCTATATGATCCTA
1 ATGCAACTATATGATCCTA
3498988 TATGAGCTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.23, G:0.10, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:3506221 original size:179 final size:179
Alignment explanation
Indices: 3505921--3506283 Score: 672
Period size: 179 Copynumber: 2.0 Consensus size: 179
3505911 GTCTTCGACA
* *
3505921 TTGATCTGTGTACCACTCCGTAGAGTTAGCACACTGCATTGTTCTTTGCCATGAGGTTTTGTGAC
1 TTGATCTGTGTACCAATCCGTAGAGTTAGCACACTGCATTGTTCTTTACCATGAGGTTTTGTGAC
3505986 TTCAGTGTCACTCGGCAAATGTCCTGGTTGTCGTTCTTGTAATGCCGTGGCAATTTGACCAACCT
66 TTCAGTGTCACTCGGCAAATGTCCTGGTTGTCGTTCTTGTAATGCCGTGGCAATTTGACCAACCT
* *
3506051 GACTCTCCAATGCCCTCAGTGATGAATTGTGGCTCTGAAGCAGGGCTCC
131 GACTCTCCAATGCCCTCAGCGATGAACTGTGGCTCTGAAGCAGGGCTCC
* *
3506100 TTGATCTGTGTACCAATCTGTAGAGTTAGCACACTGCATTGTTCTTTACCATGAGGTTTTGTTAC
1 TTGATCTGTGTACCAATCCGTAGAGTTAGCACACTGCATTGTTCTTTACCATGAGGTTTTGTGAC
3506165 TTCAGTGTCACTCGGCAAATGTCCTGGTTGTCGTTCTTGTAATGCCGTGGCAATTTGACCAACCT
66 TTCAGTGTCACTCGGCAAATGTCCTGGTTGTCGTTCTTGTAATGCCGTGGCAATTTGACCAACCT
3506230 GACTCTCCAATGCCCTCAGCGATGAACTGTGGCTCTGAAGCAGGGCTCC
131 GACTCTCCAATGCCCTCAGCGATGAACTGTGGCTCTGAAGCAGGGCTCC
3506279 TTGAT
1 TTGAT
3506284 TTTTGATGGA
Statistics
Matches: 178, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
179 178 1.00
ACGTcount: A:0.20, C:0.24, G:0.23, T:0.33
Consensus pattern (179 bp):
TTGATCTGTGTACCAATCCGTAGAGTTAGCACACTGCATTGTTCTTTACCATGAGGTTTTGTGAC
TTCAGTGTCACTCGGCAAATGTCCTGGTTGTCGTTCTTGTAATGCCGTGGCAATTTGACCAACCT
GACTCTCCAATGCCCTCAGCGATGAACTGTGGCTCTGAAGCAGGGCTCC
Found at i:3508762 original size:18 final size:20
Alignment explanation
Indices: 3508725--3508764 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
3508715 AAAATAGTAA
*
3508725 ATTTAAGTTTTAATTTATTT
1 ATTTAAGTTCTAATTTATTT
3508745 ATTTAA-TTCTAA-TTATTT
1 ATTTAAGTTCTAATTTATTT
3508763 AT
1 AT
3508765 CGTTGATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 8 0.42
19 5 0.26
20 6 0.32
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.62
Consensus pattern (20 bp):
ATTTAAGTTCTAATTTATTT
Found at i:3514534 original size:18 final size:18
Alignment explanation
Indices: 3514513--3514550 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
3514503 CCTTACACAC
3514513 TTTGCCACAACAACACCA
1 TTTGCCACAACAACACCA
*
3514531 TTTGCCACGACAACACCA
1 TTTGCCACAACAACACCA
3514549 TT
1 TT
3514551 CATACTTCAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.34, C:0.37, G:0.08, T:0.21
Consensus pattern (18 bp):
TTTGCCACAACAACACCA
Found at i:3520805 original size:18 final size:18
Alignment explanation
Indices: 3520784--3520821 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
3520774 CCTTACACAC
3520784 TTTGCCACAACAACACCA
1 TTTGCCACAACAACACCA
*
3520802 TTTGCCACGACAACACCA
1 TTTGCCACAACAACACCA
3520820 TT
1 TT
3520822 CATACTTCAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.34, C:0.37, G:0.08, T:0.21
Consensus pattern (18 bp):
TTTGCCACAACAACACCA
Found at i:3522032 original size:37 final size:37
Alignment explanation
Indices: 3521990--3522063 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
3521980 AAGAGAAAAC
3521990 ATCTTTCACACTCGTTGTCATGTAAACAACAAAGTTT
1 ATCTTTCACACTCGTTGTCATGTAAACAACAAAGTTT
3522027 ATCTTTCACACTCGTTGTCATGTAAACAACAAAGTTT
1 ATCTTTCACACTCGTTGTCATGTAAACAACAAAGTTT
3522064 GTTTCATGAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.32, C:0.22, G:0.11, T:0.35
Consensus pattern (37 bp):
ATCTTTCACACTCGTTGTCATGTAAACAACAAAGTTT
Found at i:3526346 original size:69 final size:69
Alignment explanation
Indices: 3526230--3526395 Score: 260
Period size: 69 Copynumber: 2.4 Consensus size: 69
3526220 TACATCACTT
* * * * *
3526230 ACTCAAGATTGAATTTCAACTTCACAACGAAGGATATCCAATTCAAAGCCAATTTGGTGAAGCAA
1 ACTCGAGATTGGATTTCAACTTCACAACAAAGGATATCCAACTCAAAGCCAATTTAGTGAAGCAA
3526295 TACA
66 TACA
* * *
3526299 ACTCGAGATTGGATTTCAACTTCACAACAAAGGATATCCAACTCAAAGCTAATTTAGTTAAGTAA
1 ACTCGAGATTGGATTTCAACTTCACAACAAAGGATATCCAACTCAAAGCCAATTTAGTGAAGCAA
3526364 TACA
66 TACA
3526368 ACTCGAGATTGGATTTCAACTTCACAAC
1 ACTCGAGATTGGATTTCAACTTCACAAC
3526396 GAAATATATC
Statistics
Matches: 89, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
69 89 1.00
ACGTcount: A:0.39, C:0.20, G:0.14, T:0.27
Consensus pattern (69 bp):
ACTCGAGATTGGATTTCAACTTCACAACAAAGGATATCCAACTCAAAGCCAATTTAGTGAAGCAA
TACA
Found at i:3528026 original size:22 final size:21
Alignment explanation
Indices: 3528001--3528055 Score: 64
Period size: 18 Copynumber: 2.7 Consensus size: 21
3527991 TAAGGGATCA
3528001 AATTGAATTAATTATAAAAT-G
1 AATT-AATTAATTATAAAATCG
3528022 TAATTAATT-ATT-T-AAATCG
1 -AATTAATTAATTATAAAATCG
3528041 AATTAATTAATTATA
1 AATTAATTAATTATA
3528056 TATATATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
18 12 0.41
19 5 0.17
20 4 0.14
21 4 0.14
22 4 0.14
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (21 bp):
AATTAATTAATTATAAAATCG
Found at i:3529018 original size:23 final size:23
Alignment explanation
Indices: 3528975--3529018 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
3528965 AGAACTATTA
*
3528975 TATAATAAAATTAATTTAATAAT
1 TATAATAAAATTAATTAAATAAT
*
3528998 TATAATTAAAATTTA-TAAATA
1 TATAA-TAAAATTAATTAAATA
3529019 TAAGGATTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 10 0.56
24 8 0.44
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
TATAATAAAATTAATTAAATAAT
Found at i:3529197 original size:16 final size:16
Alignment explanation
Indices: 3529176--3529210 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
3529166 TTTATTACTT
*
3529176 TCAAGTTAGGTAAATA
1 TCAAGTCAGGTAAATA
*
3529192 TCAAGTCATGTAAATA
1 TCAAGTCAGGTAAATA
3529208 TCA
1 TCA
3529211 TATCAGTACA
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:0.43, C:0.11, G:0.14, T:0.31
Consensus pattern (16 bp):
TCAAGTCAGGTAAATA
Found at i:3529236 original size:21 final size:21
Alignment explanation
Indices: 3529207--3529257 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
3529197 TCATGTAAAT
*
3529207 ATCATATCAGTACAATAACAA
1 ATCAGATCAGTACAATAACAA
*
3529228 ATTAGATCAGTACAATAACAA
1 ATCAGATCAGTACAATAACAA
3529249 ATCAGATCA
1 ATCAGATCA
3529258 TTTGAGTCAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.51, C:0.18, G:0.08, T:0.24
Consensus pattern (21 bp):
ATCAGATCAGTACAATAACAA
Found at i:3531510 original size:50 final size:51
Alignment explanation
Indices: 3531392--3531515 Score: 162
Period size: 51 Copynumber: 2.5 Consensus size: 51
3531382 GCAGTAAAGT
* **
3531392 GCGCCCACTGCACCGCGCTATACGATGATTTGGCGCAACGTGGGGTATAGC
1 GCGCCCCCTGCACCGCGCTATACGATGAGCTGGCGCAACGTGGGGTATAGC
*
3531443 GCGCCCCCTGCACCGCGCTATACGGTGAGCTGGCGTC-ACGT-GGGTATAGC
1 GCGCCCCCTGCACCGCGCTATACGATGAGCTGGCG-CAACGTGGGGTATAGC
* * *
3531493 GCGGCCCCTTCAGCGCGCTATAC
1 GCGCCCCCTGCACCGCGCTATAC
3531516 CTGTATATCT
Statistics
Matches: 65, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
50 29 0.45
51 35 0.54
52 1 0.02
ACGTcount: A:0.16, C:0.34, G:0.31, T:0.19
Consensus pattern (51 bp):
GCGCCCCCTGCACCGCGCTATACGATGAGCTGGCGCAACGTGGGGTATAGC
Found at i:3531667 original size:12 final size:10
Alignment explanation
Indices: 3531626--3531666 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
3531616 TTTATCACAC
3531626 CAAATTCTCT
1 CAAATTCTCT
3531636 CAAATTCTCT
1 CAAATTCTCT
3531646 -AAATTTCTCT
1 CAAA-TTCTCT
*
3531656 CAAATACTCT
1 CAAATTCTCT
3531666 C
1 C
3531667 TTTTTAAGGT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 3 0.11
10 22 0.79
11 3 0.11
ACGTcount: A:0.32, C:0.29, G:0.00, T:0.39
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:3531924 original size:105 final size:106
Alignment explanation
Indices: 3531790--3531992 Score: 327
Period size: 105 Copynumber: 1.9 Consensus size: 106
3531780 TGGAAATCAT
* * *
3531790 ATATCTCTACACTTTGCTGATGCGATAACATTTTAATGTTTTAATTTAATTTAAATTATTAGCAA
1 ATATCTCGACACTTTGCTGATACGATAACATTTTAACGTTTTAATTTAATTTAAATTATTAGCAA
* *
3531855 TATTTAGTT-ATTTATTTAATGCATGATTATTATTAATTAA
66 TAATTAGTTGATTCATTTAATGCATGATTATTATTAATTAA
* **
3531895 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTATTAA
1 ATATCTCGACACTTTGCTGATACGATAACATTTTAACGTTTTAATTTAATTTAAATTATTAGCAA
3531960 TAATTAGTTGATTCATTTAATGCATGATTATTA
66 TAATTAGTTGATTCATTTAATGCATGATTATTA
3531993 GATTTAGAAT
Statistics
Matches: 89, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
105 67 0.75
106 22 0.25
ACGTcount: A:0.34, C:0.09, G:0.09, T:0.47
Consensus pattern (106 bp):
ATATCTCGACACTTTGCTGATACGATAACATTTTAACGTTTTAATTTAATTTAAATTATTAGCAA
TAATTAGTTGATTCATTTAATGCATGATTATTATTAATTAA
Found at i:3533900 original size:3 final size:3
Alignment explanation
Indices: 3533892--3533944 Score: 88
Period size: 3 Copynumber: 17.7 Consensus size: 3
3533882 ACCTACGCAA
* *
3533892 GAC GAC GAC AAC GAC GAC GAC GAC GAT GAC GAC GAC GAC GAC GAC GAC
1 GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC
3533940 GAC GA
1 GAC GA
3533945 TGGTGATGAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.36, C:0.30, G:0.32, T:0.02
Consensus pattern (3 bp):
GAC
Found at i:3537792 original size:49 final size:51
Alignment explanation
Indices: 3537687--3537807 Score: 185
Period size: 49 Copynumber: 2.4 Consensus size: 51
3537677 ATACAAAACG
*
3537687 CGGTACCTGCCCCGCGCTATATAAAATTATGTCAGGAGTAAAGGTATGTCG
1 CGGTACCTGCCCCGCGCTATATAAAATTATGTCAGGAGTAAAGGTATGTCA
3537738 CGGTACCTGCCCCGCGCTATATAAAATTAT-T-AGGAGTAAAGGTATAG-CA
1 CGGTACCTGCCCCGCGCTATATAAAATTATGTCAGGAGTAAAGGTAT-GTCA
**
3537787 CGGTACCTGATCCGCGCTATA
1 CGGTACCTGCCCCGCGCTATA
3537808 CCCCTACGTG
Statistics
Matches: 66, Mismatches: 3, Indels: 4
0.90 0.04 0.05
Matches are distributed among these distances:
49 34 0.52
50 2 0.03
51 30 0.45
ACGTcount: A:0.28, C:0.23, G:0.24, T:0.25
Consensus pattern (51 bp):
CGGTACCTGCCCCGCGCTATATAAAATTATGTCAGGAGTAAAGGTATGTCA
Found at i:3537936 original size:51 final size:50
Alignment explanation
Indices: 3537820--3537946 Score: 128
Period size: 51 Copynumber: 2.5 Consensus size: 50
3537810 CCTACGTGGT
* * * * **
3537820 GTATAGCGCGCTGCAGGTGCCACGCTATACCCACGTGGCACCAGCTCACC
1 GTATAGCGCGATGCAGGGGGCGCGCTATACCCACGTGGCACCAAATCACC
* * * * * *
3537870 GTATAGTGTGGTGCAGGGGGCGCGCTATACCCCATGTGGCGCCAAATCATC
1 GTATAGCGCGATGCAGGGGGCGCGCTATA-CCCACGTGGCACCAAATCACC
*
3537921 GTATAGCGCGATGCAGGGGGAGCGCT
1 GTATAGCGCGATGCAGGGGGCGCGCT
3537947 TTACTGCTAA
Statistics
Matches: 61, Mismatches: 15, Indels: 1
0.79 0.19 0.01
Matches are distributed among these distances:
50 23 0.38
51 38 0.62
ACGTcount: A:0.20, C:0.29, G:0.33, T:0.18
Consensus pattern (50 bp):
GTATAGCGCGATGCAGGGGGCGCGCTATACCCACGTGGCACCAAATCACC
Found at i:3542127 original size:28 final size:29
Alignment explanation
Indices: 3542095--3542154 Score: 104
Period size: 29 Copynumber: 2.1 Consensus size: 29
3542085 ACAACTCCTT
3542095 ATAGTCGGG-GACCATTTTGTAACTTTTA
1 ATAGTCGGGAGACCATTTTGTAACTTTTA
*
3542123 ATAGTCGGGAGATCATTTTGTAACTTTTA
1 ATAGTCGGGAGACCATTTTGTAACTTTTA
3542152 ATA
1 ATA
3542155 ATCGAAAGAC
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
28 9 0.30
29 21 0.70
ACGTcount: A:0.28, C:0.12, G:0.20, T:0.40
Consensus pattern (29 bp):
ATAGTCGGGAGACCATTTTGTAACTTTTA
Found at i:3543828 original size:12 final size:12
Alignment explanation
Indices: 3543811--3543849 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
3543801 AGATATATTA
3543811 ATGCATGAATGT
1 ATGCATGAATGT
3543823 ATGCATGATATGT
1 ATGCATGA-ATGT
* *
3543836 ATGTATGTATGT
1 ATGCATGAATGT
3543848 AT
1 AT
3543850 TATGTAGAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
12 14 0.58
13 10 0.42
ACGTcount: A:0.31, C:0.05, G:0.23, T:0.41
Consensus pattern (12 bp):
ATGCATGAATGT
Found at i:3543840 original size:4 final size:4
Alignment explanation
Indices: 3543819--3544014 Score: 100
Period size: 4 Copynumber: 48.8 Consensus size: 4
3543809 TAATGCATGA
* * **
3543819 ATGT ATGC ATGAT ATGT ATGT ATGT ATGT AT-T ATGT A-GAAC ATAC ATGT
1 ATGT ATGT ATG-T ATGT ATGT ATGT ATGT ATGT ATGT ATG--T ATGT ATGT
* * * * * * *
3543868 ATGT ATG- ATGC ATGT A-GAAC ATTT ATGC ATAT ATGT AT-A ATGT ATGC
1 ATGT ATGT ATGT ATGT ATG--T ATGT ATGT ATGT ATGT ATGT ATGT ATGT
**
3543915 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATAC ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
*** * * *
3543963 AAAAC ATGT ATGC ATGT ATAT AT-A ATGT ATGT ATGTT ATAG- ATGT ATGT
1 -ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATG-T AT-GT ATGT ATGT
3544012 ATG
1 ATG
3544015 CATATCATAT
Statistics
Matches: 143, Mismatches: 34, Indels: 30
0.69 0.16 0.14
Matches are distributed among these distances:
3 13 0.09
4 120 0.84
5 9 0.06
6 1 0.01
ACGTcount: A:0.33, C:0.05, G:0.20, T:0.42
Consensus pattern (4 bp):
ATGT
Found at i:3544049 original size:17 final size:17
Alignment explanation
Indices: 3544027--3544068 Score: 84
Period size: 17 Copynumber: 2.5 Consensus size: 17
3544017 TATCATATGT
3544027 ACATACATGCATCAATA
1 ACATACATGCATCAATA
3544044 ACATACATGCATCAATA
1 ACATACATGCATCAATA
3544061 ACATACAT
1 ACATACAT
3544069 ATATACAAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.48, C:0.24, G:0.05, T:0.24
Consensus pattern (17 bp):
ACATACATGCATCAATA
Done.